//genesis // kkit Version 7 dumpfile // Saved on Mon Aug 7 19:12:04 2000 include kkit {argv 1} FASTDT = 0.001 SIMDT = 0.01 CONTROLDT = 10 PLOTDT = 1 MAXTIME = 200 float TRANSIENT_TIME = 2 int VARIABLE_DT_FLAG = 1 kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump table input output alloced step_mode stepsize 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 kpool CoTotal CoInit Co CoRemaining n nInit nTotal nMin vol \ slave_enable notes xtree_fg_req xtree_textfg_req simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req plotfield manageclass baselevel last_x last_y \ is_running simobjdump group notes editfunc xtree_fg_req xtree_textfg_req plotfield \ manageclass expanded movealone simobjdump kreac A B kf kb is_active oldmsgmode notes editfunc xtree_fg_req \ xtree_textfg_req plotfield manageclass simundump group /kinetics/Gs 1 \ "We assume GTP is present in fixed amounts, so we leave it out\nof the explicit equations in this model. Normally we would expect it\nto associate along with the G-Receptor-ligand complex.\nMost info is from Berstein et al JBC 267:12 8081-8088 1992\nStructure of rec activation of Gq from Fay et al Biochem 30 5066-5075 1991" \ edit_group blue black x group 0 0 simundump kpool /kinetics/Gs/R 1 0.083333 0.083333 0.0009862 0.082347 591.72 \ 50000 50000 0 6e+05 0 \ "A typical number of receptors per cell is about 50000." green blue simundump kpool /kinetics/Gs/L.R 1 0 0 0.0011282 -0.0011282 676.94 0 0 0 \ 6e+05 0 "Ligand.Receptor complex\n" green blue simundump kreac /kinetics/Gs/L-bind-R 1 67.694 59.173 1.6667e-07 0.1 1 0 \ "Ligand binding to receptor.\n\nFrom Gether et al JBC 270:28268-28275 (1995) the binding\nto the purified receptor is at about 1 uM, but the\nconformational change only happens at 30 uM. We'll take\n1 uM for this, since it is already much weaker binding\nthan to the R.Gs complex. The time-course from this\npaper appears remarkably slow, based on physiological data\nI estimate more like 10 sec.\n" \ edit_reac white blue A group simundump kpool /kinetics/Gs/GDP.Gabc 1 1 1 0.88025 0.11975 5.2815e+05 6e+05 \ 6e+05 0 6e+05 0 \ "The resting state of Gs: GDP bound to trimer.\n\nFrom Pang and Sternweis JBC 265:30 18707-12 1990 we get \nconc est 1.6 uM to 0.8 uM. We'll use 1 uM.\n" \ yellow blue simundump kpool /kinetics/Gs/L.R.GDP.Gabc 1 0 0 0.079566 -0.079566 47740 0 0 \ 0 6e+05 0 \ "This is the ternary complex, where all the action\nhappens. There are actually a lot more steps here, \nincluding a final step where the GTP binds the\nL.R.Ga complex and causes the release of GTP.Ga from\nthe L.R. For simplicity this is excluded." \ orange blue simundump kpool /kinetics/Gs/L 1 10 1 1 0 6e+05 6e+05 6e+06 0 6e+05 4 \ "This ligand could be any of several which bind\nto the beta adrenergic receptor and other G-protein\ncoupled receptors which activate AC. For the\nsake of argument, call it isoproterenol." \ green blue simundump kpool /kinetics/Gs/GDP.Ga 1 0 0 0.0086187 -0.0086187 5171.2 0 0 0 \ 6e+05 0 "The inactive GDP-bound form of Gs alpha." yellow blue simundump kpool /kinetics/Gs/Gbg 1 0 0 0.038465 -0.038465 23079 0 0 0 6e+05 0 \ "The Gbetagamma dimer." yellow blue simundump kreac /kinetics/Gs/Activate-Gs 1 0 1193.5 0.025 0 1 0 \ "This step combines several stages in GTP.Galpha release.\n\nFrom Berstein et al activation is at .35 - 0.7/min\nFrom Fay et al Biochem 30 5066-5075 1991 kf = .01/sec.\nFrom Brandt and Ross JBC 261(4):1656-1664 (1986)\nand Ransan et al Biochem J 283(2):519-524 (1992) rates\naround 2.5/min to 1.5/min are better." \ edit_reac white blue A group simundump kreac /kinetics/Gs/Trimerize-Gs 1 0 1193.5 1e-05 0 1 0 \ "Negligible back-reaction.\n" edit_reac white blue A group simundump kreac /kinetics/Gs/GTPase 1 0 1193.5 0.066667 0 1 0 \ "From Brandt and Ross JBC 261(4):1656-1664,\nrate is 4/min and is agonist independent.\nI treat this as irreversible." \ edit_reac white blue A group simundump kpool /kinetics/Gs/R.GDP.Gabc 1 0 0 0.0015942 -0.0015942 956.5 0 0 \ 0 6e+05 0 \ "Fraction of R.GDP.Gabc is about 50% of total R,\nfrom Fay et al. Biochemistry 30:5066-5075(1991)\nSince this is not the same receptor, this value is a bit\nuncertain.. \n" \ green blue simundump kreac /kinetics/Gs/L-bind-R.Gabc 1 4774 4782.5 8.3333e-06 0.1 1 0 \ "From Seifert et al Mol. Pharmacol 56:348-358 (1999)\nThe EC50 for ISO is about 20 nM." \ edit_reac white blue A group simundump kreac /kinetics/Gs/R-bind-Gabc 1 95.65 104.17 3.3333e-07 0.1 1 0 \ "Receptor binding to Gs. Scale it to the same\nslow rates described by Fay et al for L.R to L.R.G.\nFrom detailed balance, Kd is 50." \ edit_reac white blue A group simundump kreac /kinetics/Gs/L.R-bind-Gabc 1 4774 5958.9 1.6667e-05 0.1 1 0 \ "See Fay et al Biochem 30 5066-5075 1991.\nkf is 0.01/sec but does not account for Gs levels.