//genesis // kkit Version 9 flat dumpfile // Saved on Mon Dec 22 14:54:02 2003 include kkit {argv 1} FASTDT = 0.001 SIMDT = 0.005 CONTROLDT = 10 PLOTDT = 10 MAXTIME = 2000 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1e-15 VERSION = 9.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump table input output alloced step_mode stepsize x y z simobjdump xtree path script namemode sizescale simobjdump xcoredraw xmin xmax ymin ymax simobjdump xtext editable simobjdump xgraph xmin xmax ymin ymax overlay simobjdump xplot pixflags script fg ysquish do_slope wy simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ link savename file version md5sum mod_save_flag x y z simobjdump kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \ xtree_fg_req xtree_textfg_req x y z simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ xtree_textfg_req x y z simobjdump transport input output alloced step_mode stepsize dt delay clock \ kf xtree_fg_req xtree_textfg_req x y z simobjdump proto x y z simobjdump linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z simobjdump uplink xtree_fg_req xtree_textfg_req x y z simobjdump downlink xtree_fg_req xtree_textfg_req x y z simobjdump mirror notes xtree_fg_req x y z simundump kpool /kinetics/PKC-active 1 0.15 0.09 0.09 54000 54000 90000 0 \ 6e+05 6 "" red black 7 22 0 simundump kenz /kinetics/PKC-active/PKC-act-raf 1 0 0 0 0 6e+05 5e-07 16 4 0 \ 0 "" red yellow "" 8 7 0 simundump kenz /kinetics/PKC-active/PKC-inact-GAP 1 0 0 0 0 1 1e-05 16 4 0 0 \ "" red yellow "" 3 13 0 simundump kenz /kinetics/PKC-active/PKC-act-GEF 1 0 0 0 0 1 1e-05 16 4 0 0 "" \ red yellow "" 7.2909 20.733 0 simundump kpool /kinetics/MAPK* 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" orange \ yellow 12 1 0 simundump kenz /kinetics/MAPK*/MAPK*-feedback 1 0 0 0 0 6e+05 3.25e-06 40 10 \ 0 0 "" red orange "" 4.934 23.653 0 simundump kenz /kinetics/MAPK*/phosph_Sos 1 0 0 0 0 6e+05 3.25e-05 40 10 0 0 \ "" red orange "" 18 40 0 simundump kpool /kinetics/BetaGamma 1 1.6 0.0094 0.0094 5640 5640 9.6e+05 0 \ 6e+05 4 "" yellow black 18 16 0 simundump group /kinetics/MAPK 0 brown black x 0 0 "" defaultfile \ defaultfile.g 0 0 0 14.616 11.191 0 simundump kpool /kinetics/MAPK/craf-1 0 0.2 0.2 0.2 1.2e+05 1.2e+05 1.2e+05 0 \ 6e+05 0 "" pink brown 6.326 8.1168 0 simundump kpool /kinetics/MAPK/craf-1* 0 0.2 0 0 0 0 1.2e+05 0 6e+05 0 "" \ pink brown 9.2401 7.7115 0 simundump kpool /kinetics/MAPK/MAPKK 0 0.18 0.18 0.18 1.08e+05 1.08e+05 \ 1.08e+05 0 6e+05 0 "" pink brown 6.3315 3.9894 0 simundump kpool /kinetics/MAPK/MAPK 0 0.36 0.36 0.36 2.16e+05 2.16e+05 \ 2.16e+05 0 6e+05 0 "" pink brown 6.0656 1.0863 0 simundump kpool /kinetics/MAPK/craf-1** 1 0.2 0 0 0 0 1.2e+05 0 6e+05 0 "" \ hotpink brown 12.464 7.9022 0 simundump kpool /kinetics/MAPK/MAPK-tyr 1 0.36 0 0 0 0 2.16e+05 0 6e+05 0 "" \ orange brown 8.4147 0.82034 0 simundump kpool /kinetics/MAPK/MAPKK* 0 0.18 0 0 0 0 1.08e+05 0 6e+05 0 "" \ pink brown 12.548 4.0256 0 simundump kenz /kinetics/MAPK/MAPKK*/MAPKKtyr 0 0 0 0 0 6e+05 2.7e-05 0.6 \ 0.15 0 0 "" red pink "" 8.8914 3.5531 0 simundump kenz /kinetics/MAPK/MAPKK*/MAPKKthr 1 0 0 0 0 6e+05 2.7e-05 0.6 \ 0.15 0 0 "" red pink "" 12.961 3.0363 0 simundump kpool /kinetics/MAPK/MAPKK-ser 1 0.18 0 0 0 0 1.08e+05 0 6e+05 0 "" \ pink brown 9.2652 4.1657 0 simundump kpool /kinetics/MAPK/Raf-GTP-Ras* 1 0.0104 0 0 0 0 6240 0 6e+05 0 \ "" red brown 4.9054 6.7814 0 simundump kenz /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1 1 0 0 0 0 1 5.5e-06 \ 0.42 0.105 0 0 "" red red "" 7.6179 6.2189 0 simundump kenz /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2 1 0 0 0 0 1 5.5e-06 \ 0.42 0.105 0 0 "" red red "" 10.698 6.0688 0 simundump kpool /kinetics/MKP-1 1 0.008 0.0024 0.0024 1440 1440 4800 0 6e+05 \ 0 "" hotpink black 5.0816 2.4407 0 simundump kenz /kinetics/MKP-1/MKP1-tyr-deph 1 0 0 0 0 6e+05 0.000125 4 1 0 0 \ "" red hotpink "" 6.2781 3.0684 0 simundump kenz /kinetics/MKP-1/MKP1-thr-deph 1 0 0 0 0 6e+05 0.000125 4 1 0 0 \ "" red hotpink "" 10.789 2.9311 0 simundump kreac /kinetics/Ras-act-craf 1 4e-05 0.5 "" white black 3.5614 \ 10.091 0 simundump kpool /kinetics/PPhosphatase2A 1 0.224 0.224 0.224 1.344e+05 \ 1.344e+05 1.344e+05 0 6e+05 0 "" hotpink yellow 9.3898 9.1309 0 simundump kenz /kinetics/PPhosphatase2A/craf-deph 1 0 0 0 0 6e+05 3.3e-06 25 \ 6 0 0 "" red hotpink "" 7.8013 10.215 0 simundump kenz /kinetics/PPhosphatase2A/MAPKK-deph 1 0 0 0 0 6e+05 3.3e-06 25 \ 6 0 0 "" red hotpink "" 13.159 6.0736 0 simundump kenz /kinetics/PPhosphatase2A/MAPKK-deph-ser 1 0 0 0 0 6e+05 \ 3.3e-06 25 6 0 0 "" red hotpink "" 4.8651 5.9208 0 simundump kenz /kinetics/PPhosphatase2A/craf**-deph 1 0 0 0 0 1 3.3e-06 25 6 \ 0 0 "" red hotpink "" 12.446 9.9054 0 simundump group /kinetics/Ras 1 blue black x 0 0 "" defaultfile defaultfile.g \ 0 0 0 14.513 16.351 0 simundump kreac /kinetics/Ras/bg-act-GEF 1 1e-05 1 "" white blue 13.468 \ 14.838 0 simundump kpool /kinetics/Ras/GEF-Gprot-bg 1 0.1 0 0 0 0 60000 0 6e+05 0 "" \ hotpink blue 