//  DOQCS : http://doqcs.ncbs.res.in/ 
//  Accession Name = NonOsc_Ca_IP3metabolism 
//  Accession Number = 31 
//  Transcriber = Jyoti Mishra, NCBS 
//  Developer = Jyoti Mishra, NCBS 
//  Species = Generic mammalian 
//  Tissue = Brain - Neuronal 
//  Cell Compartment = Cytosol 
//  Notes =  This network models detailed metabolism of Ins(145)P3, integrated with GPCR mediated PLCbeta activation and Ca release by the InsP3 receptor in the neuron. It is similar to the NonOsc_Ca_IP3metab model (accession 23) except that some enzymes have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. These modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12202356&query_hl=5"> Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316</a>. 
 
 //genesis
// kkit Version 11 flat dumpfile
 
// Saved on Thu Dec  8 15:07:16 2005
 
include kkit {argv 1}
 
FASTDT = 1e-05
SIMDT = 0.0002
CONTROLDT = 1
PLOTDT = 1
MAXTIME = 1000
TRANSIENT_TIME = 10
VARIABLE_DT_FLAG = 0
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
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simundump geometry /kinetics/geometry[1] 0 1e-15 3 sphere "" white black 9 23 \
  0
simundump geometry /kinetics/geometry[2] 0 1e-13 3 sphere "" white black 23 \
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simundump group /kinetics/MIPP 0 blue black x 1 0 "" defaultfile \
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simundump kpool /kinetics/MIPP/IP5(12456)_ER 0 0 0 0 0 0 0 0 96000 0 \
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simundump kpool /kinetics/MIPP/IP5(13456)_ER 0 0 0 0 0 0 0 0 96000 0 \
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simundump kpool /kinetics/MIPP/IP4(1456)_ER 0 0 0 0 0 0 0 0 96000 0 \
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simundump kpool /kinetics/MIPP/MIPP 0 0 0.398 0.398 38208 38208 0 0 96000 0 \
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simundump kenz /kinetics/MIPP/MIPP/ip6_pase 0 0 0 0 0 1 0.0022917 0.0528 \
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simundump group /kinetics/CaMKII 1 purple black x 1 0 "" defaultfile \
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simundump kpool /kinetics/CaMKII/CaMKII-CaM 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kpool /kinetics/CaMKII/CaMKII-thr286*-CaM 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kpool /kinetics/CaMKII/CaMKII*** 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kreac /kinetics/CaMKII/CaMKII-bind-CaM 1 8.3333e-05 5 "" white \
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simundump kreac /kinetics/CaMKII/CaMK-thr286-bind-CaM 1 0.001667 0.1 "" white \
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simundump kpool /kinetics/CaMKII/CaMKII-thr286 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kpool /kinetics/CaMKII/CaMK-thr306 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kpool /kinetics/CaMKII/total-CaMKII 1 0 70 70 4.2e+07 4.2e+07 0 0 \
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simundump kreac /kinetics/CaMKII/basal-activity 1 0.003 0 "" white purple \
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simundump kpool /kinetics/CaMKII/tot_CaM_CaMKII 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kenz /kinetics/CaMKII/tot_CaM_CaMKII/CaM_act_305 1 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/tot_CaM_CaMKII/CaM_act_286 1 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/tot_CaM_CaMKII/CaM-CaMK-phos 0 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/tot_CaM_CaMKII/CaM-CaMK-phos1 0 0 0 0 0 6e+05 \
