//genesis // kkit Version 9 flat dumpfile // Original file saved on Thu May 15 12:32:42 2003 // Corrections made for units, file saved on Thu Sep 23 15:13:42 2004 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.001 CONTROLDT = 5 PLOTDT = 1 MAXTIME = 120 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 0 DEFAULT_VOL = 1.6667e-21 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/RP 0 0 0 0 0 0 0 0 0.001 0 "" grey black 3 -24 0 simundump kpool /kinetics/R2 0 0 0 0 0 0 0 0 0.001 0 "" grey black 3 -18 0 simundump kpool /kinetics/enz4 0 0.001 0.001 0.001 1e-06 1e-06 1e-06 0 0.001 \ 0 "" blue black 0 -21 0 simundump kenz /kinetics/enz4/r4 0 0 0 0 0 0.001 4.5e+07 1800 450 0 1 "" red \ blue "" 1 -21 0 simundump kreac /kinetics/r3 0 1 0.01 "" white black 5 -21 0 simundump kreac /kinetics/r2 0 10000 0.1 "" white black 0 -18 0 simundump kpool /kinetics/Ra 0 0 0 0 0 0 0 0 0.001 0 "" grey black -3 -18 0 simundump kpool /kinetics/R 0 0.4 0.1 0.1 1e-04 1e-04 0.0004 0 0.001 0 "" \ grey black -4 -15 0 simundump kpool /kinetics/EGF 0 0.666 0.666 0.666 0.000666 0.000666 0.000666 \ 0 0.001 0 "" white black -8 -15 0 simundump kreac /kinetics/r1 0 3000 0.06 "" white black -6 -18 0 simundump kpool /kinetics/R-PL 0 0 0 0 0 0 0 0 0.001 0 "" blue black 11 -20 0 simundump kpool /kinetics/R-PLP 0 0 0 0 0 0 0 0 0.001 0 "" blue black 14 -25 \ 0 simundump kpool /kinetics/PLCrP 0 0 0 0 0 0 0 0 0.001 0 "" blue black 11 -31 \ 0 simundump kpool /kinetics/PLCr 0 0.105 0.105 0.105 0.000105 0.000105 0.000105 \ 0 0.001 0 "" blue black 8 -25 0 simundump kreac /kinetics/r5 0 60000 0.2 "" white black 8 -22 0 simundump kreac /kinetics/r6 0 1 0.05 "" white black 14 -22 0 simundump kreac /kinetics/r7 0 0.3 6000 "" white black 14 -28 0 simundump kreac /kinetics/r25 0 1 0.03 "" white black 14 -33 0 simundump kpool /kinetics/PLCr-I 0 0 0 0 0 0 0 0 0.001 0 "" blue black 14 -37 \ 0 simundump kreac /kinetics/r13 0 90000 0.6 "" white black -7 -22 0 simundump kpool /kinetics/Shc 0 0.15 0.15 0.15 0.00015 0.00015 0.00015 0 \ 0.001 0 "" blue black -2 -24 0 simundump kpool /kinetics/R-Sh 0 0 0 0 0 0 0 0 0.001 0 "" blue black -11 -24 \ 0 simundump kreac /kinetics/r14 0 6 0.06 "" white black -11 -27 0 simundump kpool /kinetics/R-ShP 0 0 0 0 0 0 0 0 0.001 0 "" blue black -11 -30 \ 0 simundump kreac /kinetics/r15 0 0.3 900 "" white black -7 -30 0 simundump kpool /kinetics/ShP 0 0 0 0 0 0 0 0 0.001 0 "" blue black -2 -30 0 simundump kreac /kinetics/r17 0 3000 0.1 "" white black -11 -35 0 simundump kpool /kinetics/R-Sh-G 0 0 0 0 0 0 0 0 0.001 0 "" blue black -11 \ -39 0 simundump kreac /kinetics/r19 0 10000 0.0214 "" white black -11 -43 0 simundump kpool /kinetics/R-Sh-G-S 0 0 0 0 0 0 0 0 0.001 0 "" blue black -11 \ -47 0 simundump kreac /kinetics/r24 0 9000 0.0429 "" white black -15 -39 0 simundump kreac /kinetics/r18 0 0.3 900 "" white black -7 -39 0 simundump kreac /kinetics/r20 0 0.12 240 "" white black -7 -47 0 simundump kpool /kinetics/Sh-G-S 0 0 0 0 0 0 0 0 0.001 0 "" 52 black -2 -47 0 simundump kreac /kinetics/r22 0 30000 0.064 "" white black -2 -43 0 simundump kpool /kinetics/Sh-G 0 0 0 0 0 0 0 0 0.001 0 "" blue black -2 -39 0 simundump kreac /kinetics/r21 0 3000 0.1 "" white black -2 -35 0 simundump kreac /kinetics/r23 0 0.1 21000 "" white black 1 -47 0 simundump kpool /kinetics/G-S 0 0.033046 0.033046 0.033046 3.3046e-05 \ 3.3046e-05 3.3046e-05 0 0.001 0 "" blue black 4 -47 0 simundump kreac /kinetics/r11 0 0.03 4500 "" white black 7 -47 0 simundump kpool /kinetics/Grb 0 0.34 0.051954 0.051954 5.1954e-05 5.1954e-05 \ 0.00034 0 0.001 0 "" blue black 4 -39 0 simundump kreac /kinetics/r9 0 3000 0.05 "" white black 7 -34 0 simundump kreac /kinetics/r12 0 0.0015 100 "" white black 4 -43 0 simundump kpool /kinetics/R-G 0 0 0 0 0 0 0 0 0.001 0 "" blue black 10 -39 0 simundump kreac /kinetics/r10 0 10 0.06 "" white black 10 -43 0 simundump kpool /kinetics/SOS 0 0.034 0.00095421 0.00095421 9.5421e-07 \ 9.5421e-07 3.4e-05 0 0.001 0 "" blue black 1 -51 0 simundump kpool /kinetics/R-G-S 0 0 0 0 0 0 0 0 0.001 0 "" blue black 10 -47 \ 0 simundump kpool /kinetics/enz8 0 0.001 0.001 0.001 1e-06 1e-06 1e-06 0 0.001 \ 0 "" blue black 7 -29 0 simundump kenz /kinetics/enz8/r8 0 0 0 0 0 0.001 50000 4 1 0 1 "" red blue "" \ 8 -29 0 simundump kpool /kinetics/enz16 0 0.001 0.001 0.001 1e-06 1e-06 1e-06 0 0.001 \ 0 "" blue black 0 -27 0 simundump kenz /kinetics/enz16/r16 0 0 0 0 0 0.001 25000 6.8 1.7 0 1 "" red \ blue "" -2 -27 0 simundump kpool /kinetics/pEGFRtot 0 0 0 0 0 0 0 0 0.00050001 0 "" 2 yellow \ -17 -16 0 simundump kpool /kinetics/pShctot 0 0 0 0 0 0 0 0 0.001 0 "" blue yellow -18 \ -30 0 simundump kpool /kinetics/Grb2_Shc 0 0 0 0 0 0 0 0 0.001 0 "" 53 yellow -17 \ -50 0 simundump kpool /kinetics/Shc_EGFR 0 0 0 0 0 0 0 0 0.001 0 "" 58 yellow -18 \ -42 0 simundump kpool /kinetics/Grb_EGFR 0 0 0 0 0 0 0 0 0.001 0 "" 23 yellow 12 \ -51 0 simundump kpool /kinetics/SOS_EGFR 0 0 0 0 0 0 0 0 0.001 0 "" blue yellow -10 \ -51 0 simundump kpool /kinetics/pPLCr 0 0 0 0 0 0 0 0 0.001 0 "" blue yellow 20 -29 \ 0 simundump xgraph /graphs/conc1 0 0 119 0 148.78 0 simundump xgraph /graphs/conc2 0 0 68 0 22.716 0 simundump xplot /graphs/conc1/pEGFRtot.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 2 0 0 1 simundump xplot /graphs/conc1/pShctot.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc1/Grb2_Shc.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 53 0 0 1 simundump xplot /graphs/conc2/Shc_EGFR.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 58 0 0 1 simundump xplot /graphs/conc2/Grb_EGFR.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 23 0 0 1 simundump xgraph /moregraphs/conc3 0 0 106 0 29.433 0 simundump xgraph /moregraphs/conc4 0 0 119 0 13.695 0 simundump xplot /moregraphs/conc3/SOS_EGFR.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /moregraphs/conc3/Sh-G-S.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 52 0 0 1 simundump xplot /moregraphs/conc4/pPLCr.