//genesis
// kkit Version 8 flat dumpfile
 
// Saved on Mon Nov 12 18:58:06 2001
 
include kkit {argv 1}
 
FASTDT = 1e-05
SIMDT = 0.001
CONTROLDT = 1
PLOTDT = 0.1
MAXTIME = 600
TRANSIENT_TIME = 10
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/NOS 0 yellow black x 0 0 "" NOS \
  /home2/bhalla/scripts/modules/NOS_0.g 0 0 0 -30 -34 0
simundump kreac /kinetics/NOS/k3 0 104 0 "" white yellow -41 -28 0
simundump kreac /kinetics/NOS/k6 0 104 0 "" white yellow -41 -30 0
simundump kreac /kinetics/NOS/k5 0 3.6 0 "" white yellow -43 -32 0
simundump kpool /kinetics/NOS/FeIII_NO 0 0 0 0 0 0 0 0 1 0 "" 42 yellow -39 \
  -34 0
simundump kpool /kinetics/NOS/FeII-O2_a 0 0 0 0 0 0 0 0 1 0 "" 1 yellow -41 \
  -34 0
simundump kpool /kinetics/NOS/FeII_a 0 0 0 0 0 0 0 0 1 0 "" 26 yellow -43 -29 \
  0
simundump kpool /kinetics/NOS/FeIII_a 0 0 0 0 0 0 0 0 1 0 "" 51 yellow -41 \
  -25 0
simundump kpool /kinetics/NOS/CaM-Ca4 1 0 0 0 0 0 0 0 1 0 "" blue yellow -30 \
  -19 0
simundump kpool /kinetics/NOS/L-Arg 0 100 100 100 100 100 100 0 1 0 "" 9 \
  yellow -33 -22 0
simundump kpool /kinetics/NOS/FeIII 0 0 0 0 0 0 0 0 1 0 "" 57 yellow -35 -25 \
  0
simundump kpool /kinetics/NOS/FeII 0 0 0 0 0 0 0 0 1 0 "" 22 yellow -37 -25 0
simundump kpool /kinetics/NOS/FeII-O2 0 0 0 0 0 0 0 0 1 0 "" 29 yellow -39 \
  -25 0
simundump kpool /kinetics/NOS/nNOS 0 10 10 10 10 10 10 0 1 0 "" 27 yellow -30 \
  -30 0
simundump kreac /kinetics/NOS/Ca-CaMbind-nNOS 0 3.25 0.05 "" white yellow -30 \
  -23 0
simundump kpool /kinetics/NOS/Ca-CaM_nNOS 0 0 0 0 0 0 0 0 1 0 "" 33 yellow \
  -31 -27 0
simundump kreac /kinetics/NOS/arg_bind_nNOS 0 0.5 81 "" white yellow -33 -25 \
  0
simundump kpool /kinetics/NOS/O2 0 100 0.5 0.5 0.5 0.5 100 0 1 0 "" 4 yellow \
  -33 -27 0
simundump kpool /kinetics/NOS/NO3 0 0 0 0 0 0 0 0 1 0 "" 56 yellow -34 -34 0
simundump kpool /kinetics/NOS/FeII_NO 0 0 0 0 0 0 0 0 1 0 "" 62 yellow -36 \
  -34 0
simundump kreac /kinetics/NOS/k2 0 3.6 0 "" white yellow -39 -28 0
simundump kreac /kinetics/NOS/k1 0 10.4 0 "" white yellow -37 -28 0
simundump kreac /kinetics/NOS/kF 0 20 0 "" white yellow -35 -28 0
simundump kreac /kinetics/NOS/kG 0 10.4 0 "" white yellow -39 -30 0
simundump kreac /kinetics/NOS/k9 0 0.0004 0 "" white yellow -36 -30 0
simundump kreac /kinetics/NOS/k10 0 1.2 0 "" white yellow -34 -30 0
simundump kreac /kinetics/NOS/k4 0 10.4 0 "" white yellow -43 -26 0
simundump xgraph /graphs/conc1 0 0 600 0 0.68446 1
simundump xgraph /graphs/conc2 0 0 600 0 0.02648 1
simundump xplot /graphs/conc1/FeIII_NO.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 42 0 0 1
simundump xplot /graphs/conc1/Ca-CaM.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 57 0 0 1
simundump xplot /graphs/conc1/FeII_NO.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 62 0 0 1
simundump xplot /graphs/conc2/FeIII.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 57 0 0 1
