// DOQCS : http://doqcs.ncbs.res.in/ // Accession Name = Huang_Ferrell_MAPK // Accession Number = 30 // Transcriber = Sridhar Hariharaputran, NCBS // Developer = Huang, C.-Y.F. and Ferrell Jr., J.E. // Species = Xenopus // Tissue = Oocytes extract // Cell Compartment = Cytosol // Notes = This is the Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83 model for the MAPK cascade in Xenopus oocytes extracts. //genesis // kkit Version 11 flat dumpfile // Saved on Thu Dec 8 12:11:21 2005 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.0001 CONTROLDT = 10 PLOTDT = 1 MAXTIME = 100 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1.6667e-21 VERSION = 11.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump doqcsinfo filename accessname accesstype transcriber developer \ citation species tissue cellcompartment methodology sources \ model_implementation model_validation x y z 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 geometry size dim shape outside xtree_fg_req xtree_textfg_req x y \ z simobjdump kpool DiffConst CoInit Co n nInit mwt nMin vol slave_enable \ geomname 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 simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black 4 \ -1 0 simundump group /kinetics/MAPK 0 19 black x 0 0 "" MAPK \ /home2/bhalla/scripts/modules/MAPK_0.g 0 0 0 -5 -2 0 simundump kpool /kinetics/MAPK/INPUT(E1) 0 0 0.1 0.1 0.1 0.1 0 0 1 0 \ /kinetics/geometry 30 19 -1 -2 0 simundump kenz /kinetics/MAPK/INPUT(E1)/INPUT(E1) 0 0 0 0 0 1 1000 150 150 0 \ 0 "" red 30 "" -1 -3 0 simundump kpool /kinetics/MAPK/MAPKKK 0 0 0.003 0.003 0.003 0.003 0 0 1 0 \ /kinetics/geometry 34 19 -5 -5 0 simundump kpool /kinetics/MAPK/MAPKKK* 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 2 19 3 -5 0 simundump kenz /kinetics/MAPK/MAPKKK*/MAPKKK* 0 0 0 0 0 1 1000 150 150 0 0 "" \ red 2 "" -3 -9 0 simundump kenz /kinetics/MAPK/MAPKKK*/MAPKKK*[1] 0 0 0 0 0 1 1000 150 150 0 0 \ "" red 2 "" 1 -9 0 simundump kpool /kinetics/MAPK/E2 0 0 0.0003 0.0003 0.0003 0.0003 0 0 1 0 \ /kinetics/geometry 52 19 -1 -8 0 simundump kenz /kinetics/MAPK/E2/E2 0 0 0 0 0 1 1000 150 150 0 0 "" red 52 "" \ -1 -7 0 simundump kpool /kinetics/MAPK/MAPKK 0 0 1.2 1.2 1.2 1.2 0 0 1 0 \ /kinetics/geometry 46 19 -5 -11 0 simundump kpool /kinetics/MAPK/MAPKK-P 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 61 19 -1 -11 0 simundump kpool /kinetics/MAPK/MAPKK-PP 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 5 19 3 -11 0 simundump kenz /kinetics/MAPK/MAPKK-PP/MAPKK-PP 0 0 0 0 0 1 1000 150 150 0 0 \ "" red 5 "" -3 -16 0 simundump kenz /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1] 0 0 0 0 0 1 1000 150 150 0 \ 0 "" red 5 "" 1 -16 0 simundump kpool /kinetics/MAPK/MAPKKPase 0 0 0.0003 0.0003 0.0003 0.0003 0 0 \ 1 0 /kinetics/geometry 29 19 -3 -14 0 simundump kenz /kinetics/MAPK/MAPKKPase/MAPKKPase 0 0 0 0 0 1 1000 150 150 0 \ 0 "" red 29 "" -3 -13 0 simundump kpool /kinetics/MAPK/MAPKKPase[1] 0 0 0.0003 0.0003 0.0003 0.0003 0 \ 0 1 0 /kinetics/geometry 29 19 1 -14 0 simundump kenz /kinetics/MAPK/MAPKKPase[1]/MAPKKPase 0 0 0 0 0 1 1000 150 150 \ 0 0 "" red 29 "" 1 -13 0 simundump kpool /kinetics/MAPK/MAPK 