// DOQCS :http://doqcs.ncbs.res.in/
// Accession Name = PKA_2003
// Accession Number = 47
// Pathway Name = Gs
// Pathway Number = 198
// Transcriber = Upinder S. Bhalla, NCBS
// Developer = Upinder S. Bhalla, NCBS
// Species = Generic mammalian
// Tissue = Generic
// Cell Compartment = Cytosol + Cell membrane
// Notes = We assume GTP is present in fixed amounts, so we leave it out of the explicit equations in this model. Normally we would expect it to associate along with the G-Receptor-ligand complex. Most info is from Berstein et al JBC 267:12 8081-8088 1992 Structure of rec activation of Gq from Fay et al Biochem 30 5066-5075 1991
//genesis
// kkit Version 11 flat dumpfile
// Saved on Tue Dec 13 11:51:10 2005
include kkit {argv 1}
FASTDT = 0.001
SIMDT = 0.01
CONTROLDT = 10
PLOTDT = 1
MAXTIME = 200
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 1e-15 3 sphere "" white black 15 5 0
simundump group /kinetics/Gs 1 blue black x 0 0 "" defaultfile defaultfile.g \
0 0 0 2.7372 5.9293 0
simundump kpool /kinetics/Gs/R 1 0 0.083333 0.083333 50000 50000 0 0 6e+05 0 \
/kinetics/geometry green blue -1.1225 1.4779 0
simundump kpool /kinetics/Gs/L.R 1 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \
green blue 4.2957 1.2379 0
simundump kreac /kinetics/Gs/L-bind-R 1 1.6667e-07 0.1 "" white blue 2.9982 \
4.3281 0
simundump kpool /kinetics/Gs/GDP.Gabc 1 0 1 1 6e+05 6e+05 0 0 6e+05 0 \
/kinetics/geometry yellow blue 8.7578 1.1979 0
simundump kpool /kinetics/Gs/L.R.GDP.Gabc 1 0 0 0 0 0 0 0 6e+05 0 \
/kinetics/geometry orange blue 4.1506 -2.1065 0
simundump kpool /kinetics/Gs/L 1 0 1 1 6e+05 6e+05 0 0 6e+05 4 \
/kinetics/geometry green blue 1.3077 1.3179 0
simundump kpool /kinetics/Gs/GDP.Ga 1 0 0 0 0 0 0 0 6e+05 0 \
/kinetics/geometry yellow blue 13.115 1.0819 0
simundump kpool /kinetics/Gs/Gbg 1 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \
yellow blue 8.748 -2.0335 0
simundump kreac /kinetics/Gs/Activate-Gs 1 0.025 0 "" white blue 6.6355 \
-3.9534 0
simundump kreac /kinetics/Gs/Trimerize-Gs 1 1e-05 0 "" white blue 11.224 4.05 \
0
simundump kreac /kinetics/Gs/GTPase 1 0.066667 0 "" white blue 15.368 \
-0.55117 0
simundump kpool /kinetics/Gs/R.GDP.Gabc 1 0 0 0 0 0 0 0 6e+05 0 \
/kinetics/geometry green blue -1.2708 -2.0093 0
simundump kreac /kinetics/Gs/L-bind-R.Gabc 1 8.3333e-06 0.1 "" white blue \
1.4399 -3.7914 0
simundump kreac /kinetics/Gs/R-bind-Gabc 1 3.3333e-07 0.1 "" white blue \
0.21361 4.2768 0
simundump kreac /kinetics/Gs/L.R-bind-Gabc 1 1.6667e-05 0.1 "" white blue \
