# AMR-English alignment release (generated on Mon Mar 14, 2016 at 23:18:32) # ::id a_pmid_2488_5690.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Genetic targeting of mutant BRAF resulted in restoration of sensitivity to serum starvation @-@ induced apoptosis and efficiently inhibited cell proliferation in the absence of growth factors . # ::alignments 1-1.1.1 2-1.1.1.1.r 3-1.1.1.1 3-1.1.1.1.3 3-1.1.1.1.3.r 5-1.1.1.1.2.1 7-1.1 8-1.1.2.r 9-1.1.2 10-1.1.2.1.r 11-1.1.2.1 12-1.1.2.1.1.r 13-1.1.2.1.1.1.1.1 14-1.1.2.1.1.1.1 16-1.1.2.1.1.1 17-1.1.2.1.1 18-1 19-1.2.3 20-1.2 21-1.2.2.1 22-1.2.2 23-1.2.2.2.r 25-1.2.2.2 26-1.2.2.2.1.r 27-1.2.2.2.1 28-1.2.2.2.1 (a / and~e.18 :op1 (r2 / result-01~e.7 :ARG1 (t / target-01~e.1 :ARG1~e.2 (g2 / gene~e.3 :wiki "BRAF_(gene)" :name (n / name :op1 "BRAF"~e.5) :ARG1-of~e.3 (m / mutate-01~e.3)) :mod (g / gene)) :ARG2~e.8 (r / restore-01~e.9 :ARG1~e.10 (s / sensitive-03~e.11 :ARG1~e.12 (a2 / apoptosis~e.17 :ARG2-of (i / induce-01~e.16 :ARG0 (s2 / starve-01~e.14 :ARG2 (s3 / serum~e.13))))))) :op2 (i2 / inhibit-01~e.20 :ARG0 t :ARG1 (p / proliferate-01~e.22 :ARG0 (c / cell~e.21) :condition~e.23 (a3 / absent-01~e.25 :ARG1~e.26 (g3 / growth-factor~e.27,28))) :ARG2-of (e / efficient-01~e.19) :condition a3)) # ::id a_pmid_2488_5690.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Among tested agents , the B @-@ Raf inhibitor dabrafenib was found to induce a strong V600E @-@ dependent shift in cell viability . # ::alignments 1-1.1.1.3.1.1 2-1.1.1.3.1 5-1.1.1.2.1.1.1 7-1.1.1.2.1.1.1 8-1.1.1 8-1.1.1.2 8-1.1.1.2.r 9-1.1.1.1.1 11-1 13-1.1 15-1.1.2.3 16-1.1.2.2.1.1 18-1.1.2.2 19-1.1.2 20-1.1.2.1.r 21-1.1.2.1.1 22-1.1.2.1 (f / find-01~e.11 :ARG1 (i2 / induce-01~e.13 :ARG0 (s / small-molecule~e.8 :name (n3 / name :op1 "dabrafenib"~e.9) :ARG0-of~e.8 (i3 / inhibit-01~e.8 :ARG1 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.5,7))) :ARG1-of (i4 / include-01 :ARG2 (a / agent~e.2 :ARG1-of (t2 / test-01~e.1)))) :ARG2 (s2 / shift-01~e.19 :ARG1~e.20 (v / viability~e.22 :mod (c / cell~e.21)) :ARG0-of (d / depend-01~e.18 :ARG1 (m / mutate-01 :value "V600E"~e.16)) :mod (s3 / strong~e.15)))) # ::id a_pmid_2488_5690.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , no differential sensitizing effect was observed for conventional chemotherapeutic agents ( mitomycin C , oxaliplatin , paclitaxel , etoposide , 5 @-@ fluorouracil ) , nor for the targeted agents cetuximab , sorafenib , vemurafenib , RAF265 , or for inhibition of PI3 kinase . # ::alignments 1-1 3-1.1.1.1 3-1.1.1.1.r 4-1.1.1.4 5-1.1.1.3 6-1.1.1 8-1.1 9-1.1.1.2.r 10-1.1.1.2.1.1 11-1.1.1.2.1.2 12-1.1.1.2.1 14-1.1.1.2.1.3.1.1.1.1 15-1.1.1.2.1.3.1.1.1.2 17-1.1.1.2.1.3.1.2.1.1 19-1.1.1.2.1.3.1.3.1.1 21-1.1.1.2.1.3.1.4.1.1 23-1.1.1.2.1.3.1.5.1.1 25-1.1.1.2.1.3.1.5.1.1 28-1.1.1.1.r 31-1.1.1.2.2.1 32-1.1.1.2.2 33-1.1.1.2.2.2.1.1.1.1 35-1.1.1.2.2.2.1.2.1.1 37-1.1.1.2.2.2.1.3.1.1 39-1.1.1.2.2.2.1.4.1.1 43-1.1.1.2.3 44-1.1.1.2.3.1.r 45-1.1.1.2.3.1.1.1 46-1.1.1.2.3.1 (c / contrast-01~e.1 :ARG2 (o / observe-01~e.8 :ARG1 (a / affect-01~e.6 :polarity~e.3,28 -~e.3 :ARG0~e.9 (a2 / and :op1 (a3 / agent~e.12 :mod (c2 / conventional~e.10) :mod (c3 / chemotherapy~e.11) :ARG1-of (m / mean-01 :ARG2 (a5 / and :op1 (s2 / small-molecule :name (n / name :op1 "mitomycin"~e.14 :op2 "C"~e.15)) :op2 (s3 / small-molecule :name (n2 / name :op1 "oxaliplatin"~e.17)) :op3 (s4 / small-molecule :name (n3 / name :op1 "paclitaxel"~e.19)) :op4 (s5 / small-molecule :name (n4 / name :op1 "etoposide"~e.21)) :op5 (s6 / small-molecule :name (n5 / name :op1 "5-fluorouracil"~e.23,25))))) :op2 (a4 / agent~e.32 :ARG1-of (t / target-01~e.31) :ARG1-of (m2 / mean-01 :ARG2 (a6 / and :op1 (s7 / small-molecule :name (n6 / name :op1 "cetuximab"~e.33)) :op2 (s8 / small-molecule :name (n7 / name :op1 "sorafenib"~e.35)) :op3 (s9 / small-molecule :name (n8 / name :op1 "vemurafenib"~e.37)) :op4 (s10 / small-molecule :name (n9 / name :op1 "RAF265"~e.39))))) :op3 (i / inhibit-01~e.43 :ARG1~e.44 (k / kinase~e.46 :name (n10 / name :op1 "PI3"~e.45)))) :ARG2 (s / sensitize-01~e.5) :ARG1-of (d / differ-02~e.4)))) # ::id a_pmid_2488_5690.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Treatment with dabrafenib efficiently inhibited phosphorylation of the B @-@ Raf downstream targets Mek 1 @/@ 2 and Erk 1 @/@ 2 . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.1 3-1.3 4-1 5-1.2 6-1.2.1.r 8-1.2.1.3.1.1.1 10-1.2.1.3.1.1.1 11-1.2.1.4 12-1.2.1.3 16-1.2.1.1.1.1 16-1.2.1.2.1.1 17-1.2.1 21-1.2.1.1.1.1 21-1.2.1.2.1.1 (i / inhibit-01~e.4 :ARG0 (t / treat-04~e.0 :ARG2~e.1 (s / small-molecule :name (n5 / name :op1 "dabrafenib"~e.2))) :ARG1 (p2 / phosphorylate-01~e.5 :ARG1~e.6 (a / and~e.17 :op1 (e3 / enzyme :name (n3 / name :op1 "Mek1/2"~e.16,21)) :op2 (e4 / enzyme :name (n4 / name :op1 "Erk1/2"~e.16,21)) :ARG1-of (t2 / target-01~e.12 :ARG0 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.8,10))) :direction (d / downstream~e.11))) :ARG2-of (e / efficient-01~e.3 :ARG1 t)) # ::id a_pmid_2488_5690.33 ::amr-annotator SDL-AMR-09 ::preferred # ::tok BRAF targeting in RKO # ::alignments 1-1.1.1.1 3-1 4-1.2.r 5-1.2.1.1 (t / target-01~e.3 :ARG1 (g / gene :name (n / name :op1 "BRAF"~e.1)) :location~e.4 (c / cell-line :name (n2 / name :op1 "RKO"~e.5))) # ::id a_pmid_2488_5690.34 ::amr-annotator SDL-AMR-09 ::preferred # ::tok It has been shown that B @-@ Raf @^V600E is sufficient to promote proliferation via Erk 1 @/@ 2 signaling independently of exogenous growth factors and confers mechanisms to evade apoptosis [ @ 14 @ - @ 16 @ ] . # ::alignments 3-1 4-1.2.r 5-1.2.1.1.1.1 7-1.2.1.1.1.1 9-1.2.1.1.2.1 12-1.2.1 14-1.2.1.2 15-1.2.1.2.2 20-1.2.1.2.2.1.1.1.1 21-1.2.1.2.2.1 22-1.2.1.2.2.2.1 24-1.2.1.2.2.2.2.1 25-1.2.1.2.2.2.2 26-1.2.1.2.2.2.2 27-1.2 28-1.2.2 29-1.2.2.2 31-1.2.2.2.1 32-1.2.2.2.1.1 35-1.1.1.1.1 39-1.1.1.1.2 (s / show-01~e.3 :ARG0 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 (v / value-interval :op1 14~e.35 :op2 16~e.39))) :ARG1~e.4 (a / and~e.27 :op1 (s2 / suffice-01~e.12 :ARG0 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.5,7) :ARG1-of (m / mutate-01 :value "V600E"~e.9)) :ARG1 (p / promote-01~e.14 :ARG0 e2 :ARG1 (p2 / proliferate-01~e.15 :instrument (s3 / signal-07~e.21 :ARG0 (e3 / enzyme :name (n3 / name :op1 "Erk1/2"~e.20))) :ARG0-of (d / depend-01 :polarity -~e.22 :ARG1 (g / growth-factor~e.25,26 :mod (e4 / exogenous~e.24)))))) :op2 (c / confer-02~e.28 :ARG0 e2 :ARG1 (m2 / mechanism~e.29 :purpose (e5 / evade-01~e.31 :ARG1 (a2 / apoptosis~e.32)))))) # ::id a_pmid_2488_5690.35 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , these results are primarily based on non @-@ quantitative RNA interference ( RNAi ) methods which are prone to artifacts in mammalian cells due to nonspecific defense mechanisms [ @ 17 @ ] . # ::alignments 0-1 2-1.1.1.2 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 5-1.1.3 5-1.1.3.r 6-1.1 7-1.1.2.r 8-1.1.2.2.1 8-1.1.2.2.1.r 10-1.1.2.2 11-1.1.2.3.1.1.1 12-1.1.2.3 16-1.1.2 19-1.1.2.1 20-1.1.2.1.1.r 20-1.1.2.1.3 21-1.1.2.1.1 22-1.1.2.1.2.r 23-1.1.2.1.2.1.1.1 24-1.1.2.1.2 25-1.1.2.1.3 26-1.1.2.1.3 27-1.1.2.1.3.1.2 27-1.1.2.1.3.1.2.1 27-1.1.2.1.3.1.2.1.r 28-1.1.2.1.3.1.1 29-1.1.2.1.3.1 32-1.2.1.1.1 (c / contrast-01~e.0 :ARG2 (b / base-02~e.6 :ARG1 (t2 / thing~e.3 :ARG2-of~e.3 (r / result-01~e.3) :mod (t / this~e.2)) :ARG2~e.7 (m / method~e.16 :ARG1-of (p / prone-01~e.19 :ARG2~e.20 (a / artifact~e.21) :location~e.22 (c2 / cell~e.24 :part-of (a2 / animal :name (n2 / name :op1 "Mammalia"~e.23))) :ARG1-of (c3 / cause-01~e.20,25,26 :ARG0 (m2 / mechanism~e.29 :purpose (d / defend-01~e.28) :ARG1-of (s / specific-02~e.27 :polarity~e.27 -~e.27)))) :mod (q / quantitative~e.10 :polarity~e.8 -~e.8) :manner-of (i / interfere-01~e.12 :ARG1 (n / nucleic-acid :name (n3 / name :op1 "RNA"~e.11)))) :manner~e.5 (p3 / primary~e.5)) :ARG1-of (d2 / describe-01 :ARG0 (p2 / publication :ARG1-of (c4 / cite-01 :ARG2 17~e.32)))) # ::id a_pmid_2488_5690.36 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , somatic cell gene targeting enables quantitative knockouts of single alleles ( Figure 1 @ A ) and the generation of endogenous models featuring well @-@ defined genetic backgrounds [ @ 18 @ ] . # ::alignments 1-1 3-1.1.1.1.1.1 4-1.1.1.1.1 5-1.1.1.1 5-1.1.2.2.1.2.1.1 6-1.1.1 7-1.1 8-1.1.2.1.2 9-1.1.2.1 10-1.1.2.1.1.r 11-1.1.2.1.1.1 12-1.1.2.1.1 14-1.1.2.1.3.1 20-1.1.2 22-1.1.2.2 23-1.1.2.2.1.r 24-1.1.2.2.1.1 25-1.1.2.2.1 26-1.1.2.2.1.2 27-1.1.2.2.1.2.1.2.1 29-1.1.2.2.1.2.1.2 31-1.1.2.2.1.2.1 34-1.2.1.1.1 (c / contrast-01~e.1 :ARG2 (e / enable-01~e.7 :ARG0 (t / target-01~e.6 :ARG1 (g / gene~e.5 :part-of (c2 / cell~e.4 :mod (s / somatic~e.3)))) :ARG1 (a / and~e.20 :op1 (k / knock-out-03~e.9 :ARG1~e.10 (a2 / allele~e.12 :ARG1-of (s2 / single-02~e.11)) :mod (q / quantity~e.8) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.14 :mod "1A"))) :op2 (g2 / generate-01~e.22 :ARG1~e.23 (m / model~e.25 :mod (e2 / endogenous~e.24) :ARG0-of (f2 / feature-01~e.26 :ARG1 (b / background~e.31 :mod (g3 / gene~e.5) :ARG1-of (d2 / define-01~e.29 :manner (w / well~e.27)))))))) :ARG1-of (d3 / describe-01 :ARG0 (p / publication :ARG1-of (c3 / cite-01 :ARG2 18~e.34)))) # ::id a_pmid_2488_5690.37 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Utilizing this method , we have disrupted BRAF alleles in the colorectal cancer cell line RKO and established syngeneic clones which harbor a single BRAF allele of either wild @-@ type or mutant genotype . # ::alignments 0-1.3 1-1.3.2.1 2-1.3.2 4-1.1.1 6-1.1 8-1.1.2.1.1 8-1.2.2.2.1.2.1.1 10-1.1.2 11-1.1.3.r 13-1.1.3.2.2.1 14-1.1.3.2.2.2 15-1.1.3 16-1.1.3 17-1.1.3.1.1 18-1 19-1.2 20-1.2.2.1 21-1.2.2 23-1.2.2.2 25-1.2.2.2.1.1.3 27-1.2.2.2.1.1.1.1 29-1.2.2.2.1.1 29-1.2.2.2.1.2 32-1.2.2.2.1.1.2 34-1.2.2.2.1.1.2 35-1.2.2.2.1 36-1.2.2.2.1.2.2 (a / and~e.18 :op1 (d2 / disrupt-01~e.6 :ARG0 (w2 / we~e.4) :ARG1 (a2 / allele~e.10 :name (n2 / name :op1 "BRAF"~e.8)) :location~e.11 (c / cell-line~e.15,16 :name (n3 / name :op1 "RKO"~e.17) :mod (d3 / disease :wiki "Colorectal_cancer" :name (n6 / name :op1 "colorectal"~e.13 :op2 "cancer"~e.14)))) :op2 (e / establish-01~e.19 :ARG0 w2 :ARG1 (c2 / clone~e.21 :mod (s / syngeneic~e.20) :ARG0-of (h2 / harbor-01~e.23 :ARG1 (o / or~e.35 :op1 (a3 / allele~e.29 :name (n4 / name :op1 "BRAF"~e.27) :mod (w3 / wild-type~e.32,34) :ARG1-of (s2 / single-02~e.25)) :op2 (a4 / allele~e.29 :name (n5 / name :op1 "BRAF"~e.8) :ARG1-of (m / mutate-01~e.36) :ARG1-of s2))))) :manner (u / utilize-01~e.0 :ARG0 w2 :ARG1 (m2 / method~e.2 :mod (t / this~e.1)))) # ::id a_pmid_2488_5690.38 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Despite its near @-@ diploid karyotype and MSI phenotype , the colorectal cancer cell line RKO carries a stable triplication of the BRAF gene locus ( dup ( 7 ) ( q21q36 )) with one wild @-@ type and two mutant alleles present in parental cells [ @ 13 @ ] . # ::alignments 0-1.3.r 1-1.3.1 1-1.3.1.r 2-1.3.2.1.1 4-1.3.2.1.1.1 5-1.3.2.1 6-1.3.2 8-1.3.2.2 11-1.1.2.2.1 12-1.1.2.2.2 13-1.1 14-1.1 15-1.1.1.1 16-1 18-1.2.2 23-1.2.1.1.1.1 25-1.2.1.1 26-1.2.1 36-1.2.3.1.1.1.1 37-1.2.3.1.1.1.2 39-1.2.3.1.1.1.2 40-1.2.3.1.1 41-1.2.3.1.1.2.1 42-1.2.3.1.1.2.2 43-1.2.3.1.1.1 43-1.2.3.1.1.2 46-1.2.3.1.2.1 47-1.2.3.1.2 50-1.4.1.1.1 (c / carry-01~e.16 :ARG0 (c2 / cell-line~e.13,14 :name (n2 / name :op1 "RKO"~e.15) :mod (d / disease :wiki "Colorectal_cancer" :name (n / name :op1 "colorectal"~e.11 :op2 "cancer"~e.12))) :ARG1 (t / triplicate-00 :ARG1 (l / locus~e.26 :mod (g / gene~e.25 :name (n3 / name :op1 "BRAF"~e.23)) :ARG1-of (l2 / label-01 :ARG2 (s2 / string-entity :value "dup(7)(q21q36)"))) :ARG1-of (s / stable-03~e.18) :ARG1-of (m / mean-01 :ARG2 (b / be-located-at-91 :ARG1 (a / and~e.40 :op1 (a2 / allele~e.43 :quant 1~e.36 :mod (w / wild-type~e.37,39)) :op2 (a3 / allele~e.43 :quant 2~e.41 :ARG1-of (m2 / mutate-01~e.42))) :ARG2 (c3 / cell~e.47 :mod (p / parent~e.46))))) :concession~e.0 (h2 / have-03 :ARG0~e.1 c2~e.1 :ARG1 (a4 / and~e.6 :op1 (k / karyotype~e.5 :ARG1-of (n4 / near-01~e.2 :ARG2 (d3 / diploid~e.4))) :op2 (p2 / phenotype~e.8 :name (n5 / name :op1 "microsattelite" :op2 "instability")))) :ARG1-of (d2 / describe-01 :ARG0 (p3 / publication :ARG1-of (c4 / cite-01 :ARG2 13~e.50)))) # ::id a_pmid_2488_5690.39 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This genotype was verified by DNA sequencing in RKO @-@ E1 , a subclone obtained from RKO that was found to be comparable to the parental cell line in terms of morphology and proliferation ( Figure 1 @ B and data not shown ) . # ::alignments 0-1.1.1 1-1.1 3-1 4-1.4.r 5-1.4.1.2.1 6-1.4 7-1.2.r 8-1.2.1.1 10-1.2.1.1 13-1.2.2 14-1.2.2.1 15-1.2.2.1.1.r 16-1.2.2.1.1.1.1 19-1.2.2.2.4 25-1.2.2.2.1.1 26-1.2.2.2.1 27-1.2.2.2.1 31-1.2.2.2.3.1 32-1.2.2.2.3 33-1.2.2.2.3.2 35-1.3.1.1 40-1.3.1 41-1.3.1.2 42-1.3.1.2.1.1 42-1.3.1.2.1.1.r 43-1.3.1.2.1 (v / verify-01~e.3 :ARG1 (g / genotype~e.1 :mod (t / this~e.0)) :location~e.7 (c / cell-line :name (n2 / name :op1 "RKO-E1"~e.8,10) :ARG3-of (s2 / subclone-01~e.13 :ARG1-of (o / obtain-01~e.14 :ARG2~e.15 (c2 / cell-line :name (n3 / name :op1 "RKO"~e.16))) :ARG1-of (c3 / compare-01 :ARG2 (c4 / cell-line~e.26,27 :mod (p2 / parent~e.25)) :ARG1-of (p / possible-01) :topic (a / and~e.32 :op1 (m / morphology~e.31) :op2 (p3 / proliferate-01~e.33)) :ARG1-of (f / find-01~e.19)))) :ARG1-of (d / describe-01 :ARG0 (a2 / and~e.40 :op1 (f2 / figure~e.35 :mod "1B") :op2 (d2 / data~e.41 :ARG1-of (s / show-01~e.43 :polarity~e.42 -~e.42)))) :manner~e.4 (s3 / sequence-01~e.6 :ARG1 (n / nucleic-acid :wiki "DNA" :name (n4 / name :op1 "DNA"~e.5)))) # ::id a_pmid_2488_5690.40 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In the first targeting round , an oncogenic allele of BRAF exon 15 was recombined and deleted by somatic cell gene targeting to generate the cell clone RBOW ( RKO @-@ derived BRAF @ ^onc/wt/- ) . # ::alignments 2-1.3.2 2-1.3.2.1 2-1.3.2.1.r 3-1.3.1 4-1.3 7-1.1.1.1 8-1.1.1 11-1.1.1.2.2.1.1 13-1.1.1.2 14-1.1.1.2.1 16-1.1 17-1 18-1.2 20-1.4.1.1.1 21-1.4.1.1 21-1.5.1.2.1 22-1.4.1 23-1.4 25-1.5 27-1.5.1 27-1.5.1.2.1.1.2.1 28-1.5.1.3 29-1.5.1.1.1 31-1.5.1.2.1.1.2.1.1.1 33-1.5.1.2.1.1.2 35-1.5.1.2.1.1.1.1 38-1.5.1.2.1.1.3.1.1 (a / and~e.17 :op1 (r / recombine-01~e.16 :ARG1 (a2 / allele~e.8 :mod (o2 / oncogenic~e.7) :mod (e / exon~e.13 :mod 15~e.14 :part-of (g / gene :name (n / name :op1 "BRAF"~e.11))))) :op2 (d / delete-01~e.18 :ARG1 a2) :time (r2 / round-05~e.4 :ARG1 (t / target-01~e.3) :ord (o / ordinal-entity~e.2 :value~e.2 1~e.2)) :instrument (t2 / target-01~e.23 :ARG1 (g4 / gene~e.22 :part-of (c / cell~e.21 :mod (s / somatic~e.20)))) :purpose (g2 / generate-01~e.25 :ARG1 (c2 / cell~e.27 :name (n2 / name :op1 "RBOW"~e.29) :ARG1-of (m / mean-01 :ARG2 (c4 / cell-line~e.21 :location-of (g3 / gene :name (n3 / name :op1 "BRAF"~e.35) :ARG1-of (d2 / derive-01~e.33 :ARG2 (c3 / cell-line~e.27 :name (n4 / name :op1 "RKO"~e.31))) :ARG1-of (l / label-01 :ARG2 (s2 / string-entity :value "onc/wt/-"~e.38))))) :ARG1-of (c5 / clone-01~e.28)))) # ::id a_pmid_2488_5690.41 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Subsequently , either wild @-@ type or V600E @-@ mutant B @-@ Raf was disrupted by targeting a second allele in RBOW , yielding six BRAF @ -@ mutant and one wild @-@ type clone from approximately 10 @⁴ screened colonies . # ::alignments 0-1.4 0-1.4.r 3-1.1.1.2 5-1.1.1.2 6-1.1 7-1.1.2.2.1 9-1.1.2 9-1.1.2.2 9-1.1.2.2.r 10-1.1.1.1.1 10-1.1.2.1.1 12-1.1.1.1.1 12-1.1.2.1.1 14-1 15-1.2.r 16-1.2 18-1.2.1.2 18-1.2.1.2.1 18-1.2.1.2.1.r 19-1.2.1 20-1.2.1.1.r 21-1.2.1.1.1.1 23-1.3 24-1.3.1.1.1 26-1.3.1.1.2.1.1.1 29-1.3.1.1.2 30-1.3.1 31-1.3.1.2.1 32-1.3.1.2.2 33-1.3.1.2.2 34-1.3.1.2.2 35-1.3.1.1 35-1.3.1.2 36-1.3.2.r 37-1.3.2.2 42-1.3.2.1 43-1.3.2 (d / disrupt-01~e.14 :ARG1 (o2 / or~e.6 :op1 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.10,12) :mod (w / wild-type~e.3,5)) :op2 (e / enzyme~e.9 :name (n / name :op1 "B-Raf"~e.10,12) :ARG2-of~e.9 (m / mutate-01~e.9 :value "V600E"~e.7))) :manner~e.15 (t2 / target-01~e.16 :ARG1 (a2 / allele~e.19 :part-of~e.20 (c / cell :name (n3 / name :op1 "RBOW"~e.21)) :mod (o / ordinal-entity~e.18 :value~e.18 2~e.18))) :ARG0-of (y / yield-01~e.23 :ARG1 (a3 / and~e.30 :op1 (c2 / clone~e.35 :quant 6~e.24 :mod (m2 / mutate-01~e.29 :ARG1 (g / gene :name (n4 / name :op1 "BRAF"~e.26)))) :op2 (c3 / clone~e.35 :quant 1~e.31 :mod w~e.32,33,34)) :source~e.36 (c4 / colony~e.43 :ARG1-of (s2 / screen-01~e.42) :quant (a / approximately~e.37 :op1 10000))) :time~e.0 (s3 / subsequent~e.0)) # ::id a_pmid_2488_5690.42 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Out of these double positive clones , BRAF knockout cell lines RBO @-@ 1 and RBO @-@ 2 ( RKO @-@ derived BRAF @ ^onc/-/- 1 and 2 ) as well as RBW @-@ 1 ( RKO @-@ derived BRAF @ ^wt/-/- ) were established ( Figure 1 @ B ) . # ::alignments 0-1.1.1.3 2-1.1.4.2 3-1.1.4.1.1 4-1.1.4.1 5-1.1.4 8-1.1.1.2.1.2.1.1 8-1.1.1.3.1.1.1 8-1.1.3.2.1.1.1.1 10-1.1.1.3 11-1.1.3.2.1 12-1.1.1.2.1 12-1.1.2.2.1 12-1.1.3.2.1 13-1.1.1.1.1 13-1.1.2.1.1 15-1.1.1.1.1 15-1.1.1.2.1.1 15-1.1.3.1.1 16-1.1 17-1.1.1.1.1 17-1.1.2.1.1 19-1.1.2.1.1 19-1.1.2.2.1.1 21-1.1.1.2.1.2.2.1.1.1 23-1.1.1.2.1.2.2 25-1.1.1.2.1.2.1.1 25-1.1.1.3.1.1.1 25-1.1.3.2.1.1.1.1 30-1.1.1.1.1 30-1.1.1.2.1.1 30-1.1.3.1.1 31-1.1 32-1.1.2.1.1 32-1.1.2.2.1.1 34-1.1 35-1.1 36-1.1 37-1.1.3.1.1 39-1.1.1.1.1 39-1.1.1.2.1.1 39-1.1.3.1.1 41-1.1.1.2.1.2.2.1.1.1 43-1.1.1.2.1.2.2 45-1.1.1.2.1.2.1.1 45-1.1.3.2.1.1.1.1 52-1 54-1.2.1 56-1.1.1.1.1 56-1.1.1.2.1.1 56-1.1.3.1.1 (e / establish-01~e.52 :ARG1 (a / and~e.16,31,34,35,36 :op1 (c / cell-line :name (n / name :op1 "RBO-1"~e.13,15,17,30,39,56) :ARG1-of (m / mean-01 :ARG2 (c3 / cell-line~e.12 :mod 1~e.15,30,39,56 :location-of (g2 / gene :name (n4 / name :op1 "BRAF"~e.8,25,45) :ARG1-of (d / derive-01~e.23,43 :ARG2 (c4 / cell-line :name (n5 / name :op1 "RKO"~e.21,41))) :ARG2-of (m2 / mutate-01 :mod "−/−") :ARG0-of (c9 / cause-01 :ARG1 (d4 / disease :wiki "Cancer" :name (n8 / name :op1 "cancer")))))) :location-of (k / knock-out-03~e.0,10 :ARG1 (g / gene :name (n3 / name :op1 "BRAF"~e.8,25)))) :op2 (c2 / cell-line :name (n2 / name :op1 "RBO-2"~e.13,17,19,32) :ARG1-of (m3 / mean-01 :ARG2 (c5 / cell-line~e.12 :mod 2~e.19,32 :location-of g2)) :location-of k) :op3 (c6 / cell-line :name (n6 / name :op1 "RBW-1"~e.15,30,37,39,56) :ARG1-of (m4 / mean-01 :ARG2 (c7 / cell-line~e.11,12 :location-of (g3 / gene :name (n7 / name :op1 "BRAF"~e.8,25,45) :ARG2-of (m5 / mutate-01 :mod "−/−") :ARG1-of d :mod (w / wild-type))))) :source (c8 / clone~e.5 :mod (p / positive~e.4 :mod (d2 / double~e.3)) :mod (t / this~e.2))) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.54 :mod "1B"))) # ::id a_pmid_2488_5690.43 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The apparent counterselection against inactivation of B Raf @^V600E might indicate the presence of an oncogene addiction for B @-@ Raf @^V600E as a cancer cell trait in RKO [ @ 19 @ ] . # ::alignments 1-1.1.1.1 3-1.1.1.2 4-1.1.1.2.1 4-1.1.1.2.1.1 4-1.1.1.2.1.1.r 5-1.1.1.2.1.2.r 6-1.1.1.2.1.2.1.1 7-1.1.1.2.1.2.1.1 9-1.1.1.2.1.2.2.1 11-1 12-1.1 15-1.1.2.r 17-1.1.2.1.2 18-1.1.2.1 19-1.1.2.1.1.r 20-1.1.2.1.1 21-1.1.2.1.1 22-1.1.2.1.1 23-1.1.2.1.1 24-1.1.2.1.1 28-1.1.2.2.1.2.1 29-1.1.2.2 30-1.1.2 31-1.1.2.3.r 32-1.1.2.3.1.1 35-1.2.1.1.1 (p2 / possible-01~e.11 :ARG1 (i / indicate-01~e.12 :ARG0 (c / counterselect-00 :mod (a / apparent~e.1) :ARG0-of (c6 / counter-01~e.3 :ARG1 (a3 / activate-01~e.4 :polarity~e.4 -~e.4 :ARG1~e.5 (e3 / enzyme :name (n3 / name :op1 "B-Raf"~e.6,7) :ARG2-of (m / mutate-01 :value "V600E"~e.9))))) :ARG1~e.15 (t / trait~e.30 :domain (a2 / addict-01~e.18 :ARG1~e.19 e3~e.20,21,22,23,24 :ARG2 (o / oncogene~e.17)) :mod (c2 / cell~e.29 :mod (d / disease :wiki "Cancer" :name (n / name :op1 "cancer"~e.28))) :location~e.31 (c4 / cell-line :name (n5 / name :op1 "RKO"~e.32)))) :ARG1-of (d2 / describe-01 :ARG0 (p3 / publication :ARG1-of (c5 / cite-01 :ARG2 19~e.35)))) # ::id a_pmid_2488_5690.44 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For structural confirmation of the deleted alleles , DNA sequencing was performed and all genotypes were verified ( Figure 1 @ B ) . # ::alignments 1-1.3.2 2-1.3 3-1.3.1.r 5-1.3.1.1 6-1.3.1 8-1.1.1.1.2.1 9-1.1.1 11-1.1 12-1 13-1.2.1.1 14-1.2.1 16-1.2 18-1.4.1 (a / and~e.12 :op1 (p / perform-01~e.11 :ARG1 (s / sequence-01~e.9 :ARG1 (n / nucleic-acid :wiki "DNA" :name (n2 / name :op1 "DNA"~e.8)))) :op2 (v / verify-01~e.16 :ARG1 (g / genotype~e.14 :mod (a2 / all~e.13))) :purpose (c / confirm-01~e.2 :ARG1~e.3 (a3 / allele~e.6 :ARG1-of (d / delete-01~e.5)) :mod (s2 / structure~e.1)) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.18 :mod "1B"))) # ::id a_pmid_2488_5690.45 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Furthermore , all cells expressed BRAF protein at comparable levels ( Figure 1 @ C ) . # ::alignments 0-1 2-1.1.1.1.1.2.1 3-1.1.1.1.1.2 4-1.1.1.1.1 6-1.1.1.1.1.1.2.1 11-1.1.1.1 13-1.2.1 (a / and~e.0 :op2 (p2 / possible-01 :ARG1 (c2 / compare-01 :ARG1 (l / level~e.11 :quant-of (e / express-03~e.4 :ARG2 (e2 / enzyme :wiki - :name (n / name :op1 "BRAF"~e.6)) :ARG3 (c / cell~e.3 :mod (a2 / all~e.2)))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.13 :mod "1C"))) # ::id a_pmid_2488_5690.46 ::amr-annotator SDL-AMR-09 ::preferred # ::tok While the expression of Mek 1 @/@ 2 and Erk 1 @/@ 2 was independent of serum concentration and BRAF status , the phosphorylation of these effector kinases was constantly active in the BRAF @ -@ mutant clones but low in BRAF @ -@ wild @-@ type cells ( Figure 1 @ C ) . # ::alignments 0-1 2-1.2.2 7-1.2.2.1.1.1.1 7-1.2.2.1.2.1.1 8-1.2.2.1 12-1.2.2.1.1.1.1 12-1.2.2.1.2.1.1 14-1.2 14-1.2.1 14-1.2.1.r 15-1.2.3.r 16-1.2.3.1.1 17-1.2.3.1 18-1.2.3 20-1.2.3.2.1.1.1 22-1.2.3.2 25-1.1.1.1 29-1.1.1.1.1 30-1.1.1.1.r 31-1.1.1.2 31-1.1.1.2.r 32-1.1.1 36-1.1.1.3.1.1.1 39-1.1.1.3.1 39-1.1.1.3.1.2 39-1.1.1.3.1.2.r 40-1.1.1.3 41-1.1 42-1.1.2 45-1.1.2.1.1.1.1 48-1.1.2.1.1.2 50-1.1.2.1.1.2 51-1.1.2.1 53-1.3.1 (c / contrast-01~e.0 :ARG1 (c3 / contrast-01~e.41 :ARG1 (a3 / active~e.32 :domain~e.30 (p / phosphorylate-01~e.25 :ARG1 a~e.29) :manner~e.31 (c4 / constant~e.31) :location (c5 / clone~e.40 :location-of (g2 / gene~e.39 :name (n4 / name :op1 "BRAF"~e.36) :ARG2-of~e.39 (m / mutate-01~e.39)))) :ARG2 (l / low-04~e.42 :ARG1 (c6 / cell~e.51 :location-of (g3 / gene :name (n5 / name :op1 "BRAF"~e.45) :mod (w / wild-type~e.48,50))) :ARG2 p)) :ARG2 (d / depend-01~e.14 :polarity~e.14 -~e.14 :ARG0 (e3 / express-03~e.2 :ARG2 (a / and~e.8 :op1 (k / kinase :name (n / name :op1 "Mek1/2"~e.7,12)) :op2 (k2 / kinase :name (n2 / name :op1 "Erk1/2"~e.7,12)) :ARG0-of (e / effect-03))) :ARG1~e.15 (a2 / and~e.18 :op1 (c2 / concentrate-02~e.17 :ARG1 (s / serum~e.16)) :op2 (s2 / status~e.22 :mod (g / gene :name (n3 / name :op1 "BRAF"~e.20))))) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.53 :mod "1C"))) # ::id a_pmid_2488_5690.47 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This was found to be independent of the serum concentration , indicating that the phosphorylation status of Mek and Erk is dependent on mutant BRAF in RKO . # ::alignments 0-1.1.2 2-1 5-1.1 5-1.1.1 5-1.1.1.r 6-1.1.3.r 8-1.1.3.1 9-1.1.3 11-1.1.4 12-1.1.4.1.r 14-1.1.4.1.1.1 15-1.1.4.1.1 16-1.1.4.1.1.1.1.r 17-1.1.4.1.1.1.1.1.1.1 18-1.1.4.1.1.1.1 19-1.1.4.1.1.1.1.2.1.1 21-1.1.4.1 22-1.1.4.1.2.r 23-1.1.4.1.2 23-1.1.4.1.2.2 23-1.1.4.1.2.2.r 25-1.1.4.1.2.1.1 27-1.1.4.1.3.r 28-1.1.4.1.3.1.1 (f / find-01~e.2 :ARG1 (d / depend-01~e.5 :polarity~e.5 -~e.5 :ARG0 (t / this~e.0) :ARG1~e.6 (c / concentrate-02~e.9 :ARG1 (s / serum~e.8)) :ARG0-of (i / indicate-01~e.11 :ARG1~e.12 (d2 / depend-01~e.21 :ARG0 (s2 / status~e.15 :mod (p / phosphorylate-01~e.14 :ARG1~e.16 (a / and~e.18 :op1 (e / enzyme :name (n / name :op1 "Mek"~e.17)) :op2 (e2 / enzyme :name (n2 / name :op1 "Erk"~e.19))))) :ARG1~e.22 (g / gene~e.23 :name (n3 / name :op1 "BRAF"~e.25) :ARG2-of~e.23 (m / mutate-01~e.23)) :location~e.27 (c2 / cell-line :name (n4 / name :op1 "RKO"~e.28)))))) # ::id a_pmid_2488_5690.48 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Cell @-@ biological phenotypes related to mutant BRAF # ::alignments 0-1.1.1 2-1.1 3-1 4-1.2 5-1.2.1.r 6-1.2.1 6-1.2.1.2 6-1.2.1.2.r 8-1.2.1.1.1 (p / phenotype~e.3 :mod (b / biology~e.2 :mod (c / cell~e.0)) :ARG1-of (r / relate-01~e.4 :ARG2~e.5 (g / gene~e.6 :name (n / name :op1 "BRAF"~e.8) :ARG2-of~e.6 (m / mutate-01~e.6)))) # ::id a_pmid_2488_5690.49 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Under standard long @-@ term cell culture conditions no differences in morphology or growth were observed between the cell clones ( Figures 1 @ B and 2 @ A ) . # ::alignments 1-1.2.1 2-1.2.2.2 5-1.2.2.1 6-1.2.2 7-1.2 7-1.2.r 8-1.1.1 8-1.1.1.r 9-1.1 10-1.1.3.r 11-1.1.3.1 12-1.1.3 13-1.1.3.2 15-1 18-1.1.2 19-1.1.2.1 21-1.3.1.1 21-1.3.1.2 26-1.3.1 (o / observe-01~e.15 :ARG1 (d / differ-02~e.9 :polarity~e.8 -~e.8 :ARG1 (c2 / cell~e.18 :ARG1-of (c / clone-01~e.19)) :ARG3~e.10 (o2 / or~e.12 :op1 (m / morphology~e.11) :op2 (g / grow-01~e.13))) :condition~e.7 (c3 / condition~e.7 :ARG1-of (s / standard-02~e.1) :mod (c4 / culture-01~e.6 :ARG1 (c5 / cell~e.5) :ARG1-of (l2 / long-03~e.2))) :ARG1-of (d2 / describe-01 :ARG0 (a / and~e.26 :op1 (f / figure~e.21 :mod "1B") :op2 (f2 / figure~e.21 :mod "2A")))) # ::id a_pmid_2488_5690.50 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Expectedly , decreased serum concentrations led to lower proliferation rates in these cells , but exponential growth was sustained under all applied conditions . # ::alignments 2-1.1.1.2 3-1.1.1.1 4-1.1.1 5-1.1 6-1.1.2.r 7-1.1.2.1 7-1.1.2.1.2 7-1.1.2.1.2.r 8-1.1.2 10-1.1.2.1.1.r 11-1.1.2.1.1.1 12-1.1.2.1.1 14-1 15-1.2.1.1 16-1.2.1 18-1.2 20-1.2.2.2 21-1.2.2.1 22-1.2.2 22-1.2.2.r (c3 / contrast-01~e.14 :ARG1 (l2 / lead-03~e.5 :ARG0 (c / concentrate-02~e.4 :ARG1 (s / serum~e.3) :ARG1-of (d / decrease-01~e.2)) :ARG2~e.6 (p / proliferate-01~e.8 :ARG2-of (l / low-04~e.7 :ARG1~e.10 (c2 / cell~e.12 :mod (t / this~e.11)) :degree~e.7 (m / more~e.7))) :ARG1-of (e2 / expect-01)) :ARG2 (s2 / sustain-01~e.18 :ARG1 (g / grow-01~e.16 :ARG2 (e / exponential~e.15)) :condition~e.22 (c4 / condition~e.22 :ARG1-of (a / apply-02~e.21) :mod (a2 / all~e.20)))) # ::id a_pmid_2488_5690.51 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , the withdrawal of serum resulted in the inhibition of cell growth of the wild @-@ type cells RBW @-@ 1 ( Figure 2 @ B and C ) . # ::alignments 0-1 3-1.1.1 4-1.1.1.1.r 5-1.1.1.1 6-1.1 7-1.1.2.r 9-1.1.2 10-1.1.2.1.r 11-1.1.2.1.1 12-1.1.2.1 15-1.1.2.1.1.2 17-1.1.2.1.1.2 18-1.1.2.1.1 19-1.1.2.1.1.1.1 21-1.1.2.1.1.1.1 23-1.2.1.1 23-1.2.1.2 28-1.2.1 (c / contrast-01~e.0 :ARG2 (r / result-01~e.6 :ARG1 (w / withdraw-01~e.3 :ARG1~e.4 (s / serum~e.5)) :ARG2~e.7 (i / inhibit-01~e.9 :ARG1~e.10 (g / grow-01~e.12 :ARG0 (c2 / cell-line~e.11,18 :name (n / name :op1 "RBW-1"~e.19,21) :mod (w2 / wild-type~e.15,17))))) :ARG1-of (d / describe-01 :ARG0 (a / and~e.28 :op1 (f / figure~e.23 :mod "2B") :op2 (f2 / figure~e.23 :mod "2C")))) # ::id a_pmid_2488_5690.52 ::amr-annotator SDL-AMR-09 ::preferred # ::tok It has been shown previously that BRAF wild @-@ type cells require glucose supply for survival whereas BRAF @ -@ mutant cell clones maintain proliferation in low @-@ glucose environments [ @ 20 @ ] . # ::alignments 3-1.3 4-1.3.2 7-1.1.1.1.1.1 7-1.2.1.1.1.1.1 9-1.1.1.1.2 11-1.1.1.1.2 12-1.1.1 13-1.1 14-1.1.2.1.1.1 15-1.1.2 16-1.1.3.r 17-1.1.3 18-1 20-1.2.1.1.1.1.1 23-1.2.1.1.1 23-1.2.1.1.1.2 23-1.2.1.1.1.2.r 24-1.2.1 25-1.2.1.1 26-1.2 27-1.2.2 28-1.2.3.r 29-1.2.3.1 31-1.2.3.1.1 32-1.2.3 35-1.3.1.1.1 (c / contrast-01~e.18 :ARG1 (r / require-01~e.13 :ARG0 (c2 / cell~e.12 :location-of (g / gene :name (n / name :op1 "BRAF"~e.7) :mod (w / wild-type~e.9,11))) :ARG1 (s2 / supply-01~e.15 :ARG1 (s3 / small-molecule :name (n2 / name :op1 "glucose"~e.14))) :purpose~e.16 (s4 / survive-01~e.17 :ARG0 c2)) :ARG2 (m / maintain-01~e.26 :ARG0 (c4 / cell~e.24 :ARG1-of (c3 / clone-01~e.25 :location-of (g2 / gene~e.23 :name (n3 / name :op1 "BRAF"~e.7,20) :ARG1-of~e.23 (m2 / mutate-01~e.23)))) :ARG1 (p2 / proliferate-01~e.27) :location~e.28 (e / environment~e.32 :ARG1-of (l / low-04~e.29 :ARG2 s3~e.31))) :ARG1-of (s / show-01~e.3 :ARG0 (p3 / publication :ARG1-of (c5 / cite-01 :ARG2 20~e.35)) :time (p / previous~e.4))) # ::id a_pmid_2488_5690.53 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Here we show that the V600E mutation of B @-@ Raf also provides independency of serum @-@ derived growth signals in RKO and that targeting of oncogenically mutant BRAF is sufficient to deprive this vital feature of malignancy from the cells , thereby corroborating previous reports [ @ 6 @ ] . # ::alignments 0-1.3.2 1-1.3.1 2-1.3 5-1.1.1.2.1 6-1.1.1 6-1.1.1.2 6-1.1.1.2.r 8-1.1.1.1.1 10-1.1.1.1.1 11-1.1.3 12-1.1 13-1.1.2 13-1.1.2.1 13-1.1.2.1.r 14-1.1.2.2.r 15-1.1.2.2.2.1 17-1.1.2.2.2 18-1.1.2.2.1 19-1.1.2.2 20-1.1.4.r 21-1.1.4.1.1 22-1 24-1.2.1 27-1.2.1.1 27-1.2.1.1.2 27-1.2.1.1.2.r 29-1.2.1.1.1.1 32-1.2 34-1.2.2 35-1.2.2.2.3 36-1.2.2.2.4 37-1.2.2.2 38-1.2.2.2.2.r 39-1.2.2.2.2 40-1.2.2.3.r 42-1.2.2.3 45-1.3.3.1 46-1.3.3.1.1.1 47-1.3.3.1.1 50-1.3.3.1.1.2.1.1.1 (a / and~e.22 :op1 (p / provide-01~e.12 :ARG0 (e2 / enzyme~e.6 :name (n2 / name :op1 "B-Raf"~e.8,10) :ARG2-of~e.6 (m / mutate-01~e.6 :value "V600E"~e.5)) :ARG1 (d / depend-01~e.13 :polarity~e.13 -~e.13 :ARG1~e.14 (s / signal-07~e.19 :ARG1 (g / grow-01~e.18) :ARG1-of (d2 / derive-01~e.17 :ARG2 (s2 / serum~e.15)))) :mod (a2 / also~e.11) :location~e.20 (c / cell-line :name (n3 / name :op1 "RKO"~e.21))) :op2 (s3 / suffice-01~e.32 :ARG0 (t / target-01~e.24 :ARG1 (g2 / gene~e.27 :name (n4 / name :op1 "BRAF"~e.29) :ARG1-of~e.27 (m2 / mutate-01~e.27 :ARG0-of (c6 / cause-01 :ARG1 (d5 / disease :wiki "Cancer" :name (n / name :op1 "cancer")))))) :ARG1 (d3 / deprive-01~e.34 :ARG0 t :ARG1 (f / feature-01~e.37 :ARG0 c2 :ARG1~e.38 (m3 / malignancy~e.39) :mod (t2 / this~e.35) :mod (v / vital~e.36)) :ARG2~e.40 (c2 / cell~e.42))) :ARG1-of (s4 / show-01~e.2 :ARG0 (w / we~e.1) :location (h / here~e.0) :ARG0-of (c3 / cause-01 :ARG1 (c4 / corroborate-01~e.45 :ARG1 (r / report~e.47 :time (p2 / previous~e.46) :ARG1-of (d4 / describe-01 :ARG0 (p3 / publication :ARG1-of (c5 / cite-01 :ARG2 6~e.50)))))))) # ::id a_pmid_2488_5690.54 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Sustained proliferative signaling is considered one of the major traits of cancer cells and is therefore used as a target mechanism of individualized therapy approaches including anti EGFR therapy strategies in colorectal cancer [ @ 21 , 22 @ ] . # ::alignments 0-1.1.1.2 2-1.1.1 4-1 8-1.1.2.2 9-1.1.2 10-1.1.2.1.r 11-1.1.2.1.1.2.1 12-1.1.2.1 15-1.2 16-1.2.1 17-1.2.1.2.r 19-1.2.1.2.1 20-1.2.1.2 21-1.2.1.2.2.r 22-1.2.1.2.2.1.1 23-1.2.1.2.2.1 24-1.2.1.2.2 25-1.1 25-1.2.1.2.2.2 26-1.2.1.2.2.2.1.1.1 27-1.2.1.2.2.2.1.1.1.1.1.1 28-1.2.1.2.2.2.1.1 29-1.2.1.2.2.2.1 30-1.2.1.2.2.2.1.2.r 31-1.2.1.2.2.2.1.2.2.1 32-1.1.2.1.1.2.1 32-1.2.1.2.2.2.1.2.2.2 35-1.3.1.1.1 39-1.2.1.2.2.2.2.1.1.1 (c / consider-01~e.4 :ARG1 (i / include-01~e.25 :ARG1 (s / signal-07~e.2 :ARG0-of (p / proliferate-01) :ARG1-of (s2 / sustain-01~e.0)) :ARG2 (t / trait~e.9 :poss~e.10 (c2 / cell~e.12 :mod (d2 / disease :wiki "Cancer" :name (n3 / name :op1 "cancer"~e.11,32))) :ARG1-of (m / major-02~e.8))) :ARG0-of (c4 / cause-01~e.15 :ARG1 (u / use-01~e.16 :ARG1 s :ARG2~e.17 (m2 / mechanism~e.20 :ARG1-of (t2 / target-01~e.19) :poss~e.21 (a / approach-02~e.24 :mod (t3 / therapy~e.23 :ARG1-of (i2 / individualize-02~e.22)) :ARG2-of (i3 / include-91~e.25 :ARG1 (s3 / strategy~e.29 :mod (t4 / therapy~e.28 :ARG0-of (c7 / counter-01~e.26 :ARG1 (e / enzyme :name (n2 / name :op1 "EGFR"~e.27)))) :prep-in~e.30 (d / disease :wiki "Colorectal_cancer" :name (n / name :op1 "colorectal"~e.31 :op2 "cancer"~e.32))) :ARG1-of (d4 / describe-01 :ARG0 (p3 / publication :ARG1-of (c6 / cite-01 :ARG2 22~e.39)))))))) :ARG1-of (d3 / describe-01 :ARG0 (p2 / publication :ARG1-of (c5 / cite-01 :ARG2 21~e.35)))) # ::id a_pmid_2488_5690.55 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In another context , mutant B @-@ Raf induced cellular senescence rather than proliferation [ @ 23 , 24 @ ] . # ::alignments 1-1.3.1 2-1.3 4-1.1 4-1.1.2 4-1.1.2.r 5-1.1.1.1 7-1.1.1.1 8-1 9-1.2.1 10-1.2 11-1.2.2 13-1.2.2.1 16-1.4.1.1.1.1 20-1.4.1.1.1.2 (i / induce-01~e.8 :ARG0 (e2 / enzyme~e.4 :name (n2 / name :op1 "B-Raf"~e.5,7) :ARG2-of~e.4 (m / mutate-01~e.4)) :ARG2 (s / senescence~e.10 :mod (c / cell~e.9) :ARG1-of (i2 / instead-of-91~e.11 :ARG2 (p / proliferate-01~e.13 :ARG0 c))) :condition (c2 / context~e.2 :mod (a / another~e.1)) :ARG1-of (d / describe-01 :ARG0 (p2 / publication :ARG1-of (c3 / cite-01 :ARG2 (a2 / and :op1 23~e.16 :op2 24~e.20))))) # ::id a_pmid_2488_5690.56 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , senescence can be overcome by phosphoinositide 3 @-@ kinase ( PI3K ) / AKT signaling [ @ 24 @ ] which is hyperactivated in RKO due to a PIK3CA mutation . # ::alignments 0-1 2-1.1.1.2 3-1.1 5-1.1.1 6-1.1.1.1.r 7-1.1.1.1.1.1.1 8-1.1.1.1.1.1.2 10-1.1.1.1.1.1.2 15-1.1.1.1.1.1.3 16-1.1.1.1 19-1.1.2.1.1.1 26-1.1.1.1.2.2.1.1 27-1.1.1.1.2.3 28-1.1.1.1.2.3 31-1.1.1.1.2.3.1.1.1.1 33-1.1.1.1.2.3.1 (c / contrast-01~e.0 :ARG2 (p / possible-01~e.3 :ARG1 (o / overcome-01~e.5 :ARG0~e.6 (s2 / signal-07~e.16 :ARG0 (p2 / pathway :name (n2 / name :op1 "phosphoinositide"~e.7 :op2 "3-kinase"~e.8,10 :op3 "AKT"~e.15)) :ARG1-of (a / activate-01 :degree (h / hyper) :location (c3 / cell-line :name (n3 / name :op1 "RKO"~e.26)) :ARG1-of (c4 / cause-01~e.27,28 :ARG0 (m / mutate-01~e.33 :ARG1 (g / gene :name (n / name :op1 "PIK3CA"~e.31)))))) :ARG1 (s / senescence~e.2)) :ARG1-of (d / describe-01 :ARG0 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 24~e.19))))) # ::id a_pmid_2488_5690.57 ::amr-annotator SDL-AMR-09 ::preferred # ::tok By staining of senescence @-@ associated β-galactosidase activity [ @ 25 @ ] we examined whether the differential proliferation rates observed upon serum deprivation were attributable to cellular senescence . # ::alignments 1-1.3 2-1.3.1.r 3-1.3.1.1.1.1 5-1.3.1.1.1.1 6-1.3.1.1.1.2 7-1.3.1 10-1.3.2.1.1.1 13-1.1 14-1 15-1.2.1 15-1.2.1.r 17-1.2.2.1.2 18-1.2.2.1.1 19-1.2.2.1 20-1.2.2.1.3 22-1.2.2.1.3.1.1 23-1.2.2.1.3.1 27-1.2.2.2.1 28-1.2.2.2 (e / examine-01~e.14 :ARG0 (w / we~e.13) :ARG1 (p / possible-01 :mode~e.15 interrogative~e.15 :ARG1 (a / attribute-01 :ARG1 (r / rate~e.19 :mod (p2 / proliferate-01~e.18) :ARG1-of (d / differ-02~e.17) :ARG1-of (o / observe-01~e.20 :condition (d3 / deprive-01~e.23 :ARG1 (s3 / serum~e.22)))) :ARG2 (s / senescence~e.28 :mod (c / cell~e.27)))) :manner (s2 / stain-01~e.1 :ARG1~e.2 (a2 / activity-06~e.7 :ARG0 (e2 / enzyme :name (n / name :op1 "senescence-associated"~e.3,5 :op2 "β-galactosidase"~e.6))) :ARG1-of (d2 / describe-01 :ARG0 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 25~e.10))))) # ::id a_pmid_2488_5690.58 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Cellular senescence was detected at very low levels in less than 5 % of cells ( Figure 2 @ D @-@ E ) , indicating that senescence alone cannot explain the strong reduction in cell growth observed upon withdrawal of serum . # ::alignments 0-1.1.1.1 0-1.2 1-1.1.1 3-1 5-1.1.2.1 6-1.1.2 7-1.1 9-1.2.1 10-1.2.1 11-1.2.1.1.1 12-1.2.1.1 14-1.2 16-1.3.1.1 16-1.3.1.2 25-1.4 26-1.4.1.r 27-1.4.1.2.1 28-1.4.1.2.1.1 29-1.4.1 29-1.4.1.1 29-1.4.1.1.r 30-1.4.1.2 32-1.4.1.2.2.2 33-1.4.1.2.2 34-1.4.1.2.2.1.r 35-1.4.1.2.2.1.1 36-1.4.1.2.2.1 37-1.4.1.2.2.3 39-1.4.1.2.2.3.1 40-1.4.1.2.2.3.1.1.r 41-1.4.1.2.2.3.1.1 (d / detect-01~e.3 :ARG1 (l2 / level~e.7 :quant-of (s / senescence~e.1 :mod (c / cell~e.0)) :ARG1-of (l3 / low-04~e.6 :degree (v / very~e.5))) :location (c2 / cell~e.0,14 :quant (l / less-than~e.9,10 :op1 (p / percentage-entity~e.12 :value 5~e.11))) :ARG1-of (d2 / describe-01 :ARG0 (a / and :op1 (f / figure~e.16 :name (n / name :op1 "2D")) :op2 (f2 / figure~e.16 :name (n2 / name :op1 "2E")))) :ARG0-of (i / indicate-01~e.25 :ARG1~e.26 (p2 / possible-01~e.29 :polarity~e.29 -~e.29 :ARG1 (e / explain-01~e.30 :ARG0 (s2 / senescence~e.27 :mod (a2 / alone~e.28)) :ARG1 (r / reduce-01~e.33 :ARG1~e.34 (g / grow-01~e.36 :ARG1 (c3 / cell~e.35)) :ARG2 (s4 / strong~e.32) :ARG1-of (o / observe-01~e.37 :condition (w / withdraw-01~e.39 :ARG1~e.40 (s3 / serum~e.41)))))))) # ::id a_pmid_2488_5690.59 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Flow cytometry revealed a significant increase of apoptotic cells in wild @-@ type compared to mutant clones upon withdrawal of serum ( Figure 2 @ F and G ) . # ::alignments 0-1.1.1.1 1-1.1.1.2 2-1 4-1.2.2 5-1.2 7-1.2.1.1 8-1.2.1 8-1.2.3 9-1.2.3.1.r 10-1.2.3.1 12-1.2.3.1 13-1.2.3.2.r 15-1.2.3.2.1 16-1.2.3.2 18-1.2.4 19-1.2.4.1.r 20-1.2.4.1 22-1.3.1.1 22-1.3.1.2 27-1.3.1 (r / reveal-01~e.2 :ARG0 (t / thing :name (n / name :op1 "flow"~e.0 :op2 "cytometry"~e.1)) :ARG1 (i / increase-01~e.5 :ARG1 (c / cell~e.8 :mod (a / apoptosis~e.7)) :ARG2 (s / significant-02~e.4) :location (c2 / cell~e.8 :mod~e.9 (w / wild-type~e.10,12) :compared-to~e.13 (c3 / clone~e.16 :ARG2-of (m / mutate-01~e.15))) :condition (w2 / withdraw-01~e.18 :ARG1~e.19 (s2 / serum~e.20))) :ARG1-of (d / describe-01 :ARG0 (a2 / and~e.27 :op1 (f / figure~e.22 :mod "2F") :op2 (f2 / figure~e.22 :mod "2G")))) # ::id a_pmid_2488_5690.60 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Apoptosis was confirmed by the detection of cleaved caspase 3 at considerable levels in serum @-@ starved RBW @-@ 1 , while all other samples showed full @-@ length protein only ( Figure 2 @ H ) . # ::alignments 0-1.1.2 2-1.1 3-1.1.1.r 5-1.1.1 6-1.1.1.1.r 7-1.1.1.1.1.2 8-1.1.1.1.1.1.1 9-1.1.1.1.1.1.2 11-1.1.1.1.2 12-1.1.1.1 13-1.1.1.2.r 14-1.1.1.2.2.1 16-1.1.1.2.2 17-1.1.1.2.1.1 19-1.1.1.2.1.1 21-1 22-1.2.1.1 23-1.2.1.2 24-1.2.1 24-1.2.1.3 24-1.2.1.3.r 25-1.2 26-1.2.2.1.1 28-1.2.2.1 29-1.2.2 30-1.2.3 32-1.3.1 (c5 / contrast-01~e.21 :ARG1 (c / confirm-01~e.2 :ARG0~e.3 (d / detect-01~e.5 :ARG1~e.6 (l / level~e.12 :quant-of (p2 / protein :name (n / name :op1 "caspase"~e.8 :op2 3~e.9) :ARG1-of (c2 / cleave-01~e.7)) :quant (c3 / considerable~e.11)) :location~e.13 (c4 / cell-line :name (n2 / name :op1 "RBW-1"~e.17,19) :ARG1-of (s / starve-01~e.16 :ARG2 (s2 / serum~e.14)))) :ARG1 (a / apoptosis~e.0)) :ARG2 (s3 / show-01~e.25 :ARG0 (t / thing~e.24 :mod (a2 / all~e.22) :mod (o / other~e.23) :ARG1-of~e.24 (s4 / sample-01~e.24)) :ARG1 (p / protein~e.29 :ARG1-of (l2 / long-03~e.28 :degree (f / full~e.26))) :mod (o2 / only~e.30)) :ARG1-of (d2 / describe-01 :ARG0 (f2 / figure~e.32 :mod "2H"))) # ::id a_pmid_2488_5690.61 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Consistent with RKO modeling a distinct subpopulation of patients characterized by the presence of certain molecular features and the absence of others [ @ 7 @ ] , no implication of p53 in apoptosis was observed ( Figure 2 @ H ) . # ::alignments 0-1.2 1-1.2.1.r 2-1.2.1.1.1.1 3-1.2.1 5-1.2.1.2.2 6-1.2.1.2 7-1.2.1.2.1.r 8-1.2.1.2.1 9-1.2.1.2.3 13-1.2.1.2.3.1.r 14-1.2.1.2.3.1.1.2.2 15-1.2.1.2.3.1.1.2.1 16-1.2.1.2.3.1.1.2 16-1.2.1.2.3.1.2.2 17-1.2.1.2.3.1 20-1.2.1.2.3.1.2.2.2.r 21-1.2.1.2.3.1.2.2.2 24-1.2.1.3.1.1.1 28-1.1.1 28-1.1.1.r 29-1.1 30-1.1.2.r 31-1.1.2.1.1 32-1.1.3.r 33-1.1.3 35-1 37-1.3.1 (o / observe-01~e.35 :ARG1 (i / implicate-01~e.29 :polarity~e.28 -~e.28 :ARG1~e.30 (p / protein :name (n / name :op1 "p53"~e.31)) :ARG2~e.32 (a / apoptosis~e.33)) :ARG1-of (c / consistent-01~e.0 :ARG2~e.1 (m / model-01~e.3 :ARG0 (c2 / cell-line :name (n2 / name :op1 "RKO"~e.2)) :ARG1 (s / subpopulation~e.6 :mod~e.7 (p2 / patient~e.8) :mod (d / distinct~e.5) :ARG1-of (c3 / characterize-01~e.9 :ARG2~e.13 (a2 / and~e.17 :op1 (h / have-03 :ARG0 s :ARG1 (f / feature~e.16 :mod (m2 / molecule~e.15) :mod (c4 / certain~e.14))) :op2 (l / lack-01 :ARG0 s :ARG1 (f2 / feature~e.16 :mod m2 :mod~e.20 (o2 / other~e.21)))))) :ARG1-of (d2 / describe-01 :ARG0 (p3 / publication :ARG1-of (c5 / cite-01 :ARG2 7~e.24))))) :ARG1-of (d3 / describe-01 :ARG0 (f3 / figure~e.37 :mod "2H"))) # ::id a_pmid_2488_5690.62 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Since serum starvation is often used to model apoptosis mediated via the PUMA pathway [ @ 26 @ ] , we also analyzed PUMA protein levels . # ::alignments 0-1.3.1.3.r 1-1.3.1.1.1 2-1.3.1.1 4-1.3.1.2 5-1.3.1 5-1.3.1.3.r 7-1.3.1.3 8-1.3.1.3.2 9-1.3.1.3.2.1 12-1.3.1.3.2.1.1.1.1 13-1.3.1.3.2.1.1 16-1.3.1.4.1.1.1 20-1.1 21-1.4 22-1 23-1.2.1.1.1 24-1.2.1 25-1.2 (a / analyze-01~e.22 :ARG0 (w / we~e.20) :ARG1 (l / level~e.25 :quant-of (p / protein~e.24 :name (n / name :op1 "PUMA"~e.23))) :ARG1-of (c / cause-01 :ARG0 (u / use-01~e.5 :ARG1 (s / starve-01~e.2 :ARG2 (s2 / serum~e.1)) :frequency (o / often~e.4) :purpose~e.0,5 (m / model-01~e.7 :ARG0 s :ARG1 (a2 / apoptosis~e.8 :ARG1-of (m2 / mediate-01~e.9 :instrument (p2 / pathway~e.13 :name (n2 / name :op1 "PUMA"~e.12))))) :ARG1-of (d / describe-01 :ARG0 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 26~e.16))))) :mod (a3 / also~e.21)) # ::id a_pmid_2488_5690.63 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PUMA was found to be highly abundant specifically in serum starved RBW @-@ 1 ( Figure 2 @ H ) . # ::alignments 0-1.3.1.1 1-1.3.r 2-1.4 4-1.3.r 5-1.2 6-1 7-1.6 8-1.1.r 9-1.1.2.1 10-1.1.2 11-1.1.1.1 13-1.1.1.1 15-1.5.1 (a / abundant~e.6 :op1~e.8 (c / cell-line :name (n2 / name :op1 "RBW-1"~e.11,13) :ARG1-of (s / starve-01~e.10 :ARG2 (s2 / serum~e.9))) :ARG1-of (h / high-02~e.5) :domain~e.1,4 (p / protein :name (n / name :op1 "PUMA"~e.0)) :ARG1-of (f / find-01~e.2) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.15 :mod "2H")) :ARG1-of (s3 / specific-02~e.7)) # ::id a_pmid_2488_5690.64 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Consistent with data previously shown by others , starvation @-@ induced apoptosis is mediated by PUMA in a p53 @-@ independent fashion in our experiments [ @ 27 @ ] . # ::alignments 0-1.5 1-1.5.1.r 2-1.5.1 3-1.5.1.1.2 4-1.5.1.1 5-1.5.1.1.1.r 6-1.5.1.1.1.1 8-1.2.1.1 10-1.2.1 11-1.2 13-1 14-1.1.r 15-1.1.1.1 16-1.3.r 18-1.3.2.1.1 20-1.3 20-1.3.1 20-1.3.1.r 22-1.4.r 23-1.4.1 23-1.4.1.r 24-1.4 27-1.5.1.2.1.1.1 (m / mediate-01~e.13 :ARG0~e.14 (p / protein :name (n / name :op1 "PUMA"~e.15)) :ARG1 (a / apoptosis~e.11 :ARG2-of (i / induce-01~e.10 :ARG0 (s / starve-01~e.8))) :manner~e.16 (d / depend-01~e.20 :polarity~e.20 -~e.20 :ARG1 (p2 / protein :name (n2 / name :op1 "p53"~e.18))) :time~e.22 (e / experiment-01~e.24 :ARG0~e.23 (w / we~e.23)) :ARG1-of (c / consistent-01~e.0 :ARG2~e.1 (d2 / data~e.2 :ARG1-of (s2 / show-01~e.4 :ARG0~e.5 (p5 / person :mod (o / other~e.6)) :time (p3 / previous~e.3)) :ARG1-of (d3 / describe-01 :ARG0 (p4 / publication :ARG1-of (c2 / cite-01 :ARG2 27~e.27)))))) # ::id a_pmid_2488_5690.65 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Programmed cell death is a key feature of proliferation control in homeostasis and overcoming apoptosis is considered another hallmark of cancer cells [ @ 28 @ ] . # ::alignments 0-1.1.1.1.2 1-1.1.1.1.1 2-1.1.1.1 5-1.1.1 6-1.1 7-1.1.2.r 8-1.1.2.1 9-1.1.2 10-1.1.3.r 11-1.1.3 12-1 13-1.2.1.2 14-1.2.1.2.1 15-1.2.1.2.r 16-1.2 17-1.2.1.3 18-1.2.1 19-1.2.1.1.r 20-1.2.1.1.1.2.1 21-1.2.1.1 24-1.2.2.1.1.1 (a / and~e.12 :op1 (f / feature~e.6 :ARG1-of (k / key-02~e.5 :ARG2 (d2 / die-01~e.2 :ARG1 (c / cell~e.1) :ARG1-of (p / program-01~e.0))) :part-of~e.7 (c2 / control-01~e.9 :ARG1 (p2 / proliferate-01~e.8)) :prep-in~e.10 (h / homeostasis~e.11)) :op2 (c3 / consider-01~e.16 :ARG1 (h2 / hallmark~e.18 :mod~e.19 (c4 / cell~e.21 :mod (d / disease :wiki "Cancer" :name (n / name :op1 "cancer"~e.20))) :domain~e.15 (o / overcome-01~e.13 :ARG1 (a2 / apoptosis~e.14)) :mod (a3 / another~e.17)) :ARG1-of (d3 / describe-01 :ARG0 (p3 / publication :ARG1-of (c6 / cite-01 :ARG2 28~e.24))))) # ::id a_pmid_2488_5690.66 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Since virtually all malignant cancer cells show apoptosis resistance , the induction of apoptotic pathways is considered a particularly promising approach for therapeutic strategies [ @ 29 @ ] . # ::alignments 0-1.2 1-1.2.1.1.1.1 2-1.2.1.1.1 3-1.2.1.1.2 3-1.2.1.1.2.3 3-1.2.1.1.2.3.r 4-1.2.1.1.2.2.1 5-1.2.1.1 6-1.2.1 7-1.2.1.2.2 8-1.2.1.2 11-1.1.1 12-1.1.1.1.r 13-1.1.1.1.1 14-1.1.1.1 16-1 18-1.1.3.1 19-1.1.3 20-1.1 21-1.1.2.r 22-1.1.2.1 23-1.1.2 26-1.3.1.1.1 (c / consider-01~e.16 :ARG1 (a / approach-02~e.20 :ARG0 (i / induce-01~e.11 :ARG2~e.12 (p3 / pathway~e.14 :mod a4~e.13)) :ARG1~e.21 (s / strategy~e.23 :mod (t / therapy~e.22)) :ARG2-of (p / promise-01~e.19 :degree (p2 / particular~e.18))) :ARG1-of (c2 / cause-01~e.0 :ARG0 (s2 / show-01~e.6 :ARG0 (c3 / cell~e.5 :mod (a3 / all~e.2 :degree (v / virtual~e.1)) :mod (d / disease~e.3 :wiki "Cancer" :name (n / name :op1 "cancer"~e.4) :ARG2-of~e.3 (m / malignant-02~e.3))) :ARG1 (r / resist-01~e.8 :ARG0 c3 :ARG1 (a4 / apoptosis~e.7)))) :ARG1-of (d2 / describe-01 :ARG0 (p4 / publication :ARG1-of (c5 / cite-01 :ARG2 29~e.26)))) # ::id a_pmid_2488_5690.67 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Our results show that in RKO this particular cancer cell trait is modulated by and dependent on B @-@ Raf @^V600E and that targeting mutant BRAF is sufficient to restore sensitivity to caspase @-@ dependent apoptosis after serum withdrawal via p53 @-@ independent PUMA induction [ @ 27 @ ] . # ::alignments 0-1.1.2 0-1.1.2.r 1-1.1 1-1.1.1 1-1.1.1.r 2-1 5-1.2.1.3.1.1 6-1.2.1.1.2.3 7-1.2.1.1.2.2 8-1.2.1.1.2.1.1.2.1 9-1.2.1.1.2.1 10-1.2.1.1.2 12-1.2.1.1 14-1.2.1 15-1.2.1.2 17-1.2.1.1.1.1.1 19-1.2.1.1.1.1.1 21-1.2.1.1.1.2.1 23-1.2 23-1.2.1 23-1.2.1.r 24-1.2.r 25-1.2.2.1 26-1.2.1.1.1 26-1.2.1.1.1.2 26-1.2.1.1.1.2.r 26-1.2.2.1.1 26-1.2.2.1.1.2 26-1.2.2.1.1.2.r 28-1.2.2.1.1.1.1 31-1.2.2 33-1.2.2.2 34-1.2.2.2.2 35-1.2.2.2.2.1.r 36-1.2.2.2.2.1.1.1.1.1 38-1.2.2.2.2.1.1 39-1.2.2.2.2.1 40-1.2.2.2.2.1.2 41-1.2.2.2.2.1.2.1.1 42-1.2.2.2.2.1.2.1 44-1.2.2.2.2.1.3.2.2.1.1 46-1.2.2.2.2.1.3.2 46-1.2.2.2.2.1.3.2.1 46-1.2.2.2.2.1.3.2.1.r 47-1.2.2.2.2.1.3.1.1.1 48-1.2.2.2.2.1.3 51-1.2.2.2.2.1.3.3.1.1.1 (s / show-01~e.2 :ARG0 (t4 / thing~e.1 :ARG1-of~e.1 (r / result-01~e.1) :poss~e.0 (w / we~e.0)) :ARG1~e.24 (a / and~e.23 :op1~e.23 (a2 / and~e.14,23 :op1 (m / modulate-01~e.12 :ARG0 (e2 / enzyme~e.26 :name (n3 / name :op1 "B-Raf"~e.17,19) :ARG2-of~e.26 (m2 / mutate-01~e.26 :value "V600E"~e.21)) :ARG1 (t / trait~e.10 :mod (c / cell~e.9 :mod (d5 / disease :wiki "Cancer" :name (n / name :op1 "cancer"~e.8))) :mod (p / particular~e.7) :mod (t3 / this~e.6))) :op2 (d2 / depend-01~e.15 :ARG0 t :ARG1 e2) :location (c3 / cell-line :name (n4 / name :op1 "RKO"~e.5))) :op2 (s2 / suffice-01~e.31 :ARG0 (t2 / target-01~e.25 :ARG1 (g / gene~e.26 :name (n5 / name :op1 "BRAF"~e.28) :ARG2-of~e.26 (m3 / mutate-01~e.26))) :ARG1 (r2 / restore-01~e.33 :ARG0 t2 :ARG1 (s3 / sensitive-03~e.34 :ARG1~e.35 (a3 / apoptosis~e.39 :ARG0-of (d3 / depend-01~e.38 :ARG1 (p2 / protein :name (n6 / name :op1 "caspase"~e.36))) :time (a4 / after~e.40 :op1 (w2 / withdraw-01~e.42 :ARG1 (s4 / serum~e.41))) :instrument (i / induce-01~e.48 :ARG2 (p3 / protein :name (n7 / name :op1 "PUMA"~e.47)) :ARG0-of (d4 / depend-01~e.46 :polarity~e.46 -~e.46 :ARG1 (p4 / protein :name (n8 / name :op1 "p53"~e.44))) :ARG1-of (d / describe-01 :ARG0 (p5 / publication :ARG1-of (c4 / cite-01 :ARG2 27~e.51)))))))))) # ::id a_pmid_2488_5690.68 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Complementing and extending previous studies , we thus provide evidence from an endogenous and quantitative genetic model of BRAF @ -@ mutant colorectal cancer cells , thereby ruling out the occurrence of artifacts caused by unspecific cellular response or incomplete knockdown in RNAi setups and , likewise , avoiding inter @-@ species bias potentially experienced in mouse models of colorectal cancer [ @ 30 @ ] . # ::alignments 0-1.2 2-1.3 3-1.2.1.1 4-1.2.1 6-1.1.1 7-1.1.3 8-1.1 9-1.1.2 10-1.1.2.1.r 12-1.1.2.1.3 14-1.1.2.1.2 16-1.1.2.1 19-1.1.2.1.1.1.1.1 22-1.1.2.1.1.1 22-1.1.2.1.1.1.2 22-1.1.2.1.1.1.2.r 23-1.1.2.1.1.2.2.1 24-1.1.2.1.1.2.2.2 25-1.1.2.1.1 28-1.1.3.1.1 29-1.1.3.1.1 32-1.1.3.1.1.1.r 33-1.1.3.1.1.1 34-1.1.3.1.1.1.1 35-1.1.3.1.1.1.1.1.r 36-1.1.3.1.1.1.1.1.1.2 36-1.1.3.1.1.1.1.1.1.2.1 36-1.1.3.1.1.1.1.1.1.2.1.r 37-1.1.3.1.1.1.1.1.1.1 38-1.1.3.1.1.1.1.1.1 39-1.1.3.1.1.1.1.1 40-1.1.3.1.1.1.1.1.2.1 40-1.1.3.1.1.1.1.1.2.1.1 40-1.1.3.1.1.1.1.1.2.1.1.r 41-1.1.3.1.1.1.1.1.2 44-1.1.3.1.1.1.1.1.2.2 45-1.1.3.1 49-1.1.3.1.2 50-1.1.3.1.2.1.1 52-1.1.3.1.2.1.1 53-1.1.3.1.2.1 55-1.1.3.1.2.1.2 56-1.1.3.1.2.1.2.2.r 57-1.1.3.1.2.1.2.2.2 58-1.1.3.1.2.1.2.2 60-1.1.2.1.1.2.2.1 61-1.1.2.1.1.2.2.2 64-1.1.3.1.2.1.2.2.3.1.1.1 (i / infer-01 :ARG1 (p / provide-01~e.8 :ARG0 (w / we~e.6) :ARG1 (e / evidence~e.9 :source~e.10 (m2 / model~e.16 :mod (c / cell~e.25 :location-of (g / gene~e.22 :name (n3 / name :op1 "BRAF"~e.19) :ARG2-of~e.22 (m / mutate-01~e.22)) :mod (d / disease :wiki "Colorectal_cancer" :name (n / name :op1 "colorectal"~e.23,60 :op2 "cancer"~e.24,61))) :mod (q / quantity~e.14) :mod (e2 / endogenous~e.12) :mod (g2 / gene))) :ARG0-of (c2 / cause-01~e.7 :ARG1 (a / and~e.45 :op1 (r / rule-out-02~e.28,29 :ARG1~e.32 (a2 / artifact~e.33 :ARG1-of (c3 / cause-01~e.34 :ARG0~e.35 (o2 / or~e.39 :op1 (r2 / respond-01~e.38 :ARG0 (c4 / cell~e.37) :ARG1-of (s / specific-02~e.36 :polarity~e.36 -~e.36)) :op2 (k / knock-down-02~e.41 :ARG1-of (c5 / complete-01~e.40 :polarity~e.40 -~e.40) :location (s2 / setup~e.44 :mod (i3 / interfere-01 :ARG1 (n2 / nucleic-acid :name (n4 / name :op1 "RNA"))))))))) :op2 (a3 / avoid-01~e.49 :ARG1 (b / bias-01~e.53 :mod (i2 / inter-species~e.50,52) :ARG1-of (e3 / experience-01~e.55 :ARG1-of (p2 / possible-01) :location~e.56 (m3 / model~e.58 :mod (d2 / disease) :mod (m4 / mouse~e.57) :ARG1-of (d3 / describe-01 :ARG0 (p3 / publication :ARG1-of (c6 / cite-01 :ARG2 30~e.64)))))))))) :ARG1-of (c7 / complement-01~e.0 :ARG2 (s3 / study-01~e.4 :time (p4 / previous~e.3))) :ARG0-of (e4 / extend-01~e.2 :ARG1 s3)) # ::id bel_pmid_1064_0734.39802 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In this paper we demonstrate that expression of CD72 down @-@ modulates both extracellular signal @-@ related kinase ( ERK ) activation and Ca2+ mobilization induced by BCR ligation in the mouse B lymphoma line K46^mA , whereas BCR @-@ mediated ERK activation was not reduced by the ITIM @-@ mutated form of CD72 . # ::alignments 1-1.3.1 2-1.3 3-1.1 4-1 6-1.2.2 7-1.2.2.1.r 8-1.2.2.1.1.1 13-1.2.1.1.1.1.1 14-1.2.1.1.1.1.2 16-1.2.1.1.1.1.2 17-1.2.1.1.1.1.3 19-1.2.1.1.1.2.1.1.1 21-1.2.1.1 22-1.2.1 24-1.2.1.2 25-1.2.1.3 26-1.2.1.3.1.r 27-1.2.1.3.1.1.1.1 28-1.2.1.3.1 29-1.2.1.3.2.r 31-1.2.1.3.2.2 32-1.2.1.3.2.3.1.1 33-1.2.1.3.2.3.2 34-1.2.1.3.2 35-1.2.1.3.2.1.1 37-1.2.3 38-1.2.3.1.3.2.1 40-1.2.3.1.3.2 41-1.2.3.1.3.1 42-1.2.3.1.3 44-1.2.3.1.1 44-1.2.3.1.1.r 45-1.2.3.1 46-1.2.3.1.2.r 48-1.2.3.1.2.2.1.1.1 50-1.2.3.1.2.2 53-1.2.2.1.1.1 53-1.2.3.1.2.1.1 (d / demonstrate-01~e.4 :ARG0 (w / we~e.3) :ARG1 (d2 / downmodulate-01 :ARG1 (a / and~e.22 :op1 (a2 / activate-01~e.21 :ARG1 (e4 / enzyme :name (n3 / name :op1 "extracellular"~e.13 :op2 "signal-related"~e.14,16 :op3 "kinase"~e.17) :ARG1-of (d3 / describe-01 :ARG2 (e3 / enzyme :name (n4 / name :op1 "ERK"~e.19))))) :op2 (m / mobilize-01~e.24 :ARG1 (c4 / calcium :ARG1-of (i2 / ionize-01 :value "2+"))) :ARG2-of (i / induce-01~e.25 :ARG0~e.26 (l / ligate-01~e.28 :ARG1 (p3 / protein :name (n6 / name :op1 "BCR"~e.27))) :location~e.29 (c / cell-line~e.34 :name (n7 / name :op1 "K46^mA"~e.35) :mod (m2 / mouse~e.31) :consist-of (c3 / cell :name (n / name :op1 "B"~e.32) :part-of (l2 / lymphoma~e.33))))) :ARG2 (e2 / express-03~e.6 :ARG2~e.7 (p2 / protein :name (n2 / name :op1 "CD72"~e.8,53))) :ARG1-of (c2 / contrast-01~e.37 :ARG2 (r / reduce-01~e.45 :polarity~e.44 -~e.44 :ARG0~e.46 (p4 / protein :name (n8 / name :op1 "CD72"~e.53) :ARG2-of (m4 / mutate-01~e.50 :ARG0 (p5 / protein-segment :name (n9 / name :op1 "ITIM"~e.48)))) :ARG1 (a3 / activate-01~e.42 :ARG1 e3~e.41 :ARG1-of (m3 / mediate-01~e.40 :ARG0 p3~e.38))))) :medium (p / paper~e.2 :mod (t / this~e.1))) # ::id bel_pmid_1064_0734.39804 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Results CD72 negatively regulates both ERK activation and Ca2+ mobilization induced by BCR ligation in the K46^mk B lymphoma cells To investigate the signaling function of CD72 , we assessed CD72 expression on the surface of B cell lines by flow cytometry . # ::alignments 0-1.1 0-1.1.1 0-1.1.1.r 1-1.2.2.1.1 2-1.2 3-1.2 5-1.2.1.1.1.1.1 6-1.2.1.1 7-1.2.1 9-1.2.1.2 10-1.2.1.3 11-1.2.1.3.1.r 12-1.2.1.3.1.1.1.1 13-1.2.1.3.1 14-1.2.3.r 16-1.2.3.1.1 17-1.2.3.2.1.1 18-1.2.3.2.2 19-1.2.3 19-1.2.3.2 19-1.2.3.2.r 21-1.3.4 23-1.3.4.2.2 24-1.3.4.2 25-1.3.4.2.1.r 26-1.3.4.2.1 28-1.3.1 29-1.3 30-1.3.2.1.1.1 31-1.3.2 32-1.3.2.2.r 34-1.3.2.2 35-1.3.2.2.1.r 36-1.3.2.2.1.1.1.1 37-1.3.2.2.1 38-1.3.2.2.1 39-1.3.3.r 40-1.3.3.1 41-1.3.3 (m / multi-sentence :snt1 (t / thing~e.0 :ARG2-of~e.0 (r / result-01~e.0)) :snt1 (d / downregulate-01~e.2,3 :ARG1 (a / and~e.7 :op1 (a2 / activate-01~e.6 :ARG1 (e2 / enzyme :name (n4 / name :op1 "ERK"~e.5))) :op2 (m2 / mobilize-01~e.9 :ARG1 (c6 / calcium :ARG1-of (i3 / ionize-01 :value "2+"))) :ARG2-of (i / induce-01~e.10 :ARG0~e.11 (l / ligate-01~e.13 :ARG1 (p2 / protein :name (n6 / name :op1 "BCR"~e.12))))) :ARG2 (p / protein :name (n3 / name :op1 "CD72"~e.1)) :location~e.14 (c / cell-line~e.19 :name (n7 / name :op1 "K46^mk"~e.16) :consist-of~e.19 (c5 / cell~e.19 :name (n9 / name :op1 "B"~e.17) :part-of (l2 / lymphoma~e.18)))) :snt3 (a3 / assess-01~e.29 :ARG0 (w / we~e.28) :ARG1 (e3 / express-03~e.31 :ARG2 (p3 / protein :name (n8 / name :op1 "CD72"~e.30)) :location~e.32 (s2 / surface~e.34 :part-of~e.35 (c2 / cell-line~e.37,38 :consist-of (c4 / cell :name (n / name :op1 "B"~e.36))))) :instrument~e.39 (c3 / cytometry~e.41 :mod (f / flow~e.40)) :purpose (i2 / investigate-01~e.21 :ARG0 w :ARG1 (f2 / function-01~e.24 :ARG0~e.25 p3~e.26 :ARG1 (s3 / signal-07~e.23))))) # ::id bel_pmid_1064_0734.39810 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , both of the CD72 transfectants showed reduced phosphorylation of ERK1 and ERK2 compared to that of the parent cells regardless of the duration of Ag stimulation . # ::alignments 0-1 2-1.1.1.1 5-1.1.1.2.1.1.1 6-1.1.1 6-1.1.1.2 6-1.1.1.2.r 7-1.1 8-1.1.2.2 9-1.1.2 10-1.1.2.1.r 11-1.1.2.1.1.1.1 12-1.1.2.1 13-1.1.2.1.2.1.1 14-1.1.2.2.1.r 19-1.1.2.2.1.1 20-1.1.2.2.1 21-1.1.2.2.2 24-1.1.2.2.2.1 27-1.1.2.2.2.1.1 (h / have-concession-91~e.0 :ARG1 (s2 / show-01~e.7 :ARG0 (m / molecular-physical-entity~e.6 :mod (b / both~e.2) :ARG1-of~e.6 (t / transfect-01~e.6 :ARG2 (p2 / protein :name (n2 / name :op1 "CD72"~e.5)))) :ARG1 (p / phosphorylate-01~e.9 :ARG1~e.10 (a / and~e.12 :op1 (e / enzyme :name (n3 / name :op1 "ERK1"~e.11)) :op2 (e2 / enzyme :name (n4 / name :op1 "ERK2"~e.13))) :ARG1-of (r / reduce-01~e.8 :compared-to~e.14 (c3 / cell~e.20 :mod (p4 / parent~e.19)) :ARG1-of (r2 / regardless-91~e.21 :ARG2 (d / duration~e.24 :poss (s / stimulate-01~e.27 :ARG2 (a2 / antigen)))))))) # ::id bel_pmid_1064_0734.39812 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Taken together , expression of CD72 most probably down @-@ modu @-@ lates phosphorylation of ERK induced by BCR signaling . # ::alignments 0-1.2 1-1.2.1 3-1.1.2.2 4-1.1.2.2.1.r 5-1.1.2.2.1.1.1 6-1.1.1 7-1.1 13-1.1.2.1 14-1.1.2.1.1.r 15-1.1.2.1.1.1.1 16-1.1.2.1.2 17-1.1.2.1.2.1.r 18-1.1.2.1.2.1.1.1.1 19-1.1.2.1.2.1 (h / have-condition-91 :ARG1 (p3 / probable~e.7 :degree (m / most~e.6) :domain (d / downmodulate-01 :ARG1 (p / phosphorylate-01~e.13 :ARG1~e.14 (e / enzyme :name (n / name :op1 "ERK"~e.15)) :ARG2-of (i / induce-01~e.16 :ARG0~e.17 (s / signal-07~e.19 :ARG0 (p4 / protein :name (n3 / name :op1 "BCR"~e.18))))) :ARG2 (e2 / express-03~e.3 :ARG2~e.4 (p2 / protein :name (n2 / name :op1 "CD72"~e.5))))) :ARG2 (t / take-01~e.0 :mod (t2 / together~e.1))) # ::id bel_pmid_1064_0734.39814 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Indeed , in vitro kinase assay showed that the activity of ERK2 in Ag @-@ stimulated K46^mA CD72 transfectants was lower than that of Ag @-@ stimulated K46^mA ( Fig . 3 ) . # ::alignments 0-1.3 2-1.1.2 3-1.1.2 4-1.1.1 5-1.1 6-1 7-1.2.r 9-1.2.1 9-1.2.3 10-1.2.1.1.r 11-1.2.1.1.1.1 12-1.1.2 15-1.2.1.2.1.2 16-1.2.1.2.1.1.1 17-1.2.1.2.2.1.1.1 18-1.2.1.2 18-1.2.1.2.2 18-1.2.1.2.2.r 20-1.2 20-1.2.2 20-1.2.2.r 21-1.2.3.r 26-1.2.3.1 27-1.2.3.1 29-1.4.1 31-1.4.1.1 (s / show-01~e.6 :ARG0 (a / assay-01~e.5 :ARG1 (k / kinase~e.4) :manner (i / in-vitro~e.2,3,12)) :ARG1~e.7 (l / low-04~e.20 :ARG1 (a2 / activity-06~e.9 :ARG0~e.10 (e / enzyme :name (n / name :op1 "ERK2"~e.11)) :location (m2 / molecular-physical-entity~e.18 :part-of (c2 / cell-line :name (n4 / name :op1 "K46^mA"~e.16) :ARG1-of (s2 / stimulate-01~e.15 :ARG2 (a4 / antigen))) :ARG1-of~e.18 (t / transfect-01~e.18 :ARG2 (p / protein :name (n3 / name :op1 "CD72"~e.17))))) :degree~e.20 (m / more~e.20) :compared-to~e.21 (a3 / activity-06~e.9 :location c2~e.26,27)) :mod (i2 / indeed~e.0) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.29 :mod 3~e.31))) # ::id bel_pmid_1064_0734.39818 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , the CD72 transfectants showed less increase in the intracellular Ca2+ concentration than the parent K46^mA cells did . # ::alignments 0-1 3-1.1.1.1.1.1.1 4-1.1.1 4-1.1.1.1 4-1.1.1.1.r 5-1.1 6-1.1.2.2 7-1.1.2 8-1.1.2.1.r 10-1.1.2.1.2 12-1.1.2.1 13-1.1.2.3.r 15-1.1.2.3.2 16-1.1.2.3.1.1 17-1.1.2.3 (h / have-concession-91~e.0 :ARG1 (s / show-01~e.5 :ARG0 (m / molecular-physical-entity~e.4 :ARG1-of~e.4 (t / transfect-01~e.4 :ARG2 (p / protein :name (n2 / name :op1 "CD72"~e.3)))) :ARG1 (i / increase-01~e.7 :ARG1~e.8 (c3 / concentrate-02~e.12 :ARG0 (c / calcium :ARG1-of (i3 / ionize-01 :value "2+")) :mod (i2 / intracellular~e.10)) :ARG2 (l / less~e.6) :compared-to~e.13 (c4 / cell-line~e.17 :name (n4 / name :op1 "K46^mA"~e.16) :mod (p2 / parent~e.15))))) # ::id bel_pmid_1064_0734.39820 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Thus , expression of CD72 appears to negatively regulate BCR @-@ mediated Ca2+ mobilization in K46^mA cells . # ::alignments 2-1.1.1.2 3-1.1.1.2.1.r 4-1.1.1.2.1.1.1 5-1.1 7-1.1.1 8-1.1.1 9-1.1.1.1.2.1.1.1 11-1.1.1.1.2 13-1.1.1.1 14-1.1.1.3.r 15-1.1.1.3.1.1 16-1.1.1.3 (i / infer-01 :ARG1 (a / appear-02~e.5 :ARG1 (d / downregulate-01~e.7,8 :ARG1 (m / mobilize-01~e.13 :ARG1 (c2 / calcium :ARG1-of (i2 / ionize-01 :value "2+")) :ARG1-of (m2 / mediate-01~e.11 :ARG0 (p2 / protein :name (n4 / name :op1 "BCR"~e.9)))) :ARG2 (e / express-03~e.2 :ARG2~e.3 (p / protein :name (n / name :op1 "CD72"~e.4))) :location~e.14 (c / cell-line~e.16 :name (n5 / name :op1 "K46^mA"~e.15))))) # ::id bel_pmid_1064_0734.39822 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Taken together , CD72 down @-@ modulates both ERK activation and Ca2+ mobilization induced by BCR ligation , strongly suggesting that CD72 negatively regulates BCR signaling in K46^mA cells . # ::alignments 0-1.2 1-1.2.1 3-1.1.2.1.1 8-1.1.1.1.1.1.1 9-1.1.1.1 10-1.1.1 12-1.1.1.2 13-1.1.1.3 14-1.1.1.3.1.r 15-1.1.1.3.1.1.1.1 16-1.1.1.3.1 18-1.1.3.2 19-1.1.3 20-1.1.3.1.r 21-1.1.3.1.2 22-1.1.3.1 23-1.1.3.1 24-1.1.3.1.1.1 25-1.1.3.1.1 26-1.1.3.1.3.r 27-1.1.3.1.3.1.1 28-1.1.3.1.3 (h / have-condition-91 :ARG1 (d / downmodulate-01 :ARG1 (a / and~e.10 :op1 (a2 / activate-01~e.9 :ARG1 (e2 / enzyme :name (n3 / name :op1 "ERK"~e.8))) :op2 (m / mobilize-01~e.12 :ARG1 (c2 / calcium :ARG1-of (i2 / ionize-01 :value "2+"))) :ARG2-of (i / induce-01~e.13 :ARG0~e.14 (l / ligate-01~e.16 :ARG1 (p2 / protein :name (n5 / name :op1 "BCR"~e.15))))) :ARG2 (p / protein :name (n2 / name :op1 "CD72"~e.3)) :ARG0-of (s2 / suggest-01~e.19 :ARG1~e.20 (d2 / downregulate-01~e.22,23 :ARG1 (s4 / signal-07~e.25 :ARG0 p2~e.24) :ARG2 p~e.21 :location~e.26 (c / cell-line~e.28 :name (n6 / name :op1 "K46^mA"~e.27))) :ARG1-of (s3 / strong-02~e.18))) :ARG2 (t / take-01~e.0 :mod (t2 / together~e.1))) # ::id bel_pmid_1064_0734.39824 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Western blotting of total cell lysates using anti @-@ phospho @-@ ERK Ab showed that both ERK1 and ERK2 were phosphorylated by either BCR ligation alone or coligation of BCR and CD72 ( Fig . 6B ) . # ::alignments 0-1.1 1-1.1 2-1.1.1.r 3-1.1.1.2 4-1.1.1.1 5-1.1.1 7-1.1.2.1 9-1.1.2.1.1.2 11-1.1.2.1.1.1.1 13-1 16-1.2.1.1.1.1 17-1.2.1 18-1.2.1.2.1.1 20-1.2 23-1.2.2.1.1.1.1 24-1.2.2.1 24-1.2.2.2 25-1.2.2.1.2 26-1.2.2 28-1.2.2.2.1.r 29-1.2.2.2.1 31-1.2.2.2.2.1.1 33-1.3.1 35-1.3.1.1 (s / show-01~e.13 :ARG0 (i / immunoblot-01~e.0,1 :ARG2~e.2 (l / lysate~e.5 :mod (c / cell~e.4) :quant (t2 / total~e.3)) :ARG3 (a / antibody :ARG0-of (c2 / counter-01~e.7 :ARG1 (e / enzyme :name (n / name :op1 "ERK"~e.11) :ARG3-of (p / phosphorylate-01~e.9))))) :ARG1 (p2 / phosphorylate-01~e.20 :ARG1 (a2 / and~e.17 :op1 (e2 / enzyme :name (n3 / name :op1 "ERK1"~e.16)) :op2 (e3 / enzyme :name (n4 / name :op1 "ERK2"~e.18))) :ARG2 (o / or~e.26 :op1 (l2 / ligate-01~e.24 :ARG1 (p3 / protein :name (n5 / name :op1 "BCR"~e.23)) :mod (a3 / alone~e.25)) :op2 (l3 / ligate-01~e.24 :ARG1~e.28 p3~e.29 :ARG3 (p4 / protein :name (n6 / name :op1 "CD72"~e.31)) :mod (t3 / together)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.33 :mod "6B"~e.35))) # ::id bel_pmid_1064_0734.39826 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , BCR ligation induced stronger ERK phosphorylation than coligation of CD72 with BCR did , indicating that BCR ligation @-@ induced phosphorylation of ERK is down @-@ modulated when CD72 is coligated with BCR . # ::alignments 0-1 2-1.1.1.1.1.1 3-1.1.1 3-1.1.2.2.2 4-1.1 5-1.1.2.2 5-1.1.2.2.1 5-1.1.2.2.1.r 6-1.1.2.1.1.1 7-1.1.2 8-1.1.2.2.2.r 10-1.1.2.2.2.1.r 11-1.1.2.2.2.1.1.1 13-1.1.1.1.1.1 16-1.1.3 18-1.1.1.1.1.1 19-1.1.1 21-1.1 21-1.1.3.1.1.2 22-1.1.2 22-1.1.3.1.1 24-1.1.2.1.1.1 29-1.1.3.1.2.r 30-1.1.3.1.2 33-1.1.2.2.2.2.r 34-1.1.2.2.2.2 (h / have-concession-91~e.0 :ARG1 (i / induce-01~e.4,21 :ARG0 (l / ligate-01~e.3,19 :ARG1 (p2 / protein :name (n2 / name :op1 "BCR"~e.2,13,18))) :ARG2 (p / phosphorylate-01~e.7,22 :ARG1 (e / enzyme :name (n / name :op1 "ERK"~e.6,24)) :ARG1-of (s / strong-02~e.5 :degree~e.5 (m / more~e.5) :compared-to~e.8 (l2 / ligate-01~e.3 :ARG1~e.10 (p3 / protein :name (n3 / name :op1 "CD72"~e.11)) :ARG3~e.33 p2~e.34 :mod (t / together)))) :ARG0-of (i2 / indicate-01~e.16 :ARG1 (d / downmodulate-01 :ARG1 (p4 / phosphorylate-01~e.22 :ARG1 e :ARG2-of (i3 / induce-01~e.21 :ARG0 l)) :time~e.29 l2~e.30)))) # ::id bel_pmid_1064_0734.39828 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Phosphorylation of both ERK1 and ERK2 induced by coligation of BCR and CD72 was weaker than that induced by BCR ligation alone ( Fig . 6 C ) , indicating that coligation with CD72 reduced BCR ligation @-@ mediated phosphorylation of ERK in DBA/2 spleen cells . # ::alignments 0-1.1 0-1.3 3-1.1.1.1.1.1 4-1.1.1 5-1.1.1.2.1.1 6-1.1.2 10-1.1.2.1.1.1.1 12-1.1.2.1.2.1.1 14-1 14-1.2 14-1.2.r 15-1.3.r 17-1.3.1 19-1.3.1.1.1 20-1.3.1.1 21-1.3.1.1.2 23-1.4.1 29-1.5 32-1.5.1.r 33-1.5.1.1 34-1.5.1 35-1.5.1.1 36-1.1.2.1 36-1.3.1.1 38-1.5.1.2.2 39-1.5.1.2 40-1.5.1.2.1.r 41-1.5.1.2.1.1.1 42-1.5.1.2.3.r 43-1.5.1.2.3.1.1.1.1 44-1.5.1.2.3.1 45-1.5.1.2.3 (w / weak-02~e.14 :ARG1 (p / phosphorylate-01~e.0 :ARG1 (a / and~e.4 :op1 (e2 / enzyme :name (n2 / name :op1 "ERK1"~e.3)) :op2 (e3 / enzyme :name (n3 / name :op1 "ERK2"~e.5))) :ARG2-of (i / induce-01~e.6 :ARG0 (l / ligate-01~e.36 :ARG1 (p2 / protein :name (n4 / name :op1 "BCR"~e.10)) :ARG3 (p3 / protein :name (n5 / name :op1 "CD72"~e.12)) :mod (t / together)))) :degree~e.14 (m / more~e.14) :compared-to~e.15 (p4 / phosphorylate-01~e.0 :ARG2-of (i2 / induce-01~e.17 :ARG0 (l2 / ligate-01~e.20,36 :ARG1 p2~e.19 :mod (a2 / alone~e.21)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.23 :mod "6C")) :ARG0-of (i3 / indicate-01~e.29 :ARG1~e.32 (r / reduce-01~e.34 :ARG0 l~e.33,35 :ARG1 (p5 / phosphorylate-01~e.39 :ARG1~e.40 (e / enzyme :name (n / name :op1 "ERK"~e.41)) :ARG1-of (m2 / mediate-01~e.38 :ARG0 l2) :location~e.42 (c / cell~e.45 :part-of (s / spleen~e.44 :source (o / organism :name (n6 / name :op1 "DBA/2"~e.43 :op2 "mouse")))))))) # ::id bel_pmid_1064_0734.39830 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Coligation of CD72 with BCR showed a reduced Ca2+ flux compared to that with BCR ligation alone in spleen B cells ( Fig . 6D ) . # ::alignments 2-1.1.1.1.1 4-1.1.2.1.1 5-1 7-1.2.2 9-1.2 9-1.2.3 10-1.2.3.r 11-1.2.3.1 14-1.1.2.1.1 15-1.1 15-1.2.3.1.1 16-1.2.3.1.1.2 17-1.3.r 18-1.3.2 19-1.3.1.1 20-1.3 22-1.4.1 24-1.4.1.1 (s / show-01~e.5 :ARG0 (l / ligate-01~e.15 :ARG1 (p / protein :name (n / name :op1 "CD72"~e.2)) :ARG3 (p2 / protein :name (n2 / name :op1 "BCR"~e.4,14)) :mod (t / together)) :ARG1 (f / flux~e.9 :quant-of (c3 / calcium :ARG1-of (i / ionize-01 :value "2+")) :ARG1-of (r / reduce-01~e.7) :compared-to~e.10 (f2 / flux~e.9 :ARG1-of (c / cause-01~e.11 :ARG0 (l2 / ligate-01~e.15 :ARG1 p2 :mod (a / alone~e.16))))) :location~e.17 (c2 / cell~e.20 :name (n4 / name :op1 "B"~e.19) :part-of (s3 / spleen~e.18)) :ARG1-of (d / describe-01 :ARG0 (f3 / figure~e.22 :mod "6D"~e.24))) # ::id bel_pmid_1064_0734.39832 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Taken together , these results indicate that coligation with CD72 negatively regulates BCR @-@ induced ERK activation and Ca2+ concentration in normal spleen B cells . # ::alignments 0-1.2 1-1.1.2.2.2 3-1.1.1.2 4-1.1.1 4-1.1.1.1 4-1.1.1.1.r 5-1.1 9-1.1.2.2.1.1.1 10-1.1.2 11-1.1.2 12-1.1.2.1.1.2.1.1.1 14-1.1.2.1.1.2 15-1.1.2.1.1.1.1.1 16-1.1.2.1.1 17-1.1.2.1 19-1.1.2.1.2 20-1.1.2.3.r 21-1.1.2.3.2 22-1.1.2.3.3 23-1.1.2.3.1.1 24-1.1.2.3 (h / have-condition-91 :ARG1 (i / indicate-01~e.5 :ARG0 (t / thing~e.4 :ARG1-of~e.4 (r / result-01~e.4) :mod (t2 / this~e.3)) :ARG1 (d / downregulate-01~e.10,11 :ARG1 (a2 / and~e.17 :op1 (a / activate-01~e.16 :ARG1 (e / enzyme :name (n / name :op1 "ERK"~e.15)) :ARG2-of (i2 / induce-01~e.14 :ARG0 (p2 / protein :name (n4 / name :op1 "BCR"~e.12)))) :op2 (c / concentrate-02~e.19 :ARG1 (c3 / calcium :ARG1-of (i3 / ionize-01 :value "2+")))) :ARG2 (l / ligate-01 :ARG3 (p / protein :name (n3 / name :op1 "CD72"~e.9)) :mod (t3 / together~e.1)) :location~e.20 (c2 / cell~e.24 :name (n6 / name :op1 "B"~e.23) :ARG1-of (n2 / normal-02~e.21) :part-of (s2 / spleen~e.22)))) :ARG2 (t4 / take-01~e.0 :mod t3)) # ::id bel_pmid_1064_4693.7794 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Furthermore , the hCdc14 phosphatases were found to dephosphorylate p53 specifically at the p34( Cdc2 ) / clb phosphorylation site ( p53 @-@ phosphor @-@ Ser( 315 )) . # ::alignments 0-1 3-1.1.1.2.1.1 4-1.1.1.2.1.2 6-1.1 8-1.1.1 9-1.1.1.1.3.1.1 10-1.1.1.3 17-1.1.1.1.1.1.1.1 18-1.1.1.1.1 19-1.1.1.1 21-1.1.1.1.2.1.4 26-1.1.1.1.2.1.1 (a / and~e.0 :op2 (f / find-01~e.6 :ARG1 (d / dephosphorylate-01~e.8 :ARG1 (p3 / protein-segment~e.19 :ARG1-of (p / phosphorylate-01~e.18 :ARG2 (e / enzyme :name (n3 / name :op1 "p34Cdc2/clb"~e.17))) :ARG1-of (d2 / describe-01 :ARG2 (a2 / amino-acid :mod 315~e.26 :name (n4 / name :op1 "serine") :ARG1-of p :part-of p2~e.21)) :part-of (p2 / protein :name (n / name :op1 "p53"~e.9))) :ARG2 (e2 / enzyme :name (n2 / name :op1 "hCdc14"~e.3 :op2 "phosphatase"~e.4)) :manner (s / specific-02~e.10)))) # ::id bel_pmid_1064_8414.21216 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Overexpression of mutant FGFR3 resulted in IL @-@ 6 independence , decreased apoptosis , and an enhanced proliferative response to IL @-@ 6 . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1 2-1.1.1.2 2-1.1.1.2.r 3-1.1.1.1.1 4-1 5-1.2.r 6-1.2.1.2.1.1 8-1.2.1.2.1.1 9-1.2.1 9-1.2.1.1 9-1.2.1.1.r 11-1.2.2.1 12-1.2.2 14-1.2 16-1.2.3.3 18-1.2.3 19-1.2.3.1.r 20-1.2.3.1 21-1.2.3.1 22-1.2.3.1 (r / result-01~e.4 :ARG1 (o / overexpress-01~e.0 :ARG1~e.1 (p / protein~e.2 :name (n / name :op1 "FGFR3"~e.3) :ARG1-of~e.2 (m / mutate-01~e.2))) :ARG2~e.5 (a / and~e.14 :op1 (d / depend-01~e.9 :polarity~e.9 -~e.9 :ARG1 (p2 / protein :name (n2 / name :op1 "IL-6"~e.6,8))) :op2 (a2 / apoptosis~e.12 :ARG1-of (d2 / decrease-01~e.11)) :op3 (r2 / respond-01~e.18 :ARG1~e.19 p2~e.20,21,22 :ARG2 (p3 / proliferate-01) :ARG1-of (e / enhance-01~e.16)))) # ::id bel_pmid_1064_8414.21218 ::amr-annotator SDL-AMR-09 ::preferred # ::tok B9 clones expressing either wild @-@ type FGFR3 at high levels or mutant FGFR3 displayed increased phosphorylation of STAT3 and higher levels of bcl @-@ x( L ) expression than did parental B9 cells after cytokine withdrawal . # ::alignments 0-1.1.1 1-1.1 2-1.1.2 4-1.1.2.1.1.2 6-1.1.2.1.1.2 7-1.1.2.1.1.1.1 7-1.1.2.1.2.1.1 9-1.1.2.1.1.3.1 10-1.1.2.1.1.3 11-1.1.2.1 12-1.1.2.1.2 12-1.1.2.1.2.2 12-1.1.2.1.2.2.r 13-1.1.2.1.1.1.1 13-1.1.2.1.2.1.1 14-1 15-1.2.1.2 16-1.2.1 17-1.2.1.1.r 18-1.2.1.1.1.1 19-1.2 20-1.2.2.1 20-1.2.2.1.1 20-1.2.2.1.1.r 21-1.2.2 22-1.2.2.2.r 23-1.2.2.2.1.1.1 28-1.2.2.2 29-1.2.3.r 31-1.2.3.2 32-1.2.3.1.1 33-1.2.3 34-1.2.3.3 35-1.2.3.3.1.1.1.1 36-1.2.3.3.1 (d / display-01~e.14 :ARG0 (c3 / clone-01~e.1 :ARG1 c2~e.0 :ARG3-of (e / express-03~e.2 :ARG2 (o / or~e.11 :op1 (p2 / protein :name (n2 / name :op1 "FGFR3"~e.7,13) :mod (w / wild-type~e.4,6) :degree (l / level~e.10 :ARG1-of (h2 / high-02~e.9))) :op2 (p3 / protein~e.12 :name (n3 / name :op1 "FGFR3"~e.7,13) :ARG2-of~e.12 (m2 / mutate-01~e.12))))) :ARG1 (a / and~e.19 :op1 (p / phosphorylate-01~e.16 :ARG1~e.17 (p4 / protein :name (n4 / name :op1 "STAT3"~e.18)) :ARG1-of (i / increase-01~e.15)) :op2 (l2 / level~e.21 :ARG1-of (h / high-02~e.20 :degree~e.20 (m / more~e.20)) :degree-of~e.22 (e2 / express-03~e.28 :ARG2 (p5 / protein :name (n5 / name :op1 "bcl-xL"~e.23)))) :compared-to~e.29 (c2 / cell~e.33 :name (n6 / name :op1 "B9"~e.32) :mod (p6 / parental~e.31) :time (a2 / after~e.34 :op1 (w2 / withdraw-01~e.36 :ARG1 (p7 / protein :name (n7 / name :op1 "cytokine"~e.35))))))) # ::id bel_pmid_1066_0621.6864 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Treatment of cells expressing SRC @-@ 1 with epidermal growth factor enhanced the ligand @-@ dependent , progesterone receptor @-@ mediated activation of a target reporter gene . These results identify phosphorylation as a regulatory modification of SRC @-@ 1 and provide a basis upon which to identify signaling pathways that regulate SRC @-@ 1 function and , consequently , modify steroid @/@ nuclear receptor action . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1 3-1.1.1.1.1 4-1.1.1.1.1.1.1.1 6-1.1.1.1.1.1.1.1 7-1.1.1.2.r 8-1.1.1.2.1.1 9-1.1.1.2.1.2 10-1.1.1.2.1.3 11-1.1 13-1.1.2.2.1 15-1.1.2.2 17-1.1.2.3.1.1.1 18-1.1.2.3.1.1.2 20-1.1.2.3 21-1.1.2 22-1.1.2.1.r 24-1.1.2.1 24-1.1.2.1.2 24-1.1.2.1.2.r 25-1.1.2.1.1.1 26-1.1.2.1.1.2 28-1.2.1.1.2 29-1.2.1.1 29-1.2.1.1.1 29-1.2.1.1.1.r 30-1.2.1 31-1.2.1.2 32-1.2.1.3.r 34-1.2.1.3.2 35-1.2.1.3 36-1.2.1.3.1.r 37-1.2.1.3.1.1.1 39-1.2.1.3.1.1.1 40-1.2 41-1.2.2 43-1.2.2.2 47-1.2.2.3 48-1.2.2.3.1.1 49-1.2.2.3.1 51-1.2.2.3.1.2 52-1.2.2.3.1.2.1.1 53-1.2.2.3.1.2.1.1 54-1.2.2.3.1.2.1.1 55-1.2.2.3.1.3.2.1 58-1.2.2.3.1.3.2 60-1.2.2.3.1.3 61-1.2.2.3.1.3.1.1.1.1 63-1.2.2.3.1.3.1.1.1.1 64-1.2.2.3.1.3.1.1.1.2 65-1.2.2.3.1.3.1 (m / multi-sentence :snt1 (e / enhance-01~e.11 :ARG0 (t / treat-04~e.0 :ARG1~e.1 (c / cell~e.2 :ARG3-of (e2 / express-03~e.3 :ARG2 (p3 / protein :name (n2 / name :op1 "SRC-1"~e.4,6)))) :ARG2~e.7 (p8 / protein :name (n / name :op1 "epidermal"~e.8 :op2 "growth"~e.9 :op3 "factor"~e.10))) :ARG1 (a2 / activate-01~e.21 :ARG1~e.22 (g / gene~e.24 :name (n4 / name :op1 "reporter"~e.25 :op2 "gene"~e.26) :ARG1-of~e.24 (t2 / target-01~e.24)) :ARG0-of (d / depend-01~e.15 :ARG1 (l / ligand~e.13)) :ARG1-of (m2 / mediate-01~e.20 :ARG0 (p4 / protein :name (n3 / name :op1 "progesterone"~e.17 :op2 "receptor"~e.18))))) :snt2 (a3 / and~e.40 :op1 (i / identify-01~e.30 :ARG0 (t3 / thing~e.29 :ARG1-of~e.29 (r2 / result-01~e.29) :mod (t4 / this~e.28)) :ARG1 (p2 / phosphorylate-01~e.31) :ARG2~e.32 (m3 / modify-01~e.35 :ARG1~e.36 (p / protein :name (n5 / name :op1 "SRC-1"~e.37,39)) :ARG0-of (r / regulate-01~e.34))) :op2 (p5 / provide-01~e.41 :ARG0 t3 :ARG1 (b / basis~e.43) :purpose (i2 / identify-01~e.47 :ARG1 (p6 / pathway~e.49 :ARG0-of (s2 / signal-07~e.48) :ARG0-of (r3 / regulate-01~e.51 :ARG1 (f / function-01 :ARG0 p~e.52,53,54)) :ARG0-of (m4 / modify-01~e.60 :ARG1 (a4 / act-01~e.65 :ARG0 (p7 / protein :name (n6 / name :op1 "steroid/nuclear"~e.61,63 :op2 "receptor"~e.64))) :ARG1-of (c2 / cause-01~e.58 :ARG0 r3~e.55))))))) # ::id bel_pmid_1066_0621.21334 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Furthermore , Erk @-@ 2 phosphorylated threonine 1179 and serine 1185 ( and to a lesser extent , serine 395 ) in vitro , suggesting the importance of this pathway for SRC @-@ 1 regulation . # ::alignments 0-1 2-1.1.2.1.1 4-1.1.2.1.1 5-1.1 6-1.1.1.1.2.1 7-1.1.1.1.1 8-1.1.1 9-1.1.1.2.2.1 9-1.1.1.3.2.1 10-1.1.1.2.1 13-1.1.1.r 15-1.1.1.3.3.1 15-1.1.1.3.3.1.1 15-1.1.1.3.3.1.1.r 16-1.1.1.3.3 18-1.1.1.3.2.1 19-1.1.1.3.1 21-1.1.3 22-1.1.3 24-1.1.4 26-1.1.4.1 27-1.1.4.1.1.r 28-1.1.4.1.1.1 29-1.1.4.1.1 30-1.1.4.1.2.r 31-1.1.4.1.2.1.1.1 33-1.1.4.1.2.1.1.1 34-1.1.4.1.2 (a3 / and~e.0 :op2 (p / phosphorylate-01~e.5 :ARG1~e.13 (a4 / and~e.8 :op1 (a / amino-acid :mod 1179~e.7 :name (n / name :op1 "threonine"~e.6)) :op2 (a2 / amino-acid :mod 1185~e.10 :name (n2 / name :op1 "serine"~e.9)) :op3 (a5 / amino-acid :mod 395~e.19 :name (n4 / name :op1 "serine"~e.9,18) :degree (e2 / extent~e.16 :mod (l / less~e.15 :degree~e.15 (m / more~e.15))))) :ARG2 (e / enzyme :name (n3 / name :op1 "Erk-2"~e.2,4)) :manner (i / in-vitro~e.21,22) :ARG0-of (s / suggest-01~e.24 :ARG1 (i2 / important~e.26 :domain~e.27 (p2 / pathway~e.29 :mod (t / this~e.28)) :purpose~e.30 (r / regulate-01~e.34 :ARG1 (p3 / protein :name (n5 / name :op1 "SRC-1"~e.31,33))))))) # ::id bel_pmid_1066_6199.2154 ::amr-annotator SDL-AMR-09 ::preferred # ::tok overexpressions of cyclin D1 or bcl @-@ 2 inhibited only differentiation or apoptosis , respectively # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.1.1 3-1.1.1.1.1.2 4-1.1.1 5-1.1.1.2.1.1 7-1.1.1.2.1.1 8-1 9-1.3 10-1.2.1 11-1.2 12-1.2.2 14-1.4 14-1.4.r (i / inhibit-01~e.8 :ARG0 (o3 / overexpress-01~e.0 :ARG1~e.1 (o4 / or~e.4 :op1 (p / protein :name (n / name :op1 "cyclin"~e.2 :op2 "D1"~e.3)) :op2 (p2 / protein :name (n2 / name :op1 "bcl-2"~e.5,7)))) :ARG1 (o2 / or~e.11 :op1 (d / differentiate-01~e.10) :op2 (a / apoptosis~e.12)) :mod (o / only~e.9) :manner~e.14 (r / respective~e.14)) # ::id bel_pmid_1066_6199.28424 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Although STAT3 is essential for IL @-@ 6 @-@ induced macrophage differentiation of M1 cells , GATA @-@ 1 had little or no effect on tyrosine phosphorylation , DNA binding , and transcriptional activities of STAT3 in Western blot analysis , electropholic mobility shift assay ( EMSA ) , and luciferase assays . # ::alignments 0-1 1-1.2.1 2-1.2.1.r 3-1.2 4-1.2.2.r 5-1.2.2.2.1.1.1 7-1.2.2.2.1.1.1 9-1.2.2.2 10-1.2.2.3 11-1.2.2 12-1.2.2.1.r 13-1.2.2.1.1.1 14-1.2.2.1 16-1.1.1.1.1.1 18-1.1.1.1.1.1 20-1.1.1.3 21-1.1 22-1.1.2.1 22-1.1.2.1.r 23-1.1.1 23-1.1.2 24-1.1.1.2.r 25-1.1.1.2.1.1.1.1 26-1.1.1.2.1 28-1.1.1.2.2.1.2.1 29-1.1.1.2.2 31-1.1.1.2 32-1.1.1.2.3.2 33-1.1.1.2.3 34-1.1.1.2.3.1.r 35-1.1.1.2.3.1.1.1 36-1.1.3.r 37-1.1.3.1 38-1.1.3.1 42-1.1.3.2.1.1 43-1.1.3.2.1 44-1.1.3.2 49-1.1.3 50-1.1.3.3.1 51-1.1.3.3 (h / have-concession-91~e.0 :ARG1 (o2 / or~e.21 :op1 (a / affect-01~e.23 :ARG0 (p2 / protein :name (n / name :op1 "GATA-1"~e.16,18)) :ARG1~e.24 (a2 / and~e.31 :op1 (p / phosphorylate-01~e.26 :ARG1 (a3 / amino-acid :name (n3 / name :op1 "tyrosine"~e.25))) :op2 (b / bind-01~e.29 :ARG1 (n2 / nucleic-acid :wiki "DNA" :name (n9 / name :op1 "DNA"~e.28))) :op3 (a4 / activity-06~e.33 :ARG0~e.34 (p3 / protein :name (n4 / name :op1 "STAT3"~e.35)) :ARG1 (t / transcribe-01~e.32))) :degree (l / little~e.20)) :op2 (a6 / affect-01~e.23 :polarity~e.22 -~e.22 :ARG0 p2 :ARG1 a2) :time~e.36 (a5 / and~e.49 :op1 (i / immunoblot-01~e.37,38) :op2 (a7 / assay-01~e.44 :ARG1 (s / shift-01~e.43 :ARG1 (m2 / mobility~e.42 :mod (e2 / elecropholic)))) :op3 (a8 / assay-01~e.51 :ARG1 (l2 / luciferase~e.50)))) :ARG2 (e / essential~e.3 :domain~e.2 p3~e.1 :purpose~e.4 (d3 / differentiate-01~e.11 :ARG1~e.12 (c2 / cell~e.14 :name (n10 / name :op1 "M1"~e.13)) :ARG2-of (i2 / induce-01~e.9 :ARG0 (p4 / protein :name (n11 / name :op1 "IL-6"~e.5,7))) :mod (m / macrophage~e.10)))) # ::id bel_pmid_1066_6199.38222 ::amr-annotator SDL-AMR-09 ::preferred # ::tok During IL @-@ 6 @-@ induced macrophage differentiation of M1 cells , IL @-@ 6 down @-@ regulated cyclin D1 expression and induced p19( INK4D ) expression , leading to reduction in cdk4 activities . In contrast , sustained expression of cyclin D1 and a significantly lesser amount of p19( INK4D ) induction were observed in IL @-@ 6 @-@ treated M1 cells overexpressing GATA @-@ 1 . # ::alignments 0-1.1.4.r 1-1.1.4.2.1 2-1.1.4.2.1 3-1.1.4.2.1 5-1.1.4.2 6-1.1.4.3 7-1.1.4 8-1.1.4.1.r 9-1.1.4.1.1.1 10-1.1.4.1 12-1.1.1.2.1.1 14-1.1.1.2.1.1 18-1.1.1.1.1.1.1 19-1.1.1.1.1.1.2 20-1.1.1.1 20-1.1.2.2 21-1.1 22-1.1.2 26-1.1.1.1 26-1.1.2.2 28-1.1.3 29-1.1.3.1.r 30-1.1.3.1 31-1.1.3.1.1.r 32-1.1.3.1.1.1.1.1 33-1.1.3.1.1 36-1.2 38-1.2.1.1.1.2 39-1.2.1.1.1 40-1.2.1.1.1.1.r 41-1.2.1.1.1.1.1.1 42-1.2.1.1.1.1.1.2 43-1.2.1.1 45-1.2.1.1.2.1.1 46-1.2.1.1.2.1 47-1.2.1.1.2 52-1.2.1.1.2.2 54-1.2.1 55-1.2.1.2.r 56-1.2.1.2.2.1.1.1 58-1.2.1.2.2.1.1.1 60-1.2.1.2.2 61-1.2.1.2.1.1 62-1.2.1.2 63-1.2.1.2.3 64-1.2.1.2.3.1.1.1 66-1.2.1.2.3.1.1.1 (m / multi-sentence :snt1 (a / and~e.21 :op1 (d / downregulate-01 :ARG1 (e / express-03~e.20,26 :ARG2 (p2 / protein :name (n2 / name :op1 "cyclin"~e.18 :op2 "D1"~e.19))) :ARG2 (p / protein :name (n / name :op1 "IL-6"~e.12,14))) :op2 (i / induce-01~e.22 :ARG0 p :ARG2 (e2 / express-03~e.20,26 :ARG1 (g / gene :name (n7 / name :op1 "p19(INK4D)")))) :ARG0-of (l / lead-03~e.28 :ARG2~e.29 (r / reduce-01~e.30 :ARG1~e.31 (a2 / activity-06~e.33 :ARG0 (e3 / enzyme :name (n3 / name :op1 "cdk4"~e.32))))) :time~e.0 (d2 / differentiate-01~e.7 :ARG1~e.8 (c / cell~e.10 :name (n4 / name :op1 "M1"~e.9)) :ARG2-of (i2 / induce-01~e.5 :ARG0 p~e.1,2,3) :mod (m2 / macrophage~e.6))) :snt2 (c3 / contrast-01~e.36 :ARG2 (o / observe-01~e.54 :ARG1 (a3 / and~e.43 :op1 (e4 / express-03~e.39 :ARG1~e.40 (p3 / protein :name (n6 / name :op1 "cyclin"~e.41 :op2 "D1"~e.42)) :ARG1-of (s / sustain-01~e.38)) :op2 (a4 / amount~e.47 :mod (l2 / less~e.46 :degree (s2 / significant~e.45) :degree (m3 / more)) :degree-of (i4 / induce-01~e.52 :ARG2 (g2 / gene :name (n8 / name :op1 "p19(INK4D)"))))) :location~e.55 (c4 / cell~e.62 :name (n9 / name :op1 "M1"~e.61) :ARG1-of (t / treat-04~e.60 :ARG2 (p4 / protein :name (n10 / name :op1 "IL-6"~e.56,58))) :location-of (o2 / overexpress-01~e.63 :ARG1 (p5 / protein :name (n11 / name :op1 "GATA-1"~e.64,66))))))) # ::id bel_pmid_1067_7502.3614 ::amr-annotator SDL-AMR-09 ::preferred # ::tok High concentrations of stauro of up to 1 microM only partially inhibit IL @-@ 3 @-@ stimulated Bcl2 phosphorylation but completely block PKC @-@ mediated Bcl2 phosphorylation in vitro # ::alignments 0-1.1.1.2 1-1.1.1 1-1.1.1.3.1 2-1.1.1.1.r 3-1.1.1.1.1.1 4-1.1.1.3.r 5-1.1.1.3 6-1.1.1.3 7-1.1.1.3.1.1 9-1.1.4 10-1.1.3 10-1.1.3.r 11-1.1 12-1.1.2.2.1.1.1 14-1.1.2.2.1.1.1 16-1.1.2.2 17-1.1.2.1.1.1 18-1.1.2 19-1 20-1.2.3 21-1.2 22-1.2.2.2.1.1.1 24-1.2.2.2 25-1.2.2.1 26-1.2.2 27-1.2.4 28-1.2.4 (c / contrast-01~e.19 :ARG1 (i / inhibit-01~e.11 :ARG0 (c2 / concentrate-02~e.1 :ARG0~e.2 (s / small-molecule :name (n4 / name :op1 "stauro"~e.3)) :ARG1-of (h / high-02~e.0) :quant~e.4 (u / up-to~e.5,6 :op1 (c4 / concentration-quantity~e.1 :quant 1~e.7 :unit (m2 / micromolar)))) :ARG1 (p3 / phosphorylate-01~e.18 :ARG1 (p4 / protein :name (n / name :op1 "Bcl2"~e.17)) :ARG1-of (s2 / stimulate-01~e.16 :ARG0 (p5 / protein :name (n2 / name :op1 "IL-3"~e.12,14)))) :degree~e.10 (p2 / part~e.10) :mod (o / only~e.9)) :ARG2 (b / block-01~e.21 :ARG0 c2 :ARG1 (p / phosphorylate-01~e.26 :ARG1 p4~e.25 :ARG1-of (m / mediate-01~e.24 :ARG0 (e / enzyme :name (n3 / name :op1 "PKC"~e.22)))) :ARG1-of (c3 / complete-02~e.20) :manner (i2 / in-vitro~e.27,28))) # ::id bel_pmid_1067_7502.21952 ::amr-annotator SDL-AMR-09 ::preferred # ::tok p44MAPK @/@ extracellular signal @-@ regulated kinase 1 ( ERK1 ) and p42 MAPK @/@ ERK2 are activated by IL @-@ 3 , colocalize with mitochondrial Bcl2 , and can directly phosphorylate Bcl2 on Ser @-@ 70 in a stauro @-@ resistant manner both in vitro and in vivo # ::alignments 0-1.1.2.1.1.1 2-1.1.2.1.2.1.1.1 3-1.1.2.1.2.1.1.2 5-1.1.2.1.2.1.1.2 6-1.1.2.1.2.1.1.3 7-1.1.2.1.2.1.1.4 9-1.1.2.1.2.1.2.1.1.1 11-1.1.2 15-1.1.2.2.2.1.1.1 17-1.1 18-1.1.1.r 19-1.1.1.1.1 21-1.1.1.1.1 23-1.2 26-1.2.1.2.1.1 28-1 28-1.2.1 29-1.3 30-1.3.1.5 31-1.3.1 32-1.3.1.1.3 34-1.3.1.1.2.1 36-1.3.1.1.1 37-1.3.1.3.r 37-1.3.1.4.1 39-1.3.1.3.1.1.1 41-1.3.1.3 42-1.3.1.4.r 44-1.3.1.4.1 45-1.3.1.4.1 46-1.3.1.4 47-1.3.1.4.1 47-1.3.1.4.2 48-1.3.1.4.2 (a / and~e.28 :op1 (a2 / activate-01~e.17 :ARG0~e.18 (p / protein :name (n6 / name :op1 "IL-3"~e.19,21)) :ARG1 (a3 / and~e.11 :op1 (e / enzyme :name (n / name :op1 "p44MAPK"~e.0) :ARG1-of (m / mean-01 :ARG2 (e2 / enzyme :name (n2 / name :op1 "extracellular"~e.2 :op2 "signal-regulated"~e.3,5 :op3 "kinase"~e.6 :op4 1~e.7) :ARG1-of (d / describe-01 :ARG2 (e3 / enzyme :name (n3 / name :op1 "ERK1"~e.9)))))) :op2 (e4 / enzyme :name (n4 / name :op1 "p42MAPK") :ARG1-of (m2 / mean-01 :ARG2 (e5 / enzyme :name (n5 / name :op1 "ERK2"~e.15)))))) :op2 (c / colocalize-01~e.23 :ARG1 (a6 / and~e.28 :op1 a3 :op2 (p2 / protein :name (n7 / name :op1 "Bcl2"~e.26) :part-of (m3 / mitochondrion)))) :op3 (p3 / possible-01~e.29 :ARG1 (p4 / phosphorylate-01~e.31 :ARG1 (a4 / amino-acid :mod 70~e.36 :name (n8 / name :op1 "serine"~e.34) :part-of p2~e.32) :ARG2 a3 :manner~e.37 (r / resist-01~e.41 :ARG1 (s / small-molecule :name (n9 / name :op1 "stauro"~e.39))) :manner~e.42 (a5 / and~e.46 :op1 (i / in-vitro~e.37,44,45,47) :op2 (i2 / in-vivo~e.47,48)) :ARG1-of (d2 / direct-02~e.30)))) # ::id bel_pmid_1068_1535.5746 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We found that TPO stimulation or Ha @-@ Ras G12V expression led to up @-@ regulation of cyclin D1 , cyclin D2 , and cyclin D3 expression . # ::alignments 0-1.1 1-1 2-1.2.r 3-1.2.1.1.1.1.1 4-1.2.1.1 5-1.2.1 6-1.2.1.2.1.1.1 8-1.2.1.2.1.1.1 9-1.2.1.2.1.2.1 10-1.2.1.2 11-1.2 12-1.2.2.r 13-1.2.2 14-1.2.2 15-1.2.2 16-1.2.2.1.r 17-1.2.2.1.1.1.1.1 18-1.2.2.1.1.1.1.2 20-1.2.2.1.2.1.1.1 21-1.2.2.1.2.1.1.2 23-1.2.2.1 24-1.2.2.1.3.1.1.1 25-1.2.2.1.3.1.1.2 26-1.2.2.1.1 26-1.2.2.1.2 26-1.2.2.1.3 (f / find-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (l / lead-03~e.11 :ARG0 (o / or~e.5 :op1 (s / stimulate-01~e.4 :ARG1 (p / protein :name (n / name :op1 "TPO"~e.3))) :op2 (e / express-03~e.10 :ARG2 (e5 / enzyme :name (n2 / name :op1 "Ha-Ras"~e.6,8) :ARG2-of (m / mutate-01 :value "G12V"~e.9)))) :ARG2~e.12 (u / upregulate-01~e.13,14,15 :ARG1~e.16 (a2 / and~e.23 :op1 (e2 / express-03~e.26 :ARG2 (p3 / protein :name (n3 / name :op1 "cyclin"~e.17 :op2 "D1"~e.18))) :op2 (e3 / express-03~e.26 :ARG2 (p4 / protein :name (n4 / name :op1 "cyclin"~e.20 :op2 "D2"~e.21))) :op3 (e4 / express-03~e.26 :ARG2 (p5 / protein :name (n5 / name :op1 "cyclin"~e.24 :op2 "D3"~e.25))))))) # ::id bel_pmid_1068_1535.24496 ::amr-annotator SDL-AMR-09 ::preferred # ::tok By using a refined model of megakaryocytic differentiation , we found that either TPO stimulation or Ha @-@ Ras G12V expression could up @-@ regulate the expression of cyclin D1 and cyclin D2 in addition to cyclin D3 , and that , when cdc2 activity was suppressed , each of cyclin D1 , cyclin D2 , and cyclin D3 expression was able to induce megakaryocytic differentiation with a similar efficiency . # ::alignments 1-1.3 3-1.3.1.1 4-1.3.1 5-1.3.1.2.r 6-1.3.1.2 7-1.3.1.2 9-1.1 10-1 13-1.2.1.1.2.1.1.1.1 14-1.2.1.1.2.1 15-1.2.1.1.2 16-1.2.1.1.2.2.1.1.1 18-1.2.1.1.2.2.1.1.1 19-1.2.1.1.2.2.1.2.1 20-1.2.1.1.2.2 21-1.2.2 26-1.2.2.1.1.1 28-1.2.2.1.1.1.1.1.1 29-1.2.2.1.1.1.1.1.2 30-1.2.2.1.1 31-1.2.2.1.1.2.1.1.1 32-1.2.2.1.1.2.1.1.2 33-1.2.2.1.1 34-1.2.2.1.1 36-1.2.2.1.1.3.1.1.1 37-1.2.2.1.1.3.1.1.2 39-1.2.2.1.1 42-1.2.2.2.r 43-1.2.2.2.1.1.1.1 44-1.2.2.2.1 46-1.2.2.2 48-1.2.2.1.1.4 50-1.2.2.1.1.1.1.1.1 51-1.2.2.1.1.1.1.1.2 53-1.2.2.1.1.2.1.1.1 54-1.2.2.1.1.2.1.1.2 56-1.2.2.1.1 57-1.2.2.1.1.3.1.1.1 58-1.2.2.1.1.3.1.1.2 59-1.2.2.1.1.1 59-1.2.2.1.1.2 59-1.2.2.1.1.3 61-1.2.1 61-1.2.2 63-1.2.2.1 64-1.2.2.1.2.1.1.1 65-1.2.2.1.2 66-1.2.2.1.3.r 68-1.2.2.1.3.1 69-1.2.2.1.3 (f / find-01~e.10 :ARG0 (w / we~e.9) :ARG1 (a / and :op1 (p2 / possible-01~e.61 :ARG1 (u / upregulate-01 :ARG1 a3 :ARG2 (o / or~e.15 :op1 (s / stimulate-01~e.14 :ARG1 (p3 / protein :name (n / name :op1 "TPO"~e.13))) :op2 (e / express-03~e.20 :ARG2 (e7 / enzyme :name (n2 / name :op1 "Ha-Ras"~e.16,18) :ARG2-of (m / mutate-01 :value "G12V"~e.19)))))) :op2 (p8 / possible-01~e.21,61 :ARG1 (i / induce-01~e.63 :ARG0 (a3 / and~e.30,33,34,39,56 :op1 (e3 / express-03~e.26,59 :ARG2 (p9 / protein :name (n6 / name :op1 "cyclin"~e.28,50 :op2 "D1"~e.29,51))) :op2 (e4 / express-03~e.59 :ARG2 (p10 / protein :name (n7 / name :op1 "cyclin"~e.31,53 :op2 "D2"~e.32,54))) :op3 (e5 / express-03~e.59 :ARG2 (p11 / protein :name (n8 / name :op1 "cyclin"~e.36,57 :op2 "D3"~e.37,58))) :mod (e6 / each~e.48)) :ARG2 (d / differentiate-01~e.65 :ARG1 (c / cell :name (n10 / name :op1 "megakaryocyte"~e.64))) :ARG1-of~e.66 (e2 / efficient-01~e.69 :ARG1-of (r2 / resemble-01~e.68))) :time~e.42 (s2 / suppress-01~e.46 :ARG1 (a2 / activity-06~e.44 :ARG0 (e8 / enzyme :name (n9 / name :op1 "cdc2"~e.43)))))) :manner (u2 / use-01~e.1 :ARG1 (m3 / model~e.4 :ARG1-of (r / refine-01~e.3) :topic~e.5 d~e.6,7))) # ::id bel_pmid_1069_9758.15770 ::amr-annotator SDL-AMR-09 ::preferred # ::tok which are dual @-@ specificity ( serine/threonine and tyrosine ) kinases that regulate downstream responses to a broad range of mitogenic , apoptotic , and differentiation @-@ inducing stimuli [ 368 @-@ 372 ] . Interestingly , MEK1 but not MEK2 is stimulated by H2O2 treatment , suggesting that only MEK1 is redox @-@ sensitive [ 154 ] . # ::alignments 2-1.1.1.1.2 4-1.1.1.1 7-1.1.1.1.1.1 8-1.1.1.1.1.1.2.2.1 10-1.1.1 12-1.1 13-1.1.3 14-1.1.2 17-1.1.2.1.2 18-1.1.2.1 19-1.1.2.1.1.r 20-1.1.2.1.1.1 22-1.1.2.1.1.2 25-1.1.2.1.1.3.1 27-1.1.2.1.1.3 28-1.1.2.1.1 30-1.1.4.1.1.1.1 32-1.1.4.1.1.1.2 35-1.2.3 35-1.2.4.2 37-1.2.1.2.2.1 38-1.2 39-1.2.2.1 39-1.2.2.1.r 40-1.2.2.3.2.1 42-1.2.1 42-1.2.2 43-1.2.1.1.r 44-1.2.1.1.1.2.1 45-1.2.1.1 47-1.2.4 48-1.2.4.1.r 49-1.2.4.1.3 50-1.2.4.1.1 52-1.2.4.1.2 54-1.2.4.1 56-1.2.4.3.1.1.1 (m / multi-sentence :snt1 (r / regulate-01~e.12 :ARG0 (k / kinase~e.10 :mod (s7 / specificity~e.4 :ARG1-of (m2 / mean-01 :ARG2 (a / and~e.7 :op1 (s / slash :op1 (a2 / amino-acid :wiki "Serine" :name (n / name :op1 "serine")) :op2 (a3 / amino-acid :wiki "Threonine" :name (n2 / name :op1 "threonine"))) :op2 (a4 / amino-acid :wiki "Tyrosine" :name (n3 / name :op1 "tyrosine"~e.8)))) :mod (d / dual~e.2))) :ARG1 (r2 / respond-01~e.14 :ARG1 (r4 / range-01~e.18 :ARG1~e.19 (s5 / stimulus~e.28 :mod (m3 / mitogenic~e.20) :mod (a5 / apoptosis~e.22) :ARG0-of (i / induce-01~e.27 :ARG2 (d3 / differentiate-01~e.25))) :ARG1-of (b / broad-02~e.17))) :direction (d2 / downstream~e.13) :ARG1-of (d4 / describe-01 :ARG0 (p / publication :ARG1-of (c / cite-01 :ARG2 (v / value-interval :op1 368~e.30 :op2 372~e.32))))) :snt2 (c2 / contrast-01~e.38 :ARG1 (s2 / stimulate-01~e.42 :ARG0~e.43 (t / treat-04~e.45 :ARG2 (s8 / small-molecule :wiki "Hydrogen_peroxide" :name (n6 / name :op1 "H2O2"~e.44))) :ARG1 (e / enzyme :wiki "MAP2K1" :name (n4 / name :op1 "MEK1"~e.37))) :ARG2 (s3 / stimulate-01~e.42 :polarity~e.39 -~e.39 :ARG0 t :ARG1 (e2 / enzyme :wiki "MAP2K2" :name (n5 / name :op1 "MEK2"~e.40))) :ARG2-of (i2 / interest-01~e.35) :ARG0-of (s4 / suggest-01~e.47 :ARG1~e.48 (s6 / sensitive-03~e.54 :ARG0 e~e.50 :ARG1 (r3 / redox~e.52) :mod (o / only~e.49)) :ARG2-of (i3 / interest-01~e.35) :ARG1-of (d5 / describe-01 :ARG0 (p2 / publication :ARG1-of (c3 / cite-01 :ARG2 154~e.56)))))) # ::id bel_pmid_1069_9758.24188 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Additionally , several studies have shown that antioxidant enzymes and mimics also block NF @-@ kB activation by various stimuli . For example , overexpression of peroxiredoxin [ 247 ] or thioredoxin [ 111 ] blocks NF @-@ kB activation by H2O2 . # ::alignments 0-1.1.3 2-1.1.1.1 3-1.1.1 5-1.1 6-1.1.2.r 7-1.1.2.1.1.1 8-1.1.2.1.1 9-1.1.2.1 10-1.1.2.1.2 11-1.1.2.4 12-1.1.2 13-1.1.2.2.1.1.1 15-1.1.2.2.1.1.1 16-1.1.2.2 17-1.1.2.3.r 18-1.1.2.3.1 19-1.1.2.3 21-1.2.4 22-1.2.4 24-1.2.1.1 24-1.2.1.2 25-1.2.1.1.1.r 26-1.2.1.1.1.1.1 28-1.2.1.1.2.1.1.1 30-1.2.1 31-1.2.1.2.1.1.1 33-1.2.1.2.2.1.1.1 35-1.2 36-1.2.2.1.1.1 38-1.2.2.1.1.1 39-1.2.2 40-1.2.3.r 41-1.2.3.1.1 (m / multi-sentence :snt1 (s / show-01~e.5 :ARG0 (s2 / study-01~e.3 :quant (s3 / several~e.2)) :ARG1~e.6 (b / block-01~e.12 :ARG0 (a7 / and~e.9 :op1 (e2 / enzyme~e.8 :mod (a2 / antioxidant~e.7)) :op2 (m2 / mimic-01~e.10)) :ARG1 (a4 / activate-01~e.16 :ARG1 (p / protein :name (n / name :op1 "NF-kB"~e.13,15))) :ARG3~e.17 (s4 / stimulus~e.19 :mod (v / various~e.18)) :mod (a / also~e.11)) :mod (a6 / additional~e.0)) :snt2 (b3 / block-01~e.35 :ARG0 (o4 / or~e.30 :op1 (o / overexpress-01~e.24 :ARG1~e.25 (e4 / enzyme :name (n2 / name :op1 "peroxiredoxin"~e.26)) :ARG1-of (d / describe-01 :ARG0 (p2 / publication :ARG1-of (c / cite-01 :ARG2 247~e.28)))) :op2 (o2 / overexpress-01~e.24 :ARG1 (p4 / protein :name (n4 / name :op1 "thioredoxin"~e.31)) :ARG1-of (d2 / describe-01 :ARG0 (p5 / publication :ARG1-of (c2 / cite-01 :ARG2 111~e.33))))) :ARG1 (a5 / activate-01~e.39 :ARG1 (p3 / protein :name (n3 / name :op1 "NF-kB"~e.36,38))) :ARG3~e.40 (s5 / small-molecule :name (n5 / name :op1 "H2O2"~e.41)) :ARG0-of (e / exemplify-01~e.21,22))) # ::id bel_pmid_1069_9758.34686 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Furthermore , in many types of cells , antioxidants diminish or completely eliminate NF @-@ kB activation ( Table 1 ) . For example , H2O2 , UV , and ionizing radiation have all been observed to stimulate degradation of IkB ( Table 1 ) . Conversely , antioxidants and reductants such as BHA , NGA , a @-@ tocopherol , NAC , and PDTC decrease NF @-@ kB activity and translocation [ 12,253 ] . # ::alignments 0-1.1 0-1.3.1.3.1.1.1 2-1.1.1.r 3-1.1.1.3.2 4-1.1.1.3 5-1.1.1.3.1.r 6-1.1.1.3.1 8-1.1.1.1.1 9-1.1.1.1 10-1.1.1 11-1.1.1.2.2 12-1.1.1.2 13-1.1.1.1.2.1.1.1 15-1.1.1.1.2.1.1.1 16-1.1.1.1.2 18-1.1.2.1 18-1.2.2.1 19-1.1.2.1.1 19-1.2.2.1.1 23-1.2.3 25-1.2.1.1.1.2.1 29-1.2.1.1 30-1.2.1.1.3.1 31-1.2.1.1.3 33-1.2.1.1.4 35-1.2 37-1.2.1 38-1.2.1.2 39-1.2.1.2.1.r 40-1.2.1.2.1.1.1 42-1.1.2.1 42-1.2.2.1 43-1.1.2.1.1 43-1.2.2.1.1 48-1.3.1.1.1 48-1.3.1.1.1.1.1 48-1.3.1.1.1.1.2 49-1.3.1.1.1.1 51-1.3.1.1.1.1.r 52-1.3.1.1.1.1.r 53-1.3.1.1.1.1.1.1.1 55-1.3.1.1.1.1.2.1.1 57-1.3.1.1.2.1.1.1.1 59-1.3.1.1.2.1.1.1.1 61-1.3.1.1.2.1.2.1.1 63-1.3.1.1.2.1 64-1.3.1.1.2.1.3.1.1 65-1.3.1 66-1.3.1.2.1.1.1.1 68-1.3.1.2.1.1.1.1 69-1.3.1.2.1 70-1.3.1.2 71-1.3.1.2.2 (m / multi-sentence :snt1 (a / and~e.0 :op2~e.2 (o / or~e.10 :op1 (d / diminish-01~e.9 :ARG0 (a10 / antioxidant~e.8) :ARG1 (a2 / activate-01~e.16 :ARG1 (p / protein :name (n2 / name :op1 "NF-kB"~e.13,15)))) :op2 (e2 / eliminate-01~e.12 :ARG1 a2 :ARG1-of (c4 / complete-02~e.11)) :location (t / type-03~e.4 :ARG1~e.5 (c / cell~e.6) :mod (m3 / many~e.3))) :ARG1-of (d2 / describe-01 :ARG0 (t2 / table~e.18,42 :mod 1~e.19,43))) :snt2 (o2 / observe-01~e.35 :ARG1 (s / stimulate-01~e.37 :ARG0 (a3 / and~e.29 :op1 (s2 / small-molecule :wiki "Hydrogen_peroxide" :name (n5 / name :op1 "H2O2"~e.25)) :op2 (l / light :mod (u / ultraviolet)) :op3 (r / radiate-01~e.31 :ARG0-of (i / ionize-01~e.30)) :mod (a11 / all~e.33)) :ARG1 (d3 / degrade-01~e.38 :ARG1~e.39 (p4 / protein :name (n3 / name :op1 "IkB"~e.40)))) :ARG1-of (d4 / describe-01 :ARG0 (t3 / table~e.18,42 :mod 1~e.19,43)) :ARG0-of (e / exemplify-01~e.23)) :snt3 (c2 / contrast-01 :ARG2 (d5 / decrease-01~e.65 :ARG0 (a12 / and :op1 (a7 / antioxidant~e.48 :example~e.51,52 (a13 / and~e.49 :op1 (a14 / antioxidant~e.48 :name (n / name :op1 "BHA"~e.53)) :op2 (a15 / antioxidant~e.48 :name (n12 / name :op1 "NGA"~e.55)))) :op2 (r2 / reductant :example (a6 / and~e.63 :op1 (r3 / reductant :name (n4 / name :op1 "a-tocopherol"~e.57,59)) :op2 (r4 / reductant :name (n6 / name :op1 "NAC"~e.61)) :op3 (r5 / reductant :name (n7 / name :op1 "PDTC"~e.64))))) :ARG1 (a4 / and~e.70 :op1 (a5 / activity-06~e.69 :ARG0 (p2 / protein :name (n11 / name :op1 "NF-kB"~e.66,68))) :op2 (t4 / translocate-01~e.71 :ARG1 p2)) :ARG1-of (d7 / describe-01 :ARG0 (p3 / publication :ARG1-of (c3 / cite-01 :ARG2 (a9 / and~e.0 :op1 12 :op2 253))))))) # ::id bel_pmid_1069_9758.36926 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Once activated , Raf @-@ 1 phosphorylates serines in the catalytic sites of MKK @/@ MEK [ 345,367 ] . MKK1 @/@ MEK1 and MKK2 @/@ MEK2 activate members of the MAP kinase family ( ERK @-@ 1/ERK @-@ 2 ) , # ::alignments 0-1.2.2.1.1.1.1.1 1-1.1.3 3-1.1.2.1.1 5-1.1.2.1.1 6-1.1 7-1.1.1.1.1 10-1.1.1.2.2 11-1.1.1.2 12-1.1.1.2.1.r 13-1.1.1.2.1.1.1.1 14-1.1.1.2.1 15-1.1.1.2.1.2.1.1 20-1.2.1.1.1.1.1 21-1.2.1.1 22-1.2.1.1.2.1.1 23-1.2.1 24-1.2.1.2.1.1.1 25-1.2.1.2 25-1.2.2.1.1 26-1.2.1.2.2.1.1 27-1.2 28-1.2.2 31-1.2.2.2.1.1.1 32-1.2.2.2.1.1.2 33-1.2.2.2.1 35-1.2.2.1.1.1.1.1 35-1.2.2.1.1.2.1.1 39-1.2.2.1.1.2.1.1 (m / multi-sentence :snt1 (p / phosphorylate-01~e.6 :ARG1 (a / amino-acid :name (n2 / name :op1 "serine"~e.7) :part-of (p3 / protein-segment~e.11 :part-of~e.12 (s2 / slash~e.14 :op1 (e5 / enzyme :name (n6 / name :op1 "MKK"~e.13)) :op2 (e6 / enzyme :name (n7 / name :op1 "MEK"~e.15))) :mod (c / catalysis~e.10))) :ARG2 (e / enzyme :name (n / name :op1 "Raf-1"~e.3,5)) :time (a2 / activate-01~e.1 :ARG1 e) :ARG1-of (d / describe-01 :ARG0 (p2 / publication :ARG1-of (c2 / cite-01 :ARG2 (a3 / and :op1 345 :op2 367))))) :snt2 (a5 / activate-01~e.27 :ARG0 (a7 / and~e.23 :op1 (s3 / slash~e.21 :op1 (e4 / enzyme :name (n5 / name :op1 "MKK1"~e.20)) :op2 (e2 / enzyme :name (n3 / name :op1 "MEK1"~e.22))) :op2 (s5 / slash~e.25 :op1 (e9 / enzyme :name (n10 / name :op1 "MKK2"~e.24)) :op2 (e10 / enzyme :name (n11 / name :op1 "MEK2"~e.26)))) :ARG1 (m2 / member~e.28 :ARG1-of (m3 / mean-01 :ARG2 (s4 / slash~e.25 :op1 (e7 / enzyme :name (n8 / name :op1 "ERK-1"~e.0,35)) :op2 (e8 / enzyme :name (n9 / name :op1 "ERK-2"~e.35,39)))) :ARG1-of (i / include-91 :ARG2 (p4 / protein-family~e.33 :name (n4 / name :op1 "MAP"~e.31 :op2 "kinase"~e.32)))))) # ::id bel_pmid_1072_9607.86 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results are consistent with our previous data showing that PAF is able to translocate PKCa and PKCe from cytosol to plasma membrane # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 4-1.2.r 5-1.2.1 5-1.2.1.r 6-1.2.2 7-1.2 8-1.3 9-1.3.1.r 10-1.3.1.1.1.1.1 12-1.3.1 14-1.3.1.1 15-1.3.1.1.2.1.1.1 16-1.3.1.1.2 17-1.3.1.1.2.2.1.1 18-1.3.1.1.4.r 19-1.3.1.1.4 20-1.3.1.1.3.r 21-1.3.1.1.3.1 22-1.3.1.1.3 (c / consistent-01~e.3 :ARG1 (t3 / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :mod (t / this~e.0)) :ARG2~e.4 (d / data~e.7 :poss~e.5 (w / we~e.5) :time (p2 / previous~e.6)) :ARG0-of (s / show-01~e.8 :ARG1~e.9 (p / possible-01~e.12 :ARG1 (t2 / translocate-01~e.14 :ARG0 (s2 / small-molecule :name (n / name :op1 "PAF"~e.10)) :ARG1 (a / and~e.16 :op1 (e / enzyme :name (n2 / name :op1 "PKCa"~e.15)) :op2 (e2 / enzyme :name (n3 / name :op1 "PKCe"~e.17))) :ARG2~e.20 (m2 / membrane~e.22 :mod (p3 / plasma~e.21)) :ARG3~e.18 (c2 / cytosol~e.19))))) # ::id bel_pmid_1072_9607.18666 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Eosinophils Human Superoxide production Human Transmigration through epithelial cells Human Transmigration through Matrigel Human CD11b @/@ CD18 ( Mac @-@ 1 ) translocation , degranulation Human IL @-@ 8 release # ::alignments 0-1.1.1.2.1.1 1-1.1.1.1 2-1.1.1 3-1.1 4-1.2.2 4-1.3.1.2 4-1.3.2 7-1.2.1.1 8-1.2.1 9-1.2.2 9-1.3.1.2 9-1.3.2 12-1.3.1.1.1 13-1.2.2 13-1.3.1.2 13-1.3.2 14-1.4.1.1.1.1.1 16-1.4.1.1.2.1.1 18-1.4.1.1.3.1.1.1 20-1.4.1.1.3.1.1.1 22-1.4.1 25-1.4.2.1.1.2 26-1.4.2.1.1.1.1 28-1.4.2.1.1.1.1 29-1.4.2.1 (m / multi-sentence :snt1 (p / produce-01~e.3 :ARG1 (s / superoxide~e.2 :mod (h / human~e.1) :mod (c / cell :name (n / name :op1 "eosinophil"~e.0)))) :snt2 (t / transmigrate-01 :ARG1 (c2 / cell~e.8 :mod (e / epithelium~e.7)) :mod (h5 / human~e.4,9,13)) :snt3 (t2 / transmigrate-01 :ARG1 (p5 / protein :name (n3 / name :op1 "Matrigel"~e.12) :mod (h3 / human~e.4,9,13)) :mod (h2 / human~e.4,9,13)) :snt4 (a / and :op1 (t4 / translocate-01~e.22 :ARG1 (m2 / macro-molecular-complex :part (p2 / protein :name (n4 / name :op1 "CD11b"~e.14)) :part (p3 / protein :name (n5 / name :op1 "CD18"~e.16)) :ARG1-of (m3 / mean-01 :ARG2 (s2 / small-molecule :name (n2 / name :op1 "Mac-1"~e.18,20))))) :op2 (d / degranulate-00 :ARG1 (r / release-01~e.29 :ARG0 (p4 / protein :name (n6 / name :op1 "IL-8"~e.26,28) :mod (h4 / human~e.25)))))) # ::id bel_pmid_1072_9607.19486 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Activation of tyrosine kinases Fyn and Lyn , but not Lck , also occurred within 2 min after PAF stimulation in the cells # ::alignments 0-1.1 0-1.2 1-1.1.1.r 2-1.1.1.1.1.1 2-1.1.1.2.1.1 3-1.1.1.1.1.2 3-1.1.1.2.1.2 4-1.1.1.1.1.3 5-1.1.1 6-1.1.1.2.1.3 8-1 9-1.2.1 9-1.2.1.r 10-1.2.2.1.1 12-1.1.3 14-1.1.2 14-1.1.2.2 14-1.1.2.2.1.1.r 14-1.1.2.2.r 15-1.1.2.2.1.1 16-1.1.2.2.1.2 17-1.1.2 18-1.1.2.1.1.1.1 19-1.1.2.1 20-1.1.2.1.2.r 22-1.1.2.1.2 (c3 / contrast-01~e.8 :ARG1 (a3 / activate-01~e.0 :ARG1~e.1 (a / and~e.5 :op1 (e / enzyme :name (n / name :op1 "tyrosine"~e.2 :op2 "kinase"~e.3 :op3 "Fyn"~e.4)) :op2 (e2 / enzyme :name (n2 / name :op1 "tyrosine"~e.2 :op2 "kinase"~e.3 :op3 "Lyn"~e.6))) :time (a6 / after~e.14,17 :op1 (s / stimulate-01~e.19 :ARG1 (s2 / small-molecule :name (n4 / name :op1 "PAF"~e.18)) :location~e.20 (c2 / cell~e.22)) :quant~e.14 (u / up-to~e.14 :op1 (t / temporal-quantity :quant~e.14 2~e.15 :unit (m2 / minute~e.16)))) :mod (a2 / also~e.12)) :ARG2 (a5 / activate-01~e.0 :polarity~e.9 -~e.9 :ARG1 (e3 / enzyme :name (n3 / name :op1 "Lck"~e.10)))) # ::id bel_pmid_1072_9607.19488 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PAFR promoter 2 contained AP @-@ 2 and Sp @-@ 1 binding sites we demonstrated that PAF activates p44ERK1 @/@ p42ERK2 in CHO cells stably expressing PAF receptor # ::alignments 0-1.1.1.1.1.1.1 1-1.1.1 1-1.1.1.1 1-1.1.1.1.r 2-1.1.2.1.1.1.1.1.1 3-1.1 4-1.1.2.1.1.1.1.1.1 6-1.1.2.1.1.1.1.1.1 7-1.1.2.1 8-1.1.2.1.2.1.1.1.1 10-1.1.2.1.2.1.1.1.1 11-1.1.2 11-1.1.2.1.1.1 11-1.1.2.1.2.1 12-1.1.2.1.1 12-1.1.2.1.2 13-1.2.1 14-1.2 15-1.2.2.r 16-1.2.2.1.1.1 17-1.2.2 18-1.2.2.2.1.1.1 20-1.2.2.2.2.1.1 21-1.2.2.3.r 22-1.2.2.3.1.1 23-1.2.2.3 24-1.2.2.3.2.2 25-1.2.2.3.2 26-1.2.2.3.2.1 27-1.2.2.3.2.1 (m3 / multi-sentence :snt1 (c2 / contain-01~e.3 :ARG0 (m4 / molecular-physical-entity~e.1 :ARG0-of~e.1 (p / promote-01~e.1 :ARG1 (p6 / protein :name (n5 / name :op1 "PAFR"~e.0)))) :ARG1 (b / bind-01~e.11 :ARG1 (a2 / and~e.7 :op1 (p4 / protein-segment~e.12 :ARG1-of (b2 / bind-01~e.11 :ARG2 (p2 / protein :name (n6 / name :op1 "AP-2"~e.2,4,6)))) :op2 (p5 / protein-segment~e.12 :ARG1-of (b3 / bind-01~e.11 :ARG2 (p3 / protein :name (n8 / name :op1 "Sp-1"~e.8,10))))))) :snt2 (d / demonstrate-01~e.14 :ARG0 (w / we~e.13) :ARG1~e.15 (a / activate-01~e.17 :ARG0 (p7 / protein :name (n / name :op1 "PAF"~e.16 :op2 "receptor")) :ARG1 (m2 / macro-molecular-complex :part (e / enzyme :name (n2 / name :op1 "p44ERK1"~e.18)) :part (e2 / enzyme :name (n3 / name :op1 "p42ERK2"~e.20))) :location~e.21 (c / cell-line~e.23 :name (n4 / name :op1 "CHO"~e.22) :ARG1-of (e3 / express-03~e.25 :ARG2 p7~e.26,27 :ARG1-of (s / stable-03~e.24)))))) # ::id bel_pmid_1072_9607.19490 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PAF induced tyrosine phosphorylation and activation of focal adhesion kinase ( FAK ) in human endothelial cells derived from vein umbilical cord # ::alignments 0-1.1.1.1 1-1 2-1.2.1.1.1.1 3-1.2.1 4-1.2 5-1.2.2 6-1.2.2.1.r 7-1.2.2.1.1.1 8-1.2.2.1.1.2 9-1.2.2.1.1.3 13-1.3.r 14-1.3.2 15-1.3.1 16-1.3 17-1.3.3 18-1.3.3.1.r 19-1.3.3.1.2 20-1.3.3.1.1 21-1.3.3.1 (i / induce-01~e.1 :ARG0 (s / small-molecule :name (n / name :op1 "PAF"~e.0)) :ARG2 (a / and~e.4 :op1 (p / phosphorylate-01~e.3 :ARG1 (a2 / amino-acid :name (n2 / name :op1 "tyrosine"~e.2) :part-of e)) :op2 (a3 / activate-01~e.5 :ARG1~e.6 (e / enzyme :name (n3 / name :op1 "focal"~e.7 :op2 "adhesion"~e.8 :op3 "kinase"~e.9)))) :location~e.13 (c / cell~e.16 :mod (e2 / endothelium~e.15) :mod (h / human~e.14) :ARG1-of (d / derive-01~e.17 :ARG2~e.18 (c2 / cord~e.21 :mod (n4 / navel~e.20) :mod (v / vein~e.19))))) # ::id bel_pmid_1072_9607.22074 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Suppression of the PAF effects by calphostin C , a PKC inhibitor , suggests that PKC is an upstream activator of FAK # ::alignments 0-1.1 1-1.1.1.r 3-1.1.1.2.1.1 4-1.1.1 5-1.1.1.1.r 6-1.1.1.1 7-1.1.1.1.1.1 10-1.1.1.1.2.1.1.1.1.1 11-1.1.1.1.2.1 11-1.1.1.1.2.1.1 11-1.1.1.1.2.1.1.r 13-1 14-1.2.r 15-1.2.1 18-1.2.3 19-1.2 20-1.2.2.r 21-1.2.2.1.1 (s / suggest-01~e.13 :ARG0 (s2 / suppress-01~e.0 :ARG1~e.1 (a / affect-01~e.4 :ARG0~e.5 (c / calphostin~e.6 :name (n2 / name :op1 "C"~e.7) :ARG1-of (m2 / mean-01 :ARG2 (m3 / molecular-physical-entity~e.11 :ARG0-of~e.11 (i2 / inhibit-01~e.11 :ARG1 (e2 / enzyme :name (n3 / name :op1 "PKC"~e.10)))))) :ARG1 (s3 / small-molecule :name (n / name :op1 "PAF"~e.3)))) :ARG1~e.14 (a2 / activate-01~e.19 :ARG0 e2~e.15 :ARG1~e.20 (e3 / enzyme :name (n4 / name :op1 "FAK"~e.21)) :direction (u / upstream~e.18))) # ::id bel_pmid_1072_9607.31242 ::amr-annotator SDL-AMR-09 ::preferred # ::tok transforming growth factor @-@ b2 ( TGF @-@ b2 ) was shown to upregulate the transcription rate of PAFR transcript 1 in Ramos human lymphoblastoid cells # ::alignments 0-1.1.2.1.1 1-1.1.2.1.2 2-1.1.2.1.3 4-1.1.2.1.3 4-1.1.2.2.1.1.1 6-1.1.2.2.1.1.1 8-1.1.2.1.3 8-1.1.2.2.1.1.1 11-1 13-1.1 15-1.1.1.1 16-1.1.1 17-1.1.1.1.1.r 18-1.1.1.1.1.1.1 19-1.1.1.1.1.1.2 20-1.1.1.1.1.1.3 21-1.1.3.r 22-1.1.3.1.1 23-1.1.3.1.2 24-1.1.3.1.3 25-1.1.3 (s / show-01~e.11 :ARG1 (u / upregulate-01~e.13 :ARG1 (r / rate~e.16 :degree-of (t2 / transcribe-01~e.15 :ARG1~e.17 (p3 / protein :name (n2 / name :op1 "PAFR"~e.18 :op2 "transcript"~e.19 :op3 1~e.20)))) :ARG2 (p2 / protein :name (n3 / name :op1 "transforming"~e.0 :op2 "growth"~e.1 :op3 "factor-b2"~e.2,4,8) :ARG1-of (m / mean-01 :ARG2 (p / protein :name (n / name :op1 "TGF-b2"~e.4,6,8)))) :location~e.21 (c / cell~e.25 :name (n4 / name :op1 "Ramos"~e.22 :op2 "human"~e.23 :op3 "lymphoblastoid"~e.24)))) # ::id bel_pmid_1073_7606.7132 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We have further identified , in the GFAP promoter region , a STAT3 site at which nucleotide substitutions almost completely abolished the IL @-@ 11 @-@ induced GFAP promoter activation . # ::alignments 0-1.1 2-1.4 3-1 5-1.5.r 7-1.5.1.1.1 8-1.5.1 8-1.5.1.1 8-1.5.1.1.r 9-1.5 12-1.2.1.1.1 13-1.2 16-1.3.1.1 17-1.3.1 18-1.3.3.1 19-1.3.3 20-1.3 22-1.3.2.2.1.1.1 24-1.3.2.2.1.1.1 26-1.3.2.2 27-1.3.2.1.1.1.1.1 28-1.3.2.1 28-1.3.2.1.1 28-1.3.2.1.1.r 29-1.3.2 (i / identify-01~e.3 :ARG0 (w / we~e.0) :ARG1 (p3 / protein-segment~e.13 :part-of (p / protein :name (n / name :op1 "STAT3"~e.12))) :ARG2 (a / abolish-01~e.20 :ARG0 (s2 / substitute-01~e.17 :ARG2 (n3 / nucleotide~e.16)) :ARG1 (a3 / activate-01~e.29 :ARG1 (m2 / molecular-physical-entity~e.28 :ARG0-of~e.28 (p4 / promote-01~e.28 :ARG1 (p5 / protein :name (n4 / name :op1 "GFAP"~e.27)))) :ARG2-of (i2 / induce-01~e.26 :ARG0 (p6 / protein :name (n5 / name :op1 "IL-11"~e.22,24)))) :ARG1-of (c / complete-02~e.19 :degree (a2 / almost~e.18))) :degree (f / further~e.2) :location~e.5 (r / region~e.9 :part-of (m / molecular-physical-entity~e.8 :ARG0-of~e.8 (p2 / promote-01~e.8 :ARG1 p5~e.7)))) # ::id bel_pmid_1073_7606.22816 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Activation of the GFAP gene promoter by IL @-@ 11 and related cytokines Previous studies have shown that stimulation of gp130 molecules on neuroepithelial cells by LIF , CNTF , or the IL @-@ 6/sIL @-@ 6R complex induces activation of the GFAP gene promoter ( Bonni et al. , 1997 ; Nakashima et al. , 1999 b ) . # ::alignments 0-1.2 1-1.2.2.r 3-1.2.2.1.1.1.1 4-1.2.2.1.1 5-1.2.2 5-1.2.2.1 5-1.2.2.1.r 6-1.2.1.r 7-1.2.1.1.1.1 9-1.2.1.1.1.1 10-1.2.1 11-1.2.1.2.2 12-1.2.1.2.1.1 13-1.1.1.1 14-1.1.1 16-1.1 17-1.1.2.r 18-1.1.2.1 19-1.1.2.1.1.r 20-1.1.2.1.1.1.1 21-1.1.2.1.3.3 24-1.1.2.1.2 25-1.1.2.1.3.r 26-1.1.2.1.3.1.1.1 28-1.1.2.1.3.2.1.1 30-1.1.2.1.3 32-1.1.2.1.3.3.1.1.1 36-1.1.2.1.3.3.2.1.1 37-1.1.2.1.3.3 38-1.1.2 39-1.1.2.2 40-1.1.2.2.1.r 42-1.1.2.2.1.1.1.1.1 43-1.1.2.2.1.1.1 44-1.1.2.2.1 44-1.1.2.2.1.1 44-1.1.2.2.1.1.r 46-1.1.3.1.1.1.1.1.1 47-1.1.3.1.1.1 48-1.1.3.1.1.1.2.1 50-1.1.3.1.1.2.1 52-1.1.3.1.2.1.1.1.1 53-1.1.3.1 53-1.1.3.1.2.1 54-1.1.3.1.2.1.2.1 56-1.1.3.1.2.2.1 (m / multi-sentence :snt2 (s2 / show-01~e.16 :ARG0 (s3 / study-01~e.14 :time (p9 / previous~e.13)) :ARG1~e.17 (i / induce-01~e.38 :ARG0 (s / stimulate-01~e.18 :ARG0~e.19 (p5 / protein :name (n5 / name :op1 "gp130"~e.20)) :ARG1 (c / cell~e.24 :mod (n6 / neuroepithelium)) :ARG2~e.25 (o3 / or~e.30 :op1 (p4 / protein :name (n4 / name :op1 "LIF"~e.26)) :op2 (p6 / protein :name (n7 / name :op1 "CNTF"~e.28)) :op3 (m3 / macro-molecular-complex~e.21,37 :part (p7 / protein :name (n8 / name :op1 "IL-6"~e.32)) :part (p8 / protein :name (n9 / name :op1 "sIL-6R"~e.36))))) :ARG2 (a3 / activate-01~e.39 :ARG1~e.40 (m4 / molecular-physical-entity~e.44 :ARG0-of~e.44 (p10 / promote-01~e.44 :ARG1 (g2 / gene~e.43 :name (n10 / name :op1 "GFAP"~e.42)))))) :ARG1-of (d3 / describe-01 :ARG0 (a7 / and~e.53 :op1 (p11 / publication-91 :ARG0 (a5 / and~e.47 :op1 (p12 / person :name (n11 / name :op1 "Bonni"~e.46)) :op2 (p13 / person :mod (o / other~e.48))) :time (d / date-entity :year 1997~e.50)) :op2 (p14 / publication-91 :ARG0 (a6 / and~e.53 :op1 (p15 / person :name (n12 / name :op1 "Nakashima"~e.52)) :op2 (p16 / person :mod (o2 / other~e.54))) :time (d2 / date-entity :year 1999~e.56))))) :snt1 (a2 / activate-01~e.0 :ARG0~e.6 (a8 / and~e.10 :op1 (p2 / protein :name (n2 / name :op1 "IL-11"~e.7,9)) :op2 (p3 / protein :name (n3 / name :op1 "cytokine"~e.12) :ARG1-of (r / relate-01~e.11))) :ARG1~e.1 (m2 / molecular-physical-entity~e.5 :ARG0-of~e.5 (p / promote-01~e.5 :ARG1 (g / gene~e.4 :name (n / name :op1 "GFAP"~e.3)))))) # ::id bel_pmid_1074_4722.88 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 5B , immediately after -@ irradiation , the amount of threonine 68 @- phosphorylated Chk2 increased ( lane 2 ) , and prior treatment of cells with caffeine markedly reduced this increase ( lane 4 ) . # ::alignments 0-1.1.3.r 0-1.2.1.3.r 1-1.3 3-1.4 4-1.4.1 6-1.2.2 7-1.2.2 8-1.2.2 9-1.2.2 10-1.2.2 11-1.2.2 12-1.2.2 13-1.2.2 14-1.2.2 15-1.2.2 16-1.2.2 17-1.2.2 18-1.2.2 19-1.2.2 20-1.2.2 21-1.2.2 22-1.2.2 25-1 26-1.2.1.3 27-1.2.1 28-1.2.1.1.r 29-1.2.1.1 30-1.2.1.2.r 31-1.2.1.2 32-1.2.3 32-1.2.3.r 33-1.2 35-1.2.2 37-1.2.4.1 38-1.2.4.1.1 (a5 / and~e.25 :op1 (i / increase-01 :ARG1 (a3 / amount :quant-of (e / enzyme :name (n2 / name :op1 "Chk2") :part (a / amino-acid :mod 68 :name (n / name :op1 "threonine") :ARG1-of (p / phosphorylate-01)))) :ARG1-of (d / describe-01 :ARG2 (l / lane :mod 2)) :time~e.0 (a4 / after :op1 (i2 / irradiate-01) :mod (i3 / immediate))) :op2 (r / reduce-01~e.33 :ARG0 (t / treat-03~e.27 :ARG1~e.28 (c / cell~e.29) :ARG3~e.30 (c2 / caffeine~e.31) :time~e.0 (p2 / prior~e.26)) :ARG1 i~e.6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,35 :manner~e.32 (m2 / marked~e.32) :ARG1-of (d2 / describe-01 :ARG2 (l2 / lane~e.37 :mod 4~e.38))) :ARG1-of (s / show-01~e.1) :location (f / figure~e.3 :mod "5B"~e.4)) # ::id bel_pmid_1074_4722.15494 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 3A in normal cells , IR causes activation of Chk2 @/@ Cds1 ( lane 2 ) , and this activation is inhibited by prior treatment of cells with caffeine ( lane 4 ) . # ::alignments 0-1.2.1.3.r 1-1.3 2-1.3.1.r 3-1.3.1 4-1.3.1.1 6-1.4.1 7-1.4 9-1.1.1 9-1.1.1.1 9-1.1.1.1.r 10-1.1 11-1.1.2 13-1.1.2.1.1.1.1 15-1.1.2.1.2.1.1 17-1.1.3.1 18-1.1.3.1.1 23-1.1.2 25-1.2 27-1.2.1.3 28-1.2.1 29-1.2.1.1.r 30-1.2.1.1 31-1.2.1.2.r 32-1.2.1.2 34-1.2.3.1 35-1.2.3.1.1 (a / and :op1 (c / cause-01~e.10 :ARG0 (r / radiate-01~e.9 :ARG0-of~e.9 (i2 / ionize-01~e.9)) :ARG1 (a2 / activate-01~e.11,23 :ARG1 (m / macro-molecular-complex :part (e / enzyme :name (n2 / name :op1 "Chk2"~e.13)) :part (e2 / enzyme :name (n3 / name :op1 "Cds1"~e.15)))) :ARG1-of (d2 / describe-01 :ARG2 (l / lane~e.17 :mod 2~e.18))) :op1 (i / inhibit-01~e.25 :ARG0 (t2 / treat-03~e.28 :ARG1~e.29 (c2 / cell~e.30) :ARG3~e.31 (c3 / caffeine~e.32) :time~e.0 (p / prior~e.27)) :ARG1 a2 :ARG1-of (d / describe-01 :ARG2 (l2 / lane~e.34 :mod 4~e.35))) :ARG1-of (s / show-01~e.1 :location~e.2 (f / figure~e.3 :mod "3A"~e.4)) :location (c4 / cell~e.7 :ARG1-of (n4 / normal-02~e.6))) # ::id bel_pmid_1074_4722.15496 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Immediately after IR , an increase in serine 216 @-@ phosphorylated Cdc25C was observed in the nuclear fraction ( Fig . 1B , lane 2 ) , and prior treatment of cells with caffeine inhibited this increase ( Fig . 1B , lane 4 ) . # ::alignments 0-1.1.3.2 1-1.1.3 2-1.1.3.1 2-1.1.3.1.1 2-1.1.3.1.1.r 5-1.1.1 7-1.1.1.1.2.2.1 8-1.1.1.1.2.1 10-1.1.1.1.2.3 11-1.1.1.1.1.1 13-1.1 14-1.1.2.r 16-1.1.2.1 17-1.1.2 19-1.2.3.1.1 21-1.2.3.1.1.1 23-1.1.4.1.2 24-1.1.4.1.2.1 27-1 27-1.1.4.1 28-1.2.1.3 29-1.2.1 30-1.2.1.1.r 31-1.2.1.1 32-1.2.1.2.r 33-1.2.1.2 34-1.2 36-1.1.1 38-1.1.4.1.1 40-1.1.4.1.1.1 42-1.2.3.1.2 43-1.2.3.1.2.1 (a2 / and~e.27 :op1 (o / observe-01~e.13 :ARG1 (i / increase-01~e.5,36 :ARG1 (e / enzyme :name (n3 / name :op1 "Cdc25C"~e.11) :part (a3 / amino-acid :mod 216~e.8 :name (n2 / name :op1 "serine"~e.7) :ARG0-of (p / phosphorylate-01~e.10)))) :location~e.14 (f / fraction-01~e.17 :mod (n4 / nucleus~e.16)) :time (a / after~e.1 :op1 (r / radiate-01~e.2 :ARG0-of~e.2 (i4 / ionize-01~e.2)) :mod (i2 / immediate~e.0)) :ARG1-of (d / describe-01 :ARG0 (a4 / and~e.27 :op1 (f2 / figure~e.38 :mod "1B"~e.40) :op2 (l / lane~e.23 :mod 2~e.24)))) :op2 (i3 / inhibit-01~e.34 :ARG0 (t2 / treat-03~e.29 :ARG1~e.30 (c / cell~e.31) :ARG3~e.32 (c2 / caffeine~e.33) :time (p2 / prior~e.28)) :ARG1 i :ARG1-of (d2 / describe-01 :ARG0 (a5 / and :op1 (f3 / figure~e.19 :mod "1B"~e.21) :op2 (l2 / lane~e.42 :mod 4~e.43))))) # ::id bel_pmid_1074_4722.15498 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 6A , ATM immunoprecipitated from irradiated cells was more active than that from unirradiated cells , and both the basal and radiationinduced ATM activities were inhibited by caffeine with an IC50 at around 200 M. # ::alignments 1-1.3 2-1.3.1.r 3-1.3.1 4-1.3.1.1 6-1.1.1.1.1 6-1.1.3.1.1 7-1.1.1.2 7-1.1.3.2 9-1.1.1.2.1.1 9-1.1.3.2.1.1 9-1.1.3.2.1.1.1 9-1.1.3.2.1.1.1.r 10-1.1.1.2.1 10-1.1.3.2.1 12-1.1.2 13-1.1 14-1.1.3.r 17-1.1.1.2.1.1 17-1.1.3.2.1.1 17-1.1.3.2.1.1.1 17-1.1.3.2.1.1.1.r 18-1.1.1.2.1 20-1.2.2 23-1.2.2.1.2 24-1.2.2 26-1.2.2.1.1.1.1 27-1.2.2.1 27-1.2.2.2 29-1.2 30-1.2.1.r 31-1.2.1 36-1.2.1.1.2 37-1.2.1.1.2.1.1 (a2 / and :op1 (a3 / activity-06~e.13 :ARG0 (e / enzyme :name (n / name :op1 "ATM"~e.6) :ARG1-of (i / immunoprecipitate-01~e.7 :ARG2 (c / cell~e.10,18 :ARG1-of (i2 / irradiate-01~e.9,17)))) :degree (m2 / more~e.12) :compared-to~e.14 (e2 / enzyme :name (n2 / name :op1 "ATM"~e.6) :ARG1-of (i3 / immunoprecipitate-01~e.7 :ARG2 (c2 / cell~e.10 :ARG1-of (i8 / irradiate-01~e.9,17 :polarity~e.9,17 -~e.9,17))))) :op2 (i5 / inhibit-01~e.29 :ARG0~e.30 (c3 / caffeine~e.31 :ARG1-of (h / have-percentage-maximal-inhibitory-concentration-01 :ARG2 50 :ARG4 (a / around~e.36 :op1 (c4 / concentration-quantity :quant 200~e.37 :unit (m / molar))))) :ARG1 (a5 / and~e.20,24 :op1 (a4 / activity-06~e.27 :ARG0 (e3 / enzyme :name (n3 / name :op1 "ATM"~e.26)) :mod (b / basal~e.23)) :op2 (a6 / activity-06~e.27 :ARG0 e3 :ARG2-of (i6 / induce-01 :ARG0 (r / radiate-01))))) :ARG1-of (s / show-01~e.1 :location~e.2 (f / figure~e.3 :mod "6A"~e.4))) # ::id bel_pmid_1074_4722.15500 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , no such activation was found in A @-@ T cells indicating that caffeine inhibited the ATM @-@ dependent Chk2 @/@ Cds1 activation ( Fig . 3A , lanes 6 and 8 ) . # ::alignments 0-1 2-1.1.1.1 2-1.1.1.1.r 3-1.1.1.2 4-1.1.1 6-1.1 7-1.1.2.r 8-1.1.2.1.1 10-1.1.2.1.1 11-1.1.2 12-1.1.3 13-1.1.3.1.r 14-1.1.3.1.1 15-1.1.3.1 17-1.1.3.1.2.1.1.1 19-1.1.3.1.2.1 19-1.1.3.1.2.1.2 19-1.1.3.1.2.1.2.r 20-1.1.3.1.2.1.2.1.1.1.1 22-1.1.3.1.2.1.2.1.2.1.1 23-1.1.3.1.2 25-1.2.1.1 27-1.2.1.1.1 29-1.2.1.2.1 29-1.2.1.2.2 30-1.2.1.2.1.1 31-1.2.1.2 32-1.2.1.2.2.1 (h / have-concession-91~e.0 :ARG1 (f / find-01~e.6 :ARG1 (a / activate-01~e.4 :polarity~e.2 -~e.2 :mod (s / such~e.3)) :location~e.7 (c / cell~e.11 :name (n / name :op1 "A-T"~e.8,10)) :ARG0-of (i / indicate-01~e.12 :ARG1~e.13 (i2 / inhibit-01~e.15 :ARG0 (c2 / caffeine~e.14) :ARG1 (a2 / activate-01~e.23 :ARG1 (e / enzyme~e.19 :name (n2 / name :op1 "ATM"~e.17) :ARG0-of~e.19 (d / depend-01~e.19 :ARG1 (m / macro-molecular-complex :part (e2 / enzyme :name (n3 / name :op1 "Chk2"~e.20)) :part (e3 / enzyme :name (n4 / name :op1 "Cds1"~e.22))))))))) :ARG1-of (d2 / describe-01 :ARG0 (a3 / and :op1 (f2 / figure~e.25 :mod "3A"~e.27) :op2 (a4 / and~e.31 :op1 (l / lane~e.29 :op1 6~e.30) :op2 (l2 / lane~e.29 :mod 8~e.32))))) # ::id bel_pmid_1074_4722.21126 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Substitution of threonine 68 by alanine in the full @-@ length kinase @-@ dead Chk2 dramatically reduced but did not abolish the ATM phosphorylation of Chk2 @/@ Cds1 in vitro ( Fig . 4B ; threonine 68 accounts for approximately 70 % of the total phosphorylation ) . # ::alignments 0-1.1.1.1 2-1.1.1.1.2.1.1 2-1.2.1.2.1 3-1.2.1.1 4-1.1.1.1.1.r 5-1.1.1.1.1.1.1 6-1.1.1.1.3.r 6-1.1.1.2.3 8-1.1.1.1.3.2.2.1.1 10-1.1.1.1.3.2.2.1 11-1.1.1.1.3.2.2 14-1.1.1.1.3.1.1 14-1.1.1.2.1.1.1.1 15-1.1.1.3 16-1.1.1 17-1.1 19-1.1.2.1 20-1.1.2 22-1.1.2.2 23-1.1.2.2 24-1.1.2.2 25-1.1.2.2 26-1.1.2.2 27-1.1.2.2 28-1.1.2.2 29-1.1.2.2 31-1.1.3.1 33-1.1.3.1.1 35-1.2.1.2.1 36-1.2.1.1 37-1.2 39-1.2.1.3.2 40-1.2.1.3.2.1.1 41-1.2.1.3.2.1 44-1.2.1.3.1 45-1.2.1.3.1.1 (m / multi-sentence :snt1 (c / contrast-01~e.17 :ARG1 (r / reduce-01~e.16 :ARG0 (s / substitute-01~e.0 :ARG1~e.4 (a2 / amino-acid :name (n2 / name :op1 "alanine"~e.5)) :ARG2 (a / amino-acid :name (n / name :op1 "threonine"~e.2)) :location~e.6 (e / enzyme :name (n3 / name :op1 "Chk2"~e.14) :ARG0-of (f3 / function-01 :polarity - :ARG1 (k / kinase~e.11 :ARG1-of (l / long-03~e.10 :degree (f / full~e.8)))))) :ARG1 (p3 / phosphorylate-01 :ARG1 (m2 / macro-molecular-complex :part (e2 / enzyme :name (n4 / name :op1 "Chk2"~e.14)) :part (e4 / enzyme :name (n6 / name :op1 "Cds1"))) :ARG2 (e3 / enzyme :name (n5 / name :op1 "ATM")) :manner (i / in-vitro~e.6)) :manner (d2 / dramatic~e.15)) :ARG2 (a3 / abolish-01~e.20 :ARG0 s~e.19 :ARG1 p3~e.22,23,24,25,26,27,28,29) :ARG1-of (d3 / describe-01 :ARG0 (f2 / figure~e.31 :mod "4B"~e.33))) :snt2 (a4 / account-01~e.37 :ARG1 (a5 / amino-acid :mod 68~e.3,36 :name (n7 / name :op1 "threonine"~e.2,35) :ARG1-of (i2 / include-91 :ARG2 (t / total-01~e.44 :ARG1 (p2 / phosphorylate-01~e.45)) :ARG3 (a7 / approximately~e.39 :op1 (p / percentage-entity~e.41 :value 70~e.40)))))) # ::id bel_pmid_1074_4722.21132 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Serine 15 in the N terminus of p53 has been shown to be the preferred ATM phosphorylation site ( 27 , 29 , 30 ) . As shown in Fig. 7A , ATM immunoprecipitated from irradiated cells was more active than that from control cells , and both ATM activities were inhibited by caffeine with IC50 at around 200 M. # ::alignments 0-1.1.1.3.2.1 1-1.1.1.3.1 4-1.1.1.3.3.1.1 5-1.1.1.3.3.1.2 7-1.1.1.3.3.2.1.1 9-1.1.1.3.r 10-1.1 12-1.1.1.3.r 14-1.1.1.2 15-1.1.1.1.1.1.1 16-1.1.1.1 17-1.1.1 19-1.1.2.1.1.1.1 21-1.1.2.1.1.1.2 23-1.1.2.1.1.1.3 27-1.2.3 28-1.2.3.1.r 29-1.2.3.1 30-1.2.3.1.1 32-1.2.1.3.1.1 33-1.2.1.1.2 33-1.2.1.3.2 34-1.2.1.1.2.1.r 35-1.2.1.1.2.1.1 36-1.2.1.1.2.1 38-1.2.1.2 39-1.2.1 40-1.2.1.3.r 42-1.2.1.3.2.1.r 43-1.2.1.3.2.1.1 44-1.2.1.3.2.1 46-1.2 46-1.2.2.2.1 48-1.2.1.1.1.1 48-1.2.1.3.1.1 49-1.2.2.2 51-1.2.2 52-1.2.2.1.r 53-1.2.2.1 57-1.2.2.1.1.2 58-1.2.2.1.1.2.1.1 (m2 / multi-sentence :snt1 (s / show-01~e.10 :ARG1 (p / protein-segment~e.17 :ARG1-of (p5 / phosphorylate-01~e.16 :ARG2 (e / enzyme :name (n5 / name :op1 "ATM"~e.15))) :ARG1-of (p4 / prefer-01~e.14) :domain~e.9,12 (a3 / amino-acid :mod 15~e.1 :name (n2 / name :op1 "serine"~e.0) :part-of (p2 / protein-segment :name (n3 / name :op1 "N"~e.4 :op2 "terminus"~e.5) :part-of (p3 / protein :name (n4 / name :op1 "p53"~e.7))))) :ARG1-of (d2 / describe-01 :ARG0 (p6 / publication :ARG1-of (c / cite-01 :ARG2 (a4 / and :op1 27~e.19 :op2 29~e.21 :op3 30~e.23))))) :snt2 (a2 / and~e.46 :op1 (a7 / activity-06~e.39 :ARG0 (e2 / enzyme :name (n / name :op1 "ATM"~e.48) :ARG1-of (i / immunoprecipitate-01~e.33 :ARG2~e.34 (c2 / cell~e.36 :ARG1-of (i2 / irradiate-01~e.35)))) :degree (m3 / more~e.38) :compared-to~e.40 (e3 / enzyme :name (n6 / name :op1 "ATM"~e.32,48) :ARG1-of (i3 / immunoprecipitate-01~e.33 :ARG2~e.42 (c3 / cell~e.44 :mod (c5 / control-01~e.43))))) :op2 (i4 / inhibit-01~e.51 :ARG0~e.52 (c4 / caffeine~e.53 :ARG1-of (h / have-percentage-maximal-inhibitory-concentration-01 :ARG2 50 :ARG4 (a / around~e.57 :op1 (c6 / concentration-quantity :quant 200~e.58 :unit (m / molar))))) :ARG1 (a5 / activity-06~e.49 :ARG0 (a6 / and~e.46 :op1 e2 :op2 e3))) :ARG1-of (s3 / show-01~e.27 :location~e.28 (f / figure~e.29 :mod "7A"~e.30)))) # ::id bel_pmid_1074_4722.21168 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Both Chk1 and Chk2 @/@ Cds1 have been shown to localize to the nucleus and to phosphorylate serine 216 of Cdc25C in vitro ( 13 , 15 ) ( 18 @–@ 21 ) . # ::alignments 1-1.1.1.1.1.1.1 3-1.1.1.1.2.1.1.1 5-1.1.1.1.2.2.1.1 7-1.1.1 8-1 10-1.1.1 13-1.1.1.2 14-1.1 16-1.1.2 17-1.1.2.1.2.1 18-1.1.2.1.1 20-1.1.2.1.3.1.1 21-1.1.2.3 22-1.1.2.3 24-1.2.1.1.1.1.1 26-1.2.1.1.1.1.2 29-1.2.1.2.1.1.1 31-1.2.1.2.1.1.2 (s / show-01~e.8 :ARG1 (a2 / and~e.14 :op1 (b / be-located-at-91~e.7,10 :ARG1 (a5 / and :op1 (e / enzyme :name (n2 / name :op1 "Chk1"~e.1)) :op2 (m / macro-molecular-complex :part (e2 / enzyme :name (n3 / name :op1 "Chk2"~e.3)) :part (e3 / enzyme :name (n4 / name :op1 "Cds1"~e.5)))) :ARG2 (n5 / nucleus~e.13)) :op2 (p / phosphorylate-01~e.16 :ARG1 (a / amino-acid :mod 216~e.18 :name (n / name :op1 "serine"~e.17) :part-of (e4 / enzyme :name (n6 / name :op1 "Cdc25C"~e.20))) :ARG2 a5 :manner (i / in-vitro~e.21,22))) :ARG1-of (d2 / describe-01 :ARG0 (a4 / and :op1 (p2 / publication :ARG1-of (c / cite-01 :ARG2 (a3 / and :op1 13~e.24 :op2 15~e.26))) :op2 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 (v / value-interval :op1 18~e.29 :op2 21~e.31)))))) # ::id bel_pmid_1074_4722.21170 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in the Western blot ( Fig . 1A , lane 3 ) , the phospho @-@ S216 antibody recognized Cdc25C that was incubated with a wild type Chk2 in the in vitro kinase assay but failed to recognize unphosphorylated Cdc25C , incubated with a kinase @-@ dead mutant ( D347A ) ( Fig . 1A , lane 2 ) . # ::alignments 0-1.1.2.2.2.r 1-1.3 2-1.1.2.2.2.2 2-1.3.1.r 4-1.3.1 5-1.3.1 7-1.3.1.1.1.1 9-1.3.1.1.1.1.1 11-1.3.1.1.1.2 12-1.3.1.1.1.2.1 16-1.2.2.2.2 19-1.1.1 20-1.1 21-1.1.2.1.1 24-1.1.2.2 25-1.1.2.2.1.r 27-1.1.2.2.1.2 28-1.1.2.2.1.2 29-1.1.2.2.1.1.1 30-1.1.2.2.2.2 32-1.1.2.2.2.2 33-1.1.2.2.2.2 34-1.1.2.2.2.1 35-1.1.2.2.2 36-1 37-1.2 39-1.2.2 41-1.2.2.2.1.1 43-1.2.2.2.3 44-1.2.2.2.3.1.r 46-1.2.2.2.3.1.2.2 49-1.2.2.2.3.1 49-1.2.2.2.3.1.1 49-1.2.2.2.3.1.1.r 51-1.2.2.2.3.1.1.1 54-1.2.3.1.1 56-1.2.3.1.1.1 58-1.2.3.1.2 59-1.2.3.1.2.1 (c / contrast-01~e.36 :ARG1 (r / recognize-01~e.20 :ARG0 (a / antibody~e.19 :ARG0-of (c2 / counter-01 :ARG1 (a5 / amino-acid :mod 216 :name (n / name :op1 "serine")))) :ARG1 (e / enzyme :name (n3 / name :op1 "Cdc25C"~e.21) :ARG1-of (i / incubate-01~e.24 :ARG2~e.25 (e2 / enzyme :name (n4 / name :op1 "Chk2"~e.29) :mod (w / wild-type~e.27,28)) :time~e.0 (a3 / assay-01~e.35 :ARG1 (k / kinase~e.34) :manner (i2 / in-vitro~e.2,30,32,33))))) :ARG2 (f2 / fail-01~e.37 :ARG1 a :ARG2 (r2 / recognize-01~e.39 :ARG0 a :ARG1 (e3 / enzyme :name (n5 / name :op1 "Cdc25C"~e.41) :ARG3-of (p / phosphorylate-01~e.16 :polarity -) :ARG1-of (i3 / incubate-01~e.43 :ARG2~e.44 (m2 / molecular-physical-entity~e.49 :ARG2-of~e.49 (m / mutate-01~e.49 :value "D347A"~e.51) :ARG0-of (f / function-01 :polarity - :ARG1 (k2 / kinase~e.46)))))) :ARG1-of (d / describe-01 :ARG0 (a2 / and :op1 (f3 / figure~e.54 :mod "1A"~e.56) :op2 (l / lane~e.58 :mod 2~e.59)))) :ARG1-of (s / show-01~e.1 :ARG0~e.2 (i4 / immunoblot-01~e.4,5 :ARG1-of (d2 / describe-01 :ARG0 (a4 / and :op1 (f4 / figure~e.7 :mod "1A"~e.9) :op2 (l2 / lane~e.11 :mod 3~e.12)))))) # ::id bel_pmid_1074_7872.20016 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We found that STAT3 , but not STAT5 , was activated in response to IGF @-@ I in 293T cells cotransfected with IGF @-@ IR and STAT expression vectors . Moreover , tyrosine phosphorylation of STAT3 , JAK1 , and JAK2 was increased upon IGF @-@ I stimulation of endogenous IGF @-@ IR in 293T cells transfected with the respective STAT or JAK expression vector . # ::alignments 0-1.2.1 1-1.2 2-1.2.2.r 3-1.2.2.1.1.1.1 5-1.2.2 6-1.2.2.2.1 6-1.2.2.2.1.r 7-1.2.2.2.2.1.1 10-1.2.2.1 10-1.2.2.2 11-1.2.2.1.2.r 12-1.2.2.1.2 13-1.2.2.1.2.1.r 14-1.2.2.1.2.1.1.1 16-1.2.2.1.2.1.1.1 18-1.2.2.1.2.1.2.1.1 19-1.2.2.1.2.1.2 20-1.2.2.1.2.1.2.2 21-1.2.2.1.2.1.2.2.1.r 22-1.2.2.1.2.1.2.2.1.1.1.1 24-1.2.2.1.2.1.2.2.1.1.1.1 25-1.2.2.1.2.1.2.2.1 26-1.2.2.1.2.1.2.2.1.2.1.1.1.1 27-1.2.2.1.2.1.2.2.1.2.1 28-1.2.2.1.2.1.2.2.1.2 30-1.1.1.1.1 30-1.2.2.1.2.1.2.2.1 32-1.1.1.1.1.1.1.1 32-1.1.1.1.1.2.1.1 32-1.1.1.1.1.3.1.1 33-1.1.1.1 34-1.1.1.1.1.r 35-1.1.1.1.1.1.2.1.1 37-1.1.1.1.1.2.2.1.1 40-1.1.1.1.1.3.2.1.1 42-1.1.1 44-1.1.1.2.1.1.1 46-1.1.1.2.1.1.1 47-1.1.1.2 48-1.1.1.2.2.r 49-1.1.1.2.2.2 50-1.1.1.2.2.1.1 52-1.1.1.2.2.1.1 54-1.1.1.2.2.3.1.1 55-1.1.1.2.2.3 56-1.1.1.2.2.3.2 57-1.1.1.2.2.3.2.1.r 59-1.1.1.2.2.3.2.1.1.1.1.2 60-1.1.1.2.2.3.2.1.1.1.1.1.1 61-1.1.1.2.2.3.2.1 62-1.1.1.2.2.3.2.1.2.1.1.1.1 63-1.1.1.2.2.3.2.1.1.1 63-1.1.1.2.2.3.2.1.2.1 64-1.1.1.2.2.3.2.1.1 64-1.1.1.2.2.3.2.1.2 (m / multi-sentence :snt2 (a4 / and :op2 (i / increase-01~e.42 :ARG1 (p / phosphorylate-01~e.33 :ARG1~e.34 (a5 / and~e.30 :op1 (a6 / amino-acid :name (n7 / name :op1 "tyrosine"~e.32) :part-of (p6 / protein :name (n8 / name :op1 "STAT3"~e.35))) :op2 (a7 / amino-acid :name (n16 / name :op1 "tyrosine"~e.32) :part-of (e7 / enzyme :name (n9 / name :op1 "JAK1"~e.37))) :op3 (a8 / amino-acid :name (n17 / name :op1 "tyrosine"~e.32) :part-of (e8 / enzyme :name (n10 / name :op1 "JAK2"~e.40))))) :time (s / stimulate-01~e.47 :ARG0 (p9 / protein :name (n11 / name :op1 "IGF-I"~e.44,46)) :ARG1~e.48 (p8 / protein :name (n12 / name :op1 "IGF-IR"~e.50,52) :mod (m2 / monocot~e.49) :location (c3 / cell-line~e.55 :name (n13 / name :op1 "293T"~e.54) :ARG1-of (t / transfect-01~e.56 :ARG2~e.57 (o / or~e.61 :op1 (v3 / vector~e.64 :ARG1-of (e5 / express-03~e.63 :ARG2 (p10 / protein :name (n14 / name :op1 "STAT"~e.60) :mod (r2 / respective~e.59)))) :op2 (v2 / vector~e.64 :ARG1-of (e4 / express-03~e.63 :ARG2 (e6 / enzyme :name (n15 / name :op1 "JAK"~e.62))))))))))) :snt1 (f / find-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (c / contrast-01~e.5 :ARG1 (a / activate-01~e.10 :ARG1 (p2 / protein :name (n / name :op1 "STAT3"~e.3)) :ARG2-of~e.11 (r / respond-01~e.12 :ARG1~e.13 (p3 / protein :name (n2 / name :op1 "IGF-I"~e.14,16) :location (c2 / cell-line~e.19 :name (n3 / name :op1 "293T"~e.18) :ARG1-of (c4 / cotransfect-01~e.20 :ARG2~e.21 (a2 / and~e.25,30 :op1 (p7 / protein :name (n4 / name :op1 "IGF-IR"~e.22,24)) :op2 (v / vector~e.28 :ARG1-of (e2 / express-03~e.27 :ARG2 (p4 / protein :name (n5 / name :op1 "STAT"~e.26)))))))))) :ARG2 (a3 / activate-01~e.10 :polarity~e.6 -~e.6 :ARG1 (p5 / protein :name (n6 / name :op1 "STAT5"~e.7)) :ARG2-of r)))) # ::id bel_pmid_1074_7872.21236 ::amr-annotator SDL-AMR-09 ::preferred # ::tok tyrosine phosphorylation of STAT3 , JAK1 , and JAK2 was increased upon IGF @-@ I stimulation of endogenous IGF @-@ IR in 293T cells transfected with the respective STAT or JAK expression vector . # ::alignments 0-1.1.1.1.1.1 0-1.1.1.2.1.1 0-1.1.1.3.1.1 1-1.1 2-1.1.1.r 3-1.1.1.1.2.1.1 5-1.1.1.2.2.1.1 7-1.1.1 8-1.1.1.3.2.1.1 10-1 12-1.2.1.1.1 14-1.2.1.1.1 15-1.2 16-1.2.2.r 17-1.2.2.2 18-1.2.2.1.1 20-1.2.2.1.1 22-1.2.2.3.1.1 23-1.2.2.3 24-1.2.2.3.2 25-1.2.2.3.2.1.r 27-1.2.2.3.2.1.1.1.1.2 28-1.2.2.3.2.1.1.1.1.1.1 29-1.2.2.3.2.1 30-1.2.2.3.2.1.2.1.1.1.1 31-1.2.2.3.2.1.1.1 31-1.2.2.3.2.1.2.1 32-1.2.2.3.2.1.1 32-1.2.2.3.2.1.2 (i / increase-01~e.10 :ARG1 (p / phosphorylate-01~e.1 :ARG1~e.2 (a2 / and~e.7 :op1 (a / amino-acid :name (n / name :op1 "tyrosine"~e.0) :part-of (p2 / protein :name (n2 / name :op1 "STAT3"~e.3))) :op2 (a3 / amino-acid :name (n10 / name :op1 "tyrosine"~e.0) :part-of (e6 / enzyme :name (n3 / name :op1 "JAK1"~e.5))) :op3 (a4 / amino-acid :name (n11 / name :op1 "tyrosine"~e.0) :part-of (e5 / enzyme :name (n9 / name :op1 "JAK2"~e.8))))) :time (s / stimulate-01~e.15 :ARG0 (p4 / protein :name (n4 / name :op1 "IGF-I"~e.12,14)) :ARG1~e.16 (p3 / protein :name (n5 / name :op1 "IGF-IR"~e.18,20) :mod (m / monocot~e.17) :location (c / cell-line~e.23 :name (n6 / name :op1 "293T"~e.22) :ARG1-of (t / transfect-01~e.24 :ARG2~e.25 (o / or~e.29 :op1 (v2 / vector~e.32 :ARG1-of (e3 / express-03~e.31 :ARG2 (p5 / protein :name (n7 / name :op1 "STAT"~e.28) :mod (r / respective~e.27)))) :op2 (v / vector~e.32 :ARG1-of (e2 / express-03~e.31 :ARG2 (e4 / enzyme :name (n8 / name :op1 "JAK"~e.30)))))))))) # ::id bel_pmid_1074_7872.21238 ::amr-annotator SDL-AMR-09 ::preferred # ::tok STAT3 , but not STAT5 , was activated in response to IGF @-@ I in 293T cells cotransfected with IGF @-@ IR and STAT expression vectors . # ::alignments 0-1.1.1.1.1 2-1 3-1.2.1 3-1.2.1.r 4-1.2.2.1.1 7-1.1 7-1.2 8-1.1.2.r 9-1.1.2 10-1.1.2.1.r 11-1.1.2.1.1.1 13-1.1.2.1.1.1 15-1.1.2.1.2.1.1 16-1.1.2.1.2 17-1.1.2.1.2.2 18-1.1.2.1.2.2.1.r 19-1.1.2.1.2.2.1.1.1.1.1.1 21-1.1.2.1.2.2.1.1.1.1.1.1 22-1.1.2.1.2.2.1 23-1.1.2.1.2.2.1.2.1.1.1.1 24-1.1.2.1.2.2.1.1.1 24-1.1.2.1.2.2.1.2.1 25-1.1.2.1.2.2.1.1 25-1.1.2.1.2.2.1.2 (c / contrast-01~e.2 :ARG1 (a / activate-01~e.7 :ARG1 (p / protein :name (n / name :op1 "STAT3"~e.0)) :ARG2-of~e.8 (r / respond-01~e.9 :ARG1~e.10 (p2 / protein :name (n2 / name :op1 "IGF-I"~e.11,13) :location (c2 / cell-line~e.16 :name (n3 / name :op1 "293T"~e.15) :ARG1-of (c3 / cotransfect-01~e.17 :ARG2~e.18 (a2 / and~e.22 :op1 (v2 / vector~e.25 :ARG1-of (e2 / express-03~e.24 :ARG2 (p3 / protein :name (n4 / name :op1 "IGF-IR"~e.19,21)))) :op2 (v / vector~e.25 :ARG1-of (e / express-03~e.24 :ARG2 (p4 / protein :name (n5 / name :op1 "STAT"~e.23)))))))))) :ARG2 (a3 / activate-01~e.7 :polarity~e.3 -~e.3 :ARG1 (p5 / protein :name (n6 / name :op1 "STAT5"~e.4)) :ARG2-of r)) # ::id bel_pmid_1074_7872.21262 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Dominant @-@ negative JAK1 or JAK2 was able to block the IGF @-@ IR @-@ mediated tyrosine phosphorylation of STAT3 in 293T cells . # ::alignments 3-1.1.1.1.1.1 4-1.1.1 5-1.1.1.2.1.1 7-1 9-1.1 11-1.1.2.4.1.1.1 13-1.1.2.4.1.1.1 15-1.1.2.4 16-1.1.2.1.1.1 17-1.1.2 18-1.1.2.2.r 19-1.1.2.2.1.1 20-1.1.2.3.r 21-1.1.2.3.1.1 22-1.1.2.3 (p3 / possible-01~e.7 :ARG1 (b / block-01~e.9 :ARG0 (o / or~e.4 :op1 (e2 / enzyme :name (n / name :op1 "JAK1"~e.3) :ARG2-of (m2 / mutate-01 :mod "-/-")) :op2 (e / enzyme :name (n7 / name :op1 "JAK2"~e.5) :ARG2-of (m3 / mutate-01 :mod "-/-"))) :ARG1 (p2 / phosphorylate-01~e.17 :ARG0 (a2 / amino-acid :name (n4 / name :op1 "tyrosine"~e.16)) :ARG1~e.18 (p6 / protein :name (n5 / name :op1 "STAT3"~e.19)) :location~e.20 (c / cell-line~e.22 :name (n6 / name :op1 "293T"~e.21)) :ARG1-of (m / mediate-01~e.15 :ARG0 (p5 / protein :name (n3 / name :op1 "IGF-IR"~e.11,13)))))) # ::id bel_pmid_1077_7583.7596 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Inhibition of SHP2 activation leads to increased SOCS3 @-@ mRNA levels , whereas increased expression of SOCS3 results in a reduction of SHP2 phosphorylation after activation of the interleukin @-@ 6 signal transduction pathway . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1.1 3-1.1.1.1 4-1.1 5-1.1.2.r 6-1.1.2.1 7-1.1.2.2.2.1.1 9-1.1.2.2.1.1 10-1.1.2 12-1 13-1.1.2.1 13-1.2.1.2 14-1.2.1 15-1.2.1.1.r 16-1.2.1.1 17-1.2 18-1.2.2.r 20-1.2.2 21-1.2.2.2.r 22-1.2.2.2.1 23-1.2.2.2 24-1.2.3 25-1.2.3.1 26-1.2.3.1.1.r 28-1.2.3.1.1.1.1.1.1.1 30-1.2.3.1.1.1.1.1.1.1 31-1.2.3.1.1.1.1 32-1.2.3.1.1.1 33-1.2.3.1.1 (c / contrast-01~e.12 :ARG1 (l / lead-03~e.4 :ARG0 (i / inhibit-01~e.0 :ARG1~e.1 (a / activate-01~e.3 :ARG1 (e3 / enzyme :name (n3 / name :op1 "SHP2"~e.2)))) :ARG2~e.5 (l2 / level~e.10 :ARG1-of (i2 / increase-01~e.6,13) :quant-of (n5 / nucleic-acid :name (n / name :op1 "mRNA"~e.9) :mod (p / protein :name (n2 / name :op1 "SOCS3"~e.7))))) :ARG2 (r2 / result-01~e.17 :ARG1 (e / express-03~e.14 :ARG2~e.15 p~e.16 :ARG1-of (i3 / increase-01~e.13)) :ARG2~e.18 (r3 / reduce-01~e.20 :ARG0 e :ARG2~e.21 (p3 / phosphorylate-01~e.23 :ARG1 e3~e.22)) :time (a2 / after~e.24 :op1 (a3 / activate-01~e.25 :ARG1~e.26 (p4 / pathway~e.33 :ARG2-of (t / transduce-01~e.32 :ARG1 (s / signal-07~e.31 :ARG1 (p2 / protein :name (n4 / name :op1 "interleukin-6"~e.28,30))))))))) # ::id bel_pmid_1079_1191.20850 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In situ end @-@ labeling detection showed that apoptotic cell death was significantly increased in cells with 5 @-@ day treatment of antisense H @-@ ras oligodeoxynucleotide ( 34.0 +/- 4.5 %) in comparing with cells without treatment ( 2.5 +/- 1.2 % , t = 13.434 , P < 0.01 ) or treated with non @-@ specific antisense oligodeoxynucleotide ( 4.8 +/- 1.4 % , t = 12.453 , P < 0.01 ) at the corresponding time . # ::alignments 0-1.1.2 1-1.1.2 2-1.1.1.1 4-1.1.1 5-1.1 6-1 7-1.2.r 8-1.2.1.1 9-1.2.1 12-1.2.2 13-1.2 14-1.1.2 14-1.2.3.r 15-1.2.3 16-1.2.3.1.r 17-1.2.3.1.2.1 19-1.2.3.1.2.2 20-1.2.3.1 21-1.2.3.1.1.r 22-1.2.3.1.1.2.2 23-1.2.3.1.1.2.1.1 25-1.2.3.1.1.2.1.1 26-1.2.3.1.1.1.1 30-1.2.3.1.1.4.1 32-1.1.2 33-1.2.4.r 35-1.2.4.1 35-1.2.4.2 36-1.2.4.1.1.1 37-1.2.4.2.1 41-1.2.4.1.3.1 42-1.2.3.1.1.4 42-1.2.4.1.3 46-1.2.4.1.2.1 48-1.2.4.1.1.2 48-1.2.4.2.1.2 49-1.2.4.1.1.2.1 50-1.2.4.1.1.2.1.1 52-1.2.4 53-1.2.4.1.1 55-1.2.1.2.1 55-1.2.4.2.1.1.2.1.1 55-1.2.4.2.1.1.2.1.1.r 57-1.2.4.2.1.1.2.1 58-1.2.4.2.1.1.2 59-1.2.4.2.1.1.1.1 63-1.2.4.2.1.1.3.1 64-1.2.4.2.1.1.3 68-1.2.4.2.1.1.4.1 70-1.2.4.1.1.2 71-1.2.4.1.1.2.1 72-1.2.4.1.1.2.1.1 76-1.2.4.3.1 77-1.2.3.1.2 77-1.2.4.3 77-1.2.4.3.r (s / show-01~e.6 :ARG0 (d / detect-01~e.5 :ARG2 (l / label-01~e.4 :mod (e2 / end~e.2)) :mod (i / in-situ~e.0,1,14,32)) :ARG1~e.7 (i2 / increase-01~e.13 :ARG1 (c / cell~e.9 :mod (a / apoptosis~e.8) :ARG0-of (f / function-01 :polarity -~e.55)) :ARG2 (s2 / significant-02~e.12) :location~e.14 (c2 / cell~e.15 :ARG1-of~e.16 (t / treat-04~e.20 :ARG2~e.21 (s7 / small-molecule :name (n / name :op1 "oligodeoxynucleotide"~e.26) :mod (e / enzyme :name (n2 / name :op1 "H-ras"~e.23,25) :mod (a2 / antisense~e.22)) :quant (c6 / concentration-quantity :quant 34 :unit (m3 / micromolar)) :quant (p2 / percentage-entity~e.42 :value 4.5~e.30)) :duration (t2 / temporal-quantity~e.77 :quant 5~e.17 :unit (d3 / day~e.19)))) :compared-to~e.33 (o / or~e.52 :op1 (c3 / cell~e.35 :ARG1-of (t3 / treat-04~e.53 :polarity -~e.36 :ARG1-of (s4 / statistical-test-91~e.48,70 :ARG2 (l2 / less-than~e.49,71 :op1 0.01~e.50,72))) :quant (t6 / temperature-quantity :value 13.434~e.46) :quant (p4 / percentage-entity~e.42 :value 1.2~e.41)) :op2 (c4 / cell~e.35 :ARG1-of (t4 / treat-04~e.37 :ARG2 (s6 / small-molecule :name (n3 / name :op1 "oligodeoxynucleotide"~e.59) :mod (a3 / antisense~e.58 :ARG1-of (s3 / specific-02~e.57 :polarity~e.55 -~e.55)) :quant (p3 / percentage-entity~e.64 :value 1.4~e.63) :quant (c7 / concentration-quantity :quant 12.453~e.68 :unit (m4 / micromolar))) :ARG1-of (s5 / statistical-test-91~e.48 :ARG2 l2))) :time~e.77 (t5 / time~e.77 :ARG1-of (c5 / correspond-02~e.76))))) # ::id bel_pmid_1084_2184.19138 ::amr-annotator SDL-AMR-09 ::preferred # ::tok \" Negative regulation of growth hormone receptor @/@ JAK2 signaling by signal regulatory protein alpha.\" # ::alignments 1-1 2-1 3-1.1.r 4-1.1.1.1.1 5-1.1.1.1.2 6-1.1.1.1.3 8-1.1.2.1.1 9-1.2.1.1 11-1.2.1.1 12-1.2.1.2 13-1.2.1.3 (d / downregulate-01~e.1,2 :ARG1~e.3 (m / macro-molecular-complex :part (p / protein :name (n2 / name :op1 "growth"~e.4 :op2 "hormone"~e.5 :op3 "receptor"~e.6)) :part (e / enzyme :name (n3 / name :op1 "JAK2"~e.8))) :ARG2 (p3 / protein :name (n / name :op1 "signal"~e.9,11 :op2 "regulatory"~e.12 :op3 "protein"~e.13 :op4 "alpha")) :ARG2-of (c / cite-01)) # ::id bel_pmid_1085_1026.6144 ::amr-annotator SDL-AMR-09 ::preferred # ::tok FGFs activate the endogenous FGFRs leading to the formation of a Grb2/FRS2/Shp2 complex and activation of MAP kinase . # ::alignments 1-1 3-1.2.2 5-1.2.3 6-1.2.3.1.r 8-1.2.3.1.1 12-1.2.3.1.1.2 13-1.2.3.1 14-1.2.3.1.2 15-1.2.3.1.2.2.r 16-1.2.3.1.2.2.1.1 17-1.2.3.1.2.2 (a / activate-01~e.1 :ARG0 (p / protein :name (n / name :op1 "FGF")) :ARG1 (p2 / protein :name (n2 / name :op1 "FGFR") :mod (m2 / monocot~e.3) :ARG0-of (l / lead-03~e.5 :ARG2~e.6 (a2 / and~e.13 :op1 (f / form-01~e.8 :ARG0 p2 :ARG1 (m / macro-molecular-complex~e.12 :part (p3 / protein :name (n3 / name :op1 "Grb2")) :part (p4 / protein :name (n4 / name :op1 "FRS2")) :part (e / enzyme :name (n5 / name :op1 "Shp2")))) :op2 (a3 / activate-01~e.14 :ARG0 p2 :ARG1~e.15 (k / kinase~e.17 :name (n6 / name :op1 "MAP"~e.16))))))) # ::id bel_pmid_1085_1026.8692 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , immature osteoblasts respond to FGF treatment with increased proliferation , whereas in differentiating cells FGF does not induce DNA synthesis but causes apoptosis . # ::alignments 0-1 0-1.1 0-1.1.r 2-1.1.1.1.1 2-1.1.1.1.1.1 2-1.1.1.1.1.1.r 3-1.1.1.1 4-1.1.1 5-1.1.1.2.r 6-1.1.1.2.2.1.1 7-1.1.1.2 8-1.1.1.3.r 9-1.1.1.3.2 10-1.1.1.3 12-1.1.2 14-1.1.2.1.4 15-1.1.2.1.4.2 16-1.1.2.1.4.1 18-1.1.2.1.1 18-1.1.2.1.1.r 19-1.1.2.1 20-1.1.2.1.3.1.2.1 21-1.1.2.1.3 22-1.1.2 23-1.1.2.2 24-1.1.2.2.2 (h / have-concession-91~e.0 :ARG1~e.0 (c2 / contrast-01~e.0 :ARG1 (r / respond-01~e.4 :ARG0 (o / osteoblast~e.3 :ARG1-of (m / mature-02~e.2 :polarity~e.2 -~e.2)) :ARG1~e.5 (t / treat-04~e.7 :ARG1 o :ARG2 (p / protein :name (n / name :op1 "FGF"~e.6))) :ARG2~e.8 (p2 / proliferate-01~e.10 :ARG0 o :ARG1-of (i2 / increase-01~e.9))) :ARG2 (c3 / contrast-01~e.12,22 :ARG1 (i / induce-01~e.19 :polarity~e.18 -~e.18 :ARG0 p :ARG2 (s / synthesize-01~e.21 :ARG1 (n2 / nucleic-acid :wiki "DNA" :name (n3 / name :op1 "DNA"~e.20))) :time (d2 / differentiate-01~e.14 :ARG0 p~e.16 :ARG1 (c5 / cell~e.15))) :ARG2 (c4 / cause-01~e.23 :ARG0 p :ARG1 (a / apoptosis~e.24))))) # ::id bel_pmid_1085_1026.8694 ::amr-annotator SDL-AMR-09 ::preferred # ::tok When either primary or OB1 osteoblasts are induced to differentiate , FGF signaling inhibits expression of alkaline phosphatase , and blocks mineralization . # ::alignments 0-1.3.r 1-1.3.1.3 2-1.3.1.1.1 3-1.3.1 4-1.3.1.2.1.1.1 5-1.3.1.1 5-1.3.1.2 7-1.3 9-1.3.2 11-1.1.1.1.1 12-1.1.1.1.2 13-1.1 14-1.1.2 15-1.1.2.1.r 16-1.1.2.1.1.1 17-1.1.2.1.1.2 19-1 20-1.2 (a / and~e.19 :op1 (i2 / inhibit-01~e.13 :ARG0 (p2 / protein :name (n / name :op1 "FGF"~e.11 :op2 "signaling"~e.12)) :ARG1 (e2 / express-03~e.14 :ARG1~e.15 (e3 / enzyme :name (n3 / name :op1 "alkaline"~e.16 :op2 "phosphatase"~e.17)))) :op2 (b / block-01~e.20 :ARG0 p2 :ARG1 (m / mineralize-01)) :time~e.0 (i / induce-01~e.7 :ARG1 (o / or~e.3 :op1 (o3 / osteoblast~e.5 :mod (p / primary~e.2)) :op2 (o2 / osteoblast~e.5 :mod (d2 / dna-sequence :name (n2 / name :op1 "OB1"~e.4))) :mod (e / either~e.1)) :ARG2 (d / differentiate-01~e.9 :ARG0 o))) # ::id bel_pmid_1085_1055.19244 ::amr-annotator SDL-AMR-09 ::preferred # ::tok IL @-@ 2 @-@ mediated hetero @-@ dimerization of its receptor triggers a rapid increase in the recruitment of Jak3 and activation of both Jak1 and Jak3 # ::alignments 0-1.1.2.1.1.1 2-1.1.2.1.1.1 4-1.1.2 9-1.1.1.1 9-1.1.1.1.r 10-1.1.1 11-1 13-1.2.2 14-1.2 15-1.2.1.r 17-1.2.1.1 18-1.2.1.1.1.r 19-1.2.1.1.1.1.1 20-1.2.1 21-1.2.1.2 24-1.2.1.2.1.1.1.1 25-1.2.1 26-1.2.1.2.1.2 (t / trigger-01~e.11 :ARG0 (h2 / heterodimerize-01 :ARG1 (r3 / receptor~e.10 :poss~e.9 p3~e.9) :ARG1-of (m / mediate-01~e.4 :ARG0 (p3 / protein :name (n2 / name :op1 "IL-2"~e.0,2)))) :ARG1 (i / increase-01~e.14 :ARG1~e.15 (a / and~e.20,25 :op1 (r2 / recruit-01~e.17 :ARG1~e.18 (e2 / enzyme :name (n / name :op1 "Jak3"~e.19))) :op2 (a2 / activate-01~e.21 :ARG1 (a3 / and :op1 (e / enzyme :name (n3 / name :op1 "Jak1"~e.24)) :op2 e2~e.26))) :manner (r / rapid~e.13))) # ::id bel_pmid_1088_0513.7274 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We show that IL @-@ 6 triggers selective activation of SHP2 and its association with RAFTK in Dex @-@ treated MM cells . # ::alignments 0-1.1 1-1 2-1.2.r 3-1.2.1.1.1 5-1.2.1.1.1 6-1.2 7-1.2.2.1.3 8-1.2.2.1 9-1.2.2.1.2.r 10-1.2.2.1.2.1.1 11-1.2.2 13-1.2.2.2 14-1.2.2.2.2.r 15-1.2.2.2.2.1.1 16-1.2.2.2.3.r 17-1.2.2.2.3.1.1.1.1 19-1.2.2.2.3.1 20-1.2.2.2.3.2.1.1 20-1.2.2.2.3.2.1.2 21-1.2.2.2.3 (s / show-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (t / trigger-01~e.6 :ARG0 (p / protein :name (n2 / name :op1 "IL-6"~e.3,5)) :ARG1 (a / and~e.11 :op1 (a2 / activate-01~e.8 :ARG0 p :ARG1~e.9 (e / enzyme :name (n / name :op1 "SHP2"~e.10)) :mod (s2 / selective~e.7)) :op2 (a3 / associate-01~e.13 :ARG1 e :ARG2~e.14 (e2 / enzyme :name (n3 / name :op1 "RAFTK"~e.15)) :location~e.16 (c / cell~e.21 :ARG1-of (t2 / treat-04~e.19 :ARG2 (s3 / small-molecule :name (n4 / name :op1 "Dex"~e.17))) :mod (d / disease :name (n5 / name :op1 "multiple"~e.20 :op2 "myeloma"~e.20))))))) # ::id bel_pmid_1088_0513.23686 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We and others have shown that IL @-@ 6 induces growth in MM cells via the MAPK pathway , which includes activation of protein @-@ tyrosine phosphatase SHP2 ( 16 , 28 ) # ::alignments 0-1.1.1 1-1.1 2-1.1.2.1 4-1 5-1.2.r 6-1.2.1.1.1 8-1.2.1.1.1 9-1.2 10-1.2.2 11-1.2.2.1.r 12-1.2.2.1.1.1.1 12-1.2.2.1.1.1.2 13-1.2.2.1 16-1.2.2.2.1.1 17-1.2.2.2 20-1.2.2.2.2 21-1.2.2.2.2.1 23-1.2.1 23-1.2.2.2.2.1.1 25-1.2.2.2.2.1.1 26-1.2.2.2.2.1.1 27-1.2.2.2.2.1.1.1.1 29-1.3.1.1.1.1 31-1.3.1.1.1.2 (s / show-01~e.4 :ARG0 (a2 / and~e.1 :op1 (w / we~e.0) :op2 (p2 / person :mod (o / other~e.2))) :ARG1~e.5 (i2 / induce-01~e.9 :ARG0 (p3 / protein~e.23 :name (n / name :op1 "IL-6"~e.6,8)) :ARG2 (g / grow-01~e.10 :ARG1~e.11 (c2 / cell~e.13 :mod (d2 / disease :name (n4 / name :op1 "multiple"~e.12 :op2 "myeloma"~e.12))) :instrument (p4 / pathway~e.17 :name (n3 / name :op1 "MAPK"~e.16) :ARG2-of (i / include-01~e.20 :ARG1 (a3 / activate-01~e.21 :ARG1 (p6 / protein-tyrosine-phosphatase~e.23,25,26 :name (n6 / name :op1 "SHP2"~e.27))))))) :ARG1-of (d / describe-01 :ARG0 (p / publication :ARG1-of (c / cite-01 :ARG2 (a / and :op1 16~e.29 :op2 28~e.31))))) # ::id bio-exp_0001.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We next examined the mechanisms accounting for the increase in HER3 by MAPK pathway inhibitors in BRAF mutant thyroid cell lines . # ::alignments 0-1.1 1-1.3 2-1 4-1.2 5-1.2.1 6-1.2.1.1.r 8-1.2.1.1 9-1.2.1.1.2.r 10-1.2.1.1.2.1.1 11-1.2.1.1.1.r 12-1.2.1.1.1.1.1.1.1 13-1.2.1.1.1.1.1 14-1.2.1.1.1 14-1.2.1.1.1.1 14-1.2.1.1.1.1.r 15-1.2.1.1.1.1.2.r 16-1.2.1.1.1.1.2.2.1.3.1.1 17-1.2.1.1.1.1.2.2.1.3 17-1.2.1.1.1.1.2.2.1.3.2 17-1.2.1.1.1.1.2.2.1.3.2.r 18-1.2.1.1.1.1.2.1 19-1.2.1.1.1.1.2 20-1.2.1.1.1.1.2 (e / examine-01~e.2 :ARG0 (w / we~e.0) :ARG1 (m / mechanism~e.4 :ARG0-of (a / account-01~e.5 :ARG1~e.6 (i / increase-01~e.8 :ARG0~e.11 (m2 / molecular-physical-entity~e.14 :ARG0-of~e.14 (i2 / inhibit-01~e.14 :ARG1 (p / pathway~e.13 :name (n3 / name :op1 "MAPK"~e.12)) :location~e.15 (c / cell-line~e.19,20 :source (t / thyroid~e.18) :ARG1-of (e3 / encode-01 :ARG0 (n5 / nucleic-acid :wiki "DNA" :name (n6 / name :op1 "DNA") :part (g / gene~e.17 :name (n4 / name :op1 "BRAF"~e.16) :ARG2-of~e.17 (m3 / mutate-01~e.17))))))) :ARG1~e.9 (e2 / enzyme :name (n2 / name :op1 "HER3"~e.10))))) :time (n / next~e.1)) # ::id bio-exp_0001.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Upregulation of HER3 has been found to mediate resistance to PI3K @/@ AKT ( 26 ) or HER2 ( 27 ) inhibitors in HER2 @-@ amplified breast cancer cell lines , which is caused in part through a FoxO3A @-@ dependent induction of HER3 gene transcription . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1 5-1 6-1.1.3 7-1.1 8-1.1.2 9-1.1.2.1.r 10-1.1.2.1.1.1.1.1.1 12-1.1.2.1.1.1.1.1.1 14-1.1.2.1.1.1.1.2.1.1.1 16-1.1.2.1.1.1 17-1.1.2.1.1.1.2.1.1 19-1.1.2.1.1.1.2.2.1.1.1 21-1.1.2.1 21-1.1.2.1.1 21-1.1.2.1.1.r 22-1.1.2.2.r 23-1.1.2.2.1.1 25-1.1.2.2.1 26-1.1.2.2.2.2.1 27-1.1.2.2.2.2.2 28-1.1.2.2 29-1.1.2.2 33-1.1.3 34-1.1.3.2 34-1.1.3.2.r 35-1.1.3.2.r 38-1.1.3.1.2.1.1.1 40-1.1.3.1.2 41-1.1.3.1 42-1.1.3.1.1.r 43-1.1.3.1.1.1.1.1 44-1.1.3.1.1.1 45-1.1.3.1.1 (f / find-01~e.5 :ARG1 (m / mediate-01~e.7 :ARG0 (u / upregulate-01~e.0 :ARG1~e.1 (e / enzyme :name (n / name :op1 "HER3"~e.2))) :ARG1 (r / resist-01~e.8 :ARG1~e.9 (m2 / molecular-physical-entity~e.21 :ARG0-of~e.21 (i / inhibit-01~e.21 :ARG1 (o / or~e.16 :op1 (p / pathway :name (n2 / name :op1 "PI3K/AKT"~e.10,12) :ARG1-of (d2 / describe-01 :ARG0 (p5 / publication :ARG1-of (c4 / cite-01 :ARG2 26~e.14)))) :op2 (e3 / enzyme :name (n3 / name :op1 "HER2"~e.17) :ARG1-of (d3 / describe-01 :ARG0 (p6 / publication :ARG1-of (c5 / cite-01 :ARG2 27~e.19))))))) :location~e.22 (c / cell-line~e.28,29 :ARG0-of (a / amplify-01~e.25 :ARG1 e3~e.23) :source (d4 / disease :wiki "Breast_cancer" :name (n5 / name :op1 "breast"~e.26 :op2 "cancer"~e.27)))) :ARG1-of (c3 / cause-01~e.6,33 :ARG0 (i2 / induce-01~e.41 :ARG2~e.42 (t / transcribe-01~e.45 :ARG1 (g / gene~e.44 :ARG0-of (e2 / encode-01 :ARG1 e~e.43))) :ARG0-of (d / depend-01~e.40 :ARG1 (p4 / protein :name (n4 / name :op1 "FoxO3A"~e.38)))) :degree~e.34,35 (p3 / part~e.34)))) # ::id bio-exp_0001.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 5A , PLX4032 treatment increased HER3 and HER2 mRNAs in all six BRAF @-@ mutant thyroid cancer cell lines tested . # ::alignments 1-1.3 2-1.3.1.r 3-1.3.1 4-1.3.1.1 6-1.1.1.1.1 7-1.1 8-1 9-1.2.2.1.1.1.1 10-1.2.2.1 11-1.2.2.1.2.1.1 12-1.2.1.1 13-1.4.r 14-1.4.2.2 15-1.4.2.1.1 16-1.4.1.1.3.1.1 18-1.4.1.1.3 18-1.4.1.1.3.2 18-1.4.1.1.3.2.r 19-1.4.3.2.1 20-1.4.3.2.2 21-1.4 21-1.4.2.1 22-1.4.2.1 23-1.4.2.1.2 (i / increase-01~e.8 :ARG0 (t / treat-04~e.7 :ARG2 (s2 / small-molecule :name (n / name :op1 "PLX4032"~e.6))) :ARG1 (n8 / nucleic-acid :name (n9 / name :op1 "mRNA"~e.12) :ARG0-of (e / encode-01 :ARG1 (a / and~e.10 :op1 (e3 / enzyme :name (n2 / name :op1 "HER3"~e.9)) :op2 (e4 / enzyme :name (n3 / name :op1 "HER2"~e.11))))) :ARG1-of (s / show-01~e.1 :location~e.2 (f / figure~e.3 :mod "5A"~e.4)) :location~e.13 (c / cell-line~e.21 :ARG1-of (e2 / encode-01 :ARG0 (n5 / nucleic-acid :wiki "DNA" :name (n6 / name :op1 "DNA") :part (g / gene~e.18 :name (n4 / name :op1 "BRAF"~e.16) :ARG2-of~e.18 (m2 / mutate-01~e.18)))) :ARG1-of (i2 / include-91 :ARG2 (c3 / cell-line~e.21,22 :quant 6~e.15 :ARG1-of (t3 / test-01~e.23)) :ARG3 (a2 / all~e.14)) :source (d / disease :wiki "Thyroid_cancer" :name (n7 / name :op1 "thyroid"~e.19 :op2 "cancer"~e.20)))) # ::id bio-exp_0001.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Similar results were found following treatment with the MEK inhibitor AZD6244 ( not shown ) . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 4-1.2 5-1.2.1 6-1.2.1.1.r 8-1.2.1.1.2.1.1.1 9-1.2.1.1 9-1.2.1.1.2 9-1.2.1.1.2.r 10-1.2.1.1.1.1 12-1.1.3.1 12-1.1.3.1.r 13-1.1.3 (f / find-01~e.3 :ARG1 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :ARG1-of (r2 / resemble-01~e.0) :ARG1-of (s / show-01~e.13 :polarity~e.12 -~e.12)) :ARG1-of (f2 / follow-01~e.4 :ARG2 (t2 / treat-04~e.5 :ARG2~e.6 (s2 / small-molecule~e.9 :name (n2 / name :op1 "AZD6244"~e.10) :ARG0-of~e.9 (i / inhibit-01~e.9 :ARG1 (p / protein-family :name (n / name :op1 "MEK"~e.8))))))) # ::id bio-exp_0001.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The effects of the MEK inhibitor on total HER2 , HER3 protein and on pHER3 were dose dependent , and inversely associated with the degree of inhibition of pERK ( Fig. 5B ) . # ::alignments 1-1.1.1 2-1.1.1.1.r 4-1.1.1.1.1.1.1.1 5-1.1.1.1 5-1.1.1.1.1 5-1.1.1.1.1.r 6-1.1.1.2.r 7-1.1.1.2.1.2 8-1.1.1.2.1.1.1 10-1.1.1.2.2.1.1 10-1.1.1.2.3.1.1 11-1.1.1.1.1.1 16-1.1.2 17-1.1 19-1 20-1.2.3 20-1.2.3.r 21-1.2 22-1.2.2.r 24-1.2.2.1.r 26-1.2.2.1 28-1.1.1.2.3.2 28-1.2.2.1.1.1.1 30-1.3.1 31-1.3.1.1 (a / and~e.19 :op1 (d / depend-01~e.17 :ARG0 (a2 / affect-01~e.1 :ARG0~e.2 (m / molecular-physical-entity~e.5 :ARG0-of~e.5 (i / inhibit-01~e.5 :ARG1 (p2 / protein-family~e.11 :name (n / name :op1 "MEK"~e.4)))) :ARG1~e.6 (a3 / and :op1 (e2 / enzyme :name (n2 / name :op1 "HER2"~e.8) :mod (t / total~e.7)) :op2 (e3 / enzyme :name (n3 / name :op1 "HER3"~e.10)) :op3 (e4 / enzyme :name (n4 / name :op1 "HER3"~e.10) :ARG3-of (p / phosphorylate-01~e.28)))) :ARG1 (d2 / dose-01~e.16)) :op2 (a4 / associate-01~e.21 :ARG1 a2 :ARG2~e.22 (t2 / thing :degree-of~e.24 (i2 / inhibit-01~e.26 :ARG1 (e5 / enzyme :name (n5 / name :op1 "ERK"~e.28) :ARG3-of p))) :manner~e.20 (i3 / inverse~e.20)) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.30 :mod "5B"~e.31))) # ::id bio-exp_0001.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok RAF or MEK inhibitors induced luciferase activity of a HER3 promoter construct spanning ~ 1 kb upstream of the transcriptional start site in 8505C cells . # ::alignments 0-1.1.1.1.1.2.1 1-1.1 2-1.1.2.1.1.2.1 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 3-1.1.2 3-1.1.2.1 3-1.1.2.1.r 4-1 5-1.2.2 6-1.2 7-1.2.1.r 9-1.2.1.1.1.2.1 10-1.2.1.1 11-1.2.1 12-1.2.1.2 13-1.2.1.2.3 14-1.2.1.2.3.1.1 16-1.2.1.2.1.2 19-1.2.1.2.1.1.1.1 20-1.2.1.2.1.1.1 21-1.2.1.2.1.1 22-1.2.1.2.2.r 23-1.2.1.2.2.2.1 24-1.2.1.2.2 (i / induce-01~e.4 :ARG0 (o / or~e.1 :op1 (m / molecular-physical-entity~e.3 :ARG0-of~e.3 (i2 / inhibit-01~e.3 :ARG1 (p3 / protein-family :wiki "RAF_kinase" :name (n / name :op1 "RAF"~e.0)))) :op2 (m2 / molecular-physical-entity~e.3 :ARG0-of~e.3 (i3 / inhibit-01~e.3 :ARG1 (p4 / protein-family :wiki "Mitogen-activated_protein_kinase_kinase" :name (n2 / name :op1 "MEK"~e.2))))) :ARG2 (a / activity-06~e.6 :ARG0~e.7 (c / construct-01~e.11 :ARG0-of (p / promote-01~e.10 :ARG1 (e3 / enzyme :wiki "ERBB3" :name (n3 / name :op1 "HER3"~e.9))) :ARG0-of (s / span-01~e.12 :ARG1 (r / relative-position :op1 (p2 / protein-segment~e.21 :location-of (s3 / start-01~e.20 :ARG1 (t / transcribe-01~e.19))) :direction (u / upstream~e.16)) :location~e.22 (c2 / cell-line~e.24 :wiki - :name (n4 / name :op1 "8505C"~e.23)) :quant (a2 / approximately~e.13 :op1 (d / distance-quantity :quant 1~e.14 :unit (k / kilo-base-pair))))) :ARG1 (l / luciferase~e.5))) # ::id bio-exp_0001.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Serial deletions identified a minimal HER3 promoter retaining transcriptional response to vemurafenib and AZD6244 , which was located between -@ 401 and -@ 42 bp ( Fig. 5C ) . # ::alignments 0-1.1.1 1-1.1 2-1 4-1.2.2 5-1.2.1.1.1.1 6-1.2 6-1.2.1 6-1.2.1.r 7-1.2.3 8-1.2.3.2 9-1.2.3.1 9-1.2.3.1.1 9-1.2.3.1.1.r 10-1.2.3.1.1.1.r 11-1.2.3.1.1.1.1.1.1 12-1.2.3.1.1.1 13-1.2.3.1.1.1.2.1.1 17-1.2.4.r 18-1.2.4 20-1.2.4.1.1 23-1.2.4.2.1 26-1.3.1 27-1.3.1.1 (i / identify-01~e.2 :ARG0 (d / delete-01~e.1 :manner (s2 / serial~e.0)) :ARG1 (m / molecular-physical-entity~e.6 :ARG0-of~e.6 (p / promote-01~e.6 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.5))) :ARG1-of (m2 / minimal-02~e.4) :ARG0-of (r / retain-01~e.7 :ARG1 (t / thing~e.9 :ARG2-of~e.9 (r2 / respond-01~e.9 :ARG1~e.10 (a / and~e.12 :op1 (s3 / small-molecule :name (n3 / name :op1 "vemurafenib"~e.11)) :op2 (s / small-molecule :name (n2 / name :op1 "AZD6244"~e.13))))) :mod (t2 / transcribe-01~e.8)) :location~e.17 (b / between~e.18 :op1 (d2 / distance-quantity :quant -401~e.20 :unit (b2 / base-pair)) :op2 (d3 / distance-quantity :quant -42~e.23 :unit (b3 / base-pair)))) :ARG1-of (d4 / describe-01 :ARG0 (f / figure~e.26 :mod "5C"~e.27))) # ::id bio-exp_0001.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This region does not contain any predicted FoxO binding sites . # ::alignments 0-1.2.1 1-1.2 3-1.1 3-1.1.r 4-1 5-1.3.1 6-1.3.2 7-1.3.3.1.1.1 8-1.3.3 9-1.3 (c / contain-01~e.4 :polarity~e.3 -~e.3 :ARG0 (r / region~e.1 :mod (t / this~e.0)) :ARG1 (p3 / protein-segment~e.9 :mod (a / any~e.5) :ARG1-of (p / predict-01~e.6) :ARG1-of (b / bind-01~e.8 :ARG2 (p2 / protein :name (n / name :op1 "FoxO"~e.7))))) # ::id bio-exp_0001.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Moreover , PLX4032 led to an increase in phosphorylation of FoxO1 @/@ 3A between 4 – 10 h after addition of compound ( not shown ) , which is known to promote its dissociation from DNA , and likely discards involvement of these factors as transcriptional regulators of HER3 in response to MAPK pathway inhibition . # ::alignments 0-1 2-1.1.1.1.1 3-1.1 6-1.1.2 7-1.1.2.1.r 8-1.1.2.1 9-1.1.2.1.1.r 10-1.1.2.1.1.1.1 12-1.1.2.1.1.1.1 13-1.1.2.2.2 14-1.1.2.2.2.1.1 16-1.1.2.2.2.2.1 17-1.1.2.2.2.1.2 17-1.1.2.2.2.2.2 18-1.1.2.2 19-1.1.2.2.1 20-1.1.2.2.1.1.r 21-1.1.2.2.1.1 23-1.1.2.3.1 23-1.1.2.3.1.r 24-1.1.2.3 29-1.1.2.4.2 31-1.1.2.4 32-1.1.2.4.1.1 32-1.1.2.4.1.1.r 33-1.1.2.4.1 34-1.1.2.4.1.2.r 35-1.1.2.4.1.2.2.1 37-1.1.2.2.2 38-1.1.2.5.2 39-1.1.2.5 40-1.1.2.5.1 41-1.1.2.5.1.1.r 42-1.1.2.5.1.1.1 43-1.1.2.5.1.1 44-1.1.2.2.r 44-1.1.2.5.1.2.r 45-1.1.2.5.1.2.2 46-1.1.2.5.1.2 46-1.1.2.5.1.2.1 46-1.1.2.5.1.2.1.r 47-1.1.2.5.1.2.1.1.r 48-1.1.2.5.1.2.1.1.1.1 49-1.1.2.5.3.r 50-1.1.2.5.3 51-1.1.2.5.3.1.r 52-1.1.2.5.3.1.1.1.1 53-1.1.2.5.3.1.1 54-1.1.2.5.3.1 (a / and~e.0 :op2 (l / lead-03~e.3 :ARG0 (s / small-molecule :name (n / name :op1 "PLX4032"~e.2)) :ARG1 (i / increase-01~e.6 :ARG1~e.7 (p / phosphorylate-01~e.8 :ARG1~e.9 (p2 / protein :name (n2 / name :op1 "FoxO1/3A"~e.10,12))) :time~e.44 (a2 / after~e.18 :op1 (a3 / add-02~e.19 :ARG1~e.20 (c / compound~e.21)) :quant (b / between~e.13,37 :op1 (t / temporal-quantity :quant 4~e.14 :unit (h / hour~e.17)) :op2 (t2 / temporal-quantity :quant 10~e.16 :unit (h2 / hour~e.17)))) :ARG1-of (s2 / show-01~e.24 :polarity~e.23 -~e.23) :ARG0-of (p3 / promote-01~e.31 :ARG1 (d / dissociate-01~e.33 :ARG1~e.32 p2~e.32 :ARG2~e.34 (n5 / nucleic-acid :wiki "DNA" :name (n6 / name :op1 "DNA"~e.35))) :ARG1-of (k / know-01~e.29)) :ARG0-of (d3 / discard-01~e.39 :ARG1 (i2 / involve-01~e.40 :ARG1~e.41 (f / factor~e.43 :mod (t3 / this~e.42)) :mod~e.44 (m / molecular-physical-entity~e.46 :ARG0-of~e.46 (r / regulate-01~e.46 :ARG1~e.47 (e / enzyme :name (n3 / name :op1 "HER3"~e.48))) :ARG0-of (t4 / transcribe-01~e.45))) :ARG1-of (l2 / likely-01~e.38) :ARG2-of~e.49 (r2 / respond-01~e.50 :ARG1~e.51 (i3 / inhibit-01~e.54 :ARG1 (p4 / pathway~e.53 :name (n4 / name :op1 "MAPK"~e.52)))))))) # ::id bio-exp_0001.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The minimal HER3 promoter region regulated by MAPK inhibitors overlaps with sequences previously described to be immunoprecipitated using antibodies against the ZFN217 transcription factor and CtBP1 @/@ CtBP2 corepressors ( 28 @–@ 30 ) . # ::alignments 1-1.1.1.2 2-1.1.1.1.1.1.1 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 4-1.1 5-1.1.2 6-1.1.2.1.r 7-1.1.2.1.1.1.1.1 8-1.1.2.1 8-1.1.2.1.1 8-1.1.2.1.1.r 9-1 10-1.2.r 11-1.2 12-1.2.1.2.1 13-1.2.1.2 13-1.3 16-1.2.1 17-1.2.1.1 18-1.2.1.1.1 19-1.2.1.1.1.1 21-1.2.1.1.1.1.1.1.1.1.1.1 22-1.2.1.1.1.1.1.1.1 23-1.2.1.1.1.1.1.1 24-1.2.1.1.1.1.1 25-1.2.1.1.1.1.1.2.1.1.1.1.1 27-1.2.1.1.1.1.1.2.1.1.2.1.1 30-1.3.1.1.1.1 32-1.3.1.1.1.2 (o / overlap-01~e.9 :ARG0 (r / region~e.4 :part (m / molecular-physical-entity~e.3 :ARG0-of~e.3 (p2 / promote-01~e.3 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.2))) :ARG1-of (m2 / minimal-02~e.1)) :ARG1-of (r2 / regulate-01~e.5 :ARG0~e.6 (m3 / molecular-physical-entity~e.8 :ARG0-of~e.8 (i / inhibit-01~e.8 :ARG1 (p / pathway :name (n2 / name :op1 "MAPK"~e.7)))))) :ARG1~e.10 (s / sequence~e.11 :ARG1-of (i2 / immunoprecipitate-01~e.16 :ARG2-of (u / use-01~e.17 :ARG1 (a / antibody~e.18 :ARG0-of (o2 / oppose-01~e.19 :ARG1 (a2 / and~e.24 :op1 (f / factor~e.23 :ARG0-of (t / transcribe-01~e.22 :ARG1 (e2 / enzyme :name (n3 / name :op1 "ZFN217"~e.21)))) :op2 (m4 / molecular-physical-entity :ARG0-of (r3 / repress-01 :ARG1 (o3 / or :op1 (p5 / protein :name (n4 / name :op1 "CtBP1"~e.25)) :op2 (p6 / protein :name (n5 / name :op1 "CtBP2"~e.27))))))))) :ARG1-of (d / describe-01~e.13 :time (p3 / previous~e.12)))) :ARG1-of (d2 / describe-01~e.13 :ARG0 (p4 / publication :ARG1-of (c3 / cite-01 :ARG2 (v / value-interval :op1 28~e.30 :op2 30~e.32))))) # ::id bio-exp_0001.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok CtBPs have also been described to negatively regulate transcriptional activity of the HER3 promoter in breast carcinoma cell lines ( 30 ) . # ::alignments 2-1.4 4-1 4-1.5 4-1.5.r 5-1.2.r 6-1.2 7-1.2 8-1.2.1.2 9-1.2.1 10-1.2.1.1.r 12-1.2.1.1.1.1.1.1 13-1.2.1.1 13-1.2.1.1.1 13-1.2.1.1.1.r 14-1.3.r 15-1.3.1.2 16-1.3.1.1.1 17-1.3 18-1.3 20-1.5.1.1.1 (d / describe-01~e.4 :ARG1 (p / protein :name (n2 / name :op1 "CtBP")) :ARG2~e.5 (d2 / downregulate-01~e.6,7 :ARG1 (a / activity-06~e.9 :ARG0~e.10 (m / molecular-physical-entity~e.13 :ARG0-of~e.13 (p2 / promote-01~e.13 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.12)))) :ARG1 (t / transcribe-01~e.8)) :ARG2 p) :location~e.14 (c / cell-line~e.17,18 :mod (m2 / medical-condition :name (n3 / name :op1 "carcinoma"~e.16) :mod (b / breast~e.15))) :mod (a2 / also~e.2) :ARG1-of~e.4 (d3 / describe-01~e.4 :ARG0 (p3 / publication :ARG1-of (c3 / cite-01 :ARG2 30~e.20)))) # ::id bio-exp_0001.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Silencing of CtBP1 , and to a lesser extent CtBP2 , increased basal HER3 in 8505C cells , and markedly potentiated the effects of PLX4032 ( Fig. 5D and 5E ) . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1.1 4-1.1.1.1 7-1.1.1.1.2.2 7-1.1.1.1.2.2.1 7-1.1.1.1.2.2.1.r 9-1.1.1.1.2.1.1 11-1.1 12-1.1.2.2 13-1.1.2.1.1 14-1.1.3.r 15-1.1.3.1.1 16-1.1.3 18-1 18-1.3.1 19-1.2.3 22-1.2.1 23-1.2.1.1.r 24-1.2.1.1.1.1 26-1.3.1.1 26-1.3.1.2 27-1.3.1.1.1 28-1.3.1 29-1.3.1.2.1 (a / and~e.18 :op1 (i / increase-01~e.11 :ARG0 (s / silence-01~e.0 :ARG1~e.1 (a2 / and~e.4 :op1 (p / protein :name (n2 / name :op1 "CtBP1"~e.2)) :op2 (p2 / protein :name (n3 / name :op1 "CtBP2"~e.9) :degree (l / less~e.7 :degree~e.7 (m / more~e.7))))) :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.13) :mod (b / basal~e.12)) :location~e.14 (c / cell-line~e.16 :name (n4 / name :op1 "8505C"~e.15))) :op2 (p3 / potentiate-01 :ARG1 (a3 / affect-01~e.22 :ARG0~e.23 (s2 / small-molecule :name (n5 / name :op1 "PLX4032"~e.24))) :ARG2 s :ARG3 (m2 / marked~e.19)) :ARG1-of (d / describe-01 :ARG0 (a4 / and~e.18,28 :op1 (f / figure~e.26 :mod "5D"~e.27) :op2 (f2 / figure~e.26 :mod "5E"~e.29)))) # ::id bio-exp_0001.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Knockdown of these factors modestly increased basal and PLX4032 - induced HER2 levels , which likely contributes to the remarkable increase in pHER3 we observed ( Fig. 5D and 5E ) . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1 3-1.1.1 4-1.3 5-1 6-1.2.1.1.2 7-1.2 8-1.2.2.1.2.1.1.1 10-1.2.2.1.2 11-1.2.1.1.1.1 11-1.2.2.1.1.1 12-1.2.1 12-1.2.2 15-1.4.2 16-1.4 19-1.4.1.3 20-1.4.1 23-1.4.1.2.1 24-1.4.1.2 26-1.5.1.1 26-1.5.1.2 27-1.5.1.1.1 28-1.5.1 29-1.5.1.2.1 (i / increase-01~e.5 :ARG0 (k / knock-down-02~e.0 :ARG1~e.1 (f / factor~e.3 :mod (t / this~e.2))) :ARG1 (a / and~e.7 :op1 (l / level~e.12 :quant-of (e / enzyme :name (n / name :op1 "HER2"~e.11) :mod (b / basal~e.6))) :op2 (l2 / level~e.12 :quant-of (e2 / enzyme :name (n2 / name :op1 "HER2"~e.11) :ARG2-of (i2 / induce-01~e.10 :ARG0 (s / small-molecule :name (n3 / name :op1 "PLX4032"~e.8)))))) :degree (m / modest~e.4) :ARG0-of (c / contribute-01~e.16 :ARG1 (i3 / increase-01~e.20 :ARG1 (e3 / enzyme :name (n4 / name :op1 "HER3") :ARG3-of (p / phosphorylate-01)) :ARG1-of (o / observe-01~e.24 :ARG0 (w / we~e.23)) :ARG1-of (r / remarkable-02~e.19)) :ARG1-of (l3 / likely-01~e.15)) :ARG1-of (d / describe-01 :ARG0 (a2 / and~e.28 :op1 (f2 / figure~e.26 :mod "5D"~e.27) :op2 (f3 / figure~e.26 :mod "5E"~e.29)))) # ::id bio-exp_0001.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Finally , CtBP1 and CtBP2 chromatin immunoprecipitation assays showed decreased binding to the HER3 promoter after treatment with PLX4032 ( Fig. 5F ) . # ::alignments 0-1.1 0-1.1.r 2-1.2.1.1.1.1.1 3-1.2.1.1 4-1.2.1.1.2.1.1 5-1.2.1.2 6-1.2.1 7-1.2 8-1 9-1.3.2 10-1.3 11-1.3.1.r 13-1.3.1.1.1.1.1 14-1.3.1 14-1.3.1.1 14-1.3.1.1.r 15-1.3.2.1 16-1.3.2.1.1 17-1.3.2.1.1.1.r 18-1.3.2.1.1.1.1.1 20-1.4.1 21-1.4.1.1 (s / show-01~e.8 :li~e.0 -1~e.0 :ARG0 (a / assay-01~e.7 :ARG1 (i / immunoprecipitate-01~e.6 :ARG1 (a2 / and~e.3 :op1 (p / protein :name (n2 / name :op1 "CtBP1"~e.2)) :op2 (p2 / protein :name (n3 / name :op1 "CtBP2"~e.4))) :mod (c / chromatin~e.5))) :ARG1 (b / bind-01~e.10 :ARG2~e.11 (m / molecular-physical-entity~e.14 :ARG0-of~e.14 (p3 / promote-01~e.14 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.13)))) :ARG1-of (d / decrease-01~e.9 :time (a3 / after~e.15 :op1 (t / treat-04~e.16 :ARG2~e.17 (s2 / small-molecule :name (n4 / name :op1 "PLX4032"~e.18)))))) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.20 :mod "5F"~e.21))) # ::id bio-exp_0001.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These findings were confirmed in a second cell line ( Supplementary Fig. S5A ) . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 4-1.2.r 6-1.2.1 6-1.2.1.1 6-1.2.1.1.r 7-1.2 8-1.2 10-1.3.1.2 11-1.3.1 12-1.3.1.1 (c / confirm-01~e.3 :ARG1 (t2 / thing~e.1 :ARG1-of~e.1 (f / find-01~e.1) :mod (t / this~e.0)) :location~e.4 (c2 / cell-line~e.7,8 :ord (o / ordinal-entity~e.6 :value~e.6 2~e.6)) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.11 :mod "S5A"~e.12 :ARG2-of (s / supplement-01~e.10)))) # ::id bio-kappa_0001.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Activation of Raf occurs via a complex , yet incompletely understood mechanism requiring membrane translocation , regulatory phosphorylation / dephosphorylation events and , crucially , allosteric activation in the context of a side @-@ to @-@ side dimer comprising two Raf molecules or a Raf and a Ksr molecule . # ::alignments 0-1 1-1.1.r 2-1.1.1.1 6-1.2.1 9-1.2.2.1 9-1.2.2.1.1 9-1.2.2.1.1.r 10-1.2.2 11-1.2 12-1.2.3 13-1.2.3.1.1.1 14-1.2.3.1.1 16-1.2.3.1.2.1 16-1.2.3.1.3.1 17-1.2.3.1.2 19-1.2.3.1.3 21-1.2.3.1 23-1.2.3.1.4.2 25-1.2.3.1.4.1 26-1.2.3.1.4 32-1.2.3.1.4.3.1.1 32-1.2.3.1.4.3.1.1.1 34-1.2.3.1.4.3.1.1.1.r 36-1.2.3.1.4.3.1.1 36-1.2.3.1.4.3.1.1.1 37-1.2.3.1.4.3.1 38-1.2.3.1.4.3.1.2 39-1.2.3.1.4.3.1.2.1.1.1 40-1.2.3.1.4.3.1.2.1.1.2 41-1.2.3.1.4.3.1.2.1.1 42-1.2.3.1.4.3.1.2.1 44-1.1.1.1 45-1.2.3.1.4.3.1.2.1.2 47-1.2.3.1.4.3.1.2.1.2.2.1.1.1 48-1.2.3.1.4.3.1.2.1.2.1 48-1.2.3.1.4.3.1.2.1.2.2 (a / activate-01~e.0 :ARG1~e.1 (e / enzyme :name (n / name :op1 "Raf"~e.2,44)) :manner (m / mechanism~e.11 :mod (c / complex~e.6) :ARG1-of (u / understand-01~e.10 :ARG1-of (c2 / complete-02~e.9 :polarity~e.9 -~e.9)) :ARG0-of (r / require-01~e.12 :ARG1 (a2 / and~e.21 :op1 (t / translocate-01~e.14 :ARG2 (m2 / membrane~e.13)) :op2 (p2 / phosphorylate-01~e.17 :ARG0-of (r2 / regulate-01~e.16)) :op3 (d / dephosphorylate-01~e.19 :ARG0-of (r3 / regulate-01~e.16)) :op4 (a3 / activate-01~e.26 :mod (a4 / allosteric~e.25) :mod (c3 / crucial~e.23) :condition (h / have-part-91 :ARG1 (d2 / dimer~e.37 :mod (s / side~e.32,36 :prep-to~e.34 (s2 / side~e.32,36)) :ARG1-of (c5 / comprise-01~e.38 :ARG2 (o / or~e.42 :op1 (m3 / molecule~e.41 :quant 2~e.39 :mod e~e.40) :op2 (a5 / and~e.45 :op1 (m4 / molecule~e.48 :mod e) :op2 (m5 / molecule~e.48 :mod (e4 / enzyme :name (n4 / name :op1 "Ksr"~e.47))))))))))))) # ::id bio-kappa_0001.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Of the three Raf kinases , only B @-@ Raf is able to function as an allosteric activator in the context of the Raf heterodimers , a role independent of B @-@ Raf kinase activity . # ::alignments 2-1.1.1.2.1.1 3-1.1.1.2.1.2.1 4-1.1.1 4-1.1.1.2.1 6-1.1.1.3 7-1.1.1.1.1 9-1.1.1.2.1.2.1 9-1.1.3.1.1.1.1 11-1 16-1.1.2 17-1.1 23-1.1.1.2.1.2.1 23-1.1.3.1.1.1.1 24-1.1.3.1 28-1.1.4 28-1.1.4.1 28-1.1.4.1.r 29-1.1.4.2.r 30-1.1.4.2.1 31-1.1.4.2.1 32-1.1.4.2.1 33-1.1.4.2.1 34-1.1.4.2 (p / possible-01~e.11 :ARG1 (a / activate-01~e.17 :ARG0 (k / kinase~e.4 :name (n / name :op1 "B-Raf"~e.7) :ARG1-of (i / include-91 :ARG2 (k2 / kinase~e.4 :quant 3~e.2 :name (n2 / name :op1 "Raf"~e.3,9,23))) :mod (o / only~e.6)) :mod (a2 / allosteric~e.16) :condition (h2 / have-part-91 :ARG1 (h / heterodimer~e.24 :part (e / enzyme :name (n3 / name :op1 "Raf"~e.9,23))) :ARG2 k) :ARG0-of (d / depend-01~e.28 :polarity~e.28 -~e.28 :ARG1~e.29 (a3 / activity-06~e.34 :ARG0 k~e.30,31,32,33)))) # ::id bio-kappa_0001.