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xcoredraw /edit/draw 0 -22.1 19.9 -53 -13 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 \ "This model is based on the model and parameters published in paper:" \ "Quantificaion of Short Term Signaling by the EGFR;" \ "Kholodenko et al, The Journal of Biological Chemistry Vol 274, No. 42, Issue of October 15, pp. " \ "30169 - 30181, 1999." \ "Note: There are ambiguties in the paper about initial conditions employed for obtaining the results." \ "Thanks to Dr. Kholodenko for clarifying those ambiguties and passing on the actual values used." \ " [G-S]=33.04579, [Grb]=51.95431, [SOS]=0.95421." addmsg /kinetics/r3 /kinetics/RP REAC B A addmsg /kinetics/enz4/r4 /kinetics/RP REAC sA B addmsg /kinetics/r5 /kinetics/RP REAC A B addmsg /kinetics/r7 /kinetics/RP REAC B A addmsg /kinetics/r13 /kinetics/RP REAC A B addmsg /kinetics/r15 /kinetics/RP REAC B A addmsg /kinetics/r18 /kinetics/RP REAC B A addmsg /kinetics/r20 /kinetics/RP REAC B A addmsg /kinetics/r9 /kinetics/RP REAC A B addmsg /kinetics/r11 /kinetics/RP REAC B A addmsg /kinetics/r2 /kinetics/R2 REAC B A addmsg /kinetics/r3 /kinetics/R2 REAC A B addmsg /kinetics/enz4/r4 /kinetics/R2 MM_PRD pA addmsg /kinetics/enz4 /kinetics/enz4/r4 ENZYME n addmsg /kinetics/RP /kinetics/enz4/r4 SUBSTRATE n addmsg /kinetics/R2 /kinetics/r3 SUBSTRATE n addmsg /kinetics/RP /kinetics/r3 PRODUCT n addmsg /kinetics/Ra /kinetics/r2 SUBSTRATE n addmsg /kinetics/R2 /kinetics/r2 PRODUCT n addmsg /kinetics/Ra /kinetics/r2 SUBSTRATE n addmsg /kinetics/r1 /kinetics/Ra REAC B A addmsg /kinetics/r2 /kinetics/Ra REAC A B addmsg /kinetics/r2 /kinetics/Ra REAC A B addmsg /kinetics/r1 /kinetics/R REAC A B addmsg /kinetics/r1 /kinetics/EGF REAC A B addmsg /kinetics/EGF /kinetics/r1 SUBSTRATE n addmsg /kinetics/Ra /kinetics/r1 PRODUCT n addmsg /kinetics/R /kinetics/r1 SUBSTRATE n addmsg /kinetics/r5 /kinetics/R-PL REAC B A addmsg /kinetics/r6 /kinetics/R-PL REAC A B addmsg /kinetics/r6 /kinetics/R-PLP REAC B A addmsg /kinetics/r7 /kinetics/R-PLP REAC A B addmsg /kinetics/r7 /kinetics/PLCrP REAC B A addmsg /kinetics/r25 /kinetics/PLCrP REAC A B addmsg /kinetics/enz8/r8 /kinetics/PLCrP REAC sA B addmsg /kinetics/r5 /kinetics/PLCr REAC A B addmsg /kinetics/enz8/r8 /kinetics/PLCr MM_PRD pA addmsg /kinetics/RP /kinetics/r5 SUBSTRATE n addmsg /kinetics/R-PL /kinetics/r5 PRODUCT n addmsg /kinetics/PLCr /kinetics/r5 SUBSTRATE n addmsg /kinetics/R-PL /kinetics/r6 SUBSTRATE n addmsg /kinetics/R-PLP /kinetics/r6 PRODUCT n addmsg /kinetics/R-PLP /kinetics/r7 SUBSTRATE n addmsg /kinetics/PLCrP /kinetics/r7 PRODUCT n addmsg /kinetics/RP /kinetics/r7 PRODUCT n addmsg /kinetics/PLCrP /kinetics/r25 SUBSTRATE n addmsg /kinetics/PLCr-I /kinetics/r25 PRODUCT n addmsg /kinetics/r25 /kinetics/PLCr-I REAC B A addmsg /kinetics/RP /kinetics/r13 SUBSTRATE n addmsg /kinetics/R-Sh /kinetics/r13 PRODUCT n addmsg /kinetics/Shc /kinetics/r13 SUBSTRATE n addmsg /kinetics/r13 /kinetics/Shc REAC A B addmsg /kinetics/enz16/r16 /kinetics/Shc MM_PRD