6.5451 4.2768 0
simundump kpool /kinetics/GTP.Ga 1 0 0 0 0 0 0 0 6e+05 0 /kinetics/geometry \
red yellow 13.044 -1.9445 0
simundump doqcsinfo /kinetics/doqcsinfo 0 pdb198.g Gs pathway \
"Upinder S. Bhalla, NCBS" "Upinder S. Bhalla, NCBS" "citation here" \
"Generic Mammalian" Generic "Cytosol+Cell membrane" Qualitative \
"Bhalla US. (2004) Biophys J. 87(2):733-44 ( peer-reviewed publication )" \
"Exact GENESIS implementation" "Approximates original data " 15 6 0
simundump xgraph /graphs/conc1 0 0 200 0 0.1 0
simundump xgraph /graphs/conc2 0 0 200 0 0.1 0
simundump xplot /graphs/conc1/L.R.GDP.Gabc.Co 3 524288 \
"delete_plot.w ; edit_plot.D " orange 0 0 1
simundump xplot /graphs/conc1/L.R.Co 3 524288 \
"delete_plot.w ; edit_plot.D " green 0 0 1
simundump xplot /graphs/conc1/Gbg.Co 3 524288 \
"delete_plot.w ; edit_plot.D " yellow 0 0 1
simundump xplot /graphs/conc2/GTP.Ga.Co 3 524288 \
"delete_plot.w ; edit_plot.D " red 0 0 1
simundump xplot /graphs/conc2/GDP.Ga.Co 3 524288 \
"delete_plot.w ; edit_plot.D " yellow 0 0 1
simundump xplot /graphs/conc2/R.GDP.Gabc.Co 3 524288 \
"delete_plot.w ; edit_plot.D " green 0 0 1
simundump xgraph /moregraphs/conc3 0 0 200 0 0.1 0
simundump xgraph /moregraphs/conc4 0 0 200 0 0.1 0
simundump xcoredraw /edit/draw 0 -3.2708 17.368 -5.9534 8
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 \
"Based on Gs5.g" \
"Incorporated much better known numbers," \
"results seem reasonable."
addmsg /kinetics/Gs/L-bind-R /kinetics/Gs/R REAC A B
addmsg /kinetics/Gs/R-bind-Gabc /kinetics/Gs/R REAC A B
addmsg /kinetics/Gs/L-bind-R /kinetics/Gs/L.R REAC B A
addmsg /kinetics/Gs/L.R-bind-Gabc /kinetics/Gs/L.R REAC A B
addmsg /kinetics/Gs/Activate-Gs /kinetics/Gs/L.R REAC B A
addmsg /kinetics/Gs/R /kinetics/Gs/L-bind-R SUBSTRATE n
addmsg /kinetics/Gs/L /kinetics/Gs/L-bind-R SUBSTRATE n
addmsg /kinetics/Gs/L.R /kinetics/Gs/L-bind-R PRODUCT n
addmsg /kinetics/Gs/Trimerize-Gs /kinetics/Gs/GDP.Gabc REAC B A
addmsg /kinetics/Gs/L.R-bind-Gabc /kinetics/Gs/GDP.Gabc REAC A B
addmsg /kinetics/Gs/R-bind-Gabc /kinetics/Gs/GDP.Gabc REAC A B
addmsg /kinetics/Gs/L.R-bind-Gabc /kinetics/Gs/L.R.GDP.Gabc REAC B A
addmsg /kinetics/Gs/L-bind-R.Gabc /kinetics/Gs/L.R.GDP.Gabc REAC B A
addmsg /kinetics/Gs/Activate-Gs /kinetics/Gs/L.R.GDP.Gabc REAC A B
addmsg /kinetics/Gs/L-bind-R /kinetics/Gs/L REAC A B
addmsg /kinetics/Gs/L-bind-R.Gabc /kinetics/Gs/L REAC A B
addmsg /kinetics/Gs/GTPase /kinetics/Gs/GDP.Ga REAC B A