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The molecular basis for this has recently been elucidated by the Shaw lab , who has shown that the ability of acting as an activator depends on the presence of negative charges in the Raf N @-@ terminal acidic motif . # ::alignments 1-1.2.2 2-1.2 3-1.2.1.r 4-1.2.1 6-1.3 8-1 9-1.1.r 11-1.1.1.1 12-1.1 16-1.1.2 22-1.1.2.1.r 22-1.3.r 24-1.1.2.1.1.1 25-1.1.2.1 26-1.1.2.1.2.r 28-1.1.2.1.2 29-1.1.2.1.2.1.r 30-1.1.2.1.2.1.1 31-1.1.2.1.2.1 32-1.1.2.1.2.1.2.r 34-1.1.2.1.2.1.2.2.2.1.1 35-1.1.2.1.2.1.2.2.1.1 37-1.1.2.1.2.1.2.2.1.1 38-1.1.2.1.2.1.2.1 39-1.1.2.1.2.1.2 (e / elucidate-01~e.8 :ARG0~e.9 (l / lab~e.12 :name (n / name :op1 "Shaw"~e.11) :ARG0-of (s / show-01~e.16 :ARG1~e.22 (d / depend-01~e.25 :ARG0 (p / possible-01 :ARG1 (a / activate-01~e.24)) :ARG1~e.26 (p2 / present-02~e.28 :ARG1~e.29 (c / charge~e.31 :ARG2-of (n2 / negative-06~e.30) :location~e.32 (m3 / motif~e.39 :mod (a2 / acid~e.38) :part-of (p3 / protein-segment :name (n3 / name :op1 "N-terminus"~e.35,37) :part-of (e2 / enzyme :name (n4 / name :op1 "Raf"~e.34))))))))) :ARG1 (b / base-02~e.2 :ARG1~e.3 (t / this~e.4) :mod (m2 / molecule~e.1)) :time~e.22 (r / recent~e.6)) # ::id bio-kappa_0001.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In B @-@ Raf , this motif is negatively charged due to the constitutive phosphorylation of Ser446 and @/@ or 447 , and to the presence of two aspartates at position 448 @/@ 9 ( Fig. 2A ) . # ::alignments 1-1.1.2.1.1 3-1.1.2.1.1 5-1.1.1 6-1.1 6-1.3.1.2.2.1 6-1.3.1.2.2.2 8-1.2 9-1 10-1.3 11-1.3 13-1.3.1.1.2 14-1.3.1.1 17-1.3.1.1.1 19-1.3.1.1.1 20-1.3.1.1.1.2.1 22-1.3.1 23-1.3.1.r 25-1.3.1.2 26-1.3.1.2.1.r 27-1.3.1.2.1.1 31-1.3.1.2.2.1.1 35-1.4.1 36-1.4.1.1 (c / charge-03~e.9 :ARG1 (m / motif~e.6 :mod (t / this~e.5) :part-of (e2 / enzyme :name (n6 / name :op1 "B-Raf"~e.1,3))) :ARG2-of (n / negative-06~e.8) :ARG1-of (c2 / cause-01~e.10,11 :ARG0~e.23 (a / and~e.22 :op1 (p / phosphorylate-01~e.14 :ARG1 (a6 / and-or~e.17,19 :op1 (a2 / amino-acid :mod 446 :name (n2 / name :op1 "serine")) :op2 (a3 / amino-acid :mod 447~e.20 :name (n3 / name :op1 "serine"))) :mod (c3 / constitutive~e.13)) :op2 (p4 / present-02~e.25 :ARG1~e.26 (a4 / amino-acid :quant 2~e.27 :name (n4 / name :op1 "aspartate")) :ARG2 (a5 / and :op1 (p2 / protein-segment~e.6 :mod 448~e.31) :op2 (p3 / protein-segment~e.6 :mod 449))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.35 :mod "2A"~e.36))) # ::id bio-kappa_0001.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Allosteric activation by B @-@ Raf induces cis @-@ autophosporylation in the activation loop of the receiver kinase , i.e. C @-@ Raf , and renders it able to phosphorylate Mek . # ::alignments 0-1.1.1.2 1-1.1.1 2-1.1.1.1.r 3-1.1.1.1.1.1 5-1.1.1.1.1.1 6-1.1 12-1.1.2.3.1 13-1.1.2.3 17-1.1.2.3.1.1 20-1.1.2.3.1.1.2.1.1.1 22-1.1.1.1.1.1 22-1.1.2.3.1.1.2.1.1.1 24-1 25-1.2 26-1.2.1 27-1.2.2 29-1.1.2 29-1.2.2.1 30-1.2.2.1.1.1.1 (a3 / and~e.24 :op1 (i / induce-01~e.6 :ARG0 (a / activate-01~e.1 :ARG0~e.2 (e / enzyme :name (n / name :op1 "B-Raf"~e.3,5,22)) :mod (a2 / allosteric~e.0)) :ARG2 (p / phosphorylate-01~e.29 :ARG1 k :ARG2 k :subevent-of (l / loop~e.13 :ARG0-of (a4 / activate-01~e.12 :ARG1 (k / kinase~e.17 :ARG0-of (r2 / receive-01) :ARG1-of (m / mean-01 :ARG2 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.20,22)))))))) :op2 (r / render-01~e.25 :ARG0 a~e.26 :ARG1 (p2 / possible-01~e.27 :ARG1 (p3 / phosphorylate-01~e.29 :ARG1 (e3 / enzyme :name (n3 / name :op1 "Mek"~e.30)) :ARG2 e2)))) # ::id bio-kappa_0001.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Mek , in turn , phosphorylates the N @-@ terminal acidic motif in C @-@ Raf , converting it to an allosteric activator of other Rafs ( Fig. 2B and C ) . # ::alignments 0-1.2.1.1 2-1.4 3-1.4 5-1 7-1.1.2.1.1 9-1.1.2.1.1 10-1.1.1 11-1.1 12-1.4 13-1.1.2.2.1.1 15-1.1.2.2.2.2.1.1.1.1 17-1.1.2.2.2 18-1.1.2.2.2.1 21-1.1.2.2.2.2.1.2 22-1.1.2.2.2.2 22-1.1.2.2.2.2.1 22-1.1.2.2.2.2.1.r 24-1.1.2.2.2.2.1.1.2 27-1.3.1.1 27-1.3.1.2 28-1.3.1.1.1 29-1.3.1 30-1.1.2.2.1.1 (p / phosphorylate-01~e.5 :ARG1 (m / motif~e.11 :mod (a / acid~e.10) :part-of (p2 / protein-segment :name (n2 / name :op1 "N-terminus"~e.7,9) :part-of (e2 / enzyme :name (n3 / name :op1 "C-Raf"~e.13,30) :ARG1-of (c2 / convert-01~e.17 :ARG0 e~e.18 :ARG2 (e3 / enzyme~e.22 :ARG0-of~e.22 (a2 / activate-01~e.22 :ARG1 (e4 / enzyme :name (n4 / name :op1 "Raf"~e.15) :mod (o / other~e.24)) :mod (a3 / allosteric~e.21))))))) :ARG2 (e / enzyme :name (n / name :op1 "Mek"~e.0)) :ARG1-of (d / describe-01 :ARG0 (a4 / and~e.29 :op1 (f / figure~e.27 :mod "2B"~e.28) :op2 (f2 / figure~e.27 :mod "2C"))) :mod (i / in-turn~e.2,3,12)) # ::id bio-kappa_0001.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This model explains why C @-@ Raf mutants devoid of kinase activity cannot function as activators , and why B @-@ Raf can activate Mek directly as a homodimer . # ::alignments 0-1.1.1 1-1.1 2-1 3-1.2 3-1.2.1 3-1.2.1.r 4-1.2.1.1.1.2.1.1.1 6-1.2.1.1.1.2.1.1.1 7-1.2.1.1.1.2.1 7-1.2.1.1.1.2.1.2 7-1.2.1.1.1.2.1.2.r 10-1.2.1.1.1.2.1.3.1.1 11-1.2.1.1.1.2.1.3.1 12-1.2.1.1.1 12-1.2.1.1.1.1 12-1.2.1.1.1.1.r 15-1.2.1.1.1.2 17-1.2.1.1 18-1.2 18-1.2.1 18-1.2.1.r 19-1.2.1.1.2.1.1.1.1 21-1.2.1.1.2.1.1.1.1 22-1.2.1.1.2 23-1.2.1.1.2.1 24-1.2.1.1.2.1.2.1.1 25-1.2.1.1.2.1.3 28-1.2.1.1.2.1.1.2.1 (e / explain-01~e.2 :ARG0 (m / model~e.1 :mod (t3 / this~e.0)) :ARG1 (t2 / thing~e.3,18 :ARG0-of~e.3,18 (c2 / cause-01~e.3,18 :ARG1 (a6 / and~e.17 :op1 (p / possible-01~e.12 :polarity~e.12 -~e.12 :ARG1 (a2 / activate-01~e.15 :ARG0 (e2 / enzyme~e.7 :name (n / name :op1 "C-Raf"~e.4,6) :ARG2-of~e.7 (m2 / mutate-01~e.7) :ARG1-of (v / void-03 :ARG2 (a / activity-06~e.11 :ARG0 (k / kinase~e.10)))))) :op2 (p2 / possible-01~e.22 :ARG1 (a4 / activate-01~e.23 :ARG0 (e3 / enzyme :name (n2 / name :op1 "B-Raf"~e.19,21) :ARG0-of (a5 / act-01 :ARG1 (h / homodimer~e.28))) :ARG1 (e4 / enzyme :name (n3 / name :op1 "Mek"~e.24)) :ARG1-of (d / direct-02~e.25))))))) # ::id bio-kappa_0001.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Phosphorylated Ksr can also function as a transactivator ; however , since Raf binding to Ksr induces limited kinase activity , in quiescent cells the constitutive association of Ksr with B @-@ Raf may serve to prevent C @-@ Raf binding to B @-@ Raf , safeguarding against undue activation of the pathway . # ::alignments 0-1.1.1.2 1-1.1.1.1.1 2-1.1.3 3-1.1.2 9-1.1.3.r 11-1.1.3.3 12-1.1.3.3.1.1.1.1.1 13-1.1.3.3.1.1 14-1.1.3.3 14-1.1.3.3.1.1.2.r 15-1.1.3.3.1.1.2 16-1.1.3.3.1 17-1.1.3.3.1.2.2 18-1.1.3.3.1.2.1 19-1.1.3.3.1.2 22-1.1.3.2.1 23-1.1.3.2 25-1.1.3.1.1.3 26-1.1.3.1.1 27-1.1.3.1.1.1.r 28-1.1.3.1.1.1 29-1.1.3.1.1.2.r 30-1.1.3.1.1.2.1.1 32-1.1.3.1.1.2.1.1 33-1 33-1.1.3 34-1.1.3.1 36-1.1.3.1.2 37-1.1.3.1.2.2.1.1.1 39-1.1.3.1.2.2.1.1.1 40-1.1.3.1.2.2 41-1.1.3.1.2.2.2.r 42-1.1.3.1.2.2.2 43-1.1.3.1.2.2.2 44-1.1.3.1.2.2.2 46-1.1.3.1.2.3 48-1.1.3.1.2.3.1.2 48-1.1.3.1.2.3.1.2.1 48-1.1.3.1.2.3.1.2.1.r 49-1.1.3.1.2.3.1 50-1.1.3.1.2.3.1.1.r 52-1.1.3.1.2.3.1.1 (p / possible-01~e.33 :ARG1 (t2 / transactivate-01 :ARG2 (e / enzyme :name (n / name :op1 "Ksr"~e.1) :ARG3-of (p2 / phosphorylate-01~e.0)) :mod (a / also~e.3) :concession-of~e.9 (p3 / possible-01~e.2,33 :ARG1 (s / serve-01~e.34 :ARG0 (a3 / associate-01~e.26 :ARG1~e.27 e~e.28 :ARG2~e.29 (e3 / enzyme :name (n3 / name :op1 "B-Raf"~e.30,32)) :mod (c2 / constitutive~e.25)) :ARG1 (p4 / prevent-01~e.36 :ARG0 a3 :ARG1 (b / bind-01~e.40 :ARG1 (e4 / enzyme :name (n4 / name :op1 "C-Raf"~e.37,39)) :ARG2~e.41 e3~e.42,43,44) :ARG0-of (s2 / safeguard-01~e.46 :ARG2 (a4 / activate-01~e.49 :ARG1~e.50 (p5 / pathway~e.52) :mod (d / due~e.48 :polarity~e.48 -~e.48))))) :location (c / cell~e.23 :mod (q / quiescent~e.22)) :ARG1-of (c3 / cause-01~e.11,14 :ARG0 (i / induce-01~e.16 :ARG0 (b2 / bind-01~e.13 :ARG1 (e6 / enzyme :name (n6 / name :op1 "Raf"~e.12)) :ARG2~e.14 e~e.15) :ARG2 (a2 / activity-06~e.19 :ARG1 (k / kinase~e.18) :ARG1-of (l / limit-01~e.17))))))) # ::id bio-kappa_0001.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PSPs dephosphorylate phosphoserine and phosphothreonine residues . # ::alignments 1-1 3-1.1 5-1.1.1 5-1.1.2 (d / dephosphorylate-01~e.1 :ARG1 (a / and~e.3 :op1 (r / residue~e.5 :mod (a2 / amino-acid :name (n / name :op1 "serine") :ARG3-of (p2 / phosphorylate-01))) :op2 (r2 / residue~e.5 :mod (a3 / amino-acid :name (n2 / name :op1 "threonine") :ARG3-of (p4 / phosphorylate-01)))) :ARG2 (s / small-molecule :name (n3 / name :op1 "PSP"))) # ::id bio-kappa_0001.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok One of the most abundantly expressed PSPs , protein phosphatase 2A ( PP2A ) , can regulate the Raf / Mek / Erk pathway both positively and negatively . # ::alignments 3-1.1.1.2.2.1.2.1.1 4-1.1.1.2.2.1.2.1 5-1.1.1.2.2.1.2 8-1.1.1.2.1.1 9-1.1.1.2.1.2 10-1.1.1.2.1.3 15-1 18-1.1.1.1.1.1 20-1.1.1.1.1.1 22-1.1.1.1.1.1 23-1.1.1.1 26-1.1 (p / possible-01~e.15 :ARG1 (a3 / and~e.26 :op1 (u / upregulate-01 :ARG1 (p3 / pathway~e.23 :name (n3 / name :op1 "Raf/Mek/Erk"~e.18,20,22)) :ARG2 (e2 / enzyme :name (n2 / name :op1 "protein"~e.8 :op2 "phosphatase"~e.9 :op3 "2A"~e.10) :ARG1-of (i / include-91 :ARG2 (s / small-molecule :name (n / name :op1 "PSP") :ARG2-of (e / express-03~e.5 :degree (a / abundant~e.4 :degree (m2 / most~e.3))))))) :op2 (d / downregulate-01 :ARG1 p3 :ARG2 e2))) # ::id bio-kappa_0001.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As a positive regulator , PP2A associates with C @-@ Raf and Ksr1 and dephosphorylates negative regulatory sites on both proteins , allowing their recruitment to the membrane and leading to Mek and Erk activation . # ::alignments 5-1.1.1.1.1 6-1.1 7-1.1.2.r 8-1.1.2.1.1.1 10-1.1.2.1.1.1 12-1.1.2.2.1.1 13-1.2.1.2 15-1.2.1.1 16-1.2.1.1 17-1.2.1 20-1.2.1 22-1.3 23-1.3.1.1 23-1.3.1.1.r 24-1.3.1 25-1.3.1.2.r 27-1.3.1.2 28-1 28-1.1.2 29-1.4 30-1.4.1.r 31-1.4.1.1.1.1.1 32-1.4.1.1 33-1.4.1.1.2.1.1 34-1.4.1 (a / and~e.28 :op1 (a7 / associate-01~e.6 :ARG1 (e / enzyme :name (n / name :op1 "PP2A"~e.5)) :ARG2~e.7 (a2 / and~e.28 :op1 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.8,10)) :op2 (e3 / enzyme :name (n3 / name :op1 "Ksr1"~e.12)))) :op2 (d / dephosphorylate-01 :ARG1 (p2 / protein-segment~e.17,20 :ARG0-of (d2 / downregulate-01~e.15,16) :part-of (a3 / and~e.13 :op1 e2 :op2 e3)) :ARG2 e) :ARG0-of (a4 / allow-01~e.22 :ARG1 (r / recruit-01~e.24 :ARG1~e.23 a2~e.23 :destination~e.25 (m / membrane~e.27))) :ARG0-of (l / lead-03~e.29 :ARG2~e.30 (a5 / activate-01~e.34 :ARG1 (a6 / and~e.32 :op1 (e4 / enzyme :name (n5 / name :op1 "Mek"~e.31)) :op2 (e5 / enzyme :name (n6 / name :op1 "Erk"~e.33))))) :condition (u / upregulate-01 :ARG2 e)) # ::id bio-kappa_0001.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A similar role in C @-@ Raf activation has been described for the catalytic subunit of PP1C , which associates with C @-@ Raf in Ras @- and growth factor - stimulated cells . # ::alignments 1-1.1.1 2-1.1 3-1.1.2.r 4-1.1.2.1.1.1 6-1.1.2.1.1.1 7-1.1.2 10-1 11-1.2.r 13-1.2 13-1.2.1 13-1.2.1.r 15-1.2.2.r 16-1.2.2.1.1 21-1.2.3.1 22-1.2.3.1 23-1.2.3.1 25-1.2.3.2.1.1.1.1.1 27-1.2.3.2.1.1 28-1.2.3.2.1.1.2 29-1.2.3.2.1.1.2 31-1.2.3.2.1 32-1.2.3.2 (d / describe-01~e.10 :ARG1 (r / role~e.2 :ARG1-of (r2 / resemble-01~e.1) :purpose~e.3 (a / activate-01~e.7 :ARG1 (e / enzyme :name (n / name :op1 "C-Raf"~e.4,6)))) :topic~e.11 (p / protein-segment~e.13 :ARG0-of~e.13 (c / catalyze-01~e.13) :part-of~e.15 (e2 / enzyme :name (n2 / name :op1 "PP1C"~e.16)) :ARG1-of (b / bind-01 :ARG2 e~e.21,22,23 :location (c2 / cell~e.32 :ARG1-of (s / stimulate-01~e.31 :ARG0 (a2 / and~e.27 :op1 (e3 / enzyme :name (n3 / name :op1 "Ras"~e.25)) :op2 (g / growth-factor~e.28,29))))))) # ::id bio-kappa_0001.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In addition to promoting C @-@ Raf activation , PP2A is also able to dephosphorylate Erk - dependent sites on C @-@ Raf . # ::alignments 0-1 1-1 3-1.1 4-1.1.2.1 5-1.1.2.1 6-1.1.2.1 7-1.1.2 9-1.2.1.2.1.1 11-1.2.2 12-1.2 14-1.2.1 15-1.2.1.1.1.1.1.1 17-1.2.1.1.1 18-1.2.1.1 19-1.2.1.1.2.r 20-1.2.1.1.2.1.1 22-1.2.1.1.2.1.1 (a / and~e.0,1 :op1 (p3 / promote-02~e.3 :ARG0 e :ARG1 (a2 / activate-01~e.7 :ARG1 e3~e.4,5,6)) :op2 (p / possible-01~e.12 :ARG1 (d / dephosphorylate-01~e.14 :ARG1 (p2 / protein-segment~e.18 :ARG0-of (d2 / depend-01~e.17 :ARG1 (e2 / enzyme :name (n2 / name :op1 "Erk"~e.15))) :part-of~e.19 (e3 / enzyme :name (n3 / name :op1 "C-Raf"~e.20,22))) :ARG2 (e / enzyme :name (n / name :op1 "PP2A"~e.9))) :mod (a3 / also~e.11))) # ::id bio-kappa_0001.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Since the sites have been described alternatively as negative regulatory or activating , the significance of these dephosphorylation events for Raf activation is unclear . # ::alignments 2-1.2.1 5-1.2 6-1.2.3 6-1.2.3.r 7-1.2.2.r 8-1.2.2.1 9-1.2.2.1 10-1.2.2 11-1.2.2.2 14-1.3 15-1.3.2.r 16-1.3.2.1 17-1.3.2 19-1.3.1.r 20-1.3.1.1.1.1 21-1.3.1 23-1 23-1.1 23-1.1.r (c / clear-06~e.23 :polarity~e.23 -~e.23 :ARG0 (d2 / describe-01~e.5 :ARG1 (p / protein-segment~e.2) :ARG2~e.7 (o / or~e.10 :op1 (d3 / downregulate-01~e.8,9 :ARG2 p) :op2 (a2 / activate-01~e.11 :ARG0 p)) :manner~e.6 (a / alternative~e.6)) :ARG1 (s / significance~e.14 :topic~e.19 (a3 / activate-01~e.21 :ARG1 (e2 / enzyme :name (n2 / name :op1 "Raf"~e.20))) :mod~e.15 (d / dephosphorylate-01~e.17 :mod (t / this~e.16)))) # ::id bio-kappa_0001.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As a negative regulator of the pathway , PP2A can dephosphorylate the adapter protein Shc , required downstream of some tyrosine kinase receptors for the activation of the Raf / Mek / Erk module ; and it can dephosphorylate Mek and Erk proteins , thus inhibiting the cascade directly . # ::alignments 2-1.1.1.3 3-1.1.1.3 4-1.1.1.3.1.r 6-1.1.1.3.1 8-1.1.1.2.1.1 9-1.1 10-1.1.1 12-1.1.1.1.2 13-1.1.1.1 13-1.1.1.1.3.1.2.1 14-1.1.1.1.1.1 16-1.1.1.1.3 17-1.1.1.1.3.1.2.2 18-1.1.1.1.3.1.2.1.2.r 19-1.1.1.1.3.1.2.1.2 20-1.1.1.1.3.1.2.1.1.1 21-1.1.1.1.3.1.2.1.1.2 22-1.1.1.1.3.1.2.1.1.3 25-1.1.1.1.3.1 26-1.1.1.1.3.1.1.r 28-1.1.1.1.3.1.1.1.1 30-1.1.1.1.3.1.1.1.1 32-1.1.1.1.3.1.1.1.1 35-1 37-1.2 38-1.2.1 39-1.2.1.1.1.1.1 40-1.2.1.1 41-1.2.1.1.2.1.1 42-1.2.1.1.1 42-1.2.1.1.2 45-1.2.1.3 48-1.2.1.3.2 (a / and~e.35 :op1 (p6 / possible-01~e.9 :ARG1 (d / dephosphorylate-01~e.10 :ARG1 (p2 / protein~e.13 :name (n2 / name :op1 "Shc"~e.14) :mod (a2 / adapter~e.12) :ARG1-of (r / require-01~e.16 :ARG0 (a3 / activate-01~e.25 :ARG1~e.26 (p3 / pathway :name (n3 / name :op1 "Raf/Mek/Erk"~e.28,30,32)) :location (r3 / relative-position :op1 (p / protein~e.13 :name (n7 / name :op1 "tyrosine"~e.20 :op2 "kinase"~e.21 :op3 "receptor"~e.22) :quant~e.18 (s / some~e.19)) :direction (d2 / downstream~e.17))))) :ARG2 (e / enzyme :name (n / name :op1 "PP2A"~e.8)) :condition (d5 / downregulate-01~e.2,3 :ARG1~e.4 (p4 / pathway~e.6) :ARG2 e))) :op2 (p7 / possible-01~e.37 :ARG1 (d4 / dephosphorylate-01~e.38 :ARG1 (a4 / and~e.40 :op1 (p5 / protein-family~e.42 :name (n4 / name :op1 "Mek"~e.39)) :op2 (p8 / protein-family~e.42 :name (n5 / name :op1 "Erk"~e.41))) :ARG2 e :ARG0-of (i / inhibit-01~e.45 :ARG1 p3 :ARG1-of (d3 / direct-02~e.48))))) # ::id bio-kappa_0001.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A further negative regulator of the cascade , at the level of C @-@ Raf , is Protein phosphatase 5 ( PP5 ) , which associates with C @-@ Raf via its N @-@ terminal tetratricopeptide ( TPR ) domain in growth factor stimulated cells . # ::alignments 1-1.1.3 2-1 3-1 4-1.2.r 6-1.2 11-1.2.1.r 12-1.2.1 13-1.2.1 14-1.2.1 17-1.1.1.1 18-1.1.1.2 19-1.1.1.3 25-1.1 25-1.1.2 25-1.1.2.r 26-1.1.2.1.r 26-1.1.2.3.r 27-1.1.2.1.1.1 29-1.1.2.1.1.1 31-1.1.2.3.2.2 31-1.1.2.3.2.2.r 32-1.1.2.3.2.1.1 34-1.1.2.3.2.1.1 35-1.1.2.3.1.1 39-1.1.2.3.1.2 40-1.1.2.2.r 41-1.1.2.2.1.1 42-1.1.2.2.1.1 43-1.1.2.2.1 44-1.1.2.2 (d3 / downregulate-01~e.2,3 :ARG0 (e3 / enzyme~e.25 :name (n / name :op1 "Protein"~e.17 :op2 "phosphatase"~e.18 :op3 5~e.19) :ARG1-of~e.25 (a / associate-01~e.25 :ARG2~e.26 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.27,29)) :location~e.40 (c / cell~e.44 :ARG1-of (s / stimulate-01~e.43 :ARG0 (g / growth-factor~e.41,42))) :instrument~e.26 (p2 / protein-segment :name (n4 / name :op1 "tetratricopeptide"~e.35 :op2 "domain"~e.39) :part-of (p / protein-segment :name (n3 / name :op1 "N-terminal"~e.32,34) :part-of~e.31 e2~e.31))) :mod (f / further~e.1)) :ARG1~e.4 (c2 / cascade~e.6 :location~e.11 e2~e.12,13,14)) # ::id bio-kappa_0001.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This interaction leads to the activation of PP5 catalytic activity and to the selective dephosphorylation of the activating serine residue at position 338 , terminating the signal . # ::alignments 0-1.1.1 1-1.1 2-1 3-1.2.r 5-1.2.1 6-1.2.1.1.r 7-1.2.1.1.1.1.1 8-1.2.1.1.2 9-1.2.1.1 10-1.2 13-1.2.2.2 14-1.2.2 15-1.2.2.1.r 17-1.2.2.1.3 18-1.2.2.1.2.1.1 19-1.2.2.1 22-1.2.2.1.1 24-1.2.3 26-1.2.3.1 (l / lead-03~e.2 :ARG0 (i2 / interact-01~e.1 :mod (t / this~e.0)) :ARG2~e.3 (a3 / and~e.10 :op1 (a / activate-01~e.5 :ARG1~e.6 (a2 / activity-06~e.9 :ARG0 (e / enzyme :name (n / name :op1 "PP5"~e.7)) :ARG1 (c2 / catalyze-01~e.8))) :op2 (d / dephosphorylate-01~e.14 :ARG1~e.15 (r / residue~e.19 :mod 338~e.22 :mod (a4 / amino-acid :name (n2 / name :op1 "serine"~e.18)) :ARG0-of (a5 / activate-01~e.17)) :mod (s / selective~e.13)) :ARG0-of (t2 / terminate-01~e.24 :ARG1 (s3 / signal~e.26)))) # ::id bio-kappa_0001.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Following ligand binding , Sos is brought from the cytoplasm to the activated receptor in a phosphotyrosine - dependent manner through adapter proteins such as Grb2 . # ::alignments 0-1.6 1-1.6.1.1 2-1.6.1 4-1.1.1.1 6-1 7-1.3.r 9-1.3 10-1.2.r 12-1.2.1 13-1.2 18-1.4 19-1.4.r 21-1.5.2 22-1.5 23-1.5.1.r 24-1.5.1.r 25-1.5.1.1.1 (b / bring-01~e.6 :ARG1 (p3 / protein :name (n3 / name :op1 "Sos"~e.4)) :ARG2~e.10 (r / receptor~e.13 :ARG1-of (a / activate-01~e.12)) :ARG4~e.7 (c / cytoplasm~e.9) :manner~e.19 (d / depend-01~e.18 :ARG0 b :ARG1 (a2 / amino-acid :name (n / name :op1 "tyrosine") :ARG3-of (p4 / phosphorylate-01))) :instrument (p / protein~e.22 :example~e.23,24 (p2 / protein :name (n2 / name :op1 "Grb2"~e.25)) :mod (a3 / adapter~e.21)) :ARG1-of (f / follow-01~e.0 :ARG2 (b2 / bind-01~e.2 :ARG1 (l / ligand~e.1)))) # ::id bio-kappa_0001.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Grb2 contains SH3 domains that are bound constitutively to a carboxy - terminal proline - rich region of Sos , and the Grb2 ' 96 Sos complex is recruited to activated receptors by interactions between the SH2 domain of Grb2 and phosphotyrosine residues on the receptor . # ::alignments 0-1.1.1.1.1 1-1.1 2-1.1.2.1.1 3-1.1.2.1.2 6-1.1.2 6-1.1.2.2 6-1.1.2.2.r 7-1.1.2.2.2 8-1.1.2.2.1.r 10-1.1.2.2.1.2.1.1 12-1.1.2.2.1.2.1.1 13-1.1.2.2.1.1.1.1.1 15-1.1.2.2.1.1 16-1.1.2.2.1 18-1.1.2.2.1.2.2.1.1 22-1.1.1.1.1 25-1.2.2.2 26-1.2.2 28-1.2 29-1.2.3.r 30-1.2.3.1 31-1.2.3 32-1.2.1.r 33-1.2.1 36-1.2.1.1.1.1.1 37-1.2.1.1.1.1.2 39-1.2.1.1.1.2 40-1.2.1.1 42-1.2.1.1.2 43-1.2.1.1.2.1.r 45-1.2.1.1.2.1 (a / and :op1 (c / contain-01~e.1 :ARG0 (p / protein :name (n / name :op1 "Grb2"~e.0,22)) :ARG1 (p2 / protein-segment~e.6 :name (n2 / name :op1 "SH3"~e.2 :op2 "domain"~e.3) :ARG1-of~e.6 (b / bind-01~e.6 :ARG2~e.8 (r4 / region~e.16 :mod (r6 / rich~e.15 :topic (a3 / amino-acid :name (n3 / name :op1 "proline"~e.13))) :part-of (p5 / protein-segment :name (n4 / name :op1 "carboxy-terminus"~e.10,12) :part-of (p6 / protein :name (n5 / name :op1 "Sos"~e.18)))) :mod (c2 / constitutive~e.7)))) :op2 (r5 / recruit-01~e.28 :ARG0~e.32 (i / interact-01~e.33 :ARG0 (a5 / and~e.40 :op1 (p7 / protein-segment :name (n7 / name :op1 "SH2"~e.36 :op2 "domain"~e.37) :part-of p~e.39) :op2 (r2 / residue~e.42 :location~e.43 (r3 / receptor~e.45) :mod (a4 / amino-acid :name (n6 / name :op1 "tyrosine") :ARG3-of (p3 / phosphorylate-01))))) :ARG1 (m2 / macro-molecular-complex~e.26 :part p :part p6~e.25) :destination~e.29 (r / receptor~e.31 :ARG1-of (a2 / activate-01~e.30)))) # ::id bio-kappa_0001.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The guanine nucleotide @-@ binding switch in three dimensions . # ::alignments 1-1.1.1.1 2-1.1.1.2 4-1.1.1.2 5-1 6-1.2.r 7-1.2.1 8-1.2 (s / switch~e.5 :mod (p / protein :name (n / name :op1 "guanine"~e.1 :op2 "nucleotide-binding"~e.2,4)) :prep-in~e.6 (d / dimension~e.8 :quant 3~e.7)) # ::id bio-kappa_0001.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Activation requires dissociation of protein - bound GDP , an intrinsically slow process that is accelerated by guanine nucleotide ' 96 exchange factors ( GEFs ) . # ::alignments 0-1.1 1-1 2-1.2 3-1.2.1.r 4-1.2.1.2.1 6-1.2.1 6-1.2.1.2 6-1.2.1.2.r 7-1.2.1.1.1 10-1.2.2.1 11-1.2.2 15-1.2.3 16-1.2.3.1.r 17-1.2.3.1.1.1 18-1.2.3.1.1.2 21-1.2.3.1.1.3 22-1.2.3.1.1.4 (r / require-01~e.1 :ARG0 (a / activate-01~e.0) :ARG1 (d / dissociate-01~e.2 :ARG1~e.3 (s / small-molecule~e.6 :name (n / name :op1 "GDP"~e.7) :ARG1-of~e.6 (b / bind-01~e.6 :ARG2 (p / protein~e.4))) :ARG1-of (s2 / slow-05~e.11 :mod (i / intrinsic~e.10)) :ARG1-of (a2 / accelerate-01~e.15 :ARG0~e.16 (p2 / protein :name (n2 / name :op1 "guanine"~e.17 :op2 "nucleotide"~e.18 :op3 "exchange"~e.21 :op4 "factor"~e.22))))) # ::id bio-kappa_0001.22 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This switch - ON process involves the exchange of GDP for GTP , and is , at least in principle , reversible . # ::alignments 0-1.1.1.2 4-1.1.1 5-1.1 7-1.1.2 8-1.1.2.1.r 9-1.1.2.1.1.1 10-1.1.2.2.r 11-1.1.2.2.1.1 13-1 16-1.2.2.1 17-1.2.2.1 18-1.2.2 19-1.2.2 (a / and~e.13 :op1 (i2 / involve-01~e.5 :ARG0 (p / process-02~e.4 :ARG1 (a3 / activate-01) :mod (t / this~e.0)) :ARG1 (e / exchange-01~e.7 :ARG1~e.8 (s / small-molecule :name (n / name :op1 "GDP"~e.9)) :ARG3~e.10 (s2 / small-molecule :name (n2 / name :op1 "GTP"~e.11)))) :op2 (p3 / possible-01 :ARG1 (r / reverse-01 :ARG1 p) :mod (i / in-principle~e.18,19 :mod (a2 / at-least~e.16,17)))) # ::id bio-kappa_0001.23 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The switch - OFF process is entirely different and involves hydrolysis of GTP to GDP , the guanosine triphosphatase ( GTPase ) reaction , which is basically irreversible . # ::alignments 4-1.1.1 6-1.1.2 7-1.1 8-1 9-1.2 10-1.2.1 11-1.2.1.1.r 12-1.2.1.1.1.1 13-1.2.1.2.r 14-1.2.1.2.1.1 17-1.2.1.3.1.1.1 18-1.2.1.3.1.1.2 22-1.2.1.3 26-1.2.1.3.2.1.2 27-1.2.1.3.2.1.1 (a / and~e.8 :op1 (d2 / differ-02~e.7 :ARG1 (p / process-02~e.4 :ARG1 (d / deactivate-01)) :degree (e / entire~e.6)) :op2 (i / involve-01~e.9 :ARG1 (h / hydrolyze-01~e.10 :ARG1~e.11 (s / small-molecule :name (n / name :op1 "GTP"~e.12)) :ARG3~e.13 (s2 / small-molecule :name (n2 / name :op1 "GDP"~e.14)) :ARG2-of (r / react-01~e.22 :ARG0 (e2 / enzyme :name (n3 / name :op1 "guanosine"~e.17 :op2 "triphosphatase"~e.18)) :ARG1-of (r2 / reverse-01 :ARG1-of (p2 / possible-01 :polarity -~e.27 :mod (b / basic~e.26))))) :ARG2 p)) # ::id bio-kappa_0001.24 ::amr-annotator SDL-AMR-09 ::preferred # ::tok It is also intrinsically very slow and thus has to be accelerated by GTPase - activating proteins ( GAPs ) . # ::alignments 0-1.1 2-1.4 3-1.3 4-1.2 5-1 7-1.5 8-1.5.1 9-1.5.1 11-1.5.1.1 12-1.5.1.1.1.r 13-1.5.1.1.1.1.1.1.1 15-1.5.1.1.1.1 16-1.5.1.1.1 (s / slow-05~e.5 :ARG1 (i / it~e.0) :degree (v / very~e.4) :mod (i2 / intrinsic~e.3) :mod (a4 / also~e.2) :ARG0-of (c / cause-01~e.7 :ARG1 (o2 / obligate-01~e.8,9 :ARG2 (a / accelerate-01~e.11 :ARG0~e.12 (p / protein~e.16 :ARG0-of (a3 / activate-01~e.15 :ARG1 (e / enzyme :name (n / name :op1 "GTPase"~e.13)))) :ARG1 i)))) # ::id bio-kappa_0001.25 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The mechanism of GEF action involves a series of fast reaction steps , which lead from a binary protein - nucleotide complex via a trimeric GNBP - nucleotide - GEF complex to a binary nucleotide - free complex , which is stable in the absence of nucleotide . # ::alignments 1-1.2 2-1.2.1.r 3-1.2.1.1.1.1 4-1.2.1 5-1 7-1.1 8-1.1.1.r 9-1.1.1.1 10-1.1.1.2 11-1.1.1 17-1.1.1.3.2.3 18-1.1.1.3.2.1 20-1.1.1.3.1.1.1 21-1.1.1.3.2 21-1.1.1.3.3 22-1.1.1.3.3.r 24-1.1.1.3.3.1 25-1.1.1.3.3.2.1.1 27-1.1.1.3.3.3 29-1.2.1.1.1.1 30-1.1.1.3.2 33-1.1.1.3.2.3 34-1.1.1.3.1.1.1 36-1.1.1.3.1.1 37-1.1.1.3.1 41-1.1.1.3.1.2 42-1.1.1.3.1.2.1.r 44-1.1.1.3.1.2.1 45-1.1.1.3.1.2.1.1.r 46-1.1.1.3.1.2.1.1 (i / involve-01~e.5 :ARG1 (s / series~e.7 :consist-of~e.8 (s2 / step~e.11 :ARG1-of (f / fast-02~e.9) :mod (r / react-01~e.10) :ARG0-of (t3 / turn-02 :ARG2 (c2 / complex~e.37 :ARG1-of (f2 / free-04~e.36 :ARG2 (n3 / nucleotide~e.20,34)) :ARG1-of (s3 / stable-03~e.41 :condition~e.42 (a2 / absent-01~e.44 :ARG1~e.45 n3~e.46))) :ARG3 (m2 / macro-molecular-complex~e.21,30 :part (p2 / protein~e.18) :part n3 :mod (b2 / binary~e.17,33)) :path~e.22 (m3 / macro-molecular-complex~e.21 :mod (t2 / trimeric~e.24) :part (p3 / protein :name (n2 / name :op1 "GNBP"~e.25)) :part n3~e.27 :part p)))) :ARG2 (m / mechanism~e.1 :mod~e.2 (a / act-02~e.4 :ARG0 (p / protein :name (n / name :op1 "GEF"~e.3,29))))) # ::id bio-kappa_0001.26 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This series of reactions is reversed by rebinding of nucleotide , predominantly GTP , because of its higher concentration in the cell . # ::alignments 0-1.2.1 1-1.2 2-1.2.2.r 3-1.2.2 5-1 9-1.1.1 11-1.1.1.1.2 12-1.1.1.1.1.1.1 14-1.1.1.1.2.1 15-1.1.1.1.2.1.1.r 16-1.1.1.1.2.1.1.1 16-1.1.1.1.2.1.1.1.r 17-1.1.1.1.2.1.1.2 17-1.1.1.1.2.1.1.2.1 17-1.1.1.1.2.1.1.2.1.r 18-1.1.1.1.2.1.1 19-1.1.1.1.2.1.1.3.r 21-1.1.1.1.2.1.1.3 (r / reverse-01~e.5 :ARG0 (b / bind-01 :ARG1 (n / nucleotide~e.9 :ARG1-of (m2 / mean-01 :ARG2 (s2 / small-molecule :name (n2 / name :op1 "GTP"~e.12)) :mod (p / predominant~e.11 :ARG1-of (c / cause-01~e.14 :ARG0~e.15 (c2 / concentrate-02~e.18 :ARG1~e.16 s2~e.16 :ARG1-of (h / high-02~e.17 :degree~e.17 (m / more~e.17)) :location~e.19 (c3 / cell~e.21)))))) :mod (a / again)) :ARG1 (s / series~e.1 :mod (t / this~e.0) :consist-of~e.2 (r2 / react-01~e.3))) # ::id bio-kappa_0001.27 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In principle , these reactions are fast and fully reversible , so that the GEF merely acts as a catalyst to increase the rate at which equilibrium between the GDP @- and GTP - bound forms of the protein is reached . # ::alignments 0-1.3 1-1.3 3-1.1.1.1 4-1.1.1 6-1.1 7-1 8-1.2.1.2 11-1.4 12-1.4.1.4.r 14-1.4.1.1.1.1 15-1.4.1.3 16-1.4.1 21-1.4.1.4 23-1.4.1.4.2 29-1.4.1.4.2.1.1.1.1.1.1.1.1 31-1.4.1.4.2.1.1.1 32-1.4.1.4.2.1.1.1.2.1.1.1.1 34-1.4.1.4.2.1.1.1.1.1 34-1.4.1.4.2.1.1.1.2.1 38-1.4.1.4.2.1.1.1.1 38-1.4.1.4.2.1.1.1.2 40-1.4.1.4.2.1 (a / and~e.7 :op1 (f / fast-02~e.6 :ARG1 (r / react-01~e.4 :mod (t / this~e.3))) :op2 (p / possible-01 :ARG1 (r2 / reverse-01 :ARG1 r :degree (f2 / full~e.8))) :mod (i2 / in-principle~e.0,1) :ARG0-of (c / cause-01~e.11 :ARG1 (a2 / act-01~e.16 :ARG0 (p3 / protein :name (n / name :op1 "GEF"~e.14)) :ARG1 (c2 / catalyze-01) :degree (m / mere~e.15) :purpose~e.12 (i / increase-01~e.21 :ARG0 p3 :ARG1 (r3 / rate~e.23 :degree-of (r4 / reach-01~e.40 :ARG1 (e / equilibrate-01 :ARG1 (a4 / and~e.31 :op1 (p2 / protein~e.38 :ARG1-of (b / bind-01~e.34 :ARG2 (s / small-molecule :name (n2 / name :op1 "GDP"~e.29)))) :op2 (p5 / protein~e.38 :ARG1-of (b2 / bind-01~e.34 :ARG2 (s2 / small-molecule :name (n3 / name :op1 "GTP"~e.32)))))))))))) # ::id bio.bel_0002.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Protein kinase A @-@ dependent phosphorylation of serine 43 within the regulatory domain of Raf @-@ 1 reciprocally potentiates its interaction with Rheb and decreases its interaction with H @-@ Ras . # ::alignments 0-1.1.2.2.1.1.1 1-1.1.2.2.1.1.2 2-1.1.2.2.1.1.3 4-1.1.2.2 5-1.1.2 6-1.1.2.1.r 7-1.1.2.1.2.1 8-1.1.2.1.1 11-1.1.2.1.3.1 12-1.1.2.1.3 13-1.1.2.1.3.2.r 14-1.1.2.1.3.2.1.1 16-1.1.2.1.3.2.1.1 17-1.1.3 18-1.1 19-1.1.1.1 19-1.1.1.1.r 20-1.1.1 21-1.1.1.2.r 22-1.1.1.2.1.1 23-1 24-1.2 26-1.2.2 27-1.2.2.2.r 28-1.2.2.2.1.1 30-1.2.2.2.1.1 (a / and~e.23 :op1 (p / potentiate-01~e.18 :ARG1 (i / interact-01~e.20 :ARG0~e.19 e2~e.19 :ARG1~e.21 (p2 / protein :name (n / name :op1 "Rheb"~e.22))) :ARG2 (p3 / phosphorylate-01~e.5 :ARG1~e.6 (a2 / amino-acid :mod 43~e.8 :name (n5 / name :op1 "serine"~e.7) :part-of (d2 / domain~e.12 :mod (r / regulate-01~e.11) :part-of~e.13 (e2 / enzyme :name (n3 / name :op1 "Raf-1"~e.14,16)))) :ARG0-of (d3 / depend-01~e.4 :ARG1 (e3 / enzyme :name (n4 / name :op1 "protein"~e.0 :op2 "kinase"~e.1 :op3 "A"~e.2)))) :mod (r2 / reciprocal~e.17)) :op2 (d / decrease-01~e.24 :ARG0 p3 :ARG1 (i2 / interact-01~e.26 :ARG0 e2 :ARG1~e.27 (e / enzyme :name (n2 / name :op1 "H-Ras"~e.28,30))))) # ::id bio.bel_0002.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We show that wild @-@ type B @-@ RAF forms a complex with C @-@ RAF in a RAS @-@ dependent manner , whereas the mutants bind independently of RAS . # ::alignments 0-1.1 1-1 2-1.2.r 3-1.2.1.1.2 5-1.2.1.1.2 6-1.2.1.1.1.1 8-1.2.1.1.1.1 8-1.2.1.2.1.1 8-1.2.3.1.1.1.1 8-1.2.3.1.2.1.1 9-1.2 11-1.2.1 12-1.2.1.2.r 13-1.2.1.2.1.1 15-1.2.1.2.1.1 18-1.2.2.1.1.1 20-1.2.2 20-1.2.3.1.3 23-1.2.3 25-1.2.3.1.1 25-1.2.3.1.1.2 25-1.2.3.1.1.2.r 25-1.2.3.1.2 25-1.2.3.1.2.2 25-1.2.3.1.2.2.r 26-1.2.3.1 27-1.2.3.1.3.1 28-1.2.3.1.3.2.r 29-1.2.3.1.3.2 (s / show-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (f / form-01~e.9 :ARG1 (m / macro-molecular-complex~e.11 :part (e4 / enzyme :name (n / name :op1 "B-RAF"~e.6,8) :mod (w2 / wild-type~e.3,5)) :part~e.12 (e / enzyme :name (n2 / name :op1 "C-RAF"~e.8,13,15))) :ARG0-of (d / depend-01~e.20 :ARG1 (e3 / enzyme :name (n3 / name :op1 "RAS"~e.18))) :ARG1-of (c / contrast-01~e.23 :ARG2 (b / bind-01~e.26 :ARG1 (e5 / enzyme~e.25 :name (n4 / name :op1 "B-RAF"~e.8) :ARG2-of~e.25 (m2 / mutate-01~e.25)) :ARG2 (e2 / enzyme~e.25 :name (n5 / name :op1 "C-RAF"~e.8) :ARG2-of~e.25 (m3 / mutate-01~e.25)) :ARG0-of (d2 / depend-01~e.20 :polarity -~e.27 :ARG1~e.28 e3~e.29))))) # ::id bio.bel_0002.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Importantly , we show that wild @-@ type B @-@ RAF can also activate C @-@ RAF . # ::alignments 0-1.3 2-1.1 3-1 4-1.2.r 5-1.2.1.1.2 7-1.2.1.1.2 8-1.2.1.1.1.1 10-1.2.1.1.1.1 10-1.2.1.2.1.1 11-1.2 12-1.2.1.3 13-1.2.1 14-1.2.1.2.1.1 16-1.2.1.1.1.1 16-1.2.1.2.1.1 (s / show-01~e.3 :ARG0 (w / we~e.2) :ARG1~e.4 (p / possible-01~e.11 :ARG1 (a / activate-01~e.13 :ARG0 (e2 / enzyme :name (n / name :op1 "B-RAF"~e.8,10,16) :mod (w2 / wild-type~e.5,7)) :ARG1 (e / enzyme :name (n2 / name :op1 "C-RAF"~e.10,14,16)) :mod (a2 / also~e.12))) :mod (i / important~e.0)) # ::id bio.bel_0002.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The homologous site on B @-@ Raf , S445 , is constitutively phosphorylated , accounting for the higher basal activity of B @-@ Raf . # ::alignments 4-1.1.3.1.1 6-1.1.3.1.1 11-1.2 12-1 14-1.3 15-1.3.1.r 17-1.3.1.3 17-1.3.1.3.1 17-1.3.1.3.1.r 18-1.3.1.2 19-1.3.1 20-1.3.1.1.r 21-1.3.1.1 22-1.3.1.1 23-1.3.1.1 (p / phosphorylate-01~e.12 :ARG1 (a3 / amino-acid :mod 445 :name (n3 / name :op1 "serine") :part-of (e / enzyme :name (n4 / name :op1 "B-Raf"~e.4,6)) :mod (h2 / homologue)) :mod (c / constitutive~e.11) :ARG0-of (a / account-01~e.14 :ARG1~e.15 (a2 / activity-06~e.19 :ARG0~e.20 e~e.21,22,23 :mod (b / basal~e.18) :ARG1-of (h / high-02~e.17 :degree~e.17 (m / more~e.17))))) # ::id bio.bel_0002.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In addition , introduction of B @-@ Raf enhances and sustains integrin @-@ mediated activation of ERK in wild @-@ type primary fibroblasts # ::alignments 0-1 0-1.1 0-1.1.r 1-1 1-1.1 1-1.1.r 3-1.1.1.1 4-1.1.1.1.1.r 5-1.1.1.1.1.1.1 7-1.1.1.1.1.1.1 8-1.1.1 9-1.1 10-1.1.2 11-1.1.1.2.3.1 13-1.1.1.2.3 14-1.1.1.2 15-1.1.1.2.1.r 16-1.1.1.2.1.1.1 17-1.1.1.2.2.r 18-1.1.1.2.2.1 20-1.1.1.2.2.1 21-1.1.1.2.2.2 22-1.1.1.2.2 (a4 / and~e.0,1 :op2~e.0,1 (a / and~e.0,1,9 :op1 (e / enhance-01~e.8 :ARG0 (i / introduce-02~e.3 :ARG1~e.4 (e2 / enzyme :name (n / name :op1 "B-Raf"~e.5,7))) :ARG1 (a2 / activate-01~e.14 :ARG1~e.15 (e3 / enzyme :name (n2 / name :op1 "ERK"~e.16)) :location~e.17 (f / fibroblast~e.22 :mod (w / wild-type~e.18,20) :mod (p / primary~e.21)) :ARG1-of (m / mediate-01~e.13 :ARG0 (i2 / integrin~e.11)))) :op2 (s / sustain-01~e.10 :ARG0 i :ARG1 a2))) # ::id bio.bel_0002.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok siRNA @-@ mediated depletion of B @-@ Raf reduced cell proliferation by up to 65 % through the inhibition of ERK1 @/@ 2 activation , irrespective of the mutational status of B @-@ Raf . # ::alignments 0-1.1.2.1.1.1 2-1.1.2 3-1.1 4-1.1.1.r 5-1.1.1.1.1 7-1.1.1.1.1 8-1 9-1.2.1 10-1.2 11-1.3.r 12-1.3 13-1.3 14-1.3.1.1 15-1.3.1 18-1.4 19-1.4.1.r 20-1.4.1.1.1.1 22-1.4.1.1.1.1 23-1.4.1 25-1.5 28-1.5.1.2 29-1.5.1 30-1.5.1.1.r 31-1.5.1.1 32-1.5.1.1 33-1.5.1.1 (r / reduce-01~e.8 :ARG0 (d / deplete-01~e.3 :ARG1~e.4 (e / enzyme :name (n2 / name :op1 "B-Raf"~e.5,7)) :ARG1-of (m / mediate-01~e.2 :ARG0 (n4 / nucleic-acid :name (n / name :op1 "siRNA"~e.0)))) :ARG1 (p2 / proliferate-01~e.10 :ARG0 (c / cell~e.9)) :ARG2~e.11 (u / up-to~e.12,13 :op1 (p / percentage-entity~e.15 :value 65~e.14)) :manner (i / inhibit-01~e.18 :ARG1~e.19 (a / activate-01~e.23 :ARG1 (e2 / enzyme :name (n3 / name :op1 "ERK1/2"~e.20,22)))) :ARG1-of (r2 / regardless-91~e.25 :ARG2 (s / status~e.29 :poss~e.30 e~e.31,32,33 :mod (m2 / mutate-01~e.28)))) # ::id bio.bel_0002.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Following expression of BRAFV600E in melanocytes , the majority of cells became senescent ( Figure 1D and data not shown ) , consistent with previous studies ( Michaloglou et al. , 2005 ) # ::alignments 0-1.3 1-1.3.1 4-1.3.1.2.r 5-1.3.1.2 8-1.1.1 9-1.1.1.r 10-1.1 11-1 12-1.2 14-1.4.1.1 15-1.4.1.1.1 16-1.4.1 17-1.4.1.2 18-1.4.1.2.1.1 18-1.4.1.2.1.1.r 19-1.4.1.2.1 22-1.5 23-1.5.1.r 24-1.5.1.1 25-1.5.1 27-1.5.1.2.1.1.1.1.1 28-1.5.1.2.1.1 29-1.5.1.2.1.1.2.1 31-1.5.1.2.1.2.1 (b / become-01~e.11 :ARG1 (c / cell~e.10 :quant~e.9 (m / majority~e.8)) :ARG2 (s / senescent~e.12 :domain c) :ARG1-of (f / follow-01~e.0 :ARG2 (e / express-03~e.1 :ARG2 (e2 / enzyme :name (n / name :op1 "B-Raf") :ARG2-of (m2 / mutate-01 :value "V600E")) :ARG3~e.4 (m3 / melanocyte~e.5))) :ARG1-of (d2 / describe-01 :ARG0 (a / and~e.16 :op1 (f2 / figure~e.14 :mod "1D"~e.15) :op2 (d3 / data~e.17 :ARG1-of (s2 / show-01~e.19 :polarity~e.18 -~e.18)))) :ARG1-of (c3 / consistent-01~e.22 :ARG2~e.23 (s3 / study~e.25 :time (p / previous~e.24) :ARG1-of (d4 / describe-01 :ARG0 (p2 / publication-91 :ARG0 (a2 / and~e.28 :op1 (p3 / person :name (n2 / name :op1 "Michaloglou"~e.27)) :op2 (p4 / person :mod (o / other~e.29))) :time (d / date-entity :year 2005~e.31)))))) # ::id bio.bel_0002.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok disruption of the KSR1 @/@ CK2 interaction or inhibition of CK2 activity significantly reduces the growth @-@ factor @-@ induced phosphorylation of C @-@ Raf and B @-@ Raf on the activating serine site in the negative @-@ charge regulatory region ( N @-@ region ) . # ::alignments 0-1.1.1 1-1.1.1.1.r 3-1.1.1.1.1.1.1 5-1.1.1.1.2.1.1 6-1.1.1.1 7-1.1 8-1.1.2 9-1.1.2.1.r 10-1.1.2.1.1 11-1.1.2.1 12-1.3 13-1 15-1.2.2.1 17-1.2.2.1 19-1.2.2 20-1.2 21-1.2.1.r 22-1.2.1.3.3.1.1.1 24-1.2.1.3.3.1.1.1 24-1.2.1.3.3.2.1.1 25-1.2.1.3.3 26-1.2.1.3.3.2.1.1 28-1.2.1.3.3.1.1.1 28-1.2.1.3.3.2.1.1 31-1.2.1.1 32-1.2.1.2.1.1 33-1.2.1 36-1.2.1.3.2.1 38-1.2.1.3.2 39-1.2.1.3.1 40-1.2.1.3 44-1.2.1.3 (r / reduce-01~e.13 :ARG0 (o / or~e.7 :op1 (d / disrupt-01~e.0 :ARG1~e.1 (i / interact-01~e.6 :ARG0 (e3 / enzyme :name (n4 / name :op1 "KSR1"~e.3)) :ARG1 (e4 / enzyme :name (n5 / name :op1 "CK2"~e.5)))) :op2 (i2 / inhibit-01~e.8 :ARG1~e.9 (a3 / activity-06~e.11 :ARG0 e4~e.10))) :ARG1 (p / phosphorylate-01~e.20 :ARG1~e.21 (p2 / protein-segment~e.33 :ARG0-of (a2 / activate-01~e.31) :mod (a4 / amino-acid :name (n7 / name :op1 "serine"~e.32)) :part-of (r2 / region~e.40,44 :ARG0-of (r3 / regulate-01~e.39) :ARG1-of (c / charge-03~e.38 :ARG2-of (n3 / negative-06~e.36)) :part-of (a / and~e.25 :op1 (e / enzyme :name (n / name :op1 "C-Raf"~e.22,24,28)) :op2 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.24,26,28))))) :ARG2-of (i3 / induce-01~e.19 :ARG0 (g / growth-factor~e.15,17))) :ARG2 (s / significant-02~e.12)) # ::id bio.bel_0002.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Sorafenib is a potent TKI of VEGFR @-@ 2 , VEGFR @-@ 3 , B @-@ RAF , and PDGFR @-@ B # ::alignments 0-1.1.1.1 3-1.3 6-1.2.1.1.1 6-1.2.2.1.1 8-1.2.1.1.1 10-1.2.1.1.1 10-1.2.2.1.1 12-1.2.2.1.1 14-1.2.3.1.1 14-1.2.4.1.1 16-1.2.3.1.1 18-1.2 19-1.2.4.1.1 21-1.2.3.1.1 21-1.2.4.1.1 (i / inhibit-01 :ARG0 (s2 / small-molecule :name (n2 / name :op1 "Sorafenib"~e.0)) :ARG1 (a / and~e.18 :op1 (k / kinase :name (n / name :op1 "VEGFR-2"~e.6,8,10)) :op2 (k2 / kinase :name (n3 / name :op1 "VEGFR-3"~e.6,10,12)) :op3 (k3 / kinase :name (n4 / name :op1 "B-RAF"~e.14,16,21)) :op4 (k4 / kinase :name (n5 / name :op1 "PDGFR-B"~e.14,19,21))) :mod (p / potent~e.3)) # ::id bio.bel_0002.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In addition , we found that Rheb inhibits the association of B @-@ Raf with H @-@ Ras . # ::alignments 0-1 1-1 3-1.1.1 4-1.1 5-1.1.2.r 6-1.1.2.1.1.1 7-1.1.2 9-1.1.2.2 10-1.1.2.2.1.r 11-1.1.2.2.1.1.1 13-1.1.2.2.1.1.1 14-1.1.2.2.2.r 15-1.1.2.2.2.1.1 17-1.1.2.2.2.1.1 (a3 / and~e.0,1 :op2 (f / find-01~e.4 :ARG0 (w / we~e.3) :ARG1~e.5 (i / inhibit-01~e.7 :ARG0 (p / protein :name (n / name :op1 "Rheb"~e.6)) :ARG1 (a2 / associate-01~e.9 :ARG1~e.10 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.11,13)) :ARG2~e.14 (e3 / enzyme :name (n3 / name :op1 "H-Ras"~e.15,17)))))) # ::id bio.bel_0002.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok hKSR @-@ 2 selectively inhibited the Cot @-@ mediated activation of MEK by 60 % . # ::alignments 0-1.1.1.1 2-1.1.1.1 3-1.3 3-1.3.r 4-1 6-1.2.2.1.1.1 8-1.2.2 9-1.2 10-1.2.1.r 11-1.2.1.1.1 12-1.4.r 13-1.4.1 14-1.4 (i / inhibit-01~e.4 :ARG0 (e / enzyme :name (n / name :op1 "hKSR-2"~e.0,2)) :ARG1 (a / activate-01~e.9 :ARG1~e.10 (e2 / enzyme :name (n2 / name :op1 "MEK"~e.11)) :ARG1-of (m / mediate-01~e.8 :ARG0 (e3 / enzyme :name (n3 / name :op1 "Cot"~e.6)))) :manner~e.3 (s / selective~e.3) :quant~e.12 (p / percentage-entity~e.14 :value 60~e.13)) # ::id bio.bel_0002.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , hKSR @-@ 2 up @-@ regulated the Rafmediated MEK activation by up to 70 % . # ::alignments 1-1 3-1.1.2.1.1 5-1.1.2.1.1 6-1.1.3 11-1.1.1.1.1.1 12-1.1.1 14-1.1.3 15-1.1.3 15-1.1.3.1.r 16-1.1.3.1.1 17-1.1.3.1 (c / contrast-01~e.1 :ARG2 (u / upregulate-01 :ARG1 (a / activate-01~e.12 :ARG1 (e / enzyme :name (n / name :op1 "MEK"~e.11)) :ARG1-of (m / mediate-01 :ARG0 (e2 / enzyme :name (n2 / name :op1 "Raf")))) :ARG2 (e3 / enzyme :name (n3 / name :op1 "hKSR-2"~e.3,5)) :quant (u2 / up-to~e.6,14,15 :op1~e.15 (p / percentage-entity~e.17 :value 70~e.16)))) # ::id bio.bel_0002.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok GSK PI3K Phase 2 , part 1 : List of non @-@ position specific phosphorylation effects on parent protein 's activity , derived from existing causal assertions of position @-@ specific phosphorylations on the parent protein activity . # ::alignments 0-1.1.1.1 1-1.2.1.1 2-1.3 3-1.3.1 5-1.3.2 5-1.3.2.r 6-1.3.2.1 8-1.3.2.2 9-1.3.2.2.1.r 10-1.3.2.2.1.1.1.1 10-1.3.2.2.1.1.1.1.r 12-1.3.2.2.1.1.1.2 13-1.3.2.2.1.1.1 14-1.3.2.2.1.1 14-1.3.2.2.2.1.1 15-1.3.2.2.1 16-1.3.2.2.1.2.r 17-1.3.2.2.1.2.1.1 18-1.3.2.2.1.2.1 20-1.3.2.2.1.2 22-1.3.2.2.2 23-1.3.2.2.2.1.r 24-1.3.2.2.2.1.4 26-1.3.2.2.2.1 27-1.3.2.2.2.1.1.1.r 28-1.3.2.2.2.1.1.1 30-1.3.2.2.1.1.1 31-1.3.2.2.1.1 34-1.3.2.2.1.2.1.1 35-1.3.2.2.1.2.1 36-1.3.2.2.1.2 (a4 / and :op1 (e / enzyme :name (n / name :op1 "GSK"~e.0)) :op2 (e2 / enzyme :name (n2 / name :op1 "PI3K"~e.1)) :mod (p8 / phase~e.2 :mod 2~e.3 :part~e.5 (p9 / part~e.5 :mod 1~e.6 :topic (l / list-01~e.8 :ARG1~e.9 (a / affect-01~e.15 :ARG0 (p / phosphorylate-01~e.14,31 :ARG1-of (s / specific-02~e.13,30 :polarity~e.10 -~e.10 :ARG2 (p2 / position-01~e.12))) :ARG1~e.16 (a2 / activity-06~e.20,36 :ARG0 (p3 / protein~e.18,35 :mod (p4 / parent~e.17,34)))) :ARG1-of (d / derive-01~e.22 :ARG2~e.23 (a3 / assert-03~e.26 :ARG1 (p5 / phosphorylate-01~e.14 :mod~e.27 (p6 / position~e.28 :ARG1-of s)) :ARG0-of (c / cause-01) :topic a2 :ARG1-of (e3 / exist-01~e.24))))))) # ::id bio.bmtr_0001.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Sasaki et al. , “ Ubiquitination of Ras enhances activation and facilitates binding to select downstream effectors ” ( PMC3437993 ) # ::alignments 0-1.2.1.1.1 1-1.2 2-1.2.2.1 5-1.3.1.1 6-1.3.1.1.1.r 7-1.3.1.1.1.1.1 8-1.3.1 9-1.3.1.2 10-1.3 11-1.3.2 12-1.3.2.2 13-1.3.2.2.1.r 14-1.3.2.2.1.2 15-1.3.2.2.1.1 16-1.3.2.2.1 19-1.1 (p / publication-91 :ARG8 "PMC3437993"~e.19 :ARG0 (a / and~e.1 :op1 (p2 / person :name (n / name :op1 "Sasaki"~e.0)) :op2 (p3 / person :mod (o / other~e.2))) :ARG1 (a2 / and~e.10 :op1 (e / enhance-01~e.8 :ARG0 (u / ubiquitinate-01~e.5 :ARG1~e.6 (e3 / enzyme :name (n2 / name :op1 "Ras"~e.7))) :ARG1 (a3 / activate-01~e.9)) :op2 (f / facilitate-01~e.11 :ARG0 u :ARG1 (b / bind-01~e.12 :ARG2~e.13 (e2 / effector~e.16 :location (d / downstream~e.15) :mod (s2 / select~e.14)))))) # ::id bio.bmtr_0001.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We utilized an unbiased mass spectrometry @-@ based approach to identify ubiquitination sites of Ras . # ::alignments 0-1.1 1-1 3-1.2.2 3-1.2.2.1 3-1.2.2.1.r 4-1.2.1.1.1 5-1.2.1.1 7-1.2.1 8-1.2 10-1.3 11-1.3.2.2 12-1.3.2 13-1.3.2.1.r 14-1.3.2.1.1.1 (u / utilize-01~e.1 :ARG0 (w / we~e.0) :ARG1 (a / approach-02~e.8 :ARG1-of (b / base-02~e.7 :ARG2 (s / spectrometry~e.5 :mod (m / mass~e.4))) :ARG1-of (b2 / bias-01~e.3 :polarity~e.3 -~e.3)) :purpose (i / identify-01~e.10 :ARG0 w :ARG1 (p / protein-segment~e.12 :part-of~e.13 (e / enzyme :name (n / name :op1 "Ras"~e.14)) :ARG1-of (u2 / ubiquitinate-01~e.11)))) # ::id bio.bmtr_0001.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok His @-@ tagged ubiquitin and Flag @-@ tagged K @-@ Ras4B ( K @-@ Ras hereafter ) were expressed in HEK293T cells at levels similar to endogenous K @-@ Ras ( Fig . 1B ) and subjected to sequential affinity chromatography . # ::alignments 2-1.1.1.1.2 2-1.1.1.2.3 3-1.1.1.1.1.1 5-1.1.1.2.3.1.1.1 7-1.1.1.2.3 8-1.1.1.2.1.1 8-1.1.1.2.2.1 10-1.1.1.2.1.1 12-1.1.1.2.1.1 12-1.1.1.2.2.1 14-1.1.1.2.2.1 18-1.1 18-1.1.3.1.1.1 19-1.1.2.r 20-1.1.2.1.1 21-1.1.2 22-1.1.3.r 23-1.1.3 23-1.1.3.1.1 24-1.1.3.1 25-1.1.3.1.1.1.1.r 26-1.1.3.1.1.1.1.2 27-1.1.1.2.1.1 27-1.1.1.2.2.1 27-1.1.3.1.1.1.1.1.1 29-1.1.1.2.2.1 29-1.1.3.1.1.1.1.1.1 31-1.1.4.1 33-1.1.4.1.1 35-1 36-1.2 37-1.2.2.r 38-1.2.2.2 39-1.2.2.1 40-1.2.2 (a3 / and~e.35 :op1 (e / express-03~e.18 :ARG2 (a / and :op1 (p / protein :name (n2 / name :op1 "ubiquitin"~e.3) :ARG1-of (t / tag-01~e.2 :ARG2 (p3 / protein-segment :part (a2 / amino-acid :name (n5 / name :op1 "histidine"))))) :op2 (e5 / enzyme :name (n3 / name :op1 "K-Ras4B"~e.8,10,12,27) :name (n4 / name :op1 "K-Ras"~e.8,12,14,27,29) :ARG1-of (t2 / tag-01~e.2,7 :ARG2 (p4 / protein-segment :name (n6 / name :op1 "Flag"~e.5))))) :ARG3~e.19 (c / cell-line~e.21 :name (n / name :op1 "HEK293T"~e.20)) :degree~e.22 (l / level~e.23 :ARG1-of (r / resemble-01~e.24 :ARG2 (l2 / level~e.23 :degree-of (e3 / express-03~e.18 :ARG2~e.25 (e4 / enzyme :name (n7 / name :op1 "K-Ras"~e.27,29) :mod (e2 / endogenous~e.26)) :ARG3 c)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.31 :mod "1B"~e.33))) :op2 (s2 / subject-01~e.36 :ARG1 a :ARG2~e.37 (c2 / chromatography~e.40 :mod (a4 / affinity~e.39) :mod (s3 / sequence~e.38)))) # ::id bio.bmtr_0001.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok His @-@ ubiquitinated proteins were purified by Co2+ metal affinity chromatography in 8M urea denaturing conditions . # ::alignments 2-1.1.1 3-1.1 5-1 9-1.2.1 10-1.2 13-1.2.2.2.1.1 14-1.2.2 15-1.2.2.r (p / purify-01~e.5 :ARG1 (p2 / protein~e.3 :ARG3-of (u / ubiquitinate-01~e.2 :mod (a / amino-acid :name (n / name :op1 "histidine")))) :manner (c / chromatography~e.10 :mod (a2 / affinity~e.9 :topic (c3 / copper :ARG1-of (i / ionize-01 :value "2+"))) :condition~e.15 (d / denature-01~e.14 :ARG1 p2 :ARG4 (s / small-molecule :name (n3 / name :op1 "urea"~e.13) :mod (c2 / concentration-quantity :quant 8 :unit (m2 / molar)))))) # ::id bio.bmtr_0001.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok His @-@ ubiquitinated K @-@ Ras was subsequently purified with anti @-@ Flag resin . # ::alignments 2-1.1.2 3-1.1.1.1 5-1.1.1.1 7-1.2 7-1.2.r 8-1 9-1.3.r 10-1.3.1 12-1.3.1.1.1.1 13-1.3 (p / purify-01~e.8 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.3,5) :ARG3-of (u / ubiquitinate-01~e.2 :mod (a / amino-acid :name (n2 / name :op1 "histidine")))) :time~e.7 (s / subsequent~e.7) :instrument~e.9 (r / resin~e.13 :ARG0-of (c / counter-01~e.10 :ARG1 (p2 / protein-segment :name (n3 / name :op1 "Flag"~e.12))))) # ::id bio.bmtr_0001.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Following purification , mono @- and di @- ubiquitinated K @-@ Ras appeared to be the major ubiquitination forms , which is consistent with the endogenous K @-@ Ras ubiquitination pattern ( Fig . 1 , A and B ) . # ::alignments 0-1.3 1-1.3.1 3-1.1.3.1.1 3-1.1.3.1.1.r 5-1.1.3 6-1.1.3.2.1 6-1.1.3.2.1.r 8-1.1.3.1 8-1.1.3.2 9-1.1.3.1.2.1.1 11-1.1.3.1.2.1.1 12-1 14-1.1.3.r 16-1.1.2 17-1.1.1 18-1.1 21-1.1.3.r 22-1.1.4 23-1.1.4.1.r 25-1.1.4.1.1.1.2 26-1.1.4.1.1.1.1.1 28-1.1.4.1.1.1.1.1 29-1.1.4.1.1 30-1.1.4.1 32-1.2.1.1 32-1.2.1.2 34-1.1.3.1.1 37-1.2.1 (a / appear-02~e.12 :ARG1 (f4 / form~e.18 :mod (u3 / ubiquitinate-01~e.17) :mod (m2 / major~e.16) :domain~e.14,21 (a3 / and~e.5 :op1 (u4 / ubiquitinate-01~e.8 :quant~e.3 1~e.3,34 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.9,11))) :op2 (u5 / ubiquitinate-01~e.8 :quant~e.6 2~e.6 :ARG1 e)) :ARG1-of (c / consistent-01~e.22 :ARG2~e.23 (p2 / pattern~e.30 :topic (u2 / ubiquitinate-01~e.29 :ARG1 (e2 / enzyme :name (n2 / name :op1 "K-Ras"~e.26,28) :mod (e3 / endogenous~e.25)))))) :ARG1-of (d / describe-01 :ARG0 (a2 / and~e.37 :op1 (f2 / figure~e.32 :mod "1A") :op2 (f3 / figure~e.32 :mod "1B"))) :ARG1-of (f / follow-01~e.0 :ARG2 (p / purify-01~e.1 :ARG1 e))) # ::id bio.bmtr_0001.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok H @-@ Ras ubiquitination sites were also determined by the same approach . # ::alignments 0-1.1.2.1.1 2-1.1.2.1.1 3-1.1.1 4-1.1 6-1.3 7-1 8-1.2.r 10-1.2.1 11-1.2 (d / determine-01~e.7 :ARG1 (p / protein-segment~e.4 :ARG1-of (u / ubiquitinate-01~e.3) :part-of (e / enzyme :name (n / name :op1 "H-Ras"~e.0,2))) :manner~e.8 (a / approach-02~e.11 :ARG1-of (s / same-01~e.10)) :mod (a2 / also~e.6)) # ::id bio.bmtr_0001.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Tandem mass spectrometric analysis of tryptic fragments from the bands migrating at the positions expected for mono @- and di @-@ ubiquitinated Ras revealed ubiquitination at Lys residues 104 and 147 of K @-@ Ras , and Lys residues 117 , 147 and 170 for H @-@ Ras ( fig . S1C ) . # ::alignments 0-1.1.2.2 1-1.1.2.1 2-1.1.2 3-1.1 4-1.1.1.r 5-1.1.1.1.1.1.1 7-1.1.1.2.r 9-1.1.1.2 10-1.1.1.2.1 11-1.1.1.2.1.1.1 13-1.1.1.2.1.1 14-1.1.1.2.1.1.1.2 16-1.1.1.2.1.1.1.1.2.1.1 16-1.1.1.2.1.1.1.1.2.1.r 19-1.1.1.2.1.1.1.1.2.1.2 19-1.1.1.2.1.1.1.1.2.1.r 21-1.1.1.2.1.1.1.1.2 21-1.2 22-1.1.1.2.1.1.1.1.1.1 23-1 24-1.1.1.2.1.1.1.1.2 24-1.2 25-1.1.1.2.1.1.1 25-1.2.1.r 26-1.2.1.1.1.1.2.1 26-1.2.1.1.2.1.2.1 26-1.2.1.2.1.1.2.1 26-1.2.1.2.2.1.2.1 27-1.2.1.1.1 27-1.2.1.1.2 27-1.2.1.2.1 27-1.2.1.2.2 28-1.2.1.1.1.1.1 29-1.2.1.1 30-1.2.1.1.2.1.1 32-1.2.1.1.3.1.1 34-1.2.1.1.3.1.1 36-1.2.1 36-1.2.1.1 36-1.2.1.1.r 36-1.2.1.2 37-1.2.1.1.2.1.2.1 37-1.2.1.2.1.1.2.1 37-1.2.1.2.2.1.2.1 37-1.2.1.2.3.1.2.1 38-1.2.1.1.2 38-1.2.1.2.1 38-1.2.1.2.2 38-1.2.1.2.3 39-1.2.1.2.1.1.1 41-1.2.1.2.2.1.1 43-1.2.1.2.3.1.1 44-1.2.1.2.r 45-1.2.1.2.4.1.1 47-1.2.1.2.4.1.1 51-1.3.1.1 (r / reveal-01~e.23 :ARG0 (a / analyze-01~e.3 :ARG1~e.4 (p3 / protein-segment :ARG3-of (h / hydrolyze-01 :ARG2 (e2 / enzyme :name (n2 / name :op1 "trypsin"~e.5))) :source~e.7 (b / band~e.9 :ARG0-of (m / migrate-01~e.10 :ARG2 (p / position~e.13 :ARG2-of (b2 / be-located-at-91~e.11,25 :ARG1 (e5 / enzyme :name (n / name :op1 "Ras"~e.22) :ARG3-of (u / ubiquitinate-01~e.21,24 :quant~e.16,19 (o / or :op1 1~e.16 :op2 2~e.19))) :ARG1-of (e / expect-01~e.14)))))) :manner (s / spectrometry~e.2 :mod (m2 / mass~e.1) :mod (t / tandem~e.0))) :ARG1 (u2 / ubiquitinate-01~e.21,24 :ARG1~e.25 (a2 / and~e.36 :op1~e.36 (a8 / and~e.29,36 :op1 (r2 / residue~e.27 :mod (a3 / amino-acid :mod 104~e.28 :name (n3 / name :op1 "lysine"~e.26))) :op2 (r3 / residue~e.27,38 :mod (a4 / amino-acid :mod 147~e.30 :name (n4 / name :op1 "lysine"~e.26,37))) :part-of (e4 / enzyme :name (n5 / name :op1 "K-Ras"~e.32,34))) :op2~e.44 (a9 / and~e.36 :op1 (r4 / residue~e.27,38 :mod (a5 / amino-acid :mod 117~e.39 :name (n6 / name :op1 "lysine"~e.26,37))) :op2 (r5 / residue~e.27,38 :mod (a6 / amino-acid :mod 147~e.41 :name (n7 / name :op1 "lysine"~e.26,37))) :op3 (r6 / residue~e.38 :mod (a7 / amino-acid :mod 170~e.43 :name (n8 / name :op1 "lysine"~e.37))) :part-of (e3 / enzyme :name (n9 / name :op1 "H-Ras"~e.45,47))))) :ARG1-of (d / describe-01 :ARG0 (f / figure :mod "S1C"~e.51))) # ::id bio.bmtr_0001.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The tryptic peptide with ubiquitination at Lys147 ( K147 ) was the most frequently observed peptide for both K @-@ Ras and H @-@ Ras , while Lys117 appeared as a secondary major ubiquitination site in H @-@ Ras . # ::alignments 1-1.1.3.2.1.1.1 2-1.1 2-1.1.3 4-1.1.3.1.3 10-1.1.3.r 12-1.1.1.1.1 13-1.1.1.1 14-1.1.1 15-1.1 15-1.1.3 18-1.1.2.1.1.1.1 20-1.1.2.1.1.1.1 20-1.1.2.1.2.1.1 22-1.1.2.1.2.1.1 24-1.1.2.1.1.1.1 24-1.1.2.1.2.1.1 26-1 28-1.2 29-1.2.1.r 31-1.2.1.3 32-1.2.1.2 33-1.2.1.1 34-1.2.1 36-1.1.2.1.2.1.1 38-1.1.2.1.1.1.1 38-1.1.2.1.2.1.1 (c / contrast-01~e.26 :ARG1 (p / peptide~e.2,15 :ARG1-of (o / observe-01~e.14 :ARG1-of (f / frequent-02~e.13 :degree (m / most~e.12))) :part-of (e2 / enzyme :mod (o2 / or :op1 (e3 / enzyme :name (n3 / name :op1 "K-Ras"~e.18,20,24,38)) :op2 (e4 / enzyme :name (n4 / name :op1 "H-Ras"~e.20,22,24,36,38)))) :domain~e.10 (p2 / peptide~e.2,15 :part (a / amino-acid :mod 147 :name (n / name :op1 "lysine") :ARG3-of (u / ubiquitinate-01~e.4)) :ARG3-of (h / hydrolyze-01 :ARG2 (e / enzyme :name (n2 / name :op1 "trypsin"~e.1))) :part-of e2)) :ARG2 (a3 / appear-01~e.28 :ARG1~e.29 (p3 / protein-segment~e.34 :ARG1-of (u2 / ubiquitinate-01~e.33) :ARG1-of (m2 / major-02~e.32) :mod (s / secondary~e.31) :domain (a2 / amino-acid :mod 117 :name (n6 / name :op1 "lysine")) :part-of e4))) # ::id bio.bmtr_0001.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To examine the effect of ubiquitination on GTP loading , we purified wild @-@ type K @-@ Ras , oncogenic G12V @-@ K @-@ Ras mutant or the ubiquitinated subfraction of wild @-@ type K @-@ Ras from 32P @-@ orthophosphate labeled cells and utilized thin layer chromatography ( TLC ) and high performance liquid chromatography ( HPLC ) to assess the ratio of 32P @-@ GTP to 32P @-@ GDP that co @-@ purified with each form of K @-@ Ras . # ::alignments 1-1.3 3-1.3.2 4-1.3.2.1.r 5-1.3.2.1 6-1.3.2.2.r 7-1.3.2.2.1.1.1 8-1.3.2.2 10-1.1.1 11-1.1 12-1.1.2.1.1.2 12-1.1.2.1.3.2 14-1.1.2.1.1.2 14-1.1.2.1.3.2 15-1.1.2.1.1.1.1 15-1.1.2.1.2.1.1 15-1.1.2.1.3.1.1 17-1.1.2.1.1.1.1 17-1.1.2.1.2.1.1 17-1.1.2.1.3.1.1 19-1.1.2.1.2 19-1.1.2.1.2.2 19-1.1.2.1.2.2.1.2.1 19-1.1.2.1.2.2.r 20-1.1.2.1.2.3.1 22-1.1.2.1.2.1.1 24-1.1.2.1.2.1.1 25-1.1.2.1.2.3 26-1.1.2.1 28-1.1.2.1.3.3 29-1.1.2.1.3.4 31-1.1.2.1.1.2 31-1.1.2.1.3.2 33-1.1.2.1.1.2 33-1.1.2.1.3.2 34-1.1.2.1.1.1.1 34-1.1.2.1.2.1.1 34-1.1.2.1.3.1.1 36-1.1.2.1.1.1.1 36-1.1.2.1.2.1.1 36-1.1.2.1.3.1.1 37-1.1.3.r 38-1.1.3.1.1.2 38-1.1.3.1.1.2.1.1 40-1.1.3.1.1.1.1 41-1.1.3.1 42-1.1.3 43-1 43-1.1.2 44-1.2 45-1.2.2.1.1.1 46-1.2.2.1.1 47-1.2.2.1 51-1.2.2 52-1.2.2.2.1.1.1 53-1.2.2.2.1.1 54-1.2.2.2.1 55-1.2.2.2 60-1.2.3 62-1.2.3.2 63-1.2.3.2 64-1.2.3.2.1.2 64-1.2.3.2.1.2.1.1 64-1.2.3.2.2.2 64-1.2.3.2.2.2.1.1 66-1.2.3.2.1.1.1 68-1.2.3.2.1.2 68-1.2.3.2.1.2.1.1 68-1.2.3.2.2.2 68-1.2.3.2.2.2.1.1 70-1.2.3.2.2.1.1 74-1.1 79-1.1.2.1.1.1.1 79-1.1.2.1.2.1.1 79-1.1.2.1.3.1.1 81-1.1.2.1.1.1.1 81-1.1.2.1.2.1.1 81-1.1.2.1.3.1.1 (a2 / and~e.43 :op1 (p / purify-01~e.11,74 :ARG0 (w / we~e.10) :ARG1 (a / and~e.43 :op1 (o / or~e.26 :op1 (e / enzyme :name (n2 / name :op1 "K-Ras"~e.15,17,34,36,79,81) :mod (w2 / wild-type~e.12,14,31,33)) :op2 (e2 / enzyme~e.19 :name (n3 / name :op1 "K-Ras"~e.15,17,22,24,34,36,79,81) :ARG0-of~e.19 (c / cause-01~e.19 :ARG1 (d / disease :wiki "Cancer" :name (n8 / name :op1 "cancer"~e.19))) :ARG2-of (m / mutate-01~e.25 :value "G12V"~e.20)) :op3 (e3 / enzyme :name (n4 / name :op1 "K-Ras"~e.15,17,34,36,79,81) :mod (w3 / wild-type~e.12,14,31,33) :ARG3-of (u / ubiquitinate-01~e.28) :mod (s2 / subfraction~e.29))) :op2 s4 :op3 s5) :source~e.37 (c3 / cell~e.42 :ARG1-of (l / label-01~e.41 :ARG2 (s3 / small-molecule :name (n5 / name :op1 "orthophosphate"~e.40) :part (p2 / phosphorus~e.38 :mod (m2 / molecular-mass :value 32~e.38)))))) :op2 (u2 / utilize-01~e.44 :ARG0 w :ARG1 (a5 / and~e.51 :op1 (c4 / chromatography~e.47 :mod (l3 / layer~e.46 :ARG1-of (t / thin-03~e.45))) :op2 (c5 / chromatography~e.55 :mod (l4 / liquid~e.54 :ARG0-of (p3 / perform-02~e.53 :ARG1-of (h / high-02~e.52))))) :purpose (a3 / assess-01~e.60 :ARG0 w :ARG1 (r / ratio-of~e.62,63 :op1 (s4 / small-molecule :name (n6 / name :op1 "GTP"~e.66) :part (p4 / phosphorus~e.64,68 :mod (m3 / molecular-mass :value 32~e.64,68))) :op2 (s5 / small-molecule :name (n7 / name :op1 "GDP"~e.70) :part (p5 / phosphorus~e.64,68 :mod (m4 / molecular-mass :value 32~e.64,68)))))) :purpose (e4 / examine-01~e.1 :ARG0 w :ARG1 (a4 / affect-01~e.3 :ARG0~e.4 (u3 / ubiquitinate-01~e.5) :ARG1~e.6 (l2 / load-01~e.8 :ARG2 (s / small-molecule :name (n / name :op1 "GTP"~e.7)))))) # ::id bio.bmtr_0001.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As expected based on previous studies , wild @-@ type K @-@ Ras bound primarily 32P @-@ GDP , while G12V @-@ Ras bound 32P @-@ GTP ( Fig.2 , A and B ) . # ::alignments 0-1.4.1.1.1.r 1-1.4 2-1.4.1 4-1.4.1.1.1 5-1.4.1.1 7-1.1.1.2 9-1.1.1.2 10-1.1.1.1.1 12-1.1.1.1.1 13-1.1 14-1.1.3 15-1.1.2.2 15-1.1.2.2.1.1 17-1.1.2.1.1 19-1 20-1.2.1.2.1 22-1.2.1.1.1 23-1.2 24-1.2.2.2 24-1.2.2.2.1.1 26-1.2.2.1.1 31-1.3.1 (c / contrast-01~e.19 :ARG1 (b / bind-01~e.13 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.10,12) :mod (w / wild-type~e.7,9)) :ARG2 (s / small-molecule :name (n2 / name :op1 "GDP"~e.17) :part (p / phosphorus~e.15 :mod (m / molecular-mass :value 32~e.15))) :mod (p2 / primary~e.14)) :ARG2 (b2 / bind-01~e.23 :ARG1 (e2 / enzyme :name (n3 / name :op1 "Ras"~e.22) :ARG2-of (m2 / mutate-01 :value "G12V"~e.20)) :ARG2 (s2 / small-molecule :name (n4 / name :op1 "GTP"~e.26) :part (p3 / phosphorus~e.24 :mod (m3 / molecular-mass :value 32~e.24)))) :ARG1-of (d / describe-01 :ARG0 (a / and~e.31 :op1 (f / figure :mod "2A") :op2 (f2 / figure :mod "2B"))) :ARG1-of (e3 / expect-01~e.1 :ARG1-of (b3 / base-02~e.2 :ARG2 (s4 / study~e.5 :time~e.0 (p4 / previous~e.4))))) # ::id bio.bmtr_0001.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Interestingly , the ubiquitinated subfraction of wild @-@ type K @-@ Ras retained a significant amount of 32P @-@ GTP . # ::alignments 0-1.3 3-1.1.3 4-1.1.4 6-1.1.2 8-1.1.2 9-1.1.1.1 11-1.1.1.1 12-1 14-1.2.3.1 15-1.2.3 16-1.2.3.r 17-1.2.2 17-1.2.2.1.1 19-1.2.1.1 (r / retain-01~e.12 :ARG0 (e / enzyme :name (n / name :op1 "K-Ras"~e.9,11) :mod (w / wild-type~e.6,8) :ARG3-of (u / ubiquitinate-01~e.3) :mod (s2 / subfraction~e.4)) :ARG1 (s / small-molecule :name (n2 / name :op1 "GTP"~e.19) :part (p / phosphorus~e.17 :mod (m / molecular-mass :value 32~e.17)) :quant~e.16 (a / amount~e.15 :ARG1-of (s3 / significant-02~e.14))) :ARG2-of (i / interest-01~e.0)) # ::id bio.bmtr_0001.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results are consistent with a model in which ubiquitination of Lys147 ( or Lys117 ) , destabilizes GDP binding , allowing spontaneous GDP @/@ GTP exchange . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 4-1.2.r 6-1.2 9-1.2.1.1 13-1.2.1.1.1 17-1.2.1 18-1.2.1.2.1.1.1 19-1.2.1.2 21-1.2.1.3 22-1.2.1.3.1.3 23-1.2.1.3.1.1 25-1.2.1.3.1.2.1.1 26-1.2.1.3.1 (c / consistent-01~e.3 :ARG1 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :mod (t2 / this~e.0)) :ARG2~e.4 (m / model~e.6 :topic (d / destabilize-01~e.17 :ARG0 (u / ubiquitinate-01~e.9 :ARG1 (o / or~e.13 :op1 (a / amino-acid :mod 147 :name (n2 / name :op1 "lysine")) :op2 (a3 / amino-acid :mod 117 :name (n5 / name :op1 "lysine")))) :ARG1 (b / bind-01~e.19 :ARG2 (s / small-molecule :name (n / name :op1 "GDP"~e.18))) :ARG0-of (a2 / allow-01~e.21 :ARG1 (e / exchange-01~e.26 :ARG1 s~e.23 :ARG3 (s4 / small-molecule :name (n4 / name :op1 "GTP"~e.25)) :mod (s2 / spontaneous~e.22)))))) # ::id bio.bmtr_0001.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok It could be argued that GTP loading occurs prior to ubiquitination and that the GTP bound form of K @-@ Ras , via interaction with effectors , is preferentially mono @-@ ubiquitinated via a feedback mechanism . # ::alignments 1-1 3-1.1 4-1.1.1.r 5-1.1.1.1.1.1.1 6-1.1.1.1 8-1.1.1.1.2 9-1.1.1.1.2.1.r 10-1.1.1.1.2.1 14-1.1.1.1.1.1.1 15-1.1.1.2.2 15-1.1.1.2.2.2 15-1.1.1.2.2.2.r 18-1.1.1.2.2.1.1 20-1.1.1.2.2.1.1 23-1.1.1.2.4 24-1.1.1.2.4.2.r 25-1.1.1.2.4.2 28-1.1.1.2.3 29-1.1.1.2.1 29-1.1.1.2.1.r 31-1.1.1.2 34-1.1.1.2.5 (p / possible-01~e.1 :ARG1 (a / argue-01~e.3 :ARG1~e.4 (a2 / and :op1 (l / load-01~e.6 :ARG2 (s / small-molecule :name (n / name :op1 "GTP"~e.5,14)) :time (p2 / prior~e.8 :op1~e.9 (u / ubiquitinate-01~e.10))) :op2 (u2 / ubiquitinate-01~e.31 :quant~e.29 1~e.29 :ARG1 (e / enzyme~e.15 :name (n2 / name :op1 "K-Ras"~e.18,20) :ARG1-of~e.15 (b / bind-01~e.15 :ARG2 s)) :ARG1-of (p3 / prefer-01~e.28) :manner (i / interact-01~e.23 :ARG0 e :ARG1~e.24 (e2 / effector~e.25)) :manner (f / feedback~e.34))))) # ::id bio.bmtr_0001.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok While it is difficult to eliminate this possibility , it is unlikely since , as shown in fig. S1B , the T35 mutant of K @-@ Ras , which fails to interact with downstream effectors ( fig . S1B ) undergoes comparable monobuiquitination to wild type Ras . # ::alignments 0-1 2-1.1.1.r 3-1.1 5-1.1.1 6-1.1.1.1 7-1.1.1.1.1 9-1.2.2 10-1.1.1.r 11-1.2 11-1.2.1 11-1.2.1.r 11-1.2.3.1.2.3.1 12-1.2.3 15-1.2.3.1.3 16-1.2.3.1.3.1.r 17-1.2.3.1.3.1 18-1.2.3.1.3.1.1 21-1.2.3.1.2.2.1 22-1.2.3.1.2 22-1.2.3.1.2.2 22-1.2.3.1.2.2.r 24-1.2.3.1.2.1.1 26-1.2.3.1.2.1.1 31-1.2.3.1.2.3 32-1.2.3.1.2.3.2.r 33-1.2.3.1.2.3.2.1 34-1.2.3.1.2.3.2 38-1.2.3.1.3.1.1 41-1.2.3.1.4 44-1.2.3.1.4.1.1.2 45-1.2.3.1.4.1.1.2 46-1.2.3.1.4.1.1.1.1 (c / contrast-01~e.0 :ARG1 (d / difficult~e.3 :domain~e.2,10 (e3 / eliminate-01~e.5 :ARG1 (t / this~e.6 :ARG1-of (p / possible-01~e.7)))) :ARG2 (l / likely-01~e.11 :polarity~e.11 -~e.11 :ARG1 t~e.9 :ARG1-of (c2 / cause-01~e.12 :ARG0 (u / ubiquitinate-01 :quant 1 :ARG1 (e / enzyme~e.22 :name (n / name :op1 "K-Ras"~e.24,26) :ARG2-of~e.22 (m / mutate-01~e.22 :value "T35"~e.21) :ARG0-of (i / interact-01~e.31 :polarity -~e.11 :ARG1~e.32 (e4 / effector~e.34 :location (d2 / downstream~e.33)) :ARG1-of (d3 / describe-01 :ARG0 f))) :ARG1-of (s / show-01~e.15 :ARG0~e.16 (f / figure~e.17 :mod "S1B"~e.18,38)) :ARG1-of (c3 / comparable-03~e.41 :ARG2 (u2 / ubiquitinate-01 :ARG1 (e2 / enzyme :name (n2 / name :op1 "Ras"~e.46) :mod (w / wild-type~e.44,45)))))))) # ::id bio.bmtr_0001.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results , along with the crystal structure , support a model in which mono @-@ ubiquitination at a Lys residue directly involved in GDP binding either enhances nucleotide exchange on K @-@ Ras , impairs GTP hydrolysis , or both . # ::alignments 0-1.1.1.1 1-1.1.1 1-1.1.1.2 1-1.1.1.2.r 6-1.1.2.1 7-1.1.2 9-1 11-1.2 14-1.2.1.1.1.1 14-1.2.1.1.1.1.r 16-1.2.1.1.1 17-1.2.1.1.1.2.r 19-1.2.1.1.1.2.1.1.1 20-1.2.1.1.1.2 21-1.2.1.1.1.2.2.2 22-1.2.1.1.1.2.2 23-1.2.1.1.1.2.2.1.r 24-1.2.1.1.1.2.2.1.1.1.1 25-1.2.1.1.1.2.2.1 27-1.2.1.1 28-1.2.1.1.2.1 29-1.2.1.1.2 30-1.2.1.1.2.2.r 31-1.2.1.1.2.2.1.1 33-1.2.1.1.2.2.1.1 35-1.2.1.2 36-1.2.1.2.2.1.1.1 37-1.2.1.2.2 39-1.2.1 (s3 / support-01~e.9 :ARG0 (a / and :op1 (t / thing~e.1 :mod (t2 / this~e.0) :ARG2-of~e.1 (r / result-01~e.1)) :op2 (s4 / structure~e.7 :poss (c / crystal~e.6))) :ARG1 (m / model~e.11 :topic (o / or~e.39 :op1 (e2 / enhance-01~e.27 :ARG0 (u / ubiquitinate-01~e.16 :quant~e.14 1~e.14 :ARG1~e.17 (r2 / residue~e.20 :mod (a2 / amino-acid :name (n4 / name :op1 "lysine"~e.19)) :ARG1-of (i / involve-01~e.22 :ARG2~e.23 (b / bind-01~e.25 :ARG2 (s / small-molecule :name (n / name :op1 "GDP"~e.24))) :ARG1-of (d / direct-02~e.21)))) :ARG1 (e3 / exchange-01~e.29 :ARG1 (n5 / nucleotide~e.28) :ARG4~e.30 (e / enzyme :name (n2 / name :op1 "K-Ras"~e.31,33)))) :op2 (i2 / impair-01~e.35 :ARG0 u :ARG1 (h / hydrolyze-01~e.37 :ARG1 (s2 / small-molecule :name (n3 / name :op1 "GTP"~e.36)))) :op3 (a3 / and :op1 e2 :op2 i2)))) # ::id bio.bmtr_0001.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To corroborate this finding , we measure the activity of Ras by the GST @-@ RBD pull @-@ down assay . # ::alignments 1-1.4 2-1.4.2.2 3-1.4.2 3-1.4.2.1 3-1.4.2.1.r 5-1.1 6-1 8-1.2 9-1.2.1.r 10-1.2.1.1.1 11-1.3.r 13-1.3.1.1.1.1 15-1.3.1.1.1.1 16-1.3.1 18-1.3.1 19-1.3 (m / measure-01~e.6 :ARG0 (w / we~e.5) :ARG1 (a / activity-06~e.8 :ARG0~e.9 (e / enzyme :name (n / name :op1 "Ras"~e.10))) :ARG2~e.11 (a2 / assay-01~e.19 :ARG1 (p / pull-down-08~e.16,18 :ARG1 (p2 / protein :name (n2 / name :op1 "GST-RBD"~e.13,15)))) :purpose (c / corroborate-01~e.1 :ARG0 m :ARG1 (t / thing~e.3 :ARG1-of~e.3 (f / find-01~e.3) :mod (t2 / this~e.2)))) # ::id bio.bmtr_0001.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To ensure that ubiquitinated Ras was being detected , the protein pulled down by GST @-@ RBD was subjected to a second affinity purification on a cobalt column to purify the Flag @-@ His @-@ tagged K @-@ Ras . # ::alignments 1-1.3 2-1.3.2.r 3-1.3.2.1.2 4-1.3.2.1.1.1 7-1.3.2 10-1.1 10-1.2.5.2.2.1.2 11-1.1.1 12-1.1.1 13-1.1.1.1.r 14-1.1.1.1.1.1 16-1.1.1.1.1.1 18-1 21-1.2.2 21-1.2.2.1 21-1.2.2.1.r 22-1.2.3 23-1.2 23-1.2.5 23-1.2.5.r 26-1.2.4.1 27-1.2.4 29-1.2 29-1.2.5 29-1.2.5.r 31-1.2.5.2.2.1.1.1.1 35-1.2.5.2.2 36-1.2.5.2.1.1 38-1.2.5.2.1.1 (s / subject-01~e.18 :ARG1 (p / protein~e.10 :ARG1-of (p2 / pull-down-08~e.11,12 :ARG3~e.13 (p3 / protein :name (n3 / name :op1 "GST-RBD"~e.14,16)))) :ARG2 (p4 / purify-01~e.23,29 :ARG1 p :ord (o / ordinal-entity~e.21 :value~e.21 2~e.21) :mod (a / affinity~e.22) :location (c / column~e.27 :consist-of (c2 / cobalt~e.26)) :purpose~e.23,29 (p5 / purify-01~e.23,29 :ARG0 p4 :ARG1 (e2 / enzyme :name (n2 / name :op1 "K-Ras"~e.36,38) :ARG1-of (t / tag-01~e.35 :ARG2 (a2 / and :op1 (p6 / protein-segment :name (n4 / name :op1 "Flag"~e.31)) :op2 (p7 / protein-segment~e.10 :part (a3 / amino-acid :name (n5 / name :op1 "histidine")))))))) :purpose (e3 / ensure-01~e.1 :ARG0 s :ARG1~e.2 (d / detect-01~e.7 :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.4) :ARG3-of (u / ubiquitinate-01~e.3))))) # ::id bio.bmtr_0001.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As predicted , only a very small fraction of wild @-@ type K @-@ Ras was pulled down by the GST @-@ RBD ( Fig . 2C and fig. S1D ) , consistent with very little wild @-@ type K @-@ Ras being in the GTP state under these conditions ( Fig.2 , A and B ) . # ::alignments 1-1.3 3-1.1.3.2 5-1.1.3.1.1 6-1.1.3.1 7-1.1.3 8-1.1.3.r 9-1.1.2 11-1.1.2 12-1.1.1.1 14-1.1.1.1 16-1 17-1 18-1.2.r 20-1.2.1.1 22-1.2.1.1 24-1.4.1.1 26-1.4.1.1.1 27-1.4.1 28-1.4.1.1 28-1.4.1.2 28-1.5.1.4.1.1 28-1.5.1.4.1.2 29-1.4.1.2.1 32-1.5 34-1.5.1.1.2.1 35-1.5.1.1.2 36-1.5.1.1.3 37-1.5.1.1.3 38-1.5.1.1.3 39-1.1.1.1 39-1.5.1.1.1.1 41-1.1.1.1 41-1.5.1.1.1.1 45-1.5.1.2.1.1 48-1.5.1.3 49-1.5.1.3.r 54-1.4.1 (p / pull-down-08~e.16,17 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.12,14,39,41) :mod (w / wild-type~e.9,11) :quant~e.8 (f / fraction~e.7 :mod (s2 / small~e.6 :degree (v / very~e.5)) :mod (o / only~e.3))) :ARG3~e.18 (p2 / protein :name (n3 / name :op1 "GST-RBD"~e.20,22)) :ARG1-of (p3 / predict-01~e.1) :ARG1-of (d / describe-01 :ARG0 (a / and~e.27,54 :op1 (f2 / figure~e.24,28 :mod "2C"~e.26) :op2 (f3 / figure~e.28 :mod "S1D"~e.29))) :ARG1-of (c / consistent-01~e.32 :ARG2 (b / bind-01 :ARG1 (e2 / enzyme :name (n4 / name :op1 "K-Ras"~e.39,41) :quant (l / little~e.35 :degree (v2 / very~e.34)) :mod w~e.36,37,38) :ARG2 (s / small-molecule :name (n2 / name :op1 "GTP"~e.45)) :condition~e.49 (t / this~e.48) :ARG1-of (d2 / describe-01 :ARG0 (a2 / and :op1 (f4 / figure~e.28 :mod "2A") :op2 (f5 / figure~e.28 :mod "2B")))))) # ::id bio.bmtr_0001.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , a much greater fraction of the ubiquitinated @-@ K @-@ Ras was pulled down by the GST @-@ RBD ( Fig . 2C and fig. S1D ) . # ::alignments 0-1 3-1.1.1.3.1.2 4-1.1.1.3.1 4-1.1.1.3.1.1 4-1.1.1.3.1.1.r 5-1.1.1.3 6-1.1.1.3.r 8-1.1.1.2 10-1.1.1.1.1 12-1.1.1.1.1 14-1.1 15-1.1 16-1.1.2.r 18-1.1.2.1.1 20-1.1.2.1.1 22-1.1.3.1.1 24-1.1.3.1.1.1 25-1.1.3.1 26-1.1.3.1.1 26-1.1.3.1.2 27-1.1.3.1.2.1 (c / contrast-01~e.0 :ARG2 (p / pull-down-08~e.14,15 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.10,12) :ARG3-of (u / ubiquitinate-01~e.8) :quant~e.6 (f / fraction~e.5 :mod (g / great~e.4 :degree~e.4 (m / more~e.4) :quant (m2 / much~e.3)))) :ARG3~e.16 (p2 / protein :name (n2 / name :op1 "GST-RBD"~e.18,20)) :ARG1-of (d / describe-01 :ARG0 (a / and~e.25 :op1 (f2 / figure~e.22,26 :mod "2C"~e.24) :op2 (f3 / figure~e.26 :mod "S1D"~e.27))))) # ::id bio.bmtr_0001.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results are consistent with a greater fraction of ubiquitinated K @-@ Ras being in the GTP state ( Fig . 2 , A and B ) . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 6-1.2.1.3.1 6-1.2.1.3.1.1 6-1.2.1.3.1.1.r 7-1.2.1.3 9-1.2.1.2 10-1.2.1.1.1 12-1.2.1.1.1 16-1.2.2.1.1 19-1.3.1.1 19-1.3.1.2 24-1.3.1 (c / consistent-01~e.3 :ARG1 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :mod (t2 / this~e.0)) :ARG2 (b / bind-01 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.10,12) :ARG3-of (u / ubiquitinate-01~e.9) :degree (f3 / fraction~e.7 :mod (g / great~e.6 :degree~e.6 (m / more~e.6)))) :ARG2 (s / small-molecule :name (n2 / name :op1 "GTP"~e.16))) :ARG1-of (d / describe-01 :ARG0 (a / and~e.24 :op1 (f / figure~e.19 :mod "2A") :op2 (f2 / figure~e.19 :mod "2B")))) # ::id bio.bmtr_0002.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Turke et al. “ MEK inhibition leads to PI3K @/@ AKT activation by relieving a negative feedback on ERBB receptors ” ( PMC3515079 ) # ::alignments 0-1.2.1.1.1 1-1.2 2-1.2.2.1 4-1.3.1.1.1.1 5-1.3.1 6-1.3 7-1.3.2.r 8-1.3.2.1.1.1 10-1.3.2.1.1.1 11-1.3.2 12-1.3.3.r 13-1.3.3 15-1.3.3.2.1 16-1.3.3.2 17-1.3.3.2.1.1.r 18-1.3.3.2.1.1.1.1 19-1.3.3.2.1.1 22-1.1 (p / publication-91 :ARG8 "PMC3515079"~e.22 :ARG0 (a / and~e.1 :op1 (p2 / person :name (n / name :op1 "Turke"~e.0)) :op2 (p3 / person :mod (o / other~e.2))) :ARG1 (l / lead-03~e.6 :ARG0 (i / inhibit-01~e.5 :ARG1 (e / enzyme :name (n2 / name :op1 "MEK"~e.4))) :ARG2~e.7 (a2 / activate-01~e.11 :ARG1 (p4 / pathway :name (n3 / name :op1 "PI3K/AKT"~e.8,10))) :manner~e.12 (r / relieve-01~e.13 :ARG0 i :ARG1 (f / feedback~e.16 :ARG0-of (n4 / negative-03~e.15 :ARG1~e.17 (r2 / receptor~e.19 :name (n5 / name :op1 "ERBB"~e.18))))))) # ::id bio.bmtr_0002.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We hypothesized that the MEK @/@ ERK pathway may suppress trans @-@ phosphorylation of ERBB3 by directly phosphorylating the JM domains of EGFR and HER2 , and that this could be a dominant MEK inhibitor @-@ induced feedback leading to AKT activation in these cancers . # ::alignments 0-1.1 1-1 2-1.2.r 4-1.2.1.1.1.1.1 6-1.2.1.1.1.1.1 7-1.2.1.1.1 8-1.2.1 9-1.2.1.1 12-1.2.1.1.2 12-1.2.1.1.3 13-1.2.1.1.2.1.r 14-1.2.1.1.2.1.1.1 16-1.2.1.1.3.3 17-1.2.1.1.3 19-1.2.1.1.3.2.1.1.1 19-1.2.1.1.3.2.2.1.1 20-1.2.1.1.3.2.1.1.2 20-1.2.1.1.3.2.2.1.2 21-1.2.1.1.3.2.r 22-1.2.1.1.3.2.1.2.1.1 23-1.2.1.1.3.2 24-1.2.1.1.3.2.2.2.1.1 26-1.2 27-1.2.r 28-1.2.2.1.3.1.2.3 29-1.2.2 30-1.2.2.1.4.r 32-1.2.2.1.2 33-1.2.2.1.1.1.1.1.1.1 34-1.2.2.1.1.1 34-1.2.2.1.1.1.1 34-1.2.2.1.1.1.1.r 36-1.2.2.1.1 37-1.2.2.1 38-1.2.2.1.3 40-1.2.2.1.3.1.1.1.1 41-1.2.2.1.3.1 43-1.2.2.1.3.1.2.3 44-1.2.2.1.3.1.2.2.1 (h / hypothesize-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2,27 (a / and~e.26 :op1 (p / possible-01~e.8 :ARG1 (s / suppress-01~e.9 :ARG0 (p2 / pathway~e.7 :name (n / name :op1 "MEK/ERK"~e.4,6)) :ARG1 (p3 / phosphorylate-01~e.12 :ARG1~e.13 (e / enzyme :name (n2 / name :op1 "ERBB3"~e.14))) :manner (p4 / phosphorylate-01~e.12,17 :ARG0 p2 :ARG1~e.21 (a2 / and~e.23 :op1 (p5 / protein-segment :name (n3 / name :op1 "JM"~e.19 :op2 "domain"~e.20) :part-of (e2 / enzyme :name (n4 / name :op1 "EGFR"~e.22))) :op2 (p6 / protein-segment :name (n5 / name :op1 "JM"~e.19 :op2 "domain"~e.20) :part-of (e3 / enzyme :name (n6 / name :op1 "HER2"~e.24)))) :ARG1-of (d / direct-02~e.16)))) :op2 (p7 / possible-01~e.29 :ARG1 (f / feedback~e.37 :ARG2-of (i / induce-01~e.36 :ARG0 (m / molecular-physical-entity~e.34 :ARG0-of~e.34 (i2 / inhibit-01~e.34 :ARG1 (p8 / protein-family :name (n7 / name :op1 "MEK"~e.33))))) :ARG0-of (d2 / dominate-01~e.32) :ARG0-of (l / lead-03~e.38 :ARG2 (a3 / activate-01~e.41 :ARG1 (e5 / enzyme :name (n8 / name :op1 "AKT"~e.40)) :location (d3 / disease :wiki "Cancer" :name (n9 / name :op1 "cancer"~e.44) :mod (t / this~e.28,43)))) :domain~e.30 s)))) # ::id bio.bmtr_0002.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We used tandem mass spectrometry to measure the effects of AZD6244 on phosphorylation of this JM domain threonine residue in both EGFR @-@ mutant and HER2 @- amplified cancer models . # ::alignments 0-1.1 1-1 2-1.2.2 3-1.2.1 4-1.2 6-1.3 8-1.3.2 9-1.3.2.1.r 10-1.3.2.1.1.1 11-1.3.2.2.r 12-1.3.2.2 13-1.3.2.2.1.r 14-1.3.2.2.1.3 15-1.3.2.2.1.2.1.1 16-1.3.2.2.1.2.1.2 17-1.3.2.2.1.1.1.1 18-1.3.2.2.1 21-1.3.2.3.1.1.3.1.1.1 23-1.3.2.3.1.1.3 24-1.3.2.3 25-1.3.2.3.2.1.3.1.1.1 27-1.3.2.3.2.1.3 28-1.3.2.3.1.1.2.1 28-1.3.2.3.2.1.2.1 29-1.3.2.3.1 29-1.3.2.3.2 (u / use-01~e.1 :ARG0 (w / we~e.0) :ARG1 (s / spectrometry~e.4 :mod (m / mass~e.3) :mod (t / tandem~e.2)) :ARG2 (m2 / measure-01~e.6 :ARG0 w :ARG1 (a / affect-01~e.8 :ARG0~e.9 (s2 / small-molecule :name (n / name :op1 "AZD6244"~e.10)) :ARG1~e.11 (p / phosphorylate-01~e.12 :ARG1~e.13 (r / residue~e.18 :mod (a2 / amino-acid :name (n2 / name :op1 "threonine"~e.17)) :part-of (p2 / protein-segment :name (n3 / name :op1 "JM"~e.15 :op2 "domain"~e.16)) :mod (t2 / this~e.14))) :condition (a4 / and~e.24 :op1 (m3 / model~e.29 :topic (d / disease :wiki "Cancer" :name (n6 / name :op1 "cancer"~e.28) :mod (m4 / mutate-01~e.23 :ARG1 (e / enzyme :name (n4 / name :op1 "EGFR"~e.21))))) :op2 (m5 / model~e.29 :topic (d2 / disease :wiki "Cancer" :name (n7 / name :op1 "cancer"~e.28) :mod (a3 / amplify-01~e.27 :ARG1 (e2 / enzyme :name (n5 / name :op1 "HER2"~e.25))))))))) # ::id bio.bmtr_0002.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Targeting both the phosphorylated and non @-@ phosphorylated peptide forms , we detected a 66 % average decrease in EGFR T669 phosphorylation and a 75 % decrease in HER2 T677 phosphorylation upon treatment with AZD6244 ( Figure 5B , Supplemental Figure 8 ) . # ::alignments 0-1.3 3-1.3.2.2.1 5-1.3.2.2.1.1 5-1.3.2.2.1.1.r 7-1.3.2.1.1 7-1.3.2.2.1 8-1.3.2.1 8-1.3.2.2 11-1.1 12-1 14-1.2.1.2.1 15-1.2.1.2 16-1.2.1.2.2 17-1.2.1 18-1.2.1.1.r 19-1.2.1.1.1.3.1.1 21-1.2.1.1 22-1.2 24-1.2.2.2.1 25-1.2.2.2 26-1.2.2 27-1.2.2.1.r 28-1.2.2.1.1.3.1.1 30-1.2.2.1 32-1.4 33-1.4.1.r 34-1.4.1.1.1 36-1.5.1.1 37-1.5.1.1.1 39-1.5.1.2.2 40-1.5.1.2 41-1.5.1.2.1 (d / detect-01~e.12 :ARG0 (w / we~e.11) :ARG1 (a / and~e.22 :op1 (d2 / decrease-01~e.17 :ARG1~e.18 (p / phosphorylate-01~e.21 :ARG1 (a3 / amino-acid :mod 669 :name (n / name :op1 "threonine") :part-of (e / enzyme :name (n2 / name :op1 "EGFR"~e.19)))) :ARG2 (p2 / percentage-entity~e.15 :value 66~e.14 :ARG2-of (a2 / average-01~e.16))) :op2 (d3 / decrease-01~e.26 :ARG1~e.27 (p3 / phosphorylate-01~e.30 :ARG1 (a4 / amino-acid :mod 677 :name (n3 / name :op1 "threonine") :part-of (e2 / enzyme :name (n4 / name :op1 "HER2"~e.28)))) :ARG2 (p4 / percentage-entity~e.25 :value 75~e.24))) :ARG2 (t2 / target-01~e.0 :ARG0 w :ARG1 (a6 / and :op1 (p5 / protein-segment~e.8 :ARG3-of (p7 / phosphorylate-01~e.7)) :op2 (p6 / protein-segment~e.8 :ARG3-of (p8 / phosphorylate-01~e.3,7 :polarity~e.5 -~e.5)))) :condition (t / treat-04~e.32 :ARG2~e.33 (s / small-molecule :name (n5 / name :op1 "AZD6244"~e.34))) :ARG1-of (d4 / describe-01 :ARG0 (a5 / and :op1 (f / figure~e.36 :mod "5B"~e.37) :op2 (f2 / figure~e.40 :mod 8~e.41 :ARG2-of (s2 / supplement-01~e.39))))) # ::id bio.bmtr_0002.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Phospho @-@ specific antibodies confirmed that treatment with AZD6244 inhibited phosphorylation of T669 of EGFR and the analogous T677 of HER2 ( Figure 5A ) . # ::alignments 0-1.1.1.1 2-1.1.1 3-1.1 4-1 5-1.2.r 6-1.2.1 7-1.2.1.1.r 8-1.2.1.1.1.1 9-1.2 10-1.2.2.1 10-1.2.2.2 13-1.2.2.1.1.r 14-1.2.2.1.1.3.1.1 15-1.2.2 17-1.2.2.2.1.3 20-1.2.2.2.1.4.1.1 22-1.3.1 23-1.3.1.1 (c / confirm-01~e.4 :ARG0 (a / antibody~e.3 :ARG1-of (s / specific-02~e.2 :ARG2 (p / phosphorylate-01~e.0))) :ARG1~e.5 (i / inhibit-01~e.9 :ARG0 (t / treat-04~e.6 :ARG2~e.7 (s2 / small-molecule :name (n / name :op1 "AZD6244"~e.8))) :ARG1 (a3 / and~e.15 :op1 (p2 / phosphorylate-01~e.10 :ARG1~e.13 (a2 / amino-acid :mod 669 :name (n2 / name :op1 "threonine") :part-of (e / enzyme :name (n3 / name :op1 "EGFR"~e.14)))) :op2 (p3 / phosphorylate-01~e.10 :ARG1 (a4 / amino-acid :mod 677 :name (n4 / name :op1 "threonine") :mod (a5 / analogous~e.17 :topic a2) :part-of (e2 / enzyme :name (n5 / name :op1 "HER2"~e.20)))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.22 :mod "5A"~e.23))) # ::id bio.bmtr_0002.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Together these data indicate that loss of this inhibitory threonine phosphorylation on the JM domains of EGFR and HER2 occurs in cancer cell lines following MEK inhibition , presumably due to differential subcellular localization and @/@ or binding proteins . # ::alignments 0-1.1.2 1-1.1.1 2-1.1 3-1 4-1.2.r 5-1.2 6-1.2.1.r 7-1.2.1.3 8-1.2.1.2 9-1.2.1.1.1.1 10-1.2.1 13-1.2.1.1.2.1.1 14-1.2.1.1.2.1.2 16-1.2.1.1.2.2.1.1.1 18-1.2.1.1.2.2.2.1.1 20-1.2.2.r 21-1.2.2.1.2.1 22-1.2.2 22-1.2.4.1.1.1 23-1.2.2 24-1.2.3 25-1.2.3.1.1.1.1 26-1.2.3.1 28-1.2.4.2 29-1.2.4 30-1.2.4 31-1.2.4.1.1 31-1.2.4.1.1.2 31-1.2.4.1.1.2.r 31-1.2.4.1.2.2 34-1.2.4.1 36-1.2.1.1.2.2 36-1.2.4.1 37-1.2.4.1.2.1 38-1.2.4.1.2 (i / indicate-01~e.3 :ARG0 (d / data~e.2 :mod (t / this~e.1) :mod (t2 / together~e.0)) :ARG1~e.4 (l / lose-01~e.5 :ARG1~e.6 (p / phosphorylate-01~e.10 :ARG1 (a / amino-acid :name (n / name :op1 "threonine"~e.9) :part-of (p2 / protein-segment :name (n2 / name :op1 "JM"~e.13 :op2 "domain"~e.14) :part-of (o / or~e.36 :op1 (e / enzyme :name (n3 / name :op1 "EGFR"~e.16)) :op2 (e2 / enzyme :name (n4 / name :op1 "HER2"~e.18))))) :ARG0-of (i2 / inhibit-01~e.8) :mod (t3 / this~e.7)) :location~e.20 (c / cell-line~e.22,23 :mod (d4 / disease :wiki "Cancer" :name (n6 / name :op1 "cancer"~e.21))) :ARG1-of (f / follow-01~e.24 :ARG2 (i3 / inhibit-01~e.26 :ARG1 (e3 / enzyme :name (n5 / name :op1 "MEK"~e.25)))) :ARG1-of (c3 / cause-01~e.29,30 :ARG0 (a2 / and-or~e.34,36 :op1 (l2 / location~e.31 :location (c4 / cell~e.22) :ARG1-of~e.31 (d2 / differ-02~e.31)) :op2 (p4 / protein~e.38 :ARG1-of (b / bind-01~e.37) :ARG1-of (d3 / differ-02~e.31))) :ARG1-of (p3 / presume-01~e.28)))) # ::id bio.bmtr_0002.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Mutation of T669 and T677 abrogates MEK inhibitor @-@ induced suppression of ERBB3 Activation # ::alignments 0-1.1 3-1.1.1 5-1 6-1.2.2.1.1.1.1.1 7-1.2.2.1 7-1.2.2.1.1 7-1.2.2.1.1.r 9-1.2.2 10-1.2 11-1.2.1.r 12-1.2.1.1.1.1 13-1.2.1 (a / abrogate-01~e.5 :ARG0 (m / mutate-01~e.0 :ARG1 (a2 / and~e.3 :op1 (a3 / amino-acid :mod 669 :name (n / name :op1 "threonine")) :op2 (a4 / amino-acid :mod 677 :name (n2 / name :op1 "threonine")))) :ARG1 (s / suppress-01~e.10 :ARG1~e.11 (a5 / activate-01~e.13 :ARG1 (e / enzyme :name (n3 / name :op1 "ERBB3"~e.12))) :ARG2-of (i / induce-01~e.9 :ARG0 (m2 / molecular-physical-entity~e.7 :ARG0-of~e.7 (i2 / inhibit-01~e.7 :ARG1 (p / protein-family :name (n4 / name :op1 "MEK"~e.6))))))) # ::id bio.bmtr_0002.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We hypothesized that MEK inhibition activates AKT by inhibiting ERK activity , which blocks an inhibitory threonine phosphorylation on the JM domains of EGFR and HER2 , thereby increasing ERBB3 phosphorylation . # ::alignments 0-1.1 1-1 2-1.2.r 3-1.2.1.1.1.1 4-1.2.1 4-1.2.3 5-1.2 6-1.2.2.1.1 8-1.2.3 9-1.2.3.2.1.1.1 10-1.2.3.2 13-1.2.3.3 15-1.2.3.3.1.2 16-1.2.3.3.1.1.1.1 17-1.2.3.3.1 20-1.2.3.3.1.1.2.1.1 21-1.2.3.3.1.1.2.1.2 23-1.2.3.3.1.1.2.2.1.1.1 25-1.2.3.3.1.1.2.2.2.1.1 27-1.2.3.r 28-1.2.3.3.2 29-1.2.3.3.2.1.1.1.1 30-1.2.3.3.2.1 (h / hypothesize-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (a / activate-01~e.5 :ARG0 (i / inhibit-01~e.4 :ARG1 (e / enzyme :name (n / name :op1 "MEK"~e.3))) :ARG1 (e2 / enzyme :name (n2 / name :op1 "AKT"~e.6)) :manner~e.27 (i2 / inhibit-01~e.4,8 :ARG0 i :ARG1 (a2 / activity-06~e.10 :ARG0 (e3 / enzyme :name (n3 / name :op1 "ERK"~e.9))) :ARG0-of (b / block-01~e.13 :ARG1 (p / phosphorylate-01~e.17 :ARG1 (a3 / amino-acid :name (n4 / name :op1 "threonine"~e.16) :part-of (p2 / protein-segment :name (n5 / name :op1 "JM"~e.20 :op2 "domain"~e.21) :part-of (o / or :op1 (e4 / enzyme :name (n6 / name :op1 "EGFR"~e.23)) :op2 (e5 / enzyme :name (n7 / name :op1 "HER2"~e.25))))) :ARG0-of (i3 / inhibit-01~e.15)) :ARG0-of (i4 / increase-01~e.28 :ARG1 (p3 / phosphorylate-01~e.30 :ARG1 (e6 / enzyme :name (n8 / name :op1 "ERBB3"~e.29)))))))) # ::id bio.bmtr_0002.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To test this hypothesis , we transiently transfected CHO @-@ KI cells , which do not express ERBB receptors endogenously , with wild @-@ type ERBB3 with either wild @-@ type EGFR or EGFR T669A . # ::alignments 1-1.5 2-1.5.2.2 3-1.5.2 3-1.5.2.1 3-1.5.2.1.r 5-1.1 6-1.4 7-1 8-1.2.1.1.1 10-1.2.1.1.1 11-1.2 15-1.2.2.1 15-1.2.2.1.r 16-1.2.2 17-1.2.2.2.1.1 18-1.2.2.2 19-1.2.2.3 22-1.3.1.2 22-1.3.2.1.2 24-1.3.1.2 24-1.3.2.1.2 25-1.3.1.1.1 28-1.3.1.2 28-1.3.2.1.2 30-1.3.1.2 30-1.3.2.1.2 31-1.3.2.1.1.1 31-1.3.2.2.1.1 32-1.3.2 33-1.3.2.1.1.1 33-1.3.2.2.1.1 34-1.3.2.2.2.1 (t / transfect-01~e.7 :ARG0 (w / we~e.5) :ARG1 (c / cell~e.11 :source (c2 / cell-line :name (n / name :op1 "CHO-KI"~e.8,10)) :ARG3-of (e3 / express-03~e.16 :polarity~e.15 -~e.15 :ARG2 (r / receptor~e.18 :name (n4 / name :op1 "ERBB"~e.17)) :mod (e4 / endogenous~e.19))) :ARG2 (a / and :op1 (e5 / enzyme :name (n5 / name :op1 "ERBB3"~e.25) :mod (w3 / wild-type~e.22,24,28,30)) :op2 (o / or~e.32 :op1 (e / enzyme :name (n2 / name :op1 "EGFR"~e.31,33) :mod (w2 / wild-type~e.22,24,28,30)) :op2 (e2 / enzyme :name (n3 / name :op1 "EGFR"~e.31,33) :ARG2-of (m / mutate-01 :value "T669A"~e.34)))) :ARG1-of (t2 / transient-02~e.6) :purpose (t3 / test-01~e.1 :ARG0 w :ARG1 (t5 / thing~e.3 :ARG1-of~e.3 (h / hypothesize-01~e.3) :mod (t4 / this~e.2)))) # ::id bio.bmtr_0002.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In cells transfected with wild @-@ type EGFR , MEK inhibition led to feedback activation of phospho @-@ ERBB3 and phosho @-@ EGFR , recapitulating the results we had observed in our panel of cancer cell lines ( Figure 6A ) . # ::alignments 1-1.3 2-1.3.1 3-1.3.1.1.r 4-1.3.1.1.2 6-1.3.1.1.2 7-1.3.1.1.1.1 9-1.1.1.1.1 10-1.1 11-1 12-1.2.r 13-1.2.2 14-1.2 15-1.2.1.r 16-1.2.1.1.2 16-1.2.1.2.2 18-1.2.1.1.1.1 19-1.2.1 22-1.2.1.2.1.1 22-1.3.1.1.1.1 24-1.4 26-1.4.1 26-1.4.1.1 26-1.4.1.1.r 27-1.4.1.2.1 29-1.4.1.2 30-1.4.1.2.2.r 31-1.4.1.2.2.2 31-1.4.1.2.2.2.r 32-1.4.1.2.2 33-1.4.1.2.2.1.r 34-1.4.1.2.2.1.1.2.1 35-1.4.1.2.2.1 36-1.4.1.2.2.1 38-1.5.1 39-1.5.1.1 (l / lead-03~e.11 :ARG0 (i / inhibit-01~e.10 :ARG1 (e / enzyme :name (n / name :op1 "MEK"~e.9))) :ARG2~e.12 (a / activate-01~e.14 :ARG1~e.15 (a2 / and~e.19 :op1 (e3 / enzyme :name (n3 / name :op1 "ERBB3"~e.18) :ARG3-of (p / phosphorylate-01~e.16)) :op2 (e4 / enzyme :name (n4 / name :op1 "EGFR"~e.22) :ARG3-of (p2 / phosphorylate-01~e.16))) :subevent-of (f / feedback~e.13)) :location (c / cell~e.1 :ARG1-of (t / transfect-01~e.2 :ARG2~e.3 (e2 / enzyme :name (n2 / name :op1 "EGFR"~e.7,22) :mod (w / wild-type~e.4,6)))) :ARG0-of (r / recapitulate-01~e.24 :ARG1 (t2 / thing~e.26 :ARG2-of~e.26 (r2 / result-01~e.26) :ARG1-of (o / observe-01~e.29 :ARG0 (w2 / we~e.27) :location~e.30 (p3 / panel~e.32 :consist-of~e.33 (c2 / cell-line~e.35,36 :mod (d2 / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.34))) :poss~e.31 w2~e.31)))) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.38 :mod "6A"~e.39))) # ::id bio.bmtr_0002.