//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