addmsg /kinetics/Gs/Trimerize-Gs /kinetics/Gs/GDP.Ga REAC A B
addmsg /kinetics/Gs/Trimerize-Gs /kinetics/Gs/Gbg REAC A B
addmsg /kinetics/Gs/Activate-Gs /kinetics/Gs/Gbg REAC B A
addmsg /kinetics/Gs/L.R.GDP.Gabc /kinetics/Gs/Activate-Gs SUBSTRATE n
addmsg /kinetics/Gs/Gbg /kinetics/Gs/Activate-Gs PRODUCT n
addmsg /kinetics/Gs/L.R /kinetics/Gs/Activate-Gs PRODUCT n
addmsg /kinetics/GTP.Ga /kinetics/Gs/Activate-Gs PRODUCT n
addmsg /kinetics/Gs/GDP.Ga /kinetics/Gs/Trimerize-Gs SUBSTRATE n
addmsg /kinetics/Gs/Gbg /kinetics/Gs/Trimerize-Gs SUBSTRATE n
addmsg /kinetics/Gs/GDP.Gabc /kinetics/Gs/Trimerize-Gs PRODUCT n
addmsg /kinetics/GTP.Ga /kinetics/Gs/GTPase SUBSTRATE n
addmsg /kinetics/Gs/GDP.Ga /kinetics/Gs/GTPase PRODUCT n
addmsg /kinetics/Gs/L-bind-R.Gabc /kinetics/Gs/R.GDP.Gabc REAC A B
addmsg /kinetics/Gs/R-bind-Gabc /kinetics/Gs/R.GDP.Gabc REAC B A
addmsg /kinetics/Gs/L /kinetics/Gs/L-bind-R.Gabc SUBSTRATE n
addmsg /kinetics/Gs/L.R.GDP.Gabc /kinetics/Gs/L-bind-R.Gabc PRODUCT n
addmsg /kinetics/Gs/R.GDP.Gabc /kinetics/Gs/L-bind-R.Gabc SUBSTRATE n
addmsg /kinetics/Gs/GDP.Gabc /kinetics/Gs/R-bind-Gabc SUBSTRATE n
addmsg /kinetics/Gs/R /kinetics/Gs/R-bind-Gabc SUBSTRATE n
addmsg /kinetics/Gs/R.GDP.Gabc /kinetics/Gs/R-bind-Gabc PRODUCT n
addmsg /kinetics/Gs/GDP.Gabc /kinetics/Gs/L.R-bind-Gabc SUBSTRATE n
addmsg /kinetics/Gs/L.R /kinetics/Gs/L.R-bind-Gabc SUBSTRATE n
addmsg /kinetics/Gs/L.R.GDP.Gabc /kinetics/Gs/L.R-bind-Gabc PRODUCT n
addmsg /kinetics/Gs/GTPase /kinetics/GTP.Ga REAC A B
addmsg /kinetics/Gs/Activate-Gs /kinetics/GTP.Ga REAC B A
addmsg /kinetics/Gs/L.R.GDP.Gabc /graphs/conc1/L.R.GDP.Gabc.Co PLOT Co *L.R.GDP.Gabc.Co *orange
addmsg /kinetics/Gs/L.R /graphs/conc1/L.R.Co PLOT Co *L.R.Co *green
addmsg /kinetics/Gs/Gbg /graphs/conc1/Gbg.Co PLOT Co *Gbg.Co *yellow
addmsg /kinetics/GTP.Ga /graphs/conc2/GTP.Ga.Co PLOT Co *GTP.Ga.Co *red
addmsg /kinetics/Gs/GDP.Ga /graphs/conc2/GDP.Ga.Co PLOT Co *GDP.Ga.Co *yellow
addmsg /kinetics/Gs/R.GDP.Gabc /graphs/conc2/R.GDP.Gabc.Co PLOT Co *R.GDP.Gabc.Co *green
enddump
// End of dump
call /kinetics/Gs/notes LOAD \
"We assume GTP is present in fixed amounts, so we leave it out" \
"of the explicit equations in this model. Normally we would expect it" \
"to associate along with the G-Receptor-ligand complex." \
"Most info is from Berstein et al JBC 267:12 8081-8088 1992" \
"Structure of rec activation of Gq from Fay et al Biochem 30 5066-5075 1991"
call /kinetics/Gs/R/notes LOAD \
"A typical number of receptors per cell is about 50000."