\nkb is 0.0001/sec. The fraction of RG is about 50%, so\nwe can estimate Kd at about the same as for Gs basal levels.\n\nThis rate has to be faster since it has to feed GTP.Ga\ninto the system faster than the GTPase.\nWaldhoer et al Mol Pharmacol 53:808-818 1988\nsay affinity for A1adenosine/Gi is 10 nM." \ edit_reac white blue A group simundump kpool /kinetics/GTP.Ga 1 0 0 0.029837 -0.029837 17902 0 0 0 6e+05 0 \ "Activated G protein. \nSupposed to be 15-40% of total Gs when max stim." \ red yellow 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 -2.6561 16.209 -10.34 8.5244 simundump xtree /edit/draw/tree 0 /kinetics/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 call /edit/draw/tree ADDMSGARROW \ select all all all none -1000 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[] /kinetics/##[TYPE=group] all all none -1001 0 \ "echo.p dragging onto group ; thing_to_group_add.p " "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kpool] SUMTOTAL kpool darkgreen -1002 0 \ "echo.p dragging to for sumtotal" "pool_to_pool_add_sumtot.p " "pool_to_pool_drop_sumtot.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kpool] CONSERVE kpool blue -1003 0 \ "echo.p dragging to for conserve" "pool_to_pool_add_consv.p " "pool_to_pool_drop_consv.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kreac] /kinetics/##[TYPE=kpool] REAC kpool none -1004 0 \ "" "reac_to_pool_add.p " "reac_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] SUBSTRATE kreac green -1005 0 \ "" "pool_to_reac_add.p " "pool_to_reac_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] KF kreac purple -1006 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] KB kreac hotpink -1007 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kreac] PRODUCT kreac green -1008 1 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=kpool] MM_PRD kpool red -1009 0 \ "echo.p dragging to for enz product" "enz_to_pool_add.p " "enz_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kenz] SUBSTRATE kenz red -1010 0 \ "echo.p dragging to for enz substrate" "pool_to_enz_add.p " "pool_to_enz_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=kpool] SUMTOTAL kpool darkgreen -1011 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kenz] /kinetics/##[TYPE=kpool] CONSERVE kpool blue -1012 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kenz] INTRAMOL kenz white -1013 0 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=stim] /kinetics/##[TYPE=kpool] SLAVE kpool orange -1014 0 \ "echo.p dragging to for stimulus" "stim_to_pool_add.p " "stim_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=stim] /kinetics/##[TYPE=stim] INPUT stim orange -1015 0 \ "echo.p dragging to for stim" "stim_to_stim_add.p " "stim_to_stim_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=xtab] /kinetics/##[TYPE=kpool] SLAVE kpool orange -1016 0 \ "echo.p dragging to for xtab" "xtab_to_pool_add.p " "xtab_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=xtab] /kinetics/##[TYPE=xtab] INPUT xtab orange -1017 0 \ "echo.p dragging to for xtab" "xtab_to_xtab_add.p " "xtab_to_xtab_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=xtab] INPUT xtab hotpink -1018 0 \ "echo.p dragging to for xtab" "pool_to_xtab_add.p " "pool_to_xtab_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kchan] /kinetics/##[TYPE=kpool] REAC kpool none -1019 0 \ "echo.p dragging to for chan product" "chan_to_pool_add.p " "chan_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kchan] PRODUCT kchan orange -1020 1 \ "" "" "" call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=kchan] SUBSTRATE kchan orange -1021 0 \ "echo.p dragging to for chan substrate" "pool_to_chan_add.p " "pool_to_chan_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=transport] /kinetics/##[TYPE=kpool] MM_PRD kpool yellow -1022 0 \ "" "transport_to_pool_add.p " "transport_to_pool_drop.p " call /edit/draw/tree ADDMSGARROW \ /kinetics/##[TYPE=kpool] /kinetics/##[TYPE=transport] SUBSTRATE transport yellow -1023 0 \ "" "pool_to_transport_add.p " "pool_to_transport_drop.p " call /edit/draw/tree UNDUMP 17 \ "/kinetics/Gs" 2.7372 5.9293 0 \ "/kinetics/Gs/R" -1.1225 1.4779 0 \ "/kinetics/Gs/L.R" 4.2957 1.2379 0 \ "/kinetics/Gs/L-bind-R" 2.9982 4.3281 0 \ "/kinetics/Gs/GDP.Gabc" 8.7578 1.1979 0 \ "/kinetics/Gs/L.R.GDP.Gabc" 4.1506 -2.1065 0 \ "/kinetics/Gs/L" 1.3077 1.3179 0 \ "/kinetics/Gs/GDP.Ga" 13.115 1.0819 0 \ "/kinetics/Gs/Gbg" 8.748 -2.0335 0 \ "/kinetics/Gs/Activate-Gs" 6.6355 -3.9534 0 \ "/kinetics/Gs/Trimerize-Gs" 11.224 4.05 0 \ "/kinetics/Gs/GTPase" 15.368 -0.55117 0 \ "/kinetics/Gs/R.GDP.Gabc" -1.2708 -2.0093 0 \ "/kinetics/Gs/L-bind-R.Gabc" 1.4399 -3.7914 0 \ "/kinetics/Gs/R-bind-Gabc" 0.21361 4.2768 0 \ "/kinetics/Gs/L.R-bind-Gabc" 6.5451 4.2768 0 \ "/kinetics/GTP.Ga" 13.044 -1.9445 0 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 /edit/draw/tree RESET reset