//genesis // kkit Version 8 flat dumpfile // Saved on Mon Dec 24 10:03:33 2001 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.01 CONTROLDT = 5 PLOTDT = 1 MAXTIME = 1000 TRANSIENT_TIME = 30 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 kpool /kinetics/GC 0 3 3 3 3 3 3 0 1 4 "" 0 black 4 2 0 simundump kpool /kinetics/NO 0 0.1 0.1 0.1 0.1 0.1 0.1 0 1 0 "" 62 black 4 4 \ 0 simundump kpool /kinetics/NO_GC 0 0 0 0 0 0 0 0 1 0 "" 47 black 8 3 0 simundump kenz /kinetics/NO_GC/kenz 0 0 0 0 0 1 0.81667 29.4 7.35 0 0 "" red \ 47 "" 8 2 0 simundump kreac /kinetics/NObindGC 0 0.01 0.0025 "" white black 6 3 0 simundump kreac /kinetics/degradeNO 0 0.673 0 "" white black 6 5 0 simundump kpool /kinetics/NOdegrade 0 0 0 0 0 0 0 0 1 0 "" 27 black 8 5 0 simundump kpool /kinetics/GTP 0 10 10 10 10 10 10 0 1 0 "" 33 black 6 0 0 simundump kpool /kinetics/cGMP 0 0 0 0 0 0 0 0 1 0 "" 52 black 10 0 0 simundump kpool /kinetics/PDE 0 5 5 5 5 5 5 0 1 0 "" 22 black 11 3 0 simundump kenz /kinetics/PDE/kenz 0 0 0 0 0 1 9.675 15.48 3.87 0 0 "" red 22 \ "" 11 2 0 simundump kpool /kinetics/5'GMP 0 0 0 0 0 0 0 0 1 0 "" 5 black 14 2 0 simundump kpool /kinetics/PKG 0 2.5 2.5 2.5 2.5 2.5 2.5 0 1 0 "" 36 black 14 \ 0 0 simundump kreac /kinetics/cGMPbindPKG 0 10 0.5 "" white black 12 -2 0 simundump kpool /kinetics/cGMP.PKG 0 0 0 0 0 0 0 0 1 0 "" 56 black 12 -4 0 simundump kenz /kinetics/cGMP.PKG/kenz 0 0 0 0 0 1 18 2.88 0.72 0 0 "" red 56 \ "" 10 -4 0 simundump kpool /kinetics/Gsub 0 10.7 10.7 10.7 10.7 10.7 10.7 0 1 0 "" 25 \ black 12 -6 0 simundump kpool /kinetics/Gsub* 0 0 0 0 0 0 0 0 1 0 "" 48 black 7 -4 0 simundump kpool /kinetics/PP2A 0 2.7 2.7 2.7 2.7 2.7 2.7 0 1 0 "" 10 black 4 \ -2 0 simundump kpool /kinetics/PP2A_Gsub* 0 0 0 0 0 0 0 0 1 0 "" 58 black 4 -6 0 simundump kreac /kinetics/PP2AbindGsub* 0 1 0.27 "" white black 4 -4 0 simundump kreac /kinetics/dephosphory 0 1e-04 0 "" white black 8 -6 0 simundump xgraph /graphs/conc1 0 0 1000 6.73e-07 0.099627 0 simundump xgraph /graphs/conc2 0 0 1000 3e-08 0.0034359 0 simundump xplot /graphs/conc1/NOdegrade.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 27 0 0 1 simundump xplot /graphs/conc1/cGMP.PKG.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 56 0 0 1 simundump xplot /graphs/conc2/NO_GC.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xgraph /moregraphs/conc3 0 0 1000 0 0.0015738 0 simundump xgraph /moregraphs/conc4 0 0 1000 0 8.0731 0 simundump xplot /moregraphs/conc3/cGMP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 52 0 0 1 simundump xplot /moregraphs/conc4/Gsub*.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 48 0 0 1 simundump xplot /moregraphs/conc4/PP2A_Gsub*.