// DOQCS : http://doqcs.ncbs.res.in/
// Accession Name = sGC_Stone_Marletta
// Accession Number = 15
// Transcriber = Sudhir Sivakumaran, NCBS
// Developer = Stone and Marletta, 1996.
// Species = Bovine
// Tissue = Lungs
// Cell Compartment = Cytosol
// Notes = This features the two step binding of NO to soluble Guanylyl Cyclase as proposed by Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9. There is a fast step binding scheme and a slow step binding scheme. The difference lies in the binding of a NO to a non-heme site on sGC, which may not necessarily be the same site of binding during the initial binding. The rates have been directly used from their models
//genesis
// kkit Version 11 flat dumpfile
// Saved on Wed Oct 18 11:13:52 2006
include kkit {argv 1}
FASTDT = 1e-05
SIMDT = 0.0001
CONTROLDT = 1
PLOTDT = 0.1
MAXTIME = 10
TRANSIENT_TIME = 3
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 17 \
-3 0
simundump doqcsinfo /kinetics/doqcsinfo 0 db15.g sGC_Stone_Marletta pathway \
"Sudhir Sivakumaran, NCBS" " Stone and Marletta, 1996." "citation here" \
Bovine Lungs Cytosol "Quantitative match to experiments" \
"Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9( Peer-reviewed publication )" \
"Mathematically equivalent" "Replicates original data " 17 -1 0
simundump group /kinetics/sGC 0 black black x 0 1 "" sGC \
/home2/bhalla/scripts/modules/defaultfile_0.g 0 0 0 18 -6 0
simundump kpool /kinetics/sGC/GTP 0 0 10 10 10 10 0 0 1 0 /kinetics/geometry \
cyan black 21 -8 0
simundump kpool /kinetics/sGC/NO.sGCfast 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 2 -9 0
simundump kpool /kinetics/sGC/NO.SGC_6coord 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 8 -9 0
simundump kpool /kinetics/sGC/sGCfast 0 0 3 3 3 3 0 0 1 0 /kinetics/geometry \
cyan black -4 -9 0
simundump kreac /kinetics/sGC/NO_bind_sGCfast 0 700 800 "" black black -3 -7 \
0
simundump kreac /kinetics/sGC/form_6coord 0 850 0 "" black black 3 -7 0
simundump kreac /kinetics/sGC/act_sGCfast 0 20 0.2 "" black black 10 -7 0
simundump kpool /kinetics/sGC/NO.sGC_5coord 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 15 -8 0
simundump kpool /kinetics/sGC/sGCtot 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \
cyan black 17 -10 0
simundump kenz /kinetics/sGC/sGCtot/kenz 0 0 0 0 0 1 6.3125 101 25.25 0 0 "" \
black black "" 19 -10 0
simundump kpool /kinetics/sGC/NO.sGC5accord 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 19 -13 0
simundump kreac /kinetics/sGC/act_sGCslow 0 1.6 0.02 "" black black 14 -14 0
simundump kreac /kinetics/sGC/NObindnonheme 0 5 25 "" black black 9 -14 0
simundump kpool /kinetics/sGC/nonhemebind_int 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 15 -12 0
simundump kpool /kinetics/sGC/NO.sGC6coord 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 8 -12 0
simundump kreac /kinetics/sGC/form6coord 0 850 0 "" black black 3 -14 0
simundump kreac /kinetics/sGC/NO_bind_sGCslow 0 700 800 "" black black -3 -14 \
0
simundump kpool /kinetics/sGC/NO.sGCslow 0 0 0 0 0 0 0 0 1 0 \
/kinetics/geometry cyan black 2 -12 0
simundump kpool /kinetics/sGC/sGCslow 0 0 3 3 3 3 0 0 1 0 /kinetics/geometry \
cyan black -4 -12 0
simundump kpool /kinetics/sGC/cGMP 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry \
cyan black 21 -12 0
simundump kpool /kinetics/sGC/NO 0 0 0 0 0 0 0 0 1 0 /kinetics/geometry cyan \
black 0 -10 0
simundump xgraph /graphs/conc1 0 0 2.1 0 3 0
simundump xgraph /graphs/conc2 0 0 5.4 -0.05 0.05 0