10.373 17.271 0 simundump kenz /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras 1 0 0 0 0 6e+05 \ 3.3e-07 0.08 0.02 0 0 "" red hotpink "" 10.402 16.523 0 simundump kreac /kinetics/Ras/dephosph-GEF 1 1 0 "" white blue 9.0702 17.881 \ 0 simundump kpool /kinetics/Ras/inact-GEF 1 0.1 0.1 0.1 60000 60000 60000 0 \ 6e+05 0 "" hotpink blue 12 20 0 simundump kpool /kinetics/Ras/GEF* 1 0.1 0 0 0 0 60000 0 6e+05 0 "" hotpink \ blue 6.4483 17.246 0 simundump kenz /kinetics/Ras/GEF*/GEF*-act-ras 1 0 0 0 0 6e+05 3.3e-07 0.08 \ 0.02 0 0 "" red hotpink "" 7.0855 16.086 0 simundump kpool /kinetics/Ras/GTP-Ras 1 0.2 0 0 0 0 1.2e+05 0 6e+05 0 "" \ orange blue 12.564 13.084 0 simundump kpool /kinetics/Ras/GDP-Ras 1 0.2 0.2 0.2 1.2e+05 1.2e+05 1.2e+05 0 \ 6e+05 0 "" pink blue 6.1309 14.165 0 simundump kreac /kinetics/Ras/Ras-intrinsic-GTPase 1 1e-04 0 "" white blue \ 9.0979 13.5 0 simundump kreac /kinetics/Ras/dephosph-GAP 1 0.1 0 "" white blue 4.0234 \ 15.524 0 simundump kpool /kinetics/Ras/GAP* 1 0.05 0 0 0 0 30000 0 6e+05 0 "" red blue \ 1.3498 14.349 0 simundump kpool /kinetics/Ras/GAP 1 0.002 0.002 0.002 1200 1200 1200 0 6e+05 \ 0 "" red blue 6.6549 12.338 0 simundump kenz /kinetics/Ras/GAP/GAP-inact-ras 1 0 0 0 0 6e+05 8.2476e-05 40 \ 10 0 0 "" red red "" 9.0121 12.403 0 simundump kpool /kinetics/Ras/inact-GEF* 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" \ hotpink blue 15 20 0 simundump kreac /kinetics/Ras/CaM-bind-GEF 1 1e-04 1 "" white blue 2.4861 \ 21.679 0 simundump kpool /kinetics/Ras/CaM-GEF 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" \ pink blue 5.3451 19.58 0 simundump kenz /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras 1 0 0 0 0 6e+05 3.3e-07 \ 0.08 0.02 0 0 "" red pink "" 5.0223 18.657 0 simundump kreac /kinetics/Ras/dephosph-inact-GEF* 1 1 0 "" white blue 14.431 \ 21.995 0 simundump kpool /kinetics/PKA-active 1 0.015 0.015 0.015 9000 9000 9000 0 \ 6e+05 4 "" yellow black 18 18 0 simundump kenz /kinetics/PKA-active/PKA-phosph-GEF 1 0 0 0 0 6e+05 1e-05 36 9 \ 0 0 "" red yellow "" 14 18 0 simundump kpool /kinetics/CaM-Ca4 1 5 0 0 0 0 3e+06 0 6e+05 4 "" blue yellow \ 0 19 0 simundump kpool /kinetics/Shc*.Sos.Grb2 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" \ brown yellow 11.263 27.112 0 simundump kenz /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF 1 0 0 0 0 6e+05 3.3e-07 \ 0.08 0.02 0 0 "" red brown "" 11.266 24.47 0 simundump group /kinetics/EGFR 1 yellow black x 0 0 "" defaultfile \ defaultfile.g 0 0 0 7.0249 39.57 0 simundump kpool /kinetics/EGFR/EGFR 1 0.16667 0.16667 0.16667 1e+05 1e+05 \ 1e+05 0 6e+05 0 "" red yellow 1.9551 39.853 0 simundump kreac /kinetics/EGFR/act_EGFR 1 7e-06 0.25 "" white yellow 4.4894 \ 38.493 0 simundump kpool /kinetics/EGFR/L.EGFR 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" red \ yellow 6.2195 36.599 0 simundump kenz /kinetics/EGFR/L.EGFR/phosph_Shc 1 0 0 0 0 6e+05 2e-06 0.8 0.2 \ 0 0 "" red red "" 9.0331 36.49 0 simundump kpool /kinetics/EGFR/EGF 1 1 0 0 0 0 6e+05 0 6e+05 4 "" red yellow \ 2.2719 36.309 0 simundump kpool /kinetics/EGFR/SHC 1 1 0.5 0.5 3e+05 3e+05 6e+05 0 6e+05 0 "" \ orange yellow 8.3857 33.936 0 simundump kpool /kinetics/EGFR/SHC* 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" \ orange yellow 12.832 33.029 0 simundump kreac /kinetics/EGFR/dephosph_Shc 1 0.0016667 0 "" white yellow \ 9.7373 31.442 0 simundump kpool /kinetics/EGFR/Internal_L.EGFR 1 1.6667e-06 0 0 0 0 1 0 6e+05 \ 0 "" red yellow 6.3061 41.93 0 simundump kreac /kinetics/EGFR/Internalize 1 0.002 0.00033 "" white yellow \ 4.5213 39.863 0 simundump group /kinetics/Sos 1 blue black x 0 0 "" defaultfile defaultfile.g \ 0 0 0 19.547 34.811 0 simundump kreac /kinetics/Sos/Shc_bind_Sos.Grb2 1 8.333e-07 0.1 "" white blue \ 10.23 29.891 0 simundump kpool /kinetics/Sos/Sos*.Grb2 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" \ orange blue 12.274 41.661 0 simundump kreac /kinetics/Sos/Grb2_bind_Sos* 1 4.1667e-08 0.0168 "" white \ blue 10.533 38.235 0 simundump kpool /kinetics/Sos/Grb2 1 1 1 1 6e+05 6e+05 6e+05 0 6e+05 0 "" \ orange blue 14.742 35.301 0 simundump kpool /kinetics/Sos/Sos.Grb2 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" \ orange blue 13.988 30.097 0 simundump kpool /kinetics/Sos/Sos* 1 1.6667e-06 0 0 0 0 1 0 6e+05 0 "" red \ blue 15.421 40.215 0 simundump kreac /kinetics/Sos/dephosph_Sos 1 0.001 0 "" white blue 13.185 \ 37.153 0 simundump kreac /kinetics/Sos/Grb2_bind_Sos 1 4.1667e-08 0.0168 "" white blue \ 16.422 33.133 0 simundump kpool /kinetics/Sos/Sos 1 0.1 0.1 0.1 60000 60000 60000 0 6e+05 0 \ "" red blue 17.381 36.794 0 simundump xgraph /graphs/conc1 0 0 2000 0 0.01146 0 simundump xgraph /graphs/conc2 0 360.16 2000 0.015494 0.49511 0 simundump xplot /graphs/conc1/MAPK*.Co 3 524288 \ "delete_plot.w ; edit_plot.D " orange 0 0 1 simundump xgraph /moregraphs/conc3 0 0 2000 -1.1176e-08 1 0 simundump xgraph /moregraphs/conc4 0 0 2000 0 1 0 simundump xcoredraw /edit/draw 0 -4.5315 19.369 -1.5185 44.269 