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 58 0 0 1 simundump xcoredraw /edit/draw 0 2 16 -8 7 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 is based directly on paper by Shinya Kuroda,2001," \ "J.Neurosci., 21(15):5693-5702. This is a simulated model with the " \ "rates and other parameters obtained from various literature. " \ "This model also involves the cGMP dep PKG activity, and includes the" \ "PDE activity on cGMP." addmsg /kinetics/NObindGC /kinetics/GC REAC A B addmsg /kinetics/NObindGC /kinetics/NO REAC A B addmsg /kinetics/degradeNO /kinetics/NO REAC A B addmsg /kinetics/NObindGC /kinetics/NO_GC REAC B A addmsg /kinetics/NO_GC/kenz /kinetics/NO_GC REAC eA B addmsg /kinetics/NO_GC /kinetics/NO_GC/kenz ENZYME n addmsg /kinetics/GTP /kinetics/NO_GC/kenz SUBSTRATE n addmsg /kinetics/NO /kinetics/NObindGC SUBSTRATE n addmsg /kinetics/GC /kinetics/NObindGC SUBSTRATE n addmsg /kinetics/NO_GC /kinetics/NObindGC PRODUCT n addmsg /kinetics/NO /kinetics/degradeNO SUBSTRATE n addmsg /kinetics/NOdegrade /kinetics/degradeNO PRODUCT n addmsg /kinetics/degradeNO /kinetics/NOdegrade REAC B A addmsg /kinetics/NO_GC/kenz /kinetics/GTP REAC sA B addmsg /kinetics/NO_GC/kenz /kinetics/cGMP MM_PRD pA addmsg /kinetics/PDE/kenz /kinetics/cGMP REAC sA B addmsg /kinetics/cGMPbindPKG /kinetics/cGMP REAC A B addmsg /kinetics/PDE/kenz /kinetics/PDE REAC eA B addmsg /kinetics/PDE /kinetics/PDE/kenz ENZYME n addmsg /kinetics/cGMP /kinetics/PDE/kenz SUBSTRATE n addmsg /kinetics/PDE/kenz /kinetics/5'GMP MM_PRD pA addmsg /kinetics/cGMPbindPKG /kinetics/PKG REAC A B addmsg /kinetics/cGMP /kinetics/cGMPbindPKG SUBSTRATE n addmsg /kinetics/PKG /kinetics/cGMPbindPKG SUBSTRATE n addmsg /kinetics/cGMP.PKG /kinetics/cGMPbindPKG PRODUCT n addmsg /kinetics/cGMPbindPKG /kinetics/cGMP.PKG REAC B A addmsg /kinetics/cGMP.PKG/kenz /kinetics/cGMP.PKG REAC eA B addmsg /kinetics/cGMP.PKG /kinetics/cGMP.PKG/kenz ENZYME n addmsg /kinetics/Gsub /kinetics/cGMP.PKG/kenz SUBSTRATE n addmsg /kinetics/cGMP.PKG/kenz /kinetics/Gsub REAC sA B addmsg /kinetics/dephosphory /kinetics/Gsub REAC B A addmsg /kinetics/cGMP.PKG/kenz /kinetics/Gsub* MM_PRD pA addmsg /kinetics/PP2AbindGsub* /kinetics/Gsub* REAC A B addmsg /kinetics/dephosphory /kinetics/Gsub* REAC A B addmsg /kinetics/PP2AbindGsub* /kinetics/PP2A REAC A B addmsg /kinetics/PP2AbindGsub* /kinetics/PP2A_Gsub* REAC B A addmsg /kinetics/PP2A /kinetics/PP2AbindGsub* SUBSTRATE n addmsg /kinetics/Gsub* /kinetics/PP2AbindGsub* SUBSTRATE n addmsg /kinetics/PP2A_Gsub* /kinetics/PP2AbindGsub* PRODUCT n addmsg /kinetics/Gsub* /kinetics/dephosphory SUBSTRATE n addmsg /kinetics/Gsub /kinetics/dephosphory PRODUCT n addmsg /kinetics/NOdegrade /graphs/conc1/NOdegrade.Co PLOT Co *NOdegrade.Co *27 addmsg /kinetics/cGMP.PKG /graphs/conc1/cGMP.PKG.Co PLOT Co *cGMP.PKG.Co *56 addmsg /kinetics/NO_GC /graphs/conc2/NO_GC.Co PLOT Co *NO_GC.Co *47 addmsg /kinetics/cGMP /moregraphs/conc3/cGMP.Co PLOT Co *cGMP.Co *52 addmsg /kinetics/Gsub* /moregraphs/conc4/Gsub*.Co PLOT Co *Gsub*.Co *48 addmsg /kinetics/PP2A_Gsub* /moregraphs/conc4/PP2A_Gsub*.Co PLOT Co *PP2A_Gsub*.Co *58 enddump // End of dump call /kinetics/GC/notes LOAD \ "Guanylyl Cyclase ..." \ "Intracellular concentration is around 3 uM, as sGC is enrcihed" \ "in the Purkinje cells (Shinya Kuroda, personal corresspondence).." \ "Conc assumed on the basis of reported data in Ariano et al.," \ "1982, PNAS,79:297-300." call /kinetics/NO/notes LOAD \ "endogenous NO concentration is the course of signal transduction" \ "processes are around ~100 nM .." \ "(Varner et al., Nitric Oxide in the Nervous System, Academic Press," \ "pp:191-206)" call /kinetics/NO_GC/kenz/notes LOAD \ "Km - 45" \ "Vamx - 7.35" \ "" \ "Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702." \ "" call /kinetics/NObindGC/notes LOAD \ "Kd 250 nM (Stone and Marletta, 1996).." \ "" \ "kf - 0.01" \ "kb - 0.0025" \ "" \ "Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702 ..." call /kinetics/degradeNO/notes LOAD \ "degradation of NO ..." \ "kf - 0.673 / sec ...." \ "Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702 " \ "" call /kinetics/GTP/notes LOAD \ "conc used from Bhalla and Iyengar,1999,Science, 283:381-387.." call /kinetics/PDE/notes LOAD \ "PhophoDiesterase ... Degrades cGMP to 5'GMP ..." \ "Conc Initially used from Kotera et al.,1997, Eur J Biochem," \ "249:434-442." call /kinetics/PDE/kenz/notes LOAD \ "Km - 2" \ "Vmax - 3.87" \ "Thru personal Correspondence with Shinya Kuroda..." \ "rates initially from Turko et al., 1998, Biochem J, 329," \ "505-510 .. " call /kinetics/PKG/notes LOAD \ "PKG inactive ... " \ "conc ~2.5 uM ..Lohmann et al., PNAS, 1981, 78:635-657. and" \ "Shinya Kuroda, personal correspondence ...." \ "" call /kinetics/cGMPbindPKG/notes LOAD \ "Kd - 0.05uM" \ "Shinya Kuroda, 2001, J.Neurosci., 21(15):5693-5702." call /kinetics/cGMP.PKG/kenz/notes LOAD \ "Km - 0.2" \ "Vmax - 0.72" \ "" \ "Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702" \ "" call /kinetics/Gsub/notes LOAD \ "Conc from Detre et al., 1984, J Neurosci, 4:2843-2849." call /kinetics/PP2A/notes LOAD \ "conc from Mumby et al., 1985, J Biol Chem, 260:13763-13770." \ "" \ "" call /kinetics/PP2AbindGsub*/notes LOAD \ "Kd - 0.27 uM" \ "" \ "Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702." call /kinetics/dephosphory/notes LOAD \ "kf - 0.0001/sec" \ "" \ "Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702 ... " \ "and thru personal correspondence ..." complete_loading