// 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