pA addmsg /kinetics/r14 /kinetics/R-Sh REAC A B addmsg /kinetics/r13 /kinetics/R-Sh REAC B A addmsg /kinetics/R-Sh /kinetics/r14 SUBSTRATE n addmsg /kinetics/R-ShP /kinetics/r14 PRODUCT n addmsg /kinetics/r15 /kinetics/R-ShP REAC A B addmsg /kinetics/r17 /kinetics/R-ShP REAC A B addmsg /kinetics/r24 /kinetics/R-ShP REAC A B addmsg /kinetics/r14 /kinetics/R-ShP REAC B A addmsg /kinetics/R-ShP /kinetics/r15 SUBSTRATE n addmsg /kinetics/ShP /kinetics/r15 PRODUCT n addmsg /kinetics/RP /kinetics/r15 PRODUCT n addmsg /kinetics/r15 /kinetics/ShP REAC B A addmsg /kinetics/r21 /kinetics/ShP REAC A B addmsg /kinetics/r23 /kinetics/ShP REAC B A addmsg /kinetics/enz16/r16 /kinetics/ShP REAC sA B addmsg /kinetics/R-ShP /kinetics/r17 SUBSTRATE n addmsg /kinetics/R-Sh-G /kinetics/r17 PRODUCT n addmsg /kinetics/Grb /kinetics/r17 SUBSTRATE n addmsg /kinetics/r17 /kinetics/R-Sh-G REAC B A addmsg /kinetics/r18 /kinetics/R-Sh-G REAC A B addmsg /kinetics/r19 /kinetics/R-Sh-G REAC A B addmsg /kinetics/R-Sh-G /kinetics/r19 SUBSTRATE n addmsg /kinetics/R-Sh-G-S /kinetics/r19 PRODUCT n addmsg /kinetics/SOS /kinetics/r19 SUBSTRATE n addmsg /kinetics/r19 /kinetics/R-Sh-G-S REAC B A addmsg /kinetics/r20 /kinetics/R-Sh-G-S REAC A B addmsg /kinetics/r24 /kinetics/R-Sh-G-S REAC B A addmsg /kinetics/R-ShP /kinetics/r24 SUBSTRATE n addmsg /kinetics/R-Sh-G-S /kinetics/r24 PRODUCT n addmsg /kinetics/G-S /kinetics/r24 SUBSTRATE n addmsg /kinetics/R-Sh-G /kinetics/r18 SUBSTRATE n addmsg /kinetics/Sh-G /kinetics/r18 PRODUCT n addmsg /kinetics/RP /kinetics/r18 PRODUCT n addmsg /kinetics/R-Sh-G-S /kinetics/r20 SUBSTRATE n addmsg /kinetics/Sh-G-S /kinetics/r20 PRODUCT n addmsg /kinetics/RP /kinetics/r20 PRODUCT n addmsg /kinetics/r22 /kinetics/Sh-G-S REAC B A addmsg /kinetics/r20 /kinetics/Sh-G-S REAC B A addmsg /kinetics/r23 /kinetics/Sh-G-S REAC A B addmsg /kinetics/Sh-G /kinetics/r22 SUBSTRATE n addmsg /kinetics/Sh-G-S /kinetics/r22 PRODUCT n addmsg /kinetics/SOS /kinetics/r22 SUBSTRATE n addmsg /kinetics/r21 /kinetics/Sh-G REAC B A addmsg /kinetics/r18 /kinetics/Sh-G REAC B A addmsg /kinetics/r22 /kinetics/Sh-G REAC A B addmsg /kinetics/ShP /kinetics/r21 SUBSTRATE n addmsg /kinetics/Sh-G /kinetics/r21 PRODUCT n addmsg /kinetics/Grb /kinetics/r21 SUBSTRATE n addmsg /kinetics/Sh-G-S /kinetics/r23 SUBSTRATE n addmsg /kinetics/G-S /kinetics/r23 PRODUCT n addmsg /kinetics/ShP /kinetics/r23 PRODUCT n addmsg /kinetics/r23 /kinetics/G-S REAC B A addmsg /kinetics/r11 /kinetics/G-S REAC B A addmsg /kinetics/r24 /kinetics/G-S REAC A B addmsg /kinetics/r12 /kinetics/G-S REAC A B addmsg /kinetics/R-G-S /kinetics/r11 SUBSTRATE n addmsg /kinetics/G-S /kinetics/r11 PRODUCT n addmsg /kinetics/RP /kinetics/r11 PRODUCT n addmsg /kinetics/r17 /kinetics/Grb REAC A B addmsg /kinetics/r21 /kinetics/Grb REAC A B addmsg /kinetics/r9 /kinetics/Grb REAC A B addmsg /kinetics/r12 /kinetics/Grb REAC B A addmsg /kinetics/RP /kinetics/r9 SUBSTRATE n addmsg /kinetics/Grb /kinetics/r9 SUBSTRATE n addmsg /kinetics/R-G /kinetics/r9 PRODUCT n addmsg /kinetics/G-S /kinetics/r12 SUBSTRATE n addmsg /kinetics/Grb /kinetics/r12 PRODUCT n addmsg /kinetics/SOS /kinetics/r12 PRODUCT n addmsg /kinetics/r9 /kinetics/R-G REAC B A addmsg /kinetics/r10 /kinetics/R-G REAC A B addmsg /kinetics/R-G /kinetics/r10 SUBSTRATE n addmsg /kinetics/R-G-S /kinetics/r10 PRODUCT n addmsg /kinetics/SOS /kinetics/r10 SUBSTRATE n addmsg /kinetics/r12 /kinetics/SOS REAC B A addmsg /kinetics/r10 /kinetics/SOS REAC A B addmsg /kinetics/r22 /kinetics/SOS REAC A B addmsg /kinetics/r19 /kinetics/SOS REAC A B addmsg /kinetics/r11 /kinetics/R-G-S REAC A B addmsg /kinetics/r10 /kinetics/R-G-S REAC B A addmsg /kinetics/enz8 /kinetics/enz8/r8 ENZYME n addmsg /kinetics/PLCrP /kinetics/enz8/r8 SUBSTRATE n addmsg /kinetics/enz16 /kinetics/enz16/r16 ENZYME n addmsg /kinetics/ShP /kinetics/enz16/r16 SUBSTRATE n addmsg /kinetics/RP /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-PL /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-PLP /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-G /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-G-S /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-Sh /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-ShP /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-Sh-G /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-Sh-G-S /kinetics/pEGFRtot SUMTOTAL n nInit addmsg /kinetics/R-ShP /kinetics/pShctot SUMTOTAL n nInit addmsg /kinetics/R-Sh-G /kinetics/pShctot SUMTOTAL n nInit addmsg /kinetics/R-Sh-G-S /kinetics/pShctot SUMTOTAL n nInit addmsg /kinetics/ShP /kinetics/pShctot SUMTOTAL n nInit addmsg /kinetics/Sh-G /kinetics/pShctot SUMTOTAL n nInit addmsg /kinetics/Sh-G-S /kinetics/pShctot SUMTOTAL n nInit addmsg /kinetics/R-Sh-G /kinetics/Grb2_Shc SUMTOTAL n nInit addmsg /kinetics/Sh-G /kinetics/Grb2_Shc SUMTOTAL n nInit addmsg /kinetics/R-Sh-G-S /kinetics/Grb2_Shc SUMTOTAL n nInit addmsg /kinetics/Sh-G-S /kinetics/Grb2_Shc SUMTOTAL n nInit addmsg /kinetics/R-ShP /kinetics/Shc_EGFR SUMTOTAL n nInit addmsg /kinetics/R-Sh-G /kinetics/Shc_EGFR SUMTOTAL n nInit addmsg /kinetics/R-Sh-G-S /kinetics/Shc_EGFR SUMTOTAL n nInit addmsg /kinetics/R-G /kinetics/Grb_EGFR SUMTOTAL n nInit addmsg /kinetics/R-G-S /kinetics/Grb_EGFR SUMTOTAL n nInit addmsg /kinetics/R-Sh-G /kinetics/Grb_EGFR SUMTOTAL n nInit addmsg /kinetics/R-Sh-G-S /kinetics/Grb_EGFR SUMTOTAL n nInit addmsg /kinetics/R-G-S /kinetics/SOS_EGFR SUMTOTAL n nInit addmsg /kinetics/R-Sh-G-S /kinetics/SOS_EGFR SUMTOTAL n nInit addmsg /kinetics/R-PLP /kinetics/pPLCr SUMTOTAL n nInit addmsg /kinetics/PLCrP /kinetics/pPLCr SUMTOTAL n nInit addmsg /kinetics/pEGFRtot /graphs/conc1/pEGFRtot.Co PLOT Co *pEGFRtot.Co *2 addmsg /kinetics/pShctot /graphs/conc1/pShctot.Co PLOT Co *pShctot.Co *blue addmsg /kinetics/Grb2_Shc /graphs/conc1/Grb2_Shc.Co PLOT Co *Grb2_Shc.Co *53 addmsg /kinetics/Shc_EGFR /graphs/conc2/Shc_EGFR.Co PLOT Co *Shc_EGFR.Co *58 addmsg /kinetics/Grb_EGFR /graphs/conc2/Grb_EGFR.Co