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simundump kpool /kinetics/CaMKII/tot_autonomous_CaMKII 1 0 0 0 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/tot_autonomous_CaMKII/auton_305 1 0 0 0 0 \
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simundump kenz /kinetics/CaMKII/tot_autonomous_CaMKII/auton_286 1 0 0 0 0 \
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simundump kenz /kinetics/CaMKII/tot_autonomous_CaMKII/CaMK-phos 0 0 0 0 0 \
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simundump kenz /kinetics/CaMKII/tot_autonomous_CaMKII/CaMK-phos1 0 0 0 0 0 \
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simundump kpool /kinetics/CaMKII/PP1-active 1 0 1.8 1.8 1.08e+06 1.08e+06 0 0 \
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simundump kenz /kinetics/CaMKII/PP1-active/Deph-thr286 1 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/PP1-active/Deph-thr305 1 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/PP1-active/Deph-thr306 1 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/PP1-active/Deph-thr286c 1 0 0 0 0 6e+05 \
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simundump kenz /kinetics/CaMKII/PP1-active/Deph_thr286b 1 0 0 0 0 6e+05 \
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simundump group /kinetics/CaM 1 blue black x 1 0 "" defaultfile \
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simundump kpool /kinetics/CaM/CaM 1 0 20 20 1.2e+07 1.2e+07 0 0 6e+05 0 \
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simundump kreac /kinetics/CaM/CaM-TR2-bind-Ca 1 2e-10 72 "" white blue \
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simundump kreac /kinetics/CaM/CaM-TR2-Ca2-bind-Ca 1 6e-06 10 "" white blue \
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simundump kreac /kinetics/CaM/CaM-Ca3-bind-Ca 1 7.75e-07 10 "" white blue \
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simundump kpool /kinetics/CaM/CaM-Ca4 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kpool /kinetics/CaM/CaM-Ca3 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump kpool /kinetics/CaM/CaM-TR2-Ca2 1 0 0 0 0 0 0 0 6e+05 0 \
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simundump group /kinetics/PKC 0 blue black x 1 0 "" defaultfile \
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simundump kreac /kinetics/PKC/PKC-act-by-Ca 0 1e-06 0.5 "" white blue 22.304 \
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simundump kreac /kinetics/PKC/PKC-act-by-DAG 0 1.3333e-08 8.6348 "" white \
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simundump kreac /kinetics/PKC/PKC-Ca-to-memb 0 1.2705 3.5026 "" white blue \
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simundump kreac /kinetics/PKC/PKC-DAG-to-memb 0 1 0.1 "" white blue 23.763 \
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simundump kreac /kinetics/PKC/PKC-act-by-Ca-AA 0 2e-09 0.1 "" white blue \
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simundump kreac /kinetics/PKC/PKC-act-by-DAG-AA 0 2 0.2 "" white blue 27.628 \
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simundump kpool /kinetics/PKC/PKC-DAG-AA* 0 0 4.9137e-18 4.9137e-18 \
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addmsg /kinetics/IHP-system/IP5-dipp-inhib /kinetics/IHP-system/IP5-DIPPcmplx REAC B A 