0 0 1.2 1.2 1.2 1.2 0 0 1 0 \ /kinetics/geometry 3 19 -5 -18 0 simundump kpool /kinetics/MAPK/MAPK-P 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 29 19 -1 -18 0 simundump kpool /kinetics/MAPK/MAPK-PP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 47 19 3 -18 0 simundump kpool /kinetics/MAPK/MAPKPase 0 0 0.12 0.12 0.12 0.12 0 0 1 0 \ /kinetics/geometry 6 19 -3 -21 0 simundump kenz /kinetics/MAPK/MAPKPase/MAPKPase 0 0 0 0 0 1 1000 150 150 0 0 \ "" red 6 "" -3 -20 0 simundump kpool /kinetics/MAPK/MAPKPase[1] 0 0 0.12 0.12 0.12 0.12 0 0 1 0 \ /kinetics/geometry 4 19 1 -21 0 simundump kenz /kinetics/MAPK/MAPKPase[1]/MAPKPase 0 0 0 0 0 1 1000 150 150 0 \ 0 "" red 4 "" 1 -20 0 simundump doqcsinfo /kinetics/doqcsinfo 0 db30.g Huang_Ferrell_MAPK pathway \ "Sridhar Hariharaputran, NCBS" "Huang, C.-Y.F. and Ferrell Jr., J.E." \ "citation here" Xenopus "Oocyte extract" Cytosol \ "Quantitative match to experiments" \ "Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83 ( peer-reviewed publication )" \ "Approximate implementation" "Approximates original data " 4 1 0 simundump xgraph /graphs/conc1 0 0 100 0 5 0 simundump xgraph /graphs/conc2 0 0 100 0 2 0 simundump xplot /graphs/conc1/MAPKKK*.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 2 0 0 1 simundump xplot /graphs/conc1/MAPKK-PP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 10 0 0 1 simundump xplot /graphs/conc1/MAPK-PP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xplot /graphs/conc2/MAPKK-P.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 61 0 0 1 simundump xplot /graphs/conc2/MAPKK-PP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 10 0 0 1 simundump xplot /graphs/conc2/MAPK-P.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 29 0 0 1 simundump xplot /graphs/conc2/MAPK-PP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xgraph /moregraphs/conc3 0 0 100 0 1 0 simundump xgraph /moregraphs/conc4 0 0 100 0 1 0 simundump xcoredraw /edit/draw 0 -7 5 -23 2 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 \ "29 Jan 2002" \ " " \ " This model is based on Huang and Ferrell PNAS Vol.93, 10078-10083, 1996." \ "" \ "Parameter values are derived from a Mathematica file received with " \ "thanks from Dr. Ferrell." \ "" \ "" \ "" \ "" \ " " \ "" \ "" addmsg /kinetics/MAPK/INPUT(E1)/INPUT(E1) /kinetics/MAPK/INPUT(E1) REAC eA B addmsg /kinetics/MAPK/INPUT(E1) /kinetics/MAPK/INPUT(E1)/INPUT(E1) ENZYME n addmsg /kinetics/MAPK/MAPKKK /kinetics/MAPK/INPUT(E1)/INPUT(E1) SUBSTRATE n addmsg /kinetics/MAPK/INPUT(E1)/INPUT(E1) /kinetics/MAPK/MAPKKK REAC sA B addmsg /kinetics/MAPK/E2/E2 /kinetics/MAPK/MAPKKK MM_PRD pA addmsg /kinetics/MAPK/MAPKKK*/MAPKKK* /kinetics/MAPK/MAPKKK* REAC eA B addmsg /kinetics/MAPK/MAPKKK*/MAPKKK*[1] /kinetics/MAPK/MAPKKK* REAC eA B addmsg /kinetics/MAPK/INPUT(E1)/INPUT(E1) /kinetics/MAPK/MAPKKK* MM_PRD pA addmsg /kinetics/MAPK/E2/E2 /kinetics/MAPK/MAPKKK* REAC sA B addmsg /kinetics/MAPK/MAPKKK* /kinetics/MAPK/MAPKKK*/MAPKKK* ENZYME n addmsg /kinetics/MAPK/MAPKK /kinetics/MAPK/MAPKKK*/MAPKKK* SUBSTRATE n addmsg /kinetics/MAPK/MAPKKK* /kinetics/MAPK/MAPKKK*/MAPKKK*[1] ENZYME n addmsg /kinetics/MAPK/MAPKK-P /kinetics/MAPK/MAPKKK*/MAPKKK*[1] SUBSTRATE n addmsg /kinetics/MAPK/E2/E2 /kinetics/MAPK/E2 REAC eA B addmsg /kinetics/MAPK/E2 /kinetics/MAPK/E2/E2 ENZYME n addmsg /kinetics/MAPK/MAPKKK* /kinetics/MAPK/E2/E2 SUBSTRATE n addmsg /kinetics/MAPK/MAPKKK*/MAPKKK* /kinetics/MAPK/MAPKK REAC sA B addmsg /kinetics/MAPK/MAPKKPase/MAPKKPase /kinetics/MAPK/MAPKK MM_PRD pA addmsg /kinetics/MAPK/MAPKKK*/MAPKKK* /kinetics/MAPK/MAPKK-P MM_PRD pA addmsg /kinetics/MAPK/MAPKKK*/MAPKKK*[1] /kinetics/MAPK/MAPKK-P REAC sA B addmsg /kinetics/MAPK/MAPKKPase/MAPKKPase /kinetics/MAPK/MAPKK-P REAC sA B addmsg /kinetics/MAPK/MAPKKPase[1]/MAPKKPase /kinetics/MAPK/MAPKK-P MM_PRD pA addmsg /kinetics/MAPK/MAPKK-PP/MAPKK-PP /kinetics/MAPK/MAPKK-PP REAC eA B addmsg /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1] /kinetics/MAPK/MAPKK-PP REAC eA B addmsg /kinetics/MAPK/MAPKKK*/MAPKKK*[1] /kinetics/MAPK/MAPKK-PP MM_PRD pA addmsg /kinetics/MAPK/MAPKKPase[1]/MAPKKPase /kinetics/MAPK/MAPKK-PP REAC sA B addmsg /kinetics/MAPK/MAPKK-PP /kinetics/MAPK/MAPKK-PP/MAPKK-PP ENZYME n addmsg /kinetics/MAPK/MAPK /kinetics/MAPK/MAPKK-PP/MAPKK-PP SUBSTRATE n addmsg /kinetics/MAPK/MAPKK-PP /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1] ENZYME n addmsg /kinetics/MAPK/MAPK-P /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1] SUBSTRATE n addmsg /kinetics/MAPK/MAPKKPase/MAPKKPase /kinetics/MAPK/MAPKKPase REAC eA B addmsg /kinetics/MAPK/MAPKKPase /kinetics/MAPK/MAPKKPase/MAPKKPase ENZYME n addmsg /kinetics/MAPK/MAPKK-P /kinetics/MAPK/MAPKKPase/MAPKKPase SUBSTRATE n addmsg /kinetics/MAPK/MAPKKPase[1]/MAPKKPase /kinetics/MAPK/MAPKKPase[1] REAC eA B addmsg /kinetics/MAPK/MAPKKPase[1] /kinetics/MAPK/MAPKKPase[1]/MAPKKPase ENZYME n addmsg /kinetics/MAPK/MAPKK-PP /kinetics/MAPK/MAPKKPase[1]/MAPKKPase SUBSTRATE n addmsg /kinetics/MAPK/MAPKK-PP/MAPKK-PP /kinetics/MAPK/MAPK REAC sA B addmsg /kinetics/MAPK/MAPKPase/MAPKPase /kinetics/MAPK/MAPK MM_PRD pA addmsg /kinetics/MAPK/MAPKK-PP/MAPKK-PP /kinetics/MAPK/MAPK-P MM_PRD pA addmsg /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1] /kinetics/MAPK/MAPK-P REAC sA B addmsg /kinetics/MAPK/MAPKPase[1]/MAPKPase /kinetics/MAPK/MAPK-P MM_PRD pA addmsg /kinetics/MAPK/MAPKPase/MAPKPase /kinetics/MAPK/MAPK-P REAC sA B addmsg /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1] /kinetics/MAPK/MAPK-PP MM_PRD pA addmsg /kinetics/MAPK/MAPKPase[1]/MAPKPase /kinetics/MAPK/MAPK-PP REAC sA B addmsg /kinetics/MAPK/MAPKPase/MAPKPase /kinetics/MAPK/MAPKPase REAC eA B addmsg /kinetics/MAPK/MAPKPase /kinetics/MAPK/MAPKPase/MAPKPase ENZYME n addmsg /kinetics/MAPK/MAPK-P /kinetics/MAPK/MAPKPase/MAPKPase SUBSTRATE n addmsg /kinetics/MAPK/MAPKPase[1]/MAPKPase /kinetics/MAPK/MAPKPase[1] REAC eA B addmsg /kinetics/MAPK/MAPKPase[1] /kinetics/MAPK/MAPKPase[1]/MAPKPase ENZYME n addmsg /kinetics/MAPK/MAPK-PP /kinetics/MAPK/MAPKPase[1]/MAPKPase SUBSTRATE n addmsg /kinetics/MAPK/MAPKKK* /graphs/conc1/MAPKKK*.Co PLOT Co *MAPKKK*.Co *2 addmsg /kinetics/MAPK/MAPKK-PP /graphs/conc1/MAPKK-PP.Co PLOT Co *MAPKK-PP.Co *10 addmsg /kinetics/MAPK/MAPK-PP /graphs/conc1/MAPK-PP.Co PLOT Co *MAPK-PP.Co *47 addmsg /kinetics/MAPK/MAPKK-P /graphs/conc2/MAPKK-P.Co PLOT Co *MAPKK-P.Co *61 addmsg /kinetics/MAPK/MAPKK-PP /graphs/conc2/MAPKK-PP.Co PLOT Co *MAPKK-PP.Co *10 addmsg /kinetics/MAPK/MAPK-P /graphs/conc2/MAPK-P.Co PLOT Co *MAPK-P.Co *29 addmsg /kinetics/MAPK/MAPK-PP /graphs/conc2/MAPK-PP.Co PLOT Co *MAPK-PP.Co *47 enddump // End of dump call /kinetics/MAPK/notes LOAD \ "MAPK model by Huang, C.