// 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