addmsg /kinetics/IHP-system/ATP /kinetics/IHP-system/PP-IP5cmplx-on SUBSTRATE n 
addmsg /kinetics/IHP-system/PP-IP5 /kinetics/IHP-system/PP-IP5cmplx-on SUBSTRATE n 
addmsg /kinetics/IHP-system/PP-IP5-K /kinetics/IHP-system/PP-IP5cmplx-on SUBSTRATE n 
addmsg /kinetics/IHP-system/PP-IP5-K-complex /kinetics/IHP-system/PP-IP5cmplx-on PRODUCT n 
addmsg /kinetics/IHP-system/PP-IP5-K-complex /kinetics/IHP-system/PP-IP5cmplx-off SUBSTRATE n 
addmsg /kinetics/IHP-system/ADP /kinetics/IHP-system/PP-IP5cmplx-off PRODUCT n 
addmsg /kinetics/IHP-system/bisPP-IP4 /kinetics/IHP-system/PP-IP5cmplx-off PRODUCT n 
addmsg /kinetics/IHP-system/PP-IP5-K /kinetics/IHP-system/PP-IP5cmplx-off PRODUCT n 
addmsg /kinetics/IHP-system/PP-IP5cmplx-on /kinetics/IHP-system/PP-IP5-K-complex REAC B A 
addmsg /kinetics/IHP-system/PP-IP5cmplx-off /kinetics/IHP-system/PP-IP5-K-complex REAC A B 
addmsg /kinetics/IHP-system/IP6cmplx-on /kinetics/IHP-system/IP6-K-complex REAC B A 
addmsg /kinetics/IHP-system/IP6cmplx-off /kinetics/IHP-system/IP6-K-complex REAC A B 
addmsg /kinetics/IHP-system/IP6-K-complex /kinetics/IHP-system/IP6cmplx-off SUBSTRATE n 
addmsg /kinetics/IHP-system/PP-IP5 /kinetics/IHP-system/IP6cmplx-off PRODUCT n 
addmsg /kinetics/IHP-system/ADP /kinetics/IHP-system/IP6cmplx-off PRODUCT n 
addmsg /kinetics/IHP-system/IP6-K /kinetics/IHP-system/IP6cmplx-off PRODUCT n 
addmsg /kinetics/IHP-system/IP6 /kinetics/IHP-system/IP6cmplx-on SUBSTRATE n 
addmsg /kinetics/IHP-system/ATP /kinetics/IHP-system/IP6cmplx-on SUBSTRATE n 
addmsg /kinetics/IHP-system/IP6-K /kinetics/IHP-system/IP6cmplx-on SUBSTRATE n 
addmsg /kinetics/IHP-system/IP6-K-complex /kinetics/IHP-system/IP6cmplx-on PRODUCT n 
addmsg /kinetics/IHP-system/PP-IP5cmplx-on /kinetics/IHP-system/PP-IP5-K REAC A B 
addmsg /kinetics/IHP-system/PP-IP5cmplx-off /kinetics/IHP-system/PP-IP5-K REAC B A 
addmsg /kinetics/IHP-system/IP6cmplx-on /kinetics/IHP-system/IP6-K REAC A B 
addmsg /kinetics/IHP-system/IP6cmplx-off /kinetics/IHP-system/IP6-K REAC B A 
addmsg /kinetics/IHP-system/IP6-K/ip5_k1 /kinetics/IHP-system/IP6-K REAC eA B 
addmsg /kinetics/IHP-system/IP6-K/pp-ip4-k1 /kinetics/IHP-system/IP6-K REAC eA B 
addmsg /kinetics/IHP-system/IP6-K /kinetics/IHP-system/IP6-K/ip5_k1 ENZYME n 
addmsg /kinetics/IP4-system/IP5(13456) /kinetics/IHP-system/IP6-K/ip5_k1 SUBSTRATE n 
addmsg /kinetics/IHP-system/IP6-K /kinetics/IHP-system/IP6-K/pp-ip4-k1 ENZYME n 
addmsg /kinetics/IHP-system/PP-IP4 /kinetics/IHP-system/IP6-K/pp-ip4-k1 SUBSTRATE n 
addmsg /kinetics/1345_dephos/1345_3pase /kinetics/1345_dephos/IP5-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/IP5-3pase-cmplx /kinetics/1345_dephos/IP5-inhib-3pase PRODUCT n 
addmsg /kinetics/IP4-system/IP5(13456) /kinetics/1345_dephos/IP5-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/IP5-inhib-3pase /kinetics/1345_dephos/IP5-3pase-cmplx REAC B A 
addmsg /kinetics/1345_dephos/1345_3pase /kinetics/1345_dephos/IP6-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/IP6-inhib-3pase-cmplx /kinetics/1345_dephos/IP6-inhib-3pase PRODUCT n 
addmsg /kinetics/IHP-system/IP6 /kinetics/1345_dephos/IP6-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/1345_3pase /kinetics/1345_dephos/145-inhib-3pase SUBSTRATE n 
addmsg /kinetics/IP3-3K/IP3(145) /kinetics/1345_dephos/145-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/IP3(145)-3pase-cmplx /kinetics/1345_dephos/145-inhib-3pase PRODUCT n 