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , the EGFR T669A mutant increased both basal EGFR and ERBB3 tyrosine phosphorylation that was not augmented by MEK inhibition . # ::alignments 1-1 4-1.1.1.1.1 4-1.1.2.1.1.2.1.1 5-1.1.1.2.1 6-1.1.1 6-1.1.1.2 6-1.1.1.2.r 7-1.1 9-1.1.2.1.2 10-1.1.2.1.1.2.1.1 11-1.1.2 12-1.1.2.2.2.1.1 13-1.1.2.1.1.1.1 13-1.1.2.2.1.1.1 14-1.1.2.1 14-1.1.2.2 17-1.1.2.3.1 17-1.1.2.3.1.r 18-1.1.2.3 19-1.1.2.3.2.r 20-1.1.2.3.2.1.1.1 21-1.1.2.3.2 (c / contrast-01~e.1 :ARG2 (i / increase-01~e.7 :ARG0 (e4 / enzyme~e.6 :name (n4 / name :op1 "EGFR"~e.4) :ARG2-of~e.6 (m / mutate-01~e.6 :value "T669A"~e.5)) :ARG1 (a / and~e.11 :op1 (p2 / phosphorylate-01~e.14 :ARG1 (a2 / amino-acid :name (n5 / name :op1 "tyrosine"~e.13) :part-of (e / enzyme :name (n / name :op1 "EGFR"~e.4,10))) :mod (b / basal~e.9)) :op2 (p3 / phosphorylate-01~e.14 :ARG1 (a3 / amino-acid :name (n6 / name :op1 "tyrosine"~e.13)) :part-of (e2 / enzyme :name (n2 / name :op1 "ERBB3"~e.12)) :mod b) :ARG1-of (a4 / augment-01~e.18 :polarity~e.17 -~e.17 :ARG0~e.19 (i2 / inhibit-01~e.21 :ARG1 (e3 / enzyme :name (n3 / name :op1 "MEK"~e.20))))))) # ::id bio.bmtr_0002.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As a control , we treated CHO @-@ KI cells expressing EGFR T669A with HRG ligand to induce maximal ERBB3 phosphorylation ( Figure 6A ) , indicating that the lack of induction of phospho @-@ ERBB3 in EGFR T669A expressing cells following MEK inhibition was not simply due to the saturation of the system with phospho @-@ ERBB3 . # ::alignments 2-1.6 4-1.1 5-1 6-1.2.1.1.1 8-1.2.1.1.1 9-1.2 10-1.2.2 11-1.2.2.1.1.1 12-1.2.2.1.2.1 13-1.3.r 14-1.3.1.1 15-1.3 17-1.4 18-1.4.2.2 19-1.4.2.1.1.1 20-1.4.2 22-1.5.1 23-1.5.1.1 26-1.4.3 27-1.4.3.1.r 29-1.4.3.1.2 30-1.4.3.1.2.1.r 31-1.4.3.1.2.1 33-1.4.3.1.2.1.1 33-1.4.3.1.3.2.2 35-1.4.3.1.3.2.1.1 36-1.4.3.1.2.1.2.r 37-1.4.3.1.2.1.2.1.1.1.1 38-1.4.3.1.2.1.2.1.1.2.1 39-1.4.3.1.2.1.2.1 40-1.4.3.1.2.1.2 41-1.4.3.1.2.1.3 42-1.4.3.1.2.1.3.1.1.1.1 43-1.4.3.1.2.1.3.1 45-1.4.3.1.1 45-1.4.3.1.1.r 46-1.4.3.1.4 47-1.4.3.1 48-1.4.3.1 50-1.4.3.1.3 51-1.4.3.1.3.1.r 53-1.4.3.1.3.1 55-1.4.2 55-1.4.3.1.3.2.2 57-1.4.2.1.1.1 57-1.4.3.1.3.2.1.1 (t / treat-04~e.5 :ARG0 (w / we~e.4) :ARG1 (c / cell~e.9 :source (c2 / cell-line :name (n / name :op1 "CHO-KI"~e.6,8)) :ARG3-of (e / express-03~e.10 :ARG2 (e2 / enzyme :name (n2 / name :op1 "EGFR"~e.11) :ARG2-of (m / mutate-01 :value "T669A"~e.12)))) :ARG2~e.13 (l / ligand~e.15 :name (n3 / name :op1 "HRG"~e.14)) :purpose (i / induce-01~e.17 :ARG0 w :ARG2 (p / phosphorylate-01~e.20,55 :ARG1 (e3 / enzyme :name (n4 / name :op1 "ERBB3"~e.19,57)) :degree (m2 / maximum~e.18)) :ARG0-of (i2 / indicate-01~e.26 :ARG1~e.27 (c3 / cause-01~e.47,48 :polarity~e.45 -~e.45 :ARG0 (l2 / lack-01~e.29 :ARG1~e.30 (i3 / induce-01~e.31 :ARG2 (p3 / phosphorylate-01~e.33 :ARG1 e3) :location~e.36 (c4 / cell~e.40 :ARG3-of (e5 / express-03~e.39 :ARG2 (e6 / enzyme :name (n6 / name :op1 "EGFR"~e.37) :ARG2-of (m3 / mutate-01 :value "T669A"~e.38)))) :ARG2-of (f2 / follow-01~e.41 :ARG1 (i4 / inhibit-01~e.43 :ARG1 (e7 / enzyme :name (n7 / name :op1 "MEK"~e.42)))))) :ARG1 (s / saturate-01~e.50 :ARG1~e.51 (s2 / system~e.53) :ARG2 (e4 / enzyme :name (n5 / name :op1 "ERBB3"~e.35,57) :ARG3-of (p2 / phosphorylate-01~e.33,55))) :mod (s3 / simple~e.46)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.22 :mod "6A"~e.23)) :ARG2-of (c5 / control-01~e.2)) # ::id bio.bmtr_0002.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We observed analogous results in CHO @-@ KI cells expressing wild @-@ type ERBB3 in combination with wild @-@ type or T677A mutant HER2 ( Figure 6B ) . # ::alignments 0-1.1 1-1 2-1.2.2 3-1.2 3-1.2.1 3-1.2.1.r 4-1.2.1.1.r 5-1.2.1.1.1.1.1 7-1.2.1.1.1.1.1 8-1.2.1.1 9-1.2.1.1.2 10-1.2.1.1.2.1.2 10-1.2.1.1.2.1.3.1.2 12-1.2.1.1.2.1.2 12-1.2.1.1.2.1.3.1.2 13-1.2.1.1.2.1.1.1 16-1.2.1.1.2.1.3.r 17-1.2.1.1.2.1.3.1.2 19-1.2.1.1.2.1.3.1.2 20-1.2.1.1.2.1.3 21-1.2.1.1.2.1.3.2.2.1 22-1.2.1.1.2.1.3.2 22-1.2.1.1.2.1.3.2.2 22-1.2.1.1.2.1.3.2.2.r 23-1.2.1.1.2.1.3.1.1.1 23-1.2.1.1.2.1.3.2.1.1 25-1.3.1 26-1.3.1.1 (o / observe-01~e.1 :ARG0 (w / we~e.0) :ARG1 (t / thing~e.3 :ARG2-of~e.3 (r / result-01~e.3 :ARG1~e.4 (c / cell~e.8 :source (c2 / cell-line :name (n / name :op1 "CHO-KI"~e.5,7)) :ARG3-of (e / express-03~e.9 :ARG2 (e2 / enzyme :name (n2 / name :op1 "ERBB3"~e.13) :mod (w2 / wild-type~e.10,12) :accompanier~e.16 (o2 / or~e.20 :op1 (e3 / enzyme :name (n3 / name :op1 "HER2"~e.23) :mod (w3 / wild-type~e.10,12,17,19)) :op2 (e4 / enzyme~e.22 :name (n4 / name :op1 "HER2"~e.23) :ARG2-of~e.22 (m / mutate-01~e.22 :value "T677A"~e.21))))))) :mod (a / analogous~e.2)) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.25 :mod "6B"~e.26))) # ::id bio.bmtr_0002.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Together these results support the hypothesis that inhibition of ERK @-@ mediated phosphorylation of a conserved JM domain threonine residue leads to feedback activation of EGFR , HER2 , and ERBB3 ( Figure 7 ) . # ::alignments 0-1.1.2 1-1.1.3 2-1.1 2-1.1.1 2-1.1.1.r 3-1 5-1.2 6-1.2.1.r 7-1.2.1.1 8-1.2.1.1.1.r 9-1.2.1.1.1.2.1.1.1 11-1.2.1.1.1.2 12-1.2.1.1.1 13-1.2.1.1.1.1.r 15-1.2.1.1.1.1.2.2 16-1.2.1.1.1.1.2.1.1 17-1.2.1.1.1.1.2.1.2 18-1.2.1.1.1.1.1.1.1 19-1.2.1.1.1.1 20-1.2.1 21-1.2.1.2.r 22-1.2.1.2.2 23-1.2.1.2 24-1.2.1.2.1.r 25-1.2.1.2.1.1.1.1 27-1.2.1.2.1.2.1.1 29-1.2.1.2.1 30-1.2.1.2.1.3.1.1 32-1.3.1 33-1.3.1.1 (s / support-01~e.3 :ARG0 (t / thing~e.2 :ARG2-of~e.2 (r / result-01~e.2) :mod (t2 / together~e.0) :mod (t3 / this~e.1)) :ARG1 (h / hypothesize-01~e.5 :ARG1~e.6 (l / lead-03~e.20 :ARG0 (i / inhibit-01~e.7 :ARG1~e.8 (p / phosphorylate-01~e.12 :ARG1~e.13 (r2 / residue~e.19 :mod (a3 / amino-acid :name (n5 / name :op1 "threonine"~e.18)) :part-of (p2 / protein-segment :name (n6 / name :op1 "JM"~e.16 :op2 "domain"~e.17) :ARG1-of (c / conserve-01~e.15))) :ARG1-of (m / mediate-01~e.11 :ARG0 (e4 / enzyme :name (n4 / name :op1 "ERK"~e.9))))) :ARG2~e.21 (a / activate-01~e.23 :ARG1~e.24 (a2 / and~e.29 :op1 (e / enzyme :name (n / name :op1 "EGFR"~e.25)) :op2 (e2 / enzyme :name (n2 / name :op1 "HER2"~e.27)) :op3 (e3 / enzyme :name (n3 / name :op1 "ERBB3"~e.30))) :subevent-of (f / feedback~e.22)))) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.32 :mod 7~e.33))) # ::id bio.bmtr_0002.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To determine if this feedback model explains the activation of PI3K signaling in EGFR @-@ mutant cancers , we used shRNA to knockdown endogenous EGFR ( which carries an exon 19 deletion ) in the HCC827 NSCLC cell line and replaced with either EGFR ( exon 19 del ) wild @-@ type at T669 , or EGFR ( exon 19 del ) carrying a T669A mutation . # ::alignments 1-1.3 2-1.3.2.3.2.r 3-1.3.2.2.2 4-1.3.2.2.1 5-1.3.2.2 6-1.3.2 8-1.3.2.3 9-1.3.2.3.1.r 10-1.3.2.3.1.1.1 11-1.3.2.3.1.2 13-1.3.2.3.2.3.1.1.1 15-1.3.2.3.2.3 16-1.3.2.3.2.2.1 18-1.1.1 19-1.1 20-1.1.2.1.1 21-1.1.3.r 22-1.1.3 23-1.1.3.2.2 24-1.1.3.2.1.1 24-1.2.3.1.1.1 24-1.3.2.3.2.3.1.1.1 27-1.2.3.1.3 29-1.1.3.2.4.1 30-1.1.3.2.4.1.1 31-1.1.3.2 31-1.1.3.2.4 31-1.1.3.2.4.r 33-1.1.3.2.3.r 35-1.1.3.2.3.1.1 36-1.1.3.2.3.2.1.1 37-1.1.3.2.3 38-1.1.3.2.3 39-1 40-1.2 43-1.1.3.2.1.1 43-1.2.3.1.1.1 43-1.2.3.2.1.1 43-1.3.2.3.2.3.1.1.1 45-1.1.3.2.4.1 46-1.1.3.2.4.1.1 49-1.2.3.1.2 51-1.2.3.1.2 55-1.2.3 56-1.1.3.2.1.1 56-1.2.3.1.1.1 56-1.2.3.2.1.1 56-1.3.2.3.2.3.1.1.1 58-1.1.3.2.4.1 59-1.1.3.2.4.1.1 62-1.2.3.1.3 64-1.2.3.2.3.1 65-1.2.3.2.3 65-1.3.2.3.2.3 (a / and~e.39 :op1 (u / use-01~e.19 :ARG0 (w / we~e.18) :ARG1 (n10 / nucleic-acid :name (n / name :op1 "shRNA"~e.20)) :ARG2~e.21 (k / knock-down-02~e.22 :ARG0 w :ARG1 (e / enzyme~e.31 :name (n2 / name :op1 "EGFR"~e.24,43,56) :mod (e2 / endogenous~e.23) :location~e.33 (c2 / cell-line~e.37,38 :name (n3 / name :op1 "HCC827"~e.35) :mod (d4 / disease :name (n11 / name :op1 "NSCLC"~e.36))) :ARG2-of~e.31 (d / delete-01~e.31 :ARG1 (e3 / exon~e.29,45,58 :mod 19~e.30,46,59))))) :op2 (r / replace-01~e.40 :ARG0 w :ARG1 e :ARG2 (o / or~e.55 :op1 (e4 / enzyme :name (n4 / name :op1 "EGFR"~e.24,43,56) :mod (w2 / wild-type~e.49,51) :ARG0-of (c / carry-01~e.27,62) :part (a2 / amino-acid :mod 669 :name (n5 / name :op1 "threonine"))) :op2 (e5 / enzyme :name (n6 / name :op1 "EGFR"~e.43,56) :ARG2-of d :part (m2 / mutate-01~e.65 :value "T669A"~e.64)))) :purpose (d2 / determine-01~e.1 :ARG0 w :ARG1 (e6 / explain-01~e.6 :mode interrogative :ARG0 (m3 / model~e.5 :mod (f / feedback~e.4) :mod (t / this~e.3)) :ARG1 (a4 / activate-01~e.8 :ARG1~e.9 (p / pathway :name (n7 / name :op1 "PI3K"~e.10) :ARG0-of (s / signal-07~e.11)) :condition~e.2 (d3 / disease :wiki "Cancer" :name (n9 / name :op1 "cancer"~e.16) :mod (m4 / mutate-01~e.15,65 :ARG1 (e7 / enzyme :name (n8 / name :op1 "EGFR"~e.13,24,43,56)))))))) # ::id bio.bmtr_0002.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Of note , this is the same EGFR @-@ mutant cell line in which we observed that EGFR T669 is phosphorylated in MEK @-@ dependent manner ( Figure 5 , Supplemental Figure 8A ) . # ::alignments 1-1 3-1.1.1 6-1.1 7-1.1.2.1.1.1 7-1.1.2.2.1.3.1.1 9-1.1.2.1 9-1.1.2.1.2 9-1.1.2.1.2.r 10-1.1.2 11-1.1.2 14-1.1.2.2.3.1 15-1.1.2.2.3 17-1.1.2.2.1.3.1.1 20-1.1.2.2 21-1.1.2.2.2.r 22-1.1.2.2.2.1.1.1 24-1.1.2.2.2 27-1.1.3.1.1 28-1.1.3.1.1.1 30-1.1.3.1.2.2 31-1.1.3.1.2 32-1.1.3.1.2.1 (n / note-02~e.1 :ARG1 (s / same-01~e.6 :ARG1 (t / this~e.3) :ARG2 (c / cell-line~e.10,11 :consist-of (e3 / enzyme~e.9 :name (n2 / name :op1 "EGFR"~e.7) :ARG2-of~e.9 (m / mutate-01~e.9)) :location-of (p / phosphorylate-01~e.20 :ARG1 (a / amino-acid :mod 669 :name (n3 / name :op1 "threonine") :part-of (e / enzyme :name (n4 / name :op1 "EGFR"~e.7,17))) :ARG0-of~e.21 (d / depend-01~e.24 :ARG1 (e2 / enzyme :name (n5 / name :op1 "MEK"~e.22))) :ARG1-of (o / observe-01~e.15 :ARG0 (w / we~e.14)))) :ARG1-of (d2 / describe-01 :ARG0 (a2 / and :op1 (f / figure~e.27 :mod 5~e.28) :op2 (f2 / figure~e.31 :mod "8A"~e.32 :ARG2-of (s2 / supplement-01~e.30)))))) # ::id bio.bmtr_0002.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok When endogenous EGFR was replaced with EGFR ( exon19 del ) wild @-@ type at T669 , MEK inhibition led to significant feedback activation of ERBB3/PI3K/AKT signaling ( Figure 6C ) . # ::alignments 0-1.4.r 1-1.4.1.2 2-1.4.1.1.1 2-1.4.2.1.1 4-1.4 6-1.4.1.1.1 6-1.4.2.1.1 11-1.4.2.2 13-1.4.2.2 17-1.1.1.1.1 18-1.1 19-1 20-1.2.r 21-1.2.3 22-1.2.2 23-1.2 24-1.2.1.r 25-1.2.1.1.1 26-1.2.1.2 28-1.3.1 29-1.3.1.1 (l / lead-03~e.19 :ARG0 (i / inhibit-01~e.18 :ARG1 (e / enzyme :name (n / name :op1 "MEK"~e.17))) :ARG2~e.20 (a / activate-01~e.23 :ARG1~e.24 (p / pathway :name (n2 / name :op1 "ERBB3/PI3K/AKT"~e.25) :ARG0-of (s / signal-07~e.26)) :subevent-of (f / feedback~e.22) :ARG1-of (s2 / significant-02~e.21)) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.28 :mod "6C"~e.29)) :time~e.0 (r / replace-01~e.4 :ARG1 (e2 / enzyme :name (n3 / name :op1 "EGFR"~e.2,6) :mod (e4 / endogenous~e.1)) :ARG2 (e3 / enzyme :name (n4 / name :op1 "EGFR"~e.2,6) :mod (w / wild-type~e.11,13) :ARG2-of (d2 / delete-01 :ARG1 (e5 / exon :mod 19)) :part (a2 / amino-acid :mod 669 :name (n5 / name :op1 "threonine"))))) # ::id bio.bmtr_0002.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , replacement with the EGFR ( exon19 del ) T669A mutant led to increased tyrosine phosphorylation of both EGFR and ERBB3 , and activation of PI3K @/@ AKT signaling , mimicking the effect of MEK inhibition ( Figure 6C ) . # ::alignments 0-1.3 2-1.1 3-1.1.1.r 5-1.1.1.1.1 10-1.1.1.2.1 11-1.1.1 11-1.1.1.2 11-1.1.1.2.r 12-1 13-1.2.r 14-1.2.1 15-1.2.1.1.1.1.1.1 15-1.2.1.1.2.1.1.1 16-1.2.1.1.1 16-1.2.1.1.2 19-1.2.1.1.1.1.2.1.1 20-1.2.1.1 21-1.2.1.1.2.1.2.1.1 23-1.2 24-1.2.2 25-1.2.2.1.r 26-1.2.2.1.1.1 28-1.2.2.1.1.1 29-1.2.2.1.2 31-1.2.3 33-1.2.3.1 34-1.2.3.1.1.r 35-1.2.3.1.1.1.1.1 36-1.2.3.1.1 38-1.4.1 39-1.4.1.1 (l / lead-03~e.12 :ARG0 (r / replace-01~e.2 :ARG2~e.3 (e / enzyme~e.11 :name (n / name :op1 "EGFR"~e.5) :ARG2-of~e.11 (m / mutate-01~e.11 :value "T669A"~e.10) :ARG2-of (d / delete-01 :ARG1 (e2 / exon :mod 19)))) :ARG2~e.13 (a6 / and~e.23 :op1 (i / increase-01~e.14 :ARG1 (a / and~e.20 :op1 (p / phosphorylate-01~e.16 :ARG1 (a2 / amino-acid :name (n2 / name :op1 "tyrosine"~e.15) :part-of (e3 / enzyme :name (n3 / name :op1 "EGFR"~e.19)))) :op2 (p3 / phosphorylate-01~e.16 :ARG1 (a3 / amino-acid :name (n4 / name :op1 "tyrosine"~e.15) :part-of (e4 / enzyme :name (n7 / name :op1 "ERBB3"~e.21)))))) :op2 (a4 / activate-01~e.24 :ARG1~e.25 (p2 / pathway :name (n5 / name :op1 "PI3K/AKT"~e.26,28) :ARG0-of (s / signal-07~e.29))) :ARG1-of (m2 / mimic-01~e.31 :ARG0 (a5 / affect-01~e.33 :ARG0~e.34 (i2 / inhibit-01~e.36 :ARG1 (e5 / enzyme :name (n6 / name :op1 "MEK"~e.35)))))) :ARG1-of (h / have-concession-91~e.0) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.38 :mod "6C"~e.39))) # ::id bio.bmtr_0002.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As expected , addition of AZD6244 failed to further augment ERBB3 and AKT phosphorylation in cells expressing the 669A mutant . # ::alignments 1-1.5 3-1.2 4-1.2.1.r 5-1.2.1.1.1 8-1.4 9-1 10-1.3.1.1.1.1 11-1.3.1 12-1.3.1.2.1.1 13-1.3 14-1.3.2.r 15-1.3.2 16-1.3.2.1 19-1.3.2.1.1 19-1.3.2.1.1.2 19-1.3.2.1.1.2.r (a4 / augment-01~e.9 :polarity - :ARG0 (a / add-02~e.3 :ARG1~e.4 (s / small-molecule :name (n / name :op1 "AZD6244"~e.5))) :ARG1 (p / phosphorylate-01~e.13 :ARG1 (a3 / and~e.11 :op1 (e / enzyme :name (n2 / name :op1 "ERBB3"~e.10)) :op2 (e4 / enzyme :name (n3 / name :op1 "AKT"~e.12))) :location~e.14 (c / cell~e.15 :ARG3-of (e2 / express-03~e.16 :ARG2 (a2 / amino-acid~e.19 :mod 669 :ARG2-of~e.19 (m / mutate-01~e.19))))) :degree (f2 / further~e.8) :ARG1-of (e3 / expect-01~e.1)) # ::id bio.bmtr_0002.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results demonstrate that EGFR T669 phosphorylation is necessary for MEK @/@ ERK to suppress EGFR @-@ mediated activation of ERBB3 . # ::alignments 0-1.1.1 1-1.1 1-1.1.2 1-1.1.2.r 2-1 3-1.2.r 4-1.2.2.1.3.1.1 6-1.2.2 8-1.2 9-1.2.1.r 10-1.2.1.1.1.1 12-1.2.1.1.1.1 14-1.2.1 15-1.2.1.2.2.1.1.1 17-1.2.1.2.2 18-1.2.1.2 19-1.2.1.2.1.r 20-1.2.1.2.1.1.1 (d / demonstrate-01~e.2 :ARG0 (t / thing~e.1 :mod (t2 / this~e.0) :ARG2-of~e.1 (r / result-01~e.1)) :ARG1~e.3 (n / need-01~e.8 :ARG0~e.9 (s / suppress-01~e.14 :ARG0 (p2 / pathway :name (n4 / name :op1 "MEK/ERK"~e.10,12)) :ARG1 (a2 / activate-01~e.18 :ARG1~e.19 (e2 / enzyme :name (n5 / name :op1 "ERBB3"~e.20)) :ARG1-of (m / mediate-01~e.17 :ARG0 (e3 / enzyme :name (n6 / name :op1 "EGFR"~e.15))))) :ARG1 (p / phosphorylate-01~e.6 :ARG1 (a / amino-acid :mod 669 :name (n2 / name :op1 "threonine") :part-of (e / enzyme :name (n3 / name :op1 "EGFR"~e.4)))))) # ::id bio.bmtr_0002.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This supports the hypothesis that a dominant ERK feedback on ERBB3/PI3K/AKT is mediated though phosphorylation of T669 on EGFR ( or T677 HER2 ) . # ::alignments 0-1.1 1-1 3-1.2 4-1.2.1.r 6-1.2.1.2.1 7-1.2.1.2.3.1.1 8-1.2.1.2 9-1.2.1.2.2.r 10-1.2.1.2.2.1.1 12-1.2.1 14-1.2.1.1.1 14-1.2.1.1.2 17-1.2.1.1.1.1.r 18-1.2.1.1.1.1.3.1.1 20-1.2.1.1 22-1.2.1.1.2.1.3.1.1 (s / support-01~e.1 :ARG0 (t / this~e.0) :ARG1 (h / hypothesize-01~e.3 :ARG1~e.4 (m / mediate-01~e.12 :ARG0 (o2 / or~e.20 :op1 (p2 / phosphorylate-01~e.14 :ARG1~e.17 (a / amino-acid :mod 669 :name (n3 / name :op1 "threonine") :part-of (e2 / enzyme :name (n4 / name :op1 "EGFR"~e.18)))) :op2 (p3 / phosphorylate-01~e.14 :ARG1 (a2 / amino-acid :mod 677 :name (n5 / name :op1 "threonine") :part-of (e3 / enzyme :name (n6 / name :op1 "HER2"~e.22))))) :ARG1 (f / feedback~e.8 :ARG0-of (d / dominate-01~e.6) :destination~e.9 (p / pathway :name (n / name :op1 "ERBB3/PI3K/AKT"~e.10)) :mod (e / enzyme :name (n2 / name :op1 "ERK"~e.7)))))) # ::id bio.bmtr_0003.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Montero @-@ Conde et al. “ Relief of feedback inhibition of HER3 transcription by RAF and MEK inhibitors attenuates their antitumor effects in BRAF mutant thyroid carcinomas.” ( PMC3651738 ) # ::alignments 0-1.2.1.1.1 2-1.2.1.1.1 3-1.2 4-1.2.2.1 6-1.3.1 7-1.3.1.1.r 8-1.3.1.1.3 9-1.3.1.1 10-1.3.1.1.2.r 11-1.3.1.1.2.1.1.1 12-1.3.1.1.2 13-1.3.1.1.1.r 14-1.3.1.1.1.1.1.1.1.1 15-1.3.1.1.1.1.1 16-1.3.1.1.1.1.1.2.1.1 17-1.3.1.1.1 17-1.3.1.1.1.1 17-1.3.1.1.1.1.r 18-1.3 19-1.3.2.1 19-1.3.2.1.r 20-1.3.2.2 20-1.3.2.2.1 20-1.3.2.2.1.r 21-1.3.2 22-1.3.2.3.r 23-1.3.2.3.3.1.1 24-1.3.2.3.3 24-1.3.2.3.3.2 24-1.3.2.3.3.2.r 25-1.3.2.3.2 28-1.1 (p / publication-91 :ARG8 "PMC3651738"~e.28 :ARG0 (a / and~e.3 :op1 (p2 / person :name (n / name :op1 "Montero-Conde"~e.0,2)) :op2 (p3 / person :mod (o / other~e.4))) :ARG1 (a3 / attenuate-01~e.18 :ARG0 (r / relieve-01~e.6 :ARG1~e.7 (i / inhibit-01~e.9 :ARG0~e.13 (m / molecular-physical-entity~e.17 :ARG0-of~e.17 (i2 / inhibit-01~e.17 :ARG1 (a2 / and~e.15 :op1 (p4 / protein-family :name (n3 / name :op1 "RAF"~e.14)) :op2 (p5 / protein-family :name (n4 / name :op1 "MEK"~e.16))))) :ARG1~e.10 (t / transcribe-01~e.12 :ARG1 (e / enzyme :name (n2 / name :op1 "HER3"~e.11))) :subevent-of (f / feedback~e.8))) :ARG1 (a4 / affect-01~e.21 :ARG0~e.19 m~e.19 :ARG2 (c / counter-01~e.20 :ARG1~e.20 (t2 / tumor~e.20)) :location~e.22 (m3 / medical-condition :name (n8 / name :op1 "carcinoma") :mod (t3 / thyroid~e.25) :mod (e4 / enzyme~e.24 :name (n5 / name :op1 "BRAF"~e.23) :ARG2-of~e.24 (m2 / mutate-01~e.24)))))) # ::id bio.bmtr_0003.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We next examined the mechanisms accounting for the increase in HER3 by MAPK pathway inhibitors in BRAF mutant thyroid cell lines . # ::alignments 0-1.1 1-1.3 2-1 4-1.2 5-1.2.1 6-1.2.1.1.r 8-1.2.1.1 9-1.2.1.1.2.r 10-1.2.1.1.2.1.1 11-1.2.1.1.1.r 12-1.2.1.1.1.1.1.1.1 13-1.2.1.1.1.1.1 14-1.2.1.1.1 14-1.2.1.1.1.1 14-1.2.1.1.1.1.r 15-1.2.1.1.3.r 16-1.2.1.1.3.2.1.3.1.1 17-1.2.1.1.3.2.1.3 17-1.2.1.1.3.2.1.3.2 17-1.2.1.1.3.2.1.3.2.r 18-1.2.1.1.3.1 19-1.2.1.1.3 20-1.2.1.1.3 (e / examine-01~e.2 :ARG0 (w / we~e.0) :ARG1 (m / mechanism~e.4 :ARG0-of (a / account-01~e.5 :ARG1~e.6 (i / increase-01~e.8 :ARG0~e.11 (m2 / molecular-physical-entity~e.14 :ARG0-of~e.14 (i2 / inhibit-01~e.14 :ARG1 (p / pathway~e.13 :name (n2 / name :op1 "MAPK"~e.12)))) :ARG1~e.9 (e2 / enzyme :name (n / name :op1 "HER3"~e.10)) :location~e.15 (c / cell-line~e.19,20 :source (t / thyroid~e.18) :ARG1-of (e3 / encode-01 :ARG0 (n5 / nucleic-acid :wiki "DNA" :name (n6 / name :op1 "DNA") :part (g / gene~e.17 :name (n3 / name :op1 "BRAF"~e.16) :ARG2-of~e.17 (m3 / mutate-01~e.17)))))))) :time (n4 / next~e.1)) # ::id bio.bmtr_0003.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Upregulation of HER3 has been found to mediate resistance to PI3K @/@ AKT ( 26 ) or HER2 ( 27 ) inhibitors in HER2 @-@ amplified breast cancer cell lines , which is caused in part through a FoxO3A @-@ dependent induction of HER3 gene transcription . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1 5-1 6-1.1.3 7-1.1 8-1.1.2 9-1.1.2.1.r 10-1.1.2.1.1.1.1.1.1 12-1.1.2.1.1.1.1.1.1 14-1.1.2.1.1.1.1.2.1.1.1 16-1.1.2.1.1.1 17-1.1.2.1.1.1.2.1.1 19-1.1.2.1.1.1.2.2.1.1 21-1.1.2.1 21-1.1.2.1.1 21-1.1.2.1.1.r 22-1.1.2.2.r 23-1.1.2.2.1.1 25-1.1.2.2.1 26-1.1.2.2.2.2.1 27-1.1.2.2.2.2.2 28-1.1.2.2 29-1.1.2.2 33-1.1.3 34-1.1.3.2 34-1.1.3.2.r 35-1.1.3.2.r 38-1.1.3.1.2.1.1.1 40-1.1.3.1.2 41-1.1.3.1 42-1.1.3.1.1.r 43-1.1.3.1.1.1.1.1 44-1.1.3.1.1.1 45-1.1.3.1.1 (f / find-01~e.5 :ARG1 (m / mediate-01~e.7 :ARG0 (u / upregulate-01~e.0 :ARG1~e.1 (e / enzyme :name (n / name :op1 "HER3"~e.2))) :ARG1 (r / resist-01~e.8 :ARG1~e.9 (m2 / molecular-physical-entity~e.21 :ARG0-of~e.21 (i / inhibit-01~e.21 :ARG1 (o / or~e.16 :op1 (p / pathway :name (n2 / name :op1 "PI3K/AKT"~e.10,12) :ARG1-of (d / describe-01 :ARG0 (p2 / publication :ARG1-of (c / cite-01 :ARG2 26~e.14)))) :op2 (e2 / enzyme :name (n3 / name :op1 "HER2"~e.17) :ARG1-of (d2 / describe-01 :ARG1-of (c2 / cite-01 :ARG2 27~e.19)))))) :location~e.22 (c3 / cell-line~e.28,29 :mod (a / amplify-01~e.25 :ARG0 e2~e.23) :source (d4 / disease :wiki "Breast_cancer" :name (n5 / name :op1 "breast"~e.26 :op2 "cancer"~e.27)))) :ARG1-of (c5 / cause-01~e.6,33 :ARG0 (i2 / induce-01~e.41 :ARG2~e.42 (t / transcribe-01~e.45 :ARG1 (g / gene~e.44 :ARG0-of (e3 / encode-01 :ARG1 e~e.43))) :ARG0-of (d3 / depend-01~e.40 :ARG1 (p3 / protein :name (n4 / name :op1 "FoxO3A"~e.38)))) :degree~e.34,35 (p4 / part~e.34)))) # ::id bio.bmtr_0003.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 5A , PLX4032 treatment increased HER3 and HER2 mRNAs in all six BRAF @-@ mutant thyroid cancer cell lines tested . # ::alignments 1-1.4 2-1.4.1.r 3-1.4.1 4-1.4.1.1 6-1.1.1.1.1 7-1.1 8-1 9-1.2.2.1.1.1.1 10-1.2.2.1 11-1.2.2.1.2.1.1 12-1.2.1.1 13-1.3.r 14-1.3.3 15-1.3.1 16-1.3.2.1.1.3.1.1 18-1.3.2.1.1.3 18-1.3.2.1.1.3.2 18-1.3.2.1.1.3.2.r 19-1.3.2 20-1.3.5.2.1 21-1.3 22-1.3 23-1.3.4 (i / increase-01~e.8 :ARG0 (t / treat-04~e.7 :ARG2 (s / small-molecule :name (n / name :op1 "PLX4032"~e.6))) :ARG1 (n8 / nucleic-acid :name (n9 / name :op1 "mRNA"~e.12) :ARG0-of (e / encode-01 :ARG1 (a / and~e.10 :op1 (e2 / enzyme :name (n2 / name :op1 "HER3"~e.9)) :op2 (e3 / enzyme :name (n3 / name :op1 "HER2"~e.11))))) :location~e.13 (c / cell-line~e.21,22 :quant 6~e.15 :source (t2 / thyroid~e.19 :ARG1-of (e4 / encode-01 :ARG0 (n5 / nucleic-acid :wiki "DNA" :name (n6 / name :op1 "DNA") :part (g / gene~e.18 :name (n4 / name :op1 "BRAF"~e.16) :ARG2-of~e.18 (m2 / mutate-01~e.18))))) :mod (a2 / all~e.14) :ARG1-of (t3 / test-01~e.23) :mod (d / disease :wiki "Cancer" :name (n7 / name :op1 "cancer"~e.20))) :ARG1-of (s2 / show-01~e.1 :ARG0~e.2 (f / figure~e.3 :mod "5A"~e.4))) # ::id bio.bmtr_0003.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Similar results were found following treatment with the MEK inhibitor AZD6244 ( not shown ) . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 4-1.2 5-1.2.1 6-1.2.1.1.r 8-1.2.1.1.2.1.1.1 9-1.2.1.1 9-1.2.1.1.2 9-1.2.1.1.2.r 10-1.2.1.1.1.1 12-1.2.1.1.3.1 12-1.2.1.1.3.1.r 13-1.2.1.1.3 (f / find-01~e.3 :ARG1 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :ARG1-of (r2 / resemble-01~e.0)) :ARG1-of (f2 / follow-01~e.4 :ARG2 (t2 / treat-04~e.5 :ARG2~e.6 (s / small-molecule~e.9 :name (n / name :op1 "AZD6244"~e.10) :ARG0-of~e.9 (i / inhibit-01~e.9 :ARG1 (p / protein-family :name (n2 / name :op1 "MEK"~e.8))) :ARG1-of (s2 / show-01~e.13 :polarity~e.12 -~e.12))))) # ::id bio.bmtr_0003.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The effects of the MEK inhibitor on total HER2 , HER3 protein and on pHER3 were dose dependent , and inversely associated with the degree of inhibition of pERK ( Fig . 5B ) . # ::alignments 1-1.1.1 2-1.1.1.1.r 4-1.1.1.1.1.1.1.1 5-1.1.1.1 5-1.1.1.1.1 5-1.1.1.1.1.r 6-1.1.1.2.r 7-1.1.1.2.1.2 8-1.1.1.2.1.1.1 10-1.1.1.2.2.1.1 10-1.1.1.2.3.1.1 11-1.1.1.1.1.1 16-1.1.2 17-1.1 19-1 20-1.2.3 21-1.2 22-1.2.2.r 24-1.2.2.1.r 26-1.2.2.1 28-1.1.1.2.3.2 28-1.2.2.1.1.1.1 30-1.3.1 32-1.3.1.1 (a / and~e.19 :op1 (d / depend-01~e.17 :ARG0 (a2 / affect-01~e.1 :ARG0~e.2 (m / molecular-physical-entity~e.5 :ARG0-of~e.5 (i / inhibit-01~e.5 :ARG1 (p2 / protein-family~e.11 :name (n / name :op1 "MEK"~e.4)))) :ARG1~e.6 (a3 / and :op1 (e2 / enzyme :name (n2 / name :op1 "HER2"~e.8) :mod (t / total~e.7)) :op2 (e3 / enzyme :name (n3 / name :op1 "HER3"~e.10)) :op3 (e4 / enzyme :name (n4 / name :op1 "HER3"~e.10) :ARG3-of (p / phosphorylate-01~e.28)))) :ARG1 (d2 / dose-01~e.16)) :op2 (a4 / associate-01~e.21 :ARG1 a2 :ARG2~e.22 (t2 / thing :degree-of~e.24 (i2 / inhibit-01~e.26 :ARG1 (e5 / enzyme :name (n5 / name :op1 "ERK"~e.28) :ARG1-of p))) :mod (i3 / inverse~e.20)) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.30 :mod "5B"~e.32))) # ::id bio.bmtr_0003.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok RAF or MEK inhibitors induced luciferase activity of a HER3 promoter construct spanning ~ 1 kb upstream of the transcriptional start site in 8505C cells . # ::alignments 0-1.1.1.1.1.1.1 1-1.1 2-1.1.2.1.1.1.1 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 3-1.1.2 3-1.1.2.1 3-1.1.2.1.r 4-1 5-1.2.2 6-1.2 7-1.2.1.r 9-1.2.1.1.1.1.1 10-1.2.1.1 11-1.2.1 12-1.2.1.2 13-1.2.1.2.2 14-1.2.1.2.2.1.1 16-1.2.1.2.1.2 19-1.2.1.2.1.1.1.1 20-1.2.1.2.1.1.1 21-1.2.1.2.1.1 22-1.2.1.2.3.r 23-1.2.1.2.3.1.1 24-1.2.1.2.3 (i / induce-01~e.4 :ARG0 (o / or~e.1 :op1 (m / molecular-physical-entity~e.3 :ARG0-of~e.3 (i2 / inhibit-01~e.3 :ARG1 (p2 / protein-family :name (n / name :op1 "RAF"~e.0)))) :op2 (m2 / molecular-physical-entity~e.3 :ARG0-of~e.3 (i3 / inhibit-01~e.3 :ARG1 (p3 / protein-family :name (n2 / name :op1 "MEK"~e.2))))) :ARG2 (a / activity-06~e.6 :ARG0~e.7 (c / construct-01~e.11 :ARG0-of (p / promote-01~e.10 :ARG1 (e3 / enzyme :name (n3 / name :op1 "HER3"~e.9))) :ARG1-of (s / span-01~e.12 :location (r / relative-position :op1 (s2 / site~e.21 :location-of (s3 / start-01~e.20 :ARG1 (t / transcribe-01~e.19))) :direction (u / upstream~e.16)) :quant (a2 / approximately~e.13 :op1 (d / distance-quantity :quant 1~e.14 :unit (k / kilo-base-pair))) :location~e.22 (c2 / cell-line~e.24 :name (n5 / name :op1 "8505C"~e.23)))) :ARG1 (l / luciferase~e.5))) # ::id bio.bmtr_0003.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Serial deletions identified a minimal HER3 promoter retaining transcriptional response to vemurafenib and AZD6244 , which was located between -@ 401 and -@ 42 bp ( Fig . 5C ) . # ::alignments 0-1.1.1 1-1.1 2-1 4-1.2.2 5-1.2.1.1.1.1 6-1.2 6-1.2.1 6-1.2.1.r 7-1.2.3 8-1.2.3.1.2 9-1.2.3.1 9-1.2.3.1.1 9-1.2.3.1.1.r 10-1.2.3.1.1.1.r 11-1.2.3.1.1.1.1.1.1 12-1.2.3.1.1.1 13-1.2.3.1.1.1.2.1.1 17-1.2.4.r 18-1.2.4 20-1.2.4.1.1 23-1.2.4.2.1 26-1.3.1 28-1.3.1.1 (i / identify-01~e.2 :ARG0 (d / delete-01~e.1 :manner (s / serial~e.0)) :ARG1 (m / molecular-physical-entity~e.6 :ARG0-of~e.6 (p / promote-01~e.6 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.5))) :ARG1-of (m2 / minimal-02~e.4) :ARG0-of (r / retain-01~e.7 :ARG1 (t / thing~e.9 :ARG2-of~e.9 (r2 / respond-01~e.9 :ARG1~e.10 (a / and~e.12 :op1 (s2 / small-molecule :name (n2 / name :op1 "vemurafenib"~e.11)) :op2 (s3 / small-molecule :name (n3 / name :op1 "AZD6244"~e.13)))) :mod (t2 / transcribe-01~e.8))) :location~e.17 (b / between~e.18 :op1 (d2 / distance-quantity :quant -401~e.20 :unit (b2 / base-pair)) :op2 (d3 / distance-quantity :quant -42~e.23 :unit (b3 / base-pair)))) :ARG1-of (d4 / describe-01 :ARG0 (f / figure~e.26 :mod "5C"~e.28))) # ::id bio.bmtr_0003.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This region does not contain any predicted FoxO binding sites . # ::alignments 0-1.2.1 1-1.2 3-1.1 3-1.1.r 4-1 5-1.3.4 6-1.3.3 7-1.3.1.1.1 8-1.3.2 9-1.3 (c / contain-01~e.4 :polarity~e.3 -~e.3 :ARG0 (r / region~e.1 :mod (t / this~e.0)) :ARG1 (p3 / protein-segment~e.9 :part-of (p / protein :name (n / name :op1 "FoxO"~e.7)) :ARG1-of (b / bind-01~e.8) :ARG1-of (p2 / predict-01~e.6) :mod (a / any~e.5))) # ::id bio.bmtr_0003.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Moreover , PLX4032 led to an increase in phosphorylation of FoxO1 @/@ 3A between 4 @–@ 10h after addition of compound ( not shown ) , which is known to promote its dissociation from DNA , and likely discards involvement of these factors as transcriptional regulators of HER3 in response to MAPK pathway inhibition . # ::alignments 0-1 2-1.1.1.1.1 3-1.1 6-1.1.2 7-1.1.2.1.r 8-1.1.2.1 9-1.1.2.1.1.r 10-1.1.2.1.1.1.1 12-1.1.2.1.1.1.1 13-1.1.2.2.2 14-1.1.2.2.2.1.1 17-1.1.2.2 18-1.1.2.2.1 19-1.1.2.2.1.1.r 20-1.1.2.2.1.1 22-1.1.2.3.1 22-1.1.2.3.1.r 23-1.1.2.3 28-1.1.2.4.2 30-1.1.2.4 31-1.1.2.4.1.1 31-1.1.2.4.1.1.r 32-1.1.2.4.1 33-1.1.2.4.1.2.r 34-1.1.2.4.1.2.2.1 36-1.1.2.2.2 37-1.1.2.5.2 38-1.1.2.5 39-1.1.2.5.1 40-1.1.2.5.1.1.r 41-1.1.2.5.1.1.1 42-1.1.2.5.1.1 43-1.1.2.2.r 43-1.1.2.5.1.2.r 44-1.1.2.5.1.2.2 45-1.1.2.5.1.2 45-1.1.2.5.1.2.1 45-1.1.2.5.1.2.1.r 46-1.1.2.5.1.2.1.1.r 47-1.1.2.5.1.2.1.1.1.1 48-1.1.2.5.3.r 49-1.1.2.5.3 50-1.1.2.5.3.1.r 51-1.1.2.5.3.1.1.1.1 52-1.1.2.5.3.1.1 53-1.1.2.5.3.1 (a / and~e.0 :op2 (l / lead-03~e.3 :ARG0 (s / small-molecule :name (n / name :op1 "PLX4032"~e.2)) :ARG1 (i / increase-01~e.6 :ARG1~e.7 (p / phosphorylate-01~e.8 :ARG1~e.9 (p2 / protein :name (n2 / name :op1 "FoxO1/3A"~e.10,12))) :time~e.43 (a2 / after~e.17 :op1 (a3 / add-02~e.18 :ARG1~e.19 (c / compound~e.20)) :quant (b / between~e.13,36 :op1 (t / temporal-quantity :quant 4~e.14 :unit (h / hour)) :op2 (t2 / temporal-quantity :quant 10 :unit (h2 / hour)))) :ARG1-of (s2 / show-01~e.23 :polarity~e.22 -~e.22) :ARG0-of (p3 / promote-01~e.30 :ARG1 (d / dissociate-01~e.32 :ARG1~e.31 p2~e.31 :ARG2~e.33 (n5 / nucleic-acid :wiki "DNA" :name (n6 / name :op1 "DNA"~e.34))) :ARG1-of (k / know-01~e.28)) :ARG0-of (d3 / discard-01~e.38 :ARG1 (i2 / involve-01~e.39 :ARG1~e.40 (f / factor~e.42 :mod (t3 / this~e.41)) :mod~e.43 (m / molecular-physical-entity~e.45 :ARG0-of~e.45 (r / regulate-01~e.45 :ARG1~e.46 (e / enzyme :name (n3 / name :op1 "HER3"~e.47))) :ARG0-of (t4 / transcribe-01~e.44))) :ARG1-of (l2 / likely-01~e.37) :ARG2-of~e.48 (r2 / respond-01~e.49 :ARG1~e.50 (i3 / inhibit-01~e.53 :ARG1 (p4 / pathway~e.52 :name (n4 / name :op1 "MAPK"~e.51)))))))) # ::id bio.bmtr_0003.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The minimal HER3 promoter region regulated by MAPK inhibitors overlaps with sequences previously described to be immunoprecipitated using antibodies against the ZFN217 transcription factor and CtBP1 @/@ CtBP2 corepressors ( 28 @–@ 30 ) . # ::alignments 1-1.1.1.2 2-1.1.1.1.1.1.1 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 4-1.1 5-1.1.2 6-1.1.2.1.r 7-1.1.2.1.1.1.1.1 8-1.1.2.1 8-1.1.2.1.1 8-1.1.2.1.1.r 9-1 10-1.2.r 11-1.2 12-1.2.1.2.1 13-1.2.1.2 13-1.3 16-1.2.1 17-1.2.1.1 18-1.2.1.1.1 19-1.2.1.1.1.1 21-1.2.1.1.1.1.1.1.1.1.1.1 22-1.2.1.1.1.1.1.1.1 23-1.2.1.1.1.1.1.1 24-1.2.1.1.1.1.1 25-1.2.1.1.1.1.1.2.1.1.1.1.1 27-1.2.1.1.1.1.1.2.1.1.2.1.1 30-1.3.1.1.1.1 32-1.3.1.1.1.2 (o / overlap-01~e.9 :ARG0 (r / region~e.4 :mod (m2 / molecular-physical-entity~e.3 :ARG0-of~e.3 (p / promote-01~e.3 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.2))) :ARG1-of (m / minimal-02~e.1)) :ARG1-of (r2 / regulate-01~e.5 :ARG0~e.6 (m3 / molecular-physical-entity~e.8 :ARG0-of~e.8 (i / inhibit-01~e.8 :ARG1 (p2 / pathway :name (n2 / name :op1 "MAPK"~e.7)))))) :ARG1~e.10 (s / sequence~e.11 :ARG1-of (i2 / immunoprecipitate-01~e.16 :ARG2-of (u / use-01~e.17 :ARG1 (a / antibody~e.18 :ARG0-of (o2 / oppose-01~e.19 :ARG1 (a2 / and~e.24 :op1 (f / factor~e.23 :ARG0-of (t / transcribe-01~e.22 :ARG1 (e2 / enzyme :name (n3 / name :op1 "ZFN217"~e.21)))) :op2 (m4 / molecular-physical-entity :ARG0-of (r3 / repress-01 :ARG1 (o3 / or :op1 (p5 / protein :name (n4 / name :op1 "CtBP1"~e.25)) :op2 (p6 / protein :name (n5 / name :op1 "CtBP2"~e.27))))))))) :ARG1-of (d / describe-01~e.13 :time (p4 / previous~e.12)))) :ARG1-of (d2 / describe-01~e.13 :ARG0 (p3 / publication :ARG1-of (c3 / cite-01 :ARG2 (v / value-interval :op1 28~e.30 :op2 30~e.32))))) # ::id bio.bmtr_0003.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok CtBPs have also been described to negatively regulate transcriptional activity of the HER3 promoter in breast carcinoma cell lines ( 30 ) . # ::alignments 2-1.3 4-1 4-1.4 4-1.4.r 5-1.2.r 6-1.2 7-1.2 8-1.2.2.2 9-1.2.2 10-1.2.2.1.r 12-1.2.2.1.1.1.1.1 13-1.2.2.1 13-1.2.2.1.1 13-1.2.2.1.1.r 14-1.2.3.r 15-1.2.3.1.2 16-1.2.3.1.1.1 17-1.2.3 18-1.2.3 20-1.4.1.1.1 (d / describe-01~e.4 :ARG1 (p / protein :name (n / name :op1 "CtBP")) :ARG2~e.5 (d3 / downregulate-01~e.6,7 :ARG0 p :ARG1 (a2 / activity-06~e.9 :ARG0~e.10 (m / molecular-physical-entity~e.13 :ARG0-of~e.13 (p2 / promote-01~e.13 :ARG1 (e / enzyme :name (n2 / name :op1 "HER3"~e.12)))) :ARG1 (t / transcribe-01~e.8)) :location~e.14 (c / cell-line~e.17,18 :mod (m2 / medical-condition :name (n4 / name :op1 "carcinoma"~e.16) :mod (b / breast~e.15)))) :mod (a / also~e.2) :ARG1-of~e.4 (d2 / describe-01~e.4 :ARG0 (p3 / publication :ARG1-of (c3 / cite-01 :ARG2 30~e.20)))) # ::id bio.bmtr_0003.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Silencing of CtBP1 , and to a lesser extent CtBP2 , increased basal HER3 in 8505C cells , and markedly potentiated the effects of PLX4032 ( Fig . 5D and 5E ) . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1.1 4-1.1.1.1 7-1.1.1.1.2.2 7-1.1.1.1.2.2.1 7-1.1.1.1.2.2.1.r 9-1.1.1.1.2.1.1 11-1.1 12-1.1.2.2 13-1.1.2.1.1 14-1.1.3.r 15-1.1.3.1.1 16-1.1.3 18-1 18-1.3.1 19-1.2.3 22-1.2.1 23-1.2.1.1.r 24-1.2.1.1.1.1 26-1.3.1.1 26-1.3.1.2 28-1.3.1.1.1 29-1.3.1 30-1.3.1.2.1 (a / and~e.18 :op1 (i / increase-01~e.11 :ARG0 (s / silence-01~e.0 :ARG1~e.1 (a2 / and~e.4 :op1 (p / protein :name (n / name :op1 "CtBP1"~e.2)) :op2 (p2 / protein :name (n2 / name :op1 "CtBP2"~e.9) :degree (l / less~e.7 :degree~e.7 (m / more~e.7))))) :ARG1 (e / enzyme :name (n3 / name :op1 "HER3"~e.13) :mod (b / basal~e.12)) :location~e.14 (c / cell-line~e.16 :name (n4 / name :op1 "8505C"~e.15))) :op2 (p3 / potentiate-01 :ARG1 (a3 / affect-01~e.22 :ARG0~e.23 (s2 / small-molecule :name (n5 / name :op1 "PLX4032"~e.24))) :ARG2 s :ARG3 (m2 / marked~e.19)) :ARG1-of (d / describe-01 :ARG0 (a4 / and~e.18,29 :op1 (f / figure~e.26 :mod "5D"~e.28) :op2 (f2 / figure~e.26 :mod "5E"~e.30)))) # ::id bio.bmtr_0003.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Knockdown of these factors modestly increased basal and PLX4032 @-@ induced HER2 levels , which likely contributes to the remarkable increase in pHER3 we observed ( Fig . 5D and 5E ) . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1 3-1.1.1 4-1.3 5-1 6-1.2.1.1.2 7-1.2 8-1.2.2.1.2.1.1.1 10-1.2.2.1.2 11-1.2.1.1.1.1 11-1.2.2.1.1.1 12-1.2.1 12-1.2.2 15-1.4.2 16-1.4 19-1.4.1.2 20-1.4.1 23-1.4.1.3.1 24-1.4.1.3 26-1.5.1.1 26-1.5.1.2 28-1.5.1.1.1 29-1.5.1 30-1.5.1.2.1 (i / increase-01~e.5 :ARG0 (k / knock-down-02~e.0 :ARG1~e.1 (f / factor~e.3 :mod (t / this~e.2))) :ARG1 (a / and~e.7 :op1 (l2 / level~e.12 :mod (e / enzyme :name (n / name :op1 "HER2"~e.11) :mod (b / basal~e.6))) :op2 (l3 / level~e.12 :mod (e2 / enzyme :name (n2 / name :op1 "HER2"~e.11) :ARG2-of (i2 / induce-01~e.10 :ARG0 (s / small-molecule :name (n3 / name :op1 "PLX4032"~e.8)))))) :degree (m / modest~e.4) :ARG0-of (c / contribute-01~e.16 :ARG1 (i3 / increase-01~e.20 :ARG1 (e3 / enzyme :name (n4 / name :op1 "HER3") :ARG3-of (p / phosphorylate-01)) :ARG1-of (r / remarkable-02~e.19) :ARG1-of (o / observe-01~e.24 :ARG0 (w / we~e.23))) :ARG1-of (l / likely-01~e.15)) :ARG1-of (d / describe-01 :ARG0 (a2 / and~e.29 :op1 (f2 / figure~e.26 :mod "5D"~e.28) :op2 (f3 / figure~e.26 :mod "5E"~e.30)))) # ::id bio.bmtr_0003.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Finally , CtBP1 and CtBP2 chromatin immunoprecipitation assays showed decreased binding to the HER3 promoter after treatment with PLX4032 ( Fig . 5F ) . # ::alignments 0-1.1 0-1.1.r 2-1.2.1.1.1.1.1 3-1.2.1.1 4-1.2.1.1.2.1.1 5-1.2.1.2 6-1.2.1 7-1.2 8-1 9-1.3.2 10-1.3 11-1.3.1.r 13-1.3.1.1.1.1.1 14-1.3.1 14-1.3.1.1 14-1.3.1.1.r 15-1.3.2.1 16-1.3.2.1.1 17-1.3.2.1.1.1.r 18-1.3.2.1.1.1.1.1 20-1.4.1 22-1.4.1.1 (s / show-01~e.8 :li~e.0 -1~e.0 :ARG0 (a / assay-01~e.7 :ARG1 (i / immunoprecipitate-01~e.6 :ARG1 (a2 / and~e.3 :op1 (p / protein :name (n / name :op1 "CtBP1"~e.2)) :op2 (p2 / protein :name (n2 / name :op1 "CtBP2"~e.4))) :mod (c / chromatin~e.5))) :ARG1 (b / bind-01~e.10 :ARG2~e.11 (m / molecular-physical-entity~e.14 :ARG0-of~e.14 (p3 / promote-01~e.14 :ARG1 (e / enzyme :name (n3 / name :op1 "HER3"~e.13)))) :ARG1-of (d / decrease-01~e.9 :time (a3 / after~e.15 :op1 (t / treat-04~e.16 :ARG2~e.17 (s2 / small-molecule :name (n4 / name :op1 "PLX4032"~e.18)))))) :ARG1-of (d2 / describe-01 :ARG0 (f2 / figure~e.20 :mod "5F"~e.22))) # ::id bio.bmtr_0003.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These findings were confirmed in a second cell line ( Supplementary Fig. S5A ) . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 3-1 4-1.2.r 6-1.2.1 6-1.2.1.1 6-1.2.1.1.r 7-1.2 8-1.2 10-1.3.1.2 11-1.3.1 12-1.3.1.1 (c / confirm-01~e.3 :ARG0 (t / thing~e.1 :ARG1-of~e.1 (f / find-01~e.1) :mod (t2 / this~e.0)) :location~e.4 (c2 / cell-line~e.7,8 :ord (o / ordinal-entity~e.6 :value~e.6 2~e.6)) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.11 :mod "S5A"~e.12 :ARG2-of (s / supplement-01~e.10)))) # ::id bio.bmtr_0003.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The increase in expression of HER3 after MAPK inhibition is due to activation of gene transcription , which was associated with a reduction of binding of the transcriptional repressors CTBP1 and CTBP2 to the HER3 gene promoter . # ::alignments 1-1.2 2-1.2.1.r 3-1.2.1 4-1.2.1.1.r 5-1.2.1.1.1.1 6-1.2.2 7-1.2.2.1.1.1.1 8-1.2.2.1 10-1 11-1 12-1.1 13-1.1.1.r 14-1.1.1.1 15-1.1.1 19-1.1.2 20-1.1.2.1.r 22-1.1.2.1 23-1.1.2.1.1.r 24-1.1.2.1.1 25-1.1.2.1.1.1.r 27-1.1.2.1.1.1.3 28-1.1.2.1.1.1.1 28-1.1.2.1.1.1.1.2 28-1.1.2.1.1.1.1.2.r 29-1.1.2.1.1.1.1.1.1 30-1.1.2.1.1.1 31-1.1.2.1.1.1.2.1.1 32-1 32-1.1.2.1.1.2.r 34-1.1.2.1.1.2.1.1.1.1 35-1.1.2.1.1.2.1.1 36-1.1.2.1.1.2 36-1.1.2.1.1.2.1 36-1.1.2.1.1.2.1.r (c / cause-01~e.10,11,32 :ARG0 (a2 / activate-01~e.12 :ARG1~e.13 (t / transcribe-01~e.15 :ARG1 (g / gene~e.14)) :ARG1-of (a3 / associate-01~e.19 :ARG2~e.20 (r / reduce-01~e.22 :ARG1~e.23 (b / bind-01~e.24 :ARG1~e.25 (a4 / and~e.30 :op1 (p3 / protein~e.28 :name (n3 / name :op1 "CTBP1"~e.29) :ARG0-of~e.28 (r2 / repress-01~e.28)) :op2 (p4 / protein :name (n4 / name :op1 "CTBP2"~e.31) :ARG0-of r2) :ARG0-of (t2 / transcribe-01~e.27)) :ARG2~e.32 (m / molecular-physical-entity~e.36 :ARG0-of~e.36 (p2 / promote-01~e.36 :ARG1 (g2 / gene~e.35 :ARG0-of (e3 / encode-01 :ARG1 e2~e.34)))))))) :ARG1 (i / increase-01~e.1 :ARG1~e.2 (e / express-03~e.3 :ARG1~e.4 (e2 / enzyme :name (n / name :op1 "HER3"~e.5))) :time (a / after~e.6 :op1 (i2 / inhibit-01~e.8 :ARG1 (p / pathway :name (n2 / name :op1 "MAPK"~e.7)))))) # ::id bio.bmtr_0003.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These corepressors have been previously linked to inhibition of HER3 transcription through promoter regions that show overlapping occupancy with ZNF217 , a transcription factor also involved in HER3 regulation ( 30 ) . # ::alignments 0-1.1.1 4-1.4 5-1 6-1.2.r 7-1.2 8-1.2.1.r 9-1.2.1.1.1.1 10-1.2.1 12-1.3.1 13-1.3 15-1.3.2 16-1.3.2.1.3 19-1.3.2.1.1.1.1 22-1.3.2.1.1.2.1 23-1.3.2.1.1.2 24-1.3.2.1.1.2.2.2 25-1.3.2.1.1.2.2 26-1.3.2.1.1.2.2.1.r 27-1.3.2.1.1.2.2.1.1 28-1.3.2.1.1.2.2.1 30-1.5.1.1.1 (l / link-01~e.5 :ARG1 (c / corepressor :mod (t / this~e.0)) :ARG2~e.6 (i / inhibit-01~e.7 :ARG1~e.8 (t2 / transcribe-01~e.10 :ARG1 (e / enzyme :name (n / name :op1 "HER3"~e.9)))) :ARG3 (r / region~e.13 :ARG0-of (p2 / promote-01~e.12) :ARG0-of (s / show-01~e.15 :ARG1 (o / occupy-01 :ARG0 (p3 / protein :name (n2 / name :op1 "ZNF217"~e.19) :mod (f / factor~e.23 :ARG0-of (t3 / transcribe-01~e.22) :ARG1-of (i2 / involve-01~e.25 :ARG2~e.26 (r2 / regulate-01~e.28 :ARG1 e~e.27) :mod (a2 / also~e.24)))) :ARG1 r :ARG0-of (o2 / overlap-01~e.16)))) :time (p / previous~e.4) :ARG1-of (d / describe-01 :ARG0 (p4 / publication :ARG1-of (c2 / cite-01 :ARG2 30~e.30)))) # ::id bio.bmtr_0003.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Accordingly , knockdown of CTBPs acutely induced HER3 expression and phosphorylation in thyroid cancer cells . # ::alignments 0-1.4 2-1.1 5-1.3 5-1.3.r 6-1 7-1.2.1.1.1.1 8-1.2.1 9-1.2 10-1.2.2 11-1.2.r 12-1.2.3.2.2.1 13-1.2.3.2.2.2 14-1.2.3 (i / induce-01~e.6 :ARG0 (k / knock-down-02~e.2 :ARG1 (p / protein :name (n / name :op1 "CTBP"))) :ARG2~e.11 (a2 / and~e.9 :op1 (e / express-03~e.8 :ARG1 (e2 / enzyme :name (n2 / name :op1 "HER3"~e.7))) :op2 (p2 / phosphorylate-01~e.10 :ARG1 e2) :location (c / cell~e.14 :source (t / thyroid) :mod (d / disease :wiki "Thyroid_cancer" :name (n3 / name :op1 "thyroid"~e.12 :op2 "cancer"~e.13)))) :manner~e.5 (a / acute~e.5) :manner (a3 / accordingly~e.0)) # ::id bio.bmtr_0003.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok MAPK inhibition may dictate a chromatin redistribution of these repressors , and thus activate HER3 transcription . # ::alignments 0-1.1.1.1.1.1 1-1.1.1 2-1 3-1.1 5-1.1.2.2 6-1.1.2 7-1.1.2.1.r 8-1.1.2.1.1 9-1.1.2.1 9-1.1.2.1.2 9-1.1.2.1.2.r 12-1.2 13-1.2.1 14-1.2.1.2.1.1.1 15-1.2.1.2 (p / possible-01~e.2 :ARG1 (d / dictate-01~e.3 :ARG0 (i / inhibit-01~e.1 :ARG1 (e2 / enzyme :name (n / name :op1 "MAPK"~e.0))) :ARG1 (r / redistribute-01~e.6 :ARG1~e.7 (m / molecular-physical-entity~e.9 :mod (t / this~e.8) :ARG0-of~e.9 (r2 / repress-01~e.9)) :mod (c / chromatin~e.5))) :ARG0-of (c2 / cause-01~e.12 :ARG1 (a2 / activate-01~e.13 :ARG0 i :ARG1 (t2 / transcribe-01~e.15 :ARG1 (e / enzyme :name (n2 / name :op1 "HER3"~e.14)))))) # ::id bio.bmtr_0003.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The biochemical mechanisms involved in delocalization of CtBPs by MAPK inhibition have not been explored , but posttranslational modifications are known to regulate the repressive activity of CtBPs either by translocation to the cytoplasm or by targeting them for degradation ( 36 , 37 ) . # ::alignments 1-1.1.2.1 2-1.1.2 3-1.1.2.2 9-1.1.2.2.1.1.1.1.1 10-1.1.2.2.1.1 12-1.1.1 12-1.1.1.r 14-1.1 16-1 17-1.2.1.1.1 17-1.2.1.1.1.1 17-1.2.1.1.1.1.r 17-1.3.1.1.1.1.r 18-1.2.1.1 20-1.2 22-1.2.1 24-1.2.1.2.2 25-1.2.1.2 29-1.2.1.3.r 30-1.2.1.3.1 31-1.2.1.3.1.2.r 33-1.2.1.3.1.2 34-1.2.1.3 36-1.2.1.3.2 38-1.2.1.3.2.2.r 39-1.2.1.3.2.2 41-1.3.1.1.1.1 43-1.3.1.1.1.2 (c / contrast-01~e.16 :ARG1 (e / explore-01~e.14 :polarity~e.12 -~e.12 :ARG1 (m / mechanism~e.2 :mod (b / biochemical~e.1) :ARG1-of (i / involve-01~e.3 :ARG2 (d / delocalize-01 :ARG0 (i2 / inhibit-01~e.10 :ARG1 (e2 / enzyme :name (n / name :op1 "MAPK"~e.9))) :ARG1 (p2 / protein :name (n2 / name :op1 "CtBP")))))) :ARG2 (k / know-01~e.20 :ARG1 (r / regulate-01~e.22 :ARG0 (m2 / modify-01~e.18 :time (a3 / after~e.17 :op1~e.17 (t3 / translate-02~e.17))) :ARG1 (a / activity-06~e.25 :ARG0 p2 :ARG1 (r2 / repress-01~e.24)) :manner~e.29 (o / or~e.34 :op1 (t / translocate-01~e.30 :ARG1 p2 :ARG2~e.31 (c2 / cytoplasm~e.33)) :op2 (t2 / target-01~e.36 :ARG1 p2 :purpose~e.38 (d2 / degrade-01~e.39 :ARG1 p2))))) :ARG1-of (d3 / describe-01 :ARG0 (p4 / publication :ARG1-of (c3 / cite-01 :ARG2 (a2 / and :op1~e.17 36~e.41 :op2 37~e.43))))) # ::id bio.bmtr_0004.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Site @-@ Specific Monoubiquitination Activates Ras by Impeding GTPase Activating Protein ( PMC3537887 ) # ::alignments 0-1.2.1.2.1 2-1.2.1.2 3-1.2.1 3-1.2.1.1 3-1.2.1.1.r 4-1.2 5-1.2.2.1.1 6-1.2.3.r 7-1.2.3 8-1.2.3.2.1.1 9-1.2.3.2.1.2 10-1.2.3.2.1.3 12-1.1 (p / publication-91 :ARG8 "PMC3537887"~e.12 :ARG1 (a / activate-01~e.4 :ARG0 (u / ubiquitinate-01~e.3 :quant~e.3 1~e.3 :ARG1-of (s / specific-02~e.2 :ARG2 (p3 / protein-segment~e.0))) :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.5)) :manner~e.6 (i / impede-01~e.7 :ARG0 u :ARG1 (p2 / protein :name (n2 / name :op1 "GTPase"~e.8 :op2 "Activating"~e.9 :op3 "Protein"~e.10))))) # ::id bio.bmtr_0004.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Passage 1 @-@ 1 ( Results ) # ::alignments 0-1 1-1.1 3-1.1 5-1.2 5-1.2.1 5-1.2.1.r (p / passage~e.0 :mod "1-1"~e.1,3 :part-of (t / thing~e.5 :ARG2-of~e.5 (r / result-01~e.5))) # ::id bio.bmtr_0004.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We next considered the effect of Ras monoubiquitination on GAP @-@ mediated hydrolysis . # ::alignments 0-1.1 1-1.3 2-1 4-1.2 5-1.2.1.r 6-1.2.1.2.1.1 7-1.2.1 7-1.2.1.1 7-1.2.1.1.r 8-1.2.2.r 9-1.2.2.1.1.1.1 11-1.2.2.1 12-1.2.2 (c / consider-02~e.2 :ARG0 (w / we~e.0) :ARG1 (a / affect-01~e.4 :ARG0~e.5 (u / ubiquitinate-01~e.7 :quant~e.7 1~e.7 :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.6))) :ARG1~e.8 (h / hydrolyze-01~e.12 :ARG1-of (m / mediate-01~e.11 :ARG0 (p / protein :name (n2 / name :op1 "GAP"~e.9))))) :time (n3 / next~e.1)) # ::id bio.bmtr_0004.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To this end we compared the rate of GTP hydrolysis for Ras and mUbRas in the presence of the catalytic domains of two GAPs , NF1 ( NF1 @-@ 333 ) and p120GAP( GAP @-@ 334 ) . # ::alignments 1-1.4 3-1.1 4-1 6-1.2 6-1.3 8-1.2.1.1.1.1 8-1.3.1.1.1.1 9-1.2.1 9-1.3.1 11-1.2.1.1.2.1.1.1 11-1.3.1.1.2.1.1.1 12-1.2.1.2.1 16-1.2.1.2 17-1.2.1.2.1.r 19-1.2.1.2.1.3 20-1.2.1.2.1.1 20-1.2.1.2.1.2 23-1.2.1.2.1.1.2.2.1.1.1 25-1.2.1.2.1.1.2.1.1 27-1.2.1.2.1.1.2.1.1 29-1.2.1.2.1.1.1.1 31-1.2.1.2.1 33-1.2.1.2.1.2.1.1 35-1.2.1.2.1.2.1.1 (c / compare-01~e.4 :ARG0 (w / we~e.3) :ARG1 (r / rate~e.6 :degree-of (h / hydrolyze-01~e.9 :ARG1 (s / small-molecule :name (n / name :op1 "GTP"~e.8) :ARG1-of (b / bind-01 :ARG2 (e / enzyme :name (n2 / name :op1 "Ras"~e.11)))) :condition (p / present-02~e.16 :ARG1~e.17 (a / and~e.12,31 :op1 (d2 / domain~e.20 :name (n10 / name :op1 "NF1-333"~e.29) :part-of (p4 / protein :name (n12 / name :op1 "NF1"~e.25,27) :ARG1-of (i / include-91 :ARG2 (p6 / protein :name (n13 / name :op1 "GAP"~e.23))))) :op2 (d3 / domain~e.20 :name (n11 / name :op1 "GAP-334"~e.33,35) :part-of (p7 / protein :name (n14 / name :op1 "p120GAP") :ARG1-of (i2 / include-91 :ARG2 p6))) :ARG0-of (c2 / catalyze-01~e.19))))) :ARG2 (r2 / rate~e.6 :degree-of (h2 / hydrolyze-01~e.9 :ARG1 (s2 / small-molecule :name (n9 / name :op1 "GTP"~e.8) :ARG1-of (b2 / bind-01 :ARG2 (e2 / enzyme :name (n3 / name :op1 "Ras"~e.11) :ARG3-of (u / ubiquitinate-01 :quant 1))))) :condition p) :purpose (t / this~e.1)) # ::id bio.bmtr_0004.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok At a GAP @-@ to @-@ Ras ratio of 1 @:@ 500 , we observed an order of magnitude increase in the rate of GTP hydrolysis for unmodified Ras relative to the intrinsic rate of GTP hydrolysis . # ::alignments 2-1.2.3.2.1.1.1 6-1.2.3.2.2.1.1 7-1.2.3.2 8-1.2.3.2 9-1.2.3.1 11-1.2.3.1 13-1.1 14-1 17-1.2.2 19-1.2 22-1.2.1 22-1.2.2.2 23-1.2.1.1.r 23-1.2.2 24-1.2.1.1.1.1.1 25-1.2.1.1 27-1.2.1.1.1.2.1.2 27-1.2.1.1.1.2.1.2.1 27-1.2.1.1.1.2.1.2.1.r 28-1.2.1.1.1.2.1.1.1 32-1.2.2.2.1 33-1.2.2.2 34-1.2.2.2.2.r 35-1.2.2.2.2.1.1.1 36-1.2.2.2.2 (o / observe-01~e.14 :ARG0 (w / we~e.13) :ARG1 (i / increase-01~e.19 :ARG1 (r / rate~e.22 :degree-of~e.23 (h / hydrolyze-01~e.25 :ARG1 (s / small-molecule :name (n / name :op1 "GTP"~e.24) :ARG1-of (b / bind-01 :ARG2 (e / enzyme :name (n2 / name :op1 "Ras"~e.28) :ARG1-of (m2 / modify-01~e.27 :polarity~e.27 -~e.27)))))) :ARG4 (p2 / product-of~e.17,23 :op1 (a / about :op1 10) :op2 (r3 / rate~e.22,33 :mod (i2 / intrinsic~e.32) :degree-of~e.34 (h2 / hydrolyze-01~e.36 :ARG1 (s2 / small-molecule :name (n5 / name :op1 "GTP"~e.35))))) :condition (e3 / equal-01 :ARG2 "1/500"~e.9,11 :ARG1 (r4 / ratio-of~e.7,8 :op1 (p / protein :name (n3 / name :op1 "GAP"~e.2)) :op2 (e2 / enzyme :name (n4 / name :op1 "Ras"~e.6)))))) # ::id bio.bmtr_0004.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok No increase in the rate of GTP hydrolysis was observed for mUbRas in the presence of the same GAP @-@ to Ras ratio ( Fig . 5b ) . # ::alignments 0-1.1.1 0-1.1.1.r 1-1.1 2-1.1.2.r 4-1.1.2 5-1.1.2.1.r 6-1.1.2.1.1.1.1 7-1.1.2.1 9-1 12-1.1.3.r 14-1.1.3 15-1.1.3.1 17-1.1.3.1.3 18-1.1.3.1.1.1.1 21-1.1.2.1.1.2.1.1.1 21-1.1.3.1.2.1.1 22-1.1.3.1 24-1.2.1 26-1.2.1.1 (o / observe-01~e.9 :ARG1 (i / increase-01~e.1 :polarity~e.0 -~e.0 :ARG1~e.2 (r / rate~e.4 :degree-of~e.5 (h / hydrolyze-01~e.7 :ARG1 (s / small-molecule :name (n / name :op1 "GTP"~e.6) :ARG1-of (b / bind-01 :ARG2 (e / enzyme :name (n4 / name :op1 "Ras"~e.21) :ARG3-of (u / ubiquitinate-01 :quant 1)))))) :condition~e.12 (p / present-02~e.14 :ARG1 (r2 / ratio-of~e.15,22 :op1 (p2 / protein :name (n2 / name :op1 "GAP"~e.18)) :op2 (e2 / enzyme :name (n3 / name :op1 "Ras"~e.21)) :ARG1-of (s2 / same-01~e.17)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.24 :mod "5b"~e.26))) # ::id bio.bmtr_0004.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Therefore , mUbRas is insensitive to GAP @-@ mediated regulation , similar to an oncogenic Ras @-@ G12V mutation . # ::alignments 0-1 4-1.1 4-1.1.1 4-1.1.1.r 5-1.1.3.r 6-1.1.3.2.1.1.1 8-1.1.3.2 9-1.1.3 11-1.1.4 12-1.1.4.1.3 14-1.1.4.1.3 14-1.1.4.1.3.1.2.1 15-1.1.2.1.1 15-1.1.4.1.2.1.1 17-1.1.4.1.1 18-1.1.4.1 (c / cause-01~e.0 :ARG1 (s / sensitive-03~e.4 :polarity~e.4 -~e.4 :ARG0 (e / enzyme :name (n / name :op1 "Ras"~e.15) :ARG3-of (u / ubiquitinate-01 :quant 1)) :ARG1~e.5 (r / regulate-01~e.9 :ARG1 e :ARG1-of (m / mediate-01~e.8 :ARG0 (p / protein :name (n2 / name :op1 "GAP"~e.6)))) :ARG1-of (r2 / resemble-01~e.11 :ARG2 (m2 / mutate-01~e.18 :value "G12V"~e.17 :ARG2 (e2 / enzyme :name (n3 / name :op1 "Ras"~e.15)) :ARG0-of (c2 / cause-01~e.12,14 :ARG1 (d / disease :wiki "Cancer" :name (n4 / name :op1 "cancer"~e.14))))))) # ::id bio.bmtr_0004.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We obtained similar results using K @-@ Ras ( Supplementary Figure 6 ) , indicating that the effects of monoubiquitination on Ras are not isoform @-@ specific . # ::alignments 0-1.1 1-1 2-1.2.2 3-1.2 3-1.2.1 3-1.2.1.r 4-1.3 5-1.3.2.1.1 7-1.3.2.1.1 9-1.2.3.1.2 10-1.2.3.1 11-1.2.3.1.1 14-1.2.4 15-1.2.4.1.r 17-1.2.4.1.2 18-1.2.4.1.2.1.r 19-1.2.4.1.2.1 19-1.2.4.1.2.1.1 19-1.2.4.1.2.1.1.r 20-1.2.4.1.2.2.r 21-1.2.4.1.2.2.1.1 23-1.2.4.1.1 23-1.2.4.1.1.r 24-1.2.4.1.3 26-1.2.4.1 (o / obtain-01~e.1 :ARG0 (w / we~e.0) :ARG1 (t / thing~e.3 :ARG2-of~e.3 (r / result-01~e.3) :ARG1-of (r2 / resemble-01~e.2) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.10 :mod 6~e.11 :ARG2-of (s / supplement-01~e.9))) :ARG0-of (i / indicate-01~e.14 :ARG1~e.15 (s2 / specific-02~e.26 :polarity~e.23 -~e.23 :ARG1 (a / affect-01~e.17 :ARG0~e.18 (u2 / ubiquitinate-01~e.19 :quant~e.19 1~e.19) :ARG1~e.20 (e2 / enzyme :name (n2 / name :op1 "Ras"~e.21))) :ARG2 (i2 / isoform~e.24)))) :manner (u / use-01~e.4 :ARG0 w :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.5,7)))) # ::id bio.bmtr_0004.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To verify that the differences between the enzymatic and chemical ubiquitination linkers ( seven bonds and five bonds , respectively ) do not alter GAP @-@ responsiveness , we placed an additional cysteine at the c @-@ terminus of Ubiquitin ( Ubiquitin @-@ C77 ) , thereby creating a linker one bond longer than the native linker . # ::alignments 1-1.6 2-1.6.2.r 4-1.6.2.2 7-1.5.1 7-1.5.1.1.3 7-1.6.2.2.1 7-1.6.2.2.1.3.1 7-1.6.2.2.2 9-1.6.2.2.2.1.1 10-1.6.2.2.1.3 10-1.6.2.2.2.1 13-1.6.2.2.1.1.1 14-1.6.2.2.1.1 16-1.6.2.2.2.2.1 17-1.6.2.2.2.2 22-1.6.2.1 22-1.6.2.1.r 23-1.6.2 24-1.6.2.3.1.1.1 28-1.1 29-1 31-1.2.2 32-1.2.1.1 32-1.4.2.2.1 37-1.3.1.1 39-1.3.2.1.1 41-1.3.2.1.1 46-1.4.r 47-1.5 50-1.5.1.1.1.1 51-1.5.1.1.1 52-1.5.1.1 52-1.5.1.1.2 52-1.5.1.1.2.r 53-1.5.1.1.3.r 55-1.5.1.1.3.1 (p / place-01~e.29 :ARG0 (w / we~e.28) :ARG1 (a / amino-acid :name (n / name :op1 "cysteine"~e.32) :mod (a2 / additional~e.31)) :ARG2 (p2 / protein-segment :name (n2 / name :op1 "C-terminus"~e.37) :part-of (p3 / protein :name (n3 / name :op1 "ubiquitin"~e.39,41))) :manner-of~e.46 (b4 / become-01 :ARG1 a :ARG2 (a5 / amino-acid :mod 77 :name (n4 / name :op1 "cysteine"~e.32) :part-of p3)) :ARG0-of (c / create-01~e.47 :ARG1 (p6 / protein-segment~e.7 :ARG1-of (l / long-03~e.52 :ARG2 (b / bond~e.51 :quant 1~e.50) :degree~e.52 (m2 / more~e.52) :compared-to~e.53 (p7 / protein-segment~e.7 :mod (n7 / native~e.55) :ARG0-of (l3 / link-01))) :ARG0-of (l2 / link-01))) :purpose (v / verify-01~e.1 :ARG0 w :ARG1~e.2 (a4 / alter-01~e.23 :polarity~e.22 -~e.22 :ARG0 (d / differ-02~e.4 :ARG1 (p8 / protein-segment~e.7 :consist-of (b2 / bond~e.14 :quant 7~e.13) :ARG0-of (l4 / link-01) :location-of (u2 / ubiquitinate-01~e.10 :mod (e / enzyme~e.7))) :ARG2 (p9 / protein-segment~e.7 :location-of (u / ubiquitinate-01~e.10 :mod (c2 / chemical~e.9)) :consist-of (b3 / bond~e.17 :quant 5~e.16) :ARG0-of (l5 / link-01))) :ARG1 (r / respond-01 :ARG0 (p5 / protein :name (n5 / name :op1 "GAP"~e.24)))))) # ::id bio.bmtr_0004.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We measured the rate of GAP @-@ mediated GTP hydrolysis and observed that the response of Ras ligated to Ubiquitin @-@ C77 was identical to Ras ligated to Ubiquitin @-@ G76C ( Fig . 5b ) . # ::alignments 0-1.1.1 1-1.1 3-1.1.2 4-1.1.2.1.r 5-1.1.2.1.2.1.1.1 7-1.1.2.1.2 8-1.1.2.1.1.1.1 9-1.1.2.1 10-1 11-1.2 12-1.2.2.r 14-1.2.2.1 14-1.2.2.1.1 14-1.2.2.1.1.r 14-1.2.2.2 14-1.2.2.2.1 14-1.2.2.2.1.r 16-1.2.2.1.1.1.1.1 16-1.2.2.2.1.1.1.1 17-1.2.2.1.1.1.2 17-1.2.2.2.1.1.2 19-1.2.2.1.1.1.2.1.3.1.1 19-1.2.2.2.1.1.2.1.3.1.1 23-1.2.2 25-1.2.2.1.1.1.1.1 25-1.2.2.2.1.1.1.1 26-1.2.2.1.1.1.2 26-1.2.2.2.1.1.2 28-1.2.2.1.1.1.2.1.3.1.1 28-1.2.2.2.1.1.2.1.3.1.1 30-1.2.2.2.1.1.2.1.3.2.1 32-1.2.2.3.1 34-1.2.2.3.1.1 (a / and~e.10 :op1 (m / measure-01~e.1 :ARG0 (w / we~e.0) :ARG1 (r / rate~e.3 :degree-of~e.4 (h / hydrolyze-01~e.9 :ARG1 (s / small-molecule :name (n / name :op1 "GTP"~e.8)) :ARG1-of (m2 / mediate-01~e.7 :ARG0 (p / protein :name (n2 / name :op1 "GAP"~e.5)))))) :op2 (o / observe-01~e.11 :ARG0 w :ARG1~e.12 (i / identical-01~e.23 :ARG1 (t / thing~e.14 :ARG2-of~e.14 (r2 / respond-01~e.14 :ARG0 (e / enzyme :name (n5 / name :op1 "Ras"~e.16,25) :ARG1-of (l / ligate-01~e.17,26 :ARG3 (a2 / amino-acid :mod 77 :name (n7 / name :op1 "cysteine") :part-of (p4 / protein :name (n8 / name :op1 "ubiquitin"~e.19,28))))))) :ARG2 (t2 / thing~e.14 :ARG2-of~e.14 (r3 / respond-01~e.14 :ARG0 (e2 / enzyme :name (n4 / name :op1 "Ras"~e.16,25) :ARG1-of (l2 / ligate-01~e.17,26 :ARG3 (a3 / amino-acid :mod 76 :name (n3 / name :op1 "cysteine") :part-of (p2 / protein :name (n9 / name :op1 "ubiquitin"~e.19,28) :ARG3-of (m3 / mutate-01 :value "G76C"~e.30))))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.32 :mod "5b"~e.34))))) # ::id bio.bmtr_0004.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results indicate that variations in the linker length on this scale ( 1 @-@ 2 bonds ) do not influence the sensitivity of mUbRas to GAP downregulation . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 2-1 3-1.2.r 4-1.2.2 8-1.2.2.3 10-1.1.2 13-1.2.2.2.1.1 13-1.2.3.1.2.1 15-1.2.2.2.2.1 16-1.2.2.2.1 16-1.2.2.2.2 19-1.2.1 19-1.2.1.r 20-1.2 22-1.2.3 25-1.2.3.2.r 26-1.2.3.2.2.1.1 27-1.2.3.2 (i / indicate-01~e.2 :ARG0 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :mod (t2 / this~e.0,10)) :ARG1~e.3 (i2 / influence-01~e.20 :polarity~e.19 -~e.19 :ARG0 (v2 / vary-01~e.4 :ARG1 (p2 / protein-segment :ARG0-of (l2 / link-01)) :ARG2 (o / or :op1 (b / bond~e.16 :quant 1~e.13) :op2 (b2 / bond~e.16 :quant 2~e.15)) :ARG5 (l / length~e.8)) :ARG1 (s / sensitive-03~e.22 :ARG0 (e / enzyme :name (n / name :op1 "Ras") :ARG3-of (u / ubiquitinate-01 :quant 1~e.13)) :ARG1~e.25 (d / downregulate-01~e.27 :ARG1 e :ARG2 (p / protein :name (n2 / name :op1 "GAP"~e.26)))))) # ::id bio.bmtr_0004.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To validate the use of an in vitro system to dissect the mechanism of Ras regulation , we measured the sensitivity of mUbRas to GAP @-@ mediated hydrolysis in a cellular reconstitution system . # ::alignments 1-1.3 3-1.3.2 3-1.3.r 4-1.3.2.2.r 6-1.3.2.2.1 7-1.3.2.2.1 8-1.3.2.2 10-1.3.2.3 12-1.3.2.3.2 14-1.2.1.1.1 14-1.3.2.3.2.1.1.1.1 15-1.3.2.3.2.1 17-1.1 18-1 20-1.2 23-1.2.2.r 24-1.2.2.1.1.1.1 26-1.2.2.1 27-1.2.2 28-1.3.2.2.1 30-1.2.3.1.1 32-1.2.3 32-1.3.2.2 (m / measure-01~e.18 :ARG0 (w / we~e.17) :ARG1 (s / sensitive-03~e.20 :ARG0 (e / enzyme :name (n / name :op1 "Ras"~e.14) :ARG3-of (u / ubiquitinate-01 :quant 1)) :ARG1~e.23 (h / hydrolyze-01~e.27 :ARG1-of (m2 / mediate-01~e.26 :ARG0 (p / protein :name (n2 / name :op1 "GAP"~e.24)))) :location (s2 / system~e.32 :ARG0-of (r / reconstitute-01 :ARG1 (c / cell~e.30)))) :purpose~e.3 (v / validate-01~e.1 :ARG0 w :ARG1 (u2 / use-01~e.3 :ARG0 w :ARG1~e.4 (s3 / system~e.8,32 :mod (i / in-vitro~e.6,7,28)) :ARG2 (d / dissect-01~e.10 :ARG0 w :ARG1 (m3 / mechanism~e.12 :instrument-of (r2 / regulate-01~e.15 :ARG1 (e2 / enzyme :name (n3 / name :op1 "Ras"~e.14)))))))) # ::id bio.bmtr_0004.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We immunoprecipitated Ras from HEK293T cells and compared the sensitivity of the monoubiquitinated and unmodified fractions of Ras to regulation by GAP . # ::alignments 0-1.1.1 1-1.1 2-1.1.2.1.1 3-1.1.3.r 4-1.1.3.1.1 5-1.1.3 6-1 7-1.2 9-1.2.2 9-1.2.3 12-1.2.2.1.2 12-1.2.2.1.2.1 12-1.2.2.1.2.1.r 14-1.2.3.1.2 14-1.2.3.1.2.1 14-1.2.3.1.2.1.r 15-1.2.2.1 15-1.2.3.1 17-1.1.2.1.1 19-1.2.2.2 19-1.2.3.2 20-1.2.2.2.1.r 21-1.2.2.2.1.1.1 (a / and~e.6 :op1 (i / immunoprecipitate-01~e.1 :ARG0 (w / we~e.0) :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.2,17)) :ARG2~e.3 (c / cell-line~e.5 :name (n2 / name :op1 "HEK293T"~e.4))) :op2 (c2 / compare-01~e.7 :ARG0 w :ARG1 (s / sensitive-03~e.9 :ARG0 (f / fraction~e.15 :part-of e :ARG1-of (u / ubiquitinate-01~e.12 :quant~e.12 1~e.12)) :ARG1 (r / regulate-01~e.19 :ARG0~e.20 (p / protein :name (n3 / name :op1 "GAP"~e.21)) :ARG1 f)) :ARG2 (s2 / sensitive-03~e.9 :ARG0 (f2 / fraction~e.15 :part-of e :ARG1-of (m / modify-01~e.14 :polarity~e.14 -~e.14)) :ARG1 (r2 / regulate-01~e.19 :ARG0 p :ARG1 f2)))) # ::id bio.bmtr_0004.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As seen in Figure 5c , monoubiquitinated K @-@ Ras is less sensitive than the unmodified protein to GAP @-@ mediated GTP hydrolysis . # ::alignments 1-1.5 2-1.5.1.r 3-1.5.1 4-1.5.1.1 6-1.1.2 6-1.1.2.1 6-1.1.2.1.r 7-1.1.1.1 7-1.4.1.1 9-1.1.1.1 9-1.4.1.1 11-1.3 12-1 13-1.4.r 15-1.4.2 15-1.4.2.1 15-1.4.2.1.r 16-1.2.2.1 18-1.2.2.1.1.1 20-1.2.2 21-1.2.1.1.1 22-1.2 (s / sensitive-03~e.12 :ARG0 (e / enzyme :name (n / name :op1 "K-Ras"~e.7,9) :ARG1-of (u / ubiquitinate-01~e.6 :quant~e.6 1~e.6)) :ARG1 (h / hydrolyze-01~e.22 :ARG1 (s2 / small-molecule :name (n2 / name :op1 "GTP"~e.21)) :ARG1-of (m2 / mediate-01~e.20 :ARG0 (p2 / protein~e.16 :name (n3 / name :op1 "GAP"~e.18)))) :degree (l / less~e.11) :compared-to~e.13 (e2 / enzyme :name (n4 / name :op1 "K-Ras"~e.7,9) :ARG1-of (m / modify-01~e.15 :polarity~e.15 -~e.15)) :ARG1-of (s3 / see-01~e.1 :medium~e.2 (f / figure~e.3 :mod "5c"~e.4))) # ::id bio.bmtr_0004.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These data support our in vitro findings that monoubiquitination increases the population of active , GTP @-@ bound Ras through a defect in sensitivity to GAP @-@ mediated regulation . # ::alignments 0-1.1.1 1-1.1 2-1 3-1.2.1 3-1.2.1.r 4-1.2.3 5-1.2.3 6-1.2 7-1.2.2.r 8-1.2.2.1 8-1.2.2.1.1 8-1.2.2.1.1.r 9-1.2.2 11-1.2.2.2 12-1.2.2.2.1.r 13-1.2.2.2.1 13-1.2.2.2.1.2 13-1.2.2.2.1.2.r 15-1.2.2.2.1.3.1.1.1 17-1.2.2.2.1.3 18-1.2.2.2.1.1.1 21-1.2.2.3 22-1.2.2.3.1.r 22-1.2.3 23-1.2.2.3.1 24-1.2.2.3.1.1.r 25-1.2.2.3.1.1.1.1.1.1 27-1.2.2.3.1.1.1 28-1.2.2.3.1.1 (s / support-01~e.2 :ARG0 (d / data~e.1 :mod (t / this~e.0)) :ARG1 (f / find-01~e.6 :ARG0~e.3 (w / we~e.3) :ARG1~e.7 (i / increase-01~e.9 :ARG0 (u / ubiquitinate-01~e.8 :quant~e.8 1~e.8) :ARG1 (p / population~e.11 :consist-of~e.12 (e / enzyme~e.13 :name (n / name :op1 "Ras"~e.18) :ARG0-of~e.13 (a / activity-06~e.13) :ARG2-of (b / bind-01~e.17 :ARG1 (s2 / small-molecule :name (n2 / name :op1 "GTP"~e.15))))) :manner (d2 / defect~e.21 :topic~e.22 (s3 / sensitive-03~e.23 :ARG1~e.24 (r / regulate-01~e.28 :ARG1-of (m / mediate-01~e.27 :ARG0 (p2 / protein :name (n3 / name :op1 "GAP"~e.25))))))) :manner (i2 / in-vitro~e.4,5,22))) # ::id bio.bmtr_0004.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Passage 1 @-@ 2 ( Discussion/Conclusion ) # ::alignments 0-1 1-1.1 3-1.1 (p / passage~e.0 :mod "1-2"~e.1,3 :part-of (s / slash :op1 (t / thing :ARG1-of (d / discuss-01)) :op2 (t2 / thing :ARG1-of (c / conclude-01)))) # ::id bio.bmtr_0004.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok It was established recently that monoubiquitination increases the proportion of Ras that is in the activated ( GTP @-@ bound ) state , that monoubiquitination enhances association with the downstream effectors Raf and PI3 @-@ Kinase , and that mutation of the primary site of monoubiquitination impairs oncogenic Ras @-@ mediated tumorigenesis . # ::alignments 2-1 3-1.2 4-1.1.r 5-1.1.1.1 6-1.1.1 8-1.1.1.2 9-1.1.1.2.1.r 10-1.1.1.2.1.1.1 13-1.1.1.2.2.r 15-1.1.1.2.2 17-1.1.1.2.3.1.1.1 19-1.1.1.2.3 24-1.1.1.1 24-1.1.1.1.1 24-1.1.1.1.1.r 25-1.1.2 26-1.1.2.2 27-1.1.2.2.1.r 29-1.1.2.2.1.1.1 30-1.1.2.2.1.1 30-1.1.2.2.1.2 31-1.1.2.2.1.1.2.1.1 32-1.1.2.2.1 33-1.1.2.2.1.2.1.1.1 35-1.1.2.2.1.2.1.1.1 37-1.1.2.2.1 38-1.1.r 39-1.1.3.1 40-1.1.3.1.1.r 42-1.1.3.1.1.1 43-1.1.3.1.1 44-1.1.3.1.1.2.r 45-1.1.3.1.1.2 46-1.1.3 47-1.1.3.2.2.1 47-1.1.3.2.2.1.2 47-1.1.3.2.2.1.2.1.2.1 47-1.1.3.2.2.1.2.r 48-1.1.3.2.2.1.1.1 50-1.1.3.2.2 51-1.1.3.2 51-1.1.3.2.1 51-1.1.3.2.1.r (e / establish-01~e.2 :ARG1~e.4,38 (a / and :op1 (i / increase-01~e.6 :ARG0 (u / ubiquitinate-01~e.5,24 :quant~e.24 1~e.24) :ARG1 (p / proportion~e.8 :quant-of~e.9 (e2 / enzyme :name (n / name :op1 "Ras"~e.10)) :ARG1-of~e.13 (a2 / activate-01~e.15) :ARG1-of (b / bind-01~e.19 :ARG2 (s / small-molecule :name (n2 / name :op1 "GTP"~e.17))))) :op2 (e3 / enhance-01~e.25 :ARG0 u :ARG1 (a3 / associate-01~e.26 :ARG2~e.27 (a4 / and~e.32,37 :op1 (e4 / effector~e.30 :mod (d / downstream~e.29) :mod (e7 / enzyme :name (n3 / name :op1 "Raf"~e.31))) :op2 (e5 / effector~e.30 :mod (e8 / enzyme :name (n4 / name :op1 "PI3-Kinase"~e.33,35)))))) :op3 (i2 / impair-01~e.46 :ARG0 (m2 / mutate-01~e.39 :ARG1~e.40 (p3 / protein-segment~e.43 :mod (p2 / primary~e.42) :part-of~e.44 u~e.45)) :ARG1 (c3 / create-01~e.51 :ARG1~e.51 (t / tumor~e.51) :ARG1-of (m3 / mediate-01~e.50 :ARG0 (e6 / enzyme~e.47 :name (n5 / name :op1 "Ras"~e.48) :ARG0-of~e.47 (c / cause-01~e.47 :ARG1 (d2 / disease :wiki "Cancer" :name (n6 / name :op1 "cancer"~e.47)))))))) :time (r / recent~e.3)) # ::id bio.bmtr_0004.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Here we show that monoubiquitination decreases the sensitivity of Ras to GAP @-@ mediated hydrolysis . # ::alignments 0-1.3 1-1.1 2-1 3-1.2.r 4-1.2.1 4-1.2.1.1 4-1.2.1.1.r 5-1.2 7-1.2.2 8-1.2.2.1.r 9-1.2.2.1.1.1 10-1.2.2.2.r 11-1.2.2.2.1.1.1.1 13-1.2.2.2.1 14-1.2.2.2 (s / show-01~e.2 :ARG0 (w / we~e.1) :ARG1~e.3 (d / decrease-01~e.5 :ARG0 (u / ubiquitinate-01~e.4 :quant~e.4 1~e.4) :ARG1 (s2 / sensitive-03~e.7 :ARG0~e.8 (e / enzyme :name (n / name :op1 "Ras"~e.9)) :ARG1~e.10 (h / hydrolyze-01~e.14 :ARG1-of (m / mediate-01~e.13 :ARG0 (p / protein :name (n2 / name :op1 "GAP"~e.11)))))) :location (h2 / here~e.0)) # ::id bio.bmtr_0004.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A major advance was our ability to easily generate mUbRas , modified at a single site , in a form suitable for detailed biophysical studies . # ::alignments 1-1.2 2-1 4-1.1.1 4-1.1.1.r 5-1.1 6-1.1.3.r 7-1.1.3 8-1.1.2 11-1.1.2.2.3 12-1.1.2.2.3.1.r 14-1.1.2.2.3.1.1 15-1.1.2.2.3.1 17-1.1.2.3.r 19-1.1.2.3 20-1.1.2.3.1 21-1.1.2.3.1.1.r 22-1.1.2.3.1.1.2 23-1.1.2.3.1.1.1 24-1.1.2.3.1.1 (a / advance-01~e.2 :ARG1 (c / capable-01~e.5 :ARG1~e.4 (w / we~e.4) :ARG2 (g / generate-01~e.8 :ARG0 w :ARG1 (e / enzyme :name (n / name :op1 "Ras") :ARG3-of (u / ubiquitinate-01 :quant 1) :ARG1-of (m2 / modify-01~e.11 :location~e.12 (p / protein-segment~e.15 :ARG1-of (s2 / single-02~e.14)))) :ARG4~e.17 (f / form~e.19 :ARG1-of (s / suitable-04~e.20 :ARG2~e.21 (s4 / study-01~e.24 :ARG1 (b / biophysical~e.23) :ARG1-of (d / detail-01~e.22))))) :ARG1-of~e.6 (e2 / easy-05~e.7)) :ARG2 (m / major-02~e.1)) # ::id bio.bmtr_0004.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This chemical ligation strategy will likely be useful for the study of other monoubiquitinated proteins . # ::alignments 0-1.1.1.2 1-1.1.1.1.1 2-1.1.1.1 3-1.1.1 5-1 7-1.1 8-1.1.2.r 10-1.1.2 11-1.1.2.1.r 12-1.1.2.1.2 13-1.1.2.1.1 13-1.1.2.1.1.1 13-1.1.2.1.1.1.r 14-1.1.2.1 (l / likely-01~e.5 :ARG1 (u / useful-05~e.7 :ARG1 (s / strategy~e.3 :mod (l2 / ligate-01~e.2 :mod (c / chemical~e.1)) :mod (t / this~e.0)) :ARG2~e.8 (s2 / study-01~e.10 :ARG1~e.11 (p / protein~e.14 :ARG1-of (u2 / ubiquitinate-01~e.13 :quant~e.13 1~e.13) :mod (o / other~e.12))))) # ::id bio.bmtr_0004.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Surprisingly , monoubiquitination did not alter the intrinsic activity of Ras , despite the size of the modification . # ::alignments 0-1 2-1.1.2 2-1.1.2.1 2-1.1.2.1.r 4-1.1.1 4-1.1.1.r 5-1.1 7-1.1.3.2 8-1.1.3 9-1.1.3.1.r 10-1.1.3.1.1.1 12-1.2.r 14-1.2 14-1.2.1 14-1.2.1.r 15-1.2.1.1.r 17-1.2.1.1 (s / surprise-01~e.0 :ARG0 (a / alter-01~e.5 :polarity~e.4 -~e.4 :ARG0 (u / ubiquitinate-01~e.2 :quant~e.2 1~e.2) :ARG1 (a2 / activity-06~e.8 :ARG0~e.9 (e / enzyme :name (n / name :op1 "Ras"~e.10)) :mod (i / intrinsic~e.7))) :concession~e.12 (t / thing~e.14 :ARG2-of~e.14 (s2 / size-01~e.14 :ARG1~e.15 (m / modify-01~e.17)))) # ::id bio.bmtr_0004.22 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Our modeling and NMR analyses indicated that Ubiquitin dynamically samples a broad surface area of Ras that alters switch region dynamics . # ::alignments 0-1.1.1.1 0-1.1.1.1.r 1-1.1.1 2-1.1 4-1.1.2 5-1 6-1.2.r 7-1.2.1.1.1 8-1.2.3 9-1.2 11-1.2.2.1.1 12-1.2.2.1 13-1.2.2 14-1.2.2.2.r 15-1.2.2.2.1.1 17-1.2.4 18-1.2.4.1.1.1 19-1.2.4.1.1 20-1.2.4.1 (i / indicate-01~e.5 :ARG0 (a / and~e.2 :op1 (m / model-01~e.1 :ARG0~e.0 (w / we~e.0)) :op2 (a2 / analyze-01~e.4 :ARG0 w :manner (r2 / resonate-01 :ARG1 (n / nucleus) :mod (m2 / magnet)))) :ARG1~e.6 (s / sample-01~e.9 :ARG0 (p / protein :name (n2 / name :op1 "ubiquitin"~e.7)) :ARG1 (a3 / area~e.13 :mod (s2 / surface~e.12 :ARG1-of (b / broad-02~e.11)) :part-of~e.14 (e / enzyme :name (n3 / name :op1 "Ras"~e.15))) :manner (d / dynamic~e.8) :ARG0-of (a4 / alter-01~e.17 :ARG1 (d2 / dynamic~e.20 :location (r / region~e.19 :mod (s3 / switch-01~e.18)))))) # ::id bio.bmtr_0004.23 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results led us to examine the effect of monoubiquitination on the interaction of Ras with its cognate GEF and GAPs , which also target the switch domains . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 2-1 3-1.2 5-1.3 7-1.3.2 8-1.3.2.1.r 9-1.3.2.1 9-1.3.2.1.1 9-1.3.2.1.1.r 10-1.3.2.2.r 12-1.3.2.2 13-1.3.2.2.1.r 14-1.3.2.2.1.1.1 15-1.3.2.2.2.3.1.r 16-1.3.2.2.2.3.1 17-1.3.2.2.2.3 18-1.3.2.2.2.1.1.1 19-1.3.2.2.2 20-1.3.2.2.2.2.1.1 23-1.3.2.2.2.4.2 24-1.3.2.2.2.4 26-1.3.2.2.2.4.1.1 27-1.3.2.2.2.4.1 (l / lead-03~e.2 :ARG0 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :mod (t2 / this~e.0)) :ARG1 (w / we~e.3) :ARG2 (e / examine-01~e.5 :ARG0 w :ARG1 (a / affect-01~e.7 :ARG0~e.8 (u / ubiquitinate-01~e.9 :quant~e.9 1~e.9) :ARG1~e.10 (i / interact-01~e.12 :ARG0~e.13 (e2 / enzyme :name (n / name :op1 "Ras"~e.14)) :ARG1 (a2 / and~e.19 :op1 (p / protein :name (n2 / name :op1 "GEF"~e.18)) :op2 (p2 / protein :name (n3 / name :op1 "GAP"~e.20)) :mod (c / cognate~e.17 :prep-with~e.15 e2~e.16) :ARG0-of (t3 / target-01~e.24 :ARG1 (d / domain~e.27 :mod (s / switch-01~e.26)) :mod (a3 / also~e.23))))))) # ::id bio.bmtr_0004.24 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The analysis revealed that monoubiquitination abrogates GAP @-@ mediated GTP hydrolysis . # ::alignments 1-1.1 2-1 3-1.2.r 4-1.2.1 4-1.2.1.1 4-1.2.1.1.r 5-1.2 6-1.2.2.2.1.1.1 8-1.2.2.2 9-1.2.2.1.1.1 10-1.2.2 (r / reveal-01~e.2 :ARG0 (a / analyze-01~e.1) :ARG1~e.3 (a2 / abrogate-01~e.5 :ARG0 (u / ubiquitinate-01~e.4 :quant~e.4 1~e.4) :ARG1 (h / hydrolyze-01~e.10 :ARG1 (s / small-molecule :name (n / name :op1 "GTP"~e.9)) :ARG1-of (m / mediate-01~e.8 :ARG0 (p / protein :name (n2 / name :op1 "GAP"~e.6)))))) # ::id bio.bmtr_0004.25 ::amr-annotator SDL-AMR-09 ::preferred # ::tok All other activities , including the ability to bind regulators , were largely preserved and our kinetic modeling suggests that the GAP defect will dominate . # ::alignments 0-1.1.1.1 1-1.1.1.2 2-1.1.1 4-1.1.1.3 8-1.1.1.3.1.1 9-1.1.1.3.1.1.1 9-1.1.1.3.1.1.1.1 9-1.1.1.3.1.1.1.1.r 12-1.1.2 13-1.1 14-1 15-1.2.1.1 15-1.2.1.1.r 16-1.2.1.2 17-1.2.1 18-1.2 19-1.2.2.r 21-1.2.2.1.1.1.1 22-1.2.2.1 24-1.2.2 (a3 / and~e.14 :op1 (p / preserve-01~e.13 :ARG1 (a / act-02~e.2 :mod (a2 / all~e.0) :mod (o / other~e.1) :ARG2-of (i / include-01~e.4 :ARG1 (p2 / possible-01 :ARG1 (b / bind-01~e.8 :ARG1 (m2 / molecular-physical-entity~e.9 :ARG0-of~e.9 (r / regulate-01~e.9)))))) :mod (l / large~e.12)) :op2 (s / suggest-01~e.18 :ARG0 (m / model-01~e.17 :ARG0~e.15 (w / we~e.15) :mod (k / kinetic~e.16)) :ARG1~e.19 (d / dominate-01~e.24 :ARG1 (d2 / defect~e.22 :mod (p3 / protein :name (n / name :op1 "GAP"~e.21)))))) # ::id bio.bmtr_0004.26 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Furthermore , this outcome was specific to monoubiquitination at position 147 . # ::alignments 0-1 2-1.1.1.1 3-1.1.1 5-1.1 6-1.1.2.r 7-1.1.2 7-1.1.2.1 7-1.1.2.1.r 10-1.1.2.2.1 (a / and~e.0 :op2 (s / specific-02~e.5 :ARG1 (o / outcome~e.3 :mod (t / this~e.2)) :ARG2~e.6 (u / ubiquitinate-01~e.7 :quant~e.7 1~e.7 :ARG1 (a2 / amino-acid :mod 147~e.10)))) # ::id bio.bmtr_0004.27 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Thus our work establishes an entirely new mode of Ras activation in which signaling is sustained even in the absence of hormone stimulus or oncogene mutation . # ::alignments 0-1.2.3.2.1.2.1 1-1.1.1 1-1.1.1.r 2-1.1 3-1 5-1.2.1.1 6-1.2.1 7-1.2 8-1.2.2.r 9-1.2.2.1.1.1 10-1.2.2 13-1.2.3.1 15-1.2.3 19-1.2.3.2 20-1.2.3.2.1.r 21-1.2.3.2.1.1.1 22-1.2.3.2.1.1 23-1.2.3.2.1 25-1.2.3.2.1.2 (e / establish-01~e.3 :ARG0 (w / work-01~e.2 :ARG0~e.1 (w2 / we~e.1)) :ARG1 (m / mode~e.7 :ARG1-of (n / new-01~e.6 :degree (e2 / entire~e.5)) :mod~e.8 (a / activate-01~e.10 :ARG1 (e3 / enzyme :name (n2 / name :op1 "Ras"~e.9))) :ARG0-of (s / sustain-01~e.15 :ARG1 (s2 / signal-07~e.13) :concession (a2 / absent-01~e.19 :ARG1~e.20 (o / or~e.23 :op1 (s3 / stimulus~e.22 :mod (h / hormone~e.21)) :op2 (m2 / mutate-01~e.25 :ARG0-of (c / cause-01~e.0 :ARG1 (d / disease :wiki "Cancer" :name (n3 / name :op1 "cancer"))))))))) # ::id bio.bmtr_0005.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Phosphorylation of ASPP2 by RAS @/@ MAPK Pathway Is Critical for Its Full Pro @-@ Apoptotic Function ( PMC3847091 ) # ::alignments 0-1.2.1 1-1.2.1.1.r 2-1.2.1.1.1.1 3-1.2.1.2.r 4-1.2.1.2.1.1 6-1.2.1.2.1.1 7-1.2.1.2 9-1.2 10-1.2.2.r 11-1.2.2.1 11-1.2.2.1.r 12-1.2.2.3 13-1.2.2.2.1 15-1.2.2.2 16-1.2.2 18-1.1 (p5 / publication-91 :ARG8 "PMC3847091"~e.18 :ARG1 (c / critical-02~e.9 :ARG1 (p / phosphorylate-01~e.0 :ARG1~e.1 (p2 / protein :name (n / name :op1 "ASPP2"~e.2)) :ARG2~e.3 (p3 / pathway~e.7 :name (n2 / name :op1 "RAS/MAPK"~e.4,6))) :ARG2~e.10 (f / function-01~e.16 :ARG0~e.11 p2~e.11 :ARG1 (a / apoptosis~e.15 :ARG1-of (f3 / favor-01~e.13)) :mod (f2 / full~e.12)))) # ::id bio.bmtr_0005.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Passage 1 @-@ 1 ( Results ) # ::alignments 0-1 1-1.1 3-1.1 5-1.2 5-1.2.1 5-1.2.1.r (p / passage~e.0 :mod "1-1"~e.1,3 :part-of (t / thing~e.5 :ARG2-of~e.5 (r / result-01~e.5))) # ::id bio.bmtr_0005.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok It has recently been shown that oncogenic RAS can enhance the apoptotic function of p53 via ASPP1 and ASPP2 . # ::alignments 2-1.2 4-1 5-1.1.r 6-1.1.1.1 6-1.1.1.1.2 6-1.1.1.1.2.1.2.1 6-1.1.1.1.2.r 7-1.1.1.1.1.1 8-1.1 9-1.1.1 11-1.1.1.2.2 12-1.1.1.2 13-1.1.1.2.1.r 14-1.1.1.2.1.1.1 16-1.1.1.3.1.1.1 17-1.1.1.3 18-1.1.1.3.2.1.1 (s / show-01~e.4 :ARG1~e.5 (p / possible-01~e.8 :ARG1 (e / enhance-01~e.9 :ARG0 (e2 / enzyme~e.6 :name (n / name :op1 "Ras"~e.7) :ARG0-of~e.6 (c / cause-01~e.6 :ARG1 (d / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.6)))) :ARG1 (f / function-01~e.12 :ARG0~e.13 (p2 / protein :name (n2 / name :op1 "p53"~e.14)) :ARG1 (a / apoptosis~e.11)) :instrument (a2 / and~e.17 :op1 (p3 / protein :name (n3 / name :op1 "ASPP1"~e.16)) :op2 (p4 / protein :name (n4 / name :op1 "ASPP2"~e.18))))) :time (r / recent~e.2)) # ::id bio.bmtr_0005.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Mechanistically ASPP1 and ASPP2 bind RAS @-@ GTP and potentiates RAS signalling to enhance p53 mediated apoptosis [ 2 ] . # ::alignments 0-1.3 1-1.1.1.1.1 2-1.1 3-1.1.2.1.1 4-1 5-1.2.1.1.1 7-1.2.2.1.1 8-1.1 9-1.4 10-1.4.1.1 11-1.4.1 13-1.4.2 14-1.4.2.2.1.1.1.1 15-1.4.2.2.1 16-1.4.2.2 18-1.5.1.1.1 (b / bind-01~e.4 :ARG1 (a2 / and~e.2,8 :op1 (p / protein :name (n / name :op1 "ASPP1"~e.1)) :op2 (p2 / protein :name (n2 / name :op1 "ASPP2"~e.3))) :ARG2 (m3 / macro-molecular-complex :part (e / enzyme :name (n3 / name :op1 "Ras"~e.5)) :part (s / small-molecule :name (n4 / name :op1 "GTP"~e.7))) :manner (m / mechanistic~e.0) :ARG2-of (p3 / potentiate-01~e.9 :ARG1 (s2 / signal-07~e.11 :ARG0 e~e.10) :purpose (e2 / enhance-01~e.13 :ARG0 b :ARG1 (a / apoptosis~e.16 :ARG1-of (m2 / mediate-01~e.15 :ARG0 (p4 / protein :name (n5 / name :op1 "p53"~e.14)))))) :ARG1-of (d / describe-01 :ARG0 (p5 / publication :ARG1-of (c / cite-01 :ARG2 2~e.18)))) # ::id bio.bmtr_0005.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As RAS is upstream of several signalling cascades [ 13 ] , we queried whether the activity of ASPP2 is regulated by the activation of a RAS @-@ mediated signalling pathway . # ::alignments 1-1.3.1.1.1.1 2-1.3.1 3-1.3.1.2.2 5-1.3.1.2.1.2 6-1.3.1.2.1.1 7-1.3.1.2.1 9-1.3.1.3.1.1.1 12-1.1 13-1 16-1.2.2 17-1.2.2.1.r 18-1.2.2.1.1.1 20-1.2 21-1.2.1.r 23-1.2.1 24-1.2.1.1.r 26-1.2.1.1.1.1.1 28-1.2.1.1.1.1 29-1.2.1.1.1 30-1.2.1.1 (q / query-01~e.13 :ARG0 (w / we~e.12) :ARG2 (r / regulate-01~e.20 :ARG0~e.21 (a / activate-01~e.23 :ARG0~e.24 (p / pathway~e.30 :ARG0-of (s / signal-07~e.29 :ARG1-of (m / mediate-01~e.28 :ARG0 e~e.26)))) :ARG1 (a2 / activity-06~e.16 :ARG0~e.17 (p2 / protein :name (n2 / name :op1 "ASPP2"~e.18)))) :ARG1-of (c / cause-01 :ARG0 (b / be-located-at-91~e.2 :ARG1 (e / enzyme :name (n / name :op1 "RAS"~e.1)) :ARG2 (r2 / relative-position :op1 (c2 / cascade~e.7 :subevent (s2 / signal-07~e.6) :quant (s3 / several~e.5)) :direction (u / upstream~e.3)) :ARG1-of (d / describe-01 :ARG0 (p3 / publication :ARG0-of (c3 / cite-01 :ARG2 13~e.9)))))) # ::id bio.bmtr_0005.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok One of the most studied downstream pathways of RAS signalling is the Raf @-@ MAPK pathway . # ::alignments 3-1.2.1.1 4-1.2.1 5-1.2.2 6-1.2 8-1.2.3.1.1.1 9-1.2.3 12-1.1.1.1 14-1.1.1.1 15-1.2 (i / include-91 :ARG1 (p / pathway :name (n / name :op1 "Raf-MAPK"~e.12,14)) :ARG2 (p2 / pathway~e.6,15 :ARG1-of (s / study-01~e.4 :degree (m / most~e.3)) :mod (d / downstream~e.5) :location-of (s2 / signal-07~e.9 :ARG0 (e / enzyme :name (n2 / name :op1 "Ras"~e.8))))) # ::id bio.bmtr_0005.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Interestingly , we observed two conserved putative MAPK phosphorylation sites in ASPP1 and ASPP2 . # ::alignments 0-1.3 2-1.1 3-1 4-1.2.1.1 5-1.2.1.2 6-1.2.1.3.2 7-1.2.1.3.1.1.1 8-1.2.1.3 9-1.2.1 10-1.2.1.4.r 11-1.2.1.4.1.1.1 12-1.2.1.4 13-1.2.1.4.2.1.1 (o / observe-01~e.3 :ARG0 (w2 / we~e.2) :ARG1 (a / and :op1 (p3 / protein-segment~e.9 :quant 2~e.4 :ARG1-of (c / conserve-01~e.5) :ARG1-of (p2 / phosphorylate-01~e.8 :ARG2 (e / enzyme :name (n / name :op1 "MAPK"~e.7)) :ARG2-of (t / think-01~e.6)) :part-of~e.10 (a2 / and~e.12 :op1 (p5 / protein :name (n2 / name :op1 "ASPP1"~e.11)) :op2 (p6 / protein :name (n3 / name :op1 "ASPP2"~e.13))))) :ARG2-of (i / interest-01~e.0 :ARG1 w2)) # ::id bio.bmtr_0005.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The ASPP1 sites are at residues 671 and 746 , and the ASPP2 sites are at residues 698 and 827 ( Figure 1A ) . # ::alignments 1-1.1.1.1.1.1 2-1.1.1 3-1.1 4-1.1 5-1.1.2.1 5-1.1.2.2 5-1.2.2.2 6-1.1.2.1.1.1 7-1.1.2 8-1.1.2.2.1.1 10-1.1.2 12-1.2.1.1.1.1 13-1.1.1 13-1.2.1 14-1.1 14-1.2 15-1.1 16-1.2.2.1 17-1.2.2.1.1.1 18-1.2.2 19-1.2.2.2.1.1 21-1.3.1 22-1.3.1.1 (a4 / and :op1 (b / be-located-at-91~e.3,4,14,15 :ARG1 (p / protein-segment~e.2,13 :part-of (p2 / protein :name (n / name :op1 "ASPP1"~e.1))) :ARG2 (a2 / and~e.7,10 :op1 (r / residue~e.5 :mod (a / amino-acid :mod 671~e.6)) :op2 (r2 / residue~e.5 :mod (a3 / amino-acid :mod 746~e.8)))) :op2 (b2 / be-located-at-91~e.14 :ARG1 (p3 / protein-segment~e.13 :part-of (p4 / protein :name (n2 / name :op1 "ASPP2"~e.12))) :ARG2 (a5 / and~e.18 :op1 (r3 / residue~e.16 :mod (a6 / amino-acid :mod 698~e.17)) :op2 (r4 / residue~e.5 :mod (a7 / amino-acid :mod 827~e.19)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.21 :mod "1A"~e.22))) # ::id bio.bmtr_0005.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We thus tested whether RAS activation may regulate ASPP2 phosphorylation . # ::alignments 0-1.1.1 1-1 2-1.1 3-1.1.2.1 3-1.1.2.1.r 4-1.1.2.2.1.1.1.1 5-1.1.2.2.1 6-1.1.2 7-1.1.2.2 8-1.1.2.2.2.1.1.1 9-1.1.2.2.2 (c / cause-01~e.1 :ARG1 (t / test-01~e.2 :ARG0 (w / we~e.0) :ARG1 (p / possible-01~e.6 :mode~e.3 interrogative~e.3 :ARG1 (r / regulate-01~e.7 :ARG0 (a / activate-01~e.5 :ARG1 (e / enzyme :name (n / name :op1 "RAS"~e.4))) :ARG1 (p2 / phosphorylate-01~e.9 :ARG1 (p3 / protein :name (n2 / name :op1 "ASPP2"~e.8))))))) # ::id bio.bmtr_0005.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok An in vitro phophorylation assay was performed with a purified C @-@ terminus fragment of ASPP2 ( 693 @-@ 1128 ) containing both MAPK putative phosphorylation sites . # ::alignments 1-1.1.2 2-1.1.2 4-1 9-1.1.1.2 10-1.1.1.1.1.1 12-1.1.1.1.1.1 15-1.1.1.1.2.1.1 17-1.1.1.3.1.1 19-1.1.1.3.2.1 21-1.1.1.4 22-1.1.1.4.1.2 23-1.1.1.4.1.1.1.1.1 24-1.1.1.4.1.1.2 25-1.1 25-1.1.1.4.1.1 26-1.1.1 26-1.1.1.4.1 (a / assay-01~e.4 :ARG1 (p / phosphorylate-01~e.25 :ARG1 (p2 / protein-segment~e.26 :part-of (p3 / protein-segment :name (n / name :op1 "C-terminus"~e.10,12) :part-of (p4 / protein :name (n2 / name :op1 "ASPP2"~e.15))) :ARG1-of (p5 / purify-01~e.9) :mod (b / between :op1 (a2 / amino-acid :mod 693~e.17) :op2 (a3 / amino-acid :mod 1128~e.19)) :ARG0-of (c / contain-01~e.21 :ARG1 (p6 / protein-segment~e.26 :ARG1-of (p7 / phosphorylate-01~e.25 :ARG2 (e / enzyme :name (n4 / name :op1 "MAPK"~e.23)) :ARG1-of (t / think-01~e.24)) :mod (b2 / both~e.22)))) :manner (i / in-vitro~e.1,2))) # ::id bio.bmtr_0005.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok When compared to p38 SAPK , MAPK1 was clearly able to phosphorylate the ASPP2 fragment in vitro ( Figure 1B , left and middle panels ) . # ::alignments 1-1.3.r 3-1.3.1.2.1.1 4-1.3.1.2.1.2 6-1.1.2.1.1 8-1.2 9-1 9-1.3 11-1.1 11-1.3.1 13-1.1.1.1.1.1 15-1.1.3 16-1.1.3 18-1.4.1.3 19-1.4.1.3.1 21-1.4.1.1.1 22-1.4.1 23-1.4.1.2.1 24-1.4.1.1 24-1.4.1.2 (p / possible-01~e.9 :ARG1 (p2 / phosphorylate-01~e.11 :ARG1 (p3 / protein-segment :part-of (p4 / protein :name (n2 / name :op1 "ASPP2"~e.13))) :ARG2 (e / enzyme :name (n / name :op1 "MAPK1"~e.6)) :manner (i / in-vitro~e.15,16)) :ARG1-of (c / clear-06~e.8) :compared-to~e.1 (p5 / possible-01~e.9 :ARG1 (p6 / phosphorylate-01~e.11 :ARG1 p3 :ARG2 (e2 / enzyme :name (n3 / name :op1 "p38"~e.3 :op2 "SAPK"~e.4)))) :ARG1-of (d / describe-01 :ARG0 (a / and~e.22 :op1 (p7 / panel~e.24 :ARG1-of (l / left-20~e.21)) :op2 (p8 / panel~e.24 :location (m / middle~e.23)) :part-of (f / figure~e.18 :mod "1B"~e.19)))) # ::id bio.bmtr_0005.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Figure S1 , histone 2B phosphorylated by p38 SAPK had high levels of incorporated 32P , suggesting that p38 SAPK was active ; while under the same conditions , ASPP2 ( 693 @-@ 1128 ) fragment phosphorylated by p38 SAPK had very low levels of incorporated 32P , indicating that p38 SAPK is not an efficient kinase for ASPP2 phosphorylation . # ::alignments 1-1 2-1.1.r 3-1.1 4-1.1.1 6-1.2.1.1.1.1 7-1.2.1.1.1.2 8-1.2.1.1.2 8-1.2.2.3.1.3 10-1.2.1.1.2.1.1.1 11-1.2.1.1.2.1.1.2 12-1.2.1 13-1.2.1.2.2.1 14-1.2.1.2.2 15-1.2.1.2.2.r 16-1.2.1.2.3 17-1.2.1.2 17-1.2.1.2.1.1 19-1.2.1.3 20-1.2.1.3.1.r 21-1.2.1.3.1.1 22-1.2.1.3.1.1 24-1.2.1.3.1 26-1.2 29-1.2.2.4 29-1.2.2.4.1 29-1.2.2.4.1.r 30-1.2.2.4.1.1.1.r 30-1.2.2.4.r 32-1.2.2.1.2.1.1 34-1.2.2.1.1.1.1 36-1.2.2.1.1.2.1 39-1.2.1.1.2 39-1.2.2.1.3 41-1.2.1.1.2.1.1.1 42-1.2.1.1.2.1.1.2 43-1.2.2 44-1.2.2.2.2.1.1 45-1.2.2.2.2.1 46-1.2.2.2.2 47-1.2.2.2.2.r 48-1.2.2.2.3 49-1.2.2.2 49-1.2.2.2.1.1 51-1.2.2.3 52-1.2.2.3.1.r 53-1.2.2.3.1.2 54-1.2.2.3.1.2 56-1.2.2.3.1.1 56-1.2.2.3.1.1.r 58-1.2.2.3.1 61-1.2.2.1.2.1.1 62-1.2.1.1.2 62-1.2.2.1.3 (s / show-01~e.1 :ARG0~e.2 (f / figure~e.3 :mod "S1"~e.4) :ARG1 (c / contrast-01~e.26 :ARG1 (h / have-part-91~e.12 :ARG1 (p8 / protein :name (n / name :op1 "Histone"~e.6 :op2 "2B"~e.7) :ARG3-of (p2 / phosphorylate-01~e.8,39,62 :ARG2 (e / enzyme :name (n2 / name :op1 "p38"~e.10,41 :op2 "SAPK"~e.11,42)))) :ARG2 (p / phosphorus~e.17 :mod (m / molecular-mass :value 32~e.17) :quant~e.15 (l / level~e.14 :ARG1-of (h2 / high-02~e.13)) :ARG1-of (i / incorporate-02~e.16 :ARG2 p8)) :ARG0-of (s2 / suggest-01~e.19 :ARG1~e.20 (a / activity-06~e.24 :ARG0 e~e.21,22))) :ARG2 (h4 / have-part-91~e.43 :ARG1 (p3 / protein-segment :mod (b / between :op1 (a2 / amino-acid :mod 693~e.34) :op2 (a3 / amino-acid :mod 1128~e.36)) :part (p5 / protein :name (n3 / name :op1 "ASPP2"~e.32,61)) :ARG3-of (p6 / phosphorylate-01~e.39,62 :ARG2 e)) :ARG2 (p4 / phosphorus~e.49 :mod (m2 / molecular-mass :value 32~e.49) :quant~e.47 (l2 / level~e.46 :ARG1-of (l3 / low-04~e.45 :degree (v / very~e.44))) :ARG1-of (i2 / incorporate-02~e.48 :ARG2 p3)) :ARG0-of (i3 / indicate-01~e.51 :ARG1~e.52 (e2 / efficient-01~e.58 :polarity~e.56 -~e.56 :ARG1 e~e.53,54 :ARG2 (p7 / phosphorylate-01~e.8 :ARG1 p5 :ARG2 e))) :condition~e.30 (t / thing~e.29 :ARG1-of~e.29 (s3 / same-01~e.29 :ARG2 (t2 / thing :condition-of~e.30 h)))))) # ::id bio.bmtr_0005.