simundump xplot /graphs/conc2/FeII.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 22 0 0 1
simundump xplot /graphs/conc2/CaM-Ca4.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" blue 0 0 1
simundump xgraph /moregraphs/conc3 0 0 600 0 0.026471 1
simundump xgraph /moregraphs/conc4 0 0 600 0 0.50003 1
simundump xplot /moregraphs/conc3/FeII-O2_a.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 1 0 0 1
simundump xplot /moregraphs/conc3/FeII_a.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 26 0 0 1
simundump xplot /moregraphs/conc3/FeIII_a.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 51 0 0 1
simundump xplot /moregraphs/conc4/FeII-O2.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 29 0 0 1
simundump xplot /moregraphs/conc4/NO3.Co 3 524288 \
  "delete_plot.w <s> <d>; edit_plot.D <w>" 56 0 0 1
simundump xcoredraw /edit/draw 0 -45 -25 -36 -5.1448
simundump xtree /edit/draw/tree 0 \
  /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \
  "edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>" auto 0.6
simundump xtext /file/notes 0 1
xtextload /file/notes \
"NO synthesis by NOS (nNOS) in the mammalian brain." \
"model based on Stuehr et al., JBC, 2001;276(2):1233-1243." \
"Rates used from the literature, increased by 2X for every 10 C rise," \
"to get the rates at the cell temperature. " \
"" \
"" \
"Incorporated basal dephosph of " \
"neurogranin which gives around 20%" \
"phosph at basal PKC activity." \
"Deleted CONSERVE msg from Ca to" \
"itself."
addmsg /kinetics/NOS/FeII-O2 /kinetics/NOS/k3 SUBSTRATE n 
addmsg /kinetics/NOS/FeIII_a /kinetics/NOS/k3 PRODUCT n 
addmsg /kinetics/NOS/FeII-O2_a /kinetics/NOS/k6 SUBSTRATE n 
addmsg /kinetics/NOS/FeIII_NO /kinetics/NOS/k6 PRODUCT n 
addmsg /kinetics/NOS/FeII_a /kinetics/NOS/k5 SUBSTRATE n 
addmsg /kinetics/NOS/FeII-O2_a /kinetics/NOS/k5 PRODUCT n 
addmsg /kinetics/NOS/k6 /kinetics/NOS/FeIII_NO REAC B A 
addmsg /kinetics/NOS/kG /kinetics/NOS/FeIII_NO REAC A B 
addmsg /kinetics/NOS/kF /kinetics/NOS/FeIII_NO REAC A B 
addmsg /kinetics/NOS/k5 /kinetics/NOS/FeII-O2_a REAC B A 
addmsg /kinetics/NOS/k6 /kinetics/NOS/FeII-O2_a REAC A B 
addmsg /kinetics/NOS/k4 /kinetics/NOS/FeII_a REAC B A 
addmsg /kinetics/NOS/k5 /kinetics/NOS/FeII_a REAC A B 
addmsg /kinetics/NOS/k3 /kinetics/NOS/FeIII_a REAC B A 
addmsg /kinetics/NOS/k4 /kinetics/NOS/FeIII_a REAC A B 
addmsg /kinetics/NOS/Ca-CaMbind-nNOS /kinetics/NOS/CaM-Ca4 REAC A B 
addmsg /kinetics/NOS/arg_bind_nNOS /kinetics/NOS/L-Arg REAC A B 
addmsg /kinetics/NOS/k1 /kinetics/NOS/FeIII REAC A B 
addmsg /kinetics/NOS/k10 /kinetics/NOS/FeIII REAC B A 
addmsg /kinetics/NOS/kF /kinetics/NOS/FeIII REAC B A 
addmsg /kinetics/NOS/arg_bind_nNOS /kinetics/NOS/FeIII REAC B A 
addmsg /kinetics/NOS/k1 /kinetics/NOS/FeII REAC B A 
addmsg /kinetics/NOS/k2 /kinetics/NOS/FeII REAC A B 