addmsg /kinetics/IP4-system/IP4(3456) /kinetics/1345_dephos/IP4-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/1345_3pase /kinetics/1345_dephos/IP4-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/IP4-3pase-cmplx /kinetics/1345_dephos/IP4-inhib-3pase PRODUCT n 
addmsg /kinetics/1345_dephos/1345_3pase /kinetics/1345_dephos/134-inhib-3pase SUBSTRATE n 
addmsg /kinetics/IP4-system/IP3(134) /kinetics/1345_dephos/134-inhib-3pase SUBSTRATE n 
addmsg /kinetics/1345_dephos/IP3(134)-3pase-cmplx /kinetics/1345_dephos/134-inhib-3pase PRODUCT n 
addmsg /kinetics/1345_dephos/IP4-inhib-3pase /kinetics/1345_dephos/IP4-3pase-cmplx REAC B A 
addmsg /kinetics/1345_dephos/145-inhib-3pase /kinetics/1345_dephos/IP3(145)-3pase-cmplx REAC B A 
addmsg /kinetics/1345_dephos/134-inhib-3pase /kinetics/1345_dephos/IP3(134)-3pase-cmplx REAC B A 
addmsg /kinetics/1345_dephos/IP6-inhib-3pase /kinetics/1345_dephos/IP6-inhib-3pase-cmplx REAC B A 
addmsg /kinetics/1345_dephos/134-inhib-3pase /kinetics/1345_dephos/1345_3pase REAC A B 
addmsg /kinetics/1345_dephos/145-inhib-3pase /kinetics/1345_dephos/1345_3pase REAC A B 
addmsg /kinetics/1345_dephos/IP4-inhib-3pase /kinetics/1345_dephos/1345_3pase REAC A B 
addmsg /kinetics/1345_dephos/IP5-inhib-3pase /kinetics/1345_dephos/1345_3pase REAC A B 
addmsg /kinetics/1345_dephos/IP6-inhib-3pase /kinetics/1345_dephos/1345_3pase REAC A B 
addmsg /kinetics/1345_dephos/1345_3pase/ip4_3pase /kinetics/1345_dephos/1345_3pase REAC eA B 
addmsg /kinetics/1345_dephos/1345_3pase /kinetics/1345_dephos/1345_3pase/ip4_3pase ENZYME n 
addmsg /kinetics/IP3-3K/IP4(1345) /kinetics/1345_dephos/1345_3pase/ip4_3pase SUBSTRATE n 
addmsg /kinetics/IHP-system/bisPP-IP4 /graphs/conc1/bisPP-IP4.Co PLOT Co *bisPP-IP4.Co *7 
addmsg /kinetics/IHP-system/PP-IP5 /graphs/conc1/PP-IP5.Co PLOT Co *PP-IP5.Co *52 
addmsg /kinetics/IHP-system/PP-IP4 /graphs/conc1/PP-IP4.Co PLOT Co *PP-IP4.Co *pink 
addmsg /kinetics/IHP-system/IP6 /graphs/conc1/IP6.Co PLOT Co *IP6.Co *39 
addmsg /kinetics/IP4-system/IP5(13456) /graphs/conc1/IP5(13456).Co PLOT Co *IP5(13456).Co *0 
addmsg /kinetics/CaRegulation/Ca-sequester /graphs/conc1/Ca-sequester.Co PLOT Co *Ca-sequester.Co *red 
addmsg /kinetics/IP3-3K/IP4(1345) /graphs/conc2/IP4(1345).Co PLOT Co *IP4(1345).Co *46 
addmsg /kinetics/IP4-system/IP4(3456) /graphs/conc2/IP4(3456).Co PLOT Co *IP4(3456).Co *61 
addmsg /kinetics/IP4-system/IP4(1456) /graphs/conc2/IP4(1456).Co PLOT Co *IP4(1456).Co *1 
addmsg /kinetics/IP4-system/IP4(1346) /graphs/conc2/IP4(1346).Co PLOT Co *IP4(1346).Co *34 
addmsg /kinetics/IP3-3K/IP3(145) /moregraphs/conc3/IP3(145).Co PLOT Co *IP3(145).Co *53 
addmsg /kinetics/IP4-system/IP3(134) /moregraphs/conc3/IP3(134).Co PLOT Co *IP3(134).Co *62 
addmsg /kinetics/134_dephos/IP2(13) /moregraphs/conc3/IP2(13).Co PLOT Co *IP2(13).Co *cyan 
addmsg /kinetics/134_dephos/IP2(34) /moregraphs/conc3/IP2(34).Co PLOT Co *IP2(34).Co *26 
addmsg /kinetics/145_dephos/IP2(14) /moregraphs/conc3/IP2(14).Co PLOT Co *IP2(14).Co *18 
addmsg /kinetics/CaRegulation/Ca /moregraphs/conc4/Ca.Co PLOT Co *Ca.Co *61 
addmsg /kinetics/145_dephos/IP1(4) /moregraphs/conc4/IP1(4).Co PLOT Co *IP1(4).Co *34 
addmsg /kinetics/134_dephos/IP1(3) /moregraphs/conc4/IP1(3).Co PLOT Co *IP1(3).Co *7 
addmsg /kinetics/134_dephos/IP1(1) /moregraphs/conc4/IP1(1).Co PLOT