simundump xplot /graphs/conc1/sGCtot.Co 3 524288 \
"delete_plot.w ; edit_plot.D " 23 0 0 1
simundump xplot /graphs/conc1/sGCfast.Co 3 524288 \
"delete_plot.w ; edit_plot.D " cyan 0 0 1
simundump xplot /graphs/conc2/NO.sGCfast.Co 3 524288 \
"delete_plot.w ; edit_plot.D " cyan 0 0 1
simundump xgraph /moregraphs/conc3 0 0 2.5 0 10 0
simundump xgraph /moregraphs/conc4 0 0 2.8 0 3 0
simundump xplot /moregraphs/conc3/cGMP.Co 3 524288 \
"delete_plot.w ; edit_plot.D " cyan 0 0 1
simundump xplot /moregraphs/conc3/GTP.Co 3 524288 \
"delete_plot.w ; edit_plot.D " 10 0 0 1
simundump xplot /moregraphs/conc4/NO.Co 3 524288 \
"delete_plot.w ; edit_plot.D " 4 0 0 1
simundump xplot /moregraphs/conc4/sGCslow.Co 3 524288 \
"delete_plot.w ; edit_plot.D " cyan 0 0 1
simundump xcoredraw /edit/draw 0 -6 23 -16 1
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 features the activation of sGC by NO, and the conversio" \
"of GTP to cGMP. This is based on Stone and Marletta, 1996, " \
"Biochemistry, 35(4):1093-1099. Rates used as directly from their paper" \
"and their exp results. The Km and Vmax for the enzyme from T.Bellamy" \
"(thru personal correspondence)." \
"This model incorporates the NO synthesis scheme from completed " \
"model." \
""
addmsg /kinetics/sGC/sGCtot/kenz /kinetics/sGC/GTP REAC sA B
addmsg /kinetics/sGC/NO_bind_sGCfast /kinetics/sGC/NO.sGCfast REAC B A
addmsg /kinetics/sGC/form_6coord /kinetics/sGC/NO.sGCfast REAC A B
addmsg /kinetics/sGC/form_6coord /kinetics/sGC/NO.SGC_6coord REAC B A
addmsg /kinetics/sGC/act_sGCfast /kinetics/sGC/NO.SGC_6coord REAC A B
addmsg /kinetics/sGC/NO_bind_sGCfast /kinetics/sGC/sGCfast REAC A B
addmsg /kinetics/sGC/sGCfast /kinetics/sGC/NO_bind_sGCfast SUBSTRATE n
addmsg /kinetics/sGC/NO.sGCfast /kinetics/sGC/NO_bind_sGCfast PRODUCT n
addmsg /kinetics/sGC/NO /kinetics/sGC/NO_bind_sGCfast SUBSTRATE n
addmsg /kinetics/sGC/NO.sGCfast /kinetics/sGC/form_6coord SUBSTRATE n
addmsg /kinetics/sGC/NO.SGC_6coord /kinetics/sGC/form_6coord PRODUCT n
addmsg /kinetics/sGC/NO.SGC_6coord /kinetics/sGC/act_sGCfast SUBSTRATE n
addmsg /kinetics/sGC/NO.sGC_5coord /kinetics/sGC/act_sGCfast PRODUCT n
addmsg /kinetics/sGC/act_sGCfast /kinetics/sGC/NO.sGC_5coord REAC B A
addmsg /kinetics/sGC/sGCtot/kenz /kinetics/sGC/sGCtot REAC eA B
addmsg /kinetics/sGC/NO.sGC_5coord /kinetics/sGC/sGCtot SUMTOTAL n nInit
addmsg /kinetics/sGC/NO.sGC5accord /kinetics/sGC/sGCtot SUMTOTAL n nInit
addmsg /kinetics/sGC/sGCtot /kinetics/sGC/sGCtot/kenz ENZYME n
addmsg /kinetics/sGC/GTP /kinetics/sGC/sGCtot/kenz SUBSTRATE n
addmsg /kinetics/sGC/act_sGCslow /kinetics/sGC/NO.sGC5accord REAC B A
addmsg /kinetics/sGC/nonhemebind_int /kinetics/sGC/act_sGCslow SUBSTRATE n
addmsg /kinetics/sGC/NO.sGC5accord /kinetics/sGC/act_sGCslow PRODUCT n
addmsg /kinetics/sGC/NO.sGC6coord /kinetics/sGC/NObindnonheme SUBSTRATE n
addmsg /kinetics/sGC/nonhemebind_int /kinetics/sGC/NObindnonheme PRODUCT n
addmsg /kinetics/sGC/NO /kinetics/sGC/NObindnonheme SUBSTRATE n
addmsg /kinetics/sGC/NObindnonheme /kinetics/sGC/nonhemebind_int REAC B A
addmsg /kinetics/sGC/act_sGCslow /kinetics/sGC/nonhemebind_int REAC A B
addmsg /kinetics/sGC/form6coord /kinetics/sGC/NO.sGC6coord REAC B A
addmsg /kinetics/sGC/NObindnonheme /kinetics/sGC/NO.sGC6coord REAC A B
addmsg /kinetics/sGC/NO.sGCslow /kinetics/sGC/form6coord SUBSTRATE n
addmsg /kinetics/sGC/NO.sGC6coord /kinetics/sGC/form6coord PRODUCT n
addmsg /kinetics/sGC/sGCslow /kinetics/sGC/NO_bind_sGCslow SUBSTRATE n
addmsg /kinetics/sGC/NO.sGCslow /kinetics/sGC/NO_bind_sGCslow PRODUCT n