call /kinetics/Gs/L.R/notes LOAD \
"Ligand.Receptor complex" \
""
call /kinetics/Gs/L-bind-R/notes LOAD \
"Ligand binding to receptor." \
"" \
"From Gether et al JBC 270:28268-28275 (1995) the binding" \
"to the purified receptor is at about 1 uM, but the" \
"conformational change only happens at 30 uM. We'll take" \
"1 uM for this, since it is already much weaker binding" \
"than to the R.Gs complex. The time-course from this" \
"paper appears remarkably slow, based on physiological data" \
"I estimate more like 10 sec." \
""
call /kinetics/Gs/GDP.Gabc/notes LOAD \
"The resting state of Gs: GDP bound to trimer." \
"" \
"From Pang and Sternweis JBC 265:30 18707-12 1990 we get " \
"conc est 1.6 uM to 0.8 uM. We'll use 1 uM." \
""
call /kinetics/Gs/L.R.GDP.Gabc/notes LOAD \
"This is the ternary complex, where all the action" \
"happens. There are actually a lot more steps here, " \
"including a final step where the GTP binds the" \
"L.R.Ga complex and causes the release of GTP.Ga from" \
"the L.R. For simplicity this is excluded."
call /kinetics/Gs/L/notes LOAD \
"This ligand could be any of several which bind" \
"to the beta adrenergic receptor and other G-protein" \
"coupled receptors which activate AC. For the" \
"sake of argument, call it isoproterenol."
call /kinetics/Gs/GDP.Ga/notes LOAD \
"The inactive GDP-bound form of Gs alpha."
call /kinetics/Gs/Gbg/notes LOAD \
"The Gbetagamma dimer."
call /kinetics/Gs/Activate-Gs/notes LOAD \
"This step combines several stages in GTP.Galpha release." \
"" \
"From Berstein et al activation is at .35 - 0.7/min" \
"From Fay et al Biochem 30 5066-5075 1991 kf = .01/sec." \
"From Brandt and Ross JBC 261(4):1656-1664 (1986)" \
"and Ransan et al Biochem J 283(2):519-524 (1992) rates" \
"around 2.5/min to 1.5/min are better."
call /kinetics/Gs/Trimerize-Gs/notes LOAD \
"Negligible back-reaction." \
""
call /kinetics/Gs/GTPase/notes LOAD \
"From Brandt and Ross JBC 261(4):1656-1664," \
"rate is 4/min and is agonist independent." \
"I treat this as irreversible."
call /kinetics/Gs/R.GDP.Gabc/notes LOAD \
"Fraction of R.GDP.Gabc is about 50% of total R," \
"from Fay et al. Biochemistry 30:5066-5075(1991)" \
"Since this is not the same receptor, this value is a bit" \
"uncertain.. " \
""
call /kinetics/Gs/L-bind-R.Gabc/notes LOAD \
"From Seifert et al Mol. Pharmacol 56:348-358 (1999)" \
"The EC50 for ISO is about 20 nM."
call /kinetics/Gs/R-bind-Gabc/notes LOAD \
"Receptor binding to Gs. Scale it to the same" \
"slow rates described by Fay et al for L.R to L.R.G." \
"From detailed balance, Kd is 50."
call /kinetics/Gs/L.R-bind-Gabc/notes LOAD \
"See Fay et al Biochem 30 5066-5075 1991." \
"kf is 0.01/sec but does not account for Gs levels." \
"kb is 0.0001/sec. The fraction of RG is about 50%, so" \
"we can estimate Kd at about the same as for Gs basal levels." \
"" \
"This rate has to be faster since it has to feed GTP.Ga" \
"into the system faster than the GTPase." \
"Waldhoer et al Mol Pharmacol 53:808-818 1988" \
"say affinity for A1adenosine/Gi is 10 nM."
call /kinetics/GTP.Ga/notes LOAD \
"Activated G protein. " \
"Supposed to be 15-40% of total Gs when max stim."
call /kinetics/doqcsinfo/notes LOAD \
" We assume GTP is present in fixed amounts, so we leave it out of the explicit equations in this model. Normally we would expect it to associate along with the G-Receptor-ligand complex. Most info is from Berstein et al JBC 267:12 8081-8088 1992 Structure of rec activation of Gq from Fay et al Biochem 30 5066-5075 1991"
complete_loading