//genesis // kkit Version 11 flat dumpfile // Saved on Mon Aug 7 16:10:22 2006 include kkit {argv 1} FASTDT = 2e-07 SIMDT = 4e-07 CONTROLDT = 0.001 PLOTDT = 0.001 MAXTIME = 0.1 TRANSIENT_TIME = 2 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 simobjdump text str simundump geometry /kinetics/geometry 0 1.6667e-21 3 sphere "" white black 3 \ 7 0 simundump kpool /kinetics/Im-nNOS 0 0 1 1 1 1 0 0 1 0 /kinetics/geometry blue \ black -4 6 0 simundump kreac /kinetics/Imidazole_release 0 42 0.2 "" white black 1 -2 0 simundump kpool /kinetics/Imidazole 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry 46 \ black -4 -4 0 simundump kpool /kinetics/Homoarginine 0 0 6000 6000 6000 6000 0 0 1 0 \ /kinetics/geometry 8 black 6 6 0 simundump kreac /kinetics/Homoarginine_binding 0 25 2.5e+05 "" white black 1 \ 4 0 simundump kpool /kinetics/Im-nNOS-Homoarginine 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 25 black 1 1 0 simundump kpool /kinetics/nNOS-Homoarginine 0 0 0 0 0 0 0 0 1 0 \ /kinetics/geometry 0 black 5 -4 0 simundump doqcsinfo /kinetics/doqcsinfo 0 \ Homoarginine.g HomoArginine pathway \ "Sharat J. Vayttaden and Prasoon Agarwal, NCBS" "Abu-Soud HM, Wang J, Rousseau DL, and Stuehr DJ" "" human \ "Kidney cell expressing the rat brain nNOS" Cytosol \ "Quantitative match to experiments" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication )" \ "Exact GENESIS implementation" "Approximates original data " 1 7 0 simundump xgraph /graphs/conc1 0 0 0.1 0 0.7 0 simundump xgraph /graphs/conc2 0 0 0.1 0 0.4 0 simundump xplot /graphs/conc1/Im-nNOS.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc2/Im-nNOS-Homoarginine.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 25 0 0 1 simundump xgraph /moregraphs/conc3 0 0 0.1 0 0.8 0 simundump xgraph /moregraphs/conc4 0 0 0.1 0 1 0 simundump xplot /moregraphs/conc3/Homoarginine.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 8 0 0 1 simundump xplot /moregraphs/conc3/Imidazole.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 46 0 0 1 simundump xplot /moregraphs/conc4/nNOS-Homoarginine.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 0 0 0 1 simundump xcoredraw /edit/draw 0 -6 8 -6 9 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 \ "Model shows the substrate (Homorginine) binding to nNOS " \ "in a two-step reversible fashion. First there is rapid " \ "binding equilibrium between Im-nNOS and Homoarginine to" \ "form an intermediate that contains bound imidazole and" \ "homoarginine. This is followed by a slower conformational" \ "change in the Im-enzyme-substrate complex that is associated" \ "with release of bound imidazole and generation of a" \ "modified enzyme-substrate complex which is detected" \ "due to spectral change." \ "" \ "Rates approximated based on data in Table 2." \ "The rates for first reaction are not exact since only" \ "Kd known and appropriate graphs do not exist for matching the" \ "kinetic profile." \ " " \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" addmsg /kinetics/Homoarginine_binding /kinetics/Im-nNOS REAC A B addmsg /kinetics/Im-nNOS-Homoarginine /kinetics/Imidazole_release SUBSTRATE n addmsg /kinetics/nNOS-Homoarginine /kinetics/Imidazole_release PRODUCT n addmsg /kinetics/Imidazole /kinetics/Imidazole_release PRODUCT n addmsg /kinetics/Imidazole_release /kinetics/Imidazole REAC B A addmsg /kinetics/Homoarginine_binding /kinetics/Homoarginine REAC A B addmsg /kinetics/Homoarginine /kinetics/Homoarginine_binding SUBSTRATE n addmsg /kinetics/Im-nNOS /kinetics/Homoarginine_binding SUBSTRATE n addmsg /kinetics/Im-nNOS-Homoarginine /kinetics/Homoarginine_binding PRODUCT n addmsg /kinetics/Homoarginine_binding /kinetics/Im-nNOS-Homoarginine REAC B A addmsg /kinetics/Imidazole_release /kinetics/Im-nNOS-Homoarginine REAC A B addmsg /kinetics/Imidazole_release /kinetics/nNOS-Homoarginine REAC B A addmsg /kinetics/Im-nNOS /graphs/conc1/Im-nNOS.Co PLOT Co *Im-nNOS.Co *blue addmsg /kinetics/Im-nNOS-Homoarginine /graphs/conc2/Im-nNOS-Homoarginine.Co PLOT Co *Im-nNOS-Homoarginine.Co *25 addmsg /kinetics/Homoarginine /moregraphs/conc3/Homoarginine.Co PLOT Co *Homoarginine.Co *8 addmsg /kinetics/Imidazole /moregraphs/conc3/Imidazole.Co PLOT Co *Imidazole.Co *46 addmsg /kinetics/nNOS-Homoarginine /moregraphs/conc4/nNOS-Homoarginine.Co PLOT Co *nNOS-Homoarginine.Co *0 enddump // End of dump call /kinetics/Im-nNOS/notes LOAD \ "Imidazole bound rat brain neuronal Nitric Oxide Synthase" \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/Imidazole_release/notes LOAD \ "Release of Imidazole from complex of " \ "Homoarginine and Imidazole bound rat brain" \ "neuronal Nitric Oxide Synthase." \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/Imidazole/notes LOAD \ "Imidazole released from the neuronal Nitric Oxide Synthase" \ "complexed to Homoarginine." \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/Homoarginine/notes LOAD \ "Homoarginine, an alternative substrate for " \ "neuronal Nitric Oxide Synthase" \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/Homoarginine_binding/notes LOAD \ "Binding of Homoarginine to Imidazole bound rat brain" \ "neuronal Nitric Oxide Synthase." \ "" \ "Only Kd is known, Kf and Kb need to be approximated" \ "accordingly to match kinetic profiles. Due to lack of " \ "appropriate graphs the choice of Kf and Kb here is " \ "arbitrary and matches only the Kd." \ "" \ "Kd = 10mM = 10000uM" \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/Im-nNOS-Homoarginine/notes LOAD \ "An intermediate formed due to rapid binding of Homoarginine " \ "to Imidazole bound neuronal Nitric Oxide Synthase." \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/nNOS-Homoarginine/notes LOAD \ "Homoarginine bound to neuronal Nitric Oxide Synthase." \ "" \ "Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" call /kinetics/doqcsinfo/notes LOAD \ "This model is taken from the Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51" \ "This model shows kinetic binding of HomoArginine to neuronal nitric oxide synthase."\ " " \ "Model shows the substrate (Homorginine) binding to nNOS " \ "in a two-step reversible fashion. First there is rapid " \ "binding equilibrium between Im-nNOS and Homoarginine to" \ "form an intermediate that contains bound imidazole and" \ "homoarginine. This is followed by a slower conformational" \ "change in the Im-enzyme-substrate complex that is associated" \ "with release of bound imidazole and generation of a" \ "modified enzyme-substrate complex which is detected" \ "due to spectral change." \ "" \ "Rates approximated based on data in Table 2." \ "The rates for first reaction are not exact since only" \ "Kd known and appropriate graphs do not exist for matching the" \ "kinetic profile." complete_loading