PLOT Co *Grb_EGFR.Co *23 addmsg /kinetics/SOS_EGFR /moregraphs/conc3/SOS_EGFR.Co PLOT Co *SOS_EGFR.Co *blue addmsg /kinetics/Sh-G-S /moregraphs/conc3/Sh-G-S.Co PLOT Co *Sh-G-S.Co *52 addmsg /kinetics/pPLCr /moregraphs/conc4/pPLCr.Co PLOT Co *pPLCr.Co *blue enddump // End of dump call /kinetics/RP/notes LOAD \ " Taken from Kholodenko et al 1999." call /kinetics/R2/notes LOAD \ "Taken form Kholodenko et al 1999." call /kinetics/enz4/notes LOAD \ " The initial conentration was set to 1nM" call /kinetics/enz4/r4/notes LOAD \ " Taken from Kholodenko et al 1999." call /kinetics/r3/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r2/notes LOAD \ " Taken from Kholodenko et al 1999" call /kinetics/Ra/notes LOAD \ " Taken form Kholodenko et al 1999" \ "" call /kinetics/R/notes LOAD \ "Taken form Kholodenko et al 1999." \ "[EGFR] = 100nM." \ "To obtain the plots as per figure-7B [EGFR] was increased " \ "4-fold (400nM) to obtain plot-1 and " \ "decreased 4-fold (25nM) to obtain plot-2." \ "" call /kinetics/EGF/notes LOAD \ "Taken from Kholodenko et al 1999" \ "Simulations were done at EGF concentration set to 20nM and 2nM" \ "concentration. This concentration was multiplied by a constant " \ "factor Vm/Vcw = 33.3 to formally rescale it to the cytoplasmic" \ "water volume. So actual concentration to which EGF was set was" \ "666nM and 66.6nM." \ "Plots 1&3 of figure-5 and plot 1 of figure 4 are obtained" \ "by setting the EGF conc to 666nM." \ "Plots 2&4 of figure-5 and plot 3 of figure 4 are obtained " \ "by setting the EGF conc to 66.6nM." \ "" \ "" call /kinetics/r1/notes LOAD \ "Taken from Kholodenko et al 1999." \ "" call /kinetics/R-PL/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/R-PLP/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/PLCrP/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/PLCr/notes LOAD \ "Taken from Kholodenko et al 1999. PLC-gamma" call /kinetics/r5/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/r6/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/r7/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/r25/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/PLCr-I/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/r13/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/Shc/notes LOAD \ "Taken from Kholodenko et al 1999." \ "To get plots in figure-4 and figure-5 [Shc] is set to 150nM" \ "To get plots in figure-7A [Shc] is set to 37.5nM" \ "(4-fold decrease)." \ "" call /kinetics/R-Sh/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r14/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/R-ShP/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r15/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/ShP/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r17/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/R-Sh-G/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r19/notes LOAD \ "Taken from Kholodenko et al 1999." \ "" call /kinetics/R-Sh-G-S/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r24/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r18/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r20/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/Sh-G-S/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Phosphorylated Shc [Sh-G-S]" call /kinetics/r22/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/Sh-G/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r21/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r23/notes LOAD \ "Taken form Kholodenko et al 1999" call /kinetics/G-S/notes LOAD \ "" \ "Thanks to Dr. Kholodenko for clarifying the ambiguity " \ "and furnishing the values." \ "" call /kinetics/r11/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/Grb/notes LOAD \ "Taken from Kholodenko et al 1999." \ "To obtain plots as per figure-4 and 5 [Grb] is set to 51.954nM." \ "instead of 85nM. Thanks to Dr. Kholodenko for clarifying the" \ "ambiguity and furnishing us the above value." \ "" \ " To obtain plots as per figure-7A [Grb] is set to 340nM " \ "(4-fold increase)." call /kinetics/r9/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/r12/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/R-G/notes LOAD \ "Taken from Kholodenko et al 1999" \ "" call /kinetics/r10/notes LOAD \ "Taken from Kholodenko et al 1999" call /kinetics/SOS/notes LOAD \ "The initial concentration is set to 0.95421nM instead of 37nM which." \ "Thanks to Dr. Kholodenko for clarifying the ambiguity and " \ "furnishing the initial concentration." call /kinetics/R-G-S/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/enz8/notes LOAD \ "The initial concentration was set ot 1nM." call /kinetics/enz8/r8/notes LOAD \ "Taken from Kholodenko et al 1999. " call /kinetics/enz16/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/enz16/r16/notes LOAD \ "Taken from Kholodenko et al 1999." call /kinetics/pEGFRtot/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Total phosphorylated EGFR = 2.([RP] + [R-PL] + [R-PLP] + [R-G]" \ "+ [R-G-S] + [R-Sh] + [R-ShP] + [R-Sh-G] + [R-Sh-G-S] )" call /kinetics/pShctot/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Total phosphorylated Shc = [ShP] + [Sh-G] + [ Sh-G-S] + [R-ShP]" \ "[R-Sh-G] + [R-Sh-G-S]" call /kinetics/Grb2_Shc/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Total Concentration of Grb2 bound to Shc isoforms= [Sh-G-S]" \ "[R-Sh-G] +[R-Sh-G-S] + [Sh-G]" \ "" call /kinetics/Shc_EGFR/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Shc bound to EGFR = [R-ShP] + [ R-Sh-G] + [R-Sh-G-S]" call /kinetics/Grb_EGFR/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Total concentration of Grb2 bound to EGFR forms =" \ "[R-G] + [R-G-S] + [R-Sh-G] + [R-Sh-G-S]" \ "" call /kinetics/SOS_EGFR/notes LOAD \ "Taken from Kholodenko et al 1999." \ "Total Sos bound to EGFR = [R-G-S] + [R-Sh-G-S]" \ "" call /kinetics/pPLCr/notes LOAD \ "According to Kholodenko et al 1999." \ "" \ "Total Phosphorylated PLCr = [R-PLP] + [PLCrP]." \ "" complete_loading