// DOQCS : http://doqcs.ncbs.res.in/ // Accession Name = NOS_Iwanaga // Accession Number = 11 // Transcriber = Sudhir Sivakumaran, NCBS // Developer = Iwanaga, Yamazaki and Kominami // Species = Rat; Mammalian // Tissue = Neuronal; Expression in E.coli // Cell Compartment = Cytosol // Notes = This model is based on Iwanaga T et al. Biochemistry (1999) 38(50):16629-35.The model features the catalytic activity of neuronal Nitric Oxide Synthase expressed in Escherichia coli in a four step reaction mechanism. The rates found in the model are used directly from their paper and have been determined from experiments performed at 25 C. //genesis // kkit Version 11 flat dumpfile // Saved on Thu Dec 8 14:07:19 2005 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 0.1 MAXTIME = 400 TRANSIENT_TIME = 5 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 1.6667e-21 3 sphere "" white black -9 \ -14 0 simundump doqcsinfo /kinetics/doqcsinfo 0 db11.g NOS_Iwanaga pathway \ "Sudhir Sivakumaran, NCBS" "Iwanaga, Yamazaki and Kominami" "citation here" \ "Rat; Mammalian" "Neuronal ; Expression in E.coli" Cytosol \ "Quantitative match to experiments" In-house "Exact GENESIS implementation" \ "Replicates original data " -9 -11 0 simundump group /kinetics/NOS 0 yellow black x 0 0 "" NOS \ /home2/bhalla/scripts/modules/neuroNOS_0.g 0 0 0 -19 -20 0 simundump kpool /kinetics/NOS/nNOS 0 0 0.5 0.5 0.5 0.5 0 0 1 0 \ /kinetics/geometry 27 yellow -15 -17 0 simundump kpool /kinetics/NOS/Ca-CaM_nNOS 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 33 yellow -17 -11 0 simundump kreac /kinetics/NOS/Ca-CaMbind-nNOS 0 3.25 0.05 "" white yellow -16 \ -14 0 simundump kreac /kinetics/NOS/nNOSbindArg 0 0.5 81 "" white yellow -18 -14 0 simundump kpool /kinetics/NOS/L-Arg 0 0 100 100 100 100 0 0 1 0 \ /kinetics/geometry 9 yellow -17 -17 0 simundump kreac /kinetics/NOS/k1 0 25 0 "" white yellow -20 -14 0 simundump kreac /kinetics/NOS/k3 0 19 0 "" white yellow -22 -14 0 simundump kpool /kinetics/NOS/OH.Arg 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 34 yellow -25 -11 0 simundump kpool /kinetics/NOS/nNOS.Cit+NO 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 62 yellow -21 -17 0 simundump kpool /kinetics/NOS/Cit 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 12 \ yellow -23 -17 0 simundump kpool /kinetics/NOS/NO 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 4 \ yellow -25 -17 0 simundump kreac /kinetics/NOS/k4 0 2.7 0 "" white yellow -22 -20 0 simundump kpool /kinetics/NOS/nNOS.OH.Arg 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 27 yellow -21 -11 0 simundump kpool /kinetics/NOS/nNOS.arg 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ 6 yellow -19 -11 0 simundump kreac /kinetics/NOS/k2 0 4.4 0 "" white yellow -24 -14 0 simundump kpool /kinetics/NOS/CaM-Ca4 1 0 0 0 0 0 0 0 1 0 /kinetics/geometry \ blue yellow -15 -11 0 simundump xgraph /graphs/conc1 0 0 400 -0.05 0.05 0 simundump xgraph /graphs/conc2 0 0 400 0 0.0015779 0 simundump xplot /graphs/conc2/CaM-Ca4.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xgraph /moregraphs/conc3 0 0 400 99.666 100 0 simundump xgraph /moregraphs/conc4 0 0 400 0 0.27092 0 simundump xplot /moregraphs/conc3/L-Arg.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 9 0 0 1 simundump xplot /moregraphs/conc4/nNOS.OH.Arg.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 27 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 -27 2 -22 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 \ "Incorporated basal dephosph of " \ "neurogranin which gives around 20%" \ "phosph at basal PKC activity." \ "Deleted CONSERVE msg from Ca to" \ "itself." addmsg /kinetics/NOS/Ca-CaMbind-nNOS /kinetics/NOS/nNOS REAC A B addmsg /kinetics/NOS/Ca-CaMbind-nNOS /kinetics/NOS/Ca-CaM_nNOS REAC B A addmsg /kinetics/NOS/nNOSbindArg /kinetics/NOS/Ca-CaM_nNOS REAC A B addmsg /kinetics/NOS/Ca-CaM_nNOS /kinetics/NOS/Ca-CaMbind-nNOS PRODUCT n addmsg /kinetics/NOS/nNOS /kinetics/NOS/Ca-CaMbind-nNOS SUBSTRATE n addmsg /kinetics/NOS/CaM-Ca4 /kinetics/NOS/Ca-CaMbind-nNOS SUBSTRATE n addmsg /kinetics/NOS/L-Arg /kinetics/NOS/nNOSbindArg SUBSTRATE n addmsg /kinetics/NOS/nNOS.arg /kinetics/NOS/nNOSbindArg PRODUCT n addmsg /kinetics/NOS/Ca-CaM_nNOS /kinetics/NOS/nNOSbindArg SUBSTRATE