//genesis // kkit Version 8 flat dumpfile // Saved on Mon Dec 10 12:01:40 2001 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.0001 CONTROLDT = 1 PLOTDT = 0.1 MAXTIME = 10 TRANSIENT_TIME = 3 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/group 0 black black x 0 1 "" defaultfile \ /home2/bhalla/scripts/modules/defaultfile_0.g 0 0 0 18 -6 0 simundump kpool /kinetics/group/GTP 0 1000 10 10 10 10 1000 0 1 0 "" cyan \ black 21 -8 0 simundump kpool /kinetics/group/NO.sGCfast 0 0 0 0 0 0 0 0 1 0 "" cyan black \ 2 -9 0 simundump kpool /kinetics/group/NO.SGC_6coord 0 0 0 0 0 0 0 0 1 0 "" cyan \ black 8 -9 0 simundump kpool /kinetics/group/sGCfast 0 3 3 3 3 3 3 0 1 0 "" cyan black -4 \ -9 0 simundump kreac /kinetics/group/NO_bind_sGCfast 0 700 800 "" black black -3 \ -7 0 simundump kreac /kinetics/group/form_6coord 0 850 0 "" black black 3 -7 0 simundump kreac /kinetics/group/act_sGCfast 0 20 0.2 "" black black 10 -7 0 simundump kpool /kinetics/group/NO.sGC_5coord 0 0 0 0 0 0 0 0 1 0 "" cyan \ black 15 -8 0 simundump kpool /kinetics/group/sGCtot 0 0 0 0 0 0 0 0 1 0 "" cyan black 17 \ -10 0 simundump kenz /kinetics/group/sGCtot/kenz 0 0 0 0 0 1 6.3125 101 25.25 0 0 \ "" black black "" 19 -10 0 simundump kpool /kinetics/group/NO.sGC5accord 0 0 0 0 0 0 0 0 1 0 "" cyan \ black 19 -13 0 simundump kreac /kinetics/group/act_sGCslow 0 1.6 0.02 "" black black 14 -14 \ 0 simundump kreac /kinetics/group/NObindnonheme 0 5 25 "" black black 9 -14 0 simundump kpool /kinetics/group/nonhemebind_int 0 0 0 0 0 0 0 0 1 0 "" cyan \ black 15 -12 0 simundump kpool /kinetics/group/NO.sGC6coord 0 0 0 0 0 0 0 0 1 0 "" cyan \ black 8 -12 0 simundump kreac /kinetics/group/form6coord 0 850 0 "" black black 3 -14 0 simundump kreac /kinetics/group/NO_bind_sGCslow 0 700 800 "" black black -3 \ -14 0 simundump kpool /kinetics/group/NO.sGCslow 0 0 0 0 0 0 0 0 1 0 "" cyan black \ 2 -12 0 simundump kpool /kinetics/group/sGCslow 0 3 3 3 3 3 3 0 1 0 "" cyan black -4 \ -12 0 simundump kpool /kinetics/group/cGMP 0 0 0 0 0 0 0 0 1 0 "" cyan black 21 -12 \ 0 simundump kpool /kinetics/group/NO 0 5 0 0 0 0 5 0 1 0 "" cyan black 0 -10 0 simundump xgraph /graphs/conc1 0 0 10 0 0.20109 0 simundump xgraph /graphs/conc2 0 0 10 0.05 0.1 0 simundump xplot /graphs/conc1/sGCtot.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 23 0 0 1 simundump xplot /graphs/conc2/CaM-Ca4.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xgraph /moregraphs/conc3 0 0 10 0 1000.6 0 simundump xgraph /moregraphs/conc4 0 0 10 0 0.00012091 0 simundump xplot /moregraphs/conc3/cGMP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " cyan 0 0 1 simundump xplot /moregraphs/conc4/NO.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 4 0 0 1 simundump xcoredraw /edit/draw 0 -6 23 -16.6 -4.6 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 \ "This model features the activation of sGC by NO, and the conversio" \ "of GTP to cGMP. This is based on Stone and Marletta, 1996, " \ "Biochemistry, 35(4):1093-1099. Rates used as directly from their paper" \ "and their exp results. The Km and Vmax for the enzyme from T.Bellamy" \ "(thru personal correspondence)." \ "This model incorporates the NO synthesis scheme from completed " \ "model." \ "" addmsg /kinetics/group/sGCtot/kenz /kinetics/group/GTP REAC sA B addmsg /kinetics/group/NO_bind_sGCfast /kinetics/group/NO.sGCfast REAC B A addmsg /kinetics/group/form_6coord /kinetics/group/NO.sGCfast REAC A B addmsg /kinetics/group/form_6coord /kinetics/group/NO.SGC_6coord REAC B A addmsg /kinetics/group/act_sGCfast /kinetics/group/NO.SGC_6coord REAC A B addmsg /kinetics/group/NO_bind_sGCfast /kinetics/group/sGCfast REAC A B addmsg /kinetics/group/sGCfast /kinetics/group/NO_bind_sGCfast SUBSTRATE n addmsg /kinetics/group/NO.sGCfast /kinetics/group/NO_bind_sGCfast PRODUCT n addmsg /kinetics/group/NO /kinetics/group/NO_bind_sGCfast SUBSTRATE n addmsg /kinetics/group/NO.sGCfast /kinetics/group/form_6coord SUBSTRATE n addmsg /kinetics/group/NO.SGC_6coord /kinetics/group/form_6coord PRODUCT n addmsg /kinetics/group/NO.SGC_6coord /kinetics/group/act_sGCfast SUBSTRATE n addmsg /kinetics/group/NO.sGC_5coord /kinetics/group/act_sGCfast PRODUCT n addmsg /kinetics/group/act_sGCfast /kinetics/group/NO.sGC_5coord REAC B A addmsg /kinetics/group/sGCtot/kenz /kinetics/group/sGCtot REAC eA B addmsg /kinetics/group/NO.sGC_5coord /kinetics/group/sGCtot SUMTOTAL n nInit addmsg /kinetics/group/NO.sGC5accord /kinetics/group/sGCtot SUMTOTAL n nInit addmsg /kinetics/group/sGCtot /kinetics/group/sGCtot/kenz ENZYME n addmsg /kinetics/group/GTP /kinetics/group/sGCtot/kenz SUBSTRATE n addmsg /kinetics/group/act_sGCslow /kinetics/group/NO.sGC5accord REAC B A addmsg /kinetics/group/nonhemebind_int /kinetics/group/act_sGCslow SUBSTRATE n addmsg /kinetics/group/NO.sGC5accord /kinetics/group/act_sGCslow PRODUCT n addmsg /kinetics/group/NO.sGC6coord /kinetics/group/NObindnonheme SUBSTRATE n addmsg /kinetics/group/nonhemebind_int /kinetics/group/NObindnonheme PRODUCT n addmsg /kinetics/group/NO /kinetics/group/NObindnonheme SUBSTRATE n addmsg /kinetics/group/NObindnonheme /kinetics/group/nonhemebind_int REAC B A addmsg /kinetics/group/act_sGCslow /kinetics/group/nonhemebind_int REAC A B addmsg /kinetics/group/form6coord /kinetics/group/NO.sGC6coord REAC B A addmsg /kinetics/group/NObindnonheme /kinetics/group/NO.sGC6coord REAC A B addmsg /kinetics/group/NO.sGCslow /kinetics/group/form6coord SUBSTRATE n addmsg /kinetics/group/NO.sGC6coord /kinetics/group/form6coord PRODUCT n addmsg /kinetics/group/sGCslow /kinetics/group/NO_bind_sGCslow SUBSTRATE n addmsg /kinetics/group/NO.sGCslow /kinetics/group/NO_bind_sGCslow PRODUCT n addmsg /kinetics/group/NO /kinetics/group/NO_bind_sGCslow SUBSTRATE n addmsg /kinetics/group/NO_bind_sGCslow /kinetics/group/NO.sGCslow REAC B A addmsg /kinetics/group/form6coord /kinetics/group/NO.sGCslow REAC A B addmsg /kinetics/group/NO_bind_sGCslow /kinetics/group/sGCslow REAC A B addmsg /kinetics/group/sGCtot/kenz /kinetics/group/cGMP MM_PRD pA addmsg /kinetics/group/NO_bind_sGCfast /kinetics/group/NO REAC A B addmsg /kinetics/group/NO_bind_sGCslow /kinetics/group/NO REAC A B addmsg /kinetics/group/NObindnonheme /kinetics/group/NO REAC A B addmsg /kinetics/group/sGCtot /graphs/conc1/sGCtot.Co PLOT Co *sGCtot.Co *23 addmsg /kinetics/group/cGMP /moregraphs/conc3/cGMP.Co PLOT Co *cGMP.Co *cyan addmsg /kinetics/group/NO /moregraphs/conc4/NO.Co PLOT Co *NO.Co *4 enddump // End of dump call /kinetics/group/notes LOAD \ "This group features the binding reaction scheme as proposed by" \ "Stone and Marletta,1996, Biochemistry, 35(4):1093-1099. They" \ "report a two step binding step for the activation of sGC by NO." \ "Rates shown in the model are used directly from their experiments" \ "on stopped flow kinetics. " call /kinetics/group/GTP/notes LOAD \ "Concentration 10 uM" \ "(Kuroda et al., J.Neurosci., 2001, 21(15):5693-5702 ;" \ "Bhalla and Iyengar, 1999, Science, 283:381-387)" \ "" call /kinetics/group/sGCfast/notes LOAD \ "Stone and Marletta, Biochemistry,35(4), 1996," \ "" \ "They have reported that the binding of sGC with NO occurs through two" \ "phases;a slow process and a fast process. 30% of the sGC binds " \ "quickly to NO; but the rest 70% goes through a slow process which" \ "involves the binding of another NO to an unidentified non-heme " \ "site on the protein, which seems to be not necessarily the same " \ "site used in the initial two step binding to the heme." \ "" \ "Stone and Marletta,1995,34;14668-14674;-- report that the native" \ "heme stoichiometry is 2 per heterodimer. spectrally only one" \ "type of heme is observed, indicating that both hemes are in " \ "similar environment. they conclude that each subunit of the " \ "heterodimer binds 1 equiv of heme at a site conserved between" \ "the two subunits." \ "" \ "Concentration 3 uM assumed on the basis of reported data" \ "(Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ;" \ "Ariano et al., PNAS, 1982, 79:1316-1320)" \ "" \ "" \ "" \ "" call /kinetics/group/NO_bind_sGCfast/notes LOAD \ "This is the fast binding of NO to sGC, subsequently activating" \ "it, as proposed by Stone and Marletta." \ "" \ "Rates of these binding reactions used directly from Stone and" \ "Marletta,1996, Biochemistry, 35(4):1093-1099, " \ "based on whose paper this model is made. Rates obtained from" \ "stopped flow kinetics detailed in their paper." call /kinetics/group/form_6coord/notes LOAD \ "Rates used directly from Stone and Marletta,1996,Biochemistry," \ "35(4):1093-1099." call /kinetics/group/act_sGCfast/notes LOAD \ "Rates used directly from Stone and Marletta,1996,Biochemistry," \ "35(4):1093-1099." call /kinetics/group/NO.sGC_5coord/notes LOAD \ "This is the active sGC, a 5-coordinate complex formed after a " \ "series of reaction steps, involving the formation of a " \ "6 coordinate complex which converted to a 5-coordinate complex." call /kinetics/group/sGCtot/notes LOAD \ "This is the sumtotal of the sGC activated via two binding " \ "mecanisms as reported by Stone and Marletta, 1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/group/sGCtot/kenz/notes LOAD \ "The range of estimates found in the literature are:" \ "Km -> 40 - 150 uM (without NO)" \ " 20 - 40 uM (with NO)" \ "Vmax -> 10 - 100 nmol/mg/min (wihtout NO)" \ " 10 - 40 umol/mg/min (with NO)." \ "----- thru personal correspondence from T. Bellamy, Wolfson " \ "Ins. for Biomedical Sciences, UK." \ "NO increases the Vmax of sGC by 100-200 fold, and it has been " \ "proposed that this activation occurs subsequent to the binding " \ "of NO toa heme moiety on the enzyme. (Stone and Marletta,1995," \ "Biochemistry,34:14668-14674). " call /kinetics/group/NO.sGC5accord/notes LOAD \ "This is the 5-coordinate complex of the enzyme sGC. This is" \ "also the active form of the enzyme." call /kinetics/group/act_sGCslow/notes LOAD \ "Rates used directly from Stone and Marletta,1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/group/NObindnonheme/notes LOAD \ "This step is the one that differs from the fast reaction scheme," \ "as reported by Stone and Marletta. Here the reaction is dependent " \ "upon the binding of NO to an unidentified non-heme site on the" \ "protein." \ "" \ "Rates used directly from Stone and Marletta,1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/group/nonhemebind_int/notes LOAD \ "here the new NO has bound to the unidentified non-heme site on" \ "the 6-coordinate complex, and this will convert to the" \ "5-coordinate complex. this binding of a new NO to the non-heme " \ "site on the 6-coordinate complex is characteristic of the slow " \ "binding process of NO to sGC." call /kinetics/group/NO.sGC6coord/notes LOAD \ "this compoud, a 6-coordinate complex will be bound by another NO" \ "to an unidentified non-heme site in the next reaction step." call /kinetics/group/form6coord/notes LOAD \ "Rates used directly from Stone and Marletta,1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/group/NO_bind_sGCslow/notes LOAD \ "This is the slow binding of NO to sGC, as reported by Stone and " \ "Marletta,1996, Biochemistry, 35(4):1093-1099. " \ "The rates shown have been used directly from their data from" \ "stopped flow kinetics." call /kinetics/group/sGCslow/notes LOAD \ "This is the slow reaction process of the binding of NO to sGC." \ "we can notice the binding of another NO in the third reaction " \ "step to a non-heme site, which then converts to the 5-coordinate" \ "complex. this binding of another NO to an non-heme site is" \ "characteristic of the slow binding process of NO to sGC.(Stone" \ "and Marletta, 1996,35(4);1093-1099)" \ "" \ "Concentration 3 uM assumed on the basis of reported data " \ "(Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ; " \ "Ariano et al., PNAS, 1982, 79:1316-1320.)" call /kinetics/group/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