//genesis // kkit Version 8 flat dumpfile // Saved on Mon Dec 24 17:28:10 2001 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 0.1 MAXTIME = 1000 TRANSIENT_TIME = 5 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1.6667e-21 VERSION = 8.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 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 kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \ 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 proto x y z simobjdump linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z simobjdump uplink xtree_fg_req xtree_textfg_req x y z simobjdump downlink xtree_fg_req xtree_textfg_req x y z simobjdump mirror notes xtree_fg_req x y z simundump group /kinetics/condorelliGCmod 0 62 black x 0 0 "" condorelliGCmod \ /home2/bhalla/scripts/modules/condorelliGCmod_0.g 0 0 0 -9 -12 0 simundump kpool /kinetics/condorelliGCmod/NO_sGCpart_act 0 0 0 0 0 0 0 0 1 0 \ "" 23 62 -19 -4 0 simundump kreac /kinetics/condorelliGCmod/NObind_sGC 0 980 350 "" white 62 \ -13 -5 0 simundump kreac /kinetics/condorelliGCmod/NOdepPway 0 1.68 0 "" white 62 -21 \ -7 0 simundump kreac /kinetics/condorelliGCmod/NOindePway 0 0.0609 0.014 "" white \ 62 -17 -7 0 simundump kpool /kinetics/condorelliGCmod/NO_sGCfull_act 0 0 0 0 0 0 0 0 1 0 \ "" 7 62 -19 -10 0 simundump kenz /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC 0 0 0 0 \ 0 1 3.4483 160 40 0 0 "" red 7 "" -19 -11 0 simundump kpool /kinetics/condorelliGCmod/GTP 0 1000 1000 1000 1000 1000 1000 \ 0 1 0 "" 54 62 -22 -14 0 simundump kpool /kinetics/condorelliGCmod/cGMP 0 0 0 0 0 0 0 0 1 0 "" 14 62 \ -16 -14 0 simundump kpool /kinetics/condorelliGCmod/NO_a 0 0.1 0.1 0.1 0.1 0.1 0.1 0 1 \ 0 "" 47 62 -23 -4 0 simundump kpool /kinetics/condorelliGCmod/sGC_basal 0 3 3 3 3 3 3 0 1 0 "" 0 \ 62 -15 -8 0 simundump kreac /kinetics/condorelliGCmod/dissoNO 0 0.07 0 "" white 62 -13 \ -11 0 simundump kpool /kinetics/condorelliGCmod/NO 0 5 0 0 0 0 5 0 1 0 "" 4 62 -11 \ -8 0 simundump xgraph /graphs/conc1 0 0 547.8 0 0.29425 0 simundump xgraph /graphs/conc2 0 0 564.3 2.5659 3 0 simundump xplot /graphs/conc1/NO_sGCpart_act.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 23 0 0 1 simundump xplot /graphs/conc1/NO_sGCfull_act.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 7 0 0 1 simundump xplot /graphs/conc2/sGC_basal.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 0 0 0 1 simundump xgraph /moregraphs/conc3 0 0 582.6 0 1000.1 0 simundump xgraph /moregraphs/conc4 0 0 575 0 0.1 0 simundump xplot /moregraphs/conc3/cGMP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 14 0 0 1 simundump xplot /moregraphs/conc4/NO_a.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xcoredraw /edit/draw 0 -25 -7 -16 -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 \ "The model with the partial and fully active enzyme sGC as proposed by Condorelli et al. with NO activating sGC," \ "in a mechanism as proposed by Condorelli et al., 2001, Biophys J, 80:2110-2119...." \ "This is similar to condorelli_GCmodel_incNOS_Iwan.g, but the rates used here have been converted by 7X, since the" \ "original rates were obtained from experiments performed at 4C .... and the NOS reaction scheme is not included..." addmsg /kinetics/condorelliGCmod/NObind_sGC /kinetics/condorelliGCmod/NO_sGCpart_act REAC B A addmsg /kinetics/condorelliGCmod/NOindePway /kinetics/condorelliGCmod/NO_sGCpart_act REAC A B addmsg /kinetics/condorelliGCmod/NOdepPway /kinetics/condorelliGCmod/NO_sGCpart_act REAC A B addmsg /kinetics/condorelliGCmod/sGC_basal /kinetics/condorelliGCmod/NObind_sGC SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO_sGCpart_act /kinetics/condorelliGCmod/NObind_sGC PRODUCT n addmsg /kinetics/condorelliGCmod/NO /kinetics/condorelliGCmod/NObind_sGC SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO_sGCpart_act /kinetics/condorelliGCmod/NOdepPway SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO_a /kinetics/condorelliGCmod/NOdepPway SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO_sGCfull_act /kinetics/condorelliGCmod/NOdepPway PRODUCT n addmsg /kinetics/condorelliGCmod/NO_sGCpart_act /kinetics/condorelliGCmod/NOindePway SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO_sGCfull_act /kinetics/condorelliGCmod/NOindePway PRODUCT n addmsg /kinetics/condorelliGCmod/NOindePway /kinetics/condorelliGCmod/NO_sGCfull_act REAC B A addmsg /kinetics/condorelliGCmod/NOdepPway /kinetics/condorelliGCmod/NO_sGCfull_act REAC B A addmsg /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC /kinetics/condorelliGCmod/NO_sGCfull_act REAC eA B addmsg /kinetics/condorelliGCmod/dissoNO /kinetics/condorelliGCmod/NO_sGCfull_act REAC A B addmsg /kinetics/condorelliGCmod/NO_sGCfull_act /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC ENZYME n addmsg /kinetics/condorelliGCmod/GTP /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC /kinetics/condorelliGCmod/GTP REAC sA B addmsg /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC /kinetics/condorelliGCmod/cGMP MM_PRD pA addmsg /kinetics/condorelliGCmod/NOdepPway /kinetics/condorelliGCmod/NO_a REAC A B addmsg /kinetics/condorelliGCmod/NObind_sGC /kinetics/condorelliGCmod/sGC_basal REAC A B addmsg /kinetics/condorelliGCmod/dissoNO /kinetics/condorelliGCmod/sGC_basal REAC B A addmsg /kinetics/condorelliGCmod/NO_sGCfull_act /kinetics/condorelliGCmod/dissoNO SUBSTRATE n addmsg /kinetics/condorelliGCmod/NO /kinetics/condorelliGCmod/dissoNO PRODUCT n addmsg /kinetics/condorelliGCmod/sGC_basal /kinetics/condorelliGCmod/dissoNO PRODUCT n addmsg /kinetics/condorelliGCmod/NObind_sGC /kinetics/condorelliGCmod/NO REAC A B addmsg /kinetics/condorelliGCmod/dissoNO /kinetics/condorelliGCmod/NO REAC B A addmsg /kinetics/condorelliGCmod/NO_sGCpart_act /graphs/conc1/NO_sGCpart_act.Co PLOT Co *NO_sGCpart_act.Co *23 addmsg /kinetics/condorelliGCmod/NO_sGCfull_act /graphs/conc1/NO_sGCfull_act.Co PLOT Co *NO_sGCfull_act.Co *7 addmsg /kinetics/condorelliGCmod/sGC_basal /graphs/conc2/sGC_basal.Co PLOT Co *sGC_basal.Co *0 addmsg /kinetics/condorelliGCmod/cGMP /moregraphs/conc3/cGMP.Co PLOT Co *cGMP.Co *14 addmsg /kinetics/condorelliGCmod/NO_a /moregraphs/conc4/NO_a.Co PLOT Co *NO_a.Co *47 enddump // End of dump call /kinetics/condorelliGCmod/NO_sGCpart_act/notes LOAD \ "This is the partiallly active form of sGC bound with NO, as " \ "proposed by Condorelli et al., 2001, Biophys J, 80:2110-2119.." \ "based originally on Zhao et al., 1999, PNAS,96:14753-14758." call /kinetics/condorelliGCmod/NObind_sGC/notes LOAD \ "Rates at 4C..." \ "used directly from paper by Condorelli P, 2001, Biophysical J," \ "80:2110-2119, which in turn have been obtained mainly from" \ "Zhao et al., 1999, PNAS,96:14753-14758." call /kinetics/condorelliGCmod/NOdepPway/notes LOAD \ "Rates from stopped flow experiments performed at 4C from" \ "Zhao et al., 1999, PNAS,96:14753-14758." \ "" \ "Same rates used by Condorelli P, for his simulations..." call /kinetics/condorelliGCmod/NOindePway/notes LOAD \ "Rates used directly from Condorelli et al., 2001, Biophysical J," \ "80:2110-2119 ...." \ "Rates originally from Zhao et al., 1999, PNAS, 96:14753-14758" \ "from stopped flow spectroscopy experiments performed at 4C." call /kinetics/condorelliGCmod/NO_sGCfull_act/notes LOAD \ "This is the fully active form of sGC, catalysing the conversion " \ "of GTP to cGMP....as proposed by Condorelli et al., 2001, " \ "Biophys J, 80:14753-14758." \ "" call /kinetics/condorelliGCmod/NO_sGCfull_act/full_act_sGC/notes LOAD \ "Km values for the basal and fully activated forms of sGC have" \ "been determined as 85-120 uM and 58 uM, respectively ..." \ "(Ignarro et al., 1982, BBA, 718:49-59)..and the same has been" \ "used by Condorelli et al., 2001..." \ "" \ "Vmax values are around 10-100 nmol/min/mg (without NO) and" \ "10-40 umol/min/mg (with NO) ..... thru personal correspondence" \ "with T Bellamy, UK. " call /kinetics/condorelliGCmod/GTP/notes LOAD \ "Under in vivo conditions, GTP is present in excess, ~ 1 mM." \ "" call /kinetics/condorelliGCmod/sGC_basal/notes LOAD \ "Intracellular levels of sGC is around 3 uM, as sGC is enriched" \ "in Purkinje cells. (Shinya Kuroda, personal correpondence)..." call /kinetics/condorelliGCmod/dissoNO/notes LOAD \ "This is a modification by Condorelli et al., 2001, Biophys J" \ "of the recent binding scheme of Zhao et al., to include the" \ "NO dissociation from fully active complex of sGC..." \ "" \ "The dissociation is characterised by the respective first order" \ "rate constants depicted in the model... Rates are obtained at " \ "4C..." call /kinetics/condorelliGCmod/NO/notes LOAD \ "Endogenously produced NO concentrations in the course of" \ "signal transduction processes are < 100 nM. (Varner et al.," \ "Nitric oxide in the nervous system, Academic press, London, UK," \ "pp.191-206.)" complete_loading