addmsg /kinetics/NOS/k9 /kinetics/NOS/FeII REAC B A 
addmsg /kinetics/NOS/k2 /kinetics/NOS/FeII-O2 REAC B A 
addmsg /kinetics/NOS/k3 /kinetics/NOS/FeII-O2 REAC A B 
addmsg /kinetics/NOS/Ca-CaMbind-nNOS /kinetics/NOS/nNOS REAC A B 
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/Ca-CaM_nNOS /kinetics/NOS/Ca-CaMbind-nNOS PRODUCT n 
addmsg /kinetics/NOS/arg_bind_nNOS /kinetics/NOS/Ca-CaM_nNOS REAC A B 
addmsg /kinetics/NOS/Ca-CaMbind-nNOS /kinetics/NOS/Ca-CaM_nNOS REAC B A 
addmsg /kinetics/NOS/L-Arg /kinetics/NOS/arg_bind_nNOS SUBSTRATE n 
addmsg /kinetics/NOS/FeIII /kinetics/NOS/arg_bind_nNOS PRODUCT n 
addmsg /kinetics/NOS/Ca-CaM_nNOS /kinetics/NOS/arg_bind_nNOS SUBSTRATE n 
addmsg /kinetics/NOS/k10 /kinetics/NOS/O2 REAC A B 
addmsg /kinetics/NOS/k10 /kinetics/NOS/NO3 REAC B A 
addmsg /kinetics/NOS/kG /kinetics/NOS/FeII_NO REAC B A 
addmsg /kinetics/NOS/k9 /kinetics/NOS/FeII_NO REAC A B 
addmsg /kinetics/NOS/k10 /kinetics/NOS/FeII_NO REAC A B 
addmsg /kinetics/NOS/FeII /kinetics/NOS/k2 SUBSTRATE n 
addmsg /kinetics/NOS/FeII-O2 /kinetics/NOS/k2 PRODUCT n 
addmsg /kinetics/NOS/FeIII /kinetics/NOS/k1 SUBSTRATE n 
addmsg /kinetics/NOS/FeII /kinetics/NOS/k1 PRODUCT n 
addmsg /kinetics/NOS/FeIII_NO /kinetics/NOS/kF SUBSTRATE n 
addmsg /kinetics/NOS/FeIII /kinetics/NOS/kF PRODUCT n 
addmsg /kinetics/NOS/FeIII_NO /kinetics/NOS/kG SUBSTRATE n 
addmsg /kinetics/NOS/FeII_NO /kinetics/NOS/kG PRODUCT n 
addmsg /kinetics/NOS/FeII_NO /kinetics/NOS/k9 SUBSTRATE n 
addmsg /kinetics/NOS/FeII /kinetics/NOS/k9 PRODUCT n 
addmsg /kinetics/NOS/FeII_NO /kinetics/NOS/k10 SUBSTRATE n 
addmsg /kinetics/NOS/FeIII /kinetics/NOS/k10 PRODUCT n 
addmsg /kinetics/NOS/NO3 /kinetics/NOS/k10 PRODUCT n 
addmsg /kinetics/NOS/O2 /kinetics/NOS/k10 SUBSTRATE n 
addmsg /kinetics/NOS/FeIII_a /kinetics/NOS/k4 SUBSTRATE n 
addmsg /kinetics/NOS/FeII_a /kinetics/NOS/k4 PRODUCT n 
addmsg /kinetics/NOS/FeIII_NO /graphs/conc1/FeIII_NO.Co PLOT Co *FeIII_NO.Co *42 
addmsg /kinetics/NOS/CaM-Ca4 /graphs/conc1/Ca-CaM.Co PLOT Co *Ca-CaM.Co *57 
addmsg /kinetics/NOS/FeII_NO /graphs/conc1/FeII_NO.Co PLOT Co *FeII_NO.Co *62 
addmsg /kinetics/NOS/FeIII /graphs/conc2/FeIII.Co PLOT Co *FeIII.Co *57 
addmsg /kinetics/NOS/FeII /graphs/conc2/FeII.Co PLOT Co *FeII.Co *22 
addmsg /kinetics/NOS/CaM-Ca4 /graphs/conc2/CaM-Ca4.Co PLOT Co *CaM-Ca4.Co *blue 
addmsg /kinetics/NOS/FeII-O2_a /moregraphs/conc3/FeII-O2_a.Co PLOT Co *FeII-O2_a.Co *1 
addmsg /kinetics/NOS/FeII_a /moregraphs/conc3/FeII_a.Co PLOT Co *FeII_a.Co *26 
addmsg /kinetics/NOS/FeIII_a /moregraphs/conc3/FeIII_a.Co PLOT Co *FeIII_a.Co *51 
addmsg /kinetics/NOS/FeII-O2 /moregraphs/conc4/FeII-O2.Co PLOT Co *FeII-O2.Co *29 
addmsg /kinetics/NOS/NO3 /moregraphs/conc4/NO3.Co PLOT Co *NO3.Co *56 
enddump
// End of dump

call /kinetics/NOS/k3/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2):1233-1243" \