addmsg /kinetics/sGC/NO /kinetics/sGC/NO_bind_sGCslow SUBSTRATE n
addmsg /kinetics/sGC/NO_bind_sGCslow /kinetics/sGC/NO.sGCslow REAC B A
addmsg /kinetics/sGC/form6coord /kinetics/sGC/NO.sGCslow REAC A B
addmsg /kinetics/sGC/NO_bind_sGCslow /kinetics/sGC/sGCslow REAC A B
addmsg /kinetics/sGC/sGCtot/kenz /kinetics/sGC/cGMP MM_PRD pA
addmsg /kinetics/sGC/NO_bind_sGCfast /kinetics/sGC/NO REAC A B
addmsg /kinetics/sGC/NO_bind_sGCslow /kinetics/sGC/NO REAC A B
addmsg /kinetics/sGC/NObindnonheme /kinetics/sGC/NO REAC A B
addmsg /kinetics/sGC/sGCtot /graphs/conc1/sGCtot.Co PLOT Co *sGCtot.Co *23
addmsg /kinetics/sGC/sGCfast /graphs/conc1/sGCfast.Co PLOT Co *sGCfast.Co *cyan
addmsg /kinetics/sGC/NO.sGCfast /graphs/conc2/NO.sGCfast.Co PLOT Co *NO.sGCfast.Co *cyan
addmsg /kinetics/sGC/cGMP /moregraphs/conc3/cGMP.Co PLOT Co *cGMP.Co *cyan
addmsg /kinetics/sGC/GTP /moregraphs/conc3/GTP.Co PLOT Co *GTP.Co *cyan
addmsg /kinetics/sGC/NO /moregraphs/conc4/NO.Co PLOT Co *NO.Co *4
addmsg /kinetics/sGC/sGCslow /moregraphs/conc4/sGCslow.Co PLOT Co *sGCslow.Co *cyan
enddump
// End of dump
call /kinetics/doqcsinfo/notes LOAD \
"This features the two step binding of NO to soluble Guanylyl Cyclase as proposed by" \
" Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9. There is a fast step binding scheme and a slow step binding scheme. The difference lies in the binding of a NO to a non-heme site on sGC, which may not necessarily be the same site of binding during the initial binding. The rates have been directly used from models."
call /kinetics/sGC/notes LOAD \
"This group features the binding reaction scheme as proposed by" \
"Stone and Marletta,1996, Biochemistry, 35(4):1093-1099. They" \
"report a two step binding step for the activation of sGC by NO." \
"Rates shown in the model are used directly from their experiments" \
"on stopped flow kinetics. "
call /kinetics/sGC/GTP/notes LOAD \
"Concentration 10 uM" \
"(Kuroda et al., J.Neurosci., 2001, 21(15):5693-5702 ;" \
"Bhalla and Iyengar, 1999, Science, 283:381-387)" \
""
call /kinetics/sGC/sGCfast/notes LOAD \
"Stone and Marletta, Biochemistry,35(4), 1996," \
"" \
"They have reported that the binding of sGC with NO occurs through two" \
"phases;a slow process and a fast process. 30% of the sGC binds " \
"quickly to NO; but the rest 70% goes through a slow process which" \
"involves the binding of another NO to an unidentified non-heme " \
"site on the protein, which seems to be not necessarily the same " \
"site used in the initial two step binding to the heme." \
"" \
"Stone and Marletta,1995,34;14668-14674;-- report that the native" \
"heme stoichiometry is 2 per heterodimer. spectrally only one" \
"type of heme is observed, indicating that both hemes are in " \
"similar environment. they conclude that each subunit of the " \
"heterodimer binds 1 equiv of heme at a site conserved between" \
"the two subunits." \
"" \
"Concentration 3 uM assumed on the basis of reported data" \
"(Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ;" \
"Ariano et al., PNAS, 1982, 79:1316-1320)" \
"" \
"" \
"" \
""
call /kinetics/sGC/NO_bind_sGCfast/notes LOAD \
"This is the fast binding of NO to sGC, subsequently activating" \
"it, as proposed by Stone and Marletta." \
"" \
"Rates of these binding reactions used directly from Stone and" \
"Marletta,1996, Biochemistry, 35(4):1093-1099, " \
"based on whose paper this model is made. Rates obtained from" \
"stopped flow kinetics detailed in their paper."