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The phosphorylated ASPP2 fragment by MAPK1 was digested by trypsin and fractioned on a high performance liquid chromatography ( HPLC ) . # ::alignments 1-1.1.2.2 2-1.1.2.1.1.1 4-1.1.2.2.1.r 5-1.1.2.2.1.1.1 7-1.1 8-1.1.1.r 9-1.1.1.1.1 10-1 11-1.2 12-1.2.2.r 14-1.2.2.1.1.1 15-1.2.2.1.1 16-1.2.2.1 17-1.2.2 (a / and~e.10 :op1 (d / digest-01~e.7 :ARG0~e.8 (e / enzyme :name (n / name :op1 "trypsin"~e.9)) :ARG1 (p / protein-segment :part-of (p2 / protein :name (n2 / name :op1 "ASPP2"~e.2)) :ARG3-of (p3 / phosphorylate-01~e.1 :ARG2~e.4 (e2 / enzyme :name (n3 / name :op1 "MAPK1"~e.5))))) :op2 (f / fraction-01~e.11 :ARG1 p :manner~e.12 (c / chromatography~e.17 :mod (l / liquid~e.16 :ARG0-of (p4 / perform-02~e.15 :ARG1-of (h / high-02~e.14)))))) # ::id bio.bmtr_0005.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Each eluted fraction was measured for its radioactivity content ( Figure 1B , right panel ) . # ::alignments 0-1.1.2 1-1.1.1 2-1.1 4-1 7-1.2.1 8-1.2 8-1.2.2 8-1.2.2.r 10-1.3.1.2 11-1.3.1.2.1 13-1.3.1.1 14-1.3.1 (m / measure-01~e.4 :ARG1 (f / fraction~e.2 :ARG1-of (e / elute-01~e.1) :mod (e2 / each~e.0)) :purpose (t / thing~e.8 :mod (r2 / radioactive~e.7) :ARG1-of~e.8 (c / contain-01~e.8 :ARG0 f)) :ARG1-of (d / describe-01 :ARG0 (p / panel~e.14 :ARG1-of (r / right-04~e.13) :part-of (f2 / figure~e.10 :mod "1B"~e.11)))) # ::id bio.bmtr_0005.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The fractions representing these radioactive peaks were analysed by mass spectrometry . # ::alignments 1-1.1 2-1.1.1 3-1.1.1.1.2 4-1.1.1.1.1 5-1.1.1.1 7-1 8-1.2.r 9-1.2.1 10-1.2 (a / analyze-01~e.7 :ARG1 (f / fraction~e.1 :ARG0-of (r / represent-01~e.2 :ARG1 (p / peak~e.5 :mod (r2 / radioactive~e.4) :mod (t / this~e.3)))) :manner~e.8 (s / spectrometry~e.10 :mod (m / mass~e.9))) # ::id bio.bmtr_0005.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Of the two radioactive peaks , one represented the linker region between the GST and our ASPP2 fragment and the other corresponded to a fragment of the same mass as that containing the second putative phosphorylation site , serine 827 . # ::alignments 2-1.1.1.1.1.1 3-1.1.1.1.1.2 4-1.1.1 4-1.1.1.1.1 4-1.2.1 7-1.1 10-1.1.2 13-1.1.2.1.1.1.1 15-1.1.2.1.2.2 15-1.1.2.1.2.2.r 16-1.1.2.1.2.1.1.1 18-1 20-1.2.1.1 21-1.2 25-1.2.2.r 27-1.2.2.1.1.1 28-1.2.2.1.1 28-1.2.2.1.1.1.1 33-1.2.2.1.1.1.1.1.2 33-1.2.2.1.1.1.1.1.2.1 33-1.2.2.1.1.1.1.1.2.1.r 34-1.2.2.1.1.1.1.1.3.2 35-1.2.2.1.1.1.1.1.1 36-1.1.2.1.2 36-1.2.2 36-1.2.2.1.1.1.1.1 38-1.2.2.1.1.1.1.1.3.1.2.1 39-1.2.2.1.1.1.1.1.3.1.1 (a / and~e.18 :op1 (r / represent-01~e.7 :ARG0 (p / peak~e.4 :ARG1-of (i / include-91 :ARG2 (p2 / peak~e.4 :quant 2~e.2 :mod (r2 / radioactive~e.3)))) :ARG1 (r4 / region~e.10 :ARG3-of (l / link-01 :ARG1 (e / enzyme :name (n / name :op1 "GST"~e.13)) :ARG2 (p3 / protein-segment~e.36 :part-of (p4 / protein :name (n2 / name :op1 "ASPP2"~e.16)) :poss~e.15 (w / we~e.15))))) :op2 (c / correspond-02~e.21 :ARG1 (p5 / peak~e.4 :mod (o / other~e.20) :ARG1-of (i2 / include-91 :ARG2 p2)) :ARG2~e.25 (p6 / protein-segment~e.36 :ARG0-of (h / have-03 :ARG1 (m / mass~e.28 :ARG1-of (s / same-01~e.27 :ARG2 (m2 / mass~e.28 :poss (p7 / protein-segment~e.36 :ARG1-of (p8 / phosphorylate-01~e.35) :ord (o2 / ordinal-entity~e.33 :value~e.33 2~e.33) :ARG1-of (e2 / equal-01 :ARG2 (a3 / amino-acid :mod 827~e.39 :name (n3 / name :op1 "serine"~e.38)) :ARG1-of (t / think-01~e.34)))))))))) # ::id bio.bmtr_0005.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Hence ASPP2 can be phosphorylated at serine 827 by MAPK1 in vitro . # ::alignments 0-1 1-1.1.1.1.3.1.1 2-1.1 4-1.1.1 6-1.1.1.1.2.1 7-1.1.1.1.1 8-1.1.1.2.r 9-1.1.1.2.1.1 10-1.1.1.3 11-1.1.1.3 (c / cause-01~e.0 :ARG1 (p / possible-01~e.2 :ARG1 (p2 / phosphorylate-01~e.4 :ARG1 (a / amino-acid :mod 827~e.7 :name (n / name :op1 "serine"~e.6) :part-of (p3 / protein :name (n2 / name :op1 "ASPP2"~e.1))) :ARG2~e.8 (e / enzyme :name (n3 / name :op1 "MAPK1"~e.9)) :manner (i / in-vitro~e.10,11)))) # ::id bio.bmtr_0005.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Passage 1 @-@ 2 ( Discussion/Conclusion ) # ::alignments 0-1 1-1.1 3-1.1 (p / passage~e.0 :mod "1-2"~e.1,3 :part-of (s / slash :op1 (t2 / thing :ARG1-of (d / discuss-01)) :op2 (t / thing :ARG1-of (c / conclude-01)))) # ::id bio.bmtr_0005.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We and others have recently shown that ASPP2 can potentiate RAS signaling by binding directly via the ASPP2 N @-@ terminus [ 2,6 ] . # ::alignments 0-1.1.1 1-1.1 2-1.1.2.1 4-1.3 5-1 6-1.2.r 7-1.2.1.2.1.1 8-1.2 9-1.2.1 10-1.2.1.1.1.1.1 11-1.2.1.1 12-1.2.1.3.r 13-1.2.1.3 14-1.2.1.3.3 17-1.2.1.3.2.2 18-1.2.1.3.2.1.1 20-1.2.1.3.2.1.1 (s / show-01~e.5 :ARG0 (a / and~e.1 :op1 (w / we~e.0) :op2 (p / person :mod (o / other~e.2))) :ARG1~e.6 (p2 / possible-01~e.8 :ARG1 (p3 / potentiate-01~e.9 :ARG1 (s2 / signal-07~e.11 :ARG0 (e / enzyme :name (n2 / name :op1 "RAS"~e.10))) :ARG2 (p4 / protein :name (n / name :op1 "ASPP2"~e.7)) :manner~e.12 (b / bind-01~e.13 :ARG1 e :ARG2 (p5 / protein-segment :name (n3 / name :op1 "N-terminus"~e.18,20) :part-of p4~e.17) :ARG1-of (d / direct-02~e.14)))) :time (r / recent~e.4) :ARG1-of (d2 / describe-01 :ARG0 (p6 / publication :ARG1-of (c / cite-01 :ARG2 (a2 / and :op1 2 :op2 6))))) # ::id bio.bmtr_0005.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Moreover , the RAS @-@ ASPP interaction enhances the transcription function of p53 in cancer cells [ 2 ] . # ::alignments 0-1 0-1.1.1.1 3-1.1.1.1.1.1.1 5-1.1.1.1.2.1.1 6-1.1.1 7-1.1 9-1.1.2.2 10-1.1.2 11-1.1.2.1.r 12-1.1.2.1.1.1 13-1.1.2.3.r 14-1.1.2.3.1.2.1 15-1.1.2.3 17-1.1.3.1.1.1 (a / and~e.0 :op2 (e / enhance-01~e.7 :ARG0 (i / interact-01~e.6 :ARG0 (a2 / and~e.0 :op1 (e2 / enzyme :name (n / name :op1 "RAS"~e.3)) :op2 (p / protein :name (n2 / name :op1 "ASPP"~e.5)))) :ARG1 (f / function-01~e.10 :ARG0~e.11 (p2 / protein :name (n3 / name :op1 "p53"~e.12)) :ARG1 (t / transcribe-01~e.9) :location~e.13 (c2 / cell~e.15 :mod (d2 / disease :wiki "Cancer" :name (n4 / name :op1 "cancer"~e.14)))) :ARG1-of (d / describe-01 :ARG0 (p3 / publication :ARG1-of (c4 / cite-01 :ARG2 2~e.17))))) # ::id bio.bmtr_0005.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Until now , it has been unclear how RAS could affect ASPP2 to enhance p53 function . # ::alignments 0-1.3 1-1.3.1 6-1 6-1.1 6-1.1.r 7-1.2.1.r 8-1.2.1.1.1.1.1 9-1.2.1 10-1.2.1.1 11-1.2.1.1.2.1.1 13-1.2.1.1.3 14-1.2.1.1.3.1.1.1.1 15-1.2.1.1.3.1 (c / clear-06~e.6 :polarity~e.6 -~e.6 :ARG1 (t / thing :manner-of~e.7 (p / possible-01~e.9 :ARG1 (a / affect-01~e.10 :ARG0 (e / enzyme :name (n / name :op1 "RAS"~e.8)) :ARG1 (p2 / protein :name (n3 / name :op1 "ASPP2"~e.11)) :ARG2 (e2 / enhance-01~e.13 :ARG1 (f / function-01~e.15 :ARG0 (p3 / protein :name (n4 / name :op1 "p53"~e.14))))))) :time (u / until~e.0 :op1 (n2 / now~e.1))) # ::id bio.bmtr_0005.22 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We show here that ASPP2 is phosphorylated by the RAS/Raf/MAPK pathway and that this phosphorylation leads to its increased translocation to the cytosol @/@ nucleus and increased binding to p53 , providing an explanation of how RAS can activate p53 pro @-@ apoptotic functions ( Figure 5 ) . # ::alignments 0-1.1 1-1 2-1.3 3-1.2.r 4-1.2.1.1.1 6-1.2 9-1.2.2.1.1 10-1.2.2 14-1.2 15-1.2.3 18-1.2.3.1.1 19-1.2.3.1.1.1 20-1.2.3.1.1.1.2.r 22-1.2.3.1.1.1.2.1 23-1.2.3.1.1.1.2 24-1.2.3.1.1.1.2.2 25-1.2.3.1 26-1.2.3.1.1 26-1.2.3.1.2 27-1.2.3.1.2.1 28-1.2.3.1.2.1.2.r 29-1.2.3.1.2.1.2.1.1 33-1.2.4 36-1.2.4.1.1.1.1.1 37-1.2.4.1 38-1.2.4.1.1 39-1.2.4.1.1.2.1 40-1.2.4.1.1.2.2.1 42-1.2.4.1.1.2.2 43-1.2.4.1.1.2 45-1.2.5.1 46-1.2.5.1.1 (s / show-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.3 (p / phosphorylate-01~e.6,14 :ARG1 (p3 / protein :name (n2 / name :op1 "ASPP2"~e.4)) :ARG2 (p2 / pathway~e.10 :name (n / name :op1 "RAS/Raf/MAPK"~e.9)) :ARG0-of (l / lead-03~e.15 :ARG2 (a / and~e.25 :op1 (i / increase-01~e.18,26 :ARG1 (t / translocate-01~e.19 :ARG1 p3 :ARG2~e.20 (s2 / slash~e.23 :op1 (c / cytosol~e.22) :op2 (n3 / nucleus~e.24)))) :op2 (i2 / increase-01~e.26 :ARG1 (b / bind-01~e.27 :ARG1 p3 :ARG2~e.28 (p4 / protein :name (n4 / name :op1 "p53"~e.29)))))) :ARG0-of (e2 / explain-01~e.33 :ARG1 (p5 / possible-01~e.37 :ARG1 (a2 / activate-01~e.38 :ARG0 (e / enzyme :name (n5 / name :op1 "RAS"~e.36)) :ARG1 (f / function-01~e.43 :ARG0 p4~e.39 :ARG1 (a3 / apoptosis~e.42 :ARG1-of (f2 / favor-01~e.40)))))) :ARG1-of (d / describe-01 :ARG0 (f3 / figure~e.45 :mod 5~e.46))) :location (h / here~e.2)) # ::id bio.bmtr_0005.23 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Additionally , RAS/Raf/MAPK pathway activation stabilizes ASPP2 protein , although the underlying mechanism remains to be investigated . # ::alignments 0-1 2-1.1.1.1.1.1 3-1.1.1.1 4-1.1.1 5-1.1 6-1.1.2.1.1 7-1.1.2 9-1.1.3.r 11-1.1.3.1.1 12-1.1.3.1 13-1.1.3 16-1.1.3.2 (a / and~e.0 :op2 (s / stabilize-01~e.5 :ARG0 (a2 / activate-01~e.4 :ARG1 (p / pathway~e.3 :name (n / name :op1 "RAS/Raf/MAPK"~e.2))) :ARG1 (p2 / protein~e.7 :name (n2 / name :op1 "ASPP2"~e.6)) :concession~e.9 (r / remain-01~e.13 :ARG1 (m / mechanism~e.12 :ARG0-of (u / underlie-01~e.11 :ARG1 s)) :ARG3 (i / investigate-01~e.16 :ARG1 m)))) # ::id bio.chicago_2015.17089 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The analogous result for PKC interaction with Par6 in the lower panel shows that , similarly to p62 , Par6b binds to PKC only when the PKC OPCA motif is not mutated and the back of Par6b has the wild @-@ type Lys 20 . # ::alignments 1-1.1.2 2-1.1 2-1.1.1 2-1.1.1.r 3-1.1.3.r 4-1.1.3.1.1.1 5-1.1.3 8-1.1.4.r 10-1.1.4.1 10-1.1.4.1.1 10-1.1.4.1.1.r 11-1.1.4 12-1 15-1.2.5 16-1.2.5.1.r 17-1.2.5.1.1.1 19-1.2.1 20-1.2 21-1.2.2.r 22-1.2.2 23-1.2.4 26-1.2.3.1.2.1.2 27-1.2.3.1.2.1.1.1 28-1.2.3.1.2 30-1.2.3.1.1 30-1.2.3.1.1.r 31-1.2.3.1 32-1.2.3 34-1.2.3.2.1 35-1.2.3.2.1.1.r 36-1.2.3.2.1.1 37-1.2.3.2 39-1.2.3.2.2.3 41-1.2.3.2.2.3 42-1.2.3.2.2.2.1 43-1.2.3.2.2.1 (s / show-01~e.12 :ARG0 (t / thing~e.2 :ARG2-of~e.2 (r / result-01~e.2) :mod (a / analogous~e.1) :topic~e.3 (i / interact-01~e.5 :ARG0 (e / enzyme :name (n / name :op1 "PKC"~e.4)) :ARG1 (p2 / protein :name (n2 / name :op1 "Par6b"))) :location~e.8 (p3 / panel~e.11 :ARG1-of (l / low-04~e.10 :degree~e.10 (m / more~e.10)))) :ARG1 (b / bind-01~e.20 :ARG0 p2~e.19 :ARG1~e.21 e~e.22 :condition (a2 / and~e.32 :op1 (m2 / mutate-01~e.31 :polarity~e.30 -~e.30 :ARG1 (m3 / motif~e.28 :mod (p4 / protein-segment :name (n3 / name :op1 "OPCA"~e.27) :part-of e~e.26))) :op2 (h / have-03~e.37 :ARG0 (b2 / back~e.34 :poss~e.35 p2~e.36) :ARG1 (a3 / amino-acid :mod 20~e.43 :name (n7 / name :op1 "lysine"~e.42) :mod (w / wild-type~e.39,41)))) :mod (o / only~e.23) :ARG1-of (r2 / resemble-01~e.15 :ARG2~e.16 (p6 / protein :name (n6 / name :op1 "p62"~e.17))))) # ::id bio.chicago_2015.17091 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A model is proposed in which endosomal Sca and Gp150 promote Notch activation in response to Delta , by regulating acquisition of insensitivity to Delta in a subset of cells . # ::alignments 1-1.1 3-1 6-1.1.1.1.3 7-1.1.1.1.1.1.1 8-1.1.1.1 9-1.1.1.1.2.1.1 10-1.1.1 11-1.1.1.2.1.1.1 12-1.1.1.2 13-1.1.1.2.2.r 14-1.1.1.2.2 15-1.1.1.2.2.1.r 16-1.1.1.2.2.1.1.1 18-1.1.1.3.r 19-1.1.1.3 20-1.1.1.3.1 21-1.1.1.3.1.1.r 22-1.1.1.3.1.1 22-1.1.1.3.1.1.1 22-1.1.1.3.1.1.1.r 23-1.1.1.3.1.1.3.r 24-1.1.1.3.1.1.3 25-1.1.1.3.2.r 27-1.1.1.3.2 28-1.1.1.3.2.1.r 29-1.1.1.3.2.1 (p / propose-01~e.3 :ARG1 (m / model~e.1 :topic (p2 / promote-02~e.10 :ARG0 (a / and~e.8 :op1 (p3 / protein :name (n / name :op1 "Sca"~e.7)) :op2 (p4 / protein :name (n2 / name :op1 "Gp150"~e.9)) :mod (e / endosomal~e.6)) :ARG1 (a2 / activate-01~e.12 :ARG1 (p5 / protein :name (n3 / name :op1 "Notch"~e.11)) :ARG2-of~e.13 (r / respond-01~e.14 :ARG1~e.15 (p6 / protein :name (n4 / name :op1 "Delta"~e.16)))) :manner~e.18 (r2 / regulate-01~e.19 :ARG1 (a3 / acquire-01~e.20 :ARG1~e.21 (s / sensitive-03~e.22 :polarity~e.22 -~e.22 :ARG0 p5 :ARG1~e.23 p6~e.24)) :location~e.25 (s2 / subset~e.27 :consist-of~e.28 (c / cell~e.29)))))) # ::id bio.chicago_2015.17114 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Because PLD activates PKC through the formation of diacylglycerol in VSMCs , 47 PLD also may contribute to this suppression . # ::alignments 0-1 1-1.1.1.1.1 2-1.1 3-1.1.2.1.1 6-1.1.3 7-1.1.3.1.r 8-1.1.3.1.1.1 12-1.1.4.1.1.1 13-1.1.1.1.1 14-1.2.2 15-1.2 16-1.2.1 17-1.2.1.2.r 18-1.2.1.2.1 19-1.2.1.2 (c / cause-01~e.0 :ARG0 (a / activate-01~e.2 :ARG0 (e3 / enzyme :name (n / name :op1 "PLD"~e.1,13)) :ARG1 (e2 / enzyme :name (n2 / name :op1 "PKC"~e.3)) :manner (f / form-01~e.6 :ARG1~e.7 (e / enzyme :name (n3 / name :op1 "diacylglycerol"~e.8)) :location (c2 / cell :name (n4 / name :op1 "VSMC"))) :ARG1-of (d2 / describe-01 :ARG0 (p4 / publication :ARG1-of (c4 / cite-01 :ARG2 47~e.12)))) :ARG1 (p3 / possible-01~e.15 :ARG1 (c3 / contribute-01~e.16 :ARG0 e3 :ARG1~e.17 (s / suppress-01~e.19 :mod (t / this~e.18))) :mod (a2 / also~e.14))) # ::id bio.chicago_2015.17152 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Whether PKC regulation of DAT and other neurotransmitter transporters is due to direct phosphorylation of the transporter remains unclear . # ::alignments 0-1.1.1 0-1.1.1.r 1-1.1.3.1.1.1 2-1.1.3 3-1.1.3.2.r 4-1.1.3.2.1.1.1 5-1.1.3.2 6-1.1.3.2.2.2 7-1.1.3.2.2.1.1 8-1.1.3.2.2.1.2 10-1.1 11-1.1 12-1.1.2.2 13-1.1.2 16-1.1.3.2.2.1.2 17-1 18-1.2 18-1.2.1 18-1.2.1.r (r / remain-01~e.17 :ARG1 (c2 / cause-01~e.10,11 :mode~e.0 interrogative~e.0 :ARG0 (p / phosphorylate-01~e.13 :ARG1 (m / molecular-physical-entity :ARG0-of (t2 / transport-01)) :ARG1-of (d / direct-02~e.12)) :ARG1 (r2 / regulate-01~e.2 :ARG0 (e / enzyme :name (n / name :op1 "PKC"~e.1)) :ARG1~e.3 (a / and~e.5 :op1 (p3 / protein :name (n2 / name :op1 "DAT"~e.4)) :op2 (p4 / protein-family :name (n3 / name :op1 "neurotransmitter"~e.7 :op2 "transporter"~e.8,16) :mod (o / other~e.6))))) :ARG3 (c / clear-06~e.18 :polarity~e.18 -~e.18 :ARG1 c2)) # ::id bio.chicago_2015.17165 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Venable et al. ( 66 ) also described an inhibition by ceramide of PLD stimulation by PKC , but ascribed this to an upstream effect on PKC rather than a decrease in the translocation to membranes . # ::alignments 0-1.1.1.1.1.1.1 1-1.1.1.1 2-1.1.1.1.2.1 4-1.1.1.2.1 6-1.1.3 7-1.1 9-1.1.2 10-1.1.2.1.r 11-1.1.2.1.1.1 12-1.1.2.2.r 13-1.1.2.2.2.1.1 14-1.1.2.2 15-1.1.2.2.1.r 16-1.1.2.2.1.1.1 18-1 19-1.2 21-1.2.3.r 23-1.2.3.2 24-1.2.3 25-1.2.3.1.r 26-1.2.3.1 27-1.2.3.3 30-1.2.3.3.1 31-1.2.3.3.1.1.r 33-1.2.3.3.1.1 34-1.2.3.3.1.1.1.r 35-1.2.3.3.1.1.1 (c2 / contrast-01~e.18 :ARG1 (d / describe-01~e.7 :ARG0 (p / publication-91 :ARG0 (a / and~e.1 :op1 (p2 / person :name (n / name :op1 "Venable"~e.0)) :op1 (p3 / person :mod (o / other~e.2))) :ARG1-of (c / cite-01 :ARG2 66~e.4)) :ARG1 (i / inhibit-01~e.9 :ARG0~e.10 (s2 / small-molecule :name (n2 / name :op1 "ceramide"~e.11)) :ARG1~e.12 (s / stimulate-01~e.14 :ARG0~e.15 (e / enzyme :name (n4 / name :op1 "PKC"~e.16)) :ARG1 (e2 / enzyme :name (n3 / name :op1 "PLD"~e.13)))) :mod (a4 / also~e.6)) :ARG2 (a2 / ascribe-01~e.19 :ARG0 p :ARG1 i :ARG2~e.21 (a3 / affect-01~e.24 :ARG1~e.25 e~e.26 :mod (u / upstream~e.23) :ARG1-of (i2 / instead-of-91~e.27 :ARG2 (d2 / decrease-01~e.30 :ARG1~e.31 (t2 / translocate-01~e.33 :ARG2~e.34 (m / membrane~e.35))))))) # ::id bio.chicago_2015.17176 ::amr-annotator SDL-AMR-09 ::preferred # ::tok dSir2 Interacts Genetically with Hairy Embryos derived from mothers transheterozygous for hairy and dSir2 mated to wild @-@ type males exhibit moderate # ::alignments 0-1.1.1.1 1-1 2-1.3 3-1.2.r 4-1.2.1.1.1 5-1.2 6-1.2.2 7-1.2.2.1.r 8-1.2.2.1.1.1 9-1.2.2.1.2 10-1.2.2.1.2.1.r 11-1.2.2.1.2.1.1 12-1.2.2.1.2.1 13-1.1.1.1 14-1.2.2.1.3 15-1.2.2.1.3.1.r 16-1.2.2.1.3.1.1 18-1.2.2.1.3.1.1 19-1.2.2.1.3.1 20-1.2.2.1 20-1.2.2.1.4 20-1.2.2.1.4.r 21-1.2.2.1.4.1 21-1.2.2.1.4.1.1 21-1.2.2.1.4.1.1.r (i / interact-01~e.1 :ARG0 (p / protein :name (n / name :op1 "dSir2"~e.0,13)) :ARG1~e.3 (e / embryo~e.5 :mod (p3 / protein :name (n2 / name :op1 "hairy"~e.4)) :ARG1-of (d / derive-01~e.6 :ARG2~e.7 (p2 / person~e.20 :ARG0-of (h2 / have-rel-role-91 :ARG2 (m / mother~e.8)) :mod (t / transheterozygous~e.9 :topic~e.10 (a / and~e.12 :op1 p3~e.11 :op2 p)) :ARG1-of (m2 / mate-02~e.14 :ARG2~e.15 (m3 / male~e.19 :mod (w / wild-type~e.16,18))) :ARG0-of~e.20 (e2 / exhibit-01~e.20 :ARG1 (t2 / thing~e.21 :ARG1-of~e.21 (m4 / moderate-01~e.21)))))) :manner (g / genetic~e.2)) # ::id bio.chicago_2015.17177 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We now report that , although PS1 mutations augment gamma @-@ secretase cleavage at residue 42 , they in fact suppress both S3 @-@ cleavage of Notch and epsilon @-@ cleavage of APP near residue 50 . # ::alignments 0-1.1 1-1.3 2-1 5-1.2.4.r 6-1.2.4.1.1.1.1 7-1.2.4.1 8-1.2.4 9-1.2.4.2.1.1.2.1.1 11-1.2.4.2.1.1.2.1.1 12-1.2.4.2 14-1.2.4.2.1 15-1.2.4.2.1.1.1 17-1.2.1 18-1.2.3 19-1.2.3 20-1.2 22-1.2.2.1.1.1.1 24-1.2.2.1 26-1.2.2.1.1.2.1.1 27-1.2.2 28-1.2.2.2.1.1.1 30-1.2.2.2 32-1.2.2.2.1.2.1.1 33-1.2.2.1.1 33-1.2.2.1.1.3 33-1.2.2.1.1.3.r 34-1.2.2.1.1.3.1 35-1.2.2.1.1.3.1.1.1 (r3 / report-01~e.2 :ARG0 (w / we~e.0) :ARG1 (s / suppress-01~e.20 :ARG0 m~e.17 :ARG1 (a / and~e.27 :op1 (c / cleave-01~e.24 :ARG1 (p3 / protein-segment~e.33 :name (n / name :op1 "S3"~e.22) :part-of (p / protein :name (n2 / name :op1 "Notch"~e.26)) :ARG1-of~e.33 (n5 / near-02~e.33 :ARG2 (r / residue~e.34 :mod (a2 / amino-acid :mod 50~e.35))))) :op2 (c2 / cleave-01~e.30 :ARG1 (p4 / protein-segment :name (n4 / name :op1 "epsilon"~e.28) :part-of (p2 / protein :name (n3 / name :op1 "APP"~e.32)) :ARG1-of n5))) :mod (i / in-fact~e.18,19) :concession~e.5 (a3 / augment-01~e.8 :ARG0 (m / mutate-01~e.7 :ARG1 (p5 / protein :name (n6 / name :op1 "PS1"~e.6))) :ARG1 (c3 / cleave-01~e.12 :ARG1 (r2 / residue~e.14 :mod (a4 / amino-acid :mod 42~e.15 :part-of (e3 / enzyme :name (n7 / name :op1 "gamma-secretase"~e.9,11))))))) :time (n8 / now~e.1)) # ::id bio.chicago_2015.17180 ::amr-annotator SDL-AMR-09 ::preferred # ::tok At the nucleus , PKC betaII mediates direct phosphorylation of the nuclear envelope polypeptide lamin B on sites involved in mitotic nuclear lamina disassembly ( 12 , 13 , 15 ) . # ::alignments 2-1.3 4-1.1.1.1 5-1.1.1.2 6-1 7-1.2.2 8-1.2 9-1.2.1.r 11-1.2.1.2.1 12-1.2.1.2 14-1.2.1.1.1 15-1.2.1.1.2 16-1.2.3.r 17-1.2.3 18-1.2.3.1 20-1.2.3.1.1.2.1 21-1.2.3.1.1.2.2 22-1.2.3.1.1.2 25-1.4.1.1.1.1 27-1.4.1.1.1.2 29-1.4.1.1.1.3 (m / mediate-01~e.6 :ARG0 (e / enzyme :name (n / name :op1 "PKC"~e.4 :op2 "betaII"~e.5)) :ARG1 (p2 / phosphorylate-01~e.8 :ARG1~e.9 (p3 / protein-segment :name (n2 / name :op1 "lamin"~e.14 :op2 "B"~e.15) :part-of (e2 / envelope~e.12 :part-of n3~e.11)) :ARG1-of (d / direct-02~e.7) :location~e.16 (s / site~e.17 :ARG1-of (i / involve-01~e.18 :ARG2 (a / assemble-01 :polarity - :ARG1 (l / lamina~e.22 :mod (m2 / mitosis~e.20) :part-of n3~e.21))))) :location (n3 / nucleus~e.2) :ARG1-of (d2 / describe-01 :ARG0 (p4 / publication :ARG1-of (c / cite-01 :ARG2 (a2 / and :op1 12~e.25 :op2 13~e.27 :op3 15~e.29))))) # ::id bio.chicago_2015.17227 ::amr-annotator SDL-AMR-09 ::preferred # ::tok At the nucleus , PKC betaII directly phosphorylates the nuclear envelope polypeptide lamin B at sites involved in mitotic nuclear lamina disassembly ( 8 @-@ 10 ) . # ::alignments 2-1.4 4-1.2.1.1 5-1.2.1.2 6-1.3 6-1.3.r 7-1 9-1.1.2.1 10-1.1.2 12-1.1.1.1 13-1.1.1.2 14-1.5.r 15-1.5 16-1.5.1 18-1.5.1.1.2.2 19-1.5.1.1.2.1 20-1.5.1.1.2 23-1.6.1.1.1.1 25-1.6.1.1.1.2 (p / phosphorylate-01~e.7 :ARG1 (p2 / protein-segment :name (n3 / name :op1 "lamin"~e.12 :op2 "B"~e.13) :part-of (e2 / envelope~e.10 :part-of n2~e.9)) :ARG2 (e / enzyme :name (n / name :op1 "PKC"~e.4 :op2 "betaII"~e.5)) :manner~e.6 (d / direct~e.6) :location (n2 / nucleus~e.2) :location~e.14 (s / site~e.15 :ARG1-of (i / involve-01~e.16 :ARG2 (a / assemble-01 :polarity - :ARG1 (l / lamina~e.20 :part-of n2~e.19 :mod (m / mitosis~e.18))))) :ARG1-of (d2 / describe-01 :ARG0 (p3 / publication :ARG1-of (c / cite-01 :ARG2 (v / value-interval :op1 8~e.23 :op2 10~e.25))))) # ::id bio.chicago_2015.17275 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To determine whether in vitro phosphorylation of fascin with PKC occurs at the same sites as observed in vivo , two @-@ dimensional phosphopeptide mapping was performed . # ::alignments 1-1.2 2-1.2.1.1 2-1.2.1.1.r 3-1.2.1.4 4-1.2.1.4 5-1.2.1 6-1.2.1.2.r 7-1.2.1.2.1.1 8-1.2.1.3.r 9-1.2.1.3.1.1 11-1.2.1.5.r 13-1.2.1.5.1 14-1.2.1.5 14-1.2.1.5.1.1 15-1.2.1.5.1.1.2.r 16-1.2.1.5.1.1.2 17-1.2.1.5.1.1.2.1 18-1.2.1.5.1.1.2.1 20-1.1.2.1 22-1.1.2 23-1.1.1.1.1 24-1.1 26-1 (p2 / perform-02~e.26 :ARG1 (m / map-02~e.24 :ARG1 (s4 / small-molecule :name (n / name :op1 "phosphopeptide"~e.23)) :manner (d / dimension~e.22 :quant 2~e.20)) :purpose (d2 / determine-01~e.1 :ARG1 (p4 / phosphorylate-01~e.5 :mode~e.2 interrogative~e.2 :ARG1~e.6 (p5 / protein :name (n2 / name :op1 "fascin"~e.7)) :ARG2~e.8 (e / enzyme :name (n3 / name :op1 "PKC"~e.9)) :manner (i / in-vitro~e.3,4) :location~e.11 (s / site~e.14 :ARG1-of (s2 / same-01~e.13 :ARG2 (s3 / site~e.14 :location-of p4 :ARG1-of~e.15 (o2 / observe-01~e.16 :manner (i2 / in-vivo~e.17,18)))))))) # ::id bio.chicago_2015.17347 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Dl then activates Notch ( N ) in the R4 precursor ( Cooper and Bray , 1999 ; Fanto and Mlodzik , 1999 ; Tomlinson and Struhl , 1999 ) . # ::alignments 0-1.1.1.1 1-1.5 2-1 3-1.2.1.1 7-1.3.r 9-1.3.1.1 10-1.3.1.2 12-1.4.1.1.1.1.1.1 13-1.4.1.1.1 14-1.4.1.1.1.2.1.1 16-1.4.1.1.2.1 18-1.4.1.2.1.1.1.1 19-1.4.1.2.1 20-1.4.1.2.1.2.1.1 22-1.4.1.1.2.1 24-1.4.1.3.1.1.1.1 25-1.4.1.3.1 26-1.4.1.3.1.2.1.1 28-1.4.1.3.2 (a / activate-01~e.2 :ARG0 (p11 / protein :name (n9 / name :op1 "Dl"~e.0)) :ARG1 (p / protein :name (n / name :op1 "Notch"~e.3)) :location~e.7 (c / cell :name (n2 / name :op1 "R4"~e.9 :op2 "precursor"~e.10)) :ARG1-of (d3 / describe-01 :ARG0 (a2 / and :op1 (p2 / publication-91 :ARG0 (a3 / and~e.13 :op1 (p3 / person :name (n3 / name :op1 "Cooper"~e.12)) :op2 (p4 / person :name (n4 / name :op1 "Bray"~e.14))) :time (d4 / date-entity :year 1999~e.16,22)) :op2 (p5 / publication-91 :ARG0 (a4 / and~e.19 :op1 (p7 / person :name (n6 / name :op1 "Fanto"~e.18)) :op2 (p6 / person :name (n5 / name :op1 "Mlodzik"~e.20))) :time d4) :op3 (p8 / publication-91 :ARG0 (a5 / and~e.25 :op1 (p9 / person :name (n7 / name :op1 "Tomlinson"~e.24)) :op2 (p10 / person :name (n8 / name :op1 "Struhl"~e.26))) :time d4~e.28))) :time (t / then~e.1)) # ::id bio.chicago_2015.17446 ::amr-annotator SDL-AMR-09 ::preferred # ::tok to prevent the additional stabilization of U2AF65 binding conferred by the interaction between U2AF35 and the AG dinucleotide . # ::alignments 1-1.1 3-1.1.1.2 4-1.1.1 5-1.1.1.1.r 6-1.1.1.1.1.1.1 7-1.1.1.1 8-1.1.1.1.2 9-1.1.1.1.2.1.r 11-1.1.1.1.2.1 13-1.1.1.1.2.1.1.1.1 16-1.1.1.1.2.1.2.1.1 17-1.1.1.1.2.1.2 (h / have-purpose-91 :ARG2 (p / prevent-01~e.1 :ARG1 (s / stabilize-01~e.4 :ARG1~e.5 (b / bind-01~e.7 :ARG1 (p2 / protein :name (n / name :op1 "U2AF65"~e.6)) :ARG1-of (c / confer-02~e.8 :ARG0~e.9 (i / interact-01~e.11 :ARG0 (p3 / protein :name (n2 / name :op1 "U2AF35"~e.13)) :ARG1 (d / dinucleotide~e.17 :name (n3 / name :op1 "AG"~e.16))))) :mod (a / additional~e.3)))) # ::id bio.chicago_2015.17480 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Axin mutants with C @-@ terminal truncations lacked the ability to inhibit Lef @-@ 1 reporter activity , even though they bound GSK @-@ 3 beta and beta @-@ catenin . # ::alignments 0-1.1.1.1 1-1.1 1-1.1.2 1-1.1.2.r 3-1.1.3.1.1.1.1 5-1.1.3.1.1.1.1 6-1.1.3.1 7-1 9-1.2 11-1.2.2 12-1.2.2.2.1.1.1.1.1 14-1.2.2.2.1.1.1.1.1 15-1.2.2.2.1 15-1.2.2.2.1.1 15-1.2.2.2.1.1.r 16-1.2.2.2 18-1.3.r 19-1.3.r 20-1.3.1 21-1.3 22-1.3.2.1.1.1 25-1.3.2.2.1.1 27-1.3.2.2.1.1 29-1.3.2.2.1.1 (l / lack-01~e.7 :ARG0 (p2 / protein~e.1 :name (n / name :op1 "Axin"~e.0) :ARG2-of~e.1 (m / mutate-01~e.1) :ARG0-of (h / have-03 :ARG1 (t / truncate-01~e.6 :ARG1 (p3 / protein-segment :name (n2 / name :op1 "C-terminus"~e.3,5))))) :ARG1 (c / capable-01~e.9 :ARG1 p2 :ARG2 (i / inhibit-01~e.11 :ARG0 p2 :ARG1 (a / activity-06~e.16 :ARG0 (m2 / molecular-physical-entity~e.15 :ARG0-of~e.15 (r2 / report-01~e.15 :ARG1 (p / protein :name (n3 / name :op1 "Lef-1"~e.12,14))))))) :concession~e.18,19 (b / bind-01~e.21 :ARG1 p2~e.20 :ARG2 (a2 / and :op1 (e / enzyme :name (n4 / name :op1 "GSK-3beta"~e.22)) :op2 (p4 / protein :name (n5 / name :op1 "beta-catenin"~e.25,27,29))))) # ::id bio.chicago_2015.17550 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In vivo binding of GSK @-@ 3 beta with Axin or beta @-@ catenin . # ::alignments 0-1.3 1-1.3 2-1 3-1.1.r 4-1.1.1.1 7-1.2.2.1.1 8-1.2.r 9-1.2.1.1.1 10-1.2 11-1.2.2.1.1 13-1.2.2.1.1 (b / bind-01~e.2 :ARG1~e.3 (e / enzyme :name (n / name :op1 "GSK-3beta"~e.4)) :ARG2~e.8 (o / or~e.10 :op1 (p / protein :name (n2 / name :op1 "Axin"~e.9)) :op2 (p2 / protein :name (n3 / name :op1 "beta-catenin"~e.7,11,13))) :manner (i / in-vivo~e.0,1)) # ::id bio.chicago_2015.17615 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For some of these transcription factors , the domain that interacts with Groucho is mapped to a short peptide motif . # ::alignments 1-1.3.2 2-1.3.2.r 3-1.3.3 4-1.3.1 5-1.3 8-1.1 10-1.1.1 11-1.1.1.1.r 12-1.1.1.1.1.1 14-1 15-1.2.r 17-1.2.1.1 18-1.2.1 19-1.2 (m / map-02~e.14 :ARG1 (d / domain~e.8 :ARG0-of (i / interact-01~e.10 :ARG1~e.11 (p / protein :name (n / name :op1 "Groucho"~e.12))) :part-of f) :ARG2~e.15 (m2 / motif~e.19 :part-of (p2 / peptide~e.18 :ARG1-of (s / short-07~e.17))) :beneficiary (f / factor~e.5 :ARG0-of (t / transcribe-01~e.4) :quant~e.2 (s2 / some~e.1) :mod (t2 / this~e.3))) # ::id bio.chicago_2015.17655 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We may conclude that GAGA factor binds to ( CT ) n repeats independently of TBP binding and facilitates binding of the latter directly or indirectly . # ::alignments 0-1.1.1 1-1 2-1.1 3-1.1.2.r 4-1.1.2.1.1.1.1 5-1.1.2.1.1.1.2 6-1.1.2.1.3.2 12-1.1.2.1.2.1.2 13-1.1.2.1.3.1 15-1.1.2.1.3.2.1.1.1 16-1.1.2.1 16-1.1.2.1.3.2 17-1.1.2 18-1.1.2.2 19-1.1.2.2.2 23-1.1.2.2.2.2 23-1.1.2.2.2.3 25-1.1.2.2.2.3 25-1.1.2.2.2.3.1 25-1.1.2.2.2.3.1.r (p / possible-01~e.1 :ARG1 (c / conclude-01~e.2 :ARG0 (w / we~e.0) :ARG1~e.3 (a / and~e.17 :op1 (b / bind-01~e.16 :ARG1 (p2 / protein :name (n / name :op1 "GAGA"~e.4 :op2 "factor"~e.5)) :ARG2 (p3 / protein :name (n2 / name :op1 "(CT)n" :op2 "repeat"~e.12)) :ARG0-of (d / depend-01 :polarity -~e.13 :ARG1 (b2 / bind-01~e.6,16 :ARG1 (p4 / protein :name (n3 / name :op1 "TBP"~e.15))))) :op2 (f / facilitate-01~e.18 :ARG0 p2 :ARG1 (b3 / bind-01~e.19 :ARG1 p4 :ARG1-of (d2 / direct-02~e.23) :ARG1-of (d3 / direct-02~e.23,25 :polarity~e.25 -~e.25)))))) # ::id bio.chicago_2015.17666 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As - catenin interacts with transcription factors of the LEF/ TCF family to regulate target gene expression , this raises the possibility that nuclear events of Wnt/ - catenin signaling are involved in regulating convergent extension . # ::alignments 2-1.1.1.1 3-1 4-1.2.r 5-1.2.1 6-1.2 10-1.2.2.1.2 11-1.2.2 13-1.3 14-1.3.2.1.1 15-1.3.2.1 16-1.3.2 19-1.4 21-1.4.1 22-1.4.1.1.r 23-1.4.1.1.1.1 24-1.4.1.1.1 28-1.4.1.1.1.2.1.1.1.1 29-1.4.1.1.1.2.1 31-1.4.1.1 32-1.4.1.1.2.r 33-1.4.1.1.2 34-1.4.1.1.2.2.1 35-1.4.1.1.2.2 (i / interact-01~e.3 :ARG0 (p / protein :name (n / name :op1 "beta-catenin"~e.2)) :ARG1~e.4 (f / factor~e.6 :ARG0-of (t / transcribe-01~e.5) :part-of (p2 / protein-family~e.11 :name (n2 / name :op1 "LEF" :op2 "TCF"~e.10))) :ARG2 (r / regulate-01~e.13 :ARG0 p :ARG1 (e / express-03~e.16 :ARG1 (g / gene~e.15 :ARG1-of (t2 / target-01~e.14)))) :ARG0-of (r2 / raise-01~e.19 :ARG1 (p3 / possible-01~e.21 :ARG1~e.22 (i2 / involve-01~e.31 :ARG1 (e2 / event~e.24 :location (n3 / nucleus~e.23) :ARG1-of (c / cause-01 :ARG0 (s / signal-07~e.29 :ARG0 (p4 / pathway :name (n4 / name :op1 "Wnt/beta-catenin"~e.28))))) :ARG2~e.32 (r3 / regulate-01~e.33 :ARG0 e2 :ARG1 (e3 / extend-01~e.35 :ARG0-of (c2 / converge-01~e.34))))))) # ::id bio.chicago_2015.17703 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We believe that it represents an unlikely scenario as we have shown that a PS1 allele defective in beta @-@ catenin binding , while retaining full Notch processing activity , cannot suppress the elevated beta @-@ catenin signaling caused by PS1 deficiency ( Fig . 4 ) . # ::alignments 0-1.1 1-1 2-1.2.r 3-1.2.1 4-1.2 6-1.2.2.1 6-1.2.2.1.1 6-1.2.2.1.1.r 7-1.2.2 8-1.3.r 9-1.3.1.1 11-1.3.1 12-1.3.1.2.r 14-1.3.1.2.2.3.1 15-1.3.1.2.2.3.1 16-1.3.1.2.2.3.1 17-1.3.1.2.2.3.1 18-1.3.1.2.2.3.1 19-1.3.1.2.2.3.1 20-1.3.1.2.2.3.1 21-1.3.1.2.2.3.1 24-1.3.1.2.2.3 25-1.3.1.2.2.3.2.2 26-1.3.1.2.2.3.2.1.2.1.1 27-1.3.1.2.2.3.2.1 28-1.3.1.2.2.3.2 30-1.3.1.2 30-1.3.1.2.1 30-1.3.1.2.1.r 31-1.3.1.2.2 33-1.3.1.2.2.2.2 34-1.3.1.2.2.2.1 35-1.3.1.2.2.2.1 36-1.3.1.2.2.2.1 37-1.3.1.2.2.2 38-1.3 38-1.3.1.2.2.2.3 39-1.3.1.2.2.1.r 40-1.3.1.2.2.1.1.1 41-1.3.1.2.2.1 41-1.3.1.2.2.1.4 41-1.3.1.2.2.1.4.r 43-1.4.1 45-1.4.1.1 (b / believe-01~e.1 :ARG0 (w2 / we~e.0) :ARG1~e.2 (r / represent-01~e.4 :ARG1 (i / it~e.3) :ARG2 (s / scenario~e.7 :ARG1-of (l / likely-01~e.6 :polarity~e.6 -~e.6))) :ARG1-of~e.8 (c / cause-01~e.38 :ARG0 (s2 / show-01~e.11 :ARG0 w2~e.9 :ARG1~e.12 (p / possible-01~e.30 :polarity~e.30 -~e.30 :ARG1 (s3 / suppress-01~e.31 :ARG0~e.39 (p5 / protein~e.41 :name (n / name :op1 "PS1"~e.40) :mod (d / defective) :ARG1-of (b2 / bind-01 :ARG2 (p2 / protein :name (n2 / name :op1 "beta-catenin"))) :ARG2-of~e.41 (m / mutate-01~e.41)) :ARG1 (s4 / signal-07~e.37 :ARG0 p2~e.34,35,36 :ARG1-of (e / elevate-01~e.33) :ARG1-of (c2 / cause-01~e.38 :ARG0 (l2 / lack-01 :ARG1 p5))) :concession (r2 / retain-01~e.24 :ARG0 p5~e.14,15,16,17,18,19,20,21 :ARG1 (a2 / activity-06~e.28 :ARG1 (p3 / process-01~e.27 :ARG0 p5 :ARG1 (p4 / protein :name (n3 / name :op1 "Notch"~e.26))) :mod (f / full~e.25))))))) :ARG1-of (d2 / describe-01 :ARG0 (f2 / figure~e.43 :mod 4~e.45))) # ::id bio.chicago_2015.17707 ::amr-annotator SDL-AMR-09 ::preferred # ::tok CKI did not phosphorylate GSK3 beta , B56 alpha , or beta @-@ TrCP . # ::alignments 0-1.3.1.1 2-1.1 2-1.1.r 3-1 5-1.2.3.1.1 10-1.2 11-1.2.3.1.1 13-1.2.3.1.1 (p / phosphorylate-01~e.3 :polarity~e.2 -~e.2 :ARG1 (o / or~e.10 :op1 (e2 / enzyme :name (n2 / name :op1 "GSK3beta")) :op2 (e3 / enzyme :name (n3 / name :op1 "B56alpha")) :op2 (p2 / protein :name (n4 / name :op1 "beta-TrCP"~e.5,11,13))) :ARG2 (e / enzyme :name (n / name :op1 "CKI"~e.0))) # ::id bio.chicago_2015.17718 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Because the mutations in PS1 apparently inhibit transcriptional activity of beta @-@ catenin downstream of GSK 3 beta , we hypothesized that PS1 may be interacting with the binding partner of beta @-@ catenin , namely hTcf @-@ 4 . # ::alignments 0-1.3 2-1.3.1.1 3-1.3.1.1.1.r 4-1.3.1.1.1 5-1.3.1.3 6-1.3.1 7-1.3.1.2.2 8-1.3.1.2 10-1.2.1.2.1.1.1.1 10-1.3.1.2.3.1.1.2 12-1.3.1.2.1 13-1.3.1.2.3.2 17-1.2.1.2.1.1.1.1 17-1.3.1.2.3.1.1.2 19-1.1 20-1 21-1.2.r 22-1.2.1.1.1.1 23-1.2 25-1.2.1 26-1.2.1.2.r 28-1.2.1.2.1 29-1.2.1.2 30-1.2.1.2.1.1.r 31-1.2.1.2.1.1.1.1 33-1.2.1.2.1.1.1.1 35-1.2.1.2.2 36-1.2.1.2.2.1.1.1 38-1.2.1.2.2.1.1.1 (h / hypothesize-01~e.20 :ARG0 (w / we~e.19) :ARG1~e.21 (p / possible-01~e.23 :ARG1 (i / interact-01~e.25 :ARG0 (p4 / protein :name (n / name :op1 "PS1"~e.22)) :ARG1~e.26 (p2 / partner~e.29 :ARG1-of (b / bind-01~e.28 :ARG2~e.30 (p3 / protein :name (n2 / name :op1 "beta-catenin"~e.10,17,31,33))) :ARG1-of (m / mean-01~e.35 :ARG2 (p5 / protein :name (n3 / name :op1 "hTcf-4"~e.36,38)))))) :ARG1-of (c / cause-01~e.0 :ARG0 (i2 / inhibit-01~e.6 :ARG0 (m2 / mutate-01~e.2 :ARG1~e.3 p4~e.4) :ARG1 (a3 / activity-06~e.8 :ARG0 p3~e.12 :ARG1 (t2 / transcribe-01~e.7) :location (r / relative-position :op1 (e / enzyme :name (n5 / name :op1 "GSK3" :op2 "beta"~e.10,17)) :direction (d2 / downstream~e.13))) :ARG1-of (a / appear-02~e.5)))) # ::id bio.chicago_2015.17743 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Currently , a link between MAPK activation and the phosphorylation and activation of transcription factors involved in proliferation and cell growth is established by the finding that MAPK activates p90 ribosomal S6 kinase ( p90RSK ; De Cesare et al. , 1998 ; Frodin and Gammeltoft , 1999 ; Smith et al. 1999 ) . # ::alignments 0-1.4 3-1.2 4-1.2.1.r 5-1.2.1.1 6-1.2.1 7-1.2.2 9-1.2.2.1 10-1.2.2 11-1.2.2.2 12-1.2.2.1.1.r 13-1.2.2.1.1.1 14-1.2.2.1.1 15-1.2.2.1.1.2 16-1.2.2.1.1.2.1.r 17-1.2.2.1.1.2.1.1 18-1.2.2.1.1.2.1 19-1.2.2.1.1.2.1.2.1 20-1.2.2.1.1.2.1.2 22-1 23-1.1.r 25-1.1 26-1.1.1.r 27-1.1.1.1.1.1 28-1.1.1 29-1.1.1.2.1.1 30-1.1.1.2.1.2 31-1.1.1.2.1.3 32-1.1.1.2.1.4 36-1.3.1.1.1.1.1.1 37-1.3.1.1.1.1.1.2 38-1.3.1.1.1 39-1.3.1.1.1.2.1 41-1.3.1.1.2.1 43-1.3.1.2.1.1.1.1 44-1.3.1.2.1 45-1.3.1.2.1.2.1.1 47-1.3.1.2.2.1 49-1.3.1.3.1.1.1.1 50-1.3.1 50-1.3.1.2.1 50-1.3.1.3.1 51-1.3.1.3.1.2.1 52-1.3.1.3.2 (e / establish-01~e.22 :ARG0~e.23 (f / find-01~e.25 :ARG1~e.26 (a / activate-01~e.28 :ARG0 (e2 / enzyme :name (n2 / name :op1 "MAPK"~e.27)) :ARG1 (e3 / enzyme :name (n3 / name :op1 "p90"~e.29 :op2 "ribosomal"~e.30 :op3 "S6"~e.31 :op4 "kinase"~e.32)))) :ARG1 (l / link-01~e.3 :ARG1~e.4 (a2 / activate-01~e.6 :ARG0 e2~e.5) :ARG2 (a3 / and~e.7,10 :op1 (p3 / phosphorylate-01~e.9 :ARG1~e.12 (f2 / factor~e.14 :ARG0-of (t / transcribe-01~e.13) :ARG1-of (i / involve-01~e.15 :ARG2~e.16 (a5 / and~e.18 :op1 (p4 / proliferate-01~e.17) :op2 (g / grow-01~e.20 :ARG1 (c / cell~e.19)))))) :op2 (a4 / activate-01~e.11 :ARG1 f2))) :ARG1-of (d3 / describe-01 :ARG0 (a6 / and~e.50 :op1 (p5 / publication-91 :ARG0 (a7 / and~e.38 :op1 (p6 / person :name (n4 / name :op1 "De"~e.36 :op2 "Cesare"~e.37)) :op2 (p7 / person :mod (o / other~e.39))) :time (d4 / date-entity :year 1998~e.41)) :op2 (p8 / publication-91 :ARG0 (a8 / and~e.44,50 :op1 (p9 / person :name (n5 / name :op1 "Frodin"~e.43)) :op2 (p10 / person :name (n6 / name :op1 "Gammeltoft"~e.45))) :time (d5 / date-entity :year 1999~e.47)) :op3 (p11 / publication-91 :ARG0 (a9 / and~e.50 :op1 (p12 / person :name (n7 / name :op1 "Smith"~e.49)) :op2 (p13 / person :mod (o2 / other~e.51))) :time d5~e.52))) :time (c2 / current~e.0)) # ::id bio.chicago_2015.17757 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These results suggest that CBP can bind to various transcription factors of the ATF/ CREB family through the b @-@ ZIP domain . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 2-1 3-1.2.r 4-1.2.1.1.1.1 5-1.2 6-1.2.1 7-1.2.1.2.r 8-1.2.1.2.3 9-1.2.1.2.1 10-1.2.1.2 14-1.2.1.2.2.1.2 15-1.2.1.2.2 18-1.2.1.3.1.1 20-1.2.1.3.1.1 (s / suggest-01~e.2 :ARG0 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :mod (t3 / this~e.0)) :ARG1~e.3 (p / possible-01~e.5 :ARG1 (b / bind-01~e.6 :ARG1 (p2 / protein :name (n / name :op1 "CBP"~e.4)) :ARG2~e.7 (f / factor~e.10 :ARG0-of (t2 / transcribe-01~e.9) :part-of (p3 / protein-family~e.15 :name (n2 / name :op1 "ATF" :op2 "CREB"~e.14)) :mod (v / various~e.8)) :instrument (p4 / protein-segment :name (n3 / name :op1 "b-ZIP"~e.18,20))))) # ::id bio.chicago_2015.17801 ::amr-annotator SDL-AMR-09 ::preferred # ::tok GSK @-@ 3 beta , glycogen synthase kinase 3 beta ; EC , embryonal carcinoma ; RA , retinoic acid ; DMEM , Dulbecco 's modified Eagle 's medium ; FBS , fetal bovine serum ; CM , conditioned medium ; PBS , phosphate @-@ buffered saline ; RT , reverse transcriptase ; PMSF , phenylmethylsulfonyl fluoride ; MAP2 , microtubule @-@ associated protein 2 ; GFP , green fluorescence protein ; EGFP , enhanced GFP ; CMV , cytomegalovirus ; Dox , doxycycline ; Tcf/ LEF , T cell factor/ lymphoid enhancer factor ; CKI , casein kinase I ; dpc , days post @-@ coitum ; rtTA , reverse tetracycline controlled transactivator ; ICAT , inhibitor of beta @-@ catenin and Tcf @-@ 4 . # ::alignments 0-1.1.1 3-1.1.2.1.1.4 5-1.1.2.1.1.1 6-1.1.2.1.1.2 9-1.1.2.1.1.4 11-1.2.1 14-1.2.2.1.1.1 16-1.3.1 18-1.3.2.1.1.1 19-1.3.2.1.1.2 21-1.4.1 23-1.4.2.1.3.1.1 24-1.4.2.1.3.r 25-1.4.2.1.2 26-1.4.2.1.1.1.1 27-1.4.2.1.1.r 28-1.4.2.1 30-1.5.1 32-1.5.2.1.1 33-1.5.2.1.1.1 34-1.5.2.1 36-1.6.1 38-1.6.2.1.1 39-1.6.2.1 41-1.7.1 43-1.7.2.1.1.1 45-1.7.2.1.1 46-1.7.2.1 48-1.8.1 50-1.8.2.1.1.1 51-1.8.2.1.1.2 53-1.9.1 55-1.9.2.1.1.1 56-1.9.2.1.1.2 58-1.10.1 60-1.10.2.1.1.1 62-1.10.2.1.1.1 63-1.10.2.1.1.2 64-1.10.2.1.1.3 66-1.11.1 68-1.11.2.1.1.1 69-1.11.2.1.1.2 70-1.11.2.1.1.3 72-1.12.1 74-1.12.2.1.2 75-1.12.2.1.1.1 77-1.13.1 79-1.13.2.1 81-1.14.1 83-1.14.2.1.1.1 88-1.15.2.1.1.1 89-1.15.2.1.1.2 90-1.15.2.1.1.3 91-1.15.2.1.1.4 92-1.15.2.1.1.5 93-1.15.2.1.1.6 95-1.16.1 97-1.16.2.1.1.1 98-1.16.2.1.1.2 99-1.16.2.1.1.3 101-1.17.1 103-1.17.2.1.1.2 104-1.17.2.1.2 108-1.18.1 110-1.18.2.1.1.1 111-1.18.2.1.1.2 112-1.18.2.1.1.3 113-1.18.2.1.1.4 115-1.19.1 117-1.19.2.1 117-1.19.2.1.1 117-1.19.2.1.1.r 118-1.19.2.1.1.1.r 119-1.19.2.1.1.1.1.1.1 121-1.19.2.1.1.1.1.1.1 122-1.19.2.1.1.1 123-1.19.2.1.1.1.2.1.1 125-1.19.2.1.1.1.2.1.1 (a / and :op1 (n19 / name :op1 "GSK-3beta"~e.0 :ARG2-of (l / label-01 :ARG1 (e / enzyme :name (n / name :op1 "glycogen"~e.5 :op2 "synthase"~e.6 :op3 "kinase3" :op4 "beta"~e.3,9)))) :op2 (n20 / name :op1 "EC"~e.11 :ARG2-of (l2 / label-01 :ARG1 (m / medical-condition :name (n2 / name :op1 "carcinoma"~e.14) :location (e4 / embryo)))) :op3 (n21 / name :op1 "RA"~e.16 :ARG2-of (l3 / label-01 :ARG1 (p / protein :name (n17 / name :op1 "retinoic"~e.18 :op2 "acid"~e.19)))) :op4 (n22 / name :op1 "DMEM"~e.21 :ARG2-of (l4 / label-01 :ARG1 (m21 / medium~e.28 :poss~e.27 (p3 / person :name (n3 / name :op1 "Eagle"~e.26)) :ARG1-of (m22 / modify-01~e.25) :poss~e.24 (p4 / person :name (n4 / name :op1 "Dulbecco"~e.23))))) :op5 (n23 / name :op1 "FBS"~e.30 :ARG2-of (l5 / label-01 :ARG1 (s / serum~e.34 :source (f2 / fetus~e.32 :mod (b2 / bovine~e.33))))) :op6 (n24 / name :op1 "CM"~e.36 :ARG2-of (l6 / label-01 :ARG1 (m23 / medium~e.39 :ARG1-of (c4 / condition-01~e.38)))) :op7 (n25 / name :op1 "PBS"~e.41 :ARG2-of (l7 / label-01 :ARG1 (s2 / saline~e.46 :ARG1-of (b / buffer-01~e.45 :ARG0 (p5 / phosphate~e.43))))) :op8 (n26 / name :op1 "RT"~e.48 :ARG2-of (l8 / label-01 :ARG1 (e5 / enzyme :name (n6 / name :op1 "reverse"~e.50 :op2 "transcriptase"~e.51)))) :op9 (n27 / name :op1 "PMSF"~e.53 :ARG2-of (l9 / label-01 :ARG1 (s4 / small-molecule :name (n7 / name :op1 "phenylmethylsulfonyl"~e.55 :op2 "fluoride"~e.56)))) :op10 (n28 / name :op1 "MAP2"~e.58 :ARG2-of (l10 / label-01 :ARG1 (p6 / protein :name (n8 / name :op1 "microtubule-associated"~e.60,62 :op2 "protein"~e.63 :op3 2~e.64)))) :op11 (n29 / name :op1 "GFP"~e.66 :ARG2-of (l11 / label-01 :ARG1 (p7 / protein :name (n9 / name :op1 "green"~e.68 :op2 "fluorescence"~e.69 :op3 "protein"~e.70)))) :op12 (n30 / name :op1 "EGFP"~e.72 :ARG2-of (l12 / label-01 :ARG1 (p8 / protein :name (n10 / name :op1 "GFP"~e.75) :ARG1-of (e7 / enhance-01~e.74)))) :op13 (n31 / name :op1 "CMV"~e.77 :ARG2-of (l13 / label-01 :ARG1 (c / cytomegalovirus~e.79))) :op14 (n32 / name :op1 "Dox"~e.81 :ARG2-of (l14 / label-01 :ARG1 (s3 / small-molecule :name (n14 / name :op1 "doxycycline"~e.83)))) :op15 (n33 / name :op1 "TcfLEF" :ARG2-of (l15 / label-01 :ARG1 (p9 / protein-family :name (n12 / name :op1 "T"~e.88 :op2 "cell"~e.89 :op3 "factor/"~e.90 :op4 "lymphoid"~e.91 :op5 "enhancer"~e.92 :op6 "factor"~e.93)))) :op16 (n34 / name :op1 "CKI"~e.95 :ARG2-of (l16 / label-01 :ARG1 (e6 / enzyme :name (n13 / name :op1 "casein"~e.97 :op2 "kinase"~e.98 :op3 "I"~e.99)))) :op17 (n35 / name :op1 "dpc"~e.101 :ARG2-of (l17 / label-01 :ARG1 (m2 / multiple :op1 (t / temporal-quantity :quant 1 :unit (d / day~e.103)) :time (a3 / after~e.104 :op1 (c5 / coitus))))) :op18 (n18 / name :op1 "rtTA"~e.108 :ARG2-of (l18 / label-01 :ARG1 (p11 / protein :name (n15 / name :op1 "reverse"~e.110 :op2 "tetracycline"~e.111 :op3 "controlled"~e.112 :op4 "transactivator"~e.113)))) :op19 (n11 / name :op1 "ICAT"~e.115 :ARG2-of (l19 / label-01 :ARG1 (m26 / molecular-physical-entity~e.117 :ARG0-of~e.117 (i / inhibit-01~e.117 :ARG1~e.118 (a2 / and~e.122 :op1 (p12 / protein :name (n5 / name :op1 "beta-catenin"~e.119,121)) :op2 (p13 / protein :name (n16 / name :op1 "Tcf-4"~e.123,125)))))))) # ::id bio.chicago_2015.17831 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The ability to form H @-@ DNA cannot substitute for GAGA factor binding to the ( CT ) n sequence . # ::alignments 1-1.2.1 3-1.2.1.1 4-1.2.1.1.1.1.1 6-1.2.1.1.1.1.1 7-1 7-1.1 7-1.1.r 8-1.2 9-1.2.2.r 10-1.2.2.1.1.1 11-1.2.2.1.1.2 12-1.2.2 19-1.2.2.2.1.2 (p / possible-01~e.7 :polarity~e.7 -~e.7 :ARG1 (s / substitute-01~e.8 :ARG1 (c / capable-01~e.1 :ARG2 (f / form-01~e.3 :ARG1 (n / nucleic-acid :name (n2 / name :op1 "H-DNA"~e.4,6)))) :ARG2~e.9 (b / bind-01~e.12 :ARG1 (p2 / protein :name (n3 / name :op1 "GAGA"~e.10 :op2 "factor"~e.11)) :ARG2 (p3 / protein-segment :name (n4 / name :op1 "(CT)n" :op2 "sequence"~e.19))))) # ::id bio.chicago_2015.17892 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Identification of the pathway directing TCF @-@ 1 import will be an important step in determining whether different mechanisms of LEF @-@ 1 and TCF @-@ 1 nuclear transport promote different LEF @-@ 1 , TCF @-@ 1 , and beta @-@ catenin function . # ::alignments 0-1.1 1-1.1.1.r 3-1.1.1 4-1.1.1.1 5-1.1.1.1.1.1.1.1 7-1.1.1.1.1.1.1.1 8-1.1.1.1.1 12-1.3 13-1 14-1.2.r 15-1.2 16-1.2.1.1 16-1.2.1.1.r 17-1.2.1.2.1 18-1.2.1.2 19-1.2.1.2.2.r 20-1.2.1.2.2.1.1.1.1 22-1.2.1.2.2.1.1.1.1 23-1.2.1.2.2.1 24-1.1.1.1.1.1.1.1 26-1.1.1.1.1.1.1.1 26-1.2.1.2.2.1.1.1.1 27-1.2.1.2.2.2 28-1.2.1.2.2 29-1.2.1 30-1.2.1.2.1 31-1.2.1.2.2.1.1.1.1 33-1.1.1.1.1.1.1.1 33-1.2.1.2.2.1.1.1.1 35-1.1.1.1.1.1.1.1 37-1.1.1.1.1.1.1.1 37-1.2.1.2.2.1.1.1.1 39-1.2.1.3.1 40-1.2.1.3.1.3.1.1 42-1.2.1.3.1.3.1.1 43-1.2.1.3 (s / step-01~e.13 :ARG1 (i2 / identify-01~e.0 :ARG1~e.1 (p / pathway~e.3 :ARG0-of (d4 / direct-01~e.4 :ARG1 (i3 / import-01~e.8 :ARG1 (p2 / protein :name (n / name :op1 "TCF-1"~e.5,7,24,26,33,35,37)))))) :ARG2~e.14 (d / determine-01~e.15 :ARG1 (p3 / promote-01~e.29 :mode~e.16 interrogative~e.16 :ARG0 (m / mechanism~e.18 :ARG1-of (d2 / differ-02~e.17,30) :instrument-of~e.19 (t / transport-01~e.28 :ARG1 (a / and~e.23 :op1 (p4 / protein :name (n3 / name :op1 "LEF-1"~e.20,22,26,31,33,37)) :op2 p2) :ARG4 (n2 / nucleus~e.27))) :ARG1 (f / function-01~e.43 :ARG0 (a2 / and~e.39 :op1 p4 :op2 p2 :op3 (p5 / protein :name (n4 / name :op1 "beta-catenin"~e.40,42))) :ARG1-of d2))) :mod (i / important~e.12)) # ::id bio.chicago_2015.17923 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The role of other transcription factors that are regulated by PKA and that bind to the CRE of the fibronectin promoter , such as ATF @-@ 1 and ATF @-@ 2 , may also be relevant to TGF @-@ beta stimulation of fibronectin gene transcription . # ::alignments 1-1.1.1 2-1.1.1.1.r 3-1.1.1.1.4 4-1.1.1.1.1 5-1.1.1.1 8-1.1.1.1.2 9-1.1.1.1.2.1.r 10-1.1.1.1.2.1.1.1 13-1.1.1.1.3 14-1.1.1.1.3.1.r 16-1.1.1.1.3.1.1.1 19-1.1.1.1.3.1.2.1.1.1.1 20-1.1.1.1.3.1.2 20-1.1.1.1.3.1.2.1 20-1.1.1.1.3.1.2.1.r 22-1.1.1.1.3.1.2.2.r 23-1.1.1.1.3.1.2.2.r 24-1.1.1.1.3.1.2.2.1.1.1 24-1.1.1.1.3.1.2.2.2.1.1 26-1.1.1.1.3.1.2.2.1.1.1 27-1.1.1.1.3.1.2.2 28-1.1.1.1.3.1.2.2.1.1.1 28-1.1.1.1.3.1.2.2.2.1.1 30-1.1.1.1.3.1.2.2.2.1.1 32-1 33-1.1.3 35-1.1 36-1.1.2.r 37-1.1.2.1.1.1 39-1.1.2.1.1.1 40-1.1.2 41-1.1.2.2.r 42-1.1.2.2.1.1.1 43-1.1.2.2.1 44-1.1.2.2 (p / possible-01~e.32 :ARG1 (r / relevant-01~e.35 :ARG1 (r2 / role~e.1 :poss~e.2 (f / factor~e.5 :ARG0-of (t / transcribe-01~e.4) :ARG1-of (r3 / regulate-01~e.8 :ARG0~e.9 (e / enzyme :name (n / name :op1 "PKA"~e.10))) :ARG1-of (b / bind-01~e.13 :ARG2~e.14 (e3 / enzyme :name (n2 / name :op1 "CRE"~e.16) :part-of (m / molecular-physical-entity~e.20 :ARG0-of~e.20 (p2 / promote-01~e.20 :ARG1 (p3 / protein :name (n3 / name :op1 "fibronectin"~e.19))) :example~e.22,23 (a / and~e.27 :op1 (p4 / protein :name (n4 / name :op1 "ATF-1"~e.24,26,28)) :op2 (p5 / protein :name (n5 / name :op1 "ATF-2"~e.24,28,30)))))) :mod (o / other~e.3))) :ARG2~e.36 (s / stimulate-01~e.40 :ARG0 (p6 / protein :name (n6 / name :op1 "TGF-beta"~e.37,39)) :ARG1~e.41 (t2 / transcribe-01~e.44 :ARG1 (g / gene~e.43 :ARG0-of (e2 / encode-01 :ARG1 p3~e.42)))) :mod (a2 / also~e.33))) # ::id bio.chicago_2015.18003 ::amr-annotator SDL-AMR-09 ::preferred # ::tok LiCl Activates a Prosurvival Pathway through GSK @-@ 3 beta Inhibition and Activation of beta @-@ Catenincf @-@ mediated Transcription-- To determine whether LiCl had an effect on GSK @-@ 3 @-@ mediated beta @-@ catenin signaling , we used the pTopflash or pFopflash luciferase reporter plasmids . # ::alignments 0-1.1.1.1.1 0-1.2.3.3.1.1 1-1.1 4-1.1.2 6-1.1.3.1.1.1.1 6-1.2.3.3.2.1.2.1.1.1 8-1.2.3.3.2.1.2.1.1.1 9-1.1.3.2.1.1.1.1.1 9-1.2.3.3.2.1.1.1.1 10-1.1.3.1 11-1.1.3 12-1.1 12-1.1.3.2 14-1.2.3.3.2.1.1.1.1 18-1.2.3.3.2.1.2 21-1.2.3 22-1.2.3.1 22-1.2.3.1.r 23-1.2.3.3.1.1 26-1.2.3.3 26-1.2.3.3.2 26-1.2.3.3.2.r 28-1.2.3.3.2.1.2.1.1.1 30-1.2.3.3.2.1.2.1.1.1 32-1.1.3.2.1.1 32-1.2.3.3.2.1.2 33-1.2.3.3.2.1.1.1.1 35-1.2.3.3.2.1.1.1.1 36-1.2.3.3.2.1 38-1.2.1 39-1.2 39-1.2.3.r 41-1.2.2.1.1.1 42-1.2.2 43-1.2.2.2.1.1 44-1.2.2.1.2.1.1.1 45-1.2.2.1 45-1.2.2.1.2 45-1.2.2.1.2.r (m / multi-sentence :snt1 (a / activate-01~e.1,12 :ARG0 (s3 / small-molecule :name (n / name :op1 "LiCl"~e.0)) :ARG1 (p2 / pathway~e.4 :ARG0-of (f / favor-01 :ARG1 (s2 / survive-01))) :manner (a2 / and~e.11 :op1 (i / inhibit-01~e.10 :ARG1 (e / enzyme :name (n3 / name :op1 "GSK-3beta"~e.6))) :op2 (a3 / activate-01~e.12 :ARG1 (t / transcribe-01 :ARG1-of (m3 / mediate-01~e.32 :ARG0 (p3 / protein-family :name (n4 / name :op1 "beta-catenin/Tcf"~e.9))))))) :snt2 (u / use-01~e.39 :ARG0 (w / we~e.38) :ARG1 (o / or~e.42 :op1 (d / dna-sequence~e.45 :name (n5 / name :op1 "pTopflash"~e.41 :op2 "plasmid") :ARG0-of~e.45 (r2 / report-01~e.45 :ARG1 (e2 / enzyme :name (n7 / name :op1 "luciferase"~e.44)))) :op2 (d2 / dna-sequence :name (n6 / name :op1 "pFopflash"~e.43 :op2 "plasmid") :ARG0-of r2)) :purpose~e.39 (d3 / determine-01~e.21 :mode~e.22 interrogative~e.22 :ARG0 w :ARG1 (s4 / small-molecule~e.26 :name (n8 / name :op1 "LiCl"~e.0,23) :ARG0-of~e.26 (a4 / affect-01~e.26 :ARG1 (s / signal-07~e.36 :ARG0 (p4 / protein :name (n9 / name :op1 "beta-catenin"~e.9,14,33,35)) :ARG1-of (m5 / mediate-01~e.18,32 :ARG0 (e3 / enzyme :name (n10 / name :op1 "GSK-3"~e.6,8,28,30))))))))) # ::id bio.chicago_2015.18005 ::amr-annotator SDL-AMR-09 ::preferred # ::tok ILK also appears to regulate muscle differentiation by activating Erk , which suppresses transcription factors required for myogenic differentiation ( Huang et al. , 2000 ) . # ::alignments 0-1.1.1.1.1 1-1.3 2-1 4-1.1 5-1.1.2.1 6-1.1.2 7-1.1.3.r 8-1.1.3 9-1.1.3.2.1.1 12-1.1.3.2 12-1.1.3.2.2 12-1.1.3.2.2.r 13-1.1.3.2.2.1.1 14-1.1.3.2.2.1 15-1.1.3.2.2.1.2 16-1.1.3.2.2.1.2.1.r 17-1.1.3.2.2.1.2.1.1 18-1.1.3.2.2.1.2.1 20-1.2.1.1.1.1.1 21-1.2.1.1 22-1.2.1.1.2.1 24-1.2.1.2.1 (a / appear-02~e.2 :ARG1 (r / regulate-01~e.4 :ARG0 (p2 / protein :name (n2 / name :op1 "ILK"~e.0)) :ARG1 (d2 / differentiate-01~e.6 :ARG1 (m / muscle~e.5)) :manner~e.7 (a2 / activate-01~e.8 :ARG0 p2 :ARG1 (e / enzyme~e.12 :name (n4 / name :op1 "Erk"~e.9) :ARG0-of~e.12 (s / suppress-01~e.12 :ARG1 (f / factor~e.14 :ARG0-of (t / transcribe-01~e.13) :ARG1-of (r2 / require-01~e.15 :ARG0~e.16 (d3 / differentiate-01~e.18 :mod (m2 / myogenic~e.17)))))))) :ARG1-of (d4 / describe-01 :ARG0 (p3 / publication-91 :ARG0 (a3 / and~e.21 :op1 (p4 / person :name (n3 / name :op1 "Huang"~e.20)) :op2 (p5 / person :mod (o / other~e.22))) :time (d5 / date-entity :year 2000~e.24))) :mod (a4 / also~e.1)) # ::id bio.chicago_2015.18031 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This observation suggested that the 60 @-@ residue linker region may assist Ldb binding by LIM B in the 1m construct . # ::alignments 0-1.1.1 1-1.1 2-1 3-1.2.r 5-1.2.1.1.1.1.1 7-1.2.1.1.1.1 9-1.2.1.1 10-1.2 11-1.2.1 12-1.2.1.2.2.1.1 13-1.2.1.2 14-1.2.1.2.1.r 15-1.2.1.2.1.1.1 16-1.2.1.2.1.1.2 17-1.2.1.2.3.r 19-1.2.1.2.3.1.1.1 20-1.2.1.2.3 (s / suggest-01~e.2 :ARG0 (o / observe-01~e.1 :mod (t / this~e.0)) :ARG1~e.3 (p / possible-01~e.10 :ARG1 (a / assist-01~e.11 :ARG0 (r / region~e.9 :ARG3-of (l / link-01 :ARG1 (r2 / residue~e.7 :mod 60~e.5))) :ARG1 (b / bind-01~e.13 :ARG1~e.14 (p3 / protein :name (n2 / name :op1 "LIM"~e.15 :op2 "B"~e.16)) :ARG2 (p2 / protein :name (n / name :op1 "Ldb"~e.12)) :location~e.17 (c / construct~e.20 :ARG1-of (l2 / label-01 :ARG2 (n3 / name :op1 "1m"~e.19))))))) # ::id bio.chicago_2015.18065 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Again , Ser 5 phosphorylation of the CTD is seen at the promoter ( Fig . 3 , CTD @-@ S5 @-@ P ) , whereas phosphorylation at Ser 2 increases as Pol II passes through the coding region ( Fig . 3 , CTD @-@ S2 @-@ P ) . As seen with the ADH1 gene , levels of Ser 2 phosphorylation in coding regions increased in the fcp1 mutants . # ::alignments 0-1.1.3 2-1.1.1.1.1.2.1 2-1.1.2.1.1.2.1 3-1.1.1.1.1.1 4-1.1.1.1 7-1.1.1.1.1.3.1.1 9-1.1.1 10-1.1.1.2.r 12-1.1.1.2 12-1.1.1.2.1 12-1.1.1.2.1.r 14-1.1.1.3.1 16-1.1.1.3.1.1 18-1.1.1.1.1.3.1.1 20-1.1.1.1.2.1.1 22-1.1.1.1.2.1.1 22-1.1.2.1 25-1.1 26-1.1.2.1 28-1.1.2.1.1.2.1 29-1.1.2.1.1.1 30-1.1.2 31-1.1.2.2.r 32-1.1.2.2.1.1.1 33-1.1.2.2.1.1.2 34-1.1.2.2 37-1.1.2.2.2.1 38-1.1.2.2.2 40-1.1.1.3.1 42-1.1.1.3.1.1 44-1.1.2.1.2.1.1 46-1.1.2.1.2.1.1 48-1.1.2.1 48-1.1.2.1.2.1.1 51-1.1.2.2.r 52-1.2.3 55-1.2.3.1.1.1 56-1.2.2 56-1.2.3.1 58-1.2.1 59-1.2.1.1.r 60-1.2.1.1.1.2.1 61-1.2.1.1.1.1 62-1.2.1.1 63-1.2.1.1.2.r 64-1.2.1.1.2.1 65-1.2.1.1.2 66-1.2 69-1.2.2.1.1 70-1.2.2.2 (m / multi-sentence :snt1 (c / contrast-01~e.25 :ARG1 (s / see-01~e.9 :ARG1 (p2 / phosphorylate-01~e.4 :ARG1 (a / amino-acid :mod 5~e.3 :name (n / name :op1 "serine"~e.2) :part-of (p3 / protein-segment :name (n2 / name :op1 "CTD"~e.7,18))) :ARG1-of (l2 / label-01 :ARG2 (n8 / name :op1 "CTD-S5-P"~e.20,22))) :location~e.10 (m3 / molecular-physical-entity~e.12 :ARG0-of~e.12 (p4 / promote-01~e.12)) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.14,40 :mod 3~e.16,42))) :ARG2 (i / increase-01~e.30 :ARG1 (p5 / phosphorylate-01~e.22,26,48 :ARG1 (a3 / amino-acid :mod 2~e.29 :name (n3 / name :op1 "serine"~e.2,28)) :ARG1-of (l3 / label-01 :ARG2 (n9 / name :op1 "CTD-S2-P"~e.44,46,48))) :time~e.31,51 (p6 / pass-08~e.34 :ARG0 (e / enzyme :name (n4 / name :op1 "Pol"~e.32 :op2 "II"~e.33)) :ARG1 (r / region~e.38 :location-of (c3 / code-01~e.37))) :ARG1-of (d2 / describe-01 :ARG0 f)) :mod (a6 / again~e.0)) :snt2 (i2 / increase-01~e.66 :ARG1 (l / level~e.58 :degree-of~e.59 (p7 / phosphorylate-01~e.62 :ARG1 (a5 / amino-acid :mod 2~e.61 :name (n5 / name :op1 "serine"~e.60)) :location~e.63 (r2 / region~e.65 :location-of (c5 / code-01~e.64)))) :location (g / gene~e.56 :name (n6 / name :op1 "fcp1"~e.69) :ARG2-of (m2 / mutate-01~e.70)) :ARG1-of (s2 / see-01~e.52 :topic (g2 / gene~e.56 :name (n7 / name :op1 "ADH1"~e.55))))) # ::id bio.chicago_2015.18079 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Thus , these results suggest that endogenous bHLH proteins bind to the E1 E @-@ box and consequently activate GAP @-@ 43 promoter activity , an activity that is affected by the action of Id2 . # ::alignments 2-1.1.1.2 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 4-1.1 5-1.1.2.r 6-1.1.2.1.1.2 7-1.1.2.1.1.1.1 8-1.1.2.1.1 8-1.1.2.2.2.1.1.1 8-1.1.2.2.2.2.1.1 9-1.1.2.1 10-1.1.2.1.2.r 12-1.1.2.1.2.1.1 13-1.1.2.1.2.1.2 15-1.1.2.1.2.1.2 16-1.1.2 18-1.1.2.2 19-1.1.2.2.2.1.1.1.1.1 21-1.1.2.2.2.1.1.1.1.1 22-1.1.2.2.2.1 22-1.1.2.2.2.1.1 22-1.1.2.2.2.1.1.r 23-1.1.2.2.2 26-1.1.2.2.2 29-1.1.2.2.2.2 30-1.1.2.2.2.2.1.r 32-1.1.2.2.2.2.1 34-1.1.2.2.2.2.1.1.1.1 (i / infer-01 :ARG1 (s / suggest-01~e.4 :ARG0 (t / thing~e.3 :ARG2-of~e.3 (r / result-01~e.3) :mod (t2 / this~e.2)) :ARG1~e.5 (a / and~e.16 :op1 (b / bind-01~e.9 :ARG1 (p / protein~e.8 :name (n / name :op1 "bHLH"~e.7) :mod (e / endogenous~e.6)) :ARG2~e.10 (d / dna-sequence :name (n2 / name :op1 "E1"~e.12 :op2 "E-box"~e.13,15))) :op2 (a2 / activate-01~e.18 :ARG0 p :ARG1 (a3 / activity-06~e.23,26 :ARG0 (m / molecular-physical-entity~e.22 :ARG0-of~e.22 (p2 / promote-01~e.22 :ARG1 (p3 / protein~e.8 :name (n3 / name :op1 "GAP-43"~e.19,21)))) :ARG1-of (a4 / affect-01~e.29 :ARG0~e.30 (a5 / act-02~e.32 :ARG0 (p4 / protein~e.8 :name (n4 / name :op1 "Id2"~e.34))))))))) # ::id bio.chicago_2015.18091 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Inhibition of GSK @-@ 3 beta @-@ dependent phosphorylation of Axin by Dvl . # ::alignments 0-1 1-1.1.r 2-1.1.3.1.1.1 7-1.1.3 8-1.1 9-1.1.1.r 10-1.1.1.1.1 11-1.1.2.r 12-1.1.2.1.1 (i / inhibit-01~e.0 :ARG1~e.1 (p2 / phosphorylate-01~e.8 :ARG1~e.9 (p / protein :name (n2 / name :op1 "Axin"~e.10)) :ARG2~e.11 (p3 / protein :name (n3 / name :op1 "Dvl"~e.12)) :ARG0-of (d / depend-01~e.7 :ARG1 (e / enzyme :name (n / name :op1 "GSK-3beta"~e.2))))) # ::id bio.chicago_2015.18127 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Axin also blocks beta @-@ catenin @-@ mediated transcription in colon cancer cells that have a mutation in the adenomatous polyposis coli gene . # ::alignments 0-1.1.1.1 1-1.4 2-1 3-1.2.1.1.1.1 5-1.2.1.1.1.1 7-1.2.1 8-1.2 9-1.3.r 10-1.3.2.2.1 11-1.3.2.2.2 12-1.3 16-1.3.3 17-1.3.3.1.r 19-1.3.3.1.1.1 20-1.3.3.1.1.2 21-1.3.3.1.1.3 22-1.3.3.1 (b / block-01~e.2 :ARG0 (p / protein :name (n / name :op1 "Axin"~e.0)) :ARG1 (t / transcribe-01~e.8 :ARG1-of (m2 / mediate-01~e.7 :ARG0 (p2 / protein :name (n2 / name :op1 "beta-catenin"~e.3,5)))) :location~e.9 (c / cell~e.12 :poss-of (t2 / thing) :source (d / disease :wiki "Colorectal_cancer" :name (n4 / name :op1 "colon"~e.10 :op2 "cancer"~e.11)) :ARG2-of (m / mutate-01~e.16 :location~e.17 (g / gene~e.22 :name (n3 / name :op1 "adenomatous"~e.19 :op2 "polyposis"~e.20 :op3 "coli"~e.21)))) :mod (a / also~e.1)) # ::id bio.chicago_2015.18130 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Hemin treatment caused no reduction in cellular glutathione concentrations , indicating that the increased TRX expression was not due to oxidative stress . # ::alignments 0-1.2.1.1.1 1-1.2 2-1 3-1.1 3-1.1.r 4-1.3 5-1.3.1.r 6-1.3.1.2 7-1.3.1.1.1.1 8-1.3.1 10-1.4 11-1.4.1.r 13-1.4.1.3.2 14-1.4.1.3.1.1.1 15-1.4.1.3 17-1.4.1.1 17-1.4.1.1.r 18-1.4.1 19-1.4.1 20-1.4.1.2.1 21-1.4.1.2 (c / cause-01~e.2 :polarity~e.3 -~e.3 :ARG0 (t / treat-04~e.1 :ARG2 (s2 / small-molecule :name (n / name :op1 "hemin"~e.0))) :ARG1 (r / reduce-01~e.4 :ARG1~e.5 (c2 / concentrate-02~e.8 :ARG1 (e / enzyme :name (n2 / name :op1 "glutathione"~e.7)) :mod (c3 / cell~e.6))) :ARG0-of (i / indicate-01~e.10 :ARG1~e.11 (c4 / cause-01~e.18,19 :polarity~e.17 -~e.17 :ARG0 (s / stress~e.21 :mod (o / oxidative~e.20)) :ARG1 (e2 / express-03~e.15 :ARG1 (p / protein :name (n3 / name :op1 "TRX"~e.14)) :ARG1-of (i2 / increase-01~e.13))))) # ::id bio.chicago_2015.18156 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Upon CTD phosphorylation by TFIIH , RNA pol II dissociates from the initiation complex and leaves the promoter . # ::alignments 2-1.3 3-1.3.2.r 4-1.3.2.1.1 6-1.1.1.1.1 7-1.1.1.1.2 8-1.1.1.1.3 9-1.1 10-1.1.2.r 12-1.1.2.1 13-1.1.2 14-1 15-1.2 17-1.2.2 17-1.2.2.1 17-1.2.2.1.r (a / and~e.14 :op1 (d / dissociate-01~e.9 :ARG1 (e / enzyme :name (n / name :op1 "RNA"~e.6 :op2 "pol"~e.7 :op3 "II"~e.8)) :ARG2~e.10 (c / complex~e.13 :mod (i / initiate-01~e.12))) :op2 (l / leave-05~e.15 :ARG0 e :ARG1 (m / molecular-physical-entity~e.17 :ARG0-of~e.17 (p2 / promote-01~e.17))) :condition (p / phosphorylate-01~e.2 :ARG1 (p4 / protein-segment :name (n3 / name :op1 "C-terminus")) :ARG2~e.3 (p3 / protein :name (n2 / name :op1 "TFIIH"~e.4)))) # ::id bio.chicago_2015.18159 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This is supported by the in vitro observations that Dvl inhibits GSK @-@ 3 beta @-@ dependent phosphorylation of Axin , APC , and beta @-@ catenin in the Axin complex , although the bindings of GSK @-@ 3 beta , beta @-@ catenin , and APC to Axin are not changed , and that Dvl does not affect GSK @-@ 3 beta activity to phosphorylate the peptide substrate ( 22 , 26 ) . # ::alignments 0-1.2 2-1 3-1.1.r 5-1.1.2 6-1.1.2 7-1.1 9-1.1.1.1.1.1.1.1 10-1.1.1.1.1 11-1.1.1.1.1.2.2.1.1.1 14-1.1.1.1.1.2.1.3.1.1 16-1.1.1.1.1.2.2 17-1.1.1.1.1.2 18-1.1.1.1.1.2.1.r 19-1.1.1.1.1.2.1.1.1.1 21-1.1.1.1.1.2.1.2.1.1 23-1.1.1.1.1.2.1 24-1.1.1.1.1.2.1.3.1.1 26-1.1.1.1.1.2.1.3.1.1 27-1.1.2 29-1.1.1.1.1.2.1.4.1 30-1.1.1.1.1.2.1.4 32-1.1.1.1 34-1.1.1.1.2.2 36-1.1.1.1.1.2.2.1.1.1 39-1.1.1.1.1.2.1.3.1.1 41-1.1.1.1.1.2.1.3.1.1 43-1.1.1.1.1.2.1.3.1.1 46-1.1.1.1.1.2.1.2.1.1 48-1.1.1.1.1.2.1.1.1.1 50-1.1.1.1.2.1 50-1.1.1.1.2.1.r 51-1.1.1.1.2 54-1.1.1.r 55-1.1.1.2.2 57-1.1.1.2.1 57-1.1.1.2.1.r 58-1.1.1.2 59-1.1.1.1.1.2.2.1.1.1 62-1.1.1.1.1.2.1.3.1.1 63-1.1.1.2.3 65-1.1.1.2.3.2 67-1.1.1.2.3.2.1.1 68-1.1.1.2.3.2.1 70-1.3.1.1.1.1 72-1.3.1.1.1.2 (s / support-01~e.2 :ARG0~e.3 (o / observe-01~e.7 :ARG1~e.54 (a / and :op1 (h / have-concession-91~e.32 :ARG1 (i / inhibit-01~e.10 :ARG0 (p2 / protein :name (n / name :op1 "Dvl"~e.9)) :ARG1 (p / phosphorylate-01~e.17 :ARG1~e.18 (a2 / and~e.23 :op1 (p3 / protein :name (n2 / name :op1 "Axin"~e.19,48)) :op2 (p4 / protein :name (n4 / name :op1 "APC"~e.21,46)) :op3 (p5 / protein :name (n5 / name :op1 "beta-catenin"~e.14,24,26,39,41,43,62)) :location (c2 / complex~e.30 :mod p3~e.29)) :ARG0-of (d / depend-01~e.16 :ARG1 (e / enzyme :name (n3 / name :op1 "GSK-3beta"~e.11,36,59))))) :ARG2 (c / change-01~e.51 :polarity~e.50 -~e.50 :ARG1 (b / bind-01~e.34 :ARG1 (a3 / and :op1 e :op2 p5 :op3 p4) :ARG2 p3))) :op2 (a4 / affect-01~e.58 :polarity~e.57 -~e.57 :ARG0 p2~e.55 :ARG1 (a5 / activity-06~e.63 :ARG0 e :ARG1 (p6 / phosphorylate-01~e.65 :ARG1 (s2 / substrate~e.68 :mod (p7 / peptide~e.67)) :ARG2 e)))) :manner (i2 / in-vitro~e.5,6,27)) :ARG1 (t / this~e.0) :ARG1-of (d2 / describe-01 :ARG0 (p8 / publication :ARG1-of (c3 / cite-01 :ARG2 (a6 / and :op1 22~e.70 :op2 26~e.72))))) # ::id bio.chicago_2015.18163 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As demonstrated in Figure 5 , B and C , in the absence of neurotrophins , DRG neurons derived from NF1 @-@ deficient embryos exhibit elevated erk phosphorylation levels that are comparable to wild @-@ type neurons in the presence of NGF . # ::alignments 1-1.4 2-1.4.1.r 3-1.4.1.1 3-1.4.1.2 3-1.4.1.3 4-1.4.1.3.1 6-1.4.1.1.1 7-1.4.1 8-1.4.1.2.1 12-1.3 17-1.1 18-1.1.1 19-1.1.1.1.r 19-1.1.2.r 20-1.1.1.1.1.1.1.1 23-1.1.1.1 24-1 25-1.2.2 26-1.2.1.1.1.1 27-1.2.1 28-1.2 31-1.2.3 32-1.2.3.1.r 33-1.2.3.1.1 35-1.2.3.1.1 36-1.2.3.1 37-1.2.3.1.2.r 39-1.2.3.1.2 40-1.2.3.1.2.1.r 41-1.2.3.1.2.1.1.1 (e / exhibit-01~e.24 :ARG0 (n8 / neuron~e.17 :ARG1-of (d / derive-01~e.18 :ARG2~e.19 (e2 / embryo~e.23 :ARG0-of (l / lack-01 :ARG1 (p3 / protein :name (n3 / name :op1 "NF1"~e.20))))) :source~e.19 (g / ganglion :mod (r / root) :mod (d3 / dorsal))) :ARG1 (l2 / level~e.28 :degree-of (p4 / phosphorylate-01~e.27 :ARG1 (e4 / enzyme :name (n / name :op1 "ERK"~e.26))) :ARG1-of (e3 / elevate-01~e.25) :ARG1-of (c / comparable-03~e.31 :ARG2~e.32 (n4 / neuron~e.36 :mod (w / wild-type~e.33,35) :condition~e.37 (p5 / present-02~e.39 :ARG1~e.40 (p6 / protein :name (n5 / name :op1 "NGF"~e.41)))))) :condition (a / absent-01~e.12 :ARG1 (e5 / enzyme :name (n6 / name :op1 "neurotrophin"))) :ARG1-of (d2 / demonstrate-01~e.1 :ARG0~e.2 (a2 / and~e.7 :op1 (f / figure~e.3 :mod "B"~e.6) :op2 (f2 / figure~e.3 :mod "C"~e.8) :part-of (f3 / figure~e.3 :mod 5~e.4)))) # ::id bio.chicago_2015.18186 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This result suggests that Axin binding to both GSK @-@ 3 beta and beta @-@ catenin is necessary for inhibition of Lef @-@ 1 reporter gene transcription . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 2-1 3-1.2.r 4-1.2.2.1.1.1 5-1.2.2 8-1.2.2.2.1.1.1 11-1.2.2.2.2.1.1 13-1.2.2.2.2.1.1 15-1.2.2.2.2.1.1 17-1.2 18-1.2.1.r 19-1.2.1 20-1.2.1.1.r 21-1.2.1.1.1.1.1 23-1.2.1.1.1.1.1 24-1.2.1.1.1.2 25-1.2.1.1.1 26-1.2.1.1 (s / suggest-01~e.2 :ARG0 (t / thing~e.1 :ARG2-of~e.1 (r2 / result-01~e.1) :mod (t2 / this~e.0)) :ARG1~e.3 (n2 / need-01~e.17 :ARG0~e.18 (i / inhibit-01~e.19 :ARG1~e.20 (t3 / transcribe-01~e.26 :ARG1 (g / gene~e.25 :name (n / name :op1 "Lef-1"~e.21,23) :ARG0-of (r / report-01~e.24)))) :ARG1 (b / bind-01~e.5 :ARG1 (p2 / protein :name (n3 / name :op1 "Axin"~e.4)) :ARG2 (a / and :op1 (e / enzyme :name (n4 / name :op1 "GSK-3beta"~e.8)) :op2 (p4 / protein :name (n5 / name :op1 "beta-catenin"~e.11,13,15)))))) # ::id bio.chicago_2015.18196 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The major region of phosphorylation of beta @-@ catenin by CK2 is the central armadillo repeat domain , where carrier proteins like axin and the adenomatous polyposis coli gene product APC interact with beta @-@ catenin . # ::alignments 1-1.1 2-1 3-1.2.r 4-1.2 5-1.2.1.r 6-1.2.1.1.1 8-1.2.1.1.1 9-1.2.2.r 10-1.2.2.1.1 11-1.3.r 13-1.3.1.1 14-1.3.1.2 15-1.3.1.3 18-1.3.2.r 19-1.3.2.1.2 20-1.3.2.1 21-1.3.2.1.1.r 22-1.3.2.1.1.1.1.1 23-1.3.2.1.1 25-1.3.2.1.1.2.2.1.1.1 26-1.3.2.1.1.2.2.1.1.2 27-1.3.2.1.1.2.2.1.1.3 28-1.3.2.1.1.2.2.1 30-1.3.2.1.1.2.1.1 31-1.3.2 32-1.3.2.2.r 33-1.3.2.2 34-1.3.2.2 35-1.3.2.2 (r2 / region~e.2 :ARG1-of (m / major-02~e.1) :location-of~e.3 (p / phosphorylate-01~e.4 :ARG1~e.5 (p2 / protein :name (n / name :op1 "beta-catenin"~e.6,8)) :ARG2~e.9 (e / enzyme :name (n2 / name :op1 "CK2"~e.10))) :domain~e.11 (p6 / protein-segment :name (n5 / name :op1 "central"~e.13 :op2 "armadillo"~e.14 :op3 "repeat"~e.15) :location-of~e.18 (i / interact-01~e.31 :ARG0 (p3 / protein~e.20 :example~e.21 (a2 / and~e.23 :op1 (p4 / protein :name (n3 / name :op1 "axin"~e.22)) :op2 (p5 / protein :name (n6 / name :op1 "APC"~e.30) :ARG1-of (e2 / encode-01 :ARG0 (g / gene~e.28 :name (n4 / name :op1 "adenomatous"~e.25 :op2 "polyposis"~e.26 :op3 "coli"~e.27))))) :mod (c / carrier~e.19)) :ARG1~e.32 p2~e.33,34,35))) # ::id bio.chicago_2015.18258 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , the ATP binding @-@ deficient , dominant @-@ negative HA @-@ MEKK1 @-@ K1255M reduced Axin activation of JNK by 3 @-@ fold , suggesting that MEKK1 acts in the same signaling pathway in Axin @-@ mediated activation of JNK . # ::alignments 1-1 4-1.1.1.3.1.2.1.1 5-1.1.1.3.1 7-1.1.1 7-1.1.1.2 7-1.1.1.2.1 7-1.1.1.2.1.r 7-1.1.1.2.r 9-1.1.1.2.2 12-1.1.1.1.1 14-1.1.1.1.1 16-1.1.1.1.1 17-1.1 18-1.1.2.1.1.1 19-1.1.2 20-1.1.2.2.r 21-1.1.2.2.1.1 23-1.1.3.1 25-1.1.3 27-1.1.4 28-1.1.4.1.r 29-1.1.4.1.1.1.1 30-1.1.4.1 31-1.1.4.1.2.r 33-1.1.4.1.2.2 34-1.1.4.1.2.1 35-1.1.4.1.2 36-1.1.4.1.3.r 37-1.1.4.1.3.2.1 39-1.1.4.1.3.2 40-1.1.4.1.3 41-1.1.3 41-1.1.4.1.3.1.r 42-1.1.4.1.3.1 (c / contrast-01~e.1 :ARG2 (r / reduce-01~e.17 :ARG0 (e / enzyme~e.7 :name (n / name :op1 "HA-MEKK1-K1255M"~e.12,14,16) :ARG2-of~e.7 (m2 / mutate-01~e.7 :mod~e.7 "-/-"~e.7 :ARG0-of (d / dominate-01~e.9)) :ARG0-of (l / lack-01 :ARG1 (b / bind-01~e.5 :ARG1 e :ARG2 (s / small-molecule :name (n5 / name :op1 "ATP"~e.4))))) :ARG1 (a / activate-01~e.19 :ARG0 (p / protein :name (n2 / name :op1 "Axin"~e.18)) :ARG1~e.20 (e3 / enzyme :name (n3 / name :op1 "JNK"~e.21))) :ARG2 (p2 / product-of~e.25,41 :op1 3~e.23) :ARG0-of (s4 / suggest-01~e.27 :ARG1~e.28 (a2 / act-02~e.30 :ARG0 (e2 / enzyme :name (n6 / name :op1 "MEKK1"~e.29)) :location~e.31 (p3 / pathway~e.35 :ARG0-of (s2 / signal-07~e.34) :ARG1-of (s3 / same-01~e.33)) :topic~e.36 (a3 / activate-01~e.40 :ARG1~e.41 e3~e.42 :ARG1-of (m / mediate-01~e.39 :ARG0 p~e.37)))))) # ::id bio.chicago_2015.18265 ::amr-annotator SDL-AMR-09 ::preferred # ::tok First , PR facilitates binding of NF1 by an ATP @-@ dependent process that results in marked reduction of the linking number of chromosomal DNA . # ::alignments 0-1.3 2-1.1.1.1 3-1 4-1.2 5-1.2.2.r 6-1.2.2.1.1 7-1.2.1.r 9-1.2.1.1.1.1.1 11-1.2.1.1 12-1.2.1 14-1.2.1.2 15-1.2.1.2.1.r 16-1.2.1.2.1.2 17-1.2.1.2.1 18-1.2.1.2.1.1.r 20-1.2.1.2.1.1.1 21-1.2.1.2.1.1 22-1.2.1.2.1.1.2.r 23-1.2.1.2.1.1.2.2 24-1.2.1.2.1.1.2.1.1 (f / facilitate-01~e.3 :ARG0 (e / enzyme :name (n / name :op1 "PR"~e.2)) :ARG1 (b / bind-01~e.4 :ARG0~e.7 (p3 / process-02~e.12 :ARG0-of (d / depend-01~e.11 :ARG1 (s / small-molecule :name (n3 / name :op1 "ATP"~e.9))) :ARG1-of (r / result-01~e.14 :ARG2~e.15 (r2 / reduce-01~e.17 :ARG1~e.18 (n4 / number~e.21 :mod (l / link-01~e.20) :quant-of~e.22 (n5 / nucleic-acid :name (n6 / name :op1 "DNA"~e.24) :mod (c / chromosome~e.23))) :ARG2 (m / mark-01~e.16)))) :ARG1~e.5 (p2 / protein :name (n2 / name :op1 "NF1"~e.6))) :time (f2 / first~e.0)) # ::id bio.chicago_2015.18319 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Axin is also phosphorylated by GSK @-@ 3 beta and stabilized by its phosphorylation in contrast to beta @-@ catenin ( 22 ) , and the phosphorylation increases the binding of Axin to beta @-@ catenin ( 23 , 24 ) . # ::alignments 0-1.1.1.1.1.1 2-1.1.3 3-1.1.1 4-1.1.1.2.r 5-1.1.1.2.1.1 8-1.1.4.1.1.1 9-1.1 10-1.1.2 13-1.1.2.1 15-1.1.4 17-1.1.4.1.1.1 19-1.1.4.1.1.1 21-1.1.4.2.1.1.1 24-1.1 26-1.2.1 27-1.2 29-1.2.2 30-1.2.2.1.r 31-1.2.2.1 33-1.1.4.1.1.1 35-1.1.4.1.1.1 37-1.2.3.1.1.1.1 39-1.2.3.1.1.1.2 (a / and :op1 (a2 / and~e.9,24 :op1 (p2 / phosphorylate-01~e.3 :ARG1 (p3 / protein :name (n / name :op1 "Axin"~e.0)) :ARG2~e.4 (e / enzyme :name (n2 / name :op1 "GSK-3beta"~e.5))) :op2 (s / stabilize-01~e.10 :ARG0 (p / phosphorylate-01~e.13 :ARG1 p3) :ARG1 p3) :mod (a3 / also~e.2) :ARG1-of (c / contrast-01~e.15 :ARG2 (p4 / protein :name (n3 / name :op1 "beta-catenin"~e.8,17,19,33,35)) :ARG1-of (d / describe-01 :ARG0 (p5 / publication :ARG1-of (c2 / cite-01 :ARG2 22~e.21))))) :op2 (i / increase-01~e.27 :ARG0 p2~e.26 :ARG1 (b / bind-01~e.29 :ARG1~e.30 p3~e.31 :ARG2 p4) :ARG1-of (d2 / describe-01 :ARG0 (p7 / publication :ARG1-of (c3 / cite-01 :ARG2 (a4 / and :op1 23~e.37 :op2 24~e.39)))))) # ::id bio.chicago_2015.18396 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Axin enhances the phosphorylation of beta @-@ catenin by GSK @-@ 3 beta by positioning GSK @-@ 3 beta close to beta @-@ catenin , resulting in the inhibition of the Wnt signaling pathway ( 32 ) . # ::alignments 0-1.1.1.1 1-1 3-1.2 4-1.2.1.r 5-1.2.1.1.1 7-1.2.1.1.1 8-1.2.2.r 9-1.2.2.1.1 12-1.2.1.1.1 13-1.3.r 14-1.3 15-1.3.2 18-1.3.3.2 19-1.3.3 21-1.3.3.2 22-1.3.3.2 23-1.3.3.2 25-1.4 26-1.4.1.r 28-1.4.1 29-1.4.1.1.r 31-1.4.1.1.1.1 32-1.4.1.1.2 33-1.4.1.1 35-1.4.2.1.1.1 (e / enhance-01~e.1 :ARG0 (p2 / protein :name (n / name :op1 "Axin"~e.0)) :ARG1 (p3 / phosphorylate-01~e.3 :ARG1~e.4 (p4 / protein :name (n2 / name :op1 "beta-catenin"~e.5,7,12)) :ARG2~e.8 (e2 / enzyme :name (n3 / name :op1 "GSK-3beta"~e.9))) :manner~e.13 (p5 / position-01~e.14 :ARG0 p2 :ARG1 e2~e.15 :ARG2 (c / close-10~e.19 :ARG1 e2 :ARG2 n2~e.18,21,22,23)) :ARG1-of (r / result-01~e.25 :ARG2~e.26 (i / inhibit-01~e.28 :ARG1~e.29 (p / pathway~e.33 :name (n4 / name :op1 "Wnt"~e.31) :ARG0-of (s / signal-07~e.32))) :ARG1-of (d / describe-01 :ARG0 (p6 / publication :ARG1-of (c2 / cite-01 :ARG2 32~e.35))))) # ::id bio.chicago_2015.18464 ::amr-annotator SDL-AMR-09 ::preferred # ::tok ( c ) Axin inhibits secondary axis formation induced by CKI . # ::alignments 1-1.1 3-1.2.1.1 4-1 5-1.3.1.1 6-1.3.1 7-1.3 8-1.3.2 9-1.3.2.1.r 10-1.3.2.1.1.1 (i / inhibit-01~e.4 :li "c"~e.1 :ARG0 (p / protein :name (n / name :op1 "Axin"~e.3)) :ARG1 (f / form-01~e.7 :ARG1 (a / axis~e.6 :mod (s / secondary~e.5)) :ARG2-of (i2 / induce-01~e.8 :ARG0~e.9 (e / enzyme :name (n2 / name :op1 "CKI"~e.10))))) # ::id bio.chicago_2015.18510 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Full @-@ length Axin did not activate TCF @-@ dependent transcription , but unexpectedly , the introduction of L521P into full @-@ length Myc @- or Flag @-@ tagged murine Axin [ mFlagAx-( 1 @-@ 956 )] transformed it into a transcriptional activator ( Figure 5D ) . # ::alignments 0-1.1.2.2.1 2-1.1.2 2-1.1.2.2 2-1.1.2.2.r 3-1.1.2.1.1 3-1.2.1.2.2.1.1 5-1.1.1 5-1.1.1.r 6-1.1 7-1.1.3.1.1.1.1 9-1.1.3.1 10-1.1.3 12-1 13-1.1.1 13-1.2.4.1 16-1.2.1 18-1.2.1.1.2.1.1 19-1.2.1.2.r 20-1.2.1.2.1.4 21-1.2.1.2.1.4 22-1.2.1.2.1.4 23-1.2.1.2.1.3.1.1.1 25-1.2.1.2 26-1.2.1.2.2.2.1.1.1 28-1.2.1.2.1.3 28-1.2.1.2.2.2 29-1.2.1.2.1.2 30-1.2.1.2.1.1.1 37-1.2 38-1.2.2 41-1.2.3.1.1 42-1.1 42-1.2.3 42-1.2.3.1 42-1.2.3.1.r 44-1.3.1 45-1.3.1.1 (c / contrast-01~e.12 :ARG1 (a2 / activate-01~e.6,42 :polarity~e.5 -~e.5,13 :ARG0 (p / protein~e.2 :name (n / name :op1 "Axin"~e.3) :ARG1-of~e.2 (l / long-03~e.2 :ARG1-of (f / full-09~e.0))) :ARG1 (t2 / transcribe-01~e.10 :ARG0-of (d / depend-01~e.9 :ARG1 (p2 / protein :name (n2 / name :op1 "TCF"~e.7))))) :ARG2 (t3 / transform-01~e.37 :ARG0 (i / introduce-02~e.16 :ARG1 (m / mutate-01 :ARG1 p :ARG2 (p3 / protein :name (n3 / name :op1 "L521P"~e.18))) :ARG2~e.19 (o / or~e.25 :op1 (p4 / protein :name (n4 / name :op1 "Axin"~e.30) :mod (m2 / murine~e.29) :ARG1-of (t4 / tag-01~e.28 :ARG0 (p7 / protein :name (n6 / name :op1 "Myc"~e.23))) :ARG1-of l~e.20,21,22) :op2 (p5 / protein :name (n5 / name :op1 "Axin"~e.3) :ARG1-of (t5 / tag-01~e.28 :ARG0 (p6 / protein-segment :name (n7 / name :op1 "Flag"~e.26))) :mod m2 :ARG1-of l))) :ARG1 p~e.38 :ARG2 (m3 / molecular-physical-entity~e.42 :ARG0-of~e.42 (a5 / activate-01~e.42 :ARG1 (t7 / transcribe-01~e.41))) :ARG1-of (e / expect-01 :polarity -~e.13)) :ARG1-of (d2 / describe-01 :ARG0 (f2 / figure~e.44 :mod "5D"~e.45))) # ::id bio.chicago_2015.18552 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These interactions are specific , because an E1A polypeptide that binds to the ASH1 binding region in dCBP blocks the GST @-@ ASH1( 47 @-@ 456 )- dCBP interaction more efficiently than an E1A @-@ RG2 polypeptide that carries a mutation that reduces E1A binding to dCBP ( Fig . 7E ) . # ::alignments 0-1.1.1 1-1.1 3-1 5-1.2 7-1.2.1.1.1.1.1 8-1.2.1.1 10-1.2.1.1.2 11-1.2.1.1.2.1.r 13-1.2.1.1.2.1.1.1.1.1 14-1.2.1.1.2.1.1 15-1.2.1.1.2.1 16-1.2.1.1.2.1.2.r 17-1.2.1.1.2.1.2.1.1 18-1.2.1 20-1.2.1.2.1.1.1 23-1.2.1.2.2.1.1.1 25-1.2.1.2.2.1.1.2 27-1.2.1.2.2.2 28-1.2.1.2 29-1.2.1.3.1 30-1.2.1.3 31-1.2.1.3.2.r 33-1.2.1.3.2.1.1.1 35-1.2.1.3.2.1.1.1 36-1.2.1.3.2 38-1.2.1.3.2.2 40-1.2.1.3.2.2.1 42-1.2.1.3.2.2.1.1 43-1.2.1.3.2.1.1.1 44-1.2.1.3.2.2.1.1.1 45-1.2.1.3.2.2.1.1.1.2.r 46-1.2.1.3.2.2.1.1.1.2 48-1.3.1 50-1.3.1.1 (s / specific-02~e.3 :ARG1 (i / interact-01~e.1 :mod (t / this~e.0)) :ARG1-of (c / cause-01~e.5 :ARG0 (b2 / block-01~e.18 :ARG0 (p / polypeptide~e.8 :mod (p2 / protein :name (n / name :op1 "E1A"~e.7)) :ARG1-of (b3 / bind-01~e.10 :ARG2~e.11 (r / region~e.15 :location-of (b4 / bind-01~e.14 :ARG1 (e / enzyme :name (n2 / name :op1 "ASH1"~e.13))) :location~e.16 (p3 / protein :name (n3 / name :op1 "dCBP"~e.17))))) :ARG1 (i2 / interact-01~e.28 :ARG0 (e2 / enzyme :name (n4 / name :op1 "GST"~e.20)) :ARG1 (a / and :op1 (a2 / amino-acid :mod (v2 / value-interval :op1 47~e.23 :op2 456~e.25) :part-of e) :op2 p3~e.27)) :ARG1-of (e3 / efficient-01~e.30 :degree (m / more~e.29) :compared-to~e.31 (p5 / polypeptide~e.36 :mod (p6 / protein :name (n6 / name :op1 "E1A-RG2"~e.33,35,43)) :ARG0-of (c2 / carry-01~e.38 :ARG1 (m2 / mutate-01~e.40 :ARG0-of (r2 / reduce-01~e.42 :ARG1 (b5 / bind-01~e.44 :ARG1 p2 :ARG2~e.45 p3~e.46)))))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.48 :mod "7E"~e.50))) # ::id bio.chicago_2015.18587 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The copurification suggested that BMP @-@ 1 and BMP @-@ 2 might physically interact , leading to the idea that Tolloid might increase DPP activity by proteolytically processing DPP precursors ( Shimell et al. , 1991 ; Childs and O'Connor , 1994 ; Finelli et al. , 1994 ) . # ::alignments 2-1 3-1.2.r 4-1.2.1.1.1.1 4-1.2.1.2.1.1 6-1.2.1.1.1.1 8-1.2.1.1.1.1 8-1.2.1.2.1.1 10-1.2.1.2.1.1 11-1.2 12-1.2.1.3 12-1.2.1.3.r 13-1.2.1 15-1.3 16-1.3.1.r 18-1.3.1 20-1.3.1.1.1.1.1.1 21-1.3.1.1 22-1.3.1.1.1 23-1.3.1.1.1.2.1.1.1 24-1.3.1.1.1.2 27-1.3.1.1.1.3 28-1.3.1.1.1.3.1.1 29-1.3.1.1.1.3.1 31-1.4.1.1.1.1.1.1 32-1.4.1.1.1 33-1.4.1.1.1.2.1 35-1.4.1.1.2.1 37-1.4.1.2.1.1.1.1 38-1.4.1.2.1 39-1.4.1.2.1.2.1.1 41-1.4.1.2.2.1 43-1.4.1.3.1.1.1.1 44-1.4.1 44-1.4.1.2.1 44-1.4.1.3.1 45-1.4.1.3.1.2.1 47-1.4.1.3.2 (s / suggest-01~e.2 :ARG0 (c / copurify-00) :ARG1~e.3 (p2 / possible-01~e.11 :ARG1 (i / interact-01~e.13 :ARG0 (p3 / protein :name (n / name :op1 "BMP-1"~e.4,6,8)) :ARG1 (p4 / protein :name (n2 / name :op1 "BMP-2"~e.4,8,10)) :manner~e.12 (p5 / physical~e.12))) :ARG0-of (l / lead-03~e.15 :ARG2~e.16 (i2 / idea~e.18 :topic (p6 / possible-01~e.21 :ARG1 (i3 / increase-01~e.22 :ARG0 (p7 / protein :name (n3 / name :op1 "Tolloid"~e.20)) :ARG1 (a / activity-06~e.24 :ARG0 (p19 / protein :name (n4 / name :op1 "DPP"~e.23))) :manner (p8 / process-01~e.27 :ARG1 (p10 / precursor~e.29 :mod p19~e.28) :manner (p9 / proteolytical)))))) :ARG1-of (d3 / describe-01 :ARG0 (a2 / and~e.44 :op1 (p11 / publication-91 :ARG0 (a3 / and~e.32 :op1 (p12 / person :name (n5 / name :op1 "Shimell"~e.31)) :op2 (p13 / person :mod (o / other~e.33))) :time (d / date-entity :year 1991~e.35)) :op2 (p14 / publication-91 :ARG0 (a4 / and~e.38,44 :op1 (p15 / person :name (n6 / name :op1 "Childs"~e.37)) :op2 (p16 / person :name (n7 / name :op1 "O'Connor"~e.39))) :time (d2 / date-entity :year 1994~e.41)) :op3 (p / publication-91 :ARG0 (a5 / and~e.44 :op1 (p17 / person :name (n8 / name :op1 "Finelli"~e.43)) :op2 (p18 / person :mod (o2 / other~e.45))) :time d2~e.47)))) # ::id bio.chicago_2015.18599 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Moreover ectopic expression of cyclin E does not activate E2F in the absence of cdk4 and cdk6 activity ( Lukas et al. , 1997 ) . # ::alignments 0-1 0-1.2.1.1 1-1.1.2.2 2-1.1.2 3-1.1.2.1.r 4-1.1.2.1.1.1 5-1.1.2.1.1.2 7-1.1.1 7-1.1.1.r 8-1.1 9-1.1.3.1.1 10-1.1.4.r 12-1.1.4 13-1.1.4.1.r 14-1.1.4.1.1.1.1.1 15-1.1.4.1.1 16-1.1.4.1.1.2.1.1 17-1.1.4.1 19-1.2.1.1.1.1.1 20-1.2.1.1 21-1.2.1.1.2.1 23-1.2.1.2.1 (a2 / and~e.0 :op2 (a / activate-01~e.8 :polarity~e.7 -~e.7 :ARG0 (e / express-03~e.2 :ARG2~e.3 (p / protein :name (n / name :op1 "cyclin"~e.4 :op2 "E"~e.5)) :mod (e2 / ectopic~e.1)) :ARG1 (p5 / protein :name (n2 / name :op1 "E2F"~e.9)) :condition~e.10 (a3 / absent-01~e.12 :ARG1~e.13 (a4 / activity-06~e.17 :ARG0 (a5 / and~e.15 :op1 (e3 / enzyme :name (n3 / name :op1 "cdk4"~e.14)) :op2 (e4 / enzyme :name (n4 / name :op1 "cdk6"~e.16)))))) :ARG1-of (d2 / describe-01 :ARG0 (p2 / publication-91 :ARG0 (a6 / and~e.0,20 :op1 (p3 / person :name (n5 / name :op1 "Lukas"~e.19)) :op1 (p4 / person :mod (o / other~e.21))) :time (d / date-entity :year 1997~e.23)))) # ::id bio.chicago_2015.18617 ::amr-annotator SDL-AMR-09 ::preferred # ::tok DLT Interacts with CRB and NRX IV # ::alignments 0-1.1.1.1 1-1 2-1.2.r 3-1.2.1.1.1 4-1.2 5-1.2.2.1.1 6-1.2.2.1.2 (i / interact-01~e.1 :ARG0 (p / protein :name (n / name :op1 "DLT"~e.0)) :ARG1~e.2 (a / and~e.4 :op1 (p2 / protein :name (n2 / name :op1 "CRB"~e.3)) :op2 (p3 / protein :name (n3 / name :op1 "NRX"~e.5 :op2 "IV"~e.6)))) # ::id bio.chicago_2015.18666 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The negative regulation of brinker expression by Dpp signaling illustrates a significant element of regulatory versatility afforded by the use of a Type II , as compared with a Type I , switch mechanism . # ::alignments 1-1.1 2-1.1 3-1.1.1.r 4-1.1.1.1.1.1 5-1.1.1 6-1.1.2.r 7-1.1.2.1.1.1 8-1.1.2 9-1 11-1.2.1 12-1.2 13-1.2.2.r 14-1.2.2.1 15-1.2.2 16-1.2.2.2 17-1.2.2.2.1.r 19-1.2.2.2.1 20-1.2.2.2.1.1.r 22-1.2.2.2.1.1.2 23-1.2.2.2.1.1.2.1.1 26-1.2.2.2.1.1.3.r 29-1.2.2.2.1.1.3.2 30-1.2.2.2.1.1.3.2.1.1 32-1.2.2.2.1.1.1 33-1.2.2.2.1.1 33-1.2.2.2.1.1.3 (i / illustrate-01~e.9 :ARG0 (d / downregulate-01~e.1,2 :ARG1~e.3 (e / express-03~e.5 :ARG2 (p2 / protein :name (n3 / name :op1 "brinker"~e.4))) :ARG2~e.6 (s / signal-07~e.8 :ARG0 (p / pathway :name (n2 / name :op1 "Dpp"~e.7)))) :ARG1 (e2 / element~e.12 :ARG1-of (s2 / significant-02~e.11) :part-of~e.13 (v / versatility~e.15 :ARG0-of (r2 / regulate-01~e.14) :ARG1-of (a / afford-02~e.16 :ARG0~e.17 (u / use-01~e.19 :ARG1~e.20 (m / mechanism~e.33 :mod (s3 / switch-01~e.32) :ARG1-of (t / type-03~e.22 :ARG2 (s4 / string-entity :value "II"~e.23)) :compared-to~e.26 (m2 / mechanism~e.33 :mod s3 :ARG1-of (t2 / type-03~e.29 :ARG2 (s5 / string-entity :value "I"~e.30))))))))) # ::id bio.chicago_2015.18675 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Unlike known E2Fs , these E2F @-@ like proteins efficiently bind E2F sites in the monomeric form but not as a heterodimer with DP proteins and repress E2F @-@ regulated promoters . # ::alignments 0-1.1.1.2 0-1.1.1.2.1 0-1.1.1.2.1.r 1-1.1.1.2.2 1-1.1.1.2.2.2 1-1.1.1.2.2.2.r 4-1.1.1.3 5-1.1.1.1.1.1.1 5-1.1.1.2.2.1.1 7-1.1.1.1 7-1.1.1.2 8-1.1.1 9-1.1.3 10-1.1 11-1.1.1.1.1.1.1 11-1.1.1.2.2.1.1 12-1.1.2 16-1.1.4.1 17-1.1.4 18-1.1.4.2.1 18-1.1.4.2.1.r 21-1.1.4.2 22-1.1.4.2.2.r 23-1.1.4.2.2.1.1 24-1.1.1 25-1 26-1.2 27-1.2.1 29-1.2.2.2 30-1.2.2 30-1.2.2.1 30-1.2.2.1.r (a / and~e.25 :op1 (b / bind-01~e.10 :ARG1 (p / protein~e.8,24 :ARG1-of (r2 / resemble-01~e.7 :ARG2 (p4 / protein-family :name (n / name :op1 "E2F"~e.5,11))) :ARG1-of (r5 / resemble-01~e.0,7 :polarity~e.0 -~e.0 :ARG2 (p5 / protein-family~e.1 :name (n3 / name :op1 "E2F"~e.5,11) :ARG1-of~e.1 (k / know-01~e.1))) :mod (t2 / this~e.4)) :ARG2 (s / site~e.12 :mod p4) :ARG1-of (e / efficient-01~e.9) :condition (c / contrast-01~e.17 :ARG1 (f / form~e.16 :mod (m / monomer)) :ARG2 (h / heterodimer~e.21 :polarity~e.18 -~e.18 :prep-with~e.22 (p2 / protein :name (n2 / name :op1 "DP"~e.23))))) :op2 (r3 / repress-01~e.26 :ARG0 p~e.27 :ARG1 (m2 / molecular-physical-entity~e.30 :ARG0-of~e.30 (p3 / promote-01~e.30) :ARG1-of (r4 / regulate-01~e.29 :ARG0 p4)))) # ::id bio.chicago_2015.18689 ::amr-annotator SDL-AMR-09 ::preferred # ::tok By definition , PLD catalyzes the hydrolysis of PC to PA and choline . # ::alignments 1-1.3 3-1.1.1.1 4-1 6-1.2 7-1.2.1.r 8-1.2.1.1.1 9-1.2.2.r 10-1.2.2.1.1.1 11-1.2.2 12-1.2.2.2.1.1 (c / catalyze-01~e.4 :ARG0 (e / enzyme :name (n / name :op1 "PLD"~e.3)) :ARG1 (h / hydrolyze-01~e.6 :ARG1~e.7 (s / small-molecule :name (n2 / name :op1 "PC"~e.8)) :ARG3~e.9 (a / and~e.11 :op1 (s2 / small-molecule :name (n3 / name :op1 "PA"~e.10)) :op2 (s3 / small-molecule :name (n4 / name :op1 "choline"~e.12)))) :ARG1-of (d / define-01~e.1)) # ::id bio.chicago_2015.18690 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Dephosphorylation of cyclin E by Cdc14 reverses the effects of the mitotic kinases and promotes cyclin E - Cdk2 binding to chromatin . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1 3-1.1.1.1.1.2 4-1.1.1.2.r 5-1.1.1.2.1.1 6-1.1 8-1.1.2 9-1.1.2.1.r 11-1.1.2.1.1 12-1.1.2.1 13-1 14-1.2 15-1.2.2.1.1 16-1.2.2.1.1 18-1.2.2.1.2.1.1 19-1.2.2 20-1.2.2.2.r 21-1.2.2.2.1.1 (a2 / and~e.13 :op1 (r / reverse-01~e.6 :ARG0 (d / dephosphorylate-01~e.0 :ARG1~e.1 (p2 / protein :name (n2 / name :op1 "cyclin"~e.2 :op2 "E"~e.3)) :ARG2~e.4 (p / protein :name (n / name :op1 "Cdc14"~e.5))) :ARG1 (a / affect-01~e.8 :ARG0~e.9 (k / kinase~e.12 :mod (m / mitosis~e.11)))) :op2 (p3 / promote-01~e.14 :ARG0 d :ARG1 (b / bind-01~e.19 :ARG1 (m2 / macro-molecular-complex :part p2~e.15,16 :part (e / enzyme :name (n3 / name :op1 "Cdk2"~e.18))) :ARG2~e.20 (m3 / macro-molecular-complex :name (n4 / name :op1 "chromatin"~e.21))))) # ::id bio.chicago_2015.18717 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Our results demonstrate that the chromosome condensation defect caused by perturbed ISWI function is mediated through the NURF complex . # ::alignments 0-1.1.2 0-1.1.2.r 1-1.1 1-1.1.1 1-1.1.1.r 2-1 3-1.2.r 5-1.2.2.1.1 6-1.2.2.1 7-1.2.2 8-1.2.2.2 9-1.2.2.2.1.r 10-1.2.2.2.1.2 11-1.2.2.2.1.1.1.1 12-1.2.2.2.1 14-1.2 17-1.2.1.1.1 18-1.2.1 (d / demonstrate-01~e.2 :ARG0 (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1) :poss~e.0 (w / we~e.0)) :ARG1~e.3 (m / mediate-01~e.14 :ARG0 (m2 / macro-molecular-complex~e.18 :name (n2 / name :op1 "NURF"~e.17)) :ARG1 (d2 / defect~e.7 :mod (c / condense-01~e.6 :ARG1 (c2 / chromosome~e.5)) :ARG1-of (c3 / cause-01~e.8 :ARG0~e.9 (f / function-01~e.12 :ARG0 (p / protein :name (n / name :op1 "ISWI"~e.11)) :ARG1-of (p2 / perturb-01~e.10)))))) # ::id bio.chicago_2015.18724 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The Essential Activity of DSmurf Is Limited to the DPP Signaling Pathway # ::alignments 1-1.1.2 2-1.1 3-1.1.1.r 4-1.1.1.1.1 6-1 7-1.2.r 9-1.2.1.1 10-1.2.2 11-1.2 (l / limit-01~e.6 :ARG1 (a / activity-06~e.2 :ARG0~e.3 (e2 / enzyme :name (n / name :op1 "DSmurf"~e.4)) :mod (e / essential~e.1)) :ARG2~e.7 (p / pathway~e.11 :name (n2 / name :op1 "DPP"~e.9) :ARG0-of (s / signal-07~e.10))) # ::id bio.chicago_2015.18744 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Alternatively , auxilin might bind much more weakly to Hsc70 in ADP than ATP . # ::alignments 0-1.2 0-1.2.r 2-1.1.1.1.1 3-1 4-1.1 4-1.1.5 5-1.1.3.1.1 6-1.1.3.1 7-1.1.3 8-1.1.2.r 9-1.1.2.1.1 10-1.1.4.r 11-1.1.4.1.1 12-1.1.5.r 13-1.1.5.3.1.1 (p2 / possible-01~e.3 :ARG1 (b / bind-01~e.4 :ARG1 (e / enzyme :name (n / name :op1 "auxilin"~e.2)) :ARG2~e.8 (p3 / protein :name (n2 / name :op1 "Hsc70"~e.9)) :ARG1-of (w / weak-02~e.7 :degree (m / more~e.6 :quant (m2 / much~e.5))) :location~e.10 (s / small-molecule :name (n3 / name :op1 "ADP"~e.11)) :compared-to~e.12 (b2 / bind-01~e.4 :ARG1 e :ARG2 p3 :location (s2 / small-molecule :name (n4 / name :op1 "ATP"~e.13)))) :manner~e.0 (a / alternative~e.0)) # ::id bio.chicago_2015.18747 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Regulation of Dpp Targets by brinker . # ::alignments 0-1 1-1.2.r 2-1.2.1.1.1.1 3-1.2 3-1.2.1 3-1.2.1.r 4-1.1.r 5-1.1.1.1 (r / regulate-01~e.0 :ARG0~e.4 (p2 / protein :name (n2 / name :op1 "brinker"~e.5)) :ARG1~e.1 (m / molecular-physical-entity~e.3 :ARG1-of~e.3 (t / target-01~e.3 :ARG0 (p / protein :name (n / name :op1 "Dpp"~e.2))))) # ::id bio.chicago_2015.18750 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The only other known zinc finger @-@ homeodomain cooperation is in Drosophila , where it was recently shown that the orphan nuclear receptor alphaFtz @-@ F1 is a cofactor for the homeodomain protein Ftz ( Guichet et al. , 1997 ; Yu et al. , 1997 ) ; in this case , the physical association between alphaFtz @-@ F1 and Ftz is thought to enhance the binding of the Ftz to its lower @-@ affinity target sequences ( Guichet et al. , 1997 ; Yu et al. , 1997 ) , much in the same way that Extradenticle and Pbx modulate the DNA binding activity of Hox proteins ( Phelan et al. , 1995 ; Lu and Kamps , 1996 ; Peltenburg and Murre , 1997 ) . # ::alignments 1-1.1.3.5 2-1.1.3.4 3-1.1.3.3 4-1.1.3.1.1.1 5-1.1.3.1.1.2 7-1.1.3.2.1.1 8-1.1.3 11-1.1.2.1 13-1.1.3.r 13-1.1.4.r 15-1.1.4.1.1.r 16-1.1.4.2 17-1.1.4 18-1.1.4.1.r 20-1.1.4.1.1.3 21-1.1.4.1.1.2 22-1.1.4.1.1 22-1.2.1.1.1 23-1.1.4.1.1.1.1 25-1.1.4.1.1.1.1 26-1.1.4.1.1.r 28-1.1.4.1 31-1.1.3.2.1.1 32-1.1.3.1 32-1.1.3.2 32-1.1.4.1.2 32-1.2.1.1.2 33-1.1.4.1.2.1.1 35-1.1.4.3.1.1.1.1.1.1 35-1.2.2.1.1.1.1.1.1 36-1.1.4.3.1 36-1.1.4.3.1.1.1 36-1.1.4.3.1.2.1 36-1.2.2.1 36-1.2.2.1.1.1 36-1.2.2.1.2.1 37-1.1.3.4 37-1.1.4.3.1.1.1.2.1 37-1.1.4.3.1.2.1.2.1 37-1.2.2.1.1.1.2.1 37-1.2.2.1.2.1.2.1 39-1.1.4.3.1.1.2.1 41-1.1.4.3.1.2.1.1.1.1 41-1.2.2.1.2.1.1.1.1 42-1.1.4.3.1 42-1.1.4.3.1.1.1 42-1.1.4.3.1.2.1 42-1.2.2.1 42-1.2.2.1.1.1 42-1.2.2.1.2.1 43-1.1.3.4 43-1.1.4.3.1.1.1.2.1 43-1.1.4.3.1.2.1.2.1 43-1.2.2.1.1.1.2.1 43-1.2.2.1.2.1.2.1 45-1.1.4.3.1.1.2.1 49-1.2.3.1 50-1.2.3 53-1.2.1.1.3 54-1.2.1.1 55-1.1.3.1.r 56-1.2.1.1.1.1.1 58-1.2.1.1.1.1.1 59-1.1.4.3.1 59-1.1.4.3.1.1.1 59-1.1.4.3.1.2.1 60-1.1.4.1.2.1.1 62-1.2 64-1.2.1 66-1.2.1.2 69-1.2.1.1.2.1.1 70-1.2.1.2.2.r 71-1.2.1.2.2.3 71-1.2.1.2.2.3.r 72-1.2.1.2.2.2.1 72-1.2.1.2.2.2.1.1 72-1.2.1.2.2.2.1.1.r 74-1.2.1.2.2.2 75-1.2.1.2.2.1 76-1.2.1.2.2 78-1.2.2.1.1.1.1.1.1 79-1.2.2.1 79-1.2.2.1.1.1 79-1.2.2.1.2.1 80-1.2.2.1.1.1.2.1 80-1.2.2.1.2.1.2.1 82-1.2.2.1.2.2 84-1.2.2.1.2.1.1.1.1 85-1.2.2.1 85-1.2.2.1.1.1 85-1.2.2.1.2.1 86-1.2.2.1.1.1.2.1 86-1.2.2.1.2.1.2.1 88-1.2.1.3.1.3.1.3.2.1 91-1.2.1.3.2 97-1.2.1.3.1.1.1.1.1 98-1.2.1.3.1.1 99-1.2.1.3.1.1.2.1.1 100-1.2.1.3.1 102-1.2.1.3.1.2.2.1.1.1 103-1.2.1.3.1.2.2 104-1.2.1.3.1.2 106-1.2.1.3.1.2.1.1.1 107-1.2.1.3.1.1.1 107-1.2.1.3.1.1.2 107-1.2.1.3.1.2.1 109-1.2.1.3.1.3.1.1.1.1.1.1 110-1.2.1.3.1.3.1.1.1 111-1.2.1.3.1.3.1.1.1.2.1 113-1.2.1.3.1.3.1.1.2.1 115-1.2.1.3.1.3.1.2.1.1.1.1 116-1.2.1.3.1.3.1.2.1 117-1.2.1.3.1.3.1.2.1.2.1.1 119-1.2.1.3.1.3.1.2.2.1 121-1.2.1.3.1.3.1.3.1.1.1.1 122-1.2.1.3.1.3.1.3.1 123-1.2.1.3.1.3.1.3.1.2.1.1 125-1.2.1.3.1.3.1.3.2.1 (m / multi-sentence :snt1 (o / organism :wiki "Drosophila" :name (n / name :op1 "Drosophila"~e.11) :location-of~e.13 (c / cooperate-01~e.8 :ARG0~e.55 (p / protein~e.32 :name (n2 / name :op1 "zinc"~e.4 :op2 "finger"~e.5)) :ARG1 (p23 / protein~e.32 :name (n3 / name :op1 "homeodomain"~e.7,31)) :ARG1-of (k / know-01~e.3) :mod (o2 / other~e.2,37,43) :mod (o3 / only~e.1)) :location-of~e.13 (s / show-01~e.17 :ARG1~e.18 (c2 / cofactor~e.28 :domain~e.15,26 (r / receptor~e.22 :name (n4 / name :op1 "alphaFtz-F1"~e.23,25) :mod (n5 / nucleus~e.21) :mod (o4 / orphan~e.20)) :beneficiary (p4 / protein~e.32 :name (n6 / name :op1 "Ftz"~e.33,60) :mod p23)) :time (r2 / recent~e.16) :ARG1-of (d2 / describe-01 :ARG0 (a4 / and~e.36,42,59 :op1 (p2 / publication-91 :ARG0 (a2 / and~e.36,42,59 :op1 (p5 / person :name (n7 / name :op1 "Guichet"~e.35)) :op2 (p6 / person :mod (o5 / other~e.37,43))) :time (d / date-entity :year 1997~e.39,45)) :op2 (p7 / publication-91 :ARG0 (a3 / and~e.36,42,59 :op1 (p8 / person :name (n8 / name :op1 "Yu"~e.41)) :op2 (p9 / person :mod (o6 / other~e.37,43))) :time d))))) :snt2 (t / think-01~e.62 :ARG1 (e / enhance-01~e.64 :ARG0 (a5 / associate-01~e.54 :ARG1 (r4 / receptor~e.22 :name (n17 / name :op1 "alphaFtz-F1"~e.56,58)) :ARG2 (p3 / protein~e.32 :name (n18 / name :op1 "Ftz"~e.69)) :mod (p10 / physical~e.53)) :ARG1 (b / bind-01~e.66 :ARG1 p3 :ARG2~e.70 (s2 / sequence~e.76 :ARG1-of (t2 / target-01~e.75) :mod (a6 / affinity~e.74 :ARG1-of (l / low-04~e.72 :degree~e.72 (m2 / more~e.72))) :poss~e.71 p3~e.71)) :ARG1-of (r3 / resemble-01 :ARG2 (m4 / modulate-01~e.100 :ARG0 (a7 / and~e.98 :op1 (p11 / protein~e.107 :name (n9 / name :op1 "Extradenticle"~e.97)) :op2 (p12 / protein~e.107 :name (n10 / name :op1 "Pbx"~e.99))) :ARG1 (a8 / activity-06~e.104 :ARG0 (p13 / protein-family~e.107 :name (n11 / name :op1 "Hox"~e.106)) :ARG1 (b2 / bind-01~e.103 :ARG2 (n21 / nucleic-acid :name (n22 / name :op1 "DNA"~e.102)))) :ARG1-of (d8 / describe-01 :ARG0 (a9 / and :op1 (p14 / publication-91 :ARG0 (a10 / and~e.110 :op1 (p15 / person :name (n12 / name :op1 "Phelan"~e.109)) :op2 (p16 / person :mod (o7 / other~e.111))) :time (d9 / date-entity :year 1995~e.113)) :op2 (p17 / publication-91 :ARG0 (a11 / and~e.116 :op1 (p18 / person :name (n13 / name :op1 "Lu"~e.115)) :op2 (p19 / person :name (n14 / name :op1 "Kamps"~e.117))) :time (d10 / date-entity :year 1996~e.119)) :op3 (p20 / publication-91 :ARG0 (a12 / and~e.122 :op1 (p21 / person :name (n15 / name :op1 "Peltenburg"~e.121)) :op2 (p22 / person :name (n16 / name :op1 "Murre"~e.123))) :time (d11 / date-entity :year 1997~e.88,125))))) :degree (m3 / much~e.91))) :ARG1-of (d4 / describe-01 :ARG0 (a / and~e.36,42,79,85 :op1 (p24 / publication-91 :ARG0 (a13 / and~e.36,42,79,85 :op1 (p26 / person :name (n19 / name :op1 "Guichet"~e.35,78)) :op2 (p29 / person :mod (o8 / other~e.37,43,80,86))) :time d11) :op2 (p25 / publication-91 :ARG0 (a14 / and~e.36,42,79,85 :op1 (p27 / person :name (n20 / name :op1 "Yu"~e.41,84)) :op2 (p28 / person :mod (o9 / other~e.37,43,80,86))) :time d11~e.82))) :mod (c3 / case-04~e.50 :ARG1 (t3 / this~e.49)))) # ::id bio.chicago_2015.18761 ::amr-annotator SDL-AMR-09 ::preferred # ::tok During gastrulation , DLT may first form a complex with CRB to target it to the apical domain . # ::alignments 0-1.2.r 3-1.1.1.1.1.1 4-1 5-1.1.4 6-1.1 8-1.1.2 9-1.1.1.r 10-1.1.1.2.1.1 12-1.1.3 14-1.1.3.2.r 16-1.1.3.2.1 17-1.1.3.2 (p / possible-01~e.4 :ARG1 (f / form-01~e.6 :ARG0~e.9 (a2 / and :op1 (p2 / protein :name (n / name :op1 "DLT"~e.3)) :op2 (p3 / protein :name (n2 / name :op1 "CRB"~e.10))) :ARG1 (m / macro-molecular-complex~e.8) :purpose (t / target-01~e.12 :ARG0 p2 :ARG1~e.14 (d2 / domain~e.17 :mod (a / apical~e.16)) :ARG2 p3) :time (f2 / first~e.5)) :time~e.0 (g / gastrulate-00)) # ::id bio.chicago_2015.18776 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We compared cdc25A induction to that of cyclin E , which is regulated by E2F and Rb family members ( 4 , 20 , 45 ) . # ::alignments 0-1.1 1-1 2-1.2.1.1.1 3-1.2 3-1.3 6-1.3.1.r 7-1.3.1.1.1 8-1.3.1.1.2 12-1.3.2 13-1.3.2.1.r 14-1.3.2.1.1.1.1.1 15-1.3.2.1 16-1.3.2.1.2.1.1.1 17-1.3.2.1.1.1 17-1.3.2.1.2.1 18-1.3.2.1.1 18-1.3.2.1.2 20-1.4.1.1.1.1 22-1.4.1.1.1.2 24-1.4.1.1.1.3 (c / compare-01~e.1 :ARG0 (w / we~e.0) :ARG1 (i / induce-01~e.3 :ARG2 (e / enzyme :name (n / name :op1 "cdc25A"~e.2))) :ARG2 (i2 / induce-01~e.3 :ARG2~e.6 (p2 / protein :name (n2 / name :op1 "cyclin"~e.7 :op2 "E"~e.8)) :ARG1-of (r / regulate-01~e.12 :ARG0~e.13 (a / and~e.15 :op1 (m / member~e.18 :part-of (p3 / protein-family~e.17 :name (n3 / name :op1 "E2F"~e.14))) :op2 (m2 / member~e.18 :part-of (p4 / protein-family~e.17 :name (n4 / name :op1 "Rb"~e.16)))))) :ARG1-of (d / describe-01 :ARG0 (p5 / publication :ARG1-of (c2 / cite-01 :ARG2 (a2 / and :op1 4~e.20 :op2 20~e.22 :op3 45~e.24))))) # ::id bio.chicago_2015.18798 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Furthermore , during early gastrulation , DLT normally colocalizes with CRB . # ::alignments 0-1 0-1.1.1 2-1.1.3.r 3-1.1.3.1 6-1.1.1.1.1.1 7-1.1.2 8-1.1 9-1.1.1.r 10-1.1.1.2.1.1 (a / and~e.0 :op2 (c / colocalize-01~e.8 :ARG1~e.9 (a2 / and~e.0 :op1 (p / protein :name (n / name :op1 "DLT"~e.6)) :op2 (p2 / protein :name (n2 / name :op1 "CRB"~e.10))) :ARG1-of (n3 / normal-02~e.7) :time~e.2 (g / gastrulate-00 :mod (e / early~e.3)))) # ::id bio.chicago_2015.18911 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , caldesmon together with TM completely inhibits actin binding of human fascin . # ::alignments 0-1 2-1.1.1.1.1.1 5-1.1.1.2.1.1 6-1.1.3 7-1.1 8-1.1.2.1.1.1 9-1.1.2 10-1.1.2.2.r 11-1.1.2.2.2 12-1.1.2.2.1.1 (c / contrast-01~e.0 :ARG2 (i / inhibit-01~e.7 :ARG0 (a / and :op1 (p / protein :name (n / name :op1 "caldesmon"~e.2)) :op2 (p2 / protein :name (n2 / name :op1 "TM"~e.5))) :ARG1 (b / bind-01~e.9 :ARG1 (p3 / protein :name (n3 / name :op1 "actin"~e.8)) :ARG2~e.10 (p4 / protein :name (n4 / name :op1 "fascin"~e.12) :mod (h / human~e.11))) :ARG1-of (c2 / complete-02~e.6))) # ::id bio.chicago_2015.18974 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Binding of filamin to actin bundles was determined in the absence of another ABP ( curve 1 , A , B ) or in the presence of saturating quantities of calponin ( curve 2 , A ) or - actinin ( curve 2 , B ) . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.1 3-1.1.2.r 4-1.1.2.1.1.1 5-1.1.2 7-1 8-1.2.r 10-1.2.1 11-1.2.1.1.r 12-1.2.1.1.2 13-1.2.1.1.1.1 15-1.2.1.2.1.3.1 16-1.2.1.2.1.3.1.1 18-1.2.1.2.1.1.1 20-1.2.1.2.1.2.1 22-1.2 25-1.2.2 26-1.2.2.1.r 27-1.2.2.1.1 28-1.2.2.1 29-1.2.2.1.1.1.r 30-1.2.2.1.1.1.1.1.1 32-1.2.2.1.1.1.1.2.1.2.1 33-1.2.2.1.1.1.1.2.1.2.1.1 35-1.2.2.1.1.1.1.2.1.1 37-1.2.2.1.1.1 39-1.2.2.1.1.1.2.1.1 41-1.2.2.1.1.1.1.2.1.2.1 42-1.2.2.1.1.1.1.2.1.2.1.1 44-1.2.1.2.1.2.1 44-1.2.2.1.1.1.2.2.1.1 (d / determine-01~e.7 :ARG1 (b / bind-01~e.0 :ARG1~e.1 (p / protein :name (n / name :op1 "filamin"~e.2)) :ARG2~e.3 (b2 / bundle~e.5 :mod (p2 / protein :name (n2 / name :op1 "actin"~e.4)))) :condition~e.8 (o / or~e.22 :op1 (a / absent-01~e.10 :ARG1~e.11 (p3 / protein :name (n3 / name :op1 "ABP"~e.13) :mod (a2 / another~e.12)) :ARG1-of (d2 / describe-01 :ARG0 (a3 / and :op1 (f / figure :mod "A"~e.18) :op2 (f2 / figure :mod "B"~e.20,44) :part-of (f3 / figure :mod (c / curve~e.15 :mod 1~e.16))))) :op2 (p4 / present-02~e.25 :ARG1~e.26 (q / quantity~e.28 :ARG0-of (s / saturate-01~e.27 :ARG2~e.29 (o2 / or~e.37 :op1 (p5 / protein :name (n4 / name :op1 "calponin"~e.30) :ARG1-of (d3 / describe-01 :ARG0 (f4 / figure :mod "A"~e.35 :part-of (f5 / figure :mod (c2 / curve~e.32,41 :mod 2~e.33,42))))) :op2 (p6 / protein :name (n5 / name :op1 "actinin"~e.39) :ARG1-of (d4 / describe-01 :ARG0 (f6 / figure :mod "B"~e.44 :part-of f5))))))))) # ::id bio.chicago_2015.18987 ::amr-annotator SDL-AMR-09 ::preferred # ::tok During cell morphogenesis and motility , cells undergo extensive remodeling of the actin cytoskeleton , a phenomenon that is mediated by various actin @-@ binding proteins ( 1 ) . # ::alignments 0-1.3.r 1-1.3.1.1 2-1.3.2 3-1.3 4-1.3.1 6-1.1 7-1 8-1.2.2 9-1.2 10-1.2.1.r 12-1.2.1.1.1.1 13-1.2.1 19-1.4 20-1.4.1.r 21-1.4.1.2 22-1.4.1.1.1 24-1.4.1.1 25-1.4.1 27-1.5.1.1.1 (u / undergo-28~e.7 :ARG1 (c / cell~e.6) :ARG2 (r / remodel-01~e.9 :ARG1~e.10 (c2 / cytoskeleton~e.13 :mod (p / protein :name (n / name :op1 "actin"~e.12))) :ARG1-of (e / extensive-03~e.8)) :time~e.0 (a / and~e.3 :op1 (m / motility~e.4 :mod (c3 / cell~e.1)) :op2 (m2 / morphogenesis~e.2 :mod c3)) :ARG1-of (m3 / mediate-01~e.19 :ARG0~e.20 (p3 / protein~e.25 :ARG0-of (b / bind-01~e.24 :ARG1 p~e.22) :mod (v / various~e.21))) :ARG1-of (d / describe-01 :ARG0 (p4 / publication :ARG1-of (c4 / cite-01 :ARG2 1~e.27)))) # ::id bio.chicago_2015.19008 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For instance , the proposed role of Grb2 in clathrin @-@ independent endocytosis of EGFR ( Yamazaki et al. , 2002 ) may be related to the ability of Grb2 to mediate EGFR signaling to actin cytoskeleton # ::alignments 0-1.2 1-1.2 4-1.1.1.1 5-1.1.1 6-1.1.1.2.r 7-1.1.1.2.1.1 8-1.1.1.3.r 9-1.1.1.3.1.2.1.1 11-1.1.1.3.1 11-1.1.1.3.1.1 11-1.1.1.3.1.1.r 12-1.1.1.3 13-1.1.1.3.2.r 14-1.1.1.3.2.1.1 16-1.1.1.1.1.1.1.1.1.1 17-1.1.1.1.1.1.1 18-1.1.1.1.1.1.1.2.1 20-1.1.1.1.1.1.2.1 22-1 24-1.1 25-1.1.2.r 27-1.1.2 28-1.1.2.2.r 29-1.1.2.2.1 31-1.1.2.2 32-1.1.2.2.2.1 33-1.1.2.2.2 34-1.1.2.2.2.2.r 35-1.1.2.2.2.2.1.1.1 36-1.1.2.2.2.2 (p / possible-01~e.22 :ARG1 (r / relate-01~e.24 :ARG1 (r2 / role~e.5 :ARG1-of (p2 / propose-01~e.4 :ARG1-of (d4 / describe-01 :ARG0 (p5 / publication-91 :ARG0 (a / and~e.17 :op1 (p6 / person :name (n5 / name :op1 "Yamazaki"~e.16)) :op2 (p7 / person :mod (o / other~e.18))) :time (d5 / date-entity :year 2002~e.20)))) :mod~e.6 (p3 / protein :name (n2 / name :op1 "Grb2"~e.7)) :topic~e.8 (e3 / endocytosis~e.12 :ARG0-of (d3 / depend-01~e.11 :polarity~e.11 -~e.11 :ARG1 (p4 / protein :name (n3 / name :op1 "clathrin"~e.9))) :mod~e.13 (e4 / enzyme :name (n4 / name :op1 "EGFR"~e.14)))) :ARG2~e.25 (c / capable-01~e.27 :ARG1 p3 :ARG2~e.28 (m / mediate-01~e.31 :ARG0 p3~e.29 :ARG1 (s / signal-07~e.33 :ARG1 e4~e.32 :ARG2~e.34 (c2 / cytoskeleton~e.36 :mod (p8 / protein :name (n / name :op1 "actin"~e.35))))))) :ARG0-of (e / exemplify-01~e.0,1)) # ::id bio.chicago_2015.19022 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We found that the overexpression of SH3PX1 alone did not significantly affect the EGF receptor levels through a 60 @-@ min exposure to EGF ( Fig . 6 , lanes 9 @-@ 12 , upper panel ) . # ::alignments 0-1.1 1-1 2-1.2.r 4-1.2.2 5-1.2.2.1.r 6-1.2.2.1.1.1 7-1.2.2.2 9-1.2.1 9-1.2.1.r 10-1.2.4 11-1.2 13-1.2.3.1.1.1 14-1.2.3.1.1.2 15-1.2.3 18-1.2.5.2.1 20-1.2.5.2.2 21-1.2.5 25-1.3.1.2 27-1.3.1.2.1 29-1.3.1 30-1.3.1.1.1 32-1.3.1.1.2 35-1.3.1.3 (f / find-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (a / affect-01~e.11 :polarity~e.9 -~e.9 :ARG1 (o / overexpress-01~e.4 :ARG1~e.5 (g / gene :name (n / name :op1 "SH3PX1"~e.6)) :mod (a2 / alone~e.7)) :ARG2 (l / level~e.15 :quant-of (e2 / enzyme :name (n3 / name :op1 "EGF"~e.13 :op2 "receptor"~e.14))) :ARG1-of (s / significant-02~e.10) :time (e / expose-01~e.21 :ARG2 (r / receptor) :duration (t / temporal-quantity :quant 60~e.18 :unit (m / minute~e.20)))) :ARG1-of (d / describe-01 :ARG0 (l2 / lane~e.29 :value (v / value-interval :op1 9~e.30 :op2 12~e.32) :part-of (f2 / figure~e.25 :mod 6~e.27) :location (p / panel~e.35 :ARG1-of (u / up-02 :degree (m2 / more)))))) # ::id bio.chicago_2015.19058 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Overexpression of cdc5 delta N induces a disturbance in septin ring structures and Cdc5 interacts with two septins , Cdc11 and Cdc12 , in a polo @-@ box - dependent manner . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.1.1 3-1.1.1.1.1.2 4-1.1.1.1.1.3 5-1.1 7-1.1.2 8-1.1.2.1.r 9-1.1.2.1.1.1.1.1 10-1.1.2.1.1 11-1.1.2.1 12-1 13-1.2.1.1.1 14-1.2 19-1.2.2.1.1.1 20-1.2.2 21-1.2.2.2.1.1 23-1.2.3.r 25-1.2.3.1 27-1.2.3.1 29-1.2.3 (a / and~e.12 :op1 (i / induce-01~e.5 :ARG0 (o / overexpress-01~e.0 :ARG1~e.1 (p3 / protein :name (n6 / name :op1 "cdc5"~e.2 :op2 "delta"~e.3 :op3 "N"~e.4))) :ARG2 (d / disturb-01~e.7 :ARG1~e.8 (s / structure-01~e.11 :ARG1 (r / ring~e.10 :mod (p / protein-family :name (n2 / name :op1 "septin"~e.9)))))) :op2 (i2 / interact-01~e.14 :ARG0 (p4 / protein :name (n3 / name :op1 "Cdc5"~e.13)) :ARG1 (a2 / and~e.20 :op1 (s2 / septin :name (n4 / name :op1 "Cdc11"~e.19)) :op2 (s3 / septin :name (n5 / name :op1 "Cdc12"~e.21))) :ARG0-of~e.23 (d3 / depend-01~e.29 :ARG1 (p2 / polo-box~e.25,27)))) # ::id bio.chicago_2015.19083 ::amr-annotator SDL-AMR-09 ::preferred # ::tok How the interactions of filamin with actin and transmembrane proteins are regulated is largely unknown . # ::alignments 0-1.2.1.r 2-1.2.1.1 3-1.2.1.1.1.r 4-1.2.1.1.1.1.1 5-1.2.1.1.2.r 6-1.2.1.1.2.1.1.1 7-1.2.1.1.2 8-1.2.1.1.2.2.1 9-1.2.1.1.2.2 11-1.2.1 13-1.3 14-1 14-1.1 14-1.1.r (k / know-01~e.14 :polarity~e.14 -~e.14 :ARG1 (t2 / thing :manner-of~e.0 (r / regulate-01~e.11 :ARG1 (i / interact-01~e.2 :ARG0~e.3 (p / protein :name (n / name :op1 "filamin"~e.4)) :ARG1~e.5 (a / and~e.7 :op1 (p2 / protein :name (n2 / name :op1 "actin"~e.6)) :op2 (p3 / protein~e.9 :mod (t / transmembrane~e.8)))))) :degree (l / large~e.13)) # ::id bio.chicago_2015.19095 ::amr-annotator SDL-AMR-09 ::preferred # ::tok P @-@ TEFb may alter the role of Spt proteins either by phosphorylation of Pol II or Spt5 ( Ivanov et al. 2000 ) . # ::alignments 0-1.1.1.1.1 0-1.1.3 2-1.1.1.1.1 3-1 4-1.1 6-1.1.2 8-1.1.2.1.1.1 9-1.1.1 9-1.1.2.1 9-1.1.3.1.2 12-1.1.3 13-1.1.3.1.r 14-1.1.3.1.1.1.1 15-1.1.3.1.1.1.2 16-1.1.3.1 17-1.1.3.1.2.1.1 19-1.2.1.1.1.1.1 20-1.2.1.1 21-1.2.1.1.2.1 22-1.2.1.2.1 (p / possible-01~e.3 :ARG1 (a / alter-01~e.4 :ARG0 (p2 / protein~e.9 :name (n / name :op1 "P-TEFb"~e.0,2)) :ARG1 (r / role~e.6 :poss (p3 / protein~e.9 :name (n2 / name :op1 "Spt"~e.8))) :manner (p4 / phosphorylate-01~e.0,12 :ARG1~e.13 (o / or~e.16 :op1 (e / enzyme :name (n3 / name :op1 "Pol"~e.14 :op2 "II"~e.15)) :op2 (p5 / protein~e.9 :name (n4 / name :op1 "SPT5"~e.17))))) :ARG1-of (d / describe-01 :ARG0 (p6 / publication-91 :ARG0 (a2 / and~e.20 :op1 (p7 / person :name (n5 / name :op1 "Ivanov"~e.19)) :op2 (p8 / person :mod (o2 / other~e.21))) :time (d2 / date-entity :year 2000~e.22)))) # ::id bio.chicago_2015.19112 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Site II seems to be generally less well conserved ( for example , Arp1 and beta @- and gamma @-@ tubulin ) , and this may explain why these target proteins bind less well to prefoldin than actin and alpha @-@ tubulin ( see Fig. 4 ; the fragments of Arp1 and beta @- and gamma @-@ tubulin also show binding to CCT , whereas actin and alpha @-@ tubulin do not ) . # ::alignments 0-1.2.1.1 1-1.2.1.1 2-1.2.1.1 3-1.2.1.1 4-1.2.1.1 5-1.2.1.1 6-1.2.1.1 7-1.2.1.1 8-1.2.1.1 9-1.2.1.1 10-1.2.1.1 11-1.2.1.1 12-1.2.1.1 13-1.2.1.1 14-1.2.1.1 15-1.2.1.1 16-1.2.1.1 17-1.2.1.1 18-1.2.1.1 19-1.2.1.1 20-1.2.1.1 23-1 23-1.1.1.1.2 23-1.1.1.1.2.2 23-1.1.1.1.2.2.r 24-1.2.1.2.1.1.1.2 25-1.2 26-1.2.1 26-1.3.1.2 27-1.2.1.2 27-1.2.1.2.1 27-1.2.1.2.1.r 28-1.2.1.2.1.1.1.2 29-1.2.1.2.1.1.1.1 30-1.2.1.2.1.1.1 31-1.2.1.2.1.1 32-1.2.1.2.1.1.3.1 33-1.2.1.2.1.1.3 34-1.2.1.2.1.1.2.r 35-1.2.1.2.1.1.2.1.1 36-1.2.1.2.1.1.3.2.r 37-1.2.1.2.1.1.3.2.1.1.1 38-1.2.1.2.1.1.3.2 39-1.2.1.2.1.1.3.2.2.1.1 41-1.1.1.1.2.2.1.1.1 41-1.1.1.1.2.2.2.1.1 41-1.2.1.2.1.1.3.2.2.1.1 43-1.3.1.3 44-1.3.1 45-1.3.1.1 48-1.3.1.2.1.1 49-1.3.1.2.1.1.1.r 50-1.3.1.2.1.1.1.1 51-1.1.1.1.2.2 52-1.1.1.1.2.2.1.1.1 54-1.1.1.1.2.2 55-1.1.1.1.2.2.2.1.1 57-1.1.1.1.2.2.2.1.1 57-1.2.1.2.1.1.3.2.2.1.1 58-1.3.1.2.1.4 59-1.3.1.2.1 59-1.3.1.2.1.3.1 60-1.3.1.2.1.2 61-1.3.1.2.1.2.2.r 62-1.3.1.2.1.2.2.1.1 64-1.3.1.2.1.3 65-1.2.1.2.1.1.3.2.1.1.1 67-1.2.1.2.1.1.3.2.2.1.1 69-1.1.1.1.2.2.2.1.1 69-1.2.1.2.1.1.3.2.2.1.1 71-1.3.1.2.1.3.1.1 71-1.3.1.2.1.3.1.1.r (a2 / and~e.23 :op1 (s / seem-01 :ARG1 (c / conserve-01 :ARG1 (s2 / site :mod 2 :example (a4 / and~e.23 :op1 (p / protein :name (n / name :op1 "Arp1")) :op2~e.23 (a5 / and~e.23,51,54 :op1 (p7 / protein :name (n5 / name :op1 "beta-tubulin"~e.41,52)) :op2 (p8 / protein-family :name (n6 / name :op1 "gamma-tubulin"~e.41,55,57,69))))) :mod (w / well :degree (l / less)) :ARG1-of (g / general-02))) :op2 (p2 / possible-01~e.25 :ARG1 (e / explain-01~e.26 :ARG0 s~e.0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 :ARG1 (t4 / thing~e.27 :ARG0-of~e.27 (c2 / cause-01~e.27 :ARG1 (b / bind-01~e.31 :ARG1 (p3 / protein~e.30 :ARG0-of (t / target-01~e.29) :mod (t2 / this~e.24,28)) :ARG2~e.34 (p4 / protein-family :name (n2 / name :op1 "prefoldin"~e.35)) :mod (w2 / well~e.33 :degree (l2 / less~e.32) :compared-to~e.36 (a3 / and~e.38 :op1 (p5 / protein :name (n3 / name :op1 "actin"~e.37,65)) :op2 (p6 / protein :name (n4 / name :op1 "alpha-tubulin"~e.39,41,57,67,69))))))))) :ARG1-of (d / describe-01 :ARG2 (f / figure~e.44 :mod 4~e.45 :ARG0-of (e2 / explain-01~e.26 :ARG1 (s3 / show-01~e.59 :ARG0 (f2 / fragment~e.48 :part-of~e.49 (a6 / and :op1 p~e.50 :op2 a5)) :ARG1 (b2 / bind-01~e.60 :ARG1 (a7 / and :op1 p :op2 a5) :ARG2~e.61 (p9 / protein :name (n7 / name :op1 "CCT"~e.62))) :ARG1-of (c3 / contrast-01~e.64 :ARG2 (s4 / show-01~e.59 :polarity~e.71 -~e.71 :ARG0 (a8 / and :op1 p5 :op2 p6) :ARG1 b2)) :mod (a / also~e.58))) :ARG1-of (s5 / see-01~e.43 :mode imperative :ARG0 (y / you))))) # ::id bio.chicago_2015.19139 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These functions of cadherin require intracellular attachment of cadherin to the actin cytoskeleton that is dependent on binding of cadherin to catenins ( Hirano et al. , 1987 ; Nagafuchi and Takeichi , 1988 ; Ozawa et al. , 1990 ) ; beta @-@ catenin mediates the linkage of cadherins to alpha @-@ catenin , which in turn interacts with the actin cytoskeleton ( Aberle et al. , 1994 ; Hulsken et al. , 1994 ; Jou et al. , 1995 ; Rimm et al. , 1995 ) . # ::alignments 0-1.1.1.2 1-1.1.1 2-1.1.1.1.r 3-1.1.1.1.1.1 4-1.1 5-1.1.2.3 6-1.1.2 8-1.1.1.1.1.1 8-1.2.2.1.1.1 9-1.1.2.2.r 11-1.1.2.2.1.1.1 12-1.1.2.2 15-1.1.2.2.2 16-1.1.2.2.2.1.r 17-1.1.2.2.2.1 18-1.1.2.2.2.1.1.r 19-1.1.2.2.2.1.1 23-1.1.3.1.1.1.1.1.1 24-1.1.3.1.1.1 25-1.1.3.1.1.1.2.1 27-1.1.3.1.1.2.1 29-1.1.3.1.2.1.1.1.1 30-1.1.3.1.2.1 31-1.1.3.1.2.1.2.1.1 33-1.1.3.1.2.2.1 35-1.1.3.1.3.1.1.1.1 36-1.1.3.1.3.1 37-1.1.3.1.3.1.2.1 39-1.1.3.1.3.2.1 42-1.2.1.1.1 44-1.2.1.1.1 45-1.2 47-1.2.2 50-1.2.2.2.r 51-1.2.2.2.1.1 53-1.1.2.2.2.1.2.1.1 56-1.2.2.2.2.2 57-1.2.2.2.2.2 58-1.2.2.2 58-1.2.2.2.2 58-1.2.2.2.2.r 59-1.2.2.2.2.1.r 61-1.2.2.2.2.1 62-1.2.2.2.2.1 64-1.2.3.1.1.1.1.1.1 65-1.2.3.1 65-1.2.3.1.1.1 65-1.2.3.1.3.1 65-1.2.3.1.4.1 66-1.2.3.1.1.1.2.1 66-1.2.3.1.3.1.2.1 66-1.2.3.1.4.1.2.1 68-1.2.3.1.2.2.1 70-1.2.3.1.2.1.1.1.1 71-1.2.3.1.2.1 72-1.2.3.1.2.1.2.1 74-1.2.3.1.2.2.1 76-1.2.3.1.3.1.1.1.1 77-1.2.3.1.3.1 78-1.2.3.1.3.1.2.1 80-1.2.3.1.3.2.1 82-1.2.3.1.4.1.1.1.1 83-1.1.3.1 83-1.2.3.1 83-1.2.3.1.1.1 83-1.2.3.1.3.1 83-1.2.3.1.4.1 84-1.2.3.1.1.1.2.1 84-1.2.3.1.3.1.2.1 84-1.2.3.1.4.1.2.1 86-1.2.3.1.3.2.1 (m / multi-sentence :snt1 (r / require-01~e.4 :ARG0 (f / function-01~e.1 :ARG0~e.2 (p / protein-family :name (n / name :op1 "cadherin"~e.3,8)) :mod (t / this~e.0)) :ARG1 (a / attach-01~e.6 :ARG1 p :ARG2~e.9 (c / cytoskeleton~e.12 :mod (p2 / protein :name (n2 / name :op1 "actin"~e.11)) :ARG0-of (d / depend-01~e.15 :ARG1~e.16 (b / bind-01~e.17 :ARG1~e.18 p~e.19 :ARG2 (p3 / protein-family :name (n3 / name :op1 "catenin"~e.53))))) :mod (i3 / intracellular~e.5)) :ARG1-of (d2 / describe-01 :ARG0 (a2 / and~e.83 :op1 (p4 / publication-91 :ARG0 (a3 / and~e.24 :op1 (p5 / person :name (n4 / name :op1 "Hirano"~e.23)) :op2 (p6 / person :mod (o / other~e.25))) :time (d3 / date-entity :year 1987~e.27)) :op2 (p7 / publication-91 :ARG0 (a4 / and~e.30 :op1 (p8 / person :name (n5 / name :op1 "Nagafuchi"~e.29)) :op2 (p9 / person :name (n6 / name :op1 "Takeichi"~e.31))) :time (d4 / date-entity :year 1988~e.33)) :op3 (p10 / publication-91 :ARG0 (a5 / and~e.36 :op1 (p11 / person :name (n7 / name :op1 "Ozawa"~e.35)) :op2 (p12 / person :mod (o2 / other~e.37))) :time (d5 / date-entity :year 1990~e.39))))) :snt2 (m2 / mediate-01~e.45 :ARG0 (p13 / protein :name (n8 / name :op1 "beta-catenin"~e.42,44)) :ARG1 (l / link-01~e.47 :ARG1 (p14 / protein-family :name (n9 / name :op1 "cadherin"~e.8)) :ARG2~e.50 (p15 / protein~e.58 :name (n10 / name :op1 "alpha-catenin"~e.51) :ARG0-of~e.58 (i / interact-01~e.58 :ARG1~e.59 c~e.61,62 :mod (i2 / in-turn~e.56,57)))) :ARG1-of (d6 / describe-01 :ARG0 (a6 / and~e.65,83 :op1 (p16 / publication-91 :ARG0 (a7 / and~e.65,83 :op1 (p17 / person :name (n11 / name :op1 "Aberle"~e.64)) :op2 (p18 / person :mod (o3 / other~e.66,84))) :time d7) :op2 (p19 / publication-91 :ARG0 (a8 / and~e.71 :op1 (p20 / person :name (n12 / name :op1 "Hulsken"~e.70)) :op2 (p21 / person :mod (o4 / other~e.72))) :time (d7 / date-entity :year 1994~e.68,74)) :op3 (p22 / publication-91 :ARG0 (a9 / and~e.65,77,83 :op1 (p23 / person :name (n13 / name :op1 "Jou"~e.76)) :op2 (p24 / person :mod (o5 / other~e.66,78,84))) :time (d8 / date-entity :year 1995~e.80,86)) :op4 (p25 / publication-91 :ARG0 (a10 / and~e.65,83 :op1 (p26 / person :name (n14 / name :op1 "Rimm"~e.82)) :op2 (p27 / person :mod (o6 / other~e.66,84))) :time d8))))) # ::id bio.chicago_2015.19160 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Other possibilities would be that actin promotes interaction of the BR particle with a fibrous network in the nucleoplasm , allows binding to export receptors ( cf . ref . 52 ) , or is involved in the dramatic conformational change of the particle upon translocation through the nuclear pore . # ::alignments 0-1.2 1-1 4-1.1.r 5-1.1.1.1.1.1 6-1.1.1 7-1.1.1.2 8-1.1.1.2.1.r 10-1.1.1.2.1.1.1 11-1.1.1.2.1 12-1.1.1.2.2.r 14-1.1.1.2.2.1 15-1.1.1.2.2 16-1.1.1.2.3.r 18-1.1.1.2.3 20-1.1.2 21-1.1.2.2 22-1.1.2.2.1.r 23-1.1.2.2.1.1 24-1.1.2.2.1 30-1.1.2.3.1.1.1 33-1.1 35-1.1.3 36-1.1.3.2.r 38-1.1.3.2.2 39-1.1.3.2.3 40-1.1.3.2 41-1.1.3.2.4.r 43-1.1.3.2.4.1 45-1.1.3.2.4 46-1.1.3.2.4.2.r 48-1.1.3.2.4.2.1 49-1.1.3.2.4.2 (p / possible-01~e.1 :ARG1~e.4 (o2 / or~e.33 :op1 (p2 / promote-02~e.6 :ARG0 (p3 / protein :name (n / name :op1 "actin"~e.5)) :ARG1 (i / interact-01~e.7 :ARG0~e.8 (p4 / particle~e.11 :name (n2 / name :op1 "BR"~e.10)) :ARG1~e.12 (n3 / network~e.15 :mod (f / fibrous~e.14)) :location~e.16 (n4 / nucleoplasm~e.18))) :op2 (a2 / allow-01~e.20 :ARG0 p3 :ARG1 (b / bind-01~e.21 :ARG2~e.22 (r / receptor~e.24 :ARG0-of (e / export-01~e.23))) :ARG1-of (c / compare-01 :ARG2 (p5 / publication :ARG1-of (c2 / cite-01 :ARG2 52~e.30)))) :op3 (i2 / involve-01~e.35 :ARG1 p3 :ARG2~e.36 (c3 / change-01~e.40 :ARG1 p4 :degree (d / dramatic~e.38) :mod (c4 / conformational~e.39) :condition~e.41 (t / translocate-01~e.45 :ARG1 p4~e.43 :path~e.46 (p6 / pore~e.49 :mod (n5 / nucleus~e.48)))))) :mod (o / other~e.0)) # ::id bio.chicago_2015.19248 ::amr-annotator SDL-AMR-09 ::preferred # ::tok 1 ) the MLC @-@ pep blocks an interaction between vMLC @-@ 1 and actin , which releases a tethering effect that leads to the inotropic effect ; 2 ) the MLC @-@ pep blocks a site on myosin to which the vMLC @-@ 1 binds that disrupts myosin binding to actin ; and 3 ) the MLC @-@ pep exerts a direct effect on the actin @-@ myosin interaction or actin @-@ actin interactions in the presence of regulatory proteins and Ca2+, such that it cooperatively stimulates the entire thin filament . # ::alignments 0-1.1.1 3-1.1.2.1.1 5-1.1.2.1.1 6-1.1 8-1.1.3 10-1.1.3.1.1.1 12-1.1.3.1.1.1 14-1.1.3.2.1.1 17-1.1.4 19-1.1.4.1.1 20-1.1.4.1 22-1.1.4.1.2 23-1.1.4.1.2.1.r 25-1.1.4.1.2.1.1 26-1.1.4.1.2.1 28-1.2.1 31-1.2.2 32-1.2.2 33-1.2.2 34-1.2 36-1.2.3 37-1.2.3.1.r 38-1.2.3.1.1.1 42-1.1.3.1.1.1 44-1.1.1 44-1.1.3.1.1.1 45-1.2.3.2 47-1.2.4 48-1.2.4.1.1 49-1.2.4.1 50-1.2.4.1.2.r 51-1.2.4.1.2 53-1 54-1.3.1 57-1.3.2 58-1.3.2 59-1.3.2 60-1.3 62-1.3.3.1 63-1.3.3 66-1.1.3.2.1.1 68-1.2.3.1.1.1 69-1.3.4.1 69-1.3.4.2 70-1.3.4 71-1.3.4.1.1 72-1.3.4.1.1 73-1.3.4.1.1 74-1.3.4.1 75-1.3.5.r 77-1.3.5 78-1.3.5.1.r 79-1.3.5.1.1.1 80-1.3.5.1.1 81-1.3.5.1 86-1.3.6.1.3 87-1.3.6.1 89-1.3.6.1.2.1 90-1.3.6.1.2.2 91-1.3.6.1.2 (a / and~e.53 :op1 (b / block-01~e.6 :li 1~e.0,44 :ARG0 (s / small-molecule :name (n / name :op1 "MLC-pep"~e.3,5)) :ARG1 (i / interact-01~e.8 :ARG0 (p / protein :name (n2 / name :op1 "vMLC-1"~e.10,12,42,44)) :ARG1 (p2 / protein :name (n3 / name :op1 "actin"~e.14,66))) :ARG0-of (r / release-01~e.17 :ARG1 (a2 / affect-01~e.20 :ARG0-of (t / tether-01~e.19) :ARG0-of (l / lead-03~e.22 :ARG2~e.23 (a3 / affect-01~e.26 :mod (i2 / inotropic~e.25)))))) :op2 (b2 / block-01~e.34 :li 2~e.28 :ARG0 s~e.31,32,33 :ARG1 (s2 / site~e.36 :part-of~e.37 (p3 / protein :name (n4 / name :op1 "myosin"~e.38,68)) :ARG2-of (b3 / bind-01~e.45 :ARG1 p)) :ARG0-of (d / disrupt-01~e.47 :ARG1 (b4 / bind-01~e.49 :ARG1 p3~e.48 :ARG2~e.50 p2~e.51))) :op3 (e / exert-01~e.60 :li 3~e.54 :ARG0 s~e.57,58,59 :ARG1 (a4 / affect-01~e.63 :ARG1-of (d2 / direct-02~e.62)) :ARG2 (o / or~e.70 :op1 (i3 / interact-01~e.69,74 :ARG0 p2~e.71,72,73 :ARG1 p3) :op2 (i4 / interact-01~e.69 :ARG0 p2 :ARG1 p2)) :condition~e.75 (p4 / present-02~e.77 :ARG1~e.78 (a5 / and~e.81 :op1 (p5 / protein~e.80 :ARG0-of (r2 / regulate-01~e.79)) :op2 (s3 / small-molecule :name (n5 / name :op1 "calcium") :ARG0-of r2 :ARG1-of (i5 / ionize-01 :value "2+")))) :ARG0-of (c2 / cause-01 :ARG1 (s4 / stimulate-01~e.87 :ARG0 s :ARG1 (f / filament~e.91 :mod (e2 / entire~e.89) :ARG1-of (t2 / thin-03~e.90)) :ARG2-of (c / cooperate-01~e.86))))) # ::id bio.chicago_2015.19251 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In addition , in co @-@ transfection experiments , Rlf ( Zwartkruis et al. , 1998 ) , but apparently not RalGDS ( Urano et al. , 1996 ) , can mediate Rap1 @- and C3G @-@ induced Ral activation . # ::alignments 0-1 1-1 7-1.1.1.2 9-1.1.1.1.1.1.1 11-1.1.1.1.1.2.1.1.1.1.1 12-1.1.1.1.1.2.1.1 13-1.1.1.1.1.2.1.1.2.1 15-1.1.1.1.1.2.1.2.1 18-1.1 19-1.1.2.3 20-1.1.2.1 20-1.1.2.1.r 21-1.1.2.2.1.1.1 23-1.1.2.2.1.2.1.1.1.1.1 24-1.1.2.2.1.2.1.1 25-1.1.2.2.1.2.1.1.2.1 27-1.1.2.2.1.2.1.2.1 30-1.1.1 30-1.1.2 31-1.1.1.1 31-1.1.2.2 32-1.1.1.1.2.2.1.1.1.1 34-1.1.1.1.2.2.1 35-1.1.1.1.2.2.1.2.1.1 37-1.1.1.1.2.2 38-1.1.1.1.2.1.1.1 39-1.1.1.1.2 (a / and~e.0,1 :op2 (c / contrast-01~e.18 :ARG1 (p / possible-01~e.30 :ARG1 (m / mediate-01~e.31 :ARG0 (e / enzyme :name (n / name :op1 "Rlf"~e.9) :ARG1-of (d / describe-01 :ARG0 (p2 / publication-91 :ARG0 (a2 / and~e.12 :op1 (p3 / person :name (n2 / name :op1 "Zwartkruis"~e.11)) :op2 (p4 / person :mod (o / other~e.13))) :time (d4 / date-entity :year 1998~e.15)))) :ARG1 (a3 / activate-01~e.39 :ARG1 (p5 / protein :name (n3 / name :op1 "Ral"~e.38)) :ARG2-of (i / induce-01~e.37 :ARG0 (a4 / and~e.34 :op1 (e2 / enzyme :name (n4 / name :op1 "Rap1"~e.32)) :op2 (s / small-molecule :name (n5 / name :op1 "C3G"~e.35)))))) :time (e3 / experiment-01~e.7 :ARG2 (c2 / cotransfect-01))) :ARG2 (p6 / possible-01~e.30 :polarity~e.20 -~e.20 :ARG1 (m2 / mediate-01~e.31 :ARG0 (p7 / protein :name (n6 / name :op1 "RalGDS"~e.21) :ARG1-of (d2 / describe-01 :ARG0 (p8 / publication-91 :ARG0 (a5 / and~e.24 :op1 (p9 / person :name (n7 / name :op1 "Urano"~e.23)) :op2 (p10 / person :mod (o2 / other~e.25))) :time (d3 / date-entity :year 1996~e.27)))) :ARG1 a3 :time e3) :ARG1-of (a6 / appear-02~e.19)))) # ::id bio.chicago_2015.19256 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Towards the center of the gradient , high levels of Dpp signaling strongly repress brk transcription . # ::alignments 0-1.3.r 2-1.3 3-1.3.1.r 5-1.3.1 7-1.1.1 8-1.1 9-1.1.2.r 10-1.1.2.1.1.1 11-1.1.2 12-1.4 13-1 14-1.2.1.1.1 15-1.2 (r / repress-01~e.13 :ARG0 (l / level~e.8 :ARG1-of (h / high-02~e.7) :degree-of~e.9 (s / signal-07~e.11 :ARG0 (p / pathway :name (n / name :op1 "Dpp"~e.10)))) :ARG1 (t / transcribe-01~e.15 :ARG0 (p2 / protein :name (n2 / name :op1 "brk"~e.14))) :direction~e.0 (c / center~e.2 :part-of~e.3 (g2 / gradient~e.5)) :ARG1-of (s2 / strong-02~e.12)) # ::id bio.chicago_2015.19269 ::amr-annotator SDL-AMR-09 ::preferred # ::tok high amounts of Dpp signaling abolish brk transcription completely , intermediate amounts of Dpp only partially repress brk transcription , while the absence of Dpp results in high levels of brk transcription . # ::alignments 0-1.1.1.1.2 1-1.1.1.1 2-1.1.1.1.1.r 3-1.1.1.1.1.1.1.1 4-1.1.1.1.1 5-1.1.1 6-1.1.1.2.1.1.1 7-1.1.1.2 8-1.1.1.3 10-1.1.2.1.1 11-1.1.2.1 12-1.1.2.1.2.r 13-1.1.2.1.2 14-1.1.2.3.1 15-1.1.2.3 15-1.1.2.3.r 16-1.1.2 17-1.1.2.2 18-1.1.2.2 20-1 22-1.2.1 23-1.2.1.1.r 24-1.2.1.1 25-1.2 26-1.2.2.r 27-1.2.2.2 28-1.2.2 29-1.2.2.1.r 30-1.2.2.1 31-1.2.2.1 (c / contrast-01~e.20 :ARG1 (a / and :op1 (a2 / abolish-01~e.5 :ARG0 (a3 / amount~e.1 :degree-of~e.2 (s / signal-07~e.4 :ARG0 (p / pathway :name (n / name :op1 "Dpp"~e.3))) :ARG1-of (h3 / high-02~e.0)) :ARG1 (t / transcribe-01~e.7 :ARG0 (p3 / protein :name (n2 / name :op1 "brk"~e.6))) :ARG1-of (c2 / complete-02~e.8)) :op2 (r / repress-01~e.16 :ARG0 (a4 / amount~e.11 :degree (i / intermediate~e.10) :quant-of~e.12 p~e.13) :ARG1 t~e.17,18 :degree~e.15 (p4 / part~e.15 :mod (o / only~e.14)))) :ARG2 (r2 / result-01~e.25 :ARG1 (a5 / absent-01~e.22 :ARG1~e.23 p~e.24) :ARG2~e.26 (l / level~e.28 :quant-of~e.29 t~e.30,31 :ARG1-of h3~e.27))) # ::id bio.chicago_2015.19306 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Dissected wing imaginal discs stained with antibodies against the beta @-@ galactosidase and Engrailed proteins showing the induction and suppression of induction of Engrailed expression ; anterior upward , wing pouch to the left . # ::alignments 0-1.5 1-1.4 2-1.6 3-1 4-1.1 5-1.1.1.r 6-1.1.1 7-1.1.1.1 9-1.1.1.1.1.1.1.1 11-1.1.1.1.1.1.1.1 12-1.1.1.1.1 13-1.1.1.1.1.2.1.1 14-1.1.1.1.1.2 15-1.2 17-1.2.1.2.1 18-1.2.1 19-1.2.1.2 21-1.2.1.2.1 23-1.2.1.1.1.1 24-1.2.1.1.1 26-1.3.1.2 27-1.3.1.2.1 29-1.3.1.3 30-1.3.1 33-1.3.1.1 (d3 / disc~e.3 :ARG1-of (s / stain-01~e.4 :ARG2~e.5 (a2 / antibody~e.6 :ARG0-of (o / oppose-01~e.7 :ARG1 (a3 / and~e.12 :op1 (e2 / enzyme :name (n2 / name :op1 "beta-galactosidase"~e.9,11)) :op2 (p2 / protein~e.14 :name (n3 / name :op1 "Engrailed"~e.13)))))) :ARG0-of (s2 / show-01~e.15 :ARG1 (a4 / and~e.18 :op1 (i / induce-01 :ARG2 (e / express-03~e.24 :ARG2 p2~e.23)) :op2 (s3 / suppress-01~e.19 :ARG1 i~e.17,21))) :ARG1-of (d2 / describe-01 :medium (p / pouch~e.30 :ARG1-of (l / left-20~e.33) :mod (a5 / anterior~e.26 :direction (u / upward~e.27)) :mod (w2 / wing~e.29))) :mod (w / wing~e.1) :ARG1-of (d / dissect-01~e.0) :mod (i2 / imaginal~e.2)) # ::id bio.chicago_2015.19311 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To identify the site( s ) on the cytoplasmic domain of the EGFR that mediates its recruitment of PI3K @-@ C2 beta , a panel of receptor point mutations was expressed in HEK293 cells . # ::alignments 1-1.3 8-1.3.1.1.1 9-1.3.1.1 10-1.3.1.1.2.r 12-1.3.1.1.2.1.1 14-1.3.1.1.2 14-1.3.1.1.2.2 14-1.3.1.1.2.2.r 15-1.3.1.1.2.2.1.1 15-1.3.1.1.2.2.1.1.r 16-1.3.1.1.2.2.1 17-1.3.1.1.2.2.1.2.r 18-1.3.1.1.2.2.1.2.1.1 24-1.1 25-1.1.1.r 26-1.1.1.1.1 27-1.1.1.1 28-1.1.1 30-1 31-1.2.r 32-1.2.1.1 33-1.2 (e / express-03~e.30 :ARG2 (p / panel~e.24 :consist-of~e.25 (m / mutate-01~e.28 :ARG1 (p2 / point~e.27 :mod (r / receptor~e.26)))) :ARG3~e.31 (c / cell~e.33 :name (n / name :op1 "HEK293"~e.32)) :purpose (i / identify-01~e.1 :ARG1 (s / site :location (d / domain~e.9 :mod (c2 / cytoplasm~e.8) :part-of~e.10 (e2 / enzyme~e.14 :name (n2 / name :op1 "EGFR"~e.12) :ARG0-of~e.14 (m2 / mediate-01~e.14 :ARG1 (r2 / recruit-01~e.16 :ARG0~e.15 e2~e.15 :ARG1~e.17 (e3 / enzyme :name (n3 / name :op1 "PI3K-C2beta"~e.18))))))))) # ::id bio.chicago_2015.19345 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Formation of sharp borders of Iro @-@ C gene expression in response to localized EGFR signaling The lateral border delimiting Iro @-@ C expression in the wing disc is relatively straight and sharp ( e.g . Fig. 1B , Fig. 4C ) , raising the question of how such a well @-@ defined border can be established and maintained in response to EGFR signaling . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1 3-1.1.1 4-1.1.1.2.r 5-1.1.1.2.1.1.1 7-1.1.1.2.1.1.1 8-1.1.1.2.1 8-1.2.1.1.2.1.1 9-1.1.1.2 11-1.1.2 14-1.1.2.1.1.1.1 15-1.1.2.1 17-1.2.1.1.1 18-1.2.1.1 19-1.2.1.1.2 20-1.2.1.1.2.1.1.1.1 22-1.2.1.1.2.1.1.1.1 23-1.2.1.1.2.1 24-1.2.1.1.2.2.r 26-1.2.1.1.2.2.1 27-1.2.1.1.2.2 29-1.2.1.2 30-1.2.1 31-1.2 31-1.2.3.1 32-1.2.2 36-1.2.3.1.1 37-1.2.3.1.1.1 39-1.2.3.1.2 40-1.2.3.1.2.1 43-1.2.4 45-1.2.4.1 46-1.2.4.1.1.r 47-1.2.4.1.1.1.r 48-1.2.4.1.1.1.1.1.2 50-1.2.4.1.1.1.1.1.1 52-1.2.4.1.1.1.1.1 53-1.2.4.1.1.1.1 54-1.2.4.1.1.1.3 56-1.2.4.1.1.1 58-1.2.4.1.1.2 60-1.1.2 60-1.2.4.1.1.1.2 62-1.1.2.1.1.1.1 62-1.2.4.1.1.1.2.1.1.1.1 63-1.1.2.1 63-1.2.4.1.1.1.2.1 (m / multi-sentence :snt1 (f / form-01~e.0 :ARG1~e.1 (b / border~e.3 :ARG1-of (s / sharp-02~e.2) :poss~e.4 (e / express-03~e.9 :ARG1 (g / gene~e.8 :name (n / name :op1 "Iro-C"~e.5,7)))) :ARG2-of (r / respond-01~e.11,60 :ARG1 (s2 / signal-07~e.15,63 :ARG0 (e2 / enzyme :name (n2 / name :op1 "EGFR"~e.14,62)) :ARG1-of (l / local-02)))) :snt2 (a / and~e.31 :op1 (s3 / straight-04~e.30 :ARG1 (b2 / border~e.18 :mod (l2 / lateral~e.17) :ARG1-of (d / delimit-01~e.19 :ARG2 (e4 / express-03~e.23 :ARG1 (g2 / gene~e.8 :name (n3 / name :op1 "Iro-C"~e.20,22))) :location~e.24 (d2 / disc~e.27 :topic (w / wing~e.26)))) :ARG2-of (r2 / relative-05~e.29)) :op2 (s4 / sharp-02~e.32 :ARG1 b2 :degree r2) :ARG1-of (d3 / describe-01 :ARG0 (a2 / and~e.31 :op1 (f2 / figure~e.36 :mod "1B"~e.37) :op2 (f3 / figure~e.39 :mod "4C"~e.40))) :ARG0-of (r3 / raise-01~e.43 :ARG1 (q / question-01~e.45 :ARG1~e.46 (t / thing :manner-of~e.47 (e3 / establish-01~e.56 :ARG1 (b3 / border~e.53 :ARG1-of (d4 / define-01~e.52 :manner (w2 / well~e.50) :mod (s6 / such~e.48))) :ARG2-of (r4 / respond-01~e.60 :ARG1 (s5 / signal-07~e.63 :ARG0 (e5 / enzyme :name (n4 / name :op1 "EGFR"~e.62)))) :ARG1-of (p / possible-01~e.54)) :ARG0-of (m2 / maintain-01~e.58 :ARG1 b3 :ARG2-of r4)))))) # ::id bio.chicago_2015.19362 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Ectopic Gem or Rad expression inhibits ROK @-@ dependent functions such as formation of stress fibers and focal adhesions , neurite retraction , and Rho @-@ dependent transformation . # ::alignments 0-1.1.1.3 1-1.1.1.1.1.1 3-1.1.1.2.1.1 4-1.1 5-1 6-1.2.1.1.1.1 8-1.2.1 9-1.2 10-1.2.2.r 11-1.2.2.r 12-1.2.2.1 13-1.2.2.1.1.r 14-1.2.2.1.1.1.1 15-1.2.2.1.1.1 16-1.2.2.1.1 17-1.2.2.1.1.2.1 18-1.2.2.1.1.2 20-1.2.2.2.1.1.1 21-1.2.2.2 23-1.2.2 24-1.2.2.3.1.1.1.1 26-1.2.2.3.1 27-1.2.2.3 (i / inhibit-01~e.5 :ARG0 (e / express-03~e.4 :ARG2 (a / and :op1 (p / protein :name (n / name :op1 "Gem"~e.1)) :op2 (p2 / protein :name (n2 / name :op1 "Rad"~e.3)) :mod (e2 / ectopic~e.0))) :ARG1 (f / function-01~e.9 :ARG0-of (d / depend-01~e.8 :ARG1 (p3 / protein :name (n3 / name :op1 "ROK"~e.6))) :example~e.10,11 (a2 / and~e.23 :op1 (f2 / form-01~e.12 :ARG1~e.13 (a3 / and~e.16 :op1 (f3 / fiber~e.15 :mod (s / stress~e.14)) :op2 (a4 / adhere-01~e.18 :mod (f4 / focal~e.17)))) :op2 (r / retract-01~e.21 :ARG1 (c / cell :name (n4 / name :op1 "neurite"~e.20))) :op3 (t / transform-01~e.27 :ARG0-of (d2 / depend-01~e.26 :ARG1 (p4 / protein-family :name (n5 / name :op1 "Rho"~e.24))))))) # ::id bio.mskcc_0001.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We identify four S/TP sites of B @-@ Raf phosphorylated by activated ERK and find that feedback phosphorylation of B @-@ Raf inhibits binding to activated Ras and disrupts heterodimerization with C @-@ Raf , which is dependent on the B @-@ Raf pS729 @/@ 14 @-@ 3 @-@ 3 binding site . # ::alignments 0-1.1.1 1-1.1 2-1.1.2.1 4-1.1.2 6-1.1.2.3.1.1 8-1.1.2.3.1.1 9-1.1.2.2.1 11-1.1.2.2.1.1.2 12-1.1.2.2.1.1.1.1 13-1 14-1.2 16-1.1.2.2.1.2 17-1.1.2.2.1 17-1.2.2.2.2.3.1.3 19-1.1.2.3.1.1 21-1.1.2.3.1.1 22-1.2.2.1 23-1.2.2.1.2 25-1.2.2.1.2.2.2 26-1.2.2.1.2.2.1.1 27-1.2.2 28-1.2.2.2 29-1.2.2.2.2 30-1.2.2.2.2.2.r 31-1.2.2.2.2.2.1.1 33-1.2.2.2.2.2.1.1 37-1.2.2.2.2.3 40-1.1.2.3.1.1 42-1.1.2.3.1.1 42-1.2.2.2.2.2.1.1 45-1.2.2.2.2.3.1.4.1.1.1 47-1.2.2.2.2.3.1.4.1.1.1 49-1.2.2.2.2.3.1.4.1.1.1 50-1.2.2.1.2 50-1.2.2.2.2.3.1.4 51-1.1.2 (a / and~e.13 :op1 (i / identify-01~e.1 :ARG0 (w / we~e.0) :ARG1 (p / protein-segment~e.4,51 :quant 4~e.2 :part (a5 / amino-acid :ARG3-of (p2 / phosphorylate-01~e.9,17 :ARG2 (e / enzyme :name (n3 / name :op1 "ERK"~e.12) :ARG1-of (a2 / activate-01~e.11)) :subevent-of (f2 / feedback~e.16)) :mod (o / or :op1 (a6 / amino-acid :name (n / name :op1 "serine")) :op2 (a7 / amino-acid :name (n9 / name :op1 "threonine")))) :part-of (e4 / enzyme :name (n2 / name :op1 "B-Raf"~e.6,8,19,21,40,42)))) :op2 (f / find-01~e.14 :ARG0 w :ARG1 (a3 / and~e.27 :op1 (i2 / inhibit-01~e.22 :ARG0 p2 :ARG1 (b / bind-01~e.23,50 :ARG1 e4 :ARG2 (e3 / enzyme :name (n4 / name :op1 "Ras"~e.26) :ARG1-of (a4 / activate-01~e.25)))) :op2 (d / disrupt-01~e.28 :ARG0 p2 :ARG1 (h / heterodimerize-01~e.29 :ARG1 e4 :ARG2~e.30 (e2 / enzyme :name (n5 / name :op1 "C-Raf"~e.31,33,42)) :ARG0-of (d2 / depend-01~e.37 :ARG1 (a8 / amino-acid :mod 729 :name (n10 / name :op1 "serine") :ARG3-of (p4 / phosphorylate-01~e.17) :ARG1-of (b2 / bind-01~e.50 :ARG2 (p3 / protein :name (n6 / name :op1 "14-3-3"~e.45,47,49))) :part-of e4))))))) # ::id bio.mskcc_0001.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok 14 @-@ 3 @-@ 3 dimers bind to phosphorylation sites present in both the N @- and C @-@ terminal regions and stabilize the autoinhibited state ( 22 ) . # ::alignments 0-1.1.1.1.1.1 2-1.1.1.1.1.1 4-1.1.1.1.1.1 5-1.1.1 6-1.1 6-1.2 8-1.1.2.1 8-1.2.2.1 9-1.1.2 9-1.2.2 10-1.1.2.2 10-1.2.2.2 14-1.1.2.2.1.1.1 16-1 17-1.2.2.2.1.1.1 19-1.1.2.2.1.1.1 19-1.2.2.2.1.1.1 21-1 22-1.3 27-1.4.1.1.1 (a / and~e.16,21 :op1 (b / bind-01~e.6 :ARG1 (d / dimer~e.5 :part (p5 / protein :name (n / name :op1 "14-3-3"~e.0,2,4))) :ARG2 (p9 / protein-segment~e.9 :ARG1-of (p / phosphorylate-01~e.8) :ARG1-of (p11 / present-02~e.10 :ARG2 (p2 / protein-segment :name (n2 / name :op1 "N-terminus"~e.14,19))))) :op2 (b2 / bind-01~e.6 :ARG1 d :ARG2 (p10 / protein-segment~e.9 :ARG1-of (p3 / phosphorylate-01~e.8) :ARG1-of (p12 / present-02~e.10 :ARG2 (p4 / protein-segment :name (n3 / name :op1 "C-terminus"~e.17,19))))) :op3 (s3 / stabilize-01~e.22 :ARG0 d :ARG1 (i / inhibit-01 :ARG0 p5 :ARG1 p5)) :ARG1-of (d2 / describe-01 :ARG0 (p8 / publication :ARG1-of (c / cite-01 :ARG2 22~e.27)))) # ::id bio.mskcc_0001.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To activate the Raf proteins , autoinhibition mediated by the N terminus must be relieved and the kinase domain must adopt the active catalytic conformation # ::alignments 1-1.1 1-1.2.2.1 3-1.1.1.1.1 4-1.2.1.1.1.1 4-1.2.1.1.1.2 7-1.2.1.1.1.3 8-1.2.1.1.1.3.1.r 10-1.2.1.1.1.3.1.1.1 11-1.2.1.1.1.3.1.1.1 12-1.2.1 14-1.2.1.1 15-1.2 17-1.2.2.1.1.1 18-1.2.2.1.1 19-1.2.1 23-1.2.2.1.1.3 (r / require-01 :ARG0 (a / activate-01~e.1 :ARG1 (p / protein-family :name (n / name :op1 "Raf"~e.3))) :ARG1 (a2 / and~e.15 :op1 (o / obligate-01~e.12,19 :ARG2 (r2 / relieve-01~e.14 :ARG1 (i / inhibit-01 :ARG0 (p2 / protein-segment~e.4 :part-of p) :ARG1 (p3 / protein-segment~e.4 :part-of p) :ARG1-of (m / mediate-01~e.7 :ARG0~e.8 (p5 / protein-segment :name (n2 / name :op1 "N-terminus"~e.10,11) :part-of p))))) :op2 (o2 / obligate-01 :ARG2 (a3 / activate-01~e.1 :ARG1 (d / domain~e.18 :mod (k / kinase~e.17) :part-of p :ARG0-of (c / catalyze-01~e.23)))))) # ::id bio.mskcc_0001.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Under normal signaling conditions , Ras activation helps mediate these events by recruiting the Raf proteins to the plasma membrane , which induces the release of 14 @-@ 3 @-@ 3 from the N @-@ terminal binding site and facilitates phosphorylation of the Raf kinase domain ( 19 ) . # ::alignments 1-1.4 2-1.4.1 3-1.4.r 5-1.1.1.1.1 6-1.1 7-1 8-1.2 9-1.2.2.1 10-1.2.2 11-1.3.r 12-1.3 14-1.3.2.1.1 15-1.3.4.1.2 16-1.3.3.r 18-1.3.3.1 19-1.3.3 22-1.3.4 24-1.3.4.1 25-1.3.4.1.1.r 26-1.3.4.1.1.1.1 28-1.3.4.1.1.1.1 30-1.3.4.1.1.1.1 33-1.3.4.1.2.1.1.1 35-1.3.4.1.2.1.1.1 36-1.3.4.1.2.2 37-1.3.4.1.2 39-1.3.5 40-1.3.5.1 41-1.3.5.1.1.r 43-1.3.5.1.1.2 44-1.3.5.1.1.1 45-1.3.5.1.1 47-1.5.1.1.1 (h / help-01~e.7 :ARG0 (a / activate-01~e.6 :ARG1 (e3 / enzyme :name (n / name :op1 "Ras"~e.5))) :ARG1 (m / mediate-01~e.8 :ARG0 a :ARG1 (e / event~e.10 :mod (t / this~e.9))) :manner~e.11 (r / recruit-01~e.12 :ARG0 a :ARG1 (e2 / enzyme :name (n6 / name :op1 "Raf"~e.14)) :destination~e.16 (m2 / membrane~e.19 :mod (p2 / plasma~e.18)) :ARG0-of (i / induce-01~e.22 :ARG2 (r2 / release-01~e.24 :ARG1~e.25 (p3 / protein :name (n2 / name :op1 "14-3-3"~e.26,28,30)) :ARG2 (p8 / protein-segment~e.15,37 :part-of (p4 / protein-segment :name (n3 / name :op1 "N-terminus"~e.33,35)) :ARG1-of (b / bind-01~e.36)))) :ARG0-of (f / facilitate-01~e.39 :ARG1 (p5 / phosphorylate-01~e.40 :ARG1~e.41 (d / domain~e.45 :mod (k / kinase~e.44) :part-of e2~e.43)))) :condition~e.3 (n4 / normal-02~e.1 :ARG1 (s2 / signal-07~e.2 :ARG0 e3)) :ARG1-of (d2 / describe-01 :ARG0 (p6 / publication :ARG1-of (c / cite-01 :ARG2 19~e.47)))) # ::id bio.mskcc_0001.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Once activated , either by upstream signaling or by mutational events , all Raf proteins are capable of initiating the phosphorylation cascade that results in the sequential activation of MEK and ERK . # ::alignments 1-1.3 4-1.3.1.r 5-1.3.1.1.1 6-1.3.1.1 7-1.3.1 9-1.3.1.2 12-1.1.2 13-1.1.1.1 14-1.1 16-1 17-1.2.r 18-1.2 20-1.2.2.1 21-1.2.2 23-1.2.2.2 27-1.2.2.2.1.1 27-1.2.2.2.1.2 28-1.2.2.2.1.1.1.r 29-1.2.2.2.1.1.1.1.1 30-1.2.2.2.1 31-1.2.2.2.1.2.1.1.1 (c / capable-01~e.16 :ARG1 (p / protein-family~e.14 :name (n / name :op1 "Raf"~e.13) :mod (a / all~e.12)) :ARG2~e.17 (i / initiate-01~e.18 :ARG0 p :ARG1 (c2 / cascade~e.21 :subevent (p3 / phosphorylate-01~e.20) :ARG1-of (r / result-01~e.23 :ARG2 (a3 / and~e.30 :op1 (a2 / activate-01~e.27 :ARG1~e.28 (e / enzyme :name (n2 / name :op1 "MEK"~e.29))) :op2 (a4 / activate-01~e.27 :ARG1 (e2 / enzyme :name (n3 / name :op1 "ERK"~e.31)) :ARG2-of (f / follow-01 :ARG1 a2)))))) :time (a6 / activate-01~e.1 :ARG0~e.4 (o / or~e.7 :op1 (s / signal-07~e.6 :source (u / upstream~e.5)) :op2 (m / mutate-01~e.9)) :ARG1 p)) # ::id bio.mskcc_0001.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Strikingly , the Raf proteins themselves are also substrates of activated ERK . # ::alignments 0-1.3 3-1.2.1.1 4-1.2 7-1.2.2 10-1.1.2 11-1.1.1.1 (c / catalyze-01 :ARG0 (e / enzyme :name (n / name :op1 "ERK"~e.11) :ARG1-of (a / activate-01~e.10)) :ARG1 (p / protein-family~e.4 :name (n2 / name :op1 "Raf"~e.3) :mod (a2 / also~e.7)) :ARG1-of (s / strike-04~e.0)) # ::id bio.mskcc_0001.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In regard to C @-@ Raf , ERK @-@ dependent feedback phosphorylation has been shown to instigate a regulatory cycle whereby phosphorylation of the feedback sites down @-@ modulates C @-@ Raf signaling , after which the hyperphosphorylated C @-@ Raf protein is dephosphorylated and returned to a signaling @-@ competent state through dephosphorylation events involving protein phosphatase 2A ( PP2A ) and the Pin1 prolyl @-@ isomerase ( 8 ) . # ::alignments 2-1.2.1.1.2.r 3-1.2.1.1.1.1.1 5-1.2.1.1.1.1.1 7-1.2.1.2.1.1.1 9-1.2.1.2 10-1.2.1.1.2 11-1.2.1 14-1 15-1.2.1.1.2.r 16-1.2 18-1.2.2.1 19-1.2.2 21-1.2.2.2.2 22-1.2.2.2.2 23-1.2.2.2.2 24-1.2.2.2.2 25-1.2.2.2.2 26-1.2.2.2.2 27-1.2.2.2.2 28-1.2.2.2.2 29-1.2.2.2.2 30-1.2.2.2.2 31-1.2.2.2.2 32-1.2.2.2.1 34-1.2.2.2.3 37-1.2.2.2.3.1.1.2 38-1.2.2.2.3.1.1.1.1 40-1.2.2.2.3.1.1.1.1 43-1.2.2.2.3.1 48-1.2.2.2.1 53-1.2.2.2.3.1 55-1.2.2.2.3.1.3 56-1.2.2.2.3.1.3.1.1.1.1 57-1.2.2.2.3.1.3.1.1.1.2 58-1.2.2.2.3.1.3.1.1.1.3 62-1.2.2.2.3.1.3.1 64-1.2.2.2.3.1.3.1.2.1.1 65-1.2.2.2.3.1.3.1.2 67-1.2.2.2.3.1.3.1.2 69-1.1.1.1 (s / show-01~e.14 :ARG0 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 8~e.69)) :ARG1 (i / instigate-01~e.16 :ARG0 (p / phosphorylate-01~e.11 :ARG1 (p2 / protein-segment :part-of (e / enzyme :name (n / name :op1 "C-Raf"~e.3,5)) :destination-of~e.2,15 (f / feedback~e.10)) :ARG0-of (d / depend-01~e.9 :ARG1 (e2 / enzyme :name (n2 / name :op1 "ERK"~e.7)))) :ARG1 (c / cycle-02~e.19 :ARG1-of (r / regulate-01~e.18) :subevent (d2 / downmodulate-01 :ARG1 (s2 / signal-07~e.32,48 :ARG0 e) :ARG2 p~e.21,22,23,24,25,26,27,28,29,30,31 :op1-of (a / after~e.34 :time-of (d3 / dephosphorylate-01~e.43,53 :ARG1 (e3 / enzyme :name (n3 / name :op1 "C-Raf"~e.38,40) :ARG3-of (h / hyperphosphorylate-01~e.37)) :ARG0-of (a2 / activate-01 :ARG1 s2) :ARG1-of (i2 / involve-01~e.55 :ARG2 (a3 / and~e.62 :op1 (e4 / enzyme :name (n4 / name :op1 "protein"~e.56 :op2 "phosphatase"~e.57 :op3 "2A"~e.58)) :op2 (p4 / prolyl-isomerase~e.65,67 :name (n5 / name :op1 "Pin1"~e.64)))))))))) # ::id bio.mskcc_0001.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For B @-@ Raf , two ERK @-@ dependent feedback sites , S750 and T753 , have been identified , and phosphorylation of these sites has been reported to have a negative regulatory effect # ::alignments 1-1.1.1.3.1.1 3-1.1.1.3.1.1 6-1.1.1.4.1.1.1.1 8-1.1.1.4.1 9-1.1.1.4 13-1.1.1 18-1.1 20-1 21-1.2.1.1 27-1.2 31-1.2.1.2 32-1.2.1.2 33-1.2.1 (a / and~e.20 :op1 (i / identify-01~e.18 :ARG1 (a2 / and~e.13 :op1 (a3 / amino-acid :mod 750 :name (n4 / name :op1 "serine")) :op2 (a4 / amino-acid :mod 753 :name (n3 / name :op1 "threonine")) :part-of (e / enzyme :name (n / name :op1 "B-Raf"~e.1,3)) :destination-of (f / feedback~e.9 :ARG0-of (d / depend-01~e.8 :ARG1 (e2 / enzyme :name (n2 / name :op1 "ERK"~e.6)))))) :op2 (r / report-01~e.27 :ARG1 (a5 / affect-01~e.33 :ARG0 (p / phosphorylate-01~e.21 :ARG1 a2) :ARG2 (d2 / downregulate-01~e.31,32)))) # ::id bio.mskcc_0001.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Here we find that both normal and oncogenic B @-@ Raf proteins are phosphorylated on four S/TP sites ( S151 , T401 , S750 , and T753 ) by activated ERK . # ::alignments 0-1.3 1-1.1 2-1 5-1.2.3.1 7-1.2.3.2 7-1.2.3.2.2.2.1 8-1.2.1.5.1.1 10-1.2.1.5.1.1 13-1.2 25-1.2.1 28-1.2.2.r 29-1.2.2.2 30-1.2.2.1.1 (f / find-01~e.2 :ARG0 (w / we~e.1) :ARG1 (p / phosphorylate-01~e.13 :ARG1 (a / and~e.25 :op1 (a2 / amino-acid :mod 151 :name (n / name :op1 "serine")) :op2 (a3 / amino-acid :mod 401 :name (n2 / name :op1 "threonine")) :op3 (a4 / amino-acid :mod 750 :name (n3 / name :op1 "serine")) :op4 (a5 / amino-acid :mod 753 :name (n4 / name :op1 "threonine")) :part-of (e / enzyme :name (n5 / name :op1 "B-Raf"~e.8,10))) :ARG2~e.28 (e2 / enzyme :name (n7 / name :op1 "ERK"~e.30) :ARG1-of (a6 / activate-01~e.29)) :condition (o / or :op1 (n6 / normal-02~e.5 :ARG1 e) :op2 (c / cause-01~e.7 :ARG0 e :ARG1 (d / disease :wiki "Cancer" :name (n8 / name :op1 "cancer"~e.7))))) :medium (h / here~e.0)) # ::id bio.mskcc_0001.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Previously , we found that in response to growth factor treatment , signaling from C @-@ Raf is downregulated by ERK @-@ dependent feedback phosphorylation on S/TP sites and that C @-@ Raf is subsequently dephosphorylated and returned to a signaling @-@ competent state through the activities of PP2A and the Pin1 prolyl @-@ isomerase ( 8 ) # ::alignments 0-1.4 2-1.1 3-1 5-1.2.r 6-1.2.3 7-1.2.3.1.r 8-1.2.3.1.1 9-1.2.3.1.1 10-1.2.3.1 12-1.2.2.4.1 13-1.2.2.4.1 14-1.2.1.2.1 15-1.2.1.2.1 16-1.2.1.2.1 17-1.2.2.4.1 18-1.2.2.4.1 19-1.2.2.4.1 20-1.2.2.4.1 21-1.2.2.4.1 22-1.2.2.4.1 23-1.2.2.4.1 24-1.2.2.4.1 25-1.2.2.4.1 26-1.2.2.4.1 27-1.2.2.4.1 28-1.2.2.4.1 29-1.2.2.4.1 30-1.2.2.4.1 31-1.2.2.4.1 32-1.2.2.4.1 34-1.2.2.4 34-1.2.2.4.r 35-1.2.2.1 36-1.2.2 37-1.2.2.2 38-1.2.2.2.2.r 40-1.2.2.2.2.1 43-1.2.2.2.2 46-1.2.2.3 47-1.2.2.3.1.r 48-1.2.2.3.1.1.1.1 49-1.2.2.3.1 51-1.2.2.3.1.2.1.1 52-1.2.2.3.1.2 54-1.2.2.3.1.2 56-1.3.1.1.1 (f2 / find-01~e.3 :ARG0 (w / we~e.2) :ARG1~e.5 (a / and :op1 (d2 / downregulate-01 :ARG0 (p / phosphorylate-01 :ARG1 (a4 / amino-acid :mod (o / or :op1 (a6 / amino-acid :name (n7 / name :op1 "serine")) :op2 (a7 / amino-acid :name (n8 / name :op1 "threonine"))) :part-of (e / enzyme :name (n / name :op1 "C-Raf")) :destination-of (f / feedback)) :ARG0-of (d / depend-01 :ARG1 (e2 / enzyme :name (n2 / name :op1 "ERK")))) :ARG1 (s2 / signal-07 :ARG0 e~e.14,15,16)) :op2 (a8 / and~e.36 :op1 (d3 / dephosphorylate-01~e.35 :ARG1 e) :op2 (r / return-03~e.37 :ARG1 e :ARG2~e.38 (s3 / state~e.43 :mod s2~e.40)) :manner (a9 / activity-06~e.46 :ARG0~e.47 (a3 / and~e.49 :op1 (e4 / enzyme :name (n4 / name :op1 "PP2A"~e.48)) :op2 (p4 / prolyl-isomerase~e.52,54 :name (n5 / name :op1 "Pin1"~e.51)))) :time~e.34 (a5 / after~e.34 :op1 d2~e.12,13,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32)) :ARG0-of (r2 / respond-01~e.6 :ARG1~e.7 (t / treat-04~e.10 :ARG2 (g / growth-factor~e.8,9)))) :ARG1-of (d4 / describe-01 :ARG0 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 8~e.56))) :time (p2 / previous~e.0)) # ::id bio.mskcc_0001.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The Pin1 prolyl @-@ isomerase binds specifically to phosphorylated S/TP ( pS/TP ) motifs ( 33 ) , and isomerization of the pS @/@ TP bond is required for PP2A to efficiently dephosphorylate certain proteins , such as cdc25C , Myc , and C @-@ Raf ( 16 ) . # ::alignments 1-1.1.1.1.1 2-1.1.1 4-1.1.1 5-1.1 6-1.1.3 7-1.1.2.r 8-1.1.2.1 13-1.1.2 15-1.1.4.1.1.1 18-1 19-1.2.2 23-1.2.2.1.1 25-1.2.2.1 27-1.2 28-1.2.1.r 29-1.2.1.2.1.1 31-1.2.1.3 32-1.2.1 33-1.2.1.1.2 34-1.2.1.1 36-1.2.1.1.1.r 37-1.2.1.1.1.r 38-1.2.1.1.1.1.1.1 40-1.2.1.1.1.2.1.1 42-1.2.1.1.1 43-1.2.1.1.1.3.1.1 45-1.2.1.1.1.3.1.1 47-1.2.3.1.1.1 (a / and~e.18 :op1 (b / bind-01~e.5 :ARG1 (p7 / prolyl-isomerase~e.2,4 :name (n / name :op1 "Pin1"~e.1)) :ARG2~e.7 (p / protein-segment~e.13 :ARG3-of (p2 / phosphorylate-01~e.8) :mod (s2 / slash :op1 (a3 / amino-acid :name (n6 / name :op1 "serine")) :op2 (a4 / amino-acid :name (n7 / name :op1 "threonine")))) :ARG1-of (s / specific-02~e.6) :ARG1-of (d / describe-01 :ARG0 (p3 / publication :ARG1-of (c / cite-01 :ARG2 33~e.15)))) :op2 (r / require-01~e.27 :ARG0~e.28 (d2 / dephosphorylate-01~e.32 :ARG1 (p4 / protein~e.34 :example~e.36,37 (a2 / and~e.42 :op1 (e3 / enzyme :name (n3 / name :op1 "cdc25C"~e.38)) :op2 (p5 / protein :name (n4 / name :op1 "Myc"~e.40)) :op3 (e4 / enzyme :name (n5 / name :op1 "C-Raf"~e.43,45))) :mod (c3 / certain~e.33)) :ARG2 (e2 / enzyme :name (n2 / name :op1 "PP2A"~e.29)) :ARG2-of (e5 / efficient-01~e.31 :ARG1 e2)) :ARG1 (i / isomerize-01~e.19 :ARG1 (b2 / bond~e.25 :part-of p~e.23)) :ARG1-of (d3 / describe-01 :ARG0 (p6 / publication :ARG1-of (c2 / cite-01 :ARG2 16~e.47))))) # ::id bio.mskcc_0001.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Complex formation between B @-@ Raf and Pin1 correlated with the phosphorylation of B @-@ Raf on S/TP sites ( Fig . 1C ) and this interaction could be blocked when the MEK inhibitor U0126 was used to prevent ERK activation and the S/TP phosphorylation of B @-@ Raf ( Fig . 1D ) . # ::alignments 0-1.1.1.1 1-1.1.1 3-1.1.1.2.1.1.1 5-1.1.1.2.1.1.1 6-1.1.1.2 7-1.1.1.2.2.1.1 8-1.1 9-1.1.2.r 11-1.1.2 12-1.1.2.1.r 13-1.1.2.1.1 14-1.1.2.1.1 15-1.1.2.1.1 18-1.1.2.1 20-1.1.3.1 22-1.1.3.1.1 24-1 27-1.2 29-1.2.1 32-1.2.2.1.2.1.1.1 33-1.2.2.1 33-1.2.2.1.2 33-1.2.2.1.2.r 34-1.2.2.1.1.1 36-1.2.2 38-1.2.2.2 39-1.2.2.2.2.1.1.1.1 40-1.2.2.2.2.1 41-1.2.2.2.2 44-1.2.2.2.2.2 46-1.1.1.2.1.1.1 48-1.1.1.2.1.1.1 50-1.2.3.1 52-1.2.3.1.1 (a / and~e.24 :op1 (c / correlate-01~e.8 :ARG1 (f / form-01~e.1 :ARG1 (m / macro-molecular-complex~e.0) :ARG2 (a2 / and~e.6 :op1 (e / enzyme :name (n / name :op1 "B-Raf"~e.3,5,46,48)) :op2 (e2 / enzyme :name (n2 / name :op1 "Pin1"~e.7)))) :ARG2~e.9 (p / phosphorylate-01~e.11 :ARG1~e.12 (p2 / protein-segment~e.18 :part-of e~e.13,14,15 :mod (s2 / slash :op1 (a5 / amino-acid :name (n6 / name :op1 "serine")) :op2 (a6 / amino-acid :name (n7 / name :op1 "threonine"))))) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.20 :mod "1C"~e.22))) :op2 (p3 / possible-01~e.27 :ARG1 (b / block-01~e.29 :ARG1 f) :condition (u / use-01~e.36 :ARG1 (s / small-molecule~e.33 :name (n3 / name :op1 "U0126"~e.34) :ARG0-of~e.33 (i / inhibit-01~e.33 :ARG1 (p6 / protein-family :name (n4 / name :op1 "MEK"~e.32)))) :ARG2 (p4 / prevent-01~e.38 :ARG0 s :ARG1 (a3 / and~e.41 :op1 (a4 / activate-01~e.40 :ARG1 (e4 / enzyme :name (n5 / name :op1 "ERK"~e.39))) :op2 (p5 / phosphorylate-01~e.44 :ARG1 p2)))) :ARG1-of (d2 / describe-01 :ARG0 (f3 / figure~e.50 :mod "1D"~e.52)))) # ::id bio.mskcc_0001.13 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Together , these findings indicate that Pin1 is needed for the efficient dephosphorylation of B @-@ Raf and are consistent with the model that S/TP phosphorylation inhibits Raf signaling . # ::alignments 0-1.3 2-1.1.1.2 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 4-1.1 5-1.1.2.r 6-1.1.2.1.1.1 8-1.1.2 9-1.1.2.2.r 11-1.1.2.2.2 12-1.1.2.2 13-1.1.2.2.1.r 14-1.1.2.2.1.1.1 16-1.1.2.2.1.1.1 17-1 19-1.2 20-1.2.2.r 22-1.2.2 25-1.2.2.1.1 26-1.2.2.1 27-1.2.2.1.2.1.1.1 28-1.2.2.1.2 (a / and~e.17 :op1 (i / indicate-01~e.4 :ARG0 (t / thing~e.3 :ARG1-of~e.3 (f / find-01~e.3) :mod (t3 / this~e.2)) :ARG1~e.5 (n4 / need-01~e.8 :ARG1 (e / enzyme :name (n2 / name :op1 "Pin1"~e.6)) :purpose~e.9 (d / dephosphorylate-01~e.12 :ARG1~e.13 (e2 / enzyme :name (n / name :op1 "B-Raf"~e.14,16)) :ARG2-of (e3 / efficient-01~e.11)))) :op2 (c / consistent-01~e.19 :ARG1 t :ARG2~e.20 (m / model~e.22 :topic (i2 / inhibit-01~e.26 :ARG0 (p / phosphorylate-01~e.25 :ARG1 (p2 / protein-segment :mod (s2 / slash :op1 (a2 / amino-acid :name (n5 / name :op1 "serine")) :op2 (a3 / amino-acid :name (n6 / name :op1 "threonine"))))) :ARG1 (s / signal-07~e.28 :ARG0 (e4 / enzyme :name (n3 / name :op1 "Raf"~e.27)))))) :mod (t2 / together~e.0)) # ::id bio.mskcc_0001.14 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Eluting in HPLC fractions 78 to 79 was a peptide phosphorylated on S750 and T753 , the previously identified ERK sites , and eluting in fractions 26 and 58 to 59 were peptides phosphorylated at S151 and T401 , respectively . # ::alignments 0-1.1 3-1.1.2 4-1.1.2.1.1 6-1.1.2.1.2 9-1.1.1 10-1.1.1.1.4 17-1.1.1.1.3.2.1 18-1.1.1.1.3.2 19-1.1.1.1.3.1.1.1 20-1.1.1.1.3 22-1 23-1.1 23-1.2 23-1.3 25-1.1.2 25-1.2.2 25-1.3.2 26-1.2.2.1 27-1.1.2.1 27-1.3.2.1 28-1.3.2.1.1 30-1.3.2.1.2 32-1.1.1 32-1.2.1 32-1.3.1 33-1.1.1.2.3 36-1.3.2.1 (a / and~e.22 :op1 (e / elute-01~e.0,23 :ARG1 (p / peptide~e.9,32 :part (a2 / amino-acid :mod 750 :name (n / name :op1 "serine") :part-of (p4 / protein-segment~e.20 :part-of (e2 / enzyme :name (n3 / name :op1 "ERK"~e.19)) :ARG1-of (i / identify-01~e.18 :time (p5 / previous~e.17))) :ARG3-of p2~e.10) :part (a3 / amino-acid :mod 753 :name (n2 / name :op1 "threonine") :ARG3-of (p2 / phosphorylate-01~e.33) :part-of p4)) :ARG2 (f / fraction~e.3,25 :mod (b / between~e.27 :op1 78~e.4 :op2 79~e.6) :mod (c / chromatography :mod (l / liquid :ARG1-of (p10 / perform-02 :ARG1-of (h / high-02)))))) :op2 (e3 / elute-01~e.23 :ARG1 (p6 / peptide~e.32 :part (a5 / amino-acid :mod 151 :name (n4 / name :op1 "serine") :ARG3-of p2)) :ARG2 (f3 / fraction~e.25 :mod 26~e.26)) :op3 (e4 / elute-01~e.23 :ARG1 (p9 / peptide~e.32 :part (a6 / amino-acid :mod 401 :name (n5 / name :op1 "threonine") :ARG3-of p2)) :ARG2 (f4 / fraction~e.25 :mod (b2 / between~e.27,36 :op1 58~e.28 :op2 59~e.30)))) # ::id bio.mskcc_0001.15 ::amr-annotator SDL-AMR-09 ::preferred # ::tok All four of these identified sites are followed by a proline residue , and their phosphorylation could be blocked by pretreating cells with the MEK inhibitor U0126 ( Fig . 2A ) , suggesting that these residues are feedback targets of the proline @-@ directed kinase , ERK . # ::alignments 0-1.1.2.2 1-1.1.2.1 3-1.1.2.3 4-1.1.2.4 5-1.1.2 7-1.1 8-1.1.1.r 10-1.1.1.1.1.1 11-1.1.1 13-1 14-1.2.1.2.1 14-1.2.1.2.1.r 15-1.2.1.2 16-1.2 18-1.2.1 21-1.2.1.1.1 24-1.2.1.1.2.2.1.1.1 25-1.2.1.1.2 25-1.2.1.1.2.2 25-1.2.1.1.2.2.r 26-1.2.1.1.2.1.1 28-1.2.2.1 30-1.2.2.1.1 33-1.3 35-1.1.2.3 36-1.1.1 38-1.3.1 39-1.3.1.1.r 42-1.3.1.1 44-1.3.1.2.2 45-1.3.1.2 47-1.3.1.2.1.1 (a / and~e.13 :op1 (f / follow-01~e.7 :ARG1~e.8 (r / residue~e.11,36 :mod (a3 / amino-acid :name (n / name :op1 "proline"~e.10))) :ARG2 (p / protein-segment~e.5 :quant 4~e.1 :mod (a2 / all~e.0) :mod (t / this~e.3,35) :ARG1-of (i2 / identify-01~e.4))) :op2 (p2 / possible-01~e.16 :ARG1 (b / block-01~e.18 :ARG0 (t2 / treat-04 :ARG1 (c / cell~e.21) :ARG2 (s / small-molecule~e.25 :name (n2 / name :op1 "U0126"~e.26) :ARG0-of~e.25 (i / inhibit-01~e.25 :ARG1 (p4 / protein-family :name (n3 / name :op1 "MEK"~e.24)))) :time (b2 / before)) :ARG1 (p3 / phosphorylate-01~e.15 :ARG1~e.14 p~e.14)) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.28 :mod "2A"~e.30))) :ARG0-of (s2 / suggest-01~e.33 :ARG1 (f3 / feedback~e.38 :destination~e.39 r~e.42 :source (k / kinase~e.45 :name (n4 / name :op1 "ERK"~e.47) :ARG1-of (d2 / direct-01~e.44 :ARG2 p))))) # ::id bio.mskcc_0001.16 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Consistent with this model , we found that when purified activated ERK was incubated with kinase @-@ dead B @-@ Raf( K375M ) in vitro , ERK strongly phosphorylated B @-@ Raf on the S151 , S750 , and T753 sites , with phosphorylation of T401 also observed ( Fig . 2B ) . # ::alignments 0-1.3 1-1.3.1.r 2-1.3.1.1 3-1.3.1 5-1.1 6-1 9-1.2.3.1 10-1.2.3.1 11-1.2.3.1 13-1.2.3 14-1.2.3.2.r 15-1.2.3.2.3.2 18-1.2.3.2.1.1 21-1.2.3.2.2.1 23-1.2.3.3 24-1.2.3.3 26-1.2.1.2.1.1 27-1.2.1.3 28-1.2.1 29-1.2.3.2.1.1 31-1.2.3.2.1.1 38-1.2 38-1.2.1.1 42-1.2.r 43-1.2.2 46-1.2.2.3.1 47-1.2.2.3 49-1.2.4.1 51-1.2.4.1.1 (f / find-01~e.6 :ARG0 (w / we~e.5) :ARG1~e.42 (a6 / and~e.38 :op1 (p / phosphorylate-01~e.28 :ARG1 (a2 / and~e.38 :op1 (a3 / amino-acid :mod 151 :name (n4 / name :op1 "serine") :part-of e2) :op2 (a4 / amino-acid :mod 750 :name (n5 / name :op1 "serine") :part-of e2) :op3 (a5 / amino-acid :mod 753 :name (n6 / name :op1 "threonine") :part-of e2)) :ARG2 (e / enzyme :name (n / name :op1 "ERK"~e.26) :ARG1-of (a / activate-01) :ARG1-of (p2 / purify-01)) :ARG1-of (s / strong-02~e.27)) :op2 (p3 / phosphorylate-01~e.43 :ARG1 (a7 / amino-acid :mod 401 :name (n7 / name :op1 "threonine") :part-of e2) :ARG2 e :ARG1-of (o / observe-01~e.47 :mod (a8 / also~e.46))) :condition (i / incubate-01~e.13 :ARG1 e~e.9,10,11 :ARG2~e.14 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.18,29,31) :ARG2-of (m2 / mutate-01 :value "K375M"~e.21) :ARG0-of (f2 / function-01 :polarity - :ARG1 (k / kinase~e.15))) :manner (i2 / in-vitro~e.23,24)) :ARG1-of (d / describe-01 :ARG0 (f3 / figure~e.49 :mod "2B"~e.51))) :ARG1-of (c / consistent-01~e.0 :ARG2~e.1 (m / model~e.3 :mod (t / this~e.2)))) # ::id bio.mskcc_0001.17 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These findings are similar to what has been observed for C @-@ Raf ( 8 ) and suggest that feedback phosphorylation is a conserved mechanism used to disrupt the Ras @/@ Raf interaction . # ::alignments 0-1.1.1.2 1-1.1.1.1 3-1.1 5-1.1.1 5-1.1.2 8-1.1.2.1 9-1.1.2.2.r 10-1.1.2.2.1.1 12-1.1.2.2.1.1 14-1.1.3.1.1.1 16-1 17-1.2 18-1.2.2.r 19-1.2.2.3.1 20-1.2.2.3 21-1.2.2.3.r 23-1.2.2.1 24-1.2.2 25-1.2.2.2 27-1.2.2.2.1 29-1.2.2.2.1.2.1.1.1.1 31-1.2.2.2.1.2.1.2.1.1 32-1.2.2.2.1.2 (a / and~e.16 :op1 (r / resemble-01~e.3 :ARG1 (t / thing~e.5 :ARG1-of (f / find-01~e.1) :mod (t2 / this~e.0)) :ARG2 (t3 / thing~e.5 :ARG1-of (o / observe-01~e.8) :topic~e.9 (e / enzyme :name (n / name :op1 "C-Raf"~e.10,12))) :ARG1-of (d / describe-01 :ARG0 (p / publication :ARG1-of (c / cite-01 :ARG2 8~e.14)))) :op2 (s / suggest-01~e.17 :ARG0 t :ARG1~e.18 (m / mechanism~e.24 :ARG1-of (c2 / conserve-01~e.23) :ARG1-of (u / use-01~e.25 :ARG2 (d2 / disrupt-01~e.27 :ARG0 m :ARG1 (i / interact-01~e.32 :ARG0 (a2 / and :op1 (e3 / enzyme :name (n3 / name :op1 "Ras"~e.29)) :op2 (e2 / enzyme :name (n2 / name :op1 "Raf"~e.31)))))) :domain~e.21 (p3 / phosphorylate-01~e.20 :subevent-of (f2 / feedback~e.19))))) # ::id bio.mskcc_0001.18 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Consistent with these data , we found that B @-@ Raf interacted with C @-@ Raf in an inducible and transient manner following growth factor treatment ( Fig . 3B and C ) . # ::alignments 0-1.3 1-1.3.1.r 2-1.3.1.1 3-1.3.1 5-1.1 6-1 7-1.2.r 8-1.2.1.1.1 10-1.2.1.1.1 10-1.2.2.1.1 11-1.2 12-1.2.2.r 13-1.2.2.1.1 15-1.2.1.1.1 15-1.2.2.1.1 16-1.2.3.r 18-1.2.3 20-1.2.4 22-1.2.5 23-1.2.5.1.1 24-1.2.5.1.1 25-1.2.5.1 27-1.4.1.1 27-1.4.1.2 29-1.4.1.1.1 30-1.4.1 31-1.2.2.1.1 (f / find-01~e.6 :ARG0 (w / we~e.5) :ARG1~e.7 (i / interact-01~e.11 :ARG0 (e / enzyme :name (n / name :op1 "B-Raf"~e.8,10,15)) :ARG1~e.12 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.10,13,15,31)) :ARG2-of~e.16 (i2 / induce-01~e.18) :ARG1-of (t2 / transient-02~e.20) :ARG2-of (f4 / follow-01~e.22 :ARG1 (t3 / treat-04~e.25 :ARG2 (g / growth-factor~e.23,24)))) :ARG1-of (c / consistent-01~e.0 :ARG2~e.1 (d / data~e.3 :mod (t / this~e.2))) :ARG1-of (d2 / describe-01 :ARG0 (a2 / and~e.30 :op1 (f2 / figure~e.27 :mod "3B"~e.29) :op2 (f3 / figure~e.27 :mod "3C")))) # ::id bio.mskcc_0001.19 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In addition , when B @-@ Raf feedback phosphorylation was prevented , either by U0126 treatment or by mutation of all the feedback sites , an increase in the basal level of heterodimerization with C @-@ Raf was observed , and heterodimerization in response to growth factor treatment was increased and prolonged ( Fig . 3B and C ) . # ::alignments 0-1 0-1.1 0-1.1.r 1-1 1-1.1 1-1.1.r 4-1.1.4.2.1.1.1 6-1.1.4.2.1.1.1 7-1.1.4.2.2 8-1.1.4.2 10-1.1.4 13-1.1.4.1.r 14-1.1.4.1.1.1.1.1 15-1.1.4.1.1 16-1.1.4.1 18-1.1.4.1.2 19-1.1.4.1.2.1.r 20-1.1.4.1.2.1.3 22-1.1.4.1.2.1.2 23-1.1.4.1.2.1 26-1.1.1.1 27-1.1.1.1.1.r 29-1.1.1.1.1.1 30-1.1.1.1.1 31-1.1.1.1.1.2.r 32-1.1.1.1.1.2 33-1.1.1.1.1.2.2.r 34-1.1.1.1.1.2.2.1.1 36-1.1.1.1.1.2.2.1.1 38-1.1.1 40-1.1 41-1.1.2.1 42-1.1.2.1.1.r 43-1.1.2.1.1 44-1.1.2.1.1.1.r 45-1.1.2.1.1.1.1 46-1.1.2.1.1.1.1 47-1.1.2.1.1.1 49-1.1.2 50-1.1 50-1.1.5.1 51-1.1.3 53-1.1.5.1.1 53-1.1.5.1.2 55-1.1.5.1.1.1 56-1.1 56-1.1.5.1 57-1.1.1.1.1.2.2.1.1 (a2 / and~e.0,1 :op2~e.0,1 (a / and~e.0,1,40,50,56 :op1 (o / observe-01~e.38 :ARG1 (i / increase-01~e.26 :ARG1~e.27 (l / level~e.30 :mod (b / basal~e.29) :degree-of~e.31 (h / heterodimerize-01~e.32 :ARG1 e :ARG2~e.33 (e2 / enzyme :name (n3 / name :op1 "C-Raf"~e.34,36,57)))))) :op2 (i2 / increase-01~e.49 :ARG1 (h2 / heterodimerize-01~e.41 :ARG2-of~e.42 (r / respond-01~e.43 :ARG1~e.44 (t2 / treat-04~e.47 :ARG2 (g / growth-factor~e.45,46))))) :op3 (p / prolong-01~e.51 :ARG1 h2) :condition (p2 / prevent-01~e.10 :ARG0~e.13 (o2 / or~e.16 :op1 (t / treat-04~e.15 :ARG2 (s / small-molecule :name (n2 / name :op1 "U0126"~e.14))) :op2 (m / mutate-01~e.18 :ARG1~e.19 (p4 / protein-segment~e.23 :part-of e :destination-of f~e.22 :mod (a3 / all~e.20)))) :ARG1 (p3 / phosphorylate-01~e.8 :ARG1 (e / enzyme :name (n / name :op1 "B-Raf"~e.4,6)) :subevent-of (f / feedback~e.7))) :ARG1-of (d / describe-01 :ARG0 (a4 / and~e.50,56 :op1 (f2 / figure~e.53 :mod "3B"~e.55) :op2 (f3 / figure~e.53 :mod "3C"))))) # ::id bio.mskcc_0001.20 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These findings support a model whereby feedback phosphorylation disrupts Raf heterodimerization . # ::alignments 0-1.1.2 1-1.1 1-1.1.1 1-1.1.1.r 2-1 4-1.2 6-1.2.1.1.2 7-1.2.1.1 8-1.2.1 9-1.2.1.2.1.1.1 10-1.2.1.2 (s / support-01~e.2 :ARG0 (t / thing~e.1 :ARG1-of~e.1 (f / find-01~e.1) :mod (t2 / this~e.0)) :ARG1 (m / model~e.4 :topic (d / disrupt-01~e.8 :ARG0 (p / phosphorylate-01~e.7 :ARG1 e :subevent-of (f2 / feedback~e.6)) :ARG1 (h / heterodimerize-01~e.10 :ARG1 (e / enzyme :name (n / name :op1 "Raf"~e.9)))))) # ::id bio.mskcc_0001.21 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Unlike WT B @-@ Raf , oncogenic B @-@ Raf proteins have been shown to heterodimerize constitutively with C @-@ Raf in a Ras @-@ independent manner ( 11 ) . # ::alignments 0-1.2.3.1 1-1.2.1.2 2-1.1.1.1.1 2-1.2.1.1.1 4-1.1.1.1.1 4-1.2.1.1.1 6-1.1.1 6-1.1.1.2 6-1.1.1.2.1.2.1 6-1.1.1.2.r 7-1.1.1.1.1 9-1.1.1.1.1 9-1.1.2.1.1 13-1.1.5 14-1.1.1 14-1.1.1.2 14-1.1.1.2.r 15-1.1 15-1.2 16-1.1.3 16-1.2.3 17-1.1.2.r 18-1.1.2.1.1 20-1.1.1.1.1 20-1.1.2.1.1 21-1.1.4.r 23-1.1.4.2.1.1 25-1.1.4 25-1.1.4.1 25-1.1.4.1.r 28-1.1.5.1.1.1 (c5 / contrast-01 :ARG1 (h / heterodimerize-01~e.15 :ARG1 (e / enzyme~e.6,14 :name (n / name :op1 "B-Raf"~e.2,4,7,9,20) :ARG0-of~e.6,14 (c / cause-01~e.6,14 :ARG1 (d2 / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.6)))) :ARG2~e.17 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.9,18,20)) :mod (c3 / constitutive~e.16) :ARG0-of~e.21 (d / depend-01~e.25 :polarity~e.25 -~e.25 :ARG1 (e4 / enzyme :name (n3 / name :op1 "Ras"~e.23))) :ARG1-of (s / show-01~e.13 :ARG0 (p2 / publication :ARG1-of (c4 / cite-01 :ARG2 11~e.28)))) :ARG2 (h2 / heterodimerize-01~e.15 :ARG1 (e3 / enzyme :name (n4 / name :op1 "B-Raf"~e.2,4) :mod (w / wild-type~e.1)) :ARG2 e2 :mod (c6 / constitutive~e.16 :polarity -~e.0))) # ::id bio.mskcc_0001.22 ::amr-annotator SDL-AMR-09 ::preferred # ::tok When we next examined the effect of feedback phosphorylation on the ability of oncogenic B @-@ Raf to form heterodimers with C @-@ Raf , we found that the levels of endogenous C @-@ Raf associating with B @-@ Raf proteins of high ( V600E ) , intermediate ( G466A ) , and impaired ( D594G ) kinase activities all increased when the feedback sites were mutated , indicating that feedback phosphorylation also inhibits the heterodimerization of oncogenic B @-@ Raf proteins ( Fig . 3D ) . # ::alignments 0-1.3.3.r 1-1.1 2-1.3.3 3-1.3 5-1.3.2 6-1.3.2.1.r 7-1.3.2.1.1 8-1.3.2.1 13-1.3.2.2.1.1 13-1.3.2.2.1.1.2 13-1.3.2.2.1.1.2.1.2.1 13-1.3.2.2.1.1.2.r 14-1.3.2.2.1.1.1.1 16-1.3.2.2.1.1.1.1 16-1.3.2.2.1.2.1.1 17-1.3.2.2.1.1 17-1.3.2.2.1.1.2 17-1.3.2.2.1.1.2.r 21-1.3.2.2.1.2.1.1 23-1.3.2.2.1.1.1.1 23-1.3.2.2.1.2.1.1 25-1.1 26-1 27-1.2.r 29-1.2.1.1 29-1.2.1.2 29-1.2.1.3 31-1.2.1.1.1.3 31-1.2.1.2.1.3 31-1.2.1.3.1.3 32-1.2.1.1.1.1.1 32-1.2.1.2.1.1.1 32-1.2.1.3.1.1.1 34-1.2.1.1.1.1.1 34-1.2.1.1.1.2.1.1.1 34-1.2.1.2.1.1.1 34-1.2.1.2.1.2.1.1.1 34-1.2.1.3.1.1.1 34-1.2.1.3.1.2.1.1.1 35-1.2.1.1.1.2 35-1.2.1.2.1.2 35-1.2.1.3.1.2 37-1.2.1.1.1.2.1.1.1 37-1.2.1.2.1.2.1.1.1 37-1.2.1.3.1.2.1.1.1 37-1.2.2.1.1.1.1 39-1.2.1.1.1.1.1 39-1.2.1.1.1.2.1.1.1 39-1.2.1.2.1.1.1 39-1.2.1.2.1.2.1.1.1 39-1.2.1.3.1.1.1 39-1.2.1.3.1.2.1.1.1 39-1.2.2.1.1.1.1 40-1.2.2.1 41-1.2.1.1.1.2.1.r 41-1.2.1.1.1.r 42-1.2.1.1.1.2.1.3.2 44-1.2.1.1.1.2.1.2.1 47-1.2.1.2.1.2.1.3.2 49-1.2.1.2.1.2.1.2.1 52-1.2.1 53-1.2.1.3.1.2.1.3.1 55-1.2.1.3.1.2.1.2.1 57-1.2.1.1.1.2.1.3.1 57-1.2.1.2.1.2.1.3.1 58-1.2.1.3.1.2.1 58-1.2.1.3.1.2.1.3 58-1.2.1.3.1.2.1.3.r 60-1.2 61-1.3.3.r 63-1.2.2.1.2 64-1.2.2.1 66-1.2.1.1.1.2.1.2 66-1.2.1.2.1.2.1.2 66-1.2.1.3.1.2.1.2 66-1.2.2 68-1.2.3 69-1.2.3.1.r 70-1.2.3.1.1 71-1.2.3.1.1 72-1.2.3.1.3 73-1.2.3.1 75-1.2.3.1.2 75-1.3.2.2.1 77-1.3.2.2.1.1 77-1.3.2.2.1.1.2 77-1.3.2.2.1.1.2.1.2.1 77-1.3.2.2.1.1.2.r 78-1.2.1.3.1.2.1.1.1 78-1.2.2.1.1.1.1 78-1.3.2.2.1.1.1.1 80-1.2.1.3.1.1.1 80-1.2.1.3.1.2.1.1.1 80-1.2.2.1.1.1.1 80-1.3.2.2.1.1.1.1 80-1.3.2.2.1.2.1.1 81-1.2.2.1 83-1.2.4.1 85-1.2.1.3.1.r 85-1.2.4.1.1 (f / find-01~e.26 :ARG0 (w / we~e.1,25) :ARG1~e.27 (i / increase-01~e.60 :ARG1 (a / and~e.52 :op1 (l / level~e.29 :quant-of~e.41 (e / enzyme :name (n / name :op1 "C-Raf"~e.32,34,39) :ARG1-of (a2 / associate-01~e.35 :ARG2~e.41 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.34,37,39) :ARG2-of (m / mutate-01~e.66 :value "V600E"~e.44) :ARG0-of (a3 / act-01 :ARG1 (k / kinase~e.57) :ARG1-of (h / high-02~e.42)))) :mod (e7 / endogenous~e.31))) :op2 (l2 / level~e.29 :quant-of (e3 / enzyme :name (n3 / name :op1 "C-Raf"~e.32,34,39) :ARG1-of (a5 / associate-01~e.35 :ARG2 (e5 / enzyme :name (n5 / name :op1 "B-Raf"~e.34,37,39) :ARG2-of (m2 / mutate-01~e.66 :value "G466A"~e.49) :ARG0-of (a4 / act-01 :ARG1 (k2 / kinase~e.57) :degree (i2 / intermediate~e.47)))) :mod (e8 / endogenous~e.31))) :op3 (l3 / level~e.29 :quant-of~e.85 (e4 / enzyme :name (n4 / name :op1 "C-Raf"~e.32,34,39,80) :ARG1-of (a6 / associate-01~e.35 :ARG2 (e6 / enzyme~e.58 :name (n6 / name :op1 "B-Raf"~e.34,37,39,78,80) :ARG2-of (m3 / mutate-01~e.66 :value "D594G"~e.55) :ARG0-of~e.58 (a7 / activity-06~e.58 :ARG1-of (i3 / impair-01~e.53)))) :mod (e9 / endogenous~e.31)))) :condition (m4 / mutate-01~e.66 :ARG1 (p / protein-segment~e.40,64,81 :part-of (e10 / enzyme :name (n7 / name :op1 "B-Raf"~e.37,39,78,80)) :destination-of (f2 / feedback~e.63))) :ARG0-of (i4 / indicate-01~e.68 :ARG1~e.69 (i5 / inhibit-01~e.73 :ARG0 p2~e.70,71 :ARG1 (h3 / heterodimerize-01~e.75 :ARG1 e12 :ARG2 e13) :mod (a9 / also~e.72))) :ARG1-of (d / describe-01 :ARG0 (f4 / figure~e.83 :mod "3D"~e.85))) :manner (e11 / examine-01~e.3 :ARG0 w :ARG1 (a8 / affect-01~e.5 :ARG0~e.6 (p2 / phosphorylate-01~e.8 :subevent-of (f3 / feedback~e.7)) :ARG1 (p3 / possible-01 :ARG1 (h2 / heterodimerize-01~e.75 :ARG1 (e12 / enzyme~e.13,17,77 :name (n9 / name :op1 "B-Raf"~e.14,16,23,78,80) :ARG0-of~e.13,17,77 (c / cause-01~e.13,17,77 :ARG1 (d2 / disease :wiki "Cancer" :name (n11 / name :op1 "cancer"~e.13,77)))) :ARG2 (e13 / enzyme :name (n10 / name :op1 "C-Raf"~e.16,21,23,80))))) :time~e.0,61 (n8 / next~e.2))) # ::id bio.mskcc_0001.23 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Previous studies have shown that , for both normal and oncogenic B @-@ Raf proteins to heterodimerize with C @-@ Raf , the C @-@ terminal 14 @-@ 3 @-@ 3 binding site of C @-@ Raf ( S621 ) must be intact ( 11 , 27 ) ( Fig . 3E ) . # ::alignments 0-1.1.1 1-1.1 3-1 8-1.2.2.1.1 8-1.2.2.1.1.2 8-1.2.2.1.1.2.r 9-1.2 10-1.2.1.1.1 10-1.2.1.1.1.2 10-1.2.1.1.1.2.1.2.1 10-1.2.1.1.1.2.r 11-1.2.1.1.1.1.1 13-1.2.1.1.1.1.1 13-1.2.1.1.2.1.1 14-1.2.1.2.1.3 14-1.2.1.2.1.4.1 15-1.2.1.1.1 15-1.2.1.1.1.2 15-1.2.1.1.1.2.r 16-1.2.1.1 16-1.2.2.1 18-1.2.1.1.2.1.1 18-1.2.1.2.1.3.1.1 20-1.2.1.1.1.1.1 20-1.2.1.1.2.1.1 23-1.2.1.1.2.1.1 23-1.2.1.2.1.3.1.1 25-1.2.1.2.1.3.1.1 26-1.2.1.2.1.4.1.1.1 28-1.2.1.2.1.4.1.1.1 30-1.2.1.2.1.4.1.1.1 31-1.2.1.2.1.4 32-1.2.1.2.1.3 33-1.2.1.1.2.r 34-1.2.1.1.2.1.1 36-1.2.1.1.1.1.1 36-1.2.1.1.2.1.1 36-1.2.2.1.1.1.1 41-1.2.1.2.1.r 42-1.2.1.2 44-1.1.2.1.1 46-1.1.2.1.2 49-1.2.3.1 51-1.2.3.1.1 (s / show-01~e.3 :ARG0 (s2 / study~e.1 :time (p / previous~e.0) :ARG1-of (c / cite-01 :ARG2 (a / and :op1 11~e.44 :op2 27~e.46))) :ARG1 (a2 / and~e.9 :op1 (r / require-01 :ARG0 (h / heterodimerize-01~e.16 :ARG1 (e / enzyme~e.10,15 :name (n / name :op1 "B-Raf"~e.11,13,20,36) :ARG0-of~e.10,15 (c2 / cause-01~e.10,15 :ARG1 (d2 / disease :wiki "Cancer" :name (n8 / name :op1 "cancer"~e.10)))) :ARG2~e.33 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.13,18,20,23,34,36))) :ARG1 (i / intact~e.42 :domain~e.41 (a3 / amino-acid :mod 621 :name (n3 / name :op1 "serine") :part-of (p2 / protein-segment~e.14,32 :name (n4 / name :op1 "C-terminus"~e.18,23,25) :part-of e2) :ARG1-of (b / bind-01~e.31 :ARG2 (p3 / protein~e.14 :name (n5 / name :op1 "14-3-3"~e.26,28,30)))))) :op2 (r2 / require-01 :ARG0 (h2 / heterodimerize-01~e.16 :ARG1 (e3 / enzyme~e.8 :name (n6 / name :op1 "B-Raf"~e.36) :ARG1-of~e.8 (n7 / normal-02~e.8)) :ARG2 e2) :ARG1 i) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.49 :mod "3E"~e.51)))) # ::id bio.mskcc_0001.24 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To determine whether binding of 14 @-@ 3 @-@ 3 to B @-@ Raf is also required for heterodimerization , B @-@ Raf proteins containing lanine substitutions in the two 14 @-@ 3 @-@ 3 binding sites , S365 and S729 ( 2 ) , were examined for their abilities to heterodimerize with C @-@ Raf in response to growth factor treatment . # ::alignments 1-1.2 2-1.1.1 2-1.2.1.1 2-1.2.1.1.r 3-1.2.1.3 4-1.2.1.3.1.r 5-1.2.1.3.1 6-1.2.1.3.1 7-1.2.1.3.1 8-1.2.1.3.1 9-1.2.1.3.1 11-1.1.2.1.1.1 11-1.2.1.3.2.1.1 13-1.1.2.1.1.1 13-1.1.2.2.1.1 13-1.2.1.3.2.1.1 15-1.2.1.4 16-1.2.1 17-1.2.1.2.r 18-1.2.1.2 20-1.1.2.1.1.1 22-1.1.2.1.1.1 22-1.1.2.2.1.1 23-1.1.2.1.2.2.1.3.1 26-1.1.2.1.2 26-1.1.2.1.2.2 26-1.1.2.1.2.2.r 26-1.1.2.1.3 26-1.1.2.1.3.2 26-1.1.2.1.3.2.r 30-1.1.2.1.2.2.1.3.1.1.1 32-1.1.2.1.2.2.1.3.1.1.1 34-1.1.2.1.2.2.1.3.1.1.1 35-1.1.2.1.2.2.1.3 35-1.1.2.1.3.2.1.3 46-1 51-1.1.2 52-1.1.2.2.r 53-1.1.2.2.1.1 55-1.1.2.1.1.1 55-1.1.2.2.1.1 56-1.1.2.3.r 57-1.1.2.3 58-1.1.2.3.1.r 59-1.1.2.3.1.1 60-1.1.2.3.1.1 61-1.1.2.3.1 (e / examine-01~e.46 :ARG1 (p2 / possible-01 :mode interrogative~e.2 :ARG1 (h / heterodimerize-01~e.51 :ARG1 (e2 / enzyme :name (n / name :op1 "B-Raf"~e.11,13,20,22,55) :part (a / amino-acid~e.26 :name (n2 / name :op1 "alanine") :ARG1-of~e.26 (s / substitute-01~e.26 :ARG3 (a2 / amino-acid :mod 365 :name (n3 / name :op1 "serine") :ARG1-of (b / bind-01~e.35 :ARG2 (p / protein~e.23 :name (n6 / name :op1 "14-3-3"~e.30,32,34)))))) :part (a3 / amino-acid~e.26 :name (n4 / name :op1 "alanine") :ARG1-of~e.26 (s2 / substitute-01~e.26 :ARG2 (a4 / amino-acid :mod 729 :name (n5 / name :op1 "serine") :ARG1-of (b2 / bind-01~e.35 :ARG2 p))))) :ARG2~e.52 (e3 / enzyme :name (n7 / name :op1 "C-Raf"~e.13,22,53,55)) :ARG2-of~e.56 (r / respond-01~e.57 :ARG1~e.58 (t / treat-04~e.61 :ARG2 (g / growth-factor~e.59,60))))) :purpose (d / determine-01~e.1 :ARG1 (r2 / require-01~e.16 :mode~e.2 interrogative~e.2 :ARG0~e.17 (h2 / heterodimerize-01~e.18 :ARG1 e4 :ARG2 e3) :ARG1 (b3 / bind-01~e.3 :ARG1~e.4 p~e.5,6,7,8,9 :ARG2 (e4 / enzyme :name (n9 / name :op1 "B-Raf"~e.11,13))) :mod (a5 / also~e.15)))) # ::id bio.mskcc_0001.25 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Not surprisingly , given that mutation of the S365 14 @-@ 3 @-@ 3 binding site enhances the membrane localization of B @-@ Raf ( 2 ) , increased heterodimerization with C @-@ Raf was observed for S365A B @-@ Raf compared to WT B @-@ Raf ( Fig . 3F ) . # ::alignments 0-1.1.4.1 0-1.1.4.1.r 1-1.1.4 5-1.1.1.1 5-1.1.1.1.2 5-1.1.1.1.2.r 5-1.1.3.1.1 9-1.1.3.1.1.1.3.1.1.1 11-1.1.3.1.1.1.3.1.1.1 13-1.1.3.1.1.1.3.1.1.1 14-1.1.3.1.1.1.3 16-1.1.3.1 18-1.1.3.1.2.2 19-1.1.3.1.2 21-1.1.2.1.1.1 23-1.1.1.2.1.1 25-1.1.3.1.3.1.1.1 28-1.1 29-1.1.1 29-1.1.2 31-1.1.1.2.1.1 33-1.1.1.1.1.1 33-1.1.1.2.1.1 35-1 37-1.1.1.1.2.1 38-1.1.1.1.1.1 40-1.1.1.1.1.1 41-1.1.2.r 43-1.1.2.1.2 44-1.1.1.1.1.1 44-1.1.2.1.1.1 46-1.1.1.1.1.1 46-1.1.2.1.1.1 48-1.1.5.1 50-1.1.5.1.1 (o / observe-01~e.35 :ARG1 (i / increase-01~e.28 :ARG1 (h / heterodimerize-01~e.29 :ARG1 (e / enzyme~e.5 :name (n / name :op1 "B-Raf"~e.33,38,40,44,46) :ARG2-of~e.5 (m / mutate-01~e.5 :value "S365A"~e.37)) :ARG2 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.23,31,33))) :compared-to~e.41 (h2 / heterodimerize-01~e.29 :ARG1 (e3 / enzyme :name (n3 / name :op1 "B-Raf"~e.21,44,46) :mod (w / wild-type~e.43)) :ARG2 e2) :ARG1-of (c / cause-01 :ARG0 (e4 / enhance-01~e.16 :ARG0 (m2 / mutate-01~e.5 :ARG1 (a / amino-acid :mod 365 :name (n4 / name :op1 "serine") :ARG1-of (b / bind-01~e.14 :ARG2 (p / protein :name (n5 / name :op1 "14-3-3"~e.9,11,13))))) :ARG1 (b2 / be-located-at-91~e.19 :ARG1 e2 :ARG2 (m3 / membrane~e.18)) :ARG1-of (d / describe-01 :ARG0 (p2 / publication :ARG1-of (c2 / cite-01 :ARG2 2~e.25))))) :ARG0-of (s / surprise-01~e.1 :polarity~e.0 -~e.0) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.48 :mod "3F"~e.50)))) # ::id bio.mskcc_0001.26 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , S729A B @-@ Raf failed to heterodimerize with C @-@ Raf in response to growth factor treatment , and mutation of this site disrupted the constitutive interaction of oncogenic B @-@ Raf proteins and C @-@ Raf ( Fig . 