"" \
"rates increased by 2X for every 10 C rise, to get it ot the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 104"
call /kinetics/NOS/k6/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2): 1233-1243" \
"The transformation rate of FeII-O2_a to FeIII_NO was 26 /s." \
"rates increased by 2X for every 10 C to get it to the cell temp..." \
"(thru personal correspondence)" \
"" \
"kf -- 104" \
""
call /kinetics/NOS/k5/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2):1233-1243" \
"" \
"rates increased by 2X for every 10 C rise to get it to the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 3.6" \
""
call /kinetics/NOS/L-Arg/notes LOAD \
"The intracellular concentrations are atleast 100 uM."
call /kinetics/NOS/nNOS/notes LOAD \
"neuronal Nitric Oxide Synthase." \
"Found in neurons, activity dependent on CaM binding," \
"in response to Ca levels." \
"" \
"molecular weight ~160 kDa." \
""
call /kinetics/NOS/Ca-CaMbind-nNOS/notes LOAD \
"Those binding CaM have a high Kd, including nNOS, ~ <= 10 nM." \
"" \
"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/arg_bind_nNOS/notes LOAD \
"" \
"from Stuehr et al., Biochem, 1999, 38(38):12446-12451." \
"Rates used as it is from their results."
call /kinetics/NOS/k2/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2):1233-1243" \
"" \
"rates increased by 2X for every 10 C rise, to get it ot the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 3.6" \
""
call /kinetics/NOS/k1/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2):1233-1243." \
"All the rates increased by 2X for every 10 C rise to get it to" \
"the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 10.4" \
""
call /kinetics/NOS/kF/notes LOAD \
"rates from Stuehr et al., JBC, 2001; 276(2): 1233-1243." \
"" \
"rates increased by 2X for every 10 C rise, to get it ot the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 20" \
""
call /kinetics/NOS/kG/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2): 1233-1243.." \
"" \
"rates increased by 2X for every 10 C rise, to get it to the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 10.4" \
""
call /kinetics/NOS/k9/notes LOAD \
"rates from Stuehr et al., 2001, JBC 276(2): 1233-1243.." \
"" \
"rates increased by 2X for every 10 C rise, to get it to the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 0.0004" \
""
call /kinetics/NOS/k10/notes LOAD \
"The rates were obtained from Stuehr et al, JBC 2001, 276(2):" \
"1233-1243...." \
"" \
"The rates are multiplied by 2X for every 10 C rise, to get it" \
"to the cell temp." \
"" \
"kf -- 0.0052" \
""
call /kinetics/NOS/k4/notes LOAD \
"rates from Stuehr et al., 2001, JBC, 276(2):1233-1243" \
"" \
"rates increased by 2X for every 10 C rise to get it to the cell temp.." \
"(thru personal correspondence)" \
"" \
"kf -- 10.4" \
""
complete_loading