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "1 Sep 2003: Based on nonscaf_syn1c.g, which in turn is just " \ "like nonscaf_syn1b.g" \ "with all plots but MAPK* stripped out." \ "The current version provides the Ca input through a fast" \ "(10 msec) time-course reaction step so that the Ca can undergo" \ "fluctuations." \ "1 Oct 2003: Identical to nonscaf_syn1e.g, added a few plots." \ "9 Dec 2003: Identical to nonscaf_syn1f.g, added a plot for Ca" \ "22 Dec 2003: Based on nonscaf_syn1g.g, eliminated all except the" \ "core MAPK pathway and its inputs. Cleared out plots too." \ "Set basic values for PKC, PKA, CaM-Ca4 and Betagamma." addmsg /kinetics/PKC-active/PKC-act-raf /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active/PKC-inact-GAP /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active/PKC-act-GEF /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-act-raf ENZYME n addmsg /kinetics/MAPK/craf-1 /kinetics/PKC-active/PKC-act-raf SUBSTRATE n addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-inact-GAP ENZYME n addmsg /kinetics/Ras/GAP /kinetics/PKC-active/PKC-inact-GAP SUBSTRATE n addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-act-GEF ENZYME n addmsg /kinetics/Ras/inact-GEF /kinetics/PKC-active/PKC-act-GEF SUBSTRATE n addmsg /kinetics/MAPK*/MAPK*-feedback /kinetics/MAPK* REAC eA B addmsg /kinetics/MAPK/MAPKK*/MAPKKthr /kinetics/MAPK* MM_PRD pA addmsg /kinetics/MKP-1/MKP1-thr-deph /kinetics/MAPK* REAC sA B addmsg /kinetics/MAPK*/phosph_Sos /kinetics/MAPK* REAC eA B addmsg /kinetics/MAPK* /kinetics/MAPK*/MAPK*-feedback ENZYME n addmsg /kinetics/MAPK/craf-1* /kinetics/MAPK*/MAPK*-feedback SUBSTRATE n addmsg /kinetics/MAPK* /kinetics/MAPK*/phosph_Sos ENZYME n addmsg /kinetics/Sos/Sos /kinetics/MAPK*/phosph_Sos SUBSTRATE n addmsg /kinetics/Ras/bg-act-GEF /kinetics/BetaGamma REAC A B addmsg /kinetics/PKC-active/PKC-act-raf /kinetics/MAPK/craf-1 REAC sA B addmsg /kinetics/PPhosphatase2A/craf-deph /kinetics/MAPK/craf-1 MM_PRD pA addmsg /kinetics/PKC-active/PKC-act-raf /kinetics/MAPK/craf-1* MM_PRD pA addmsg /kinetics/MAPK*/MAPK*-feedback /kinetics/MAPK/craf-1* REAC sA B addmsg /kinetics/PPhosphatase2A/craf-deph /kinetics/MAPK/craf-1* REAC sA B addmsg /kinetics/PPhosphatase2A/craf**-deph /kinetics/MAPK/craf-1* MM_PRD pA addmsg /kinetics/Ras-act-craf /kinetics/MAPK/craf-1* REAC A B addmsg /kinetics/PPhosphatase2A/MAPKK-deph-ser /kinetics/MAPK/MAPKK MM_PRD pA addmsg /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1 /kinetics/MAPK/MAPKK REAC sA B addmsg /kinetics/MAPK/MAPKK*/MAPKKtyr /kinetics/MAPK/MAPK REAC sA B addmsg /kinetics/MKP-1/MKP1-tyr-deph /kinetics/MAPK/MAPK MM_PRD pA addmsg /kinetics/MAPK*/MAPK*-feedback /kinetics/MAPK/craf-1** MM_PRD pA addmsg /kinetics/PPhosphatase2A/craf**-deph /kinetics/MAPK/craf-1** REAC sA B addmsg /kinetics/MAPK/MAPKK*/MAPKKtyr /kinetics/MAPK/MAPK-tyr MM_PRD pA addmsg /kinetics/MAPK/MAPKK*/MAPKKthr /kinetics/MAPK/MAPK-tyr REAC sA B addmsg /kinetics/MKP-1/MKP1-tyr-deph /kinetics/MAPK/MAPK-tyr REAC sA B addmsg /kinetics/MKP-1/MKP1-thr-deph /kinetics/MAPK/MAPK-tyr MM_PRD pA addmsg /kinetics/MAPK/MAPKK*/MAPKKtyr /kinetics/MAPK/MAPKK* REAC eA B addmsg /kinetics/MAPK/MAPKK*/MAPKKthr /kinetics/MAPK/MAPKK* REAC eA B addmsg /kinetics/PPhosphatase2A/MAPKK-deph /kinetics/MAPK/MAPKK* REAC sA B addmsg /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2 /kinetics/MAPK/MAPKK* MM_PRD pA addmsg /kinetics/MAPK/MAPKK* /kinetics/MAPK/MAPKK*/MAPKKtyr ENZYME n addmsg /kinetics/MAPK/MAPK /kinetics/MAPK/MAPKK*/MAPKKtyr SUBSTRATE n addmsg /kinetics/MAPK/MAPKK* /kinetics/MAPK/MAPKK*/MAPKKthr ENZYME n addmsg /kinetics/MAPK/MAPK-tyr /kinetics/MAPK/MAPKK*/MAPKKthr SUBSTRATE n addmsg /kinetics/PPhosphatase2A/MAPKK-deph /kinetics/MAPK/MAPKK-ser MM_PRD pA addmsg /kinetics/PPhosphatase2A/MAPKK-deph-ser /kinetics/MAPK/MAPKK-ser REAC sA B addmsg /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1 /kinetics/MAPK/MAPKK-ser MM_PRD pA addmsg /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2 /kinetics/MAPK/MAPKK-ser REAC sA B addmsg /kinetics/Ras-act-craf /kinetics/MAPK/Raf-GTP-Ras* REAC B A addmsg /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1 /kinetics/MAPK/Raf-GTP-Ras* REAC eA B addmsg /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2 /kinetics/MAPK/Raf-GTP-Ras* REAC eA B addmsg /kinetics/MAPK/Raf-GTP-Ras* /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1 ENZYME n addmsg /kinetics/MAPK/MAPKK /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1 SUBSTRATE n addmsg /kinetics/MAPK/Raf-GTP-Ras* /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2 ENZYME n addmsg /kinetics/MAPK/MAPKK-ser /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2 SUBSTRATE n addmsg /kinetics/MKP-1/MKP1-tyr-deph /kinetics/MKP-1 REAC eA B addmsg /kinetics/MKP-1/MKP1-thr-deph /kinetics/MKP-1 REAC eA B addmsg /kinetics/MKP-1 /kinetics/MKP-1/MKP1-tyr-deph ENZYME n addmsg /kinetics/MAPK/MAPK-tyr /kinetics/MKP-1/MKP1-tyr-deph SUBSTRATE n addmsg /kinetics/MKP-1 /kinetics/MKP-1/MKP1-thr-deph