call /kinetics/sGC/form_6coord/notes LOAD \
"Rates used directly from Stone and Marletta,1996,Biochemistry," \
"35(4):1093-1099."
call /kinetics/sGC/act_sGCfast/notes LOAD \
"Rates used directly from Stone and Marletta,1996,Biochemistry," \
"35(4):1093-1099."
call /kinetics/sGC/NO.sGC_5coord/notes LOAD \
"This is the active sGC, a 5-coordinate complex formed after a " \
"series of reaction steps, involving the formation of a " \
"6 coordinate complex which converted to a 5-coordinate complex."
call /kinetics/sGC/sGCtot/notes LOAD \
"This is the sumtotal of the sGC activated via two binding " \
"mecanisms as reported by Stone and Marletta, 1996, Biochemistry," \
"35(4):1093-1099."
call /kinetics/sGC/sGCtot/kenz/notes LOAD \
"The range of estimates found in the literature are:" \
"Km -> 40 - 150 uM (without NO)" \
" 20 - 40 uM (with NO)" \
"Vmax -> 10 - 100 nmol/mg/min (wihtout NO)" \
" 10 - 40 umol/mg/min (with NO)." \
"----- thru personal correspondence from T. Bellamy, Wolfson " \
"Ins. for Biomedical Sciences, UK." \
"NO increases the Vmax of sGC by 100-200 fold, and it has been " \
"proposed that this activation occurs subsequent to the binding " \
"of NO toa heme moiety on the enzyme. (Stone and Marletta,1995," \
"Biochemistry,34:14668-14674). "
call /kinetics/sGC/NO.sGC5accord/notes LOAD \
"This is the 5-coordinate complex of the enzyme sGC. This is" \
"also the active form of the enzyme."
call /kinetics/sGC/act_sGCslow/notes LOAD \
"Rates used directly from Stone and Marletta,1996, Biochemistry," \
"35(4):1093-1099."
call /kinetics/sGC/NObindnonheme/notes LOAD \
"This step is the one that differs from the fast reaction scheme," \
"as reported by Stone and Marletta. Here the reaction is dependent " \
"upon the binding of NO to an unidentified non-heme site on the" \
"protein." \
"" \
"Rates used directly from Stone and Marletta,1996, Biochemistry," \
"35(4):1093-1099."
call /kinetics/sGC/nonhemebind_int/notes LOAD \
"here the new NO has bound to the unidentified non-heme site on" \
"the 6-coordinate complex, and this will convert to the" \
"5-coordinate complex. this binding of a new NO to the non-heme " \
"site on the 6-coordinate complex is characteristic of the slow " \
"binding process of NO to sGC."
call /kinetics/sGC/NO.sGC6coord/notes LOAD \
"this compoud, a 6-coordinate complex will be bound by another NO" \
"to an unidentified non-heme site in the next reaction step."
call /kinetics/sGC/form6coord/notes LOAD \
"Rates used directly from Stone and Marletta,1996, Biochemistry," \
"35(4):1093-1099."
call /kinetics/sGC/NO_bind_sGCslow/notes LOAD \
"This is the slow binding of NO to sGC, as reported by Stone and " \
"Marletta,1996, Biochemistry, 35(4):1093-1099. " \
"The rates shown have been used directly from their data from" \
"stopped flow kinetics."
call /kinetics/sGC/sGCslow/notes LOAD \
"This is the slow reaction process of the binding of NO to sGC." \
"we can notice the binding of another NO in the third reaction " \
"step to a non-heme site, which then converts to the 5-coordinate" \
"complex. this binding of another NO to an non-heme site is" \
"characteristic of the slow binding process of NO to sGC.(Stone" \
"and Marletta, 1996,35(4);1093-1099)" \
"" \
"Concentration 3 uM assumed on the basis of reported data " \
"(Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ; " \
"Ariano et al., PNAS, 1982, 79:1316-1320.)"
call /kinetics/sGC/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.)"
complete_loading