3F ) , indicating that heterodimerization with C @-@ Raf is dependent on the C @-@ terminal S729 14 @-@ 3 @-@ 3 binding site of B @-@ Raf . # ::alignments 1-1 3-1.1.1.1.1.2.1 4-1.1.1.1.1.1.1 6-1.1.1.1.1.1.1 6-1.1.1.1.2.1.1 7-1.1.1 9-1.1.1.1 10-1.1.1.1.2.r 11-1.1.1.1.2.1.1 13-1.1.1.1.1.1.1 13-1.1.1.1.2.1.1 14-1.1.1.1.3.r 15-1.1.1.1.3 16-1.1.1.1.3.1.r 17-1.1.1.1.3.1.1 18-1.1.1.1.3.1.1 19-1.1.1.1.3.1 22-1.1.1.1.1 22-1.1.1.1.1.2 22-1.1.1.1.1.2.r 25-1.1.4.1.2.3 26-1.1.2 28-1.1.2.2.3 29-1.1.2.2 30-1.1.2.2.1.r 31-1.1.2.2.1 31-1.1.2.2.1.2 31-1.1.2.2.1.2.1.2.1 31-1.1.2.2.1.2.r 32-1.1.1.1.1.1.1 32-1.1.2.2.1.1.1 32-1.1.4.1.1.1.1.1 34-1.1.1.1.1.1.1 34-1.1.1.1.2.1.1 34-1.1.2.2.1.1.1 34-1.1.4.1.1.1.1.1 35-1.1.4.1.2.3 35-1.1.4.1.2.4.1 36-1.1 37-1.1.1.1.2.1.1 37-1.1.4.1.2.3.1.1 39-1.1.1.1.1.1.1 39-1.1.1.1.2.1.1 39-1.1.2.2.1.1.1 39-1.1.4.1.1.1.1.1 41-1.1.3.1 43-1.1.3.1.1 46-1.1.4 48-1.1.4.1.1 50-1.1.4.1.2.3.1.1 52-1.1.4.1.1.1.1.1 54-1.1.4.1 57-1.1.4.1.2.3.1.1 59-1.1.4.1.2.3.1.1 61-1.1.4.1.2.4.1.1.1 63-1.1.4.1.2.4.1.1.1 65-1.1.4.1.2.4.1.1.1 66-1.1.4.1.2.4 67-1.1.4.1.2.3 69-1.1.1.1.1.1.1 69-1.1.2.2.1.1.1 71-1.1.1.1.1.1.1 71-1.1.1.1.2.1.1 71-1.1.2.2.1.1.1 (c / contrast-01~e.1 :ARG2 (a / and~e.36 :op1 (f / fail-01~e.7 :ARG1 (h / heterodimerize-01~e.9 :ARG1 (e / enzyme~e.22 :name (n / name :op1 "B-Raf"~e.4,6,13,32,34,39,69,71) :ARG2-of~e.22 (m / mutate-01~e.22 :value "S729A"~e.3)) :ARG2~e.10 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.6,11,13,34,37,39,71)) :ARG0-of~e.14 (r / respond-01~e.15 :ARG1~e.16 (t / treat-04~e.19 :ARG2 (g / growth-factor~e.17,18))))) :op2 (d / disrupt-01~e.26 :ARG0 m :ARG1 (i / interact-01~e.29 :ARG0~e.30 (e3 / enzyme~e.31 :name (n4 / name :op1 "B-Raf"~e.32,34,39,69,71) :ARG0-of~e.31 (c2 / cause-01~e.31 :ARG1 (d4 / disease :wiki "Cancer" :name (n9 / name :op1 "cancer"~e.31)))) :ARG1 e2 :mod (c4 / constitutive~e.28))) :ARG1-of (d2 / describe-01 :ARG0 (f2 / figure~e.41 :mod "3F"~e.43)) :ARG0-of (i2 / indicate-01~e.46 :ARG1 (d3 / depend-01~e.54 :ARG0 (h2 / heterodimerize-01~e.48 :ARG1 (e4 / enzyme :name (n5 / name :op1 "B-Raf"~e.32,34,39,52)) :ARG2 e2) :ARG1 (a2 / amino-acid :mod 729 :name (n6 / name :op1 "serine") :part-of (p / protein-segment~e.25,35,67 :name (n7 / name :op1 "C-terminus"~e.37,50,57,59) :part-of e4) :ARG1-of (b / bind-01~e.66 :ARG2 (p2 / protein~e.35 :name (n8 / name :op1 "14-3-3"~e.61,63,65)))))))) # ::id bio.mskcc_0001.27 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Previous studies have found that all oncogenic B @-@ Raf proteins can activate C @-@ Raf and that heterodimerization with C @-@ Raf is required for kinase @-@ impaired oncogenic B @-@ Raf proteins to mediate ERK activation in vivo ( 31 ) . # ::alignments 0-1.1.1 1-1.1 3-1 4-1.2.r 5-1.2.1.1.1.2 6-1.2.1.1.1 6-1.2.1.1.1.3 6-1.2.1.1.1.3.1.2.1 6-1.2.1.1.1.3.r 7-1.2.1.1.1.1.1 9-1.2.1.1.1.1.1 9-1.2.1.1.2.1.1 11-1.2.1 12-1.2.1.1 13-1.2.1.1.2.1.1 15-1.2.1.1.1.1.1 15-1.2.1.1.2.1.1 16-1.2 17-1.2.r 18-1.2.2.2 19-1.2.2.2.2.r 20-1.2.2.2.2 22-1.2.1.1.1.1.1 22-1.2.1.1.2.1.1 22-1.2.2.1.1.1.1 24-1.2.2 28-1.2.2.1.1.3.2 29-1.2.2.1.1.2 30-1.2.1.1.1.1.1 32-1.2.1.1.1.1.1 34-1.2.1.1.1 34-1.2.1.1.1.3 34-1.2.1.1.1.3.r 35-1.2.2.1 36-1.2.2.1.2.1.1.1 37-1.2.2.1.1 37-1.2.2.1.1.3 37-1.2.2.1.1.3.r 37-1.2.2.1.2 38-1.2.2.1.2.2 39-1.2.2.1.2.2 41-1.3.1.1.1 (f / find-01~e.3 :ARG0 (s / study~e.1 :time (p / previous~e.0)) :ARG1~e.4,17 (a / and~e.16 :op1 (p2 / possible-01~e.11 :ARG1 (a2 / activate-01~e.12 :ARG0 (e / enzyme~e.6,34 :name (n / name :op1 "B-Raf"~e.7,9,15,22,30,32) :mod (a3 / all~e.5) :ARG0-of~e.6,34 (c / cause-01~e.6,34 :ARG1 (d2 / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.6)))) :ARG1 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.9,13,15,22)))) :op2 (r / require-01~e.24 :ARG0 (m / mediate-01~e.35 :ARG0 (e3 / enzyme~e.37 :name (n3 / name :op1 "B-Raf"~e.22) :ARG0-of c~e.29 :ARG0-of~e.37 (a5 / activate-01~e.37 :ARG1 e2 :ARG1-of (i / impair-01~e.28))) :ARG1 (a4 / activate-01~e.37 :ARG1 (e4 / enzyme :name (n4 / name :op1 "ERK"~e.36)) :manner (i2 / in-vivo~e.38,39))) :ARG1 (h / heterodimerize-01~e.18 :ARG1 e :ARG2~e.19 e2~e.20))) :ARG1-of (d / describe-01 :ARG0 (p3 / publication :ARG1-of (c3 / cite-01 :ARG2 31~e.41)))) # ::id bio.mskcc_0001.28 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Therefore , to further investigate both the impact of feedback phosphorylation and the contribution of heterodimerization to oncogenic B @-@ Raf function , we examined the transformation potential of oncogenic B @-@ Raf proteins containing mutations in either the feedback phosphorylation sites ( which exhibit increased heterodimerization ) or the S729 14 @-@ 3 @-@ 3 binding site ( which are unable to heterodimerize ) . # ::alignments 0-1 2-1.1.2.1.1 2-1.1.2.1.1.2 2-1.1.2.1.1.2.r 3-1.1.3.3 4-1.1.3 7-1.1.3.2.1 8-1.1.3.2.1.1.r 9-1.1.3.2.1.1.1 10-1.1.3.2.1.1 11-1.1.3.2 13-1.1.3.2.2 14-1.1.3.2.2.1.r 15-1.1.3.2.2.1 16-1.1.3.2.2.2.1 17-1.1.3.2.2.2.1 18-1.1.3.2.2.2.1 19-1.1.3.2.2.2.1 20-1.1.3.2.2.2.1 21-1.1.3.2.2.2 23-1.1.1 24-1.1 26-1.1.2.1 29-1.1.2.1.1 29-1.1.2.1.1.2 29-1.1.2.1.1.2.1.2.1 29-1.1.2.1.1.2.r 30-1.1.2.1.1.1.1 32-1.1.2.1.1.1.1 33-1.1.2.1.1.3.1.1 35-1.1.2.1.1.3 39-1.1.2.1.1.3.1.1.1.1 40-1.1.2.1.1.3.1.1.1 41-1.1.2.1.1.3.1.1 44-1.1.2.1.1.3.1.1.2 45-1.1.2.1.1.3.1.1.2.1.1 46-1.1.2.1.1.3.1.1.2.1 48-1.1.2.1.1.3.1 51-1.1.2.1.1.3.1.2.3.1.1.1 53-1.1.2.1.1.3.1.2.3.1.1.1 55-1.1.2.1.1.3.1.2.3.1.1.1 56-1.1.2.1.1.3.1.2.3 57-1.1.2.1.1.3.1.1 61-1.1.2 61-1.1.2.1.1.3.1.2.4.1 61-1.1.2.1.1.3.1.2.4.1.1 61-1.1.2.1.1.3.1.2.4.1.1.r 63-1.1.2.1.1.3.1.2 63-1.1.2.1.1.3.1.2.4 63-1.1.2.1.1.3.1.2.4.r (i / infer-01~e.0 :ARG1 (e / examine-01~e.24 :ARG0 (w / we~e.23) :ARG1 (p / possible-01~e.61 :ARG1 (t / transform-01~e.26 :ARG0 (e2 / enzyme~e.2,29 :name (n / name :op1 "B-Raf"~e.30,32) :ARG0-of~e.2,29 (c / cause-01~e.2,29 :ARG1 (d / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.29))) :ARG2-of (m / mutate-01~e.35 :ARG1 (o / or~e.48 :op1 (p2 / protein-segment~e.33,41,57 :ARG1-of (p3 / phosphorylate-01~e.40 :subevent-of (f / feedback~e.39)) :ARG0-of (e3 / exhibit-01~e.44 :ARG1 (h / heterodimerize-01~e.46 :ARG1-of (i2 / increase-01~e.45)))) :op2 (a / amino-acid~e.63 :mod 729 :name (n4 / name :op1 "serine") :ARG1-of (b / bind-01~e.56 :ARG2 (p4 / protein :name (n2 / name :op1 "14-3-3"~e.51,53,55))) :ARG0-of~e.63 (h2 / heterodimerize-01~e.63 :ARG1-of (p5 / possible-01~e.61 :polarity~e.61 -~e.61)))))))) :purpose (i3 / investigate-01~e.4 :ARG0 w :ARG1 (a2 / and~e.11 :op1 (i4 / impact-01~e.7 :ARG0~e.8 (p6 / phosphorylate-01~e.10 :subevent-of (f3 / feedback~e.9)) :ARG1 f4) :op2 (c4 / contribute-01~e.13 :ARG0~e.14 (h3 / heterodimerize-01~e.15) :ARG2 (f4 / function-01~e.21 :ARG0 e2~e.16,17,18,19,20))) :degree (f2 / further~e.3)))) # ::id bio.mskcc_0001.29 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For these studies , FBm or S729A mutations were incorporated into a number of oncogenic B @-@ Raf proteins that exhibit various levels of kinase activity . # ::alignments 1-1.3.1 2-1.3 5-1.1 6-1.1.2.2.1 7-1.1.1 7-1.1.1.2 7-1.1.1.2.r 7-1.1.2 7-1.1.2.2 7-1.1.2.2.r 9-1 9-1.1.1.3.1 10-1.1.1.3.2.1.r 10-1.2.r 12-1.2.3 13-1.2.3.r 14-1.2 14-1.2.2 14-1.2.2.1.2.1 14-1.2.2.r 15-1.1.1.1.1 15-1.1.2.1.1 15-1.2.1.1 17-1.1.1.1.1 17-1.1.2.1.1 17-1.2.1.1 18-1.1.1.3.2 20-1.2.4 21-1.2.4.1.1 22-1.2.4.1 23-1.2.4.1.2.r 24-1.2.4.1.2.1 25-1.2.4.1.2 (i / incorporate-02~e.9 :ARG1 (o / or~e.5 :op1 (e3 / enzyme~e.7 :name (n3 / name :op1 "B-Raf"~e.15,17) :ARG2-of~e.7 (m / mutate-01~e.7) :ARG1-of (h / have-part-91 :polarity -~e.9 :ARG2 (p / protein-segment~e.18 :destination-of~e.10 (f / feedback)))) :op2 (e4 / enzyme~e.7 :name (n4 / name :op1 "B-Raf"~e.15,17) :ARG2-of~e.7 (m2 / mutate-01~e.7 :value "S729A"~e.6))) :ARG2~e.10 (e / enzyme~e.14 :name (n / name :op1 "B-Raf"~e.15,17) :ARG0-of~e.14 (c / cause-01~e.14 :ARG1 (d / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.14))) :quant~e.13 (n2 / number~e.12) :ARG0-of (e2 / exhibit-01~e.20 :ARG1 (l / level~e.22 :mod (v / various~e.21) :degree-of~e.23 (a / activity-06~e.25 :ARG0 (k / kinase~e.24))))) :purpose (s / study~e.2 :mod (t / this~e.1))) # ::id bio.mskcc_0001.30 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The proteins were then expressed in NIH 3T3 cells and examined for their abilities to alter cell morphology and induce focus formation . # ::alignments 1-1.1.1 3-1.3 4-1.1 5-1.1.2.r 6-1.1.2.1.1 7-1.1.2.1.2 8-1.1.2 9-1 10-1.2 12-1.2.1.2.1.1 12-1.2.1.2.1.1.r 15-1.2.1.2.1 16-1.2.1.2.1.2.1 17-1.2.1.2.1.2 18-1.2.1.2 19-1.2.1.2.2 20-1.2.1.2.2.2.1 21-1.2.1.2.2.2 (a / and~e.9 :op1 (e / express-03~e.4 :ARG2 (p / protein~e.1) :ARG3~e.5 (c / cell-line~e.8 :name (n / name :op1 "NIH"~e.6 :op2 "3T3"~e.7))) :op2 (e2 / examine-01~e.10 :ARG1 (p2 / possible-01 :mode interrogative :ARG1 (a2 / and~e.18 :op1 (a3 / alter-01~e.15 :ARG0~e.12 p~e.12 :ARG1 (m / morphology~e.17 :mod (c2 / cell~e.16))) :op2 (i / induce-01~e.19 :ARG0 p :ARG2 (f / form-01~e.21 :ARG1 (f2 / focus~e.20)))))) :time (t / then~e.3)) # ::id bio.mskcc_0001.31 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 4A , the FBm or S729A mutation had no effect on transformation induced by the V600E or G469A B @-@ Raf protein , both of which possess high kinase activity . # ::alignments 1-1.4 2-1.4.1.r 3-1.4.1 4-1.4.1.1 8-1.2 9-1.2.2.1 10-1.2.1 10-1.2.2 10-1.3.1.1.1 10-1.3.1.1.1.2 10-1.3.1.1.1.2.r 10-1.3.1.1.2 10-1.3.1.1.2.2 10-1.3.1.1.2.2.r 11-1.2.1.1.2 12-1.1 12-1.1.r 12-1.2.1.1.2.1 12-1.2.1.1.2.1.r 13-1 14-1.3.r 15-1.3 16-1.3.1 17-1.3.1.1.r 19-1.3.1.1.1.2.1 20-1.3.1.1 21-1.3.1.1.2.2.1 22-1.2.1.1.1.1 22-1.3.1.1.1.1.1 22-1.3.1.1.2.1.1 24-1.2.1.1.1.1 24-1.3.1.1.1.1.1 24-1.3.1.1.2.1.1 25-1.2.1.1.2.2 31-1.3.1.1.3.1 33-1.3.1.1.3 (a2 / affect-01~e.13 :polarity~e.12 -~e.12 :ARG0 (o / or~e.8 :op1 (m / mutate-01~e.10 :ARG1 (e / enzyme :name (n / name :op1 "B-Raf"~e.22,24) :ARG1-of (h2 / have-part-91~e.11 :polarity~e.12 -~e.12 :ARG2 (p / protein-segment~e.25 :destination-of (f2 / feedback))))) :op2 (m3 / mutate-01~e.10 :value "S729A"~e.9)) :ARG1~e.14 (t / transform-01~e.15 :ARG2-of (i / induce-01~e.16 :ARG0~e.17 (o2 / or~e.20 :op1 (e2 / enzyme~e.10 :name (n2 / name :op1 "B-Raf"~e.22,24) :ARG2-of~e.10 (m4 / mutate-01~e.10 :value "V600E"~e.19)) :op2 (e3 / enzyme~e.10 :name (n3 / name :op1 "B-Raf"~e.22,24) :ARG2-of~e.10 (m5 / mutate-01~e.10 :value "G469A"~e.21)) :ARG0-of (a / activity-06~e.33 :ARG1-of (h / high-02~e.31))))) :ARG1-of (s / show-01~e.1 :ARG0~e.2 (f / figure~e.3 :mod "4A"~e.4))) # ::id bio.mskcc_0001.32 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , mutation of the feedback sites significantly increased the transforming activities of B @-@ Raf proteins with intermediate or impaired kinase activity ( Fig . 4A ) . # ::alignments 0-1 2-1.1.1 3-1.1.1.1.r 5-1.1.1.1.1 6-1.1.1.1 7-1.1.3 8-1.1 10-1.1.2.3 11-1.1.2.1 13-1.1.2.1.1.1.1 15-1.1.2.1.1.1.1 16-1.1.1.1 18-1.1.2.1.3 19-1.1.2 20-1.1.2.2.3 21-1.1.2.1.2 22-1.1.2.1 22-1.1.2.2 24-1.1.4.1 26-1.1.4.1.1 (c / contrast-01~e.0 :ARG2 (i / increase-01~e.8 :ARG0 (m / mutate-01~e.2 :ARG1~e.3 (p / protein-segment~e.6,16 :destination-of (f / feedback~e.5))) :ARG1 (o / or~e.19 :op1 (a / activity-06~e.11,22 :ARG0 (e / enzyme :name (n / name :op1 "B-Raf"~e.13,15)) :ARG1 (k / kinase~e.21) :degree (i3 / intermediate~e.18)) :op2 (a2 / activity-06~e.22 :ARG0 e :ARG1 k :ARG1-of (i2 / impair-01~e.20)) :ARG0-of (t / transform-01~e.10)) :ARG2 (s / significant-02~e.7) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.24 :mod "4A"~e.26)))) # ::id bio.mskcc_0001.33 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The total number of foci observed and , often , the sizes of the foci were increased , and cells within the foci exhibited a more transformed appearance . # ::alignments 1-1.1.1.1.1 2-1.1.1.1 3-1.1.1.1.1.1.r 4-1.1.1.1.1.1 5-1.1.1.1.1.1.1 6-1.1.1 8-1.1.2 11-1.1.1.2 12-1.1.1.2.1.r 14-1.1.1.2.1 16-1.1 18-1 18-1.1.1 19-1.2.1 22-1.2.1.1 23-1.2 25-1.2.2.2.1 26-1.2.2.2 27-1.2.2 (a / and~e.18 :op1 (i / increase-01~e.16 :ARG1 (a3 / and~e.6,18 :op1 (n / number~e.2 :ARG2-of (t / total-01~e.1 :ARG1~e.3 (f / focus~e.4 :ARG1-of (o / observe-01~e.5)))) :op2 (s / size~e.11 :poss~e.12 f~e.14)) :frequency (o2 / often~e.8)) :op3 (e / exhibit-01~e.23 :ARG0 (c / cell~e.19 :location f~e.22) :ARG1 (a2 / appear-02~e.27 :ARG1 c :ARG1-of (t2 / transform-01~e.26 :degree (m / more~e.25))))) # ::id bio.mskcc_0001.34 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , the S729A mutation reduced the transforming activities of the oncogenic proteins with intermediate or impaired kinase activity , causing a reduction in focus number and a flatter cell morphology ( Fig . 4A ) . # ::alignments 1-1 4-1.1.1.1 5-1.1.1 6-1.1 8-1.1.2.3 9-1.1.2.1 12-1.1.2.1.1.1 12-1.1.2.1.1.1.1.2.1 13-1.1.2.1.1 13-1.1.2.2.1 15-1.1.2.1.3 16-1.1.2 17-1.1.2.2.3 18-1.1.2.1.2 19-1.1.2.1 19-1.1.2.2 21-1.1.3 23-1.1.3.1.1 24-1.1.3.1.1.1.r 25-1.1.3.1.1.1.1 26-1.1.3.1.1.1 27-1.1.3.1 29-1.1.3.1.2.2 29-1.1.3.1.2.2.1 29-1.1.3.1.2.2.1.r 30-1.1.3.1.2.1 31-1.1.3.1.2 33-1.1.4.1 35-1.1.4.1.1 (c / contrast-01~e.1 :ARG2 (r / reduce-01~e.6 :ARG0 (m / mutate-01~e.5 :value "S729A"~e.4) :ARG1 (o2 / or~e.16 :op1 (a / activity-06~e.9,19 :ARG0 (p / protein~e.13 :ARG0-of (c2 / cause-01~e.12 :ARG1 (d2 / disease :wiki "Cancer" :name (n2 / name :op1 "cancer"~e.12)))) :ARG1 (k / kinase~e.18) :degree (i / intermediate~e.15)) :op2 (a2 / activity-06~e.19 :ARG0 (p2 / protein~e.13 :ARG0-of c2) :ARG1 k :ARG1-of (i2 / impair-01~e.17)) :ARG0-of (t / transform-01~e.8)) :ARG0-of (c4 / cause-01~e.21 :ARG1 (a4 / and~e.27 :op1 (r2 / reduce-01~e.23 :ARG1~e.24 (n / number~e.26 :quant-of (f / focus~e.25))) :op2 (m2 / morphology~e.31 :mod (c5 / cell~e.30) :ARG1-of (f2 / flat-06~e.29 :degree~e.29 (m3 / more~e.29))))) :ARG1-of (d / describe-01 :ARG0 (f3 / figure~e.33 :mod "4A"~e.35)))) # ::id bio.mskcc_0001.35 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Examination of activated phospho @-@ MEK levels revealed that the FBm and S729 mutations had no effect on MEK activation induced by the high @-@ activity V600E B @-@ Raf protein ; however , the FBm and S729A mutations increased and decreased , respectively , the abilities of the intermediate G466A and kinase @-@ impaired D594G B @-@ Raf proteins to activate MEK ( Fig . 4B ) , indicating a correlation between the transformation potential of these proteins and their ability to activate ERK cascade signaling in vivo . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.3 3-1.1.1.1.2 5-1.1.1.1.1.1 6-1.1.1 7-1 11-1.2.1.2 13-1.2.1.2.1 13-1.2.1.2.2 14-1.2.1.2.1.1.2 15-1.2.1.1 15-1.2.1.1.r 15-1.2.1.2.1.1.2.1 15-1.2.1.2.1.1.2.1.r 16-1.2.1 17-1.2.1.3.r 18-1.2.1.3.1.1.1 19-1.2.1.3 20-1.2.1.3.2 23-1.2.1.3.2.1.3.1 25-1.2.1.3.2.1.3 26-1.2.1.3.2.1.2.1 27-1.2.1.2.1.1.1.1 27-1.2.1.3.2.1.1.1 29-1.2.1.2.1.1.1.1 29-1.2.1.3.2.1.1.1 30-1.2.1.2.1.1.2.2 32-1.2 36-1.2.2.1.1 37-1.2.2.1.1.2.1 38-1.2.1.3.2.1 38-1.2.1.3.2.1.2 38-1.2.1.3.2.1.2.r 38-1.2.2.1.1.2 38-1.2.2.1.2.1.1.1 38-1.2.2.1.2.1.1.1.2 38-1.2.2.1.2.1.1.1.2.r 38-1.2.2.1.2.1.1.2 38-1.2.2.1.2.1.1.2.2 38-1.2.2.1.2.1.1.2.2.r 39-1.2.2.1 40-1.2.2 40-1.2.2.1.1 41-1.2.2.2 43-1.2.2.3 47-1.2.2.1.2.1.1.1.2.2.r 49-1.2.2.1.2.1.1.1.2.2 50-1.2.2.1.2.1.1.1.2.1 52-1.2.2.1.2.1.1.2.3.1 54-1.2.2.1.2.1.1.2.3 55-1.2.2.1.2.1.1.2.2.1 56-1.2.1.2.1.1.1.1 56-1.2.1.3.2.1.1.1 56-1.2.2.1.2.1.1.2.1.1 58-1.2.1.2.1.1.1.1 58-1.2.1.3.2.1.1.1 58-1.2.2.1.2.1.1.1.1.1 58-1.2.2.1.2.1.1.2.1.1 59-1.2.1.2.1.1.2.2 60-1.2.1.2.1.1.2.2.1.r 60-1.2.2.r 61-1.2.2.5.1.2.1 62-1.2.1.3.1.1.1 64-1.2.2.4.1 66-1.2.2.4.1.1 69-1.2.2.5 71-1.2.2.5.1 74-1.2.2.5.1.1.1 78-1.2.1.2.1.1.2.2 83-1.2.2.1.2.1 83-1.2.2.5.1.2.1 84-1.2.2.5.1.2.1.2.1.1.1 85-1.2.2.5.1.2.1.2.3 86-1.2.2.5.1.2.1.2 87-1.2.2.5.1.2.1.2.2 88-1.2.2.5.1.2.1.2.2 (r2 / reveal-01~e.7 :ARG0 (e / examine-01~e.0 :ARG1~e.1 (l / level~e.6 :degree-of (e2 / enzyme :name (n / name :op1 "MEK"~e.5) :ARG3-of (p / phosphorylate-01~e.3) :ARG1-of (a / activate-01~e.2)))) :ARG1 (c / contrast-01~e.32 :ARG1 (a2 / affect-01~e.16 :polarity~e.15 -~e.15 :ARG0 (a3 / and~e.11 :op1 (m7 / mutate-01~e.13 :ARG1 (e9 / enzyme :name (n2 / name :op1 "B-Raf"~e.27,29,56,58) :ARG1-of (h2 / have-part-91~e.14 :polarity~e.15 -~e.15 :ARG2 (p5 / protein-segment~e.30,59,78 :destination-of~e.60 (f2 / feedback))))) :op2 (m / mutate-01~e.13 :ARG1 (a11 / amino-acid :mod 729 :name (n9 / name :op1 "serine")))) :ARG1~e.17 (a4 / activate-01~e.19 :ARG1 (e3 / enzyme :name (n3 / name :op1 "MEK"~e.18,62)) :ARG2-of (i / induce-01~e.20 :ARG0 (e4 / enzyme~e.38 :name (n4 / name :op1 "B-Raf"~e.27,29,56,58) :ARG2-of~e.38 (m3 / mutate-01~e.38 :value "V600E"~e.26) :ARG0-of (a5 / activity-06~e.25 :ARG1-of (h / high-02~e.23)))))) :ARG2~e.60 (a6 / and~e.40 :op1 (i2 / increase-01~e.39 :ARG0 (a7 / and~e.36,40 :op1 m7 :op2 (m4 / mutate-01~e.38 :value "S729A"~e.37)) :ARG1 (p2 / possible-01 :ARG1 (a8 / activate-01~e.83 :ARG0 (a9 / and :op1 (e5 / enzyme~e.38 :name (n5 / name :op1 "B-Raf"~e.58) :ARG2-of~e.38 (m5 / mutate-01~e.38 :value "G466A"~e.50 :degree~e.47 (i3 / intermediate~e.49))) :op2 (e6 / enzyme~e.38 :name (n6 / name :op1 "B-Raf"~e.56,58) :ARG2-of~e.38 (m6 / mutate-01~e.38 :value "D594G"~e.55) :mod (i4 / impair-01~e.54 :ARG1 (k / kinase~e.52)))) :ARG1 e3))) :op2 (d / decrease-01~e.41 :ARG0 a7) :mod (r / respective~e.43) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.64 :mod "4B"~e.66)) :ARG0-of (i5 / indicate-01~e.69 :ARG1 (c2 / correlate-01~e.71 :ARG1 (p3 / possible-01 :ARG1 (t / transform-01~e.74 :ARG0 a9)) :ARG2 (p4 / possible-01 :ARG1 (a10 / activate-01~e.61,83 :ARG0 a9 :ARG1 (s / signal-07~e.86 :ARG0 (e8 / enzyme :name (n8 / name :op1 "ERK"~e.84)) :manner (i6 / in-vivo~e.87,88) :subevent-of (c3 / cascade~e.85))))))))) # ::id bio.mskcc_0001.36 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Not unexpectedly , for all of the oncogenic B @-@ Raf proteins , the S729A mutation , which disrupts heterodimerization with C @-@ Raf , caused a > 90 % decrease in C @-@ Raf activity levels ( Fig . 5B ) . # ::alignments 4-1.1.2.2 7-1.1.2.3 7-1.1.2.3.1.2.1 8-1.1.2.1.1 10-1.1.2.1.1 14-1.1.1 15-1.1 18-1.1.3 19-1.1.3.1 20-1.1.3.1.2.r 21-1.1.3.1.2.1.1 23-1.1.2.1.1 23-1.1.3.1.2.1.1 25-1 25-1.1.2.3 27-1.2.2 28-1.2.2.1.1 29-1.2.2.1 30-1.2 32-1.1.3.1.2.1.1 34-1.1.2.1.1 34-1.1.3.1.2.1.1 35-1.2.1.1 36-1.2.1 38-1.4.1 40-1.4.1.1 (c / cause-01~e.25 :ARG0 (m / mutate-01~e.15 :value "S729A"~e.14 :ARG2 (e / enzyme :name (n / name :op1 "B-Raf"~e.8,10,23,34) :mod (a / all~e.4) :ARG0-of (c2 / cause-01~e.7,25 :ARG1 (d4 / disease :wiki "Cancer" :name (n3 / name :op1 "cancer"~e.7)))) :ARG0-of (d / disrupt-01~e.18 :ARG1 (h / heterodimerize-01~e.19 :ARG1 e :ARG2~e.20 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.21,23,32,34))))) :ARG1 (d2 / decrease-01~e.30 :ARG1 (l / level~e.36 :degree-of (a2 / activity-06~e.35 :ARG0 e2)) :ARG2 (m2 / more-than~e.27 :op1 (p / percentage-entity~e.29 :value 90~e.28))) :ARG1-of (e3 / expect-01) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.38 :mod "5B"~e.40))) # ::id bio.mskcc_0001.37 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Together , these findings indicate a correlation between the changes in the transformation potentials of the intermediate and impaired oncogenic B @-@ Raf proteins and their abilities to heterodimerize and activate C @-@ Raf . # ::alignments 0-1.3 2-1.1.2 3-1.1 3-1.1.1 3-1.1.1.r 4-1 6-1.2 9-1.2.1 12-1.2.1.1.1 14-1.2.1.1.1.1.r 16-1.2.1.1.1.1.1.2 17-1.2.1.1.1.1 18-1.2.1.1.1.1.2.2 19-1.2.1.1.1.1.1 19-1.2.1.1.1.1.1.3 19-1.2.1.1.1.1.1.3.1.2.1 19-1.2.1.1.1.1.1.3.r 20-1.2.1.1.1.1.1.1.1 20-1.2.1.1.1.1.2.1.1 22-1.2.1.1.1.1.1.1.1 22-1.2.1.1.1.1.2.1.1 24-1.2.1.1.1.1 25-1.2.2.1 25-1.2.2.1.r 26-1.2.2 27-1.2.2.2.r 28-1.2.2.2.1 29-1.2.2.2 30-1.2.2.2.2 31-1.2.2.2.1.2.1.1 33-1.2.2.2.1.2.1.1 (i / indicate-01~e.4 :ARG0 (t / thing~e.3 :ARG1-of~e.3 (f / find-01~e.3) :mod (t2 / this~e.2)) :ARG1 (c / correlate-01~e.6 :ARG1 (c2 / change-01~e.9 :ARG1 (p / possible-01 :ARG1 (t4 / transform-01~e.12 :ARG0~e.14 (a / and~e.17,24 :op1 (e / enzyme~e.19 :name (n / name :op1 "B-Raf"~e.20,22) :mod (i2 / intermediate~e.16) :ARG0-of~e.19 (c3 / cause-01~e.19 :ARG1 (d / disease :wiki "Cancer" :name (n4 / name :op1 "cancer"~e.19)))) :op2 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.20,22) :ARG1-of (i3 / impair-01~e.18)))))) :ARG2 (c5 / capable-01~e.26 :ARG1~e.25 a~e.25 :ARG2~e.27 (a2 / and~e.29 :op1 (h / heterodimerize-01~e.28 :ARG1 a :ARG2 (e3 / enzyme :name (n3 / name :op1 "C-Raf"~e.31,33))) :op2 (a3 / activate-01~e.30 :ARG0 a :ARG1 e3)))) :mod (t3 / together~e.0)) # ::id bio.mskcc_0001.38 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To investigate the contributions of the various feedback sites to the overall effect of feedback phosphorylation on B @-@ Raf function , we generated a panel of mutants in which specific feedback phosphorylation sites were incorporated into either WT B @-@ Raf or the intermediate @-@ activity G466A B @-@ Raf protein . # ::alignments 1-1.3 3-1.3.2 3-1.3.2.1 3-1.3.2.1.r 4-1.3.2.1.1.r 6-1.3.2.1.1.1 7-1.3.2.1.1.2 8-1.3.2.1.1 9-1.3.2.1.1.2.r 9-1.3.2.1.2.r 11-1.3.2.1.2.3 12-1.3.2.1.2 13-1.3.2.1.2.1.r 14-1.3.2.1.2.1 15-1.3.2.1.2.1 17-1.2.1.1.1 17-1.2.1.2.1.1.2.1.1.1 17-1.3.2.1.2.2.1.1.1 19-1.2.1.1.1 19-1.2.1.2.1.1.2.1.1.1 19-1.3.2.1.2.2.1.1.1 20-1.3.2.1.2.2 22-1.1 23-1 25-1.2 26-1.2.1.r 27-1.2.1 27-1.2.1.2 27-1.2.1.2.1.1.2.2 27-1.2.1.2.1.1.2.2.2 27-1.2.1.2.1.1.2.2.2.r 27-1.2.1.2.r 30-1.2.1.2.1.1.1.2.2 31-1.2.1.2.1.1.1.2.1 32-1.2.1.2.1.1.1.2 33-1.2.1.2.1.1.1 35-1.2.1.2.1.1 36-1.3.2.1.1.2.r 38-1.2.1.2.1.1.2.1.2 39-1.2.1.2.1.1.2.1.1.1 39-1.2.1.2.1.1.2.2.1.1 41-1.2.1.2.1.1.2.1.1.1 41-1.2.1.2.1.1.2.2.1.1 42-1.2.1.2.1.1.2 44-1.2.1.2.1.1.2.2.3.1 46-1.2.1.2.1.1.2.2.3 47-1.2.1.2.1.1.2.2.2.1 48-1.2.1.2.1.1.2.2.1.1 50-1.2.1.2.1.1.2.2.1.1 51-1.2.1.2.1.1.1 (g / generate-01~e.23 :ARG0 (w / we~e.22) :ARG1 (p / panel~e.25 :consist-of~e.26 (e / enzyme~e.27 :name (n / name :op1 "B-Raf"~e.17,19) :ARG2-of~e.27 (m / mutate-01~e.27 :ARG1-of (c2 / cause-01 :ARG0 (i / incorporate-02~e.35 :ARG1 (p2 / protein-segment~e.33,51 :part-of e :ARG1-of (p3 / phosphorylate-01~e.32 :subevent-of (f / feedback~e.31) :ARG1-of (s / specific-02~e.30))) :ARG2 (o / or~e.42 :op1 (e2 / enzyme :name (n2 / name :op1 "B-Raf"~e.17,19,39,41) :mod (w2 / wild-type~e.38)) :op2 (e3 / enzyme~e.27 :name (n3 / name :op1 "B-Raf"~e.39,41,48,50) :ARG2-of~e.27 (m2 / mutate-01~e.27 :value "G466A"~e.47) :ARG0-of (a / activity-06~e.46 :degree (i2 / intermediate~e.44))))))))) :purpose (i3 / investigate-01~e.1 :ARG0 w :ARG1 (t / thing~e.3 :ARG1-of~e.3 (c / contribute-01~e.3 :ARG0~e.4 (p4 / protein-segment~e.8 :mod (v / various~e.6) :destination-of~e.9,36 f~e.7) :ARG2~e.9 (a2 / affect-01~e.12 :ARG0~e.13 p3~e.14,15 :ARG1 (f2 / function-01~e.20 :ARG0 (e4 / enzyme :name (n4 / name :op1 "B-Raf"~e.17,19))) :mod (o2 / overall~e.11)))))) # ::id bio.mskcc_0001.39 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The mutant proteins were then examined for their abilities to heterodimerize with C @-@ Raf and to bind activated Ras under conditions where feedback phosphorylation was induced ( in cycling cells for the G466A mutants and in cells treated with PDGF for 30 min for the WT B @-@ Raf mutants ) . # ::alignments 1-1.1.2.1.1.1 2-1.1.2.1.1 4-1.2 5-1 10-1.1.2.1 11-1.1.2.1.2.r 12-1.1.2.1.2.1.1 14-1.1.2.1.2.1.1 15-1.1.2 15-1.1.2.1.1.2.1 17-1.1.2.2 18-1.1.2.2.1.2 19-1.1.2.2.1.1.1 21-1.1.2.3.r 22-1.1.2.1.1.2.1.1.3.r 22-1.1.2.1.1.2.1.2.4.r 23-1.1.2.3.1.1 24-1.1.2.3.1 26-1.1.2.3 29-1.1.2.1.1.2.1.1.3.1 30-1.1.2.1.1.2.1.1.3 33-1.1.2.1.1.2.1.1.2.1 34-1.1.2.1.1.2.1.1 34-1.1.2.1.1.2.1.1.2 34-1.1.2.1.1.2.1.1.2.r 35-1.1.2.1.1.2.1 37-1.1.2.1.1.2.1.2.4 38-1.1.2.1.1.2.1.2.4.1 39-1.1.2.1.1.2.1.2.4.1.1.r 40-1.1.2.1.1.2.1.2.4.1.1.1.1 41-1.1.2.1.1.2.1.2.4.1.2.r 42-1.1.2.1.1.2.1.2.4.1.2.1 43-1.1.2.1.1.2.1.2.4.1.2.2 46-1.1.2.1.1.2.1.2.3 47-1.1.2.1.1.2.1.1.1.1 47-1.1.2.1.1.2.1.2.1.1 49-1.1.2.1.1.2.1.1.1.1 49-1.1.2.1.1.2.1.2.1.1 50-1.1.2.1.1.2.1.1 50-1.1.2.1.1.2.1.1.2 50-1.1.2.1.1.2.1.1.2.r (e / examine-01~e.5 :ARG1 (p2 / possible-01 :mode interrogative :ARG1 (a / and~e.15 :op1 (h / heterodimerize-01~e.10 :ARG1 (p / protein~e.2 :ARG2-of (m / mutate-01~e.1) :ARG1-of (m2 / mean-01 :ARG2 (a3 / and~e.15,35 :op1 (e4 / enzyme~e.34,50 :name (n3 / name :op1 "B-Raf"~e.47,49) :ARG2-of~e.34,50 (m3 / mutate-01~e.34,50 :value "G466A"~e.33) :location~e.22 (c / cell~e.30 :ARG1-of (c2 / cycle-02~e.29))) :op2 (e5 / enzyme :name (n4 / name :op1 "B-Raf"~e.47,49) :ARG2-of m :mod (w / wild-type~e.46) :location~e.22 (c3 / cell~e.37 :ARG1-of (t2 / treat-04~e.38 :ARG2~e.39 (p4 / protein :name (n5 / name :op1 "PDGF"~e.40)) :duration~e.41 (t3 / temporal-quantity :quant 30~e.42 :unit (m4 / minute~e.43)))))))) :ARG2~e.11 (e2 / enzyme :name (n / name :op1 "C-Raf"~e.12,14))) :op2 (b / bind-01~e.17 :ARG1 (e3 / enzyme :name (n2 / name :op1 "Ras"~e.19) :ARG1-of (a2 / activate-01~e.18))) :condition~e.21 (i / induce-01~e.26 :ARG2 (p3 / phosphorylate-01~e.24 :subevent-of (f / feedback~e.23))))) :time (t / then~e.4)) # ::id bio.mskcc_0001.40 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As shown in Fig. 6A , only mutation of the S151 feedback site , which is in close proximity to the Ras binding domain ( residues 155 to 227 ) , was found to significantly increase binding to activated Ras . # ::alignments 1-1.2 2-1.2.1.r 3-1.2.1 4-1.2.1.1 6-1.1.1.2 7-1.1.1 11-1.1.1.1.3.1 12-1.1.1.1.3 16-1.1.1.1.3.2.r 17-1.1.1.1.3.2 19-1.1.1.1.3.2.1.r 21-1.1.1.1.3.2.1.1.1.1.1 22-1.1.1.1.3.2.1.1 23-1.1.1.1.3.2.1 25-1.1.1.1.3.2.1.2.1.1 25-1.1.1.1.3.2.1.2.1.2 26-1.1.1.1.3.2.1.2.1.1.1.1 27-1.1.1.1.3.2.1.2.1.2.1.r 28-1.1.1.1.3.2.1.2.1.2.1.1 32-1 34-1.1.3 35-1.1 36-1.1.2 37-1.1.2.1.r 38-1.1.2.1.2 39-1.1.2.1.1.1 (f / find-01~e.32 :ARG1 (i / increase-01~e.35 :ARG0 (m / mutate-01~e.7 :ARG1 (a / amino-acid :mod 151 :name (n / name :op1 "serine") :part-of (p / protein-segment~e.12 :destination-of (f2 / feedback~e.11) :ARG1-of~e.16 (c / close-10~e.17 :ARG2~e.19 (d / domain~e.23 :ARG2-of (b / bind-01~e.22 :ARG1 (e / enzyme :name (n2 / name :op1 "Ras"~e.21))) :ARG1-of (m2 / mean-01 :ARG2 (v / value-interval :op1 (r / residue~e.25 :mod (a3 / amino-acid :value 155~e.26)) :op2 (r2 / residue~e.25 :mod~e.27 (a4 / amino-acid :value 227~e.28)))))))) :mod (o / only~e.6)) :ARG1 (b3 / bind-01~e.36 :ARG2~e.37 (e4 / enzyme :name (n5 / name :op1 "Ras"~e.39) :ARG1-of (a2 / activate-01~e.38))) :ARG2 (s / significant-02~e.34)) :ARG1-of (s2 / show-01~e.1 :ARG0~e.2 (f3 / figure~e.3 :mod "6A"~e.4))) # ::id bio.mskcc_0001.41 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast , mutation of S151A , T401A , and S750A T753A were all found to increase C @-@ Raf binding ( Fig . 6A ) , a finding consistent with peptide studies suggesting that there are multiple points of contact between heterodimerized B @- and C @-@ Raf proteins ( 27 ) . # ::alignments 1-1 3-1.1.1.1.1 3-1.1.1.1.2 3-1.1.1.1.3 3-1.1.1.1.4 5-1.1.1.1.1.1 7-1.1.1.1.2.1 9-1.1.1.1 10-1.1.1.1.3.1 11-1.1.1.1.4.1 14-1.1 16-1.1.1 17-1.1.1.2.1.1.1 19-1.1.1.2.1.1.1 20-1.1.1.2 22-1.1.1.3.1 24-1.1.1.3.1.1 28-1.1 29-1.1.2 30-1.1.2.1.r 31-1.1.2.1.1 32-1.1.2.1 33-1.1.2.1.2 37-1.1.2.1.2.1.3 40-1.1.2.1.2.1 43-1.1.2.1.2.1.1.1.1 46-1.1.2.1.2.1.2.1.1 48-1.1.2.1.2.1.1.1.1 48-1.1.2.1.2.1.2.1.1 51-1.1.2.1.3.1.1.1 (c / contrast-01~e.1 :ARG2 (f / find-01~e.14,28 :ARG1 (i / increase-01~e.16 :ARG0 (a / and~e.9 :op1 (m / mutate-01~e.3 :value "S151A"~e.5) :op2 (m2 / mutate-01~e.3 :value "T401A"~e.7) :op3 (m3 / mutate-01~e.3 :value "S750A"~e.10) :op4 (m4 / mutate-01~e.3 :value "T753A"~e.11)) :ARG1 (b / bind-01~e.20 :ARG1 (e / enzyme :name (n5 / name :op1 "C-Raf"~e.17,19))) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.22 :mod "6A"~e.24))) :ARG1-of (c2 / consistent-01~e.29 :ARG2~e.30 (s / study-01~e.32 :ARG1 (p / peptide~e.31) :ARG0-of (s2 / suggest-01~e.33 :ARG1 (c3 / contact-01~e.40 :ARG0 (e2 / enzyme :name (n6 / name :op1 "B-Raf"~e.43,48) :ARG1-of (h / heterodimerize-01)) :ARG1 (e3 / enzyme :name (n7 / name :op1 "C-Raf"~e.46,48) :ARG1-of h) :quant (m5 / multiple~e.37))) :ARG1-of (d2 / describe-01 :ARG0 (p2 / publication :ARG1-of (c4 / cite-01 :ARG2 27~e.51))))))) # ::id bio.mskcc_0001.42 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Interestingly , when the S729A mutation was introduced into the FBm mutant , binding to C @-@ Raf was abolished ( Fig . 6A ) , indicating that the increased heterodimerization observed when the feedback sites are mutated is still dependent on 14 @-@ 3 @-@ 3 binding . # ::alignments 0-1.4 0-1.4.r 2-1.3.r 4-1.3.1.1 5-1.3.1 5-1.3.2 5-1.3.2.3 5-1.3.2.3.r 7-1.3 8-1.3.2.4.2.1.r 11-1.3.1 11-1.3.2 11-1.3.2.3 11-1.3.2.3.r 13-1.1 14-1.1.1.r 15-1.1.1.2.1 17-1.1.1.2.1 17-1.3.2.2.1 19-1 21-1.2.1 23-1.2.1.1 26-1.5 27-1.5.1.r 29-1.5.1.1.1 30-1.5.1.1 31-1.5.1.1.2 32-1.5.1.1.2.1.r 34-1.3.2.4.2.1 34-1.5.1.1.2.1.1.1 35-1.3.2.4.2 35-1.5.1.1.2.1.1 37-1.5.1.1.2.1 39-1.5.1.3 40-1.5.1 41-1.5.1.2.r 42-1.5.1.2.1.2.1 44-1.5.1.2.1.2.1 46-1.5.1.2.1.2.1 47-1.5.1.2 (a / abolish-01~e.19 :ARG1 (b / bind-01~e.13 :ARG2~e.14 (e / enzyme :wiki "C-Raf" :name (n / name :op1 "C-Raf"~e.15,17))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.21 :mod "6A"~e.23)) :time~e.2 (i / introduce-02~e.7 :ARG1 (m / mutate-01~e.5,11 :value "S729A"~e.4) :ARG2 (e2 / enzyme~e.5,11 :wiki - :name (n3 / name :op1 "B-Raf"~e.17) :ARG2-of~e.5,11 (m2 / mutate-01~e.5,11) :ARG1-of (h2 / have-part-91 :polarity - :ARG2 (p / protein-segment~e.35 :destination-of~e.8 (f3 / feedback~e.34))))) :manner~e.0 (i2 / interesting~e.0) :ARG0-of (i3 / indicate-01~e.26 :ARG1~e.27 (d2 / depend-01~e.40 :ARG0 (h / heterodimerize-01~e.30 :ARG1-of (i4 / increase-01~e.29) :ARG1-of (o / observe-01~e.31 :time~e.32 (m3 / mutate-01~e.37 :ARG1 (p2 / protein-segment~e.35 :destination-of (f2 / feedback~e.34))))) :ARG1~e.41 (b2 / bind-01~e.47 :ARG2 (p3 / protein :wiki "14-3-3_protein" :name (n4 / name :op1 "14-3-3"~e.42,44,46))) :mod (s / still~e.39)))) # ::id bio.mskcc_0001.43 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Given that oncogenic B @-@ Raf proteins are targets of feedback phosphorylation , we next examined whether they might also be dephosphorylated and recycled in a manner involving the PP2A phosphatase and the Pin1 prolyl @-@ isomerase . # ::alignments 2-1.3 2-1.3.1.2 2-1.3.1.2.2 2-1.3.1.2.2.1.2.1 2-1.3.1.2.2.r 3-1.3.1.2.1.1 5-1.3.1.2.1.1 8-1.3.1 9-1.3.1.1.r 10-1.3.1.1.1 11-1.3.1.1 13-1.1 14-1.4 15-1 16-1.2.1 16-1.2.1.r 18-1.2 19-1.2.2.3 21-1.2.2.1 22-1.2.2 23-1.2.2.2 24-1.2.2.r 26-1.2.2.4.r 27-1.2.2.4 29-1.2.2.4.1.1.1.1 30-1.2.2.4.1.1 31-1.2.2.4.1 33-1.2.2.4.1.2.1.1 34-1.2.2.4.1.2 36-1.2.2.4.1.2 (e / examine-01~e.15 :ARG0 (w / we~e.13) :ARG1 (p2 / possible-01~e.18 :mode~e.16 interrogative~e.16 :ARG1~e.24 (a / and~e.22 :op1 (d / dephosphorylate-01~e.21 :ARG1 e2) :op2 (r / recycle-01~e.23 :ARG1 e2) :mod (a2 / also~e.19) :manner~e.26 (i / involve-01~e.27 :ARG1 (a3 / and~e.31 :op1 (p4 / phosphatase~e.30 :name (n2 / name :op1 "PP2A"~e.29)) :op2 (p3 / prolyl-isomerase~e.34,36 :name (n3 / name :op1 "Pin1"~e.33))) :ARG2 a))) :ARG1-of (c / cause-01~e.2 :ARG0 (t / target-01~e.8 :ARG0~e.9 (p / phosphorylate-01~e.11 :subevent-of (f / feedback~e.10)) :ARG1 (e2 / enzyme~e.2 :name (n / name :op1 "B-Raf"~e.3,5) :ARG0-of~e.2 (c2 / cause-01~e.2 :ARG1 (d2 / disease :wiki "Cancer" :name (n5 / name :op1 "cancer"~e.2)))))) :time (n4 / next~e.14)) # ::id bio.mskcc_0001.44 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As indicated in Fig. 7A , when PP2A was inhibited with okadaic acid treatment , slower @-@ migrating forms of the V600E , G466A , and D594G B @-@ Raf proteins were found to accumulate . # ::alignments 1-1.2 2-1.2.1.r 3-1.2.1 4-1.2.1.1 7-1.1.2.1.1.1 9-1.1.2 10-1.1.2.2.r 11-1.1.2.2.1.1.1 12-1.1.2.2.1.1.2 13-1.1.2.2 15-1.1.1.4.1 15-1.1.1.4.1.1 15-1.1.1.4.1.1.r 17-1.1.1.4 21-1.1.1.1.2.1 23-1.1.1.2.2.1 25-1.1.1 26-1.1.1.3.2.1 27-1.1.1.1.1.1 27-1.1.1.2.1.1 27-1.1.1.3.1.1 29-1.1.1.1.1.1 29-1.1.1.2.1.1 29-1.1.1.3.1.1 32-1 34-1.1 (f / find-01~e.32 :ARG1 (a / accumulate-01~e.34 :ARG1 (a2 / and~e.25 :op1 (e2 / enzyme :name (n / name :op1 "B-Raf"~e.27,29) :ARG2-of (m / mutate-01 :value "V600E"~e.21)) :op2 (e3 / enzyme :name (n4 / name :op1 "B-Raf"~e.27,29) :ARG2-of (m4 / mutate-01 :value "G466A"~e.23)) :op3 (e4 / enzyme :name (n5 / name :op1 "B-Raf"~e.27,29) :ARG2-of (m5 / mutate-01 :value "D594G"~e.26)) :ARG0-of (m2 / migrate-01~e.17 :ARG1-of (s / slow-05~e.15 :degree~e.15 (m3 / more~e.15)))) :condition (i / inhibit-01~e.9 :ARG1 (e / enzyme :name (n3 / name :op1 "PP2A"~e.7)) :instrument~e.10 (t / treat-04~e.13 :ARG2 (s2 / small-molecule :name (n2 / name :op1 "okadaic"~e.11 :op2 "acid"~e.12))))) :ARG1-of (i2 / indicate-01~e.1 :ARG0~e.2 (f2 / figure~e.3 :mod "7A"~e.4))) # ::id bio.mskcc_0001.45 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Moreover , given their constitutive phosphorylation on S/TP sites ( Fig . 3D ) , these oncogenic B @-@ Raf mutants were found to interact constitutively with Pin1 ( Fig . 7B ) , indicating that oncogenic B @-@ Raf proteins are dephosphorylated and recycled . # ::alignments 0-1 4-1.1.1.6.1.2 5-1.1.1.6.1 8-1.1.1.6.1.1 10-1.1.1.6.1.3.1 12-1.1.1.6.1.3.1.1 15-1.1.1.1.4 16-1.1.1.1.3 16-1.1.1.1.3.1.2.1 17-1.1.1.1.1.1 19-1.1.1.1.1.1 20-1.1.1.1 20-1.1.1.1.2 20-1.1.1.1.2.r 22-1.1 23-1.1.1.1.3 23-1.1.1.6 24-1.1.1 25-1.1.1.3 26-1.1.1.2.r 27-1.1.1.2.1.1 29-1.1.1.4.1 31-1.1.1.4.1.1 34-1.1.1.5 36-1.1.1.1.3 36-1.1.1.1.3.1.2.1 36-1.1.1.6 37-1.1.1.6.1.1.1 38-1.1.1.6.1.1.1 39-1.1.1.6.1.1.1 40-1.1.1.6.1.1 42-1.1.1.5.1.1 43-1.1.1.5.1 44-1.1.1.5.1.2 (a / and~e.0 :op2 (f / find-01~e.22 :ARG1 (i / interact-01~e.24 :ARG0 (e / enzyme~e.20 :name (n / name :op1 "B-Raf"~e.17,19) :ARG2-of~e.20 (m / mutate-01~e.20) :ARG0-of (c3 / cause-01~e.16,23,36 :ARG1 (d4 / disease :wiki "Cancer" :name (n3 / name :op1 "cancer"~e.16,36))) :mod (t / this~e.15)) :ARG1~e.26 (e2 / enzyme :name (n2 / name :op1 "Pin1"~e.27)) :mod (c5 / constitutive~e.25) :ARG1-of (d2 / describe-01 :ARG0 (f3 / figure~e.29 :mod "7B"~e.31)) :ARG0-of (i2 / indicate-01~e.34 :ARG1 (a2 / and~e.43 :op1 (d3 / dephosphorylate-01~e.42 :ARG1 e) :op2 (r / recycle-01~e.44 :ARG1 e))) :ARG1-of (c / cause-01~e.23,36 :ARG0 (p / phosphorylate-01~e.5 :ARG2 (p2 / protein-segment~e.8,40 :part-of e~e.37,38,39 :mod (s / slash :op1 (a3 / amino-acid :name (n4 / name :op1 "serine")) :op2 (a4 / amino-acid :name (n5 / name :op1 "threonine")))) :mod (c2 / constitutive~e.4) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.10 :mod "3D"~e.12))))))) # ::id bio.mskcc_0001.46 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Consistent with the model that Pin1 influences B @-@ Raf signaling by facilitating the dephosphorylation of the feedback sites , overexpression of the Pin1 proteins had no effect on the transformation potential of G466A FBm @-@ B @-@ Raf , which lacks the sites of feedback phosphorylation . # ::alignments 0-1.4 1-1.4.1.r 3-1.4.1 5-1.4.1.1.1 6-1.4.1.1 7-1.4.1.1.2.1.1.1 9-1.4.1.1.2.1.1.1 10-1.4.1.1.2 11-1.4.1.1.3.r 12-1.4.1.1.3 14-1.4.1.1.3.2 15-1.4.1.1.3.2.1.r 17-1.4.1.1.3.2.1.2 18-1.4.1.1.3.2.1 20-1.2 21-1.2.1.r 23-1.2.1.1.1 24-1.3.1.1.3.2 25-1.3.1.1.3 26-1.1 26-1.1.r 26-1.3.1.1.3.1 26-1.3.1.1.3.1.r 27-1 30-1.3.1 33-1.3.1.1.2.1 36-1.3.1.1.1.1 36-1.4.1.1.2.1.1.1 38-1.3.1.1.1.1 38-1.4.1.1.2.1.1.1 43-1.4.1.1.3.2.1 44-1.3.1.1.3.2.1.r 45-1.3.1.1.3.2.1.1 46-1.3.1.1.3.2.1 (a / affect-01~e.27 :polarity~e.26 -~e.26 :ARG0 (o / overexpress-01~e.20 :ARG1~e.21 (e2 / enzyme :name (n / name :op1 "Pin1"~e.23))) :ARG1 (p / possible-01 :ARG1 (t2 / transform-01~e.30 :ARG0 (e3 / enzyme :name (n2 / name :op1 "B-Raf"~e.36,38) :ARG2-of (m / mutate-01 :value "G466A"~e.33) :ARG1-of (h / have-part-91~e.25 :polarity~e.26 -~e.26 :ARG2 (p2 / protein-segment~e.24 :ARG1-of~e.44 (p3 / phosphorylate-01~e.46 :subevent (f / feedback~e.45))))))) :ARG1-of (c / consistent-01~e.0 :ARG2~e.1 (m2 / model~e.3 :topic (i / influence-01~e.6 :ARG0 e2~e.5 :ARG1 (s / signal-07~e.10 :ARG0 (e5 / enzyme :name (n4 / name :op1 "B-Raf"~e.7,9,36,38))) :manner~e.11 (f2 / facilitate-01~e.12 :ARG0 (e4 / enzyme) :ARG1 (d / dephosphorylate-01~e.14 :ARG1~e.15 (p4 / protein-segment~e.18,43 :part-of e5 :destination-of (f3 / feedback~e.17)))))))) # ::id bio.mskcc_0001.47 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Previous studies have found that both the C @-@ Raf and B @-@ Raf proteins are targets of ERK @-@ dependent feedback phosphorylation # ::alignments 0-1.1.1 1-1.1 3-1 7-1.2.2.1.1.1 9-1.2.2.1.1.1 9-1.2.2.2.1.1 10-1.2.2 11-1.2.2.2.1.1 13-1.2.2.1.1.1 13-1.2.2.2.1.1 16-1.2 17-1.2.1.r 18-1.2.1.2.1.1.1 20-1.2.1.2 21-1.2.1.1 22-1.2.1 (f / find-01~e.3 :ARG0 (s / study~e.1 :time (p / previous~e.0)) :ARG1 (t / target-01~e.16 :ARG0~e.17 (p2 / phosphorylate-01~e.22 :subevent-of (f2 / feedback~e.21) :ARG0-of (d / depend-01~e.20 :ARG1 (e / enzyme :name (n / name :op1 "ERK"~e.18)))) :ARG1 (a / and~e.10 :op1 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.7,9,13)) :op2 (e3 / enzyme :name (n3 / name :op1 "B-Raf"~e.9,11,13))))) # ::id bio.mskcc_0001.48 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In the case of C @-@ Raf , six sites of feedback phosphorylation have been identified , five of which are direct targets of activated ERK ( 8 ) # ::alignments 4-1.1.2.1.1 6-1.1.2.1.1 8-1.1.1 9-1.1 9-1.1.4.1 10-1.1.3.r 11-1.1.3.1 12-1.1.3 15-1 17-1.1.4.1.1 21-1.1.4.1.2.2 22-1.1.4.1.2 23-1.1.4.1.2.1.r 24-1.1.4.1.2.1.2 25-1.1.4.1.2.1.1.1 27-1.2.1.1.1 (i / identify-01~e.15 :ARG1 (p / protein-segment~e.9 :quant 6~e.8 :part-of (e / enzyme :name (n / name :op1 "C-Raf"~e.4,6)) :ARG1-of~e.10 (p2 / phosphorylate-01~e.12 :subevent-of (f / feedback~e.11)) :ARG2-of (i2 / include-91 :ARG1 (p3 / protein-segment~e.9 :quant 5~e.17 :ARG1-of (t / target-01~e.22 :ARG0~e.23 (e2 / enzyme :name (n2 / name :op1 "ERK"~e.25) :ARG1-of (a / activate-01~e.24)) :ARG1-of (d / direct-02~e.21))))) :ARG1-of (d2 / describe-01 :ARG0 (p4 / publication :ARG1-of (c / cite-01 :ARG2 8~e.27)))) # ::id bio.mskcc_0001.49 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For B @-@ Raf , previous work by Brummer et al. ( 3 ) identified the C @-@ terminal S750 and T753 residues as sites phosphorylated by activated ERK . # ::alignments 1-1.2.1.2.2.1.1 3-1.2.1.2.2.1.1 5-1.1.1.2 6-1.1 6-1.1.1 6-1.1.1.r 7-1.1.1.1.r 8-1.1.1.1.1.1.1 9-1.1.1.1 10-1.1.1.1.2.1 12-1.1.2.1 14-1 16-1.2.1.2.1.1 18-1.2.1.2.1.1 20-1.2 22-1.2.1 22-1.2.2 23-1.1.1.2.r 23-1.3.r 24-1.3.1 25-1.3 26-1.3.2.r 27-1.3.2.2 28-1.3.2.1.1 (i / identify-01~e.14 :ARG0 (p / publication~e.6 :ARG1-of~e.6 (w / work-12~e.6 :ARG0~e.7 (a / and~e.9 :op1 (p2 / person :name (n / name :op1 "Brummer"~e.8)) :op2 (p3 / person :mod (o / other~e.10))) :time~e.23 (p6 / previous~e.5)) :ARG1-of (c / cite-01 :ARG2 3~e.12)) :ARG1 (a2 / and~e.20 :op1 (r / residue~e.22 :mod (a3 / amino-acid :mod 750 :name (n2 / name :op1 "serine")) :part-of (p4 / protein-segment :name (n4 / name :op1 "C-terminus"~e.16,18) :part-of (e2 / enzyme :name (n6 / name :op1 "B-Raf"~e.1,3)))) :op2 (r2 / residue~e.22 :mod (a4 / amino-acid :mod 753 :name (n3 / name :op1 "threonine")) :part-of p4)) :ARG2~e.23 (p5 / phosphorylate-01~e.25 :ARG1 a2~e.24 :ARG2~e.26 (e / enzyme :name (n5 / name :op1 "ERK"~e.28) :ARG1-of (a5 / activate-01~e.27)))) # ::id bio.mskcc_0001.50 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Through metabolic labeling experiments , we find here that in addition to the S750 and T753 sites , B @-@ Raf is feedback phosphorylated on two other sites , S151 and T401 . # ::alignments 1-1.4.1.1 2-1.4.1 3-1.4 5-1.1 6-1 7-1.3 8-1.2.r 9-1.2.1 10-1.2.1 14-1.2.1 18-1.2.1.5.1.1 20-1.2.1.5.1.1 22-1.2.2 23-1.2 30-1.2.1 (f / find-01~e.6 :ARG0 (w / we~e.5) :ARG1~e.8 (p / phosphorylate-01~e.23 :ARG1 (a / and~e.9,10,14,30 :op1 (a2 / amino-acid :mod 750 :name (n / name :op1 "serine")) :op2 (a3 / amino-acid :mod 753 :name (n2 / name :op1 "threonine")) :op3 (a4 / amino-acid :mod 151 :name (n3 / name :op1 "serine")) :op4 (a5 / amino-acid :mod 401 :name (n4 / name :op1 "threonine")) :part-of (e2 / enzyme :name (n5 / name :op1 "B-Raf"~e.18,20))) :subevent-of (f2 / feedback~e.22)) :medium (h / here~e.7) :manner (e / experiment-01~e.3 :ARG2 (l / label-01~e.2 :mod (m / metabolism~e.1)))) # ::id bio.mskcc_0001.51 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These residues are phosphorylated by activated ERK in vitro , # ::alignments 0-1.1.1 1-1.1 3-1 4-1.2.r 5-1.2.2 6-1.2.1.1 7-1.3 8-1.3 (p / phosphorylate-01~e.3 :ARG1 (r / residue~e.1 :mod (t / this~e.0)) :ARG2~e.4 (e / enzyme :name (n / name :op1 "ERK"~e.6) :ARG1-of (a / activate-01~e.5)) :manner (i / in-vitro~e.7,8)) # ::id bio.mskcc_0001.52 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As has been observed for C @-@ Raf , we find that the hyperphosphorylated B @-@ Raf protein is subsequently dephosphorylated in a manner requiring the activities of the PP2A phosphatase and Pin1 prolyl @-@ isomerase , indicating that the feedback phosphorylation @/@ dephosphorylation cycle is a conserved regulatory mechanism for the Raf proteins . # ::alignments 0-1.2.5.r 3-1.2.2.1.2 5-1.2.2.1.1.1.1 7-1.2.4.1.1.1.1.1 9-1.1 10-1 13-1.2.1.2 13-1.2.2.1.1.2 14-1.2.1.1.1 16-1.2.4.1.1.1.1.1 17-1.2.4.1.1.1 18-1.2.4.1.3.r 19-1.2.5 19-1.2.5.r 20-1.2 20-1.2.2.1 23-1.2.3.r 24-1.2.3 26-1.2.3.2.1 26-1.2.3.2.2 27-1.2.3.2.1.1.r 29-1.2.3.2.1.1.1.1 30-1.2.3.2.1.1 31-1.2.3.2 32-1.2.3.2.2.1.1.1 33-1.2.3.2.2.1 35-1.2.3.2.2.1 37-1.2.4 40-1.2.4.1.3.3 41-1.2.4.1.3.1 43-1.2.4.1.3.2 44-1.2.4.1.3 45-1.2.4.1.3.r 47-1.2.4.1.2 48-1.2.4.1.1 49-1.2.4.1 52-1.2.4.1.1.1.1.1 53-1.2.4.1.1.1 (f / find-01~e.10 :ARG0 (w / we~e.9) :ARG1 (d / dephosphorylate-01~e.20 :ARG1 (e / enzyme :name (n / name :op1 "B-Raf"~e.14) :ARG3-of (h / hyperphosphorylate-01~e.13)) :ARG1-of (r / resemble-01 :ARG2 (d2 / dephosphorylate-01~e.20 :ARG1 (e2 / enzyme :name (n2 / name :op1 "C-Raf"~e.5) :ARG3-of (h2 / hyperphosphorylate-01~e.13)) :ARG1-of (o / observe-01~e.3))) :manner~e.23 (r2 / require-01~e.24 :ARG0 d :ARG1 (a2 / and~e.31 :op1 (a / act-02~e.26 :ARG0~e.27 (p / phosphatase~e.30 :name (n3 / name :op1 "PP2A"~e.29))) :op2 (a4 / act-02~e.26 :ARG0 (p2 / prolyl-isomerase~e.33,35 :name (n4 / name :op1 "Pin1"~e.32))))) :ARG0-of (i / indicate-01~e.37 :ARG1 (m / mechanism~e.49 :ARG0-of (r3 / regulate-01~e.48 :ARG1 (p4 / protein-family~e.17,53 :name (n5 / name :op1 "Raf"~e.7,16,52))) :ARG1-of (c / conserve-01~e.47) :domain~e.18,45 (c2 / cycle-02~e.44 :subevent (p3 / phosphorylate-01~e.41) :subevent (d3 / dephosphorylate-01~e.43) :mod (f3 / feedback~e.40)))) :time~e.0,19 (a3 / after~e.19 :op1 h))) # ::id bio.mskcc_0001.53 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Through mutational analysis , we find that feedback phosphorylation disrupts the abilities of B @-@ Raf to bind activated Ras and to heterodimerize with C @-@ Raf . # ::alignments 1-1.3.2 2-1.3 4-1.1 5-1 6-1.2.r 7-1.2.1.1 8-1.2.1 9-1.2 11-1.2.2 12-1.2.2.1.r 13-1.2.2.1.1.1 15-1.2.2.1.1.1 16-1.2.2.2.r 17-1.2.2.2.1 18-1.2.2.2.1.2.2 19-1.2.2.2.1.2.1.1 20-1.2.2.2 22-1.2.2.2.2 23-1.2.2.2.2.2.r 24-1.2.2.2.2.2.1.1 26-1.2.2.1.1.1 26-1.2.2.2.2.2.1.1 (f / find-01~e.5 :ARG0 (w / we~e.4) :ARG1~e.6 (d / disrupt-01~e.9 :ARG0 (p / phosphorylate-01~e.8 :subevent-of (f2 / feedback~e.7)) :ARG1 (c / capable-01~e.11 :ARG1~e.12 (e / enzyme :name (n / name :op1 "B-Raf"~e.13,15,26)) :ARG2~e.16 (a2 / and~e.20 :op1 (b / bind-01~e.17 :ARG1 e :ARG2 (e2 / enzyme :name (n2 / name :op1 "Ras"~e.19) :ARG1-of (a / activate-01~e.18))) :op2 (h / heterodimerize-01~e.22 :ARG1 e :ARG2~e.23 (e3 / enzyme :name (n3 / name :op1 "C-Raf"~e.24,26)))))) :manner (a3 / analyze-01~e.2 :ARG0 w :ARG1 (m / mutate-01~e.1))) # ::id bio.mskcc_0001.54 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Although phosphorylation of the S151 site appears to have the greatest effect on Ras binding , our results indicate that phosphorylation of all the feedback sites contributes to the inhibition of C @-@ Raf binding . # ::alignments 0-1.3.r 1-1.2.1 5-1.2.1.1 6-1.3 10-1.3.1.3 10-1.3.1.3.1 10-1.3.1.3.1.r 11-1.3.1 12-1.3.1.2.r 13-1.3.1.2.1.1.1 14-1.3.1.2 16-1.1.2 16-1.1.2.r 17-1.1 17-1.1.1 17-1.1.1.r 18-1 20-1.2.1 20-1.3.1.1 22-1.2.1.1.1 24-1.2.1.1.2 25-1.2.1.1 26-1.2 27-1.2.2.r 29-1.2.2 30-1.2.2.1.r 31-1.2.2.1.1.1.1 33-1.2.2.1.1.1.1 34-1.2.2.1 (i / indicate-01~e.18 :ARG0 (t / thing~e.17 :ARG2-of~e.17 (r / result-01~e.17) :poss~e.16 (w / we~e.16)) :ARG1 (c / contribute-01~e.26 :ARG0 (p / phosphorylate-01~e.1,20 :ARG1 (p2 / protein-segment~e.5,25 :mod (a / all~e.22) :destination-of (f / feedback~e.24))) :ARG2~e.27 (i2 / inhibit-01~e.29 :ARG1~e.30 (b / bind-01~e.34 :ARG2 (e / enzyme :name (n / name :op1 "C-Raf"~e.31,33))))) :concession~e.0 (a2 / appear-02~e.6 :ARG1 (a3 / affect-01~e.11 :ARG0 (p3 / phosphorylate-01~e.20 :ARG1 (a4 / amino-acid :mod 151 :name (n2 / name :op1 "serine"))) :ARG1~e.12 (b2 / bind-01~e.14 :ARG2 (e2 / enzyme :name (n3 / name :op1 "Ras"~e.13))) :mod (g / great~e.10 :degree~e.10 (m / most~e.10))))) # ::id bio.mskcc_0001.55 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This finding is consistent with those of peptide binding studies conducted by Rushworth et al. ( 27 ) indicating that there are multiple points of contact between heterodimerized B @-@ Raf and C @-@ Raf proteins . # ::alignments 0-1.1.1 1-1.1 1-1.1.2 1-1.1.2.r 1-1.2 1-1.2.1 1-1.2.1.r 3-1 6-1.2.1.1.r 7-1.2.1.1.1.1 8-1.2.1.1.1 9-1.2.1.1 10-1.2.1.1.2 11-1.2.1.1.2.1.r 12-1.2.1.1.2.1.1.1.1 13-1.2.1.1.2.1 14-1.2.1.1.2.1.2.1 16-1.2.2.1.1.1 18-1.1.3 22-1.1.3.1.3 25-1.1.3.1 28-1.1.3.1.1.1.1 30-1.1.3.1.1.1.1 30-1.1.3.1.2.1.1 32-1.1.3.1.2.1.1 34-1.1.3.1.1.1.1 34-1.1.3.1.2.1.1 (c / consistent-01~e.3 :ARG1 (t / thing~e.1 :mod (t2 / this~e.0) :ARG1-of~e.1 (f / find-01~e.1) :ARG0-of (i / indicate-01~e.18 :ARG1 (c4 / contact-01~e.25 :ARG0 (e / enzyme :name (n2 / name :op1 "B-Raf"~e.28,30,34) :ARG1-of (h / heterodimerize-01)) :ARG1 (e2 / enzyme :name (n3 / name :op1 "C-Raf"~e.30,32,34) :ARG1-of h) :quant (m / multiple~e.22)))) :ARG2 (t3 / thing~e.1 :ARG1-of~e.1 (f2 / find-01~e.1 :ARG0~e.6 (s / study-01~e.9 :ARG1 (b / bind-01~e.8 :ARG1 (p / peptide~e.7)) :ARG1-of (c2 / conduct-01~e.10 :ARG0~e.11 (a / and~e.13 :op1 (p2 / person :name (n / name :op1 "Rushworth"~e.12)) :op2 (p3 / person :mod (o / other~e.14)))))) :ARG1-of (d / describe-01 :ARG0 (p4 / publication :ARG1-of (c3 / cite-01 :ARG2 27~e.16))))) # ::id bio.mskcc_0001.56 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Interestingly , these peptide binding studies also indicate that homodimerized B @-@ Raf and C @-@ Raf proteins have multiple contact points ( 27 ) , suggesting that feedback phosphorylation of the Raf proteins may disrupt Raf homodimers as well # ::alignments 0-1.3 0-1.3.r 2-1.1.2 3-1.1.1.1 4-1.1.1 5-1.1 6-1.4 7-1 10-1.2.1.1.2.1 12-1.2.1.1.2.1 12-1.2.1.2.2.1 13-1.2.1 14-1.2.1.2.2.1 16-1.6.1.1.1.1.2.1 17-1.6.1.1.1.1 19-1.2.2 20-1.2 23-1.5.1.1.1 26-1.6 28-1.6.1.1.1.2 29-1.6.1.1.1 32-1.6.1.1.1.1.2.1 33-1.6.1.1.1.1 34-1.6.1 35-1.6.1.1 36-1.6.1.1.1.1.2.1 38-1.6.1.1.3 39-1.6.1.1.3 (i / indicate-01~e.7 :ARG0 (s / study-01~e.5 :ARG1 (b / bind-01~e.4 :ARG1 (p / peptide~e.3)) :mod (t / this~e.2)) :ARG1 (c / contact-01~e.20 :ARG0 (a2 / and~e.13 :op1 (e / enzyme :wiki - :name (n / name :op1 "B-Raf"~e.10,12)) :op2 (e2 / enzyme :wiki "C-Raf" :name (n2 / name :op1 "C-Raf"~e.12,14)) :ARG3-of (h / homodimerize-01)) :quant (m / multiple~e.19)) :manner~e.0 (i2 / interesting~e.0) :mod (a / also~e.6) :ARG1-of (d / describe-01 :ARG0 (p2 / publication :ARG1-of (c2 / cite-01 :ARG2 27~e.23))) :ARG0-of (s2 / suggest-01~e.26 :ARG1 (p3 / possible-01~e.34 :ARG1 (d2 / disrupt-01~e.35 :ARG0 (p4 / phosphorylate-01~e.29 :ARG1 (p5 / protein-family~e.17,33 :wiki "RAF_kinase" :name (n3 / name :op1 "Raf"~e.16,32,36)) :subevent-of (f / feedback~e.28)) :ARG1 (h2 / homodimer :part p5) :mod (a3 / as-well~e.38,39))))) # ::id bio.mskcc_0001.57 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Taken together , these findings suggest a model whereby the binding of a 14 @-@ 3 @-@ 3 dimer to the C @-@ terminal pS621 site of C @-@ Raf and the C @-@ terminal pS729 site of B @-@ Raf provides the stable docking event that then allows the two proteins to make additional contacts ( Fig . 9 ) . # ::alignments 0-1.1.3 1-1.1.3.1 3-1.1.2 4-1.1 4-1.1.1 4-1.1.1.r 5-1 7-1.2 10-1.2.1.1.1 10-1.2.1.1.2 11-1.2.1.1.1.1.r 13-1.2.1.1.1.1.1.1.1 15-1.2.1.1.1.1.1.1.1 17-1.2.1.1.1.1.1.1.1 18-1.2.1.1.1.1 21-1.2.1.1.1.2.4.1.1 21-1.2.1.1.1.2.4.2.1.1 21-1.2.1.1.2.2.4.1.1 23-1.2.1.1.1.2.4.1.1 23-1.2.1.1.2.2.4.1.1 25-1.2.1.1.1.2.4 25-1.2.1.1.2.2.4 27-1.2.1.1.1.2.4.1.1 27-1.2.1.1.1.2.4.2.1.1 27-1.2.1.1.2.2.4.1.1 29-1.2.1.1.1.2.4.2.1.1 29-1.2.1.1.2.2.4.2.1.1 30-1.2.1.1 32-1.2.1.1.1.2.4.1.1 32-1.2.1.1.1.2.4.2.1.1 32-1.2.1.1.2.2.4.1.1 34-1.2.1.1.1.2.4.1.1 34-1.2.1.1.2.2.4.1.1 36-1.2.1.1.1.2.4 36-1.2.1.1.2.2.4 37-1.2.1.1.2.2.r 38-1.2.1.1.2.2.4.2.1.1 40-1.2.1.1.1.2.4.2.1.1 40-1.2.1.1.2.2.4.2.1.1 41-1.2.1 43-1.2.1.2.2 44-1.2.1.2 48-1.2.1.2.1 51-1.2.1.1.1.1.1 51-1.2.1.1.1.2.4 51-1.2.1.1.2.2.4 53-1 54-1.2.1.2.1.1.3 55-1.2.1.2.1.1 57-1.3.1 59-1.3.1.1 (s / suggest-01~e.5,53 :ARG0 (t / thing~e.4 :ARG1-of~e.4 (f / find-01~e.4) :mod (t2 / this~e.3) :ARG1-of (t3 / take-01~e.0 :mod (t4 / together~e.1))) :ARG1 (m / model~e.7 :topic (p / provide-01~e.41 :ARG0 (a / and~e.30 :op1 (b / bind-01~e.10 :ARG1~e.11 (d / dimer~e.18 :mod (p6 / protein~e.51 :name (n / name :op1 "14-3-3"~e.13,15,17))) :ARG2 (a2 / amino-acid :mod 621 :name (n2 / name :op1 "serine") :ARG3-of (p2 / phosphorylate-01) :part-of (p3 / protein-segment~e.25,36,51 :name (n3 / name :op1 "C-terminus"~e.21,23,27,32,34) :part-of (e / enzyme :name (n4 / name :op1 "C-Raf"~e.21,27,29,32,40))))) :op2 (b3 / bind-01~e.10 :ARG1 d :ARG2~e.37 (a3 / amino-acid :mod 729 :name (n5 / name :op1 "serine") :ARG3-of (p4 / phosphorylate-01) :part-of (p5 / protein-segment~e.25,36,51 :name (n6 / name :op1 "C-terminus"~e.21,23,27,32,34) :part-of (e2 / enzyme :name (n7 / name :op1 "B-Raf"~e.29,38,40)))))) :ARG1 (d2 / dock-01~e.44 :ARG0-of (a4 / allow-01~e.48 :ARG1 (c / contact-01~e.55 :ARG0 e :ARG1 e2 :mod (a5 / additional~e.54) :time (a6 / after :op1 a))) :ARG1-of (s2 / stable-03~e.43)))) :ARG1-of (d3 / describe-01 :ARG0 (f2 / figure~e.57 :mod 9~e.59))) # ::id bio.ras_0001.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The most frequently mutated oncogenes in the deadliest cancers responsible for human mortality are KRAS , PIK3CA and BRAF . # ::alignments 1-1.2.1.1 1-1.3.3.2 2-1.2.1 3-1.2 4-1 5-1.3.r 7-1.3 7-1.3.3 7-1.3.3.r 8-1.3.2.1 10-1.3.3.1.r 11-1.3.3.1 13-1.1.r 14-1.1.1.1.1 16-1.1.2.1.1 17-1.1 18-1.1.3.1.1 (o / oncogene~e.4 :domain~e.13 (a / and~e.17 :op1 (g / gene :name (n / name :op1 "KRAS"~e.14)) :op2 (g2 / gene :name (n2 / name :op1 "PIK3CA"~e.16)) :op3 (g3 / gene :name (n3 / name :op1 "BRAF"~e.18))) :ARG1-of (m2 / mutate-01~e.3 :ARG1-of (f / frequent-02~e.2 :degree (m3 / most~e.1))) :location~e.5 (d / disease~e.7 :wiki "Cancer" :name (n4 / name :op1 "cancer"~e.8) :ARG0-of~e.7 (k / kill-01~e.7 :ARG1~e.10 (h / human~e.11) :degree (m / most~e.1)))) # ::id bio.ras_0001.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Importantly the signaling enzymes encoded by PIK3CA and BRAF are , in part , regulated by direct binding to activated forms of the Ras proteins suggesting that dysregulation of this key step in signaling is critical for tumor formation . # ::alignments 0-1.4 2-1.2.1 3-1.2 4-1.2.2 5-1.2.2.1.r 6-1.2.2.1.1.1.1 7-1.2.2.1 8-1.2.2.1.2.1.1 11-1.3.r 12-1.3 12-1.3.r 14-1 16-1.1.3 17-1.1 18-1.1.2.r 19-1.1.2.2 20-1.5.1.2 23-1.1.2.1.1 25-1.5 27-1 33-1.2.1 35-1.5.1 37-1.5.1.2.1 38-1.5.1.2 (r / regulate-01~e.14,27 :ARG0 (b / bind-01~e.17 :ARG1 e :ARG2~e.18 (e3 / enzyme :name (n3 / name :op1 "Ras"~e.23) :ARG1-of (a2 / activate-01~e.19)) :ARG1-of (d / direct-02~e.16)) :ARG1 (e / enzyme~e.3 :ARG0-of (s / signal-07~e.2,33) :ARG1-of (e2 / encode-01~e.4 :ARG0~e.5 (a / and~e.7 :op1 (g / gene :name (n / name :op1 "PIK3CA"~e.6)) :op2 (g2 / gene :name (n2 / name :op1 "BRAF"~e.8))))) :degree~e.11,12 (p / part~e.12) :mod (i / important~e.0) :ARG0-of (s2 / suggest-01~e.25 :ARG1 (c / critical-02~e.35 :ARG1 (i2 / impair-01 :ARG1 r) :ARG2 (f / form-01~e.20,38 :ARG1 (t / tumor~e.37))))) # ::id bio.ras_0001.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Ras acts as a molecular switch that is activated upon GTP loading and deactivated upon hydrolysis of GTP to GDP . # ::alignments 0-1.1.1.1 4-1.4 5-1 7-1.1.r 8-1.2 10-1.2.1.2.1.1 11-1.2.1 13-1.3 15-1.3.1 16-1.3.1.1.r 17-1.3.1.1 18-1.3.1.2.r 19-1.3.1.2.1.1 (s / switch~e.5 :domain~e.7 (e / enzyme :name (n / name :op1 "Ras"~e.0)) :ARG1-of (a / activate-01~e.8 :ARG0 (l / load-01~e.11 :ARG1 e :ARG2 (s2 / small-molecule :name (n2 / name :op1 "GTP"~e.10)))) :ARG1-of (d / deactivate-01~e.13 :ARG0 (h / hydrolyze-01~e.15 :ARG1~e.16 s2~e.17 :ARG3~e.18 (s3 / small-molecule :name (n3 / name :op1 "GDP"~e.19)))) :mod (m / molecule~e.4)) # ::id bio.ras_0001.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This switch mechanism is common to a wide variety of GTP - binding proteins and is mediated by a conserved structure called the G - domain that consists of five conserved G boxes . # ::alignments 0-1.2.2 1-1.2.1 2-1.2 4-1 5-1.1.r 7-1.1.2.1 10-1.1.1.1.1.1 12-1.1.1 13-1.1 17-1.3.r 19-1.3.2 19-1.3.3.3 21-1.3.1.r 23-1.3.1.1 25-1.3.1.1 27-1.3.3.r 29-1.3.3.1 30-1.3.2 31-1.3.1.1 31-1.3.3.2.1 32-1.3.3.2.2 (s / share-01~e.4 :ARG0~e.5 (p / protein~e.13 :ARG2-of (b / bind-01~e.12 :ARG1 (s4 / small-molecule :name (n / name :op1 "GTP"~e.10))) :mod (v / various :ARG1-of (w / wide-02~e.7))) :ARG1 (m / mechanism~e.2 :topic (s2 / switch~e.1) :mod (t / this~e.0)) :manner~e.17 (p2 / protein-segment :name~e.21 (n2 / name :op1 "G-domain"~e.23,25,31) :ARG1-of (c2 / conserve-01~e.19,30) :part~e.27 (p3 / protein-segment :quant 5~e.29 :name (n3 / name :op1 "G"~e.31 :op2 "box"~e.32) :ARG1-of (c3 / conserve-01~e.19)))) # ::id bio.ras_0001.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Under physiological conditions , the rate of GDP or GTP release from the G - domain is slow . # ::alignments 1-1.2 2-1.2.r 7-1.1.1.1.1.1 8-1.1.1 9-1.1.1.2.1.1 10-1.1 11-1.1.2.r 13-1.1.2.1.1 15-1.1.2.1.1 17-1 (s / slow-05~e.17 :ARG1 (r / release-01~e.10 :ARG1 (o / or~e.8 :op1 (s2 / small-molecule :name (n / name :op1 "GDP"~e.7)) :op2 (s3 / small-molecule :name (n2 / name :op1 "GTP"~e.9))) :ARG2~e.11 (p3 / protein-segment :name (n3 / name :op1 "G-domain"~e.13,15))) :condition~e.2 (p2 / physiology~e.1)) # ::id bio.ras_0001.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As a consequence the GDP produced by GTP hydrolysis on Ras is trapped and the bulk of cellular Ras accumulates in the GDP - bound ‘ off ’ state , despite the high GTP / GDP ratio in the cytosol ( 1 – 3 ) . # ::alignments 0-1 1-1 2-1 4-1.1.1.1.1.1 7-1.1.1.1.2.1.1.1 8-1.1.1.1.2 10-1.1.1.1.2.1.2.1.1.1 12-1.1.1 13-1.1 15-1.1.2.1.2.2 17-1.1.2.1.2.1.2 18-1.1.2.1.1.1 18-1.1.2.1.2.1.1.1 19-1.1.2 22-1.1.1.1.1.1 24-1.1.1.1.2.1 24-1.1.1.1.2.1.2 24-1.1.1.1.2.1.2.r 24-1.1.2.1 24-1.1.2.1.4 24-1.1.2.1.4.r 30-1.1.2.2.r 32-1.1.2.2 33-1.1.2.2.1.2 34-1.1.2.2.1.2 35-1.1.2.2.1.2 36-1.1.2.2.1 37-1.1.2.2.1.3.r 39-1.1.2.2.1.3 41-1.2.1.1.1.1 43-1.2.1.1.1.2 (c / cause-01~e.0,1,2 :ARG1 (a / and~e.13 :op1 (t / trap-01~e.12 :ARG1 (s / small-molecule :name (n / name :op1 "GDP"~e.4,22) :ARG3-of (h / hydrolyze-01~e.8 :ARG1 (s2 / small-molecule~e.24 :name (n2 / name :op1 "GTP"~e.7) :ARG1-of~e.24 (b3 / bind-01~e.24 :ARG2 (e / enzyme :name (n3 / name :op1 "Ras"~e.10))))))) :op2 (a2 / accumulate-01~e.19 :ARG1 (e3 / enzyme~e.24 :name (n4 / name :op1 "Ras"~e.18) :ARG1-of (i / include-91 :ARG2 (e2 / enzyme :name (n5 / name :op1 "Ras"~e.18) :location (c5 / cell~e.17)) :ARG3 (b / bulk~e.15)) :ARG1-of (d / deactivate-01) :ARG2-of~e.24 (b2 / bind-01~e.24 :ARG1 s)) :concession~e.30 (h2 / high-02~e.32 :ARG1 (r / ratio-of~e.36 :op1 s2 :op2 s~e.33,34,35 :location~e.37 (c6 / cytosol~e.39))))) :ARG1-of (a3 / attest-01 :ARG0 (p4 / publication :ARG1-of (c7 / cite-01 :ARG2 (v / value-interval :op1 1~e.41 :op2 3~e.43))))) # ::id bio.ras_0001.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Growth factors can turn on Ras by activating Guanine nucleotide Exchange Factors ( GEFs ) or by inhibiting the GTPase Activating Proteins ( GAPs ) or by both mechanisms . # ::alignments 0-1.1.1 1-1.1.1 2-1 3-1.1 4-1.1 5-1.1.2.1.1 6-1.1.3.r 7-1.1.3.1 8-1.1.3.1.2.1.1 9-1.1.3.1.2.1.2 10-1.1.3.1.2.1.3 11-1.1.3.1.2.1.4 15-1.1.3 17-1.1.3.2 19-1.1.3.2.2.1.1.1.1 20-1.1.3.1 20-1.1.3.2.2.1 21-1.1.3.2.2 25-1.1.3 (p5 / possible-01~e.2 :ARG1 (t / turn-on-13~e.3,4 :ARG0 (g / growth-factor~e.0,1) :ARG1 (e2 / enzyme :name (n / name :op1 "Ras"~e.5)) :manner~e.6 (o / or~e.15,25 :op1 (a / activate-01~e.7,20 :ARG0 g :ARG1 (p2 / protein :name (n2 / name :op1 "guanine"~e.8 :op2 "nucleotide"~e.9 :op3 "exchange"~e.10 :op4 "factor"~e.11))) :op2 (i / inhibit-01~e.17 :ARG0 g :ARG1 (p3 / protein~e.21 :ARG0-of (a2 / activate-01~e.20 :ARG1 (e / enzyme :name (n3 / name :op1 "GTPase"~e.19))))) :op3 (a3 / and :op1 a :op2 i)))) # ::id bio.ras_0001.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok RasGEFs bind to Ras and lower the transition energy for the nucleotide exchange of the bound GDP for the more abundant cytosolic GTP , whereas RasGAPs bind to Ras and catalyze GTP hydrolysis . # ::alignments 0-1.1.1.1.1.1 1-1.1.1 2-1.1.1.2.r 3-1.1.1.2.1.1 4-1.1 5-1.1.2 7-1.1.2.2.1 8-1.1.2.2 12-1.1.2.2.2 15-1.1.2.2.2.1 15-1.1.2.2.2.1.2 15-1.1.2.2.2.1.2.r 16-1.1.2.2.2.1.1.1 17-1.1.2.2.2.2.r 19-1.1.2.2.2.2.2.1 20-1.1.2.2.2.2.2 21-1.1.2.2.2.2.3 22-1.1.2.2.2.2.1.1 24-1 26-1.1.2.2.2.1 26-1.1.2.2.2.1.2 26-1.1.2.2.2.1.2.r 26-1.2.1 28-1.1.1.2.1.1 29-1.2 30-1.2.2 31-1.2.2.2.1 32-1.2.2.2 (c / contrast-01~e.24 :ARG1 (a / and~e.4 :op1 (b / bind-01~e.1 :ARG1 (p / protein :name (n / name :op1 "RasGEF"~e.0)) :ARG2~e.2 (e3 / enzyme :name (n2 / name :op1 "Ras"~e.3,28))) :op2 (l / lower-05~e.5 :ARG0 p :ARG1 (e / energy~e.8 :mod (t / transition-01~e.7) :poss (e2 / exchange-01~e.12 :ARG1 (s2 / small-molecule~e.15,26 :name (n4 / name :op1 "GDP"~e.16) :ARG1-of~e.15,26 (b2 / bind-01~e.15,26 :ARG2 e3)) :ARG3~e.17 (s / small-molecule :name (n5 / name :op1 "GTP"~e.22) :mod (a2 / abundant~e.20 :degree (m / more~e.19) :compared-to s2) :location (c3 / cytosol~e.21)))))) :ARG2 (a3 / and~e.29 :op1 (b3 / bind-01~e.26 :ARG1 (p5 / protein :name (n3 / name :op1 "RasGAP")) :ARG2 e3) :op2 (c2 / catalyze-01~e.30 :ARG0 p5 :ARG1 (h / hydrolyze-01~e.32 :ARG1 s~e.31)))) # ::id bio.ras_0001.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The most prevalent oncogenic mutations in Ras ( Gly12 and Gly13 in the G1 box , and Gln61 in the G3 box ) preserve the GTP bound state by inhibiting intrinsic GTPase activity and by interfering with the ability of GAPs . # ::alignments 1-1.1.1.1 2-1.1.1 3-1.1.2 3-1.1.2.1.2.1 4-1.1 5-1.1.1.2.r 6-1.1.1.2.1.1 8-1.1.3.1.1.1 9-1.1.3 10-1.1.3.2.1.1 13-1.1.3.1.2.1.1 14-1.1.3.1.2.1.2 17-1.1.3.3.1.1 20-1.1.3.3.2.1.1 21-1.1.3.3.2.1.2 23-1 25-1.2.1.1.1 26-1.2 28-1.3.r 29-1.3.1 30-1.3.1.2.2 31-1.3.1.2.1.1.1 32-1.3.1.2 33-1.3 35-1.3.2 36-1.3.2.2.r 38-1.3.2.2 39-1.3.2.2.1.r 40-1.3.2.2.1.1.1 (p / preserve-01~e.23 :ARG0 (m / mutation~e.4 :ARG1-of (p2 / prevail-02~e.2 :degree (m2 / most~e.1) :compared-to~e.5 (e / enzyme :name (n / name :op1 "Ras"~e.6))) :ARG0-of (c / cause-01~e.3 :ARG1 (d / disease :wiki "Cancer" :name (n10 / name :op1 "cancer"~e.3))) :location (a / and~e.9 :op1 (p4 / protein-segment :name (n2 / name :op1 "Gly12"~e.8) :location (p7 / protein-segment :name (n5 / name :op1 "G1"~e.13 :op2 "box"~e.14) :location e)) :op2 (p5 / protein-segment :name (n3 / name :op1 "Gly13"~e.10) :location p7) :op3 (p6 / protein-segment :name (n4 / name :op1 "Gln61"~e.17) :location (p8 / protein-segment :name (n6 / name :op1 "G3"~e.20 :op2 "box"~e.21) :location e)))) :ARG1 (b / bind-01~e.26 :ARG1 (s / small-molecule :name (n7 / name :op1 "GTP"~e.25)) :ARG2 e) :manner~e.28 (a2 / and~e.33 :op1 (i / inhibit-01~e.29 :ARG0 m :ARG1 (a3 / activity-06~e.32 :ARG0 (e2 / enzyme :name (n8 / name :op1 "GTPase"~e.31)) :mod (i3 / intrinsic~e.30))) :op2 (i2 / interfere-01~e.35 :ARG0 m :ARG1~e.36 (c4 / capable-01~e.38 :ARG1~e.39 (p10 / protein :name (n9 / name :op1 "GAP"~e.40)))))) # ::id bio.ras_0001.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Other less frequently observed mutations , such as those found in the G4 and G5 boxes , increase the rate of nucleotide exchange , thereby mimicking the GEFs and increasing the GTP - bound state ( 1 – 7 ) . # ::alignments 0-1.1.2 1-1.1.1.1.1 2-1.1.1.1 3-1.1.1 4-1.1 4-1.1.3 6-1.1.3.r 7-1.1.3.r 10-1.1.3.1.r 12-1.1.3.1.1.1.1 14-1.1.3.1.2.1.1 15-1.1.3.1.1.1.2 15-1.1.3.1.2.1.2 17-1 17-1.4.1 19-1.2 20-1.2.1.r 21-1.2.1.1 22-1.2.1 24-1.3.r 25-1.3 27-1.3.2.1.1 29-1 29-1.4.1 31-1.4.1.1.1.2.1.1.1 33-1.4.1.1.1 33-1.4.1.1.1.2 33-1.4.1.1.1.2.r 36-1.5.1.1.1.1 38-1.5.1.1.1.2 (i / increase-01~e.17,29 :ARG0 (m / mutation~e.4 :ARG1-of (o / observe-01~e.3 :ARG1-of (f / frequent-02~e.2 :degree (l / less~e.1))) :mod (o2 / other~e.0) :example~e.6,7 (m2 / mutation~e.4 :location~e.10 (o3 / or :op1 (p / protein-segment :name (n / name :op1 "G4"~e.12 :op2 "box"~e.15)) :op2 (p2 / protein-segment :name (n2 / name :op1 "G5"~e.14 :op2 "box"~e.15))))) :ARG1 (r / rate~e.19 :degree-of~e.20 (e / exchange-01~e.22 :ARG1 (n3 / nucleotide~e.21))) :manner-of~e.24 (m3 / mimic-01~e.25 :ARG0 m :ARG1 (p3 / protein :name (n4 / name :op1 "GEF"~e.27))) :ARG0-of (c / cause-01 :ARG1 (i2 / increase-01~e.17,29 :ARG1 (n7 / number :quant-of (e2 / enzyme~e.33 :name (n5 / name :op1 "Ras") :ARG2-of~e.33 (b / bind-01~e.33 :ARG1 (s / small-molecule :name (n6 / name :op1 "GTP"~e.31))))))) :ARG1-of (a / attest-01 :ARG0 (p6 / publication :ARG1-of (c2 / cite-01 :ARG2 (v / value-interval :op1 1~e.36 :op2 7~e.38))))) # ::id bio.ras_0002.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Activated Ras controls diverse signaling pathways that ultimately determine Ras - induced cellular responses such as cell proliferation , survival , differentiation and motility . # ::alignments 0-1.1.2 1-1.1.1.1 2-1 3-1.2.1 4-1.2.2 5-1.2 7-1.2.3.2 8-1.2.3 9-1.2.3.1.3.1 11-1.2.3.1.3 12-1.2.3.1.1 13-1.2.3.1 15-1.2.3.1.2.r 15-1.2.3.2.r 16-1.2.3.1.2.1.1 17-1.2.3.1.2.1 19-1.2.3.1.2.2 21-1.2.3.1.2.3 22-1.2.3.1.2 23-1.2.3.1.2.4 (c / control-01~e.2 :ARG0 (e / enzyme :name (n / name :op1 "Ras"~e.1) :ARG1-of (a / activate-01~e.0)) :ARG1 (p / pathway~e.5 :mod (d / diverse~e.3) :ARG0-of (s / signal-07~e.4) :ARG0-of (d2 / determine-01~e.8 :ARG1 (r / respond-01~e.13 :ARG0 (c2 / cell~e.12) :ARG2~e.15 (a2 / and~e.22 :op1 (p2 / proliferate-01~e.17 :ARG0 c2~e.16) :op2 (s2 / survive-01~e.19 :ARG0 c2) :op3 (d3 / differentiate-01~e.21 :ARG1 c2) :op4 (m / motility~e.23 :mod c2)) :ARG2-of (i / induce-01~e.11 :ARG0 e~e.9)) :time~e.15 (u / ultimate~e.7)))) # ::id bio.ras_0002.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These multiple Ras functions depend on its binding to a range of functionally diverse effector molecules such as Raf , PI3K , AF6 and RASSFs ( 1 ) . # ::alignments 0-1.1.2 1-1.1.1 2-1.1.3.1.1.1 3-1.1 3-1.1.3 3-1.1.3.r 4-1 5-1.2.r 6-1.2.1 6-1.2.1.r 7-1.2 8-1.2.2.r 10-1.2.2.3 11-1.2.2.3.r 12-1.2.2.4 13-1.2.2.4.1 14-1.2.2.1 15-1.2.2 16-1.2.2.2.r 17-1.2.2.2.r 18-1.2.2.2.1.1.1 20-1.2.2.2.2.1.1 22-1.2.2.2.3.1.1 23-1.2.2.2 26-1.3.1.1.1 (d / depend-01~e.4 :ARG0 (t3 / thing~e.3 :quant (m / multiple~e.1) :mod (t / this~e.0) :ARG1-of~e.3 (f / function-01~e.3 :ARG0 (e / enzyme :name (n / name :op1 "Ras"~e.2)))) :ARG1~e.5 (b / bind-01~e.7 :ARG1~e.6 e~e.6 :ARG2~e.8 (m2 / molecule~e.15 :mod (e3 / effector~e.14) :example~e.16,17 (a / and~e.23 :op1 (e2 / enzyme :name (n2 / name :op1 "Raf"~e.18)) :op2 (e4 / enzyme :name (n3 / name :op1 "PI3K"~e.20)) :op3 (e5 / enzyme :name (n4 / name :op1 "AF6"~e.22)) :op4 (p / protein :name (n5 / name :op1 "RASSF"))) :quant~e.11 (r / range~e.10) :ARG0-of (f2 / function-01~e.12 :mod (d2 / diverse~e.13)))) :ARG1-of (d3 / describe-01 :ARG0 (p2 / publication :ARG1-of (c / cite-01 :ARG2 1~e.26)))) # ::id bio.ras_0002.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The enhancement of specific effector pathways plays a critical role in maintaining an appropriate biological response ( 8 ) . # ::alignments 1-1.1 2-1.1.1.r 3-1.1.1.2 4-1.1.1.1 5-1.1.1 6-1 8-1.2.1 9-1.2 10-1.2.1.1.r 11-1.2.1.1 13-1.2.1.1.2.3 14-1.2.1.1.2.2 15-1.2.1.1.2 15-1.2.1.1.2.1 15-1.2.1.1.2.1.r 17-1.3.1.1.1 (p / play-02~e.6 :ARG0 (e / enhance-01~e.1 :ARG1~e.2 (p2 / pathway~e.5 :mod (e2 / effector~e.4) :ARG1-of (s / specific-02~e.3))) :ARG1 (r / role~e.9 :ARG1-of (c / critical-02~e.8 :ARG2~e.10 (m / maintain-01~e.11 :ARG0 e :ARG1 (t / thing~e.15 :ARG2-of~e.15 (r2 / respond-01~e.15) :mod (b / biology~e.14) :ARG1-of (a / appropriate-02~e.13))))) :ARG1-of (d / describe-01 :ARG2 (p3 / publication :ARG1-of (c2 / cite-01 :ARG2 8~e.17)))) # ::id bio.ras_0002.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The specificity in Ras - induced signaling is primarily determined by the balance between Ras affinity for each of its effectors and the local concentrations of those effectors . # ::alignments 1-1.2 2-1.2.1.r 3-1.2.1.1.1 5-1.2.1.1 6-1.2.1 8-1.3 9-1 10-1.1.r 12-1.1 14-1.1.1.1.1.1 15-1.1.1 16-1.1.1.2.r 17-1.1.1.2.1 19-1.1.1.2.2 19-1.1.1.2.2.r 20-1.1.1.2 23-1.1.2.2 24-1.1.2 27-1.1.2.1 (d / determine-01~e.9 :ARG0~e.10 (b / balance-01~e.12 :ARG1 (a / affinity~e.15 :poss (e / enzyme :name (n / name :op1 "Ras"~e.14)) :topic~e.16 (e2 / effector~e.20 :mod (e3 / each~e.17) :poss~e.19 e~e.19)) :ARG2 (c / concentrate-02~e.24 :ARG1 e2~e.27 :ARG1-of (l / local-02~e.23))) :ARG1 (s / specificity~e.1 :mod~e.2 (s2 / signal-07~e.6 :ARG2-of (i / induce-01~e.5 :ARG0 e~e.3))) :mod (p / primary~e.8)) # ::id bio.ras_0002.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In addition , scaffold proteins have been shown to guide activation of specific effector pathway( s ) . For example , SHOC2 / Sur @-@ 8 bridges Ras and Raf to specifically enhance the Raf / MEK / ERK pathway without enhancing PI3K / AKT signaling ( 9 , 10 ) . # ::alignments 0-1.1 1-1.1 3-1.1.1.1.1.1 4-1.1.1.1.1 7-1.1.1 9-1.1.1.1 10-1.1.1.1.2 12-1.2.1.4.3 13-1.1.1.1.2.1.1 18-1.2 19-1.2 21-1.2.1.1.1.1.1 23-1.2.1.1.2.1.1 25-1.2.1.1.2.1.1 26-1.2.1 27-1.2.1.2.1.1 28-1.2.1.6.1.1.1 29-1.2.1.3.1.1 31-1.1.1.1.2.1.2 31-1.2.1.4.3 32-1.2.1.4 34-1.2.1.4.2.1.1 36-1.2.1.4.2.1.1 38-1.2.1.4.2.1.1 39-1.1.1.1.2.1 40-1.2.1.5.1 40-1.2.1.5.1.r 41-1.2.1.5 42-1.2.1.5.3.1.1.1 44-1.2.1.5.3.1.1.1 45-1.2.1.5.3 47-1.2.1.6.1.1.1.1 49-1.2.1.6.1.1.1.2 (m / multi-sentence :snt1 (a4 / and~e.0,1 :op2 (s / show-01~e.7 :ARG1 (g / guide-01~e.9 :ARG0 (p / protein~e.4 :mod (s5 / scaffold~e.3)) :ARG1 (a / activate-01~e.10 :ARG1 (p2 / pathway~e.39 :mod (e5 / effector~e.13) :mod (s2 / specific~e.31)))))) :snt2 (e8 / exemplify-01~e.18,19 :ARG0 (b / bridge-01~e.26 :ARG0 (m2 / macro-molecular-complex :part (e3 / enzyme :name (n3 / name :op1 "SHOC2"~e.21)) :part (e4 / enzyme :name (n4 / name :op1 "Sur-8"~e.23,25))) :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.27)) :ARG2 (e2 / enzyme :name (n2 / name :op1 "Raf"~e.29)) :purpose (e6 / enhance-01~e.32 :ARG0 m2 :ARG1 (p4 / pathway :name (n7 / name :op1 "Raf/MEK/ERK"~e.34,36,38)) :ARG1-of (s3 / specific-02~e.12,31)) :manner (e7 / enhance-01~e.41 :polarity~e.40 -~e.40 :ARG0 m2 :ARG1 (s4 / signal-07~e.45 :ARG0 (p5 / pathway :name (n8 / name :op1 "PI3K/AKT"~e.42,44)))) :ARG1-of (d / describe-01 :ARG0 (p6 / publication :ARG1-of (c / cite-01 :ARG2 (a3 / and~e.28 :op1 9~e.47 :op2 10~e.49))))))) # ::id bio.ras_0003.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We utilized an unbiased mass spectrometry - based approach to identify ubiquitination sites of Ras . # ::alignments 0-1.1 1-1 3-1.2.1 3-1.2.1.1 3-1.2.1.1.r 4-1.2.2.1.1 5-1.2.2.1 7-1.2.2 8-1.2 10-1.3 11-1.3.2.2 12-1.3.2 13-1.3.2.1.r 14-1.3.2.1.1.1 (u / utilize-01~e.1 :ARG0 (w / we~e.0) :ARG1 (a / approach-02~e.8 :ARG1-of (b / bias-01~e.3 :polarity~e.3 -~e.3) :ARG1-of (b2 / base-02~e.7 :ARG2 (s / spectrometry~e.5 :mod (m / mass~e.4)))) :purpose (i / identify-01~e.10 :ARG0 w :ARG1 (p / protein-segment~e.12 :part-of~e.13 (e / enzyme :name (n / name :op1 "Ras"~e.14)) :ARG1-of (u2 / ubiquitinate-01~e.11)))) # ::id bio.ras_0003.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok His - tagged ubiquitin and Flag - tagged K @-@ Ras4B ( K @-@ Ras hereafter ) were expressed in HEK293T cells at levels similar to endogenous K @-@ Ras ( Fig. 1B ) and subjected to sequential affinity chromatography . # ::alignments 2-1.1.1.1.2 2-1.1.1.2.3 3-1.1.1.1.1.1 5-1.1.1.2.3.1.1.1 7-1.1.1.2.3 8-1.1.1.2.1.1 8-1.1.1.2.2.1 10-1.1.1.2.1.1 12-1.1.1.2.1.1 12-1.1.1.2.2.1 14-1.1.1.2.2.1 18-1.1 18-1.1.3.1.1.1 19-1.1.2.r 20-1.1.2.1.1 21-1.1.2 22-1.1.3.r 23-1.1.3 23-1.1.3.1.1 24-1.1.3.1 25-1.1.3.1.1.1.1.r 26-1.1.3.1.1.1.1.2 27-1.1.1.2.1.1 27-1.1.1.2.2.1 27-1.1.3.1.1.1.1.1.1 29-1.1.1.2.2.1 29-1.1.3.1.1.1.1.1.1 31-1.1.4.1 32-1.1.4.1.1 34-1 35-1.2 36-1.2.2.r 37-1.2.2.2 38-1.2.2.1 39-1.2.2 (a3 / and~e.34 :op1 (e2 / express-03~e.18 :ARG2 (a / and :op1 (p / protein :name (n / name :op1 "ubiquitin"~e.3) :ARG1-of (t / tag-01~e.2 :ARG2 (a2 / amino-acid :name (n3 / name :op1 "histidine")))) :op2 (e / enzyme :name (n2 / name :op1 "K-Ras4B"~e.8,10,12,27) :name (n7 / name :op1 "K-Ras"~e.8,12,14,27,29) :ARG1-of (t2 / tag-01~e.2,7 :ARG2 (p2 / protein-segment :name (n4 / name :op1 "Flag"~e.5))))) :ARG3~e.19 (c / cell-line~e.21 :name (n5 / name :op1 "HEK293T"~e.20)) :degree~e.22 (l / level~e.23 :ARG1-of (r / resemble-01~e.24 :ARG2 (l2 / level~e.23 :degree-of (e4 / express-03~e.18 :ARG2~e.25 (e3 / enzyme :name (n6 / name :op1 "K-Ras"~e.27,29) :mod (e5 / endogenous~e.26)))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.31 :mod "1B"~e.32))) :op2 (s / subject-01~e.35 :ARG1 a :ARG2~e.36 (c2 / chromatography~e.39 :mod (a4 / affinity~e.38) :mod (s2 / sequence~e.37)))) # ::id bio.ras_0003.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok His - ubiquitinated proteins were purified by Co2+ metal affinity chromatography in 8M urea denaturing conditions . # ::alignments 2-1.1.1 3-1.1 5-1 9-1.2.1 10-1.2 13-1.2.2.2.1.1 14-1.2.2 15-1.2.2.r (p / purify-01~e.5 :ARG1 (p2 / protein~e.3 :ARG3-of (u / ubiquitinate-01~e.2 :mod (a / amino-acid :name (n / name :op1 "histidine")))) :manner (c / chromatography~e.10 :mod (a2 / affinity~e.9 :topic (c3 / copper :ARG1-of (i / ionize-01 :value "2+"))) :condition~e.15 (d2 / denature-01~e.14 :ARG1 p2 :ARG4 (s / small-molecule :name (n3 / name :op1 "urea"~e.13) :mod (c2 / concentration-quantity :quant 8 :unit (m / molar)))))) # ::id bio.ras_0003.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok His - ubiquitinated K @-@ Ras was subsequently purified with anti - Flag resin . # ::alignments 2-1.1.2 3-1.1.1.1 5-1.1.1.1 7-1.2 7-1.2.r 8-1 9-1.3.r 10-1.3.1 12-1.3.1.1.1.1 13-1.3 (p / purify-01~e.8 :ARG1 (e / enzyme :name (n / name :op1 "K-Ras"~e.3,5) :ARG3-of (u / ubiquitinate-01~e.2 :mod (a / amino-acid :name (n2 / name :op1 "histidine")))) :time~e.7 (s / subsequent~e.7) :instrument~e.9 (r / resin~e.13 :ARG0-of (c / counter-01~e.10 :ARG1 (p2 / protein-segment :name (n3 / name :op1 "Flag"~e.12))))) # ::id bio.ras_0003.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Following purification , mono @- and di @- ubiquitinated K @-@ Ras appeared to be the major ubiquitination forms , which is consistent with the endogenous K @-@ Ras ubiquitination pattern ( Fig. 1 , A and B ) . # ::alignments 0-1.2 1-1.2.1 3-1.2.1.1 4-1.2.1.1 5-1.2.1.1 6-1.2.1.1 7-1.2.1.1 8-1.2.1.1 9-1.2.1.1 10-1.2.1.1 11-1.2.1.1 12-1 13-1.1.r 14-1.1.3.r 16-1.1.2 17-1.1.1 17-1.1.3.2 18-1.1 21-1.1.3.r 22-1.3 23-1.3.1.r 25-1.3.1.1.1.2 26-1.3.1.1.1.1.1 28-1.3.1.1.1.1.1 29-1.3.1.1 30-1.3.1 32-1.4.1.1 32-1.4.1.2 33-1.1.3.2.1.1 36-1.4.1 (a / appear-02~e.12 :ARG1~e.13 (f2 / form~e.18 :mod (u2 / ubiquitinate-01~e.17) :ARG1-of (m / major-02~e.16) :domain~e.14,21 (e / enzyme :name (n / name :op1 "K-Ras") :ARG3-of (u / ubiquitinate-01~e.17 :quant (o / or :op1 1~e.33 :op2 2)))) :ARG1-of (f / follow-01~e.0 :ARG2 (p / purify-01~e.1 :ARG1 e~e.3,4,5,6,7,8,9,10,11)) :ARG1-of (c / consistent-01~e.22 :ARG2~e.23 (p2 / pattern~e.30 :topic (u3 / ubiquitinate-01~e.29 :ARG1 (e2 / enzyme :name (n2 / name :op1 "K-Ras"~e.26,28) :mod (e3 / endogenous~e.25))))) :ARG1-of (d / describe-01 :ARG0 (a2 / and~e.36 :op1 (f3 / figure~e.32 :mod "1A") :op2 (f4 / figure~e.32 :mod "1B")))) # ::id bio.ras_0003.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok H @-@ Ras ubiquitination sites were also determined by the same approach . # ::alignments 0-1.1.2.1.1 2-1.1.2.1.1 3-1.1.1 4-1.1 6-1.2 7-1 8-1.3.r 10-1.3.1 11-1.3 (d / determine-01~e.7 :ARG1 (p / protein-segment~e.4 :ARG1-of (u / ubiquitinate-01~e.3) :part-of (e / enzyme :name (n / name :op1 "H-Ras"~e.0,2))) :mod (a / also~e.6) :manner~e.8 (a2 / approach-02~e.11 :ARG1-of (s / same-01~e.10))) # ::id bio.ras_0003.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Tandem mass spectrometric analysis of tryptic fragments from the bands migrating at the positions expected for mono @- and di @- ubiquitinated Ras revealed ubiquitination at Lys residues 104 and 147 of K @-@ Ras , and Lys residues 117 , 147 and 170 for H @-@ Ras ( fig. S1C ) . # ::alignments 0-1.1.2.2 1-1.1.2.1 2-1.1.2 3-1.1 4-1.1.1.r 5-1.1.1.2.1.1 6-1.1.1 7-1.1.1.1.r 9-1.1.1.1 10-1.1.1.1.1 11-1.1.1.1.1.1.1 13-1.1.1.1.1.1 14-1.1.1.1.1.1.1.2 16-1.1.1.1.1.1.1.1.2.1.1 16-1.1.1.1.1.1.1.1.2.1.r 19-1.1.1.1.1.1.1.1.2.1.2 19-1.1.1.1.1.1.1.1.2.1.r 21-1.1.1.1.1.1.1.1.2 21-1.2 22-1.1.1.1.1.1.1.1.1.1 23-1 24-1.1.1.1.1.1.1.1.2 24-1.2 25-1.1.1.1.1.1.1 25-1.2.1.r 26-1.2.1.1.1.1.2.1 26-1.2.1.1.2.1.2.1 26-1.2.1.2.1.1.2.1 26-1.2.1.2.2.1.2.1 27-1.2.1.1.1 27-1.2.1.1.2 27-1.2.1.2.1 27-1.2.1.2.2 28-1.2.1.1.1.1.1 29-1.2.1.1 30-1.2.1.1.2.1.1 32-1.2.1.1.3.1.1 34-1.2.1.1.3.1.1 36-1.2.1 36-1.2.1.1 36-1.2.1.1.r 36-1.2.1.2 37-1.2.1.1.2.1.2.1 37-1.2.1.2.1.1.2.1 37-1.2.1.2.2.1.2.1 37-1.2.1.2.3.1.2.1 38-1.2.1.1.2 38-1.2.1.2.1 38-1.2.1.2.2 38-1.2.1.2.3 39-1.2.1.2.1.1.1 41-1.2.1.2.2.1.1 43-1.2.1.2.3.1.1 44-1.2.1.2.r 45-1.2.1.2.4.1.1 47-1.2.1.2.4.1.1 49-1.3.1 50-1.3.1.1 (r / reveal-01~e.23 :ARG0 (a / analyze-01~e.3 :ARG1~e.4 (f / fragment~e.6 :source~e.7 (b / band~e.9 :ARG0-of (m / migrate-01~e.10 :ARG2 (p / position~e.13 :ARG2-of (b2 / be-located-at-91~e.11,25 :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.22) :ARG3-of (u / ubiquitinate-01~e.21,24 :quant~e.16,19 (o / or :op1 1~e.16 :op2 2~e.19))) :ARG1-of (e4 / expect-01~e.14))))) :mod (e5 / enzyme :name (n9 / name :op1 "trypsin"~e.5))) :manner (s / spectrometry~e.2 :mod (m2 / mass~e.1) :mod (t2 / tandem~e.0))) :ARG1 (u2 / ubiquitinate-01~e.21,24 :ARG1~e.25 (a2 / and~e.36 :op1~e.36 (a3 / and~e.29,36 :op1 (r2 / residue~e.27 :mod (a4 / amino-acid :mod 104~e.28 :name (n4 / name :op1 "lysine"~e.26))) :op2 (r3 / residue~e.27,38 :mod (a5 / amino-acid :mod 147~e.30 :name (n5 / name :op1 "lysine"~e.26,37))) :part-of (e2 / enzyme :name (n2 / name :op1 "K-Ras"~e.32,34))) :op2~e.44 (a6 / and~e.36 :op1 (r4 / residue~e.27,38 :mod (a7 / amino-acid :mod 117~e.39 :name (n6 / name :op1 "lysine"~e.26,37))) :op2 (r5 / residue~e.27,38 :mod (a8 / amino-acid :mod 147~e.41 :name (n7 / name :op1 "lysine"~e.26,37))) :op3 (r6 / residue~e.38 :mod (a9 / amino-acid :mod 170~e.43 :name (n8 / name :op1 "lysine"~e.37))) :part-of (e3 / enzyme :name (n3 / name :op1 "H-Ras"~e.45,47))))) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.49 :mod "S1C"~e.50))) # ::id bio.ras_0003.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The tryptic peptide with ubiquitination at Lys147 ( K147 ) was the most frequently observed peptide for both K @-@ Ras and H @-@ Ras , while Lys117 appeared as a secondary major ubiquitination site in H @-@ Ras . # ::alignments 1-1.1.2.1.1.1.1 2-1.1 2-1.1.2 4-1.1.2.2 4-1.1.2.2.3 4-1.1.2.2.3.r 10-1.1.2.r 12-1.1.3.1.1 13-1.1.3.1 14-1.1.3 15-1.1 15-1.1.2 18-1.1.1.1.1.1 20-1.1.1.1.1.1 20-1.1.1.2.1.1 21-1.1.1 22-1.1.1.2.1.1 24-1.1.1.1.1.1 24-1.1.1.2.1.1 26-1 28-1.2 29-1.2.1.r 31-1.2.1.3 32-1.2.1.1 33-1.2.1.2 34-1.2.1 36-1.1.1.2.1.1 38-1.1.1.1.1.1 38-1.1.1.2.1.1 (c / contrast-01~e.26 :ARG1 (p / peptide~e.2,15 :part-of (a / and~e.21 :op1 (e / enzyme :name (n / name :op1 "K-Ras"~e.18,20,24,38)) :op2 (e2 / enzyme :name (n2 / name :op1 "H-Ras"~e.20,22,24,36,38))) :domain~e.10 (p2 / peptide~e.2,15 :ARG3-of (h / hydrolyze-01 :ARG2 (e3 / enzyme :name (n3 / name :op1 "trypsin"~e.1))) :part (a2 / amino-acid~e.4 :mod 147 :name (n4 / name :op1 "lysine") :ARG1-of~e.4 (u / ubiquitinate-01~e.4))) :ARG1-of (o / observe-01~e.14 :ARG1-of (f / frequent-02~e.13 :degree (m / most~e.12)))) :ARG2 (a3 / appear-01~e.28 :ARG1~e.29 (p3 / protein-segment~e.34 :ARG1-of (m2 / major-02~e.32) :ARG1-of (u2 / ubiquitinate-01~e.33) :mod (s / secondary~e.31) :domain (a4 / amino-acid :mod 117 :name (n5 / name :op1 "lysine")) :part-of e2))) # ::id bmtr_0006.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A New Dimension to Ras Function : A Novel Role for Nucleotide @-@ Free Ras in Class II Phosphatidylinositol 3 @-@ Kinase Beta ( PI3KC2β) Regulation ( PMC3441633 ) # ::alignments 1-1.1 2-1 4-1.2.1.1.1 5-1.2 8-1.3.1.1 9-1.3.1 10-1.3.1.2.r 11-1.3.1.2.2.1 13-1.3.1.2 13-1.3.1.2.2 13-1.3.1.2.2.r 14-1.3.1.2.1.1 15-1.3.1.3.r 16-1.3.1.3.2.2 17-1.3.1.3.2.2.1.1 18-1.3.1.3.2.1.1 19-1.3.1.3.2.1.2 21-1.3.1.3.2.1.2 22-1.3.1.3.2.1.3 25-1.3.1.3 27-1.4.1.1 (d3 / dimension~e.2 :ARG1-of (n2 / new-01~e.1) :topic (f / function-01~e.5 :ARG0 (e / enzyme :name (n / name :op1 "Ras"~e.4))) :ARG0-of (m2 / mean-01 :ARG1 (r / role~e.9 :mod (n3 / novel~e.8) :mod~e.10 (e2 / enzyme~e.13 :name (n4 / name :op1 "Ras"~e.14) :ARG1-of~e.13 (f2 / free-04~e.13 :ARG2 (n5 / nucleotide~e.11))) :purpose~e.15 (r2 / regulate-01~e.25 :ARG0 e2 :ARG1 (e3 / enzyme :name (n6 / name :op1 "Phosphatidylinositol"~e.18 :op2 "3-Kinase"~e.19,21 :op3 "Beta"~e.22) :mod (c / class~e.16 :ord (o / ordinal-entity :value 2~e.17)))))) :ARG1-of (d2 / describe-01 :ARG0 (p / publication-91 :ARG8 "PMC3441633"~e.27))) # ::id bmtr_0006.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Ras , like all GTPases , cycles between an inactive GDP @-@ bound state and an active GTP @-@ bound state . # ::alignments 0-1.1.1.1 0-1.2.1.1 0-1.3.1.1 3-1.1.2.1.2 6-1 9-1.2 9-1.2.2 9-1.2.2.1 9-1.2.2.1.r 9-1.2.2.r 9-1.3 9-1.3.2 9-1.3.2.r 10-1.2.3.1.1.1 12-1.2.3 12-1.3.3 16-1.2 16-1.2.2 16-1.2.2.r 16-1.3 16-1.3.2 16-1.3.2.r 17-1.3.3.1.1.1 19-1.2.3 19-1.3.3 (c / cycle-02~e.6 :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.0) :ARG1-of (s / same-01 :ARG2 (e2 / enzyme :name (n2 / name :op1 "GTPase") :mod (a / all~e.3)))) :ARG3 (e5 / enzyme~e.9,16 :name (n5 / name :op1 "Ras"~e.0) :ARG0-of~e.9,16 (a2 / activity-06~e.9,16 :polarity~e.9 -~e.9) :ARG1-of (b2 / bind-01~e.12,19 :ARG2 (s3 / small-molecule :name (n3 / name :op1 "GDP"~e.10)))) :ARG4 (e4 / enzyme~e.9,16 :name (n6 / name :op1 "Ras"~e.0) :ARG0-of~e.9,16 (a3 / activity-06~e.9,16) :ARG1-of (b3 / bind-01~e.12,19 :ARG2 (s5 / small-molecule :name (n4 / name :op1 "GTP"~e.17))))) # ::id bmtr_0006.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The transition from the inactive to active state requires formation of nucleotide @-@ free Ras through the action of exchange factors . # ::alignments 1-1.1 4-1.1.2.1 4-1.1.2.1.1 4-1.1.2.1.1.r 6-1.1.1.1 6-1.1.2.1 7-1.1.1 7-1.1.2 8-1 9-1.2 10-1.2.1.r 11-1.2.1.2.1 13-1.2.1 13-1.2.1.2 13-1.2.1.2.r 14-1.2.1.1.1 17-1.2.2 18-1.2.2.1.r 19-1.2.2.1.1 20-1.2.2.1 (r / require-01~e.8 :ARG0 (t / transition-01~e.1 :ARG2 (s2 / state~e.7 :ARG0-of (a2 / activity-06~e.6)) :ARG3 (s / state~e.7 :ARG0-of (a / activity-06~e.4,6 :polarity~e.4 -~e.4))) :ARG1 (f / form-01~e.9 :ARG1~e.10 (e / enzyme~e.13 :name (n / name :op1 "Ras"~e.14) :ARG1-of~e.13 (f2 / free-04~e.13 :ARG2 (n2 / nucleotide~e.11))) :manner (a3 / act-01~e.17 :ARG0~e.18 (f3 / factor~e.20 :ARG0-of (e2 / exchange-01~e.19))))) # ::id bmtr_0006.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This state is considered to be a short @-@ lived transition state intermediate in vivo [ 36 ] based on the relatively high GTP : GDP ratio in vivo [ 37 ] , the ability of GTP to dissociate the GEF @-@ Ras complex in vitro [ 31 ] , and the assumption that there are no proteins in vivo that might stabilize nucleotide @-@ free Ras and prevent GTP loading . # ::alignments 0-1.1.6 1-1.1 3-1 7-1.1.2.1 9-1.1.2 10-1.1.1 11-1.1 12-1.1.3 13-1.1.3.1 14-1.1.3.1 16-1.1.5.1.1.1 18-1.1.4 19-1.1.4.1.r 21-1.1.4.1.1.4.1 22-1.1.4.1.1.4 23-1.1.4.1.1.1.1.1 25-1.1.4.1.1.2.2.1 26-1.1.4.1.1 27-1.1.3.1 28-1.1.3.1 30-1.1.4.1.1.5.1.1.1 34-1.1.4.1.2 35-1.1.4.1.1 35-1.1.4.1.2.2.r 36-1.1.4.1.2.2.1 38-1.1.4.1.2.2 40-1.1.4.1.2.2.2.1.1.1 42-1.1.4.1.2.2.2.2.1.1 43-1.1.4.1.2.2.2 44-1.1.4.1.2.2.3 45-1.1.4.1.2.2.3 47-1.1.4.1.2.3.1.1.1 50-1.1.4.1 52-1.1.4.1.3 56-1.1.4.1.3.1.1 56-1.1.4.1.3.1.1.r 57-1.1.4.1.3.1 58-1.1.4.1.3.1.2 59-1.1.4.1.3.1.2 61-1.1.4.1.3.1.3.2 62-1.1.4.1.3.1.3 63-1.1.4.1.3.1.3.1.2.1 65-1.1.4.1.3.1.3.1 65-1.1.4.1.3.1.3.1.2 65-1.1.4.1.3.1.3.1.2.r 66-1.1.4.1.3.1.3.1.1.1 68-1.1.4.1.3.1.4 69-1.1.4.1.3.1.4.1.1 70-1.1.4.1.3.1.4.1 (c / consider-01~e.3 :ARG1 (s3 / state~e.1,11 :ARG1-of (t / transition-01~e.10) :ARG0-of (l / live-01~e.9 :ARG1-of (s4 / short-07~e.7)) :mod (i / intermediate~e.12 :manner (i2 / in-vivo~e.13,14,27,28)) :ARG1-of (b / base-02~e.18 :ARG2~e.19 (a / and~e.50 :op1 (r / ratio-of~e.26,35 :op1 (s / small-molecule :name (n / name :op1 "GTP"~e.23)) :op2 (s2 / small-molecule :wiki "Guanosine_diphosphate" :name (n2 / name :op1 "GDP"~e.25)) :manner i2 :ARG1-of (h / high-02~e.22 :ARG2-of (r2 / relative-05~e.21)) :ARG1-of (d2 / describe-01 :ARG0 (p2 / publication-91 :ARG1-of (c2 / cite-01 :ARG2 37~e.30)))) :op2 (c5 / capable-01~e.34 :ARG1 s :ARG2~e.35 (d / dissociate-01~e.38 :ARG0 s~e.36 :ARG1 (m / macro-molecular-complex~e.43 :part (p3 / protein :name (n4 / name :op1 "GEF"~e.40)) :part (e / enzyme :name (n3 / name :op1 "Ras"~e.42))) :manner (i3 / in-vitro~e.44,45)) :ARG1-of (d3 / describe-01 :ARG0 (p7 / publication-91 :ARG1-of (c3 / cite-01 :ARG2 31~e.47)))) :op3 (a2 / assume-02~e.52 :ARG1 (p4 / protein~e.57 :polarity~e.56 -~e.56 :manner i2~e.58,59 :ARG0-of (s5 / stabilize-01~e.62 :ARG1 (e2 / enzyme~e.65 :name (n5 / name :op1 "Ras"~e.66) :ARG1-of~e.65 (f / free-04~e.65 :ARG2 (n6 / nucleotide~e.63))) :ARG1-of (p5 / possible-01~e.61)) :ARG0-of (p6 / prevent-01~e.68 :ARG1 (l2 / load-01~e.70 :ARG2 s~e.69) :ARG1-of p5))))) :ARG1-of (d4 / describe-01 :ARG0 (p8 / publication-91 :ARG1-of (c4 / cite-01 :ARG2 36~e.16))) :mod (t2 / this~e.0))) # ::id bmtr_0006.