ENZYME n addmsg /kinetics/MAPK* /kinetics/MKP-1/MKP1-thr-deph SUBSTRATE n addmsg /kinetics/MAPK/Raf-GTP-Ras* /kinetics/Ras-act-craf PRODUCT n addmsg /kinetics/MAPK/craf-1* /kinetics/Ras-act-craf SUBSTRATE n addmsg /kinetics/Ras/GTP-Ras /kinetics/Ras-act-craf SUBSTRATE n addmsg /kinetics/PPhosphatase2A/craf-deph /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A/MAPKK-deph /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A/MAPKK-deph-ser /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A/craf**-deph /kinetics/PPhosphatase2A REAC eA B addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/craf-deph ENZYME n addmsg /kinetics/MAPK/craf-1* /kinetics/PPhosphatase2A/craf-deph SUBSTRATE n addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/MAPKK-deph ENZYME n addmsg /kinetics/MAPK/MAPKK* /kinetics/PPhosphatase2A/MAPKK-deph SUBSTRATE n addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/MAPKK-deph-ser ENZYME n addmsg /kinetics/MAPK/MAPKK-ser /kinetics/PPhosphatase2A/MAPKK-deph-ser SUBSTRATE n addmsg /kinetics/PPhosphatase2A /kinetics/PPhosphatase2A/craf**-deph ENZYME n addmsg /kinetics/MAPK/craf-1** /kinetics/PPhosphatase2A/craf**-deph SUBSTRATE n addmsg /kinetics/BetaGamma /kinetics/Ras/bg-act-GEF SUBSTRATE n addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/bg-act-GEF SUBSTRATE n addmsg /kinetics/Ras/GEF-Gprot-bg /kinetics/Ras/bg-act-GEF PRODUCT n addmsg /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras /kinetics/Ras/GEF-Gprot-bg REAC eA B addmsg /kinetics/Ras/bg-act-GEF /kinetics/Ras/GEF-Gprot-bg REAC B A addmsg /kinetics/Ras/GEF-Gprot-bg /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras SUBSTRATE n addmsg /kinetics/Ras/GEF* /kinetics/Ras/dephosph-GEF SUBSTRATE n addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/dephosph-GEF PRODUCT n addmsg /kinetics/Ras/bg-act-GEF /kinetics/Ras/inact-GEF REAC A B addmsg /kinetics/PKC-active/PKC-act-GEF /kinetics/Ras/inact-GEF REAC sA B addmsg /kinetics/Ras/dephosph-GEF /kinetics/Ras/inact-GEF REAC B A addmsg /kinetics/PKA-active/PKA-phosph-GEF /kinetics/Ras/inact-GEF REAC sA B addmsg /kinetics/Ras/CaM-bind-GEF /kinetics/Ras/inact-GEF REAC A B addmsg /kinetics/Ras/dephosph-inact-GEF* /kinetics/Ras/inact-GEF REAC B A addmsg /kinetics/PKC-active/PKC-act-GEF /kinetics/Ras/GEF* MM_PRD pA addmsg /kinetics/Ras/dephosph-GEF /kinetics/Ras/GEF* REAC A B addmsg /kinetics/Ras/GEF*/GEF*-act-ras /kinetics/Ras/GEF* REAC eA B addmsg /kinetics/Ras/GEF* /kinetics/Ras/GEF*/GEF*-act-ras ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/GEF*/GEF*-act-ras SUBSTRATE n addmsg /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras/GAP/GAP-inact-ras /kinetics/Ras/GTP-Ras REAC sA B addmsg /kinetics/Ras/Ras-intrinsic-GTPase /kinetics/Ras/GTP-Ras REAC A B addmsg /kinetics/Ras/GEF*/GEF*-act-ras /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras-act-craf /kinetics/Ras/GTP-Ras REAC A B addmsg /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF /kinetics/Ras/GTP-Ras MM_PRD pA addmsg /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Ras/GAP/GAP-inact-ras /kinetics/Ras/GDP-Ras MM_PRD pA addmsg /kinetics/Ras/Ras-intrinsic-GTPase /kinetics/Ras/GDP-Ras REAC B A addmsg /kinetics/Ras/GEF*/GEF*-act-ras /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF /kinetics/Ras/GDP-Ras REAC sA B addmsg /kinetics/Ras/GTP-Ras /kinetics/Ras/Ras-intrinsic-GTPase SUBSTRATE n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/Ras-intrinsic-GTPase PRODUCT n addmsg /kinetics/Ras/GAP* /kinetics/Ras/dephosph-GAP SUBSTRATE n addmsg /kinetics/Ras/GAP /kinetics/Ras/dephosph-GAP PRODUCT n addmsg /kinetics/PKC-active/PKC-inact-GAP /kinetics/Ras/GAP* MM_PRD pA addmsg /kinetics/Ras/dephosph-GAP /kinetics/Ras/GAP* REAC A B addmsg /kinetics/Ras/GAP/GAP-inact-ras /kinetics/Ras/GAP REAC eA B addmsg /kinetics/PKC-active/PKC-inact-GAP /kinetics/Ras/GAP REAC sA B addmsg /kinetics/Ras/dephosph-GAP /kinetics/Ras/GAP REAC B A addmsg /kinetics/Ras/GAP /kinetics/Ras/GAP/GAP-inact-ras ENZYME n addmsg /kinetics/Ras/GTP-Ras /kinetics/Ras/GAP/GAP-inact-ras SUBSTRATE n addmsg /kinetics/PKA-active/PKA-phosph-GEF /kinetics/Ras/inact-GEF* MM_PRD pA addmsg /kinetics/Ras/dephosph-inact-GEF* /kinetics/Ras/inact-GEF* REAC A B addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/CaM-bind-GEF SUBSTRATE n addmsg /kinetics/Ras/CaM-GEF /kinetics/Ras/CaM-bind-GEF PRODUCT n addmsg /kinetics/CaM-Ca4 /kinetics/Ras/CaM-bind-GEF SUBSTRATE n addmsg /kinetics/Ras/CaM-bind-GEF /kinetics/Ras/CaM-GEF REAC B A addmsg /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras /kinetics/Ras/CaM-GEF REAC eA B addmsg /kinetics/Ras/CaM-GEF /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras SUBSTRATE n addmsg /kinetics/Ras/inact-GEF* /kinetics/Ras/dephosph-inact-GEF* SUBSTRATE n addmsg /kinetics/Ras/inact-GEF /kinetics/Ras/dephosph-inact-GEF* PRODUCT n addmsg /kinetics/PKA-active/PKA-phosph-GEF /kinetics/PKA-active REAC eA B addmsg /kinetics/PKA-active /kinetics/PKA-active/PKA-phosph-GEF ENZYME n addmsg /kinetics/Ras/inact-GEF /kinetics/PKA-active/PKA-phosph-GEF SUBSTRATE n addmsg /kinetics/Ras/CaM-bind-GEF /kinetics/CaM-Ca4 REAC A B addmsg /kinetics/Sos/Shc_bind_Sos.Grb2 /kinetics/Shc*.Sos.Grb2 REAC B A addmsg /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF /kinetics/Shc*.Sos.Grb2 REAC eA B addmsg /kinetics/Shc*.Sos.Grb2 /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF ENZYME n addmsg /kinetics/Ras/GDP-Ras /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF SUBSTRATE n addmsg /kinetics/EGFR/act_EGFR /kinetics/EGFR/EGFR REAC A B addmsg /kinetics/EGFR/EGFR /kinetics/EGFR/act_EGFR SUBSTRATE n addmsg /kinetics/EGFR/EGF /kinetics/EGFR/act_EGFR SUBSTRATE n addmsg /kinetics/EGFR/L.EGFR /kinetics/EGFR/act_EGFR PRODUCT n addmsg /kinetics/EGFR/act_EGFR /kinetics/EGFR/L.EGFR REAC B A addmsg /kinetics/EGFR/L.EGFR/phosph_Shc /kinetics/EGFR/L.EGFR REAC eA B addmsg /kinetics/EGFR/Internalize /kinetics/EGFR/L.EGFR REAC A B addmsg /kinetics/EGFR/L.EGFR /kinetics/EGFR/L.EGFR/phosph_Shc ENZYME n addmsg /kinetics/EGFR/SHC /kinetics/EGFR/L.EGFR/phosph_Shc SUBSTRATE n addmsg /kinetics/EGFR/act_EGFR /kinetics/EGFR/EGF REAC A B addmsg /kinetics/EGFR/dephosph_Shc /kinetics/EGFR/SHC REAC B A addmsg /kinetics/EGFR/L.EGFR/phosph_Shc /kinetics/EGFR/SHC REAC sA B addmsg /kinetics/EGFR/dephosph_Shc /kinetics/EGFR/SHC* REAC A B addmsg /kinetics/Sos/Shc_bind_Sos.Grb2 /kinetics/EGFR/SHC* REAC A B addmsg /kinetics/EGFR/L.EGFR/phosph_Shc /kinetics/EGFR/SHC* MM_PRD pA addmsg /kinetics/EGFR/SHC* /kinetics/EGFR/dephosph_Shc SUBSTRATE n addmsg /kinetics/EGFR/SHC /kinetics/EGFR/dephosph_Shc PRODUCT n addmsg /kinetics/EGFR/Internalize /kinetics/EGFR/Internal_L.EGFR REAC B A addmsg /kinetics/EGFR/L.EGFR /kinetics/EGFR/Internalize SUBSTRATE n addmsg /kinetics/EGFR/Internal_L.EGFR /kinetics/EGFR/Internalize PRODUCT n addmsg /kinetics/Sos/Sos.Grb2 /kinetics/Sos/Shc_bind_Sos.Grb2 SUBSTRATE n addmsg /kinetics/EGFR/SHC* /kinetics/Sos/Shc_bind_Sos.Grb2 SUBSTRATE n addmsg /kinetics/Shc*.Sos.Grb2 /kinetics/Sos/Shc_bind_Sos.Grb2 PRODUCT n addmsg /kinetics/Sos/Grb2_bind_Sos* /kinetics/Sos/Sos*.Grb2 REAC B A addmsg /kinetics/Sos/Sos* /kinetics/Sos/Grb2_bind_Sos* SUBSTRATE n addmsg /kinetics/Sos/Grb2 /kinetics/Sos/Grb2_bind_Sos* SUBSTRATE n addmsg /kinetics/Sos/Sos*.Grb2 /kinetics/Sos/Grb2_bind_Sos* PRODUCT n addmsg /kinetics/Sos/Grb2_bind_Sos /kinetics/Sos/Grb2 REAC A B addmsg /kinetics/Sos/Grb2_bind_Sos* /kinetics/Sos/Grb2 REAC A B addmsg /kinetics/Sos/Grb2_bind_Sos /kinetics/Sos/Sos.Grb2 REAC B A addmsg /kinetics/Sos/Shc_bind_Sos.Grb2 /kinetics/Sos/Sos.Grb2 REAC A B addmsg /kinetics/MAPK*/phosph_Sos /kinetics/Sos/Sos* MM_PRD pA addmsg /kinetics/Sos/Grb2_bind_Sos* /kinetics/Sos/Sos* REAC A B addmsg /kinetics/Sos/dephosph_Sos /kinetics/Sos/Sos* REAC A B addmsg /kinetics/Sos/Sos* /kinetics/Sos/dephosph_Sos SUBSTRATE n addmsg /kinetics/Sos/Sos /kinetics/Sos/dephosph_Sos PRODUCT n addmsg /kinetics/Sos/Grb2 /kinetics/Sos/Grb2_bind_Sos SUBSTRATE n addmsg /kinetics/Sos/Sos.Grb2 /kinetics/Sos/Grb2_bind_Sos PRODUCT n addmsg /kinetics/Sos/Sos /kinetics/Sos/Grb2_bind_Sos SUBSTRATE n addmsg /kinetics/Sos/Grb2_bind_Sos /kinetics/Sos/Sos REAC A B addmsg /kinetics/MAPK*/phosph_Sos /kinetics/Sos/Sos REAC sA B addmsg /kinetics/Sos/dephosph_Sos /kinetics/Sos/Sos REAC B A addmsg /kinetics/MAPK* /graphs/conc1/MAPK*.Co PLOT Co *MAPK*.Co *orange enddump // End of dump call /kinetics/PKC-active/PKC-act-raf/notes LOAD \ "Rate consts from Chen et al Biochem 32, 1032 (1993)" \ "k3 = k2 = 4" \ "k1 = 9e-5" \ "recalculated gives 1.666e-5, which is not very different." \ "Looks like k3 is rate-limiting in this case: there is a huge amount" \ "of craf locked up in the enz complex. Let us assume a 10x" \ "higher Km, ie, lower affinity. k1 drops by 10x." \ "Also changed k2 to 4x k3." \ "Lowerd k1 to 1e-6 to balance 10X DAG sensitivity of PKC" call /kinetics/PKC-active/PKC-inact-GAP/notes LOAD \ "Rate consts copied from PCK-act-raf" \ "This reaction inactivates GAP. The idea is from the " \ "Boguski and McCormick review." call /kinetics/PKC-active/PKC-act-GEF/notes LOAD \ "Rate consts from PKC-act-raf." \ "This reaction activates GEF. It can lead to at least 2X stim of ras, and" \ "a 2X stim of MAPK over and above that obtained via direct phosph of" \ "c-raf. Note that it is a push-pull reaction, and there is also a contribution" \ "through the phosphorylation and inactivation of GAPs." \ "The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X" call /kinetics/MAPK*/MAPK*-feedback/notes LOAD \ "Ueki et al JBC 269(22):15756-15761 show the presence of" \ "this step, but not the rate consts, which are derived from" \ "Sanghera et al JBC 265(1):52-57, 1990, see the deriv in the" \ "MAPK* notes." call /kinetics/MAPK*/phosph_Sos/notes LOAD \ "See Porfiri and McCormick JBC 271:10 pp5871 1996 for the" \ "existence of this step. We'll take the rates from the ones" \ "used for the phosph of Raf by MAPK." \ "Sep 17 1997: The transient activation curve matches better" \ "with k1 up by 10 x." call /kinetics/BetaGamma/notes LOAD \ "These exist in a nebulous sense in this model, basically only to balance" \ "the conservation equations. The details of their reassociation with G-GDP" \ "are not modeled" \ "Resting level =0.0094, stim level =.0236 from all42.g ish." call /kinetics/MAPK/craf-1/notes LOAD \ "Couldn't find any ref to the actual conc of craf-1 but I" \ "should try Strom et al Oncogene 5 pp 345" \ "In line with the other kinases in the cascade, I estimate the conc to be" \ "0.2 uM. To init we use 0.15, which is close to equil" call /kinetics/MAPK/MAPKK/notes LOAD \ "Conc is from Seger et al JBC 267:20 pp14373 (1992)" \ "mwt is 45/46 Kd" \ "We assume that phosphorylation on both ser and thr is needed for" \ "activiation. See Kyriakis et al Nature 358 417 1992" \ "Init conc of total is 0.18" \ "" call /kinetics/MAPK/MAPK/notes LOAD \ "conc is from Sanghera et al JBC 265 pp 52 (1990)" \ "A second calculation gives 3.1 uM, from same paper." \ "They est MAPK is 1e-4x total protein, and protein is 15% of cell wt," \ "so MAPK is 1.5e-5g/ml = 0.36uM. which is closer to our first estimate." \ "Lets use this." call /kinetics/MAPK/craf-1**/notes LOAD \ "Negative feedback by MAPK* by hyperphosphorylating craf-1* gives" \ "rise to this pool." \ "Ueki et al JBC 269(22):15756-15761, 1994" \ "" call /kinetics/MAPK/MAPK-tyr/notes LOAD \ "Haystead et al FEBS Lett. 306(1) pp 17-22 show that phosphorylation" \ "is strictly sequential, first tyr185 then thr183." call /kinetics/MAPK/MAPKK*/notes LOAD \ "MAPKK phosphorylates MAPK on both the tyr and thr residues, first" \ "tyr then thr. Refs: Seger et al JBC267:20 pp 14373 1992" \ "The MAPKK itself is phosphorylated on ser as well as thr residues." \ "Let us assume that the ser goes first, and that the sequential phosphorylation" \ "is needed. See Kyriakis et al Nature 358 417-421 1992" call /kinetics/MAPK/MAPKK*/MAPKKtyr/notes LOAD \ "The actual MAPKK is 2 forms from Seger et al JBC 267:20 14373(1992)" \ "Vmax = 150nmol/min/mg" \ "From Haystead et al FEBS 306(1):17-22 we get Km=46.6nM for at least one" \ "of the phosphs." \ "Putting these together:" \ "k3=0.15/sec, scale to get k2=0.6." \ "k1=0.75/46.6nM=2.7e-5" call /kinetics/MAPK/MAPKK*/MAPKKthr/notes LOAD \ "Rate consts same as for MAPKKtyr." call /kinetics/MAPK/MAPKK-ser/notes LOAD \ "Intermediately phophorylated, assumed inactive, form of MAPKK" call /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1/notes LOAD \ "Kinetics are the same as for the craf-1* activity, ie.," \ "k1=1.1e-6, k2=.42, k3 =0.105" \ "These are based on Force et al PNAS USA 91 1270-1274 1994." \ "These parms cannot reach the observed 4X stim of MAPK. So lets" \ "increase the affinity, ie, raise k1 10X to 1.1e-5" \ "Lets take it back down to where it was." \ "Back up to 5X: 5.5e-6" call /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2/notes LOAD \ "Same kinetics as other c-raf activated forms. See " \ "Force et al PNAS 91 1270-1274 1994." \ "k1 = 1.1e-6, k2 = .42, k3 = 1.05" \ "raise k1 to 5.5e-6" \ "" call /kinetics/MKP-1/notes LOAD \ "MKP-1 dephosphoryates and inactivates MAPK in vivo: Sun et al Cell 75 " \ "487-493 1993. Levels of MKP-1" \ "are regulated, and rise in 1 hour. " \ "Kinetics from Charles et al PNAS 90:5292-5296 1993. They refer" \ "to Charles et al Oncogene 7 187-190 who show that half-life of MKP1/3CH134" \ "is 40 min. 80% deph of MAPK in 20 min" \ "Sep 17 1997: CoInit now 0.4x to 0.0032. See parm searches" \ "from jun96 on." call /kinetics/MKP-1/MKP1-tyr-deph/notes LOAD \ "The original kinetics have been modified to obey the k2 = 4 * k3 rule," \ "while keeping kcat and Km fixed. As noted in the NOTES, the only constraining" \ "data point is the time course of MAPK dephosphorylation, which this" \ "model satisfies. It would be nice to have more accurate estimates of" \ "rate consts and MKP-1 levels from the literature. " \ "Effective Km : 67 nM" \ "kcat = 1.43 umol/min/mg" call /kinetics/MKP-1/MKP1-thr-deph/notes LOAD \ "See MKP1-tyr-deph" call /kinetics/Ras-act-craf/notes LOAD \ "Assume the binding is fast and limited only by the amount of " \ "Ras* available. So kf=kb/[craf-1]" \ "If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 * 6e5) = 8.3e-6" \ "Later: Raise it by 10 X to 4e-5" \ "From Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is" \ "complexed with Ras. So we raise kb 4x to 4" \ "This step needed to memb-anchor and activate Raf: Leevers et al Nature" \ "369 411-414" \ "(I don't...." call /kinetics/PPhosphatase2A/notes LOAD \ "Refs: Pato et al Biochem J 293:35-41(93);" \ "Takai&Mieskes Biochem J 275:233-239" \ "k1=1.46e-4, k2=1000,k3=250. these use" \ "kcat values for calponin. Also, units of kcat may be in min!" \ "revert to Vmax base:" \ "k3=6, k2=25,k1=3.3e-6 or 6,6,1e-6" \ "CoInit assumed 0.1 uM." \ "See NOTES for MAPK_Ras50.g. CoInit now 0.08" \ "Sep 17 1997: Raise CoInt 1.4x to 0.224, see parm" \ "searches from jun 96 on." \ "" call /kinetics/PPhosphatase2A/craf-deph/notes LOAD \ "See parent PPhosphatase2A for