-Y.F. and Ferrell Jr., J.E." \ "1996 PNAS USA 93:10078-10083" \ "The parameters are based on the Mathematica code for" \ "the model which was kindly supplied by Prof. Ferrell." \ "This simulation very closely replicates figure 2" \ "from the paper." call /kinetics/MAPK/INPUT(E1)/notes LOAD \ "E1tot concn. = 0.0003 uM" \ "from" \ "Mathematica code received from Dr. Ferrell through" \ "personal communication." call /kinetics/MAPK/INPUT(E1)/INPUT(E1)/notes LOAD \ "Km is 300 nM and Vmax is 150 " \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKKK/notes LOAD \ "Concn. of MAPKKKtot=0.003 uM" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKKK*/notes LOAD \ "This is the activated form of MAPKKK" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKKK*/MAPKKK*/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKKK*/MAPKKK*[1]/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/E2/notes LOAD \ "E2tot. concn is 0.0003 uM" \ "from" \ "Huang and Ferrell" call /kinetics/MAPK/E2/E2/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKK/notes LOAD \ "Concn. is 1.2 uM" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKK-P/notes LOAD \ "This is the single phosphorylated form of MAPKK" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKK-PP/notes LOAD \ "This is the double phosphorylated form of MAPKK" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKK-PP/MAPKK-PP/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKK-PP/MAPKK-PP[1]/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKKPase/notes LOAD \ "Concn. of mekpasetot i.e.,MAPKKpasetot=0.003 uM" \ "from" \ "Huang and Ferrrell 1996" call /kinetics/MAPK/MAPKKPase/MAPKKPase/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKKPase[1]/notes LOAD \ "Concn. of mekpasetot i.e.,MAPKKpasetot=0.0003 uM" \ "from" \ "Huang and Ferrell, 1996" call /kinetics/MAPK/MAPKKPase[1]/MAPKKPase/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPK/notes LOAD \ "Concn. is 1.2 uM" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPK-P/notes LOAD \ "This is the single phosphorylated form of MAPK" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPK-PP/notes LOAD \ "This is the double phosphorylated form of MAPK" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKPase/notes LOAD \ "Concn. of mapkpasetot=0.12 uM" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKPase/MAPKPase/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKPase[1]/notes LOAD \ "Concn. of mapkpasetot =0.12 uM" \ "from" \ "Huang and Ferrell 1996" call /kinetics/MAPK/MAPKPase[1]/MAPKPase/notes LOAD \ "Km is 300 nM and Vmax is 150" \ "from" \ "Huang and Ferrell 1996" call /kinetics/doqcsinfo/notes LOAD \ "This is the Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83 model for the MAPK cascade in Xenopus oocytes extracts." complete_loading