n addmsg /kinetics/NOS/nNOSbindArg /kinetics/NOS/L-Arg REAC A B addmsg /kinetics/NOS/nNOS.arg /kinetics/NOS/k1 SUBSTRATE n addmsg /kinetics/NOS/nNOS.OH.Arg /kinetics/NOS/k1 PRODUCT n addmsg /kinetics/NOS/nNOS.OH.Arg /kinetics/NOS/k3 SUBSTRATE n addmsg /kinetics/NOS/nNOS.Cit+NO /kinetics/NOS/k3 PRODUCT n addmsg /kinetics/NOS/k2 /kinetics/NOS/OH.Arg REAC B A addmsg /kinetics/NOS/k3 /kinetics/NOS/nNOS.Cit+NO REAC B A addmsg /kinetics/NOS/k4 /kinetics/NOS/nNOS.Cit+NO REAC A B addmsg /kinetics/NOS/k4 /kinetics/NOS/Cit REAC B A addmsg /kinetics/NOS/k4 /kinetics/NOS/NO REAC B A addmsg /kinetics/NOS/nNOS.Cit+NO /kinetics/NOS/k4 SUBSTRATE n addmsg /kinetics/NOS/Cit /kinetics/NOS/k4 PRODUCT n addmsg /kinetics/NOS/NO /kinetics/NOS/k4 PRODUCT n addmsg /kinetics/NOS/k2 /kinetics/NOS/nNOS.OH.Arg REAC A B addmsg /kinetics/NOS/k3 /kinetics/NOS/nNOS.OH.Arg REAC A B addmsg /kinetics/NOS/k1 /kinetics/NOS/nNOS.OH.Arg REAC B A addmsg /kinetics/NOS/nNOSbindArg /kinetics/NOS/nNOS.arg REAC B A addmsg /kinetics/NOS/k1 /kinetics/NOS/nNOS.arg REAC A B addmsg /kinetics/NOS/nNOS.OH.Arg /kinetics/NOS/k2 SUBSTRATE n addmsg /kinetics/NOS/OH.Arg /kinetics/NOS/k2 PRODUCT n addmsg /kinetics/NOS/Ca-CaMbind-nNOS /kinetics/NOS/CaM-Ca4 REAC A B addmsg /kinetics/NOS/CaM-Ca4 /graphs/conc2/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue addmsg /kinetics/NOS/L-Arg /moregraphs/conc3/L-Arg.Co PLOT Co *L-Arg.Co *9 addmsg /kinetics/NOS/nNOS.OH.Arg /moregraphs/conc4/nNOS.OH.Arg.Co PLOT Co *nNOS.OH.Arg.Co *27 addmsg /kinetics/NOS/NO /moregraphs/conc4/NO.Co PLOT Co *NO.Co *4 enddump // End of dump call /kinetics/doqcsinfo/notes LOAD \ "This model is based on Iwanaga T et al. Biochemistry (1999) 38(50):16629-35.The model features the catalytic activity of neuronal Nitric Oxide Synthase expressed in Escherichia coli in a four step reaction mechanism. The rates found in the model are used directly from their paper and have been determined from experiments performed at 25 C." call /kinetics/NOS/nNOS/notes LOAD \ "neuronal Nitric Oxide Synthase." \ "Found in the neurons, activity is dependent on CaM binding," \ "in response to Ca levels." \ "" \ "Molecular weight ~160 kDa." \ "" call /kinetics/NOS/Ca-CaM_nNOS/notes LOAD \ "The CaM-Ca bound nNOS, which is the acitve form." call /kinetics/NOS/Ca-CaMbind-nNOS/notes LOAD \ "Those binding CaM have a high Kd, including nNOS, ~ <=10 nM." \ "Calcium mediated nNOS activity is required for NO synthesis." \ "Rates from experiments...The binding of CaM to NOS has been " \ "demonstrated to act as the trigger necessary for electron " \ "transfer and catalytic activity.(Marletta, Biochemistry," \ "1997;36:12337-12345)" \ "" call /kinetics/NOS/nNOSbindArg/notes LOAD \ "from Stuehr et al., Biochem,1999,38(38):12446-12451." \ "Steuhr et al., from stopped flow expts of sub binding to nNOS report" \ "0.5 (k-1) and 81 (k2)." \ "" \ "rates used straight from results." \ "" call /kinetics/NOS/L-Arg/notes LOAD \ "The intracellular concentrations are atleast 100 uM." \ "Substrate for nNOS." call /kinetics/NOS/k1/notes LOAD \ "Rates from Iwanaga et al., Biochem, 1999;38(50):16629-16635." \ "Obtained from rapid quenching expts at 25 C." \ "" \ ">>>>>> 25 +/- 2.0 " call /kinetics/NOS/k3/notes LOAD \ "Rate from Biochem., 1999, 38(50), 16629-16635." \ "Obtained from rapid queching expts at 25 C" \ "" \ ">>>>>> 19 +/- 3.0" call /kinetics/NOS/nNOS.Cit+NO/notes LOAD \ "Citrulline and NO basically dissociate from the NOS enzyme " \ "complex, and this is the NOS bound with Citrulline and NO, and" \ "they dissociate in the subsequent step." \ "" call /kinetics/NOS/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.)" call /kinetics/NOS/k4/notes LOAD \ "Rate from Biochem., 1999, 38(50), 16629-16635." \ "from rapid quenching expts at 25 C" \ "" \ ">>>>>> 2.7 +/- 0.3" call /kinetics/NOS/nNOS.OH.Arg/notes LOAD \ "This is the intermediate formed during the catalytic activity " \ "of NOS in synthesising NO, N-hydroxy arginine." call /kinetics/NOS/nNOS.arg/notes LOAD \ "Arginine binds to NOS first before the synthesis of NO from" \ "L-Arginine." call /kinetics/NOS/k2/notes LOAD \ "Rates from Biochem., 1999, 38(50), 16629-16635." \ "obtained from rapid quenching expts at 25 C...." \ "" \ ">>>>>> 4.4 +/- 0.5" complete_loading