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , our results provide the first direct evidence for a protein that may stabilize nucleotide @-@ free Ras in vivo . # ::alignments 0-1 2-1.1.1.2 2-1.1.1.2.r 3-1.1.1 3-1.1.1.1 3-1.1.1.1.r 4-1.1 6-1.1.2.2 6-1.1.2.2.1 6-1.1.2.2.1.r 7-1.1.2.1 8-1.1.2 9-1.1.2.3.r 11-1.1.2.3 13-1.1.2.3.1.2 14-1.1.2.3.1 15-1.1.2.3.1.1.2.1 17-1.1.2.3.1.1 17-1.1.2.3.1.1.2 17-1.1.2.3.1.1.2.r 18-1.1.2.3.1.1.1.1 19-1.1.2.3.1.3 20-1.1.2.3.1.3 (c / contrast-01~e.0 :ARG2 (p / provide-01~e.4 :ARG0 (t / thing~e.3 :ARG2-of~e.3 (r / result-01~e.3) :poss~e.2 (w / we~e.2)) :ARG1 (e2 / evidence~e.8 :ARG1-of (d / direct-02~e.7) :ord (o2 / ordinal-entity~e.6 :value~e.6 1~e.6) :topic~e.9 (p2 / protein~e.11 :ARG0-of (s / stabilize-01~e.14 :ARG1 (e / enzyme~e.17 :name (n / name :op1 "Ras"~e.18) :ARG1-of~e.17 (f / free-04~e.17 :ARG2 (n2 / nucleotide~e.15))) :ARG1-of (p3 / possible-01~e.13) :manner (i / in-vivo~e.19,20)))))) # ::id bmtr_0006.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok We demonstrate that the RBD of PI3KC2β binds nucleotide @-@ free Ras in vitro ( Fig . 5 ) . # ::alignments 0-1.1 1-1 2-1.2.r 4-1.2.1.1.1 6-1.2.1.2.1.1 7-1.2 8-1.2.2.2.1 10-1.2.2 10-1.2.2.2 10-1.2.2.2.r 11-1.2.2.1.1 12-1.2.3 13-1.2.3 15-1.3.1 17-1.3.1.1 (d / demonstrate-01~e.1 :ARG0 (w / we~e.0) :ARG1~e.2 (b / bind-01~e.7 :ARG1 (p / protein-segment :name (n2 / name :op1 "RBD"~e.4) :part-of (e2 / enzyme :name (n3 / name :op1 "PI3KC2β"~e.6))) :ARG2 (e / enzyme~e.10 :name (n / name :op1 "Ras"~e.11) :ARG1-of~e.10 (f / free-04~e.10 :ARG2 (n4 / nucleotide~e.8))) :manner (i / in-vitro~e.12,13)) :ARG1-of (d2 / describe-01 :ARG0 (f2 / figure~e.15 :mod 5~e.17))) # ::id bmtr_0006.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok In contrast to the GEF @-@ Ras complex , which is disrupted by addition of guanine nucleotides , the PI3KC2β RBD @-@ Ras complex is stable even in the presence of high concentrations of GTP or GDP . # ::alignments 1-1.2 2-1.2.1.r 4-1.2.1.1.1.1 6-1.2.1.2 7-1.2.1 11-1.2.1.3 12-1.2.1.3.1.r 13-1.2.1.3.1 14-1.2.1.3.1.1.r 15-1.2.1.3.1.1.1 16-1.2.1.3.1.1 19-1.1.1.2.1.1 20-1.1.1.1.1 22-1.1.2.1.1 23-1.1 25-1 26-1.3.2 29-1.3 30-1.3.1.r 31-1.3.1.2 32-1.3.1 33-1.3.1.1.r 34-1.3.1.1.1.1.1 35-1.3.1.1 36-1.3.1.1.2.2.1 (s3 / stable-03~e.25 :ARG1 (m / macro-molecular-complex~e.23 :part (p2 / protein-segment :name (n3 / name :op1 "RBD"~e.20) :part-of (e / enzyme :name (n4 / name :op1 "PI3KC2β"~e.19))) :part (e2 / enzyme :name (n5 / name :op1 "Ras"~e.22))) :ARG1-of (c2 / contrast-01~e.1 :ARG2~e.2 (m2 / macro-molecular-complex~e.7 :part (p3 / protein :name (n6 / name :op1 "GEF"~e.4)) :part e2~e.6 :ARG1-of (d2 / disrupt-01~e.11 :ARG0~e.12 (a / add-02~e.13 :ARG1~e.14 (n7 / nucleotide~e.16 :mod (g2 / guanine~e.15)) :ARG2 m2)))) :condition (p / present-02~e.29 :ARG1~e.30 (c / concentrate-02~e.32 :ARG0~e.33 (o / or~e.35 :op1 (s / small-molecule :name (n / name :op1 "GTP"~e.34)) :op2 (s2 / small-molecule :wiki "Guanosine_diphosphate" :name (n2 / name :op1 "GDP"~e.36))) :ARG1-of (h / high-02~e.31)) :mod (e3 / even~e.26))) # ::id bmtr_0006.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok These data suggest that PI3KC2β binding to nucleotide @-@ free Ras in vivo may prevent loading of nucleotides onto Ras . # ::alignments 0-1.1.1 1-1.1 2-1 3-1.2.r 4-1.2.1.1.1.1.1 5-1.2.1.1 6-1.2.1.1.2.r 7-1.2.1.1.2.2.1 9-1.2.1.1.2 9-1.2.1.1.2.2 9-1.2.1.1.2.2.r 10-1.2.1.1.2.1.1 11-1.2.1.1.3 12-1.2.1.1.3 13-1.2 14-1.2.1 15-1.2.1.2 16-1.2.1.2.2.r 17-1.2.1.2.2 19-1.2.1.2.1 (s / suggest-01~e.2 :ARG0 (d2 / data~e.1 :mod (t / this~e.0)) :ARG1~e.3 (p / possible-01~e.13 :ARG1 (p2 / prevent-01~e.14 :ARG0 (b / bind-01~e.5 :ARG1 (e2 / enzyme :name (n2 / name :op1 "PI3KC2β"~e.4)) :ARG2~e.6 (e / enzyme~e.9 :name (n / name :op1 "Ras"~e.10) :ARG1-of~e.9 (f / free-04~e.9 :ARG2 (n3 / nucleotide~e.7))) :manner (i / in-vivo~e.11,12)) :ARG1 (l / load-01~e.15 :ARG1 e~e.19 :ARG2~e.16 (n4 / nucleotide~e.17))))) # ::id bmtr_0006.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Although current methods do not allow for detection of nucleotide @-@ free GTPases in vivo , our BiFC results provide additional support for our model . # ::alignments 0-1.4.r 1-1.4.2.1 2-1.4.2 4-1.4.1 4-1.4.1.r 5-1.4 6-1.4.3.r 7-1.4.3 8-1.4.3.1.r 9-1.4.3.1.2.1 11-1.4.3.1 11-1.4.3.1.2 11-1.4.3.1.2.r 13-1.4.3.2 14-1.4.3.2 16-1.1.2 16-1.1.2.r 18-1.1 18-1.1.1 18-1.1.1.r 19-1 21-1.2 22-1.3.r 23-1.3.1 23-1.3.1.r 24-1.3 (p / provide-01~e.19 :ARG0 (t / thing~e.18 :ARG2-of~e.18 (r / result-01~e.18 :ARG1 (c2 / complement-01 :manner (f2 / fluorescence :mod (b / biomolecular)))) :poss~e.16 w~e.16) :ARG1 (s / support-01~e.21 :ARG1-of (a / add-02)) :ARG2~e.22 (m / model~e.24 :poss~e.23 (w / we~e.23)) :concession~e.0 (a2 / allow-01~e.5 :polarity~e.4 -~e.4 :ARG0 (m2 / method~e.2 :time (c / current~e.1)) :ARG1~e.6 (d / detect-01~e.7 :ARG1~e.8 (e / enzyme~e.11 :name (n / name :op1 "GTPase") :ARG1-of~e.11 (f / free-04~e.11 :ARG2 (n2 / nucleotide~e.9))) :manner (i / in-vivo~e.13,14)))) # ::id bmtr_0006.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PI3KC2β preferentially interacts with Ras17N , which has a 30 @-@ fold lower affinity for nucleotide compared to wild type Ras and therefore should exist for longer periods in the nucleotide @-@ free state . # ::alignments 0-1.1.1.1 1-1.3 2-1 3-1.2.r 4-1.2.1.1 7-1.2 7-1.2.2 7-1.2.2.r 9-1.2.2.1.1.3.1 11-1.2.2.1.1.3 12-1.2.2.1.1 12-1.2.2.1.1.1 12-1.2.2.1.1.1.r 13-1.2.2.1 14-1.2.2.1.2.r 15-1.2.2.1.2 16-1.2.2.1.1.2.r 18-1.2.2.1.1.2.2 19-1.2.2.1.1.2.2 20-1.2.2.1.1.2.1.1 22-1.2.2.2 23-1.2.2.2.1 24-1.2.2.2.1.1 25-1.2.2.2.1.1.3.r 26-1.2.2.2.1.1.3 26-1.2.2.2.1.1.3.1 26-1.2.2.2.1.1.3.1.r 28-1.2.2.2.1.1.2.r 30-1.2.2.2.1.1.2.1.1 32-1.2.2.2.1.1.2.1 33-1.2.2.2.1.1.2 (i / interact-01~e.2 :ARG0 (e2 / enzyme :name (n2 / name :op1 "PI3KC2β"~e.0)) :ARG1~e.3 (e / enzyme~e.7 :name (n / name :op1 "Ras17N"~e.4) :ARG0-of~e.7 (h / have-03~e.7 :ARG1 (a / affinity~e.13 :ARG1-of (l / low-04~e.12 :degree~e.12 (m / more~e.12) :compared-to~e.16 (e4 / enzyme :name (n5 / name :op1 "Ras"~e.20) :mod (w / wild-type~e.18,19)) :quant (p3 / product-of~e.11 :op1 30~e.9)) :topic~e.14 (n4 / nucleotide~e.15)) :ARG0-of (c / cause-01~e.22 :ARG1 (r / recommend-01~e.23 :ARG1 (e6 / exist-01~e.24 :ARG1 e :ARG2~e.28 (s / state~e.33 :ARG1-of (f / free-04~e.32 :ARG2 n4~e.30)) :ARG1-of~e.25 (l2 / long-03~e.26 :degree~e.26 (m3 / more~e.26))))))) :ARG1-of (p / prefer-01~e.1)) # ::id bmtr_0006.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As a result , BiFC traps this form of Ras resulting in greater fluorescence complementation for Ras17N ( and Ras17N/69N ) compared to wild type or constitutively activated Ras ( 61L or 12V ) . # ::alignments 2-1.3 5-1 6-1.2.2 7-1.2 8-1.2.1.r 9-1.2.1.1.1 10-1.3 11-1.3.1.r 12-1.3.1.3 12-1.3.1.3.1 12-1.3.1.3.1.r 13-1.3.1.2 14-1.1 14-1.3.1 15-1.3.1.1.r 16-1.3.1.1.1.1.1 18-1.3.1.1 19-1.3.1.1.2.1.1 21-1.3.1.3.2.r 23-1.3.1.3.2.1.2 24-1.3.1.3.2.1.2 25-1.3.1.3.2 26-1.3.1.3.2.3.2.1 26-1.3.1.3.2.3.2.1.r 27-1.3.1.3.2.3.2 28-1.3.1.3.2.1.1.1 28-1.3.1.3.2.2.1.1 28-1.3.1.3.2.3.1.1 30-1.3.1.3.2.2.2.1 31-1.3.1.3.2 32-1.3.1.3.2.3.3.1 (t / trap-01~e.5 :ARG0 (c2 / complement-01~e.14 :ARG1 (f3 / fluoresce-01 :mod (b2 / biomolecular))) :ARG1 (f / form~e.7 :mod~e.8 (e / enzyme :name (n / name :op1 "Ras"~e.9)) :mod (t2 / this~e.6)) :ARG1-of (r / result-01~e.2,10 :ARG2~e.11 (c / complement-01~e.14 :ARG2~e.15 (a3 / and~e.18 :op1 (e2 / enzyme :name (n2 / name :op1 "Ras17N"~e.16)) :op2 (e3 / enzyme :name (n3 / name :op1 "Ras17N/69N"~e.19))) :mod (f2 / fluorescence~e.13) :mod (g2 / great~e.12 :degree~e.12 (m2 / more~e.12) :compared-to~e.21 (o / or~e.25,31 :op1 (e4 / enzyme :name (n4 / name :op1 "Ras"~e.28) :mod (w / wild-type~e.23,24)) :op2 (e5 / enzyme :name (n5 / name :op1 "Ras"~e.28) :ARG2-of (m / mutate-01 :value "61L"~e.30) :ARG1-of a) :op3 (e6 / enzyme :name (n6 / name :op1 "Ras"~e.28) :ARG1-of (a / activate-01~e.27 :manner~e.26 (c3 / constitutive~e.26)) :ARG2-of (m3 / mutate-01 :value "12V"~e.32))))))) # ::id bmtr_0007.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Phosphorylation of ASPP2 by RAS @/@ MAPK Pathway Is Critical for Its Full Pro @-@ Apoptotic Function ( PMC3847091 ) # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.1 3-1.1.2.r 4-1.1.2.1.1 6-1.1.2.1.1 7-1.1.2 9-1 10-1.2.r 11-1.2.1 11-1.2.1.r 12-1.2.3 13-1.2.2.1 15-1.2.2 16-1.2 18-1.3.1.1 (c / critical-02~e.9 :ARG1 (p / phosphorylate-01~e.0 :ARG1~e.1 (p4 / protein :name (n / name :op1 "ASPP2"~e.2)) :ARG2~e.3 (p2 / pathway~e.7 :name (n2 / name :op1 "RAS/MAPK"~e.4,6))) :ARG3~e.10 (f / function-01~e.16 :ARG0~e.11 p4~e.11 :ARG1 (a / apoptosis~e.15 :ARG1-of (f2 / favor-01~e.13 :ARG0 p4)) :degree (f3 / full~e.12)) :ARG1-of (d / describe-01 :ARG0 (p3 / publication-91 :ARG8 "PMC3847091"~e.18))) # ::id bmtr_0007.2 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A synthetic peptide encoding amino acids 824 @-@ 832 , with a phosphoserine at residue 827 , was used to raise antibodies . # ::alignments 1-1.1.1 2-1.1 3-1.1.2 4-1.1.2.1 5-1.1.2.1 6-1.1.2.1.1.1 8-1.1.2.1.1.2 14-1.1.2.1.2.1 15-1.1.2.1.2.1.1 18-1 20-1.2 21-1.2.1 (u / use-01~e.18 :ARG1 (p / peptide~e.2 :mod (s / synthetic~e.1) :ARG0-of (e / encode-01~e.3 :ARG1 (a / amino-acid~e.4,5 :quant (b2 / between :op1 824~e.6 :op2 832~e.8) :ARG2-of (i / include-01 :ARG1 (r3 / residue~e.14 :location 827~e.15 :ARG3-of (p2 / phosphorylate-01) :mod (a3 / amino-acid :name (n / name :op1 "serine"))))))) :ARG2 (r2 / raise-01~e.20 :ARG1 (a2 / antibody~e.21))) # ::id bmtr_0007.3 ::amr-annotator SDL-AMR-09 ::preferred # ::tok A polyclonal antibody NGH.S4 was purified by affinity column purification . # ::alignments 1-1.2.2 2-1.2 3-1.2.1.1 5-1 5-1.1 6-1.1.r 7-1.1.1 8-1.1.2 9-1.1 (p / purify-01~e.5 :ARG0~e.6 (p3 / purify-01~e.5,9 :mod (a2 / affinity~e.7) :instrument (c / column~e.8)) :ARG1 (a3 / antibody~e.2 :name (n / name :op1 "NGH.S4"~e.3) :mod (p2 / polyclonal~e.1))) # ::id bmtr_0007.4 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To test the efficacy of the purified phospho @-@ specific # ::alignments 1-1 3-1.1 6-1.1.1.1 7-1.1.1.2.1 9-1.1.1.2 (t / test-01~e.1 :ARG1 (e / efficacy~e.3 :poss (a / antibody :ARG1-of (p / purify-01~e.6) :ARG1-of (s / specific-02~e.9 :ARG2 (p2 / phosphorylate-01~e.7))))) # ::id bmtr_0007.5 ::amr-annotator SDL-AMR-09 ::preferred # ::tok antibody , a non @-@ radioactive in vitro phosphorylation assay was performed on the purified GST @-@ ASPP2 fragment ( 693 @-@ 1128 ) with recombinant MAPK1 . # ::alignments 3-1.1.1.2.1 3-1.1.1.2.1.r 5-1.1.1.2 6-1.1.1.1 7-1.1.1.1 8-1.1.1 9-1.1 11-1 12-1.2.r 14-1.2.3 15-1.2.1.1.1 17-1.2.1.1.1 20-1.2.2.1 22-1.2.2.2 24-1.1.2.r 25-1.1.2 25-1.1.2.2 25-1.1.2.2.r 26-1.1.2.1.1 (p2 / perform-02~e.11 :ARG1 (a / assay-01~e.9 :ARG1 (p / phosphorylate-01~e.8 :manner (i / in-vitro~e.6,7) :mod (r / radioactive~e.5 :polarity~e.3 -~e.3)) :instrument~e.24 (e / enzyme~e.25 :name (n2 / name :op1 "MAPK1"~e.26) :ARG0-of~e.25 (r2 / recombine-01~e.25))) :location~e.12 (p4 / protein-segment :part-of (p3 / protein :name (n / name :op1 "GST-ASPP2"~e.15,17)) :quant (b / between :op1 693~e.20 :op2 1128~e.22) :ARG1-of (p5 / purify-01~e.14))) # ::id bmtr_0007.6 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Figure 1C shows that the phosphospecific antibody is specific for the ASPP2 fragment phosphorylated in vitro by MAPK . # ::alignments 0-1.1 1-1.1.1 2-1 6-1.2.1 8-1.2 8-1.2.1.1 9-1.2.2.r 11-1.2.2.1.1.1 13-1.2.1.1.1 13-1.2.2.2 14-1.2.2.2.2 15-1.2.2.2.2 16-1.2.2.2.1.r 17-1.2.2.2.1.1.1 (s / show-01~e.2 :ARG0 (f / figure~e.0 :mod "1C"~e.1) :ARG1 (s2 / specific-02~e.8 :ARG1 (a / antibody~e.6 :ARG1-of (s3 / specific-02~e.8 :ARG2 (p2 / phosphorylate-01~e.13))) :ARG2~e.9 (p4 / protein-segment :part-of (p5 / protein :name (n2 / name :op1 "ASPP2"~e.11)) :ARG1-of (p3 / phosphorylate-01~e.13 :ARG2~e.16 (e / enzyme :name (n / name :op1 "MAPK"~e.17)) :manner (i / in-vitro~e.14,15))))) # ::id bmtr_0007.7 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To test whether endogenous ASPP2 could be phosphorylated in cells , Saos2 cells were grown in low serum for 50 hours to remove all background stimulation of RAS , after which the cells were stimulated with EGF and 20 % fetal calf serum ( FCS ) . # ::alignments 1-1.5 2-1.5.1.1 2-1.5.1.1.r 3-1.5.1.2.1.2 4-1.5.1.2.1.1.1 5-1.5.1 7-1.5.1.2 8-1.5.1.2.2.r 9-1.5.1.2.2 11-1.1.1.1 12-1.1 14-1 15-1.2.r 16-1.2.1 17-1.2 18-1.3.r 19-1.3.1 20-1.3.2 22-1.4 23-1.4.1.3 24-1.4.1.2 25-1.4.1 26-1.4.1.1.r 27-1.4.1.1.1.1 29-1.6 32-1.6.1.1 34-1.6.1 35-1.6.1.2.r 36-1.6.1.2.1.1.1 37-1.6.1.2 38-1.6.1.2.2.2.1 39-1.6.1.2.2.2 40-1.6.1.2.2.1 41-1.6.1.2.2.1.1 42-1.6.1.2.2 (g / grow-03~e.14 :ARG1 (c / cell-line~e.12 :name (n2 / name :op1 "Saos2"~e.11)) :location~e.15 (s / serum~e.17 :ARG1-of (l / low-04~e.16)) :duration~e.18 (t2 / temporal-quantity :quant 50~e.19 :unit (h2 / hour~e.20)) :purpose (r / remove-01~e.22 :ARG1 (s2 / stimulate-01~e.25 :ARG1~e.26 (e / enzyme :name (n / name :op1 "Ras"~e.27)) :manner (b / background~e.24) :mod (a / all~e.23))) :purpose (t / test-01~e.1 :ARG1 (p3 / possible-01~e.5 :mode~e.2 interrogative~e.2 :ARG1 (p4 / phosphorylate-01~e.7 :ARG1 (p2 / protein :name (n3 / name :op1 "ASPP2"~e.4) :mod (e3 / endogenous~e.3)) :location~e.8 (c2 / cell~e.9)))) :op1-of (a2 / after~e.29 :time-of (s3 / stimulate-01~e.34 :ARG1 c~e.32 :ARG2~e.35 (a3 / and~e.37 :op1 (p5 / protein :name (n4 / name :op1 "EGF"~e.36)) :op2 (s5 / serum~e.42 :source (f / fetus~e.40 :mod (c3 / calf~e.41)) :quant (p / percentage-entity~e.39 :value 20~e.38)))))) # ::id bmtr_0007.8 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Phosphorylated endogenous ASPP2 was detected by the phospho @-@ specific antibody 30 minutes after RAS stimulation ( Figure 1D ) . # ::alignments 0-1.2.3 1-1.2.2 2-1.2.1.1 4-1 5-1.1.r 7-1.1.1.1 9-1.1.1 10-1.1 11-1.3.2.1 12-1.3.2.2 13-1.3 14-1.3.1.1.1.1 15-1.3.1 17-1.4.1 18-1.4.1.1 (d / detect-01~e.4 :ARG0~e.5 (a / antibody~e.10 :ARG1-of (s / specific-02~e.9 :ARG2 p~e.7)) :ARG1 (p2 / protein :name (n2 / name :op1 "ASPP2"~e.2) :mod (e3 / endogenous~e.1) :ARG3-of (p / phosphorylate-01~e.0)) :time (a2 / after~e.13 :op1 (s2 / stimulate-01~e.15 :ARG1 (e / enzyme :name (n / name :op1 "Ras"~e.14))) :quant (t / temporal-quantity :quant 30~e.11 :unit (m / minute~e.12))) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.17 :mod "1D"~e.18))) # ::id bmtr_0007.9 ::amr-annotator SDL-AMR-09 ::preferred # ::tok ASPP2 phosphorylation was rapid and transient as 3 hours after EGF stimulation phosphorylated ASPP2 was barely detectable . # ::alignments 0-1.2.1.1.1.1 1-1.2.1 2-1.1.1.r 3-1.1 4-1 5-1.2 6-1.3.1.2.r 7-1.3.1.2.2.1 8-1.3.1.2.2.2 9-1.3.1.2 10-1.3.1.2.1.1.1.1 11-1.3.1.2.1 12-1.3.1.1.1.2 13-1.3.1.1.1.1.1 15-1.3.1.1.2 16-1.3.1.1 (a / and~e.4 :op1 (r / rapid~e.3 :domain~e.2 p2) :op2 (t2 / transient-02~e.5 :ARG1 (p2 / phosphorylate-01~e.1 :ARG1 (p4 / protein :name (n / name :op1 "ASPP2"~e.0)))) :ARG1-of (i / infer-01 :ARG2 (p3 / possible-01 :ARG1 (d / detect-01~e.16 :ARG1 (p5 / protein :name (n3 / name :op1 "ASPP2"~e.13) :ARG3-of (p / phosphorylate-01~e.12)) :degree (b / bare~e.15)) :time~e.6 (a2 / after~e.9 :op1 (s / stimulate-01~e.11 :ARG2 (p6 / protein :name (n2 / name :op1 "EGF"~e.10))) :quant (t / temporal-quantity :quant 3~e.7 :unit (h / hour~e.8)))))) # ::id bmtr_0007.10 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Moreover , with another different phospho @-@ ASPP2 antibody , ES1 , ASPP2 phosphorylation was also observed in a human colon cancer cell line HKe3 ER : HRASV12 cells , in which RAS activation is induced upon the addition of 4 @-@ hydroxytamoxifen ( 4 @-@ OHT ) [ 2,10,11 ] ( Figure 1E ) . # ::alignments 0-1 0-1.2.1 0-1.2.1.2.1.1 2-1.1.4.r 3-1.1.4.3 4-1.1.4.2 5-1.1.4.4.1.2 7-1.1.4.4.1.1.1 8-1.1.4 10-1.1.4.1.1 12-1.1.1.1.1.1 12-1.1.4.4.1.1.1 13-1.1.1 13-1.1.4.4.1.2 15-1.1.2 16-1.1 17-1.1.3.r 19-1.1.3.4 20-1.1.3.5.2.1 21-1.1.3.5.2.2 22-1.1.3 22-1.1.3.3.1 23-1.1.3 24-1.1.3.1.1 25-1.1.3.1.2 27-1.1.3.3.1.1.1 28-1.1.3 28-1.1.3.3.1 32-1.1.3.2.2.1.1.1 33-1.1.3.2.2 35-1.1.3.2 38-1.1.3.2.1 39-1.1.3.2.1.1.r 40-1.1.3.2.1.1.1.1 42-1.1.3.2.1.1.1.1 44-1.1.3.2.1.1.1.1 52-1.2.1.1 53-1.2.1.1.1 (a2 / and~e.0 :op2 (o / observe-01~e.16 :ARG1 (p / phosphorylate-01~e.13 :ARG1 (p5 / protein :name (n3 / name :op1 "ASPP2"~e.12))) :mod (a / also~e.15) :location~e.17 (c2 / cell-line~e.22,23,28 :name (n4 / name :op1 "HKe3"~e.24 :op2 "ER"~e.25) :location-of (i / induce-01~e.35 :ARG0 (a6 / add-02~e.38 :ARG1~e.39 (s2 / small-molecule :name (n5 / name :op1 "4-hydroxytamoxifen"~e.40,42,44))) :ARG2 (a5 / activate-01~e.33 :ARG1 (e / enzyme :name (n2 / name :op1 "Ras"~e.32)))) :ARG0-of (m2 / mean-01 :ARG1 (c4 / cell~e.22,28 :name (n8 / name :op1 "HRASV12"~e.27))) :mod (h / human~e.19) :mod (d / disease :wiki "Colorectal_cancer" :name (n / name :op1 "colon"~e.20 :op2 "cancer"~e.21))) :instrument~e.2 (a3 / antibody~e.8 :name (n7 / name :op1 "ES1"~e.10) :ARG1-of (d2 / differ-02~e.4) :mod (a4 / another~e.3) :ARG1-of (s / specific-02 :ARG2 (p4 / protein :name (n6 / name :op1 "ASPP2"~e.7,12) :ARG3-of (p2 / phosphorylate-01~e.5,13))))) :ARG1-of (d3 / describe-01 :ARG0 (a7 / and~e.0 :op1 (f / figure~e.52 :mod "1E"~e.53) :op2 (p3 / publication-91 :ARG1-of (c3 / cite-01 :ARG2 (a8 / and~e.0 :op1 2 :op2 10 :op3 11)))))) # ::id bmtr_0007.11 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The phospho @-@ specific antibody for ASPP2 is specific as knockdown of ASPP2 resulted in a lack of detection of phospho @-@ ASPP2 . # ::alignments 1-1.2.1.2.1.1.2 3-1 3-1.1.1 4-1.1 6-1.2.1.1.1.1.1 6-1.2.1.2.1.1.1.1 8-1 10-1.2.1.1 12-1.2.1.1.1.1.1 12-1.2.1.2.1.1.1.1 13-1.2.1 16-1.2.1.2 18-1.2.1.2.1 20-1.2.1.2.1.1.2 22-1.2.1.1.1.1.1 22-1.2.1.2.1.1.1.1 (s / specific-02~e.3,8 :ARG1 (a / antibody~e.4 :ARG1-of (s2 / specific-02~e.3 :ARG2 p)) :ARG1-of (i / infer-01 :ARG2 (r / result-01~e.13 :ARG1 (k / knock-down-02~e.10 :ARG1 (p3 / protein :name (n / name :op1 "ASPP2"~e.6,12,22))) :ARG2 (l / lack-01~e.16 :ARG1 (d / detect-01~e.18 :ARG1 (p / protein :name (n2 / name :op1 "ASPP2"~e.6,12,22) :ARG3-of (p2 / phosphorylate-01~e.1,20))))))) # ::id bmtr_0007.12 ::amr-annotator SDL-AMR-09 ::preferred # ::tok All these demonstrate that ASPP2 is a novel substrate of MAPK and Ser827 of ASPP2 can be phosphorylated by RAS @/@ MAPK pathway . # ::alignments 0-1.1.1 1-1.1 2-1 4-1.2.1.2.1.1 7-1.2.1.3 10-1.2.1.1.1.1 14-1.2.1.2.1.1 15-1.2.2 17-1.2.2.1 18-1.2.2.1.2.r 19-1.2.2.1.2.1.1 21-1.2.2.1.2.1.1 22-1.2.2.1.2 (d / demonstrate-01~e.2 :ARG0 (t / this~e.1 :mod (a / all~e.0)) :ARG1 (a2 / and :op1 (c / catalyze-01 :ARG0 (e / enzyme :name (n / name :op1 "MAPK"~e.10)) :ARG1 (p5 / protein :name (n3 / name :op1 "ASPP2"~e.4,14)) :mod (n6 / novel~e.7)) :op2 (p2 / possible-01~e.15 :ARG1 (p3 / phosphorylate-01~e.17 :ARG1 (a3 / amino-acid :mod 827 :name (n4 / name :op1 "serine") :part-of p5) :ARG2~e.18 (p4 / pathway~e.22 :name (n5 / name :op1 "RAS/MAPK"~e.19,21)))))) # ::id pmid_1528_0923.1 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Dual blockade of EGFR and ERK1 @/@ 2 phosphorylation potentiates growth inhibition of breast cancer cells ( PMID : 15280923 ) # ::alignments 0-1.2.2 1-1.2 2-1.2.1.r 3-1.2.1.1.1.1.1 4-1.2.1.1 5-1.2.1.1.2.1.1 7-1.2.1.1.2.1.1 8-1.2.1 9-1 10-1.1.1 11-1.1 12-1.1.1.1.r 13-1.1.1.1.1.2.1 14-1.1.1.1.1.2.2 15-1.1.1.1 (p2 / potentiate-01~e.9 :ARG1 (i / inhibit-01~e.11 :ARG1 (g / grow-01~e.10 :ARG1~e.12 (c / cell~e.15 :source (d / disease :wiki "Breast_cancer" :name (n / name :op1 "breast"~e.13 :op2 "cancer"~e.14))))) :ARG2 (b / blockade-01~e.1 :ARG1~e.2 (p3 / phosphorylate-01~e.8 :ARG1 (a / and~e.4 :op1 (e2 / enzyme :name (n3 / name :op1 "EGFR"~e.3)) :op2 (e3 / enzyme :name (n4 / name :op1 "ERK1/2"~e.5,7)))) :mod (d2 / dual~e.0)) :ARG1-of (d3 / describe-01 :ARG0 (p4 / publication-91 :ARG8 "PMID15280923"))) # ::id pmid_1528_0923.66 ::amr-annotator SDL-AMR-09 ::preferred # ::tok RESULTS # ::alignments 1-1 1-1.1 1-1.1.r (t / thing~e.1 :ARG2-of~e.1 (r / result-01~e.1)) # ::id pmid_1528_0923.67 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Differences in activity of ERK1 @/@ 2 in the breast cancer cell lines # ::alignments 1-1 2-1.1.r 3-1.1 4-1.1.1.r 5-1.1.1.1.1 7-1.1.1.1.1 8-1.1.2.r 10-1.1.2.1.2.1 11-1.1.2.1.2.2 12-1.1.2 13-1.1.2 (d / differ-02~e.1 :ARG3~e.2 (a / act-02~e.3 :ARG0~e.4 (e / enzyme :name (n / name :op1 "ERK1/2"~e.5,7)) :location~e.8 (c / cell-line~e.12,13 :source (d2 / disease :wiki "Breast_cancer" :name (n2 / name :op1 "breast"~e.10 :op2 "cancer"~e.11))))) # ::id pmid_1528_0923.68 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Immunoblotting revealed differences in basal levels of ERK1 @/@ 2 phosphorylation in different breast cancer cell lines , while the expression of ERK1 @/@ 2 protein , normalised to actin expression , was relatively consistent ( Figure 1A ) . # ::alignments 0-1.1.1 1-1.1 2-1.1.2 3-1.1.2.1.r 4-1.1.2.1.1 5-1.1.2.1 6-1.1.2.1.2.r 7-1.1.2.1.2.1.1.1 9-1.1.2.1.2.1.1.1 10-1.1.2.1.2 11-1.1.2.1.2.2.r 12-1.1.2.1.2.2.2 13-1.1.2.1.2.2.1.2.1 14-1.1.2.1.2.2.1.2.2 15-1.1.2.1.2.2 16-1.1.2.1.2.2 18-1 20-1.2.1.3 22-1.1.2.1.2.1.1.1 24-1.1.2.1.2.1.1.1 25-1.2.1.3.1 29-1.2.1.3.1.1.1 30-1.2.1 30-1.2.1.3 30-1.2.1.3.r 33-1.2.2 34-1.2 37-1.3.1 38-1.3.1.1 (c / contrast-01~e.18 :ARG1 (r / reveal-01~e.1 :ARG0 (i / immunoblot-01~e.0) :ARG1 (d2 / differ-02~e.2 :ARG1~e.3 (l / level~e.5 :mod (b / basal~e.4) :quant-of~e.6 (p2 / phosphorylate-01~e.10 :ARG1 (e / enzyme :name (n2 / name :op1 "ERK1/2"~e.7,9,22,24)) :location~e.11 (c2 / cell-line~e.15,16 :source (d4 / disease :wiki "Breast_cancer" :name (n / name :op1 "breast"~e.13 :op2 "cancer"~e.14)) :ARG1-of (d3 / differ-02~e.12)))))) :ARG2 (c4 / consistent-01~e.34 :ARG1 (e2 / express-03~e.30 :ARG2 e :ARG1-of (n3 / normalize-01) :destination~e.30 (e3 / express-03~e.20,30 :ARG2 (p3 / protein~e.25 :name (n4 / name :op1 "actin"~e.29)))) :ARG2-of (r2 / relative-05~e.33)) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.37 :mod "1A"~e.38))) # ::id pmid_1528_0923.69 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To test whether the ERK1 @/@ 2 activity was only a tissue culture phenomenon , selected cell lines were injected into the mammary fatpads of nude mice , and protein lysates were prepared from the tumours . # ::alignments 1-1.3 2-1.3.1.3.1 2-1.3.1.3.1.r 4-1.3.1.3.2.1.1 6-1.3.1.3.2.1.1 7-1.3.1.3 8-1.3.1.3.r 9-1.3.1.2 11-1.3.1.1.1 12-1.3.1.1 13-1.3.1 15-1.1.1.1 16-1.1.1 17-1.1.1 19-1.1 25-1.1.2.2.1 26-1.1.2.2 28-1 29-1.2.1.1 30-1.2.1 32-1.2 33-1.1.2.1.r 33-1.2.2.r 35-1.2.2 (a / and~e.28 :op1 (i / inject-01~e.19 :ARG1 (c / cell-line~e.16,17 :ARG1-of (s / select-01~e.15)) :ARG2 (f / fatpad :source~e.33 (b / breast) :part-of (m / mouse~e.26 :mod (n / nude~e.25)))) :op2 (p / prepare-01~e.32 :ARG1 (l / lysate~e.30 :mod (p2 / protein~e.29)) :ARG2~e.33 (t / tumor~e.35)) :purpose (t2 / test-01~e.1 :ARG1 (p3 / phenomenon~e.13 :mod (c2 / culture-01~e.12 :ARG1 (t3 / tissue~e.11)) :mod (o / only~e.9) :domain~e.8 (a2 / activity-06~e.7 :mode~e.2 interrogative~e.2 :ARG0 (e / enzyme :name (n2 / name :op1 "ERK1/2"~e.4,6)))))) # ::id pmid_1528_0923.70 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Taking into account the fact that lysates were of a mixture of tumour cells and surrounding stromal and infiltrating host cells , the immunoblotting of the tumour @-@ derived proteins showed similar results to those obtained using lysates of cultured cells . # ::alignments 6-1.1 12-1.1.1.1.1 13-1.1.1.1 13-1.1.1.2.1 14-1.1.1.2 15-1.1.1.2.1.2 17-1.1.1.2 18-1.1.1.2.2.2 19-1.1.1.2.2.1 20-1.1.1.2.2 23-1.2.1 24-1.2.1.1.r 26-1.2.1.1.1.1 28-1.2.1.1.1 29-1.2.1.1 30-1.2 31-1.2.2 31-1.2.2.1 31-1.2.2.1.r 32-1.2.2.1.1 32-1.2.2.1.1.2 32-1.2.2.1.1.2.r 32-1.2.2.2 35-1.2.2.1.1.1 37-1.2.2.1.1.1.1 38-1.2.2.1.1.1.1.1.r 39-1.2.2.1.1.1.1.1.1 40-1.2.2.1.1.1.1.1 (c / consider-02 :ARG1 (l / lysate~e.6 :source (m / mix-01 :ARG1 (c2 / cell~e.13 :mod (t / tumor~e.12)) :ARG2 (a / and~e.14,17 :op1 (c3 / cell~e.13 :mod (s / stroma) :ARG1-of (s2 / surround-01~e.15)) :op2 (c4 / cell~e.20 :mod (h / host~e.19) :ARG0-of (i / infiltrate-01~e.18))))) :ARG2 (s3 / show-01~e.30 :ARG0 (i2 / immunoblot-01~e.23 :ARG1~e.24 (p / protein~e.29 :ARG1-of (d / derive-01~e.28 :ARG2 t~e.26))) :ARG1 (t2 / thing~e.31 :ARG1-of~e.31 (r3 / resemble-01~e.31 :ARG2 (t3 / thing~e.32 :ARG1-of (o / obtain-01~e.35 :ARG2 (l2 / lysate~e.37 :source~e.38 (c5 / cell~e.40 :ARG1-of (c6 / culture-01~e.39)))) :ARG2-of~e.32 (r2 / result-01~e.32))) :ARG2-of (r / result-01~e.32)))) # ::id pmid_1528_0923.71 ::amr-annotator SDL-AMR-09 ::preferred # ::tok MDA @-@ MB @-@ 231 and MDA @-@ MB @-@ 435 tumour lysates showed high levels of p @-@ ERK1 @/@ 2 in comparison to MDA @-@ MB @-@ 468 and GI101A tumours ( Figure 1B ) . # ::alignments 0-1.1.1.1.1.1 2-1.1.1.1.1.1 4-1.1.1.1.1.1 5-1.1.1 6-1.1.1.1.1.1 6-1.1.1.2.1.1 8-1.1.1.1.1.1 8-1.1.1.2.1.1 10-1.1.1.2.1.1 11-1.1.1.3 12-1.1 13-1 14-1.2.1 15-1.2 16-1.2.2.r 17-1.2.2.2 19-1.2.2.1.1 21-1.2.2.1.1 22-1.2.3.r 23-1.2.3 24-1.2.3.1.r 25-1.2.3.1.1.1.1 27-1.2.3.1.1.1.1 29-1.2.3.1.1.1.1 30-1.2.3.1 31-1.2.3.1.2.1.1 32-1.2.3.1.3 35-1.3.1 36-1.3.1.1 (s / show-01~e.13 :ARG0 (l / lysate~e.12 :source (a / and~e.5 :op1 (c / cell-line :name (n / name :op1 "MDA-MB-231"~e.0,2,4,6,8)) :op2 (c2 / cell-line :name (n2 / name :op1 "MDA-MB-435"~e.6,8,10)) :mod (t / tumor~e.11))) :ARG1 (l2 / level~e.15 :ARG1-of (h / high-02~e.14) :quant-of~e.16 (e / enzyme :name (n3 / name :op1 "ERK1/2"~e.19,21) :ARG3-of (p / phosphorylate-01~e.17)) :ARG1-of~e.22 (c3 / compare-01~e.23 :ARG2~e.24 (a2 / and~e.30 :op1 (c4 / cell-line :name (n4 / name :op1 "MDA-MB-468"~e.25,27,29)) :op2 (c5 / cell-line :name (n5 / name :op1 "GI101A"~e.31)) :mod (t2 / tumor~e.32)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.35 :mod "1B"~e.36))) # ::id pmid_1528_0923.72 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Elevated ERK activity does not necessarily correlate with the status of EGFR and HER2 in breast cancer cells # ::alignments 1-1.1.2 2-1.1.1.1.1 3-1.1 5-1.3.1 5-1.3.1.r 6-1.3 6-1.3.1 6-1.3.1.r 7-1 8-1.2.r 10-1.2 11-1.2.1.r 12-1.2.1.1.1.1 13-1.2.1 14-1.2.1.2.1.1 16-1.2.1.3.1.2.1 17-1.2.1.3.1.2.2 18-1.2.1.3 (c / correlate-01~e.7 :ARG1 (a / activity-06~e.3 :ARG0 (e / enzyme :name (n6 / name :op1 "ERK"~e.2)) :ARG1-of (e5 / elevate-01~e.1)) :ARG2~e.8 (s / status~e.10 :poss~e.11 (a2 / and~e.13 :op1 (e6 / enzyme :name (n7 / name :op1 "EGFR"~e.12)) :op2 (e7 / enzyme :name (n8 / name :op1 "HER2"~e.14)) :location (c2 / cell~e.18 :source (d / disease :wiki "Breast_cancer" :name (n / name :op1 "breast"~e.16 :op2 "cancer"~e.17))))) :ARG1-of (n5 / need-01~e.6 :polarity~e.5,6 -~e.5,6)) # ::id pmid_1528_0923.73 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Since ERK1 @/@ 2 can be activated via EGFR and HER2 signalling , relative expression levels of these growth factor receptors were measured in the panel of cell lines , to test if there was a correlation between ERK activation and receptor expression levels . # ::alignments 0-1 1-1.1.1.1.1.1 3-1.1.1.1.1.1 4-1.1 6-1.1.1 8-1.1.1.2.1.1.1.1 9-1.1.1.2.1 10-1.1.1.2.1.2.1.1 11-1.1.1.2 13-1.2.1.2 14-1.2.1.1 15-1.2.1 18-1.2.1.1.1.1 19-1.2.1.1.1.1 20-1.2.1.1.1 22-1.2 23-1.2.2.r 25-1.2.2 26-1.2.2.1.r 27-1.2.2.1 28-1.2.2.1 31-1.2.3 36-1.2.3.1 38-1.2.3.1.2.1.1.1.1 39-1.2.3.1.2.1 41-1.2.1.1.1 42-1.2.1.1 43-1.2.3.1.2 43-1.2.3.1.3 (c / cause-01~e.0 :ARG0 (p / possible-01~e.4 :ARG1 (a / activate-01~e.6 :ARG1 (e4 / enzyme :name (n5 / name :op1 "ERK1/2"~e.1,3)) :manner (s2 / signal-07~e.11 :ARG0 (a2 / and~e.9 :op1 (e5 / enzyme :name (n6 / name :op1 "EGFR"~e.8)) :op2 (e6 / enzyme :name (n7 / name :op1 "HER2"~e.10)))))) :ARG1 (m / measure-01~e.22 :ARG1 (l / level~e.15 :degree-of (e7 / express-03~e.14,42 :ARG2 (r2 / receptor~e.20,41 :mod (g / growth-factor~e.18,19))) :ARG1-of (r / relative-05~e.13)) :location~e.23 (p2 / panel~e.25 :consist-of~e.26 (c2 / cell-line~e.27,28)) :purpose (t / test-01~e.31 :ARG2 (c3 / correlate-01~e.36 :mode interrogative :ARG1 (l3 / level~e.43 :degree-of (a3 / activate-01~e.39 :ARG1 (e / enzyme :name (n9 / name :op1 "ERK"~e.38)))) :ARG2 (l2 / level~e.43 :degree-of e7))))) # ::id pmid_1528_0923.74 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As expected from the heterogeneity seen in clinical specimens of breast cancer , there was variability in expression of EGFR , from high expression in MDA @-@ MB @-@ 468 and minimal expression in MDA @-@ MB @-@ 435 cells ( Figure 1A ) . # ::alignments 1-1.4 2-1.4.1.r 5-1.4.1.1 6-1.4.1.1.1.r 7-1.4.1.1.1.1 8-1.4.1.1.1 10-1.4.1.1.1.2.2.1 11-1.4.1.1.1.2.2.2 17-1.1 17-1.2 18-1.1.1.r 19-1.1.1.1.1 21-1.4.1.1.1.2.r 22-1.2.2 23-1.2 25-1.2.1.1.1 27-1.2.1.1.1 29-1.2.1.1.1 31-1.3.2 32-1.3 34-1.3.1.1.1 36-1.3.1.1.1 38-1.3.1.1.1 39-1.2.1 39-1.3.1 42-1.5.1 43-1.5.1.1 (v / vary-01 :ARG1 (e2 / express-03~e.17 :ARG2~e.18 (e3 / enzyme :name (n3 / name :op1 "EGFR"~e.19))) :ARG3 (e4 / express-03~e.17,23 :ARG3 (c / cell-line~e.39 :name (n4 / name :op1 "MDA-MB-468"~e.25,27,29)) :ARG1-of (h / high-02~e.22)) :ARG4 (e5 / express-03~e.32 :ARG3 (c2 / cell-line~e.39 :name (n5 / name :op1 "MDA-MB-435"~e.34,36,38)) :ARG1-of (m / minimal-02~e.31)) :ARG1-of (e6 / expect-01~e.1 :source~e.2 (h2 / heterogenous :ARG1-of (s / see-01~e.5 :location~e.6 (s2 / specimen~e.8 :mod (c3 / clinic~e.7) :source~e.21 (d2 / disease :wiki "Breast_cancer" :name (n / name :op1 "breast"~e.10 :op2 "cancer"~e.11)))))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.42 :mod "1A"~e.43))) # ::id pmid_1528_0923.75 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Comparing these results with the level of pERK1 @/@ 2 indicated that there was no direct correlation between levels of these growth factor receptors and basal levels of ERK1 @/@ 2 phosphorylation . # ::alignments 0-1 1-1.1.1 2-1.1 2-1.1.2 2-1.1.2.r 3-1.2.r 5-1.2 9-1.2.1.1.1 10-1.3 14-1.3.1.1 14-1.3.1.1.r 15-1.3.1.4 16-1.3.1 18-1.3.1.2 19-1.3.1.2.1.r 20-1.3.1.2.1.2 21-1.3.1.2.1.1 22-1.3.1.2.1.1 23-1.3.1.2.1 25-1.3.1.3.1 26-1.3.1.3 28-1.2.1.1.1 28-1.3.1.3.2.1.1.1 30-1.2.1.1.1 30-1.3.1.3.2.1.1.1 31-1.2.1.2 31-1.3.1.3.2 (c / compare-01~e.0 :ARG1 (t3 / thing~e.2 :mod (t / this~e.1) :ARG2-of~e.2 (r / result-01~e.2)) :ARG2~e.3 (l / level~e.5 :quant-of (e / enzyme :name (n2 / name :op1 "ERK1/2"~e.9,28,30) :ARG3-of (p / phosphorylate-01~e.31))) :ARG0-of (i / indicate-01~e.10 :ARG1 (c2 / correlate-01~e.16 :polarity~e.14 -~e.14 :ARG1 (l2 / level~e.18 :quant-of~e.19 (r2 / receptor~e.23 :mod (g / growth-factor~e.21,22) :mod (t2 / this~e.20))) :ARG2 (l3 / level~e.26 :mod (b / basal~e.25) :quant-of (p2 / phosphorylate-01~e.31 :ARG1 (e2 / enzyme :name (n4 / name :op1 "ERK1/2"~e.28,30)))) :ARG1-of (d / direct-02~e.15)))) # ::id pmid_1528_0923.76 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Thus , while the MDA @-@ MB @-@ 231 cell line with highly activated ERK1 @/@ 2 expressed a relatively high level of EGFR , other combinations occur . # ::alignments 0-1 2-1.1 4-1.1.1.2.1.1 6-1.1.1.2.1.1 8-1.1.1.2.1.1 9-1.1.1.2 10-1.1.1.2 11-1.1.1.2.2.r 12-1.1.1.2.2.2.1 13-1.1.1.2.2.2 14-1.1.1.2.2.1.1 16-1.1.1.2.2.1.1 17-1.1.1 19-1.1.1.1.2.1 20-1.1.1.1.2 21-1.1.1.1 22-1.1.1.1.1.r 23-1.1.1.1.1.1.1 25-1.1.2.1 26-1.1.2 (c / cause-01~e.0 :ARG1 (c2 / contrast-01~e.2 :ARG1 (e2 / express-03~e.17 :ARG1 (l2 / level~e.21 :quant-of~e.22 (e3 / enzyme :name (n3 / name :op1 "EGFR"~e.23)) :ARG1-of (h / high-02~e.20 :ARG2-of (r / relative-05~e.19))) :ARG3 (c3 / cell-line~e.9,10 :name (n2 / name :op1 "MDA-MB-231"~e.4,6,8) :mod~e.11 (e4 / enzyme :name (n4 / name :op1 "ERK1/2"~e.14,16) :ARG1-of (a / activate-01~e.13 :ARG1-of (h2 / high-02~e.12))))) :ARG2 (c5 / combine-01~e.26 :mod (o / other~e.25)))) # ::id pmid_1528_0923.77 ::amr-annotator SDL-AMR-09 ::preferred # ::tok High pERK1 @/@ 2 levels were detected in MDA @-@ MB @-@ 435 cells , which have very little EGFR , in contrast to the SUM149 cells with high EGFR expression and low ERK1 @/@ 2 activity . # ::alignments 0-1.1.2 3-1.1.1.1.1 4-1.1 6-1 7-1.2.r 8-1.2.1.1 10-1.2.1.1 12-1.2.1.1 13-1.2 16-1.2.2 17-1.2.2.1.2.1 18-1.2.2.1.2 19-1.2.2.1.1.1 21-1.2.2.2.r 22-1.2.2.2 23-1.2.2.2.1.r 25-1.2.2.2.1.1.1 26-1.2.2.2.1 28-1.1.2 29-1.2.2.2.1.2.1.1 30-1.2.2.2.1.2.1 31-1.2.2.2.1.2 32-1.2.2.2.1.2.2.2 33-1.2.2.2.1.2.2.1.1.1 35-1.2.2.2.1.2.2.1.1.1 36-1.2.2.2.1.2.2 (d / detect-01~e.6 :ARG1 (l / level~e.4 :quant-of (e2 / enzyme :name (n2 / name :op1 "ERK1/2"~e.3) :ARG3-of (p / phosphorylate-01)) :ARG1-of (h / high-02~e.0,28)) :location~e.7 (c / cell-line~e.13 :name (n3 / name :op1 "MDA-MB-435"~e.8,10,12) :ARG0-of (h2 / have-03~e.16 :ARG1 (e3 / enzyme :name (n4 / name :op1 "EGFR"~e.19) :quant (l3 / little~e.18 :degree (v / very~e.17))) :ARG1-of~e.21 (c2 / contrast-01~e.22 :ARG2~e.23 (c3 / cell-line~e.26 :name (n5 / name :op1 "SUM149"~e.25) :poss (a / and~e.31 :op1 (e4 / express-03~e.30 :ARG2 e3~e.29 :ARG1-of h) :op2 (a2 / activity-06~e.36 :ARG0 (e / enzyme :name (n / name :op1 "ERK1/2"~e.33,35)) :ARG1-of (l2 / low-04~e.32)))))))) # ::id pmid_1528_0923.78 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Similarly , no correlation was found between the expression of HER2 receptor and the status of pERK ( Figure 1A ) . # ::alignments 0-1.2 2-1.1.1 2-1.1.1.r 3-1.1 5-1 8-1.1.2 9-1.1.2.1.r 10-1.1.2.1.1.1.1 11-1.1.2.1 14-1.1.3 15-1.1.3.1.r 16-1.1.3.1.1.1 16-1.1.3.1.2 19-1.3.1 20-1.3.1.1 (f / find-01~e.5 :ARG1 (c / correlate-01~e.3 :polarity~e.2 -~e.2 :ARG1 (e2 / express-03~e.8 :ARG2~e.9 (r2 / receptor~e.11 :mod (e3 / enzyme :name (n2 / name :op1 "HER2"~e.10)))) :ARG2 (s / status~e.14 :poss~e.15 (e / enzyme :name (n3 / name :op1 "ERK"~e.16) :ARG3-of (p / phosphorylate-01~e.16)))) :ARG1-of (r / resemble-01~e.0) :ARG1-of (d / describe-01 :ARG0 (f2 / figure~e.19 :mod "1A"~e.20))) # ::id pmid_1528_0923.79 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PKI166 inhibition of breast cancer cell proliferation # ::alignments 1-1.1.1.1 2-1 3-1.2.r 4-1.2.1.1.2.1 5-1.2.1.1.2.2 6-1.2.1 7-1.2 (i / inhibit-01~e.2 :ARG0 (s / small-molecule :name (n2 / name :op1 "PKI166"~e.1)) :ARG1~e.3 (p / proliferate-01~e.7 :ARG0 (c / cell~e.6 :source (d / disease :wiki "Breast_cancer" :name (n / name :op1 "breast"~e.4 :op2 "cancer"~e.5))))) # ::id pmid_1528_0923.80 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Six cell lines with different levels of EGFR expression were selected for treatment with PKI166 . # ::alignments 0-1.1.1 1-1.1 2-1.1 4-1.3.1 5-1.3 6-1.3.2.r 7-1.3.2.1.1.1 8-1.3.2 10-1 11-1.2.r 12-1.2 13-1.2.1.r 14-1.2.1.1.1 (s / select-01~e.10 :ARG1 (c / cell-line~e.1,2 :quant 6~e.0) :ARG3~e.11 (t / treat-04~e.12 :ARG2~e.13 (s2 / small-molecule :name (n3 / name :op1 "PKI166"~e.14))) :poss-of (l / level~e.5 :ARG1-of (d / differ-02~e.4) :quant-of~e.6 (e2 / express-03~e.8 :ARG2 (e3 / enzyme :name (n2 / name :op1 "EGFR"~e.7))))) # ::id pmid_1528_0923.81 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Initial studies used a dose range of 0.1 @–@ 5.0 μ @ M ( data not shown ) , and the results of treating cells with 0.5 and 5.0 μ @ M are shown in Table 1 @ . # ::alignments 0-1.1.1.1 1-1.1.1 2-1.1 4-1.1.2.1 5-1.1.2 6-1.1.2.2.r 7-1.1.2.2.1 9-1.1.2.3.1 17-1.1.3.2 18-1.1.3.1 18-1.1.3.1.r 19-1.1.3 22-1 24-1.2.1 24-1.2.1.1 24-1.2.1.1.r 25-1.2.1.1.1.r 26-1.2.1.1.1 27-1.2.1.1.1.1 28-1.2.1.1.1.2.r 29-1.2.1.1.1.2.1.1 30-1.2.1.1.1.2 31-1.2.1.1.1.2.2 39-1.2 42-1.2.2 43-1.2.2.1 (a / and~e.22 :op1 (u / use-01~e.2 :ARG0 (s / study-01~e.1 :mod (i / initial~e.0)) :ARG1 (r / range-01~e.5 :ARG1 (d / dose~e.4) :ARG3~e.6 (c / concentration-quantity :quant 0.1~e.7 :unit (m / micromolar)) :ARG4 (c2 / concentration-quantity :quant 5.0~e.9 :unit m)) :ARG1-of (s2 / show-01~e.19 :polarity~e.18 -~e.18 :ARG0 (d2 / data~e.17))) :op2 (s3 / show-01~e.39 :ARG1 (t3 / thing~e.24 :ARG2-of~e.24 (r2 / result-01~e.24 :ARG1~e.25 (t / treat-04~e.26 :ARG1 (c3 / cell~e.27) :ARG2~e.28 (a2 / and~e.30 :op1 (c4 / concentration-quantity :quant 0.5~e.29 :unit m) :op2 c2~e.31)))) :location (t2 / table~e.42 :mod 1~e.43))) # ::id pmid_1528_0923.82 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Growth inhibition was determined from the results of MTT assays , comparing PKI166 treated cells with cells exposed to medium with 0.1 % DMSO . # ::alignments 0-1.1.1 1-1.1 3-1 4-1.2.r 6-1.2 6-1.2.1 6-1.2.1.r 7-1.2.1.1.r 8-1.2.1.1.1.1.1 9-1.2.1.1 11-1.3 12-1.3.1.1.1.1.1 13-1.3.1.1 14-1.3.1 15-1.2.1.1.1.r 15-1.3.2.r 16-1.3.2 17-1.3.2.1 18-1.3.2.1.1.r 19-1.3.2.1.1 20-1.2.1.1.1.r 21-1.3.2.1.1.1.1.2.1 22-1.3.2.1.1.1.1.2 23-1.3.2.1.1.1.1.1.1 (d / determine-01~e.3 :ARG1 (i / inhibit-01~e.1 :ARG1 (g / grow-01~e.0)) :ARG2~e.4 (t4 / thing~e.6 :ARG2-of~e.6 (r / result-01~e.6 :ARG1~e.7 (a / assay-01~e.9 :instrument~e.15,20 (s3 / small-molecule :name (n / name :op1 "MTT"~e.8))))) :manner (c / compare-01~e.11 :ARG1 (c2 / cell~e.14 :ARG1-of (t2 / treat-04~e.13 :ARG2 (s / small-molecule :name (n2 / name :op1 "PKI166"~e.12)))) :ARG2~e.15 (c3 / cell~e.16 :ARG1-of (e / expose-01~e.17 :ARG2~e.18 (m / medium~e.19 :ARG0-of (h / have-03 :ARG1 (s2 / small-molecule :name (n3 / name :op1 "DMSO"~e.23) :quant (p2 / percentage-entity~e.22 :value 0.1~e.21)))))))) # ::id pmid_1528_0923.83 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Treatment with 0.5 μ @ M PKI166 , a concentration less than plasma and tumour concentrations achieved in preclinical models from oral administration of the drug , and the higher dose of 5.0 μ @ M , produced different levels of growth inhibition in different cell lines . # ::alignments 0-1.1.1 1-1.1.1.1.r 2-1.1.1.1.2.1 9-1.1.1.1.1.1 12-1.1.1.1.2 13-1.1.1.1.2.3 14-1.1.1.1.2.4.r 15-1.1.1.1.2.4.1.1 16-1.1.1.1.2.4.1 17-1.1.1.1.2.4.1.2 18-1.1.1.1.2.4 18-1.1.2.1 19-1.1.1.1.2.4.2 20-1.1.1.1.2.4.2.1.r 21-1.1.1.1.2.4.2.1.1 22-1.1.1.1.2.4.2.1 23-1.1.1.1.2.4.2.1.2.r 24-1.1.1.1.2.4.2.1.2.2 25-1.1.1.1.2.4.2.1.2 30-1.1 32-1.1.2.2 32-1.1.2.2.1 32-1.1.2.2.1.r 33-1.1.2 35-1.1.2.1.1 43-1 44-1.2.1 45-1.2 46-1.2.2.r 47-1.2.2.1 48-1.2.2 50-1.2.1 51-1.3 52-1.3 (p / produce-01~e.43 :ARG0 (a / and~e.30 :op1 (t / treat-04~e.0 :ARG2~e.1 (s / small-molecule :name (n / name :op1 "PKI166"~e.9) :mod (c / concentration-quantity~e.12 :quant 0.5~e.2 :unit (m / micromolar) :mod (l2 / less~e.13) :compared-to~e.14 (c4 / concentration~e.18 :poss (a2 / and~e.16 :op1 (p2 / plasma~e.15) :op2 (t2 / tumor~e.17)) :ARG1-of (a3 / achieve-01~e.19 :location~e.20 (m4 / model~e.22 :mod (p3 / preclinical~e.21) :source~e.23 (a4 / administer-01~e.25 :ARG1 s :path (m5 / mouth~e.24)))))))) :op2 (d / dose~e.33 :mod (c2 / concentration-quantity~e.18 :quant 5.0~e.35 :unit (m2 / micromolar)) :ARG1-of (h / high-02~e.32 :degree~e.32 (m3 / more~e.32)))) :ARG1 (l / level~e.45 :ARG1-of (d2 / differ-02~e.44,50) :quant-of~e.46 (i / inhibit-01~e.48 :ARG1 (g / grow-01~e.47))) :location (c3 / cell-line~e.51,52 :ARG1-of d2)) # ::id pmid_1528_0923.84 ::amr-annotator SDL-AMR-09 ::preferred # ::tok As expected , cells expressing low levels of EGFR and HER2 , GI101A , MDA @-@ MB @-@ 435 showed least growth inhibition . # ::alignments 1-1.3 3-1.1 4-1.1.1 5-1.1.1.1.1 6-1.1.1.1 7-1.1.1.1.2.r 8-1.1.1.1.2.1.1.1 9-1.1.1.1.2 10-1.1.1.1.2.2.1.1 12-1.1.2.1.1.1.1 14-1.1.2.1.2.1.1 16-1.1.2.1.2.1.1 18-1.1.2.1.2.1.1 19-1 20-1.2.2 21-1.2.1 22-1.2 (s / show-01~e.19 :ARG0 (c / cell~e.3 :ARG3-of (e3 / express-03~e.4 :ARG2 (l / level~e.6 :ARG1-of (l2 / low-04~e.5) :quant-of~e.7 (a / and~e.9 :op1 (e / enzyme :name (n / name :op1 "EGFR"~e.8)) :op2 (e2 / enzyme :name (n2 / name :op1 "HER2"~e.10))))) :ARG1-of (m / mean-01 :ARG2 (a2 / and :op1 (c2 / cell-line :name (n3 / name :op1 "GI101A"~e.12)) :op2 (c3 / cell-line :name (n4 / name :op1 "MDA-MB-435"~e.14,16,18))))) :ARG1 (i / inhibit-01~e.22 :ARG1 (g / grow-01~e.21) :degree (l3 / least~e.20)) :ARG1-of (e4 / expect-01~e.1)) # ::id pmid_1528_0923.85 ::amr-annotator SDL-AMR-09 ::preferred # ::tok However , not all of the high EGFR @-@ expressing lines were sensitive to PKI166 . # ::alignments 0-1 2-1.1.1.2.1 2-1.1.1.2.1.r 3-1.1.1.2 6-1.1.1.1.2 7-1.1.1.1.1.1.1 9-1.1.1.1 10-1.1.1 12-1.1 13-1.1.2.r 14-1.1.2.1.1 (c / contrast-01~e.0 :ARG2 (s / sensitive-03~e.12 :ARG0 (l / line~e.10 :ARG3-of (e / express-03~e.9 :ARG2 (e2 / enzyme :name (n / name :op1 "EGFR"~e.7)) :ARG1-of (h / high-02~e.6)) :mod (a / all~e.3 :polarity~e.2 -~e.2)) :ARG1~e.13 (s2 / small-molecule :name (n2 / name :op1 "PKI166"~e.14)))) # ::id pmid_1528_0923.86 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The lower dose produced 46 and 21 % growth inhibition of SUM149 and MDA @-@ MB @-@ 468 cells , respectively , but had little effect ( 3.3 % inhibition ) on the growth of MDA @-@ MB @-@ 231 cells . # ::alignments 1-1.1.1.1 1-1.1.1.1.1 1-1.1.1.1.1.r 2-1.1.1 3-1.1 4-1.1.2.1.2.1 5-1.1.2 6-1.1.2.2.2.1 7-1.1.2.2.2 8-1.1.2.1.1 8-1.1.2.2.1 9-1.1.2.1 9-1.1.2.2 11-1.1.2.1.1.1.1.1 12-1.1.2 13-1.1.2.2.1.1.1.1 15-1.1.2.2.1.1.1.1 17-1.1.2.2.1.1.1.1 18-1.1.2.1.1.1 18-1.1.2.2.1.1 20-1.1.3 22-1 24-1.2.3 25-1.2 27-1.2.4.1.1.1 28-1.1.2.1.2 28-1.2.4.1.1 29-1.2.4.1 31-1.2.2.r 33-1.2.2 34-1.2.2.1.r 35-1.2.2.1.1.1 37-1.2.2.1.1.1 39-1.2.2.1.1.1 40-1.2.2.1 (c / contrast-01~e.22 :ARG1 (p3 / produce-01~e.3 :ARG0 (d / dose~e.2 :ARG1-of (l / low-04~e.1 :degree~e.1 (m2 / more~e.1))) :ARG1 (a / and~e.5,12 :op1 (i / inhibit-01~e.9 :ARG1 (g / grow-01~e.8 :ARG1 (c2 / cell-line~e.18 :name (n / name :op1 "SUM149"~e.11))) :quant (p4 / percentage-entity~e.28 :value 46~e.4)) :op2 (i2 / inhibit-01~e.9 :ARG1 (g2 / grow-01~e.8 :ARG1 (c3 / cell-line~e.18 :name (n2 / name :op1 "MDA-MB-468"~e.13,15,17))) :quant (p5 / percentage-entity~e.7 :value 21~e.6))) :mod (r / respective~e.20)) :ARG2 (a2 / affect-01~e.25 :ARG0 d :ARG1~e.31 (g3 / grow-01~e.33 :ARG1~e.34 (c4 / cell-line~e.40 :name (n3 / name :op1 "MDA-MB-231"~e.35,37,39))) :degree (l3 / little~e.24) :ARG1-of (m3 / mean-01 :ARG2 (i3 / inhibit-01~e.29 :quant (p6 / percentage-entity~e.28 :value 3.3~e.27))))) # ::id pmid_1528_0923.87 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The SKBR3 cells , expressing EGFR and also high levels of HER2 , were most sensitive , showing 55 % growth inhibition with 0.5 μ @ M and 76 % inhibition with 5.0 μ @ M PKI166 . # ::alignments 1-1.2.1.1 2-1.2 4-1 5-1.1.1.1.1 6-1.1 8-1.1.2.1 9-1.1.2 10-1.1.2.2.r 11-1.1.2.2.1.1 14-1.3.1 15-1.3.1 17-1.3 18-1.3.2.1.3.1 19-1.3.2.1.3 20-1.3.2.1.2 21-1.3.2.1 22-1.3.2.1.1.r 23-1.3.2.1.1.2.1 30-1.3.2 31-1.3.2.2.2.1 32-1.3.2.2.2 33-1.3.2.2 34-1.3.2.2.1.r 35-1.3.2.2.1.2.1 42-1.3.2.1.1.1.1 42-1.3.2.2.1.1.1 (e / express-03~e.4 :ARG2 (a / and~e.6 :op1 (e2 / enzyme :name (n2 / name :op1 "EGFR"~e.5)) :op2 (l / level~e.9 :ARG1-of (h / high-02~e.8) :quant-of~e.10 (e3 / enzyme :name (n3 / name :op1 "HER2"~e.11)))) :ARG3 (c / cell-line~e.2 :name (n / name :op1 "SKBR3"~e.1) :ARG0-of (s / sensitive-03 :degree (m / most))) :manner (s2 / show-01~e.17 :ARG0 c~e.14,15 :ARG1 (a2 / and~e.30 :op1 (i / inhibit-01~e.21 :ARG0~e.22 (s3 / small-molecule :name (n4 / name :op1 "PKI166"~e.42) :mod (c2 / concentration-quantity :quant 0.5~e.23 :unit (m2 / micromolar))) :ARG1 (g / grow-01~e.20) :quant (p / percentage-entity~e.19 :value 55~e.18)) :op2 (i2 / inhibit-01~e.33 :ARG0~e.34 (s4 / small-molecule :name (n5 / name :op1 "PKI166"~e.42) :mod (c3 / concentration-quantity :quant 5.0~e.35 :unit m2)) :quant (p2 / percentage-entity~e.32 :value 76~e.31))))) # ::id pmid_1528_0923.88 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PKI166 inhibits phosphorylation of EGFR and HER2 in breast cancer cells # ::alignments 1-1.1.1.1 2-1 3-1.2 4-1.2.1.r 5-1.2.1.1.1.1 6-1.2.1 7-1.2.1.2.1.1 8-1.2.2.r 9-1.2.2.1.2.1 10-1.2.2.1.2.2 11-1.2.2 (i / inhibit-01~e.2 :ARG0 (s / small-molecule :name (n4 / name :op1 "PKI166"~e.1)) :ARG1 (p2 / phosphorylate-01~e.3 :ARG1~e.4 (a / and~e.6 :op1 (e3 / enzyme :name (n5 / name :op1 "EGFR"~e.5)) :op2 (e4 / enzyme :name (n6 / name :op1 "HER2"~e.7))) :location~e.8 (c / cell~e.11 :source (d / disease :wiki "Breast_cancer" :name (n / name :op1 "breast"~e.9 :op2 "cancer"~e.10))))) # ::id pmid_1528_0923.89 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To demonstrate inhibition of EGFR and HER2 phosphorylation by the concentrations of PKI166 used for the growth inhibition assays , cell lysates were prepared from MDA @-@ MB @-@ 231 , MDA @-@ MB @-@ 468 , SUM149 and SKBR3 cells after treatment with PKI166 and stimulation with EGF , and phosphorylation of the receptors assessed . # ::alignments 1-1.3 2-1.3.1 3-1.3.1.2.r 4-1.3.1.2.1.1.1.1 5-1.3.1.2.1 6-1.3.1.2.1.2.1.1 7-1.3.1.2 8-1.3.1.1.r 10-1.3.1.1 10-1.3.1.1.2 10-1.3.1.1.2.r 12-1.3.1.1.1.1 13-1.3.1.1.2.1 14-1.3.1.1.2.1.1.r 16-1.3.1.1.2.1.1.1.1 17-1.3.1.1.2.1.1.1 18-1.3.1.1.2.1.1 20-1.1.1.1 21-1.1.1 23-1.1 24-1.1.2.r 25-1.1.2.1.1.1 25-1.1.2.2.1.1 27-1.1.2.1.1.1 27-1.1.2.2.1.1 29-1.1.2.1.1.1 31-1.1.2.1.1.1 31-1.1.2.2.1.1 33-1.1.2.1.1.1 33-1.1.2.2.1.1 35-1.1.2.2.1.1 37-1.1.2.3.1.1 38-1.1.2 39-1.1.2.4.1.1 40-1.1.2.1 40-1.1.2.2 40-1.1.2.3 40-1.1.2.4 41-1.1.3 42-1.1.3.1.1 43-1.1.3.1.1.1.r 44-1.1.3.1.1.1.1.1 45-1.1.3.1 46-1.1.3.1.2 47-1.1.3.1.2.1.r 48-1.1.3.1.2.1.1.1 51-1.2.1 52-1.2.1.1.r 54-1.2.1.1 55-1.2 (a / and :op1 (p2 / prepare-01~e.23 :ARG1 (l / lysate~e.21 :mod (c / cell~e.20)) :ARG2~e.24 (a2 / and~e.38 :op1 (c2 / cell-line~e.40 :name (n3 / name :op1 "MDA-MB-231"~e.25,27,29,31,33)) :op2 (c3 / cell-line~e.40 :name (n4 / name :op1 "MDA-MB-468"~e.25,27,31,33,35)) :op3 (c4 / cell-line~e.40 :name (n5 / name :op1 "SUM149"~e.37)) :op4 (c5 / cell-line~e.40 :name (n6 / name :op1 "SKBR3"~e.39))) :time (a3 / after~e.41 :op1 (a4 / and~e.45 :op1 (t / treat-04~e.42 :ARG2~e.43 (s / small-molecule :name (n7 / name :op1 "PKI166"~e.44))) :op2 (s2 / stimulate-01~e.46 :ARG2~e.47 (p / protein :name (n8 / name :op1 "EGF"~e.48)))))) :op2 (a5 / assess-01~e.55 :ARG1 (p3 / phosphorylate-01~e.51 :ARG1~e.52 (r / receptor~e.54))) :purpose (d / demonstrate-01~e.1 :ARG1 (i / inhibit-01~e.2 :ARG0~e.8 (s4 / small-molecule~e.10 :name (n / name :op1 "PKI166"~e.12) :ARG1-of~e.10 (c6 / concentrate-02~e.10 :ARG1-of (u / use-01~e.13 :ARG2~e.14 (a7 / assay-01~e.18 :ARG1 (i2 / inhibit-01~e.17 :ARG1 (g / grow-01~e.16)))))) :ARG1~e.3 (p4 / phosphorylate-01~e.7 :ARG1 (a6 / and~e.5 :op1 (e3 / enzyme :name (n9 / name :op1 "EGFR"~e.4)) :op2 (e4 / enzyme :name (n10 / name :op1 "HER2"~e.6))))))) # ::id pmid_1528_0923.90 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PKI166 inhibited ligand @-@ induced EGFR phosphorylation in a dose dependent manner in these four cell lines , and also phosphorylation of HER2 in SKBR3 cells , in the absence or presence of 50 ng ml @⁻¹ EGF ( Figure 2 ) ( data for other cell lines not shown ) . # ::alignments 0-1.1.1.1.1 1-1.1 1-1.2 2-1.1.2.2.1 4-1.1.2.2 5-1.1.2.1.1.1 6-1.1.2 7-1.1.3.r 9-1.1.3.1 10-1.1.3 12-1.1.4.r 13-1.1.4.2 14-1.1.4.1 15-1.1.4 16-1.1.4 18-1 20-1.2.1 21-1.2.1.1.r 22-1.2.1.1.1.1 23-1.2.1.2.r 24-1.2.1.2.1.1 25-1.2.1.2 29-1.2.2.2 30-1.2.2 32-1.2.2.r 33-1.2.2.1.2.1 34-1.2.2.1.2.2 35-1.2.2.1.2.2 39-1.2.2.1.1.1 42-1.3.1 43-1.3.1.1 47-1.4.2 48-1.4.2.1.r 49-1.4.2.1.1 50-1.4.2.1 51-1.4.2.1 52-1.4.1 52-1.4.1.r 53-1.4 (a / and~e.18 :op1 (i / inhibit-01~e.1 :ARG0 (s / small-molecule :name (n3 / name :op1 "PKI166"~e.0)) :ARG1 (p2 / phosphorylate-01~e.6 :ARG1 (e3 / enzyme :name (n4 / name :op1 "EGFR"~e.5)) :ARG2-of (i3 / induce-01~e.4 :ARG0 (l / ligand~e.2))) :ARG0-of~e.7 (d / depend-01~e.10 :ARG1 (d2 / dose~e.9)) :location~e.12 (c2 / cell-line~e.15,16 :quant 4~e.14 :mod (t / this~e.13))) :op2 (i2 / inhibit-01~e.1 :ARG1 (p3 / phosphorylate-01~e.20 :ARG1~e.21 (e4 / enzyme :name (n5 / name :op1 "HER2"~e.22)) :location~e.23 (c3 / cell-line~e.25 :name (n6 / name :op1 "SKBR3"~e.24))) :condition~e.32 (o / or~e.30 :op1 (p / protein :name (n7 / name :op1 "EGF"~e.39) :quant (c5 / concentration-quantity :quant 50~e.33 :unit (n8 / nanogram-per-milliliter~e.34,35))) :op2 (a2 / absent-01~e.29 :ARG1 p))) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.42 :mod 2~e.43)) :ARG1-of (s3 / show-01~e.53 :polarity~e.52 -~e.52 :ARG0 (d4 / data~e.47 :topic~e.48 (c4 / cell-line~e.50,51 :mod (o2 / other~e.49))))) # ::id pmid_1528_0923.91 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Constitutive ERK1 @/@ 2 phosphorylation as a potential escape mechanism from inhibition by PKI166 # ::alignments 1-1.1.2 2-1.1.1.1.1 4-1.1.1.1.1 5-1.1 8-1.2.1 9-1.2.2 10-1.2 11-1.2.2.1.r 12-1.2.2.1 13-1.2.2.1.1.r 14-1.2.2.1.1.1.1 (p / provide-01 :ARG0 (p2 / phosphorylate-01~e.5 :ARG1 (e / enzyme :name (n / name :op1 "ERK1/2"~e.2,4)) :mod (c / constitutive~e.1)) :ARG1 (m / mechanism~e.10 :mod (p3 / potential~e.8) :purpose (e2 / escape-01~e.9 :ARG1~e.11 (i / inhibit-01~e.12 :ARG0~e.13 (s / small-molecule :name (n2 / name :op1 "PKI166"~e.14)))))) # ::id pmid_1528_0923.92 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Inhibition of growth by PKI166 was most effective in cells with high levels of EGFR and nonactivated ERK1 @/@ 2 ( SUM149 , MDA @-@ MB @-@ 468 ) when compared with cells with high EGFR and high basal level of phosphorylated ERK1 @/@ 2 ( MDA @-@ MB @-@ 231 ) . # ::alignments 0-1.1 1-1.1.2.r 2-1.1.2 3-1.1.1.r 4-1.1.1.1.1 6-1.2 7-1 9-1.3 9-1.4 11-1.4.1.1.1.1 12-1.3.1.1 12-1.4.1.1.1 13-1.3.1.1.2.r 14-1.3.1.1.2.1.1.1 15-1.3.1.1.2 17-1.3.1.1.2.2.1.1 19-1.3.1.1.2.2.1.1 21-1.3.2.1.1.1.1 23-1.3.2.1.2.1.1 25-1.3.2.1.2.1.1 27-1.3.2.1.2.1.1 30-1.4.r 32-1.3.2.1.1 32-1.3.2.1.2 32-1.4.2.1 33-1.3.1.1.1.r 34-1.3.1.1.1 35-1.3.1.1.2.1.1.1 36-1.3.2.1 37-1.4.1.1.2.3 38-1.4.1.1.2.1 39-1.4.1.1.2 40-1.4.1.1.2.2.r 41-1.4.1.1.2.2.2 42-1.4.1.1.2.2.1.1 44-1.4.1.1.2.2.1.1 46-1.4.2.1.1.1 48-1.4.2.1.1.1 50-1.4.2.1.1.1 (e2 / effective-04~e.7 :ARG0 (i / inhibit-01~e.0 :ARG0~e.3 (s / small-molecule :name (n2 / name :op1 "PKI166"~e.4)) :ARG1~e.1 (g / grow-01~e.2)) :degree (m / most~e.6) :location (c / cell~e.9 :ARG0-of (h / have-03 :ARG1 (l / level~e.12 :ARG1-of~e.33 (h2 / high-02~e.34) :quant-of~e.13 (a / and~e.15 :op1 (e3 / enzyme :name (n3 / name :op1 "EGFR"~e.14,35)) :op2 (e4 / enzyme :name (n4 / name :op1 "ERK1/2"~e.17,19) :ARG1-of (a2 / activate-01 :polarity -))))) :ARG1-of (m2 / mean-01 :ARG2 (a3 / and~e.36 :op1 (c2 / cell-line~e.32 :name (n5 / name :op1 "SUM149"~e.21)) :op2 (c3 / cell-line~e.32 :name (n6 / name :op1 "MDA-MB-468"~e.23,25,27))))) :compared-to~e.30 (c4 / cell~e.9 :ARG0-of (h3 / have-03 :ARG1 (a4 / and :op1 (l3 / level~e.12 :ARG1-of (h6 / high-02~e.11) :quant-of e3) :op2 (l2 / level~e.39 :mod (b / basal~e.38) :quant-of~e.40 (e6 / enzyme :name (n8 / name :op1 "ERK1/2"~e.42,44) :ARG3-of (p / phosphorylate-01~e.41)) :ARG1-of (h5 / high-02~e.37)))) :ARG1-of (m3 / mean-01 :ARG2 (c5 / cell-line~e.32 :name (n9 / name :op1 "MDA-MB-231"~e.46,48,50))))) # ::id pmid_1528_0923.93 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To test whether the basal ERK1 @/@ 2 activity was providing an escape mechanism from inhibition by PKI166 , cells were treated with a combination of PKI166 and UO126 , an inhibitor of MEK ( Table 1 ) . # ::alignments 1-1.3 2-1.3.1.1 2-1.3.1.1.r 4-1.3.1.2.1.2 5-1.3.1.2.1.1.1 7-1.3.1.2.1.1.1 8-1.3.1.2 10-1.3.1 12-1.3.1.3.1 13-1.3.1.3 14-1.3.1.3.1.1.r 15-1.3.1.3.1.1 16-1.3.1.3.1.1.1.r 17-1.3.1.3.1.1.1 19-1.1 21-1 22-1.2.r 24-1.2 25-1.2.1.r 26-1.2.1.1.1 28-1.2.2.1.1 31-1.2.2 31-1.2.2.2 31-1.2.2.2.r 32-1.2.2.2.1.r 33-1.2.2.2.1.1.1 36-1.4.1 37-1.4.1.1 (t2 / treat-04~e.21 :ARG1 (c / cell~e.19) :ARG2~e.22 (c2 / combine-01~e.24 :ARG1~e.25 (s / small-molecule :name (n2 / name :op1 "PKI166"~e.26)) :ARG2 (s2 / small-molecule~e.31 :name (n3 / name :op1 "UO126"~e.28) :ARG0-of~e.31 (i / inhibit-01~e.31 :ARG1~e.32 (p2 / protein-family :name (n / name :op1 "MEK"~e.33))))) :purpose (t3 / test-01~e.1 :ARG1 (p / provide-01~e.10 :mode~e.2 interrogative~e.2 :ARG0 (a / activity-06~e.8 :ARG0 (e3 / enzyme :name (n5 / name :op1 "ERK1/2"~e.5,7) :mod (b / basal~e.4))) :ARG1 (m2 / mechanism~e.13 :purpose (e4 / escape-01~e.12 :ARG1~e.14 (i3 / inhibit-01~e.15 :ARG0~e.16 s~e.17))))) :ARG1-of (d / describe-01 :ARG0 (t / table~e.36 :mod 1~e.37))) # ::id pmid_1528_0923.94 ::amr-annotator SDL-AMR-09 ::preferred # ::tok GI101A cells , with low EGFR and nonactivated ERK1 @/@ 2 , showed modest growth inhibition when treated with an individual inhibitor and no significant difference with the combination of the two . # ::alignments 0-1.1.1.1 1-1.1 4-1.1.2.1.1 4-1.1.2.1.1.2 4-1.1.2.1.1.2.r 5-1.1.2.1.1.1.1 6-1.1.2.1 8-1.1.2.1.2.1.1 10-1.1.2.1.2.1.1 12-1 13-1.2.1.3 14-1.2.1.1 15-1.2.1 16-1.2.1.2.r 17-1.2.1.2 20-1.2.1.2.2.2 21-1.2.1 21-1.2.1.2.2 21-1.2.1.2.2.1 21-1.2.1.2.2.1.r 22-1.2 23-1.2.2.3.1 23-1.2.2.3.1.r 24-1.2.2.3 25-1.1.2.1.2.2.1 25-1.2.2 25-1.2.2.3.1 25-1.2.2.3.1.r 26-1.2.2.2.r 28-1.2.2.2 31-1.1.2.1.2.1.1 31-1.2.2.2.1.1 (s2 / show-01~e.12 :ARG0 (c / cell-line~e.1 :name (n2 / name :op1 "GI101A"~e.0) :ARG0-of (h / have-03 :ARG1 (a2 / and~e.6 :op1 (e2 / enzyme~e.4 :name (n3 / name :op1 "EGFR"~e.5) :ARG1-of~e.4 (l / low-04~e.4)) :op2 (e3 / enzyme :name (n4 / name :op1 "ERK1/2"~e.8,10,31) :ARG1-of (a3 / activate-01 :polarity -~e.25))))) :ARG1 (a4 / and~e.22 :op1 (i2 / inhibit-01~e.15,21 :ARG1 (g / grow-01~e.14) :time~e.16 (t2 / treat-04~e.17 :ARG1 c :ARG2 (m2 / molecular-physical-entity~e.21 :ARG0-of~e.21 (i / inhibit-01~e.21) :mod (i3 / individual~e.20))) :mod (m / modest~e.13)) :op2 (d / differ-02~e.25 :ARG1 c :ARG2~e.26 (c2 / combine-01~e.28 :ARG1 (t / thing :quant 2~e.31)) :ARG1-of (s / significant-02~e.24 :polarity~e.23,25 -~e.23,25)))) # ::id pmid_1528_0923.95 ::amr-annotator SDL-AMR-09 ::preferred # ::tok MDA @-@ MB @-@ 435 cells were significantly inhibited by U0126 alone , and the addition of PKI166 made no difference . # ::alignments 0-1.1.2.1.1 2-1.1.2.1.1 4-1.1.2.1.1 5-1.1.2 7-1.1.3 8-1.1 9-1.1.1.r 10-1.1.1.1.1 11-1.1.1.2 13-1 15-1.2.2 16-1.2.2.1.r 17-1.2.2.1.1.1 18-1.2 19-1.2.1 19-1.2.1.r 20-1.2.1.r 20-1.2.3 (a / and~e.13 :op1 (i / inhibit-01~e.8 :ARG0~e.9 (s / small-molecule :name (n / name :op1 "U0126"~e.10) :mod (a2 / alone~e.11)) :ARG1 (c / cell-line~e.5 :name (n2 / name :op1 "MDA-MB-435"~e.0,2,4)) :ARG1-of (s2 / significant-02~e.7)) :op2 (m / make-01~e.18 :polarity~e.19,20 -~e.19 :ARG0 (a3 / add-02~e.15 :ARG1~e.16 (s3 / small-molecule :name (n3 / name :op1 "PKI166"~e.17))) :ARG1 (d / differ-02~e.20))) # ::id pmid_1528_0923.96 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The combination of agents significantly increased the antiproliferative action of PKI166 at the 0.5 and 5.0 μ @ M doses in cells expressing higher levels of EGFR or HER2 ( SUM149 , MDA @-@ MB @-@ 468 , SKBR3 ) , including MDA @-@ MB @-@ 231 cells . # ::alignments 1-1.1 2-1.1.1.r 3-1.1.1 4-1.3 5-1 7-1.2.2 7-1.2.2.1 7-1.2.2.1.r 8-1.2 9-1.2.1.r 10-1.2.1.1.1 13-1.2.1.2.1.1.1 14-1.2.1.2.1 22-1.2.1 22-1.2.1.2 22-1.2.1.2.r 23-1.4.r 24-1.4 25-1.4.1 26-1.4.1.1.1.2 26-1.4.1.1.1.2.1 26-1.4.1.1.1.2.1.r 27-1.4.1.1.1 27-1.4.1.1.2 28-1.4.1.1.1.1.r 29-1.4.1.1.1.1.1.1 30-1.4.1.1 31-1.4.1.1.2.1.1.1 33-1.4.2.1.1.1.1 35-1.4.2.1.2.1.1 37-1.4.2.1.2.1.1 39-1.4.2.1.2.1.1 41-1.4.2.1.3.1.1 44-1.4.3 45-1.4.3.1.1.1 47-1.4.3.1.1.1 49-1.4.3.1.1.1 50-1.4 (i / increase-01~e.5 :ARG0 (c / combine-01~e.1 :ARG1~e.2 (a / agent~e.3)) :ARG1 (a2 / act-01~e.8 :ARG0~e.9 (s2 / small-molecule~e.22 :name (n / name :op1 "PKI166"~e.10) :ARG2-of~e.22 (d3 / dose-01~e.22 :quant (a4 / and~e.14 :op1 (c2 / concentration-quantity :quant 0.5~e.13 :unit (m / micromolar)) :op2 (c3 / concentration-quantity :quant 5 :unit (m2 / micromolar))))) :ARG0-of (c9 / counter-01~e.7 :ARG1~e.7 (p / proliferate-01~e.7))) :ARG1-of (s / significant-02~e.4) :location~e.23 (c4 / cell~e.24,50 :ARG3-of (e / express-03~e.25 :ARG2 (o / or~e.30 :op1 (l / level~e.27 :quant-of~e.28 (e2 / enzyme :name (n2 / name :op1 "EGFR"~e.29)) :ARG1-of (h / high-02~e.26 :degree~e.26 (m3 / more~e.26))) :op2 (l2 / level~e.27 :quant-of (e3 / enzyme :name (n3 / name :op1 "HER2"~e.31)) :ARG1-of h))) :ARG1-of (m4 / mean-01 :ARG2 (a5 / and :op1 (c5 / cell-line :name (n4 / name :op1 "SUM149"~e.33)) :op2 (c6 / cell-line :name (n5 / name :op1 "MDA-MB-468"~e.35,37,39)) :op3 (c7 / cell-line :name (n6 / name :op1 "SKBR3"~e.41)))) :ARG2-of (i2 / include-01~e.44 :ARG1 (c8 / cell-line :name (n7 / name :op1 "MDA-MB-231"~e.45,47,49))))) # ::id pmid_1528_0923.97 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Treating the MDA @-@ MB @-@ 231 cells with U0126 alone produced 8.5 % inhibition , which was not significantly different from control values . # ::alignments 0-1.1 2-1.1.1.1.1 4-1.1.1.1.1 6-1.1.1.1.1 7-1.1.1 8-1.1.2.r 9-1.1.2.1.1 10-1.1.2.2 11-1 12-1.2.1.1 13-1.2.1 14-1.2 18-1.3.1.r 19-1.3.3 20-1.3 20-1.3.1 20-1.3.1.r 21-1.3.2.r 22-1.3.2.1 23-1.3.2 (p2 / produce-01~e.11 :ARG0 (t / treat-04~e.0 :ARG1 (c / cell-line~e.7 :name (n2 / name :op1 "MDA-MB-231"~e.2,4,6)) :ARG2~e.8 (s2 / small-molecule :name (n3 / name :op1 "U0126"~e.9) :mod (a / alone~e.10))) :ARG1 (i / inhibit-01~e.14 :quant (p / percentage-entity~e.13 :value 8.5~e.12)) :ARG1-of (d / differ-02~e.20 :polarity~e.18,20 -~e.20 :ARG2~e.21 (v / value~e.23 :mod (c2 / control~e.22)) :ARG1-of (s / significant-02~e.19))) # ::id pmid_1528_0923.98 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The addition of U0126 to 0.5 or 5.0 μ @ M PKI166 significantly increased the growth inhibition produced by the receptor tyrosine kinase inhibitor alone ( Table 1 ) . # ::alignments 1-1.1 2-1.1.1.r 3-1.1.1.1.1 4-1.1.2.r 5-1.1.2.1.2.1 6-1.1.2 14-1.1.2.1.1.1 14-1.1.2.2.1.1 15-1.3 16-1 18-1.2.1 19-1.2 20-1.2.2 21-1.2.2.1.r 23-1.2.2.1.1.1.1.1 24-1.2.2.1.1.1.1.2 25-1.2.2.1.1.1.1.3 26-1.2.2.1 26-1.2.2.1.1 26-1.2.2.1.1.r 27-1.2.2.1.2 30-1.4.1 31-1.4.1.1 (i / increase-01~e.16 :ARG0 (a / add-02~e.1 :ARG1~e.2 (s2 / small-molecule :name (n / name :op1 "U0126"~e.3)) :ARG2~e.4 (o / or~e.6 :op1 (s3 / small-molecule :name (n2 / name :op1 "PKI166"~e.14) :quant (c / concentration-quantity :quant 0.5~e.5 :unit (m / micromolar))) :op2 (s4 / small-molecule :name (n3 / name :op1 "PKI166"~e.14) :quant (c2 / concentration-quantity :quant 5 :unit (m3 / micromolar))))) :ARG1 (i2 / inhibit-01~e.19 :ARG1 (g / grow-01~e.18) :ARG1-of (p / produce-01~e.20 :ARG0~e.21 (m2 / molecular-physical-entity~e.26 :ARG0-of~e.26 (i3 / inhibit-01~e.26 :ARG1 (e / enzyme :name (n4 / name :op1 "receptor"~e.23 :op2 "tyrosine"~e.24 :op3 "kinase"~e.25))) :mod (a2 / alone~e.27)))) :ARG2 (s / significant-02~e.15) :ARG1-of (d / describe-01 :ARG0 (t / table~e.30 :mod 1~e.31))) # ::id pmid_1528_0923.99 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Apoptosis induced by PKI166 and U0126 was assessed by measuring DNA fragmentation by propidium iodide staining and FACS analysis , and determining the proportions of hypodiploid cells . # ::alignments 0-1.2 1-1.2.1 2-1.2.1.1.r 3-1.2.1.1.1.1.1 4-1.2.1.1 5-1.2.1.1.2.1.1 7-1 8-1.1.r 9-1.1.1 10-1.1.1.1.2.2.1 10-1.1.1.1.2.3.1 11-1.1.1.1 12-1.1.1.1.1.r 13-1.1.1.1.1.1.1.1.1 14-1.1.1.1.1.1.1.1.2 15-1.1.1.1.1.1 16-1.1.1.1.1 17-1.1.1.1.1.2.1.1.1 18-1.1.1.1.1.2 20-1.1 21-1.1.2 23-1.1.2.1 24-1.1.2.1.1.r 25-1.1.2.1.1.1 26-1.1.2.1.1 (a8 / assess-01~e.7 :ARG0~e.8 (a7 / and~e.20 :op1 (m / measure-01~e.9 :ARG1 (f / fragment-01~e.11 :ARG0~e.12 (a5 / and~e.16 :op1 (s4 / stain-01~e.15 :ARG2 (s3 / small-molecule :name (n4 / name :op1 "propidium"~e.13 :op2 "iodide"~e.14))) :op2 (a6 / analyze-01~e.18 :mod (t / thing :name (n5 / name :op1 "FACS"~e.17)))) :ARG1 (n6 / nucleic-acid :wiki "DNA" :name (n7 / name :op1 "DNA"~e.10) :name (n3 / name :op1 "DNA"~e.10)))) :op2 (d2 / determine-01~e.21 :ARG1 (p / proportion-01~e.23 :ARG1~e.24 (c / cell~e.26 :mod (h / hypodiploid~e.25))))) :ARG1 (a3 / apoptosis~e.0 :ARG2-of (i / induce-01~e.1 :ARG0~e.2 (a4 / and~e.4 :op1 (s2 / small-molecule :name (n2 / name :op1 "PKI166"~e.3)) :op2 (s / small-molecule :name (n / name :op1 "U0126"~e.5)))))) # ::id pmid_1528_0923.100 ::amr-annotator SDL-AMR-09 ::preferred # ::tok This showed that PKI166 alone or in combination with U0126 induced apoptosis in the EGFR or HER2 expressing cell lines MDA @-@ MB @-@ 231 , MDA @-@ MB @-@ 468 , SKBR3 and SUM149 cells ( Figure 3 ) , although the proportions of hypodiploid cells varied between the different lines . # ::alignments 0-1.1 1-1 2-1.2.r 3-1.2.1.1.1.1 3-1.2.1.2.1.1 4-1.2.1.1.2 5-1.2.1 7-1.2.1.2 7-1.2.1.2.2 7-1.2.1.2.2.r 8-1.2.1.2.2.1.r 9-1.2.1.2.2.1.1.1 10-1.2 11-1.2.2 12-1.2.5.r 14-1.2.5.5.1.1.1.1 15-1.2.5.5.1 16-1.2.5.5.1.2.1.1 17-1.2.5.5 18-1.2.5.1 19-1.2.5.1 20-1.2.5.1.1.1 22-1.2.5.1.1.1 24-1.2.5.1.1.1 26-1.2.5.1.1.1 26-1.2.5.2.1.1 28-1.2.5.1.1.1 28-1.2.5.2.1.1 30-1.2.5.2.1.1 32-1.2.5.3.1.1 33-1.2.5 34-1.2.5.4.1.1 35-1.2.5.1 35-1.2.5.2 35-1.2.5.3 35-1.2.5.4 38-1.2.3.1 39-1.2.3.1.1 43-1.2.4.r 45-1.2.4.1 46-1.2.4.1.1.r 47-1.2.4.1.1.1 48-1.2.4.1.1 49-1.2.4 52-1.2.4.2.1 53-1.2.4.2 (s2 / show-01~e.1 :ARG0 (t / this~e.0) :ARG1~e.2 (i / induce-01~e.10 :ARG0 (o / or~e.5 :op1 (s3 / small-molecule :name (n4 / name :op1 "PKI166"~e.3) :mod (a / alone~e.4)) :op2 (s4 / small-molecule~e.7 :name (n9 / name :op1 "PKI166"~e.3) :ARG1-of~e.7 (c / combine-01~e.7 :ARG2~e.8 (s / small-molecule :name (n / name :op1 "U0126"~e.9))))) :ARG2 (a2 / apoptosis~e.11) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.38 :mod 3~e.39)) :concession~e.43 (v / vary-01~e.49 :ARG1 (p / proportion-01~e.45 :ARG1~e.46 (c6 / cell~e.48 :mod (h2 / hypodiploid~e.47))) :location (l / line~e.53 :ARG1-of (d2 / differ-02~e.52))) :location~e.12 (a3 / and~e.33 :op1 (c2 / cell-line~e.18,19,35 :name (n5 / name :op1 "MDA-MB-231"~e.20,22,24,26,28)) :op2 (c3 / cell-line~e.35 :name (n6 / name :op1 "MDA-MB-468"~e.26,28,30)) :op3 (c4 / cell-line~e.35 :name (n7 / name :op1 "SKBR3"~e.32)) :op4 (c5 / cell-line~e.35 :name (n8 / name :op1 "SUM149"~e.34)) :ARG3-of (e3 / express-03~e.17 :ARG2 (o2 / or~e.15 :op1 (e / enzyme :name (n2 / name :op1 "EGFR"~e.14)) :op2 (e2 / enzyme :name (n3 / name :op1 "HER2"~e.16))))))) # ::id pmid_1528_0923.101 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Similar to the MTT results in Table 1 , SKBR3 and SUM 149 cells were most sensitive to treatment with the inhibitors , while the proportions of hypodiploid MDA @-@ MB @-@ 231 cells were lower . # ::alignments 0-1.3 1-1.3.1.r 3-1.3.1.1.1.1.1 4-1.3.1 4-1.3.1.1 4-1.3.1.1.r 7-1.3.1.2 8-1.3.1.2.1 11-1.1.1.1.1.1 12-1.1.1 15-1.1.1.1 15-1.1.1.2 17-1.1.3 18-1.1 19-1.1.2.r 20-1.1.2 21-1.1.2.2.r 23-1.1.2.2 23-1.1.2.2.1 23-1.1.2.2.1.r 25-1 27-1.2.1 28-1.2.1.1.r 29-1.2.1.1.2 30-1.2.1.1.1.1 32-1.2.1.1.1.1 34-1.2.1.1.1.1 35-1.2.1.1 37-1.2 37-1.2.2 37-1.2.2.r (c / contrast-01~e.25 :ARG1 (s / sensitive-03~e.18 :ARG0 (a / and~e.12 :op1 (c2 / cell-line~e.15 :name (n / name :op1 "SKBR3"~e.11)) :op2 (c3 / cell-line~e.15 :name (n2 / name :op1 "SUM149"))) :ARG1~e.19 (t2 / treat-04~e.20 :ARG1 a :ARG2~e.21 (m3 / molecular-physical-entity~e.23 :ARG0-of~e.23 (i2 / inhibit-01~e.23))) :degree (m2 / most~e.17)) :ARG2 (l / low-04~e.37 :ARG1 (p / proportion-01~e.27 :ARG1~e.28 (c4 / cell-line~e.35 :name (n3 / name :op1 "MDA-MB-231"~e.30,32,34) :mod (h / hypodiploid~e.29))) :degree~e.37 (m / more~e.37)) :ARG1-of (r / resemble-01~e.0 :ARG2~e.1 (t4 / thing~e.4 :ARG2-of~e.4 (r2 / result-01~e.4 :ARG1 (s2 / small-molecule :name (n4 / name :op1 "MTT"~e.3))) :location (t3 / table~e.7 :mod 1~e.8)))) # ::id pmid_1528_0923.102 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Treatment with U0126 alone significantly increased the numbers of MDA @-@ MB @-@ 231 in the G @₁ phase of the cell cycle ( 89 @–@ 93 % compared with 70 @–@ 72 % of control or PKI 166 treated cells , P @ < 0.001 ) . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.1 3-1.1.1.2 4-1.4 5-1 7-1.2 8-1.2.1.r 9-1.2.1.1.1 11-1.2.1.1.1 13-1.2.1.1.1 20-1.5.1.2 23-1.5.2.1 24-1.5.2 26-1.3.1.1 28-1.3.2.1 29-1.3.1 29-1.3.2 30-1.6.r 32-1.6.1.1 34-1.6.2.1 35-1.6.1 35-1.6.2 37-1.6.3.1.1 38-1.6.3 41-1.6.3.2.1 42-1.6.3.1 42-1.6.3.2 45-1.7 47-1.7.1 48-1.7.1.1 (i / increase-01~e.5 :ARG0 (t / treat-04~e.0 :ARG2~e.1 (s / small-molecule :name (n / name :op1 "U0126"~e.2) :mod (a / alone~e.3))) :ARG1 (n2 / number-01~e.7 :ARG1~e.8 (c / cell-line :name (n3 / name :op1 "MDA-MB-231"~e.9,11,13))) :ARG2 (v / value-interval :op1 (p4 / percentage-entity~e.29 :value 89~e.26) :op2 (p / percentage-entity~e.29 :value 93~e.28)) :ARG1-of (s2 / significant-02~e.4) :time (e / event :name (n5 / name :op1 "G1" :op2 "phase"~e.20) :part-of (c2 / cycle-02~e.24 :ARG1 (c3 / cell~e.23))) :compared-to~e.30 (v2 / value-interval :op1 (p5 / percentage-entity~e.35 :value 70~e.32) :op2 (p2 / percentage-entity~e.35 :value 72~e.34) :quant-of (o / or~e.38 :op1 (c4 / cell~e.42 :mod (c5 / control~e.37)) :op2 (c6 / cell~e.42 :ARG1-of (t2 / treat-04~e.41 :ARG2 (s3 / small-molecule :name (n4 / name :op1 "PKI166")))))) :ARG1-of (s4 / statistical-test-91~e.45 :ARG2 (l / less-than~e.47 :op1 0.001~e.48))) # ::id pmid_1528_0923.103 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The proportion of SUM149 cells in G @₁ was significantly increased by treatment with either inhibitor alone and the combination , while apoptosis was significantly increased in cells exposed to PKI166 , with or without U0126 . # ::alignments 1-1.1.2 2-1.1.2.1.r 3-1.1.2.1.1.1 4-1.1.2.1 11-1.1.3 12-1.1 13-1.1.1.r 14-1.1.1 17-1.1.1.1.1 17-1.1.1.1.1.1 17-1.1.1.1.1.1.r 17-1.1.1.1.2 17-1.1.1.1.2.1 17-1.1.1.1.2.1.r 18-1.1.1.1.1.2 19-1.1.1.1 21-1.1.1.1.2.2 23-1 23-1.1.2.2.r 24-1.2.1 26-1.2.3 27-1.2 28-1.2.2.r 29-1.2.2 30-1.2.2.1 31-1.2.2.1.1.r 32-1.2.2.1.1.1.1.1.1 35-1.2.2.1.1 37-1.2.2.1.1.1.2.1.1 (c / contrast-01~e.23 :ARG1 (i2 / increase-01~e.12 :ARG0~e.13 (t2 / treat-04~e.14 :ARG2 (a / and~e.19 :op1 (m / molecular-physical-entity~e.17 :ARG0-of~e.17 (i / inhibit-01~e.17) :mod (a2 / alone~e.18)) :op2 (m2 / molecular-physical-entity~e.17 :ARG0-of~e.17 (i4 / inhibit-01~e.17) :ARG1-of (c3 / combine-01~e.21)))) :ARG1 (p / proportion-01~e.1 :ARG1~e.2 (c2 / cell-line~e.4 :name (n2 / name :op1 "SUM149"~e.3)) :time~e.23 (e2 / event :name (n4 / name :op1 "G1"))) :ARG2 (s2 / significant-02~e.11)) :ARG2 (i3 / increase-01~e.27 :ARG1 (a3 / apoptosis~e.24) :location~e.28 (c4 / cell~e.29 :ARG1-of (e / expose-01~e.30 :ARG2~e.31 (o / or~e.35 :op1 (a4 / and :op1 (s4 / small-molecule :name (n3 / name :op1 "PKI166"~e.32)) :op2 (s / small-molecule :name (n / name :op1 "U0126"~e.37))) :op2 s4))) :ARG1-of s2~e.26)) # ::id pmid_1528_0923.104 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Induction of the cyclin @-@ dependent kinase inhibitor p27 @^KIP1 generally corresponded with increases in the proportion of cells in G @₁ , as shown for MDA @-@ MB @-@ 231 and SUM149 ( Figure 4 ) . # ::alignments 0-1.1 1-1.1.1.r 3-1.1.1.2.1.1.1 5-1.1.1.2.1.1.1 6-1.1.1.2.1.1.2 7-1.1.1 7-1.1.1.2 7-1.1.1.2.r 12-1.3 13-1 14-1.2.r 15-1.2 16-1.2.1.r 18-1.2.1 19-1.2.1.1.r 20-1.2.1.1 27-1.2.1.2.r 27-1.4.r 28-1.4 29-1.4.1.r 30-1.4.1.1.1.1 32-1.4.1.1.1.1 34-1.4.1.1.1.1 35-1.4.1 36-1.4.1.2.1.1 39-1.5.1 40-1.5.1.1 (c / correspond-02~e.13 :ARG1 (i2 / induce-01~e.0 :ARG2~e.1 (p2 / protein~e.7 :name (n4 / name :op1 "p27KIP1") :ARG0-of~e.7 (i / inhibit-01~e.7 :ARG1 (p3 / protein-family :name (n / name :op1 "cyclin-dependent"~e.3,5 :op2 "kinase"~e.6))))) :ARG2~e.14 (i3 / increase-01~e.15 :ARG1~e.16 (p / proportion-01~e.18 :ARG1~e.19 (c2 / cell~e.20) :time~e.27 (e2 / event :name (n5 / name :op1 "G1")))) :ARG1-of (g / general-02~e.12) :ARG1-of~e.27 (s / show-01~e.28 :ARG2~e.29 (a / and~e.35 :op1 (c3 / cell-line :name (n2 / name :op1 "MDA-MB-231"~e.30,32,34)) :op2 (c4 / cell-line :name (n3 / name :op1 "SUM149"~e.36)))) :ARG1-of (d / describe-01 :ARG0 (f / figure~e.39 :mod 4~e.40))) # ::id pmid_1528_0923.105 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Differential effect of PKI166 on ERK1 @/@ 2 phosphorylation # ::alignments 1-1.3 2-1 3-1.1.r 4-1.1.1.1 5-1.2.r 6-1.2.1.1.1 8-1.2.1.1.1 9-1.2 (a / affect-01~e.2 :ARG0~e.3 (s / small-molecule :name (n / name :op1 "PKI166"~e.4)) :ARG1~e.5 (p / phosphorylate-01~e.9 :ARG1 (e / enzyme :name (n2 / name :op1 "ERK1/2"~e.6,8))) :ARG1-of (d / differ-02~e.1)) # ::id pmid_1528_0923.106 ::amr-annotator SDL-AMR-09 ::preferred # ::tok To evaluate whether the antiproliferative effects of EGFR inhibition involve ERK1 @/@ 2 activation , the status of pERK1 @/@ 2 was determined in cells exposed to the same concentrations of PKI166 used for the growth inhibition assays , in the presence and absence of U0126 ( 10 μ @ M ) ( Figure 5 ) . # ::alignments 1-1.3 2-1.3.1.1 2-1.3.1.1.r 4-1.3.1.2.2 4-1.3.1.2.2.1 4-1.3.1.2.2.1.r 5-1.3.1.2 6-1.3.1.2.1.r 7-1.3.1.2.1.1.1.1 8-1.3.1.2.1 9-1.3.1 10-1.3.1.3.1.1.1 12-1.3.1.3.1.1.1 13-1.3.1.3 16-1.1 20-1.1.1.1.1 20-1.3.1.3.1.1.1 22-1 23-1.2.r 24-1.2 25-1.2.1 26-1.2.1.1.r 28-1.2.1.1.2 29-1.2.1.1 29-1.2.1.2.1.1.2 30-1.2.1.1.1.r 31-1.2.1.1.1.1.1 32-1.2.1.1.1.2 33-1.2.1.1.1.2.1.r 35-1.2.1.1.1.2.1.1.1 36-1.2.1.1.1.2.1.1 37-1.2.1.1.1.2.1 39-1.2.1.2.r 41-1.2.1.2.1 42-1.2.1.2 43-1.2.1.2.2 44-1.2.1.2.1.1.r 45-1.2.1.2.1.1.1.1 47-1.2.1.2.1.1.2.1 57-1.4.1 58-1.4.1.1 (d / determine-01~e.22 :ARG1 (s2 / status~e.16 :poss-of (e2 / enzyme :name (n3 / name :op1 "ERK1/2"~e.20) :ARG3-of (p / phosphorylate-01))) :location~e.23 (c / cell~e.24 :ARG1-of (e3 / expose-01~e.25 :ARG2~e.26 (c2 / concentrate-02~e.29 :ARG1~e.30 (s3 / small-molecule :name (n4 / name :op1 "PKI166"~e.31) :ARG1-of (u / use-01~e.32 :ARG2~e.33 (a / assay-01~e.37 :ARG1 (i / inhibit-01~e.36 :ARG1 (g / grow-01~e.35))))) :ARG1-of (s4 / same-01~e.28)) :manner~e.39 (a2 / and~e.42 :op1 (p2 / present-02~e.41 :ARG1~e.44 (s / small-molecule :name (n2 / name :op1 "U0126"~e.45) :quant (c3 / concentration-quantity~e.29 :quant 10~e.47 :unit (m / micromolar)))) :op2 (a3 / absent-01~e.43 :ARG1 s)))) :purpose (e4 / evaluate-01~e.1 :ARG1 (i3 / involve-01~e.9 :mode~e.2 interrogative~e.2 :ARG0 (a4 / affect-01~e.5 :ARG0~e.6 (i2 / inhibit-01~e.8 :ARG1 (e / enzyme :name (n / name :op1 "EGFR"~e.7))) :ARG0-of (c4 / counter-01~e.4 :ARG1~e.4 (p3 / proliferate-01~e.4))) :ARG1 (a5 / activate-01~e.13 :ARG1 (e5 / enzyme :name (n5 / name :op1 "ERK1/2"~e.10,12,20))))) :ARG1-of (d2 / describe-01 :ARG0 (f / figure~e.57 :mod 5~e.58))) # ::id pmid_1528_0923.107 ::amr-annotator SDL-AMR-09 ::preferred # ::tok U1026 alone inhibited ERK1 @/@ 2 phosphorylation in MDA @-@ MB @-@ 435 cells , with PKI 166 having no effect , as expected from minimal expression of EGFR in these cells . # ::alignments 0-1.1.1.1.1 1-1.1.1.2 2-1.1 3-1.1.2.1.1.1 5-1.1.2.1.1.1 6-1.1.2 7-1.1.3.r 8-1.1.3.1.1 10-1.1.3.1.1 12-1.1.3.1.1 13-1.1.3 19-1.2.1 19-1.2.1.r 20-1.2 23-1.3 24-1.3.1.r 25-1.3.1.3 26-1.3.1 27-1.3.1.1.r 28-1.3.1.1.1.1 31-1.3.1.2 (a / and :op1 (i / inhibit-01~e.2 :ARG0 (s / small-molecule :name (n2 / name :op1 "U1026"~e.0) :mod (a2 / alone~e.1)) :ARG1 (p / phosphorylate-01~e.6 :ARG1 (e2 / enzyme :name (n3 / name :op1 "ERK1/2"~e.3,5))) :location~e.7 (c / cell-line~e.13 :name (n4 / name :op1 "MDA-MB-435"~e.8,10,12))) :op2 (a3 / affect-01~e.20 :polarity~e.19 -~e.19 :ARG0 (s2 / small-molecule :name (n5 / name :op1 "PKI166"))) :ARG1-of (e3 / expect-01~e.23 :source~e.24 (e4 / express-03~e.26 :ARG2~e.27 (e / enzyme :name (n / name :op1 "EGFR"~e.28)) :ARG3 c~e.31 :ARG1-of (m / minimal-02~e.25)))) # ::id pmid_1528_0923.108 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PKI166 inhibited ERK1 @/@ 2 phosphorylation in SUM149 cells , as did U0126 alone , and further inhibition by the combination of drugs was barely discernible . # ::alignments 0-1.1.1.1.1 1-1.1 2-1.1.2.1.1.1 4-1.1.2.1.1.1 5-1.1.2 6-1.1.3.r 7-1.1.3.1.1 8-1.1.3 10-1.2.1.2.r 12-1.1.4.1.1.1 13-1.1.4.1.2 15-1 16-1.2.1.2 17-1.2.1 18-1.2.1.1.r 20-1.2.1.1 21-1.2.1.1.1.r 22-1.2.1.1.1 24-1.2.2 (a / and~e.15 :op1 (i / inhibit-01~e.1 :ARG0 (s2 / small-molecule :name (n2 / name :op1 "PKI166"~e.0)) :ARG1 (p / phosphorylate-01~e.5 :ARG1 (e / enzyme :name (n3 / name :op1 "ERK1/2"~e.2,4))) :location~e.6 (c / cell-line~e.8 :name (n4 / name :op1 "SUM149"~e.7)) :ARG1-of (r / resemble-01 :ARG2 (s / small-molecule :name (n / name :op1 "U0126"~e.12) :mod (a2 / alone~e.13)))) :op2 (d / discern-01 :ARG1 (i2 / inhibit-01~e.17 :ARG0~e.18 (c2 / combine-01~e.20 :ARG1~e.21 (d2 / drug~e.22)) :time~e.10 (f / further~e.16)) :degree (b / bare~e.24) :ARG1-of (p2 / possible-01))) # ::id pmid_1528_0923.109 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Treatment of MDA @-@ MB @-@ 468 with either drug resulted in similar inhibition of ERK1 @/@ 2 phosphorylation , with almost complete elimination of phosphorylated proteins by the combination . # ::alignments 0-1.1 1-1.1.1.r 2-1.1.1.1.1 4-1.1.1.1.1 6-1.1.1.1.1 7-1.1.2.r 8-1.1.2.1 9-1.1.2 10-1 11-1.2.r 12-1.2.1.2 13-1.2.1 14-1.2.1.1.r 15-1.2.1.1.1.1.1 17-1.2.1.1.1.1.1 18-1.2.1.1 21-1.2.2.3.1 22-1.2.2.3 23-1.2.2 24-1.2.2.2.r 25-1.2.2.2.1 26-1.2.2.2 27-1.2.2.1.r 29-1.2.2.1 (r2 / result-01~e.10 :ARG1 (t / treat-04~e.0 :ARG1~e.1 (c / cell-line :name (n / name :op1 "MDA-MB-468"~e.2,4,6)) :ARG2~e.7 (d / drug~e.9 :mod (e / either~e.8))) :ARG2~e.11 (a / and :op1 (i / inhibit-01~e.13 :ARG1~e.14 (p / phosphorylate-01~e.18 :ARG1 (e2 / enzyme :name (n2 / name :op1 "ERK1/2"~e.15,17))) :ARG1-of (r / resemble-01~e.12)) :op2 (e3 / eliminate-01~e.23 :ARG0~e.27 (c3 / combine-01~e.29) :ARG1~e.24 (p2 / protein~e.26 :ARG3-of (p3 / phosphorylate-01~e.25)) :ARG1-of (c2 / complete-01~e.22 :mod (a2 / almost~e.21))))) # ::id pmid_1528_0923.110 ::amr-annotator SDL-AMR-09 ::preferred # ::tok PKI166 alone minimally altered the ERK1 @/@ 2 status in the MDA @-@ MB @-@ 231 cells , and U0126 produced some inhibition , while the combination resulted in a substantial reduction , reflecting the effect on cell proliferation and apoptosis . # ::alignments 0-1.1.1.1.2.1 1-1.1.1.1.3 2-1.1.1.3 3-1.1.1 5-1.1.1.2.1.2.1 7-1.1.1.2.1.2.1 8-1.1.1.2 9-1.1.1.4.r 11-1.1.1.4.2.1 13-1.1.1.4.2.1 15-1.1.1.4.2.1 16-1.1.1.4 18-1.1 19-1.1.2.1.2.1 20-1.1.2 21-1.1.2.2.1 22-1.1.2.2 24-1 26-1.2.1 27-1.2 28-1.2.2.r 30-1.2.2.2 31-1.2.2 33-1.2.3 35-1.2.3.1 36-1.2.3.1.1.r 37-1.2.3.1.1.1.1 38-1.2.3.1.1.1 39-1.2.3.1.1 40-1.2.3.1.1.2 (c / contrast-01~e.24 :ARG1 (a / and~e.18 :op1 (a2 / alter-01~e.3 :ARG0 (s2 / small-molecule :wiki - :name (n2 / name :op1 "PKI166"~e.0) :mod (a3 / alone~e.1)) :ARG1 (s3 / status~e.8 :mod (e / enzyme :wiki "Extracellular_signal-regulated_kinases" :name (n3 / name :op1 "ERK1/2"~e.5,7))) :ARG1-of (m / minimal-02~e.2) :location~e.9 (c2 / cell-line~e.16 :wiki - :name (n4 / name :op1 "MDA-MB-231"~e.11,13,15))) :op2 (p / produce-01~e.20 :ARG0 (s4 / small-molecule :wiki "U0126" :name (n5 / name :op1 "U0126"~e.19)) :ARG1 (i / inhibit-01~e.22 :mod (s5 / some~e.21)))) :ARG2 (r / result-01~e.27 :ARG1 (c3 / combine-01~e.26) :ARG2~e.28 (r2 / reduce-01~e.31 :ARG1 s3 :degree (s6 / substantial~e.30)) :ARG1-of (r3 / reflect-01~e.33 :ARG2 (a4 / affect-01~e.35 :ARG1~e.36 (a5 / and~e.39 :op1 (p2 / proliferate-01~e.38 :ARG0 (c4 / cell~e.37)) :op2 (a6 / apoptosis~e.40)))))) # ::id pmid_1528_0923.111 ::amr-annotator SDL-AMR-09 ::preferred # ::tok For SUM149 and MDA @-@ MB @-@ 468 cells the combination of the inhibitors almost completely eliminated ERK1 @/@ 2 phosphorylation after 1 h incubation , although growth inhibition over 72 h was 54 @–@ 63 % with 0.5 μ @ M PKI166 plus 10 μ @ M U0126 , and 63 @–@ 81 % with 5.0 μ @ M PKI166 plus 10 μ @ M U0126 ( Table 1 ) . # ::alignments 1-1.3.1.1.1 2-1.3 3-1.3.2.1.1 5-1.3.2.1.1 7-1.3.2.1.1 8-1.3.1 8-1.3.2 10-1.1 11-1.1.1.r 13-1.1.1 13-1.1.1.1 13-1.1.1.1.r 14-1.4.1 15-1.4 16-1 17-1.2.1.1.1 19-1.2.1.1.1 20-1.2 21-1.5 22-1.5.2.1 23-1.5.2.2 24-1.5.1 26-1.6.r 27-1.6.1.2 27-1.6.2.2 28-1.6.1 28-1.6.2 29-1.6.1.4 30-1.6.1.4.1.1 31-1.6.1.4.1.2 33-1.6.1.3.1.1 35-1.6.1.3.2.1 36-1.6.1.3.1 36-1.6.1.3.2 36-1.6.2.3.1 37-1.6.1.1.r 38-1.6.1.1.1.2.1 45-1.6.1.1.1.1.1 45-1.6.2.1.1.1.1 46-1.6 46-1.6.2.1 47-1.6.1.1.2.2.1 54-1.6.1.1.2.1.1 56-1.6 57-1.6.2.3.1.1 59-1.6.2.3.2.1 60-1.6.2.3.2 69-1.6.1.1.1.1.1 69-1.6.2.1.1.1.1 70-1.6 71-1.6.1.1.2.2.1 78-1.6.1.1.2.1.1 81-1.7.1 82-1.5.2.1 82-1.7.1.1 (e / eliminate-01~e.16 :ARG0 (c / combine-01~e.10 :ARG1~e.11 (m / molecular-physical-entity~e.13 :ARG0-of~e.13 (i / inhibit-01~e.13))) :ARG1 (p3 / phosphorylate-01~e.20 :ARG1 (e2 / enzyme :name (n / name :op1 "ERK1/2"~e.17,19))) :ARG2 (a3 / and~e.2 :op1 (c3 / cell-line~e.8 :name (n2 / name :op1 "SUM149"~e.1)) :op2 (c4 / cell-line~e.8 :name (n3 / name :op1 "MDA-MB-468"~e.3,5,7))) :ARG1-of (c2 / complete-01~e.15 :mod (a / almost~e.14)) :time (a2 / after~e.21 :op1 (i2 / incubate-01~e.24) :quant (t / temporal-quantity :quant 1~e.22,82 :unit (h / hour~e.23))) :concession~e.26 (a5 / and~e.46,56,70 :op1 (i3 / inhibit-01~e.28 :ARG0~e.37 (a4 / and :op1 (s2 / small-molecule :name (n4 / name :op1 "PKI166"~e.45,69) :quant (c5 / concentration-quantity :quant 0.5~e.38 :unit (m2 / micromolar))) :op2 (s / small-molecule :name (n5 / name :op1 "U0126"~e.54,78) :quant (c6 / concentration-quantity :quant 10~e.47,71 :unit (m3 / micromolar)))) :ARG1 (g / grow-01~e.27) :quant (v / value-interval :op1 (p4 / percentage-entity~e.36 :value 54~e.33) :op2 (p / percentage-entity~e.36 :value 63~e.35)) :duration (o2 / over~e.29 :op1 (t2 / temporal-quantity :quant 72~e.30 :unit (h3 / hour~e.31)))) :op2 (i4 / inhibit-01~e.28 :ARG0 (a6 / and~e.46 :op1 (s3 / small-molecule :name (n6 / name :op1 "PKI166"~e.45,69) :quant (c7 / concentration-quantity :quant 5 :unit (m4 / micromolar))) :op2 s) :ARG1 (g2 / grow-01~e.27) :quant (v2 / value-interval :op1 (p5 / percentage-entity~e.36 :value 63~e.57) :op2 (p2 / percentage-entity~e.60 :value 81~e.59)) :duration o2)) :ARG1-of (d / describe-01 :ARG0 (t3 / table~e.81 :mod 1~e.82))) # ::id pmid_1528_0923.112 ::amr-annotator SDL-AMR-09 ::preferred # ::tok Recovery of ERK1 @/@ 2 phosphorylation in the U0126 @-@ treated cells over the period of the growth inhibition assays was not investigated , but the data may also suggest that other signal pathways were contributing to the growth and survival of the cells . # ::alignments 0-1.1.2 1-1.1.2.1.r 2-1.1.2.1.1.1.1 4-1.1.2.1.1.1.1 5-1.1.2.1 6-1.1.2.1.2.r 8-1.1.2.1.2.1.1.1.1 10-1.1.2.1.2.1 11-1.1.2.1.2 15-1.1.2.2.r 17-1.1.2.2.1.1 18-1.1.2.2.1 19-1.1.2.2 21-1.1.1 21-1.1.1.r 22-1.1 24-1 26-1.2.1.1 27-1.2 28-1.2.1.3 29-1.2.1 30-1.2.1.2.r 31-1.2.1.2.1.2 32-1.2.1.2.1.1 33-1.2.1.2.1 35-1.2.1.2 36-1.2.1.2.2.r 38-1.2.1.2.2.1 39-1.2.1.2.2 40-1.2.1.2.2.2 41-1.2.1.2.2.1.1.r 43-1.2.1.2.2.1.1 (c / contrast-01~e.24 :ARG1 (i / investigate-01~e.22 :polarity~e.21 -~e.21 :ARG1 (r / recover-02~e.0 :ARG1~e.1 (p / phosphorylate-01~e.5 :ARG1 (e / enzyme :name (n / name :op1 "ERK1/2"~e.2,4)) :location~e.6 (c2 / cell~e.11 :ARG1-of (t / treat-04~e.10 :ARG2 (s / small-molecule :name (n2 / name :op1 "U0126"~e.8))))) :time~e.15 (a / assay-01~e.19 :ARG1 (i2 / inhibit-01~e.18 :ARG1 (g / grow-01~e.17))))) :ARG2 (p3 / possible-01~e.27 :ARG1 (s2 / suggest-01~e.29 :ARG0 (d / data~e.26) :ARG1~e.30 (c3 / contribute-01~e.35 :ARG0 (p4 / pathway~e.33 :ARG0-of (s3 / signal-07~e.32) :mod (o2 / other~e.31)) :ARG2~e.36 (a3 / and~e.39 :op1 (g2 / grow-01~e.38 :ARG1~e.41 (c4 / cell~e.43)) :op2 (s4 / survive-01~e.40 :ARG0 c4))) :mod (a2 / also~e.28)))) # ::id pmid_1528_0923.113 ::amr-annotator SDL-AMR-09 ::preferred # ::tok The effects of the inhibitors were not related to downregulation of total ERK1 @/@ 2 proteins , as the levels did not decrease with treatment ( Figure 5 ) . # ::alignments 1-1.2 2-1.2.1.r 4-1.2.1 4-1.2.1.1 4-1.2.1.1.r 6-1.1 6-1.1.r 7-1 8-1.3.r 8-1.4 9-1.3 10-1.3.1.r 11-1.3.1.2 12-1.3.1.1.1 14-1.3.1.1.1 17-1.4.1.r 19-1.4.1.3 21-1.4.1.1 21-1.4.1.1.r 22-1.4.1 23-1.4.1.2.r 24-1.4.1.2 27-1.5.1 28-1.5.1.1 (r2 / relate-01~e.7 :polarity~e.6 -~e.6 :ARG1 (a / affect-01~e.1 :ARG0~e.2 (m / molecular-physical-entity~e.4 :ARG0-of~e.4 (i2 / inhibit-01~e.4))) :ARG2~e.8 (d / downregulate-01~e.9 :ARG1~e.10 (e / enzyme :name (n / name :op1 "ERK1/2"~e.12,14) :mod (t2 / total~e.11))) :ARG1-of (c / cause-01~e.8 :ARG0~e.17 (d2 / decrease-01~e.22 :polarity~e.21 -~e.21 :ARG0~e.23 (t3 / treat-04~e.24) :ARG1 (l / level~e.19))) :ARG1-of (d3 / describe-01 :ARG0 (f / figure~e.27 :mod 5~e.28)))