parms" \ "" call /kinetics/PPhosphatase2A/MAPKK-deph/notes LOAD \ "See: Kyriakis et al Nature 358 pp 417-421 1992" \ "Ahn et al Curr Op Cell Biol 4:992-999 1992 for this pathway." \ "See parent PPhosphatase2A for parms." call /kinetics/PPhosphatase2A/craf**-deph/notes LOAD \ "Ueki et al JBC 269(22) pp 15756-15761 1994 show hyperphosphorylation of" \ "craf, so this is there to dephosphorylate it. Identity of phosphatase is not" \ "known to me, but it may be PP2A like the rest, so I have made it so." call /kinetics/Ras/notes LOAD \ "Ras has now gotten to be a big enough component of the model to" \ "deserve its own group. The main refs are" \ "Boguski and McCormick Nature 366 643-654 '93 Major review" \ "Eccleston et al JBC 268:36 pp 27012-19" \ "Orita et al JBC 268:34 2554246" call /kinetics/Ras/bg-act-GEF/notes LOAD \ "SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4." \ "Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4." \ "so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should" \ "be reasonably fast, say 1/sec" \ "" call /kinetics/Ras/GEF-Gprot-bg/notes LOAD \ "Guanine nucleotide exchange factor. This activates raf by exchanging bound" \ "GDP with GTP. I have left the GDP/GTP out of this reaction, it would be" \ "trivial to put them in. See Boguski & McCormick." \ "Possible candidate molecules: RasGRF, smgGDS, Vav (in dispute). " \ "rasGRF: Kcat= 1.2/min Km = 680 nM" \ "smgGDS: Kcat: 0.37 /min, Km = 220 nM." \ "vav: Turnover up over baseline by 10X, " \ "" call /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras/notes LOAD \ "Kinetics based on the activation of Gq by the receptor complex in the" \ "Gq model (in turn based on the Mahama and Linderman model)" \ "k1 = 2e-5, k2 = 1e-10, k3 = 10 (I do not know why they even bother with k2)." \ "Lets put k1 at 2e-6 to get a reasonable equilibrium" \ "More specific values from, eg.g: Orita et al JBC 268(34) 25542-25546" \ "from rasGRF and smgGDS: k1=3.3e-7; k2 = 0.08, k3 = 0.02" \ "" call /kinetics/Ras/inact-GEF/notes LOAD \ "Assume that SoS is present only at 50 nM." \ "Revised to 100 nM to get equil to experimentally known levels." call /kinetics/Ras/GEF*/notes LOAD \ "phosphorylated and thereby activated form of GEF. See, e.g." \ "Orita et al JBC 268:34 25542-25546 1993, Gulbins et al." \ "It is not clear whether there is major specificity for tyr or ser/thr." call /kinetics/Ras/GEF*/GEF*-act-ras/notes LOAD \ "Kinetics same as GEF-bg-act-ras" \ "" call /kinetics/Ras/GTP-Ras/notes LOAD \ "Only a very small fraction (7% unstim, 15% stim) of ras is GTP-bound." \ "Gibbs et al JBC 265(33) 20437" \ "" call /kinetics/Ras/GDP-Ras/notes LOAD \ "GDP bound form. See Rosen et al Neuron 12 1207-1221 June 1994." \ "the activation loop is based on Boguski and McCormick Nature 366 643-654 93" \ "Assume Ras is present at about the same level as craf-1, 0.2 uM." \ "Hallberg et al JBC 269:6 3913-3916 1994 estimate upto 5-10% of cellular" \ "Raf is assoc with Ras. Given that only 5-10% of Ras is GTP-bound, we" \ "need similar amounts of Ras as Raf." call /kinetics/Ras/Ras-intrinsic-GTPase/notes LOAD \ "This is extremely slow (1e-4), but it is significant as so little GAP actually" \ "gets complexed with it that the total GTP turnover rises only by" \ "2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and " \ "Eccleston et al JBC 268(36) 27012-27019" \ "kf = 1e-4" \ "" call /kinetics/Ras/dephosph-GAP/notes LOAD \ "Assume a reasonably good rate for dephosphorylating it, 1/sec" call /kinetics/Ras/GAP/notes LOAD \ "GTPase-activating proteins. See Boguski and McCormick." \ "Turn off Ras by helping to hydrolyze bound GTP. " \ "This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids," \ "and expressed in neural cells. p120-GAP is also a possible candidate, but" \ "is less regulated. Both may exist at similar levels." \ "See Eccleston et al JBC 268(36) pp27012-19" \ "Level=.002" call /kinetics/Ras/GAP/GAP-inact-ras/notes LOAD \ "From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec" \ "From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min" \ "I will go with the Eccleston figures as there are good error bars (10%). In general" \ "the values are reasonably close." \ "k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting)" \ "5 Nov 2002: Changed ratio term to 4 from 100. Now we have" \ "k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting." call /kinetics/Ras/inact-GEF*/notes LOAD \ "Phosphorylation-inactivated form of GEF. See" \ "Hordijk et al JBC 269:5 3534-3538 1994" \ "and " \ "Buregering et al EMBO J 12:11 4211-4220 1993" \ "" call /kinetics/Ras/CaM-bind-GEF/notes LOAD \ "We have no numbers for this. It is probably between" \ "the two extremes represented by the CaMKII phosph states," \ "and I have used guesses based on this." \ "kf=1e-4" \ "kb=1" \ "The reaction is based on Farnsworth et al Nature 376 524-527" \ "1995" call /kinetics/Ras/CaM-GEF/notes LOAD \ "See Farnsworth et al Nature 376 524-527 1995" call /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras/notes LOAD \ "Kinetics same as GEF-bg_act-ras" \ "" call /kinetics/PKA-active/PKA-phosph-GEF/notes LOAD \ "This pathway inhibits Ras when cAMP is elevated. See:" \ "Hordijk et al JBC 269:5 3534-3538 1994" \ "Burgering et al EMBO J 12:11 4211-4220 1993" \ "The rates are the same as used in PKA-phosph-I1" call /kinetics/CaM-Ca4/notes LOAD \ "Resting level is ~1e-5 uM, small enough to ignore." call /kinetics/EGFR/EGFR/notes LOAD \ "Berkers et al JBC 266 say 22K hi aff recs." \ "Sherrill and Kyte Biochemistry 35 use range 4-200 nM." \ "These match, lets use them." call /kinetics/EGFR/act_EGFR/notes LOAD \ "Affinity of EGFR for EGF is complex: depends on [EGFR]." \ "We'll assume fixed [EGFR] and use exptal" \ "affinity ~20 nM (see Sherrill and Kyte" \ "Biochem 1996 35 5705-5718, Berkers et al JBC 266:2 922-927" \ "1991, Sorokin et al JBC 269:13 9752-9759 1994). " \ "Tau =~2 min (Davis et al JBC 263:11 5373-5379 1988)" \ "or Berkers Kass = 6.2e5/M/sec, Kdiss=3.5e-4/sec." \ "Sherrill and Kyte have Hill Coeff=1.7" \ "" call /kinetics/EGFR/L.EGFR/notes LOAD \ "This is terribly simplified: there are many interesting" \ "intermediate stages, including dimerization and assoc" \ "with adapter molecules like Shc, that contribute to the" \ "activation of the EGFR." call /kinetics/EGFR/L.EGFR/phosph_Shc/notes LOAD \ "Rates from Okada et al JBC 270:35 pp 20737 1995" \ "Km = 0.70 to 0.85 uM, Vmax = 4.4 to 5.0 pmol/min. Unfortunately" \ "the amount of enzyme is not known, the prep is only" \ "partially purified." \ "Time course of phosph is max within 30 sec, falls back within" \ "20 min. Ref: Sasaoka et al JBC 269:51 32621 1994." \ "Use k3 = 0.1 based on this tau." \ "" call /kinetics/EGFR/SHC/notes LOAD \ "There are 2 isoforms: 52 KDa and 46 KDa (See Okada et al" \ "JBC 270:35 pp 20737 1995). They are acted up on by the EGFR" \ "in very similar ways, and apparently both bind Grb2 similarly," \ "so we'll bundle them together here." \ "Sasaoka et al JBC 269:51 pp 32621 1994 show immunoprecs where" \ "it looks like there is at least as much Shc as Grb2. So" \ "we'll tentatively say there is 1 uM of Shc." call /kinetics/EGFR/dephosph_Shc/notes LOAD \ "Time course of decline of phosph is 20 min. Part of this is" \ "the turnoff time of the EGFR itself. Lets assume a tau of" \ "10 min for this dephosph. It may be wildly off." call /kinetics/EGFR/Internalize/notes LOAD \ "See Helin and Beguinot JBC 266:13 1991 pg 8363-8368." \ "In Fig 3 they have internalization tau about 10 min, " \ "equil at about 20% EGF available. So kf = 4x kb, and" \ "1/(kf + kb) = 600 sec so kb = 1/3K = 3.3e-4," \ "and kf = 1.33e-3. This doesn't take into account the" \ "unbound receptor, so we need to push the kf up a bit, to" \ "0.002" call /kinetics/Sos/Shc_bind_Sos.Grb2/notes LOAD \ "Sasaoka et al JBC 269:51 pp 32621 1994, table on pg" \ "32623 indicates that this pathway accounts for about " \ "50% of the GEF activation. (88% - 39%). Error is large," \ "about 20%. Fig 1 is most useful in constraining rates." \ "" \ "Chook et al JBC 271:48 pp 30472, 1996 say that the Kd is" \ "0.2 uM for Shc binding to EGFR. The Kd for Grb direct binding" \ "is 0.7, so we'll ignore it." call /kinetics/Sos/Grb2_bind_Sos*/notes LOAD \ "Same rates as Grb2_bind_Sos: Porfiri and McCormick JBC" \ "271:10 pp 5871 1996 show that the binding is not affected" \ "by the phosph." call /kinetics/Sos/Grb2/notes LOAD \ "There is probably a lot of it in the cell: it is also known" \ "as Ash (abundant src homology protein I think). Also " \ "Waters et al JBC 271:30 18224 1996 say that only a small" \ "fraction of cellular Grb is precipitated out when SoS is" \ "precipitated. As most of the Sos seems to be associated" \ "with Grb2, it would seem like there is a lot of the latter." \ "Say 1 uM. I haven't been able to find a decent...." call /kinetics/Sos/dephosph_Sos/notes LOAD \ "The only clue I have to these rates is from the time" \ "courses of the EGF activation, which is around 1 to 5 min." \ "The dephosph would be expected to be of the same order," \ "perhaps a bit longer. Lets use 0.002 which is about 8 min." \ "Sep 17: The transient activation curve matches better with" \ "kf = 0.001" call /kinetics/Sos/Grb2_bind_Sos/notes LOAD \ "As there are 2 SH3 domains, this reaction could be 2nd order." \ "I have a Kd of 22 uM from peptide binding (Lemmon et al " \ "JBC 269:50 pg 31653). However, Chook et al JBC 271:48 pg30472" \ "say it is 0.4uM with purified proteins, so we believe them." \ "They say it is 1:1 binding." call /kinetics/Sos/Sos/notes LOAD \ "I have tried using low (0.02 uM) initial concs, but these" \ "give a very flat response to EGF stim although the overall" \ "activation of Ras is not too bad. I am reverting to 0.1 " \ "because we expect a sharp initial response, followed by" \ "a decline." \ "Sep 17 1997: The transient activation curve looks better with" \ "[Sos] = 0.05." \ "Apr 26 1998: Some error there, it is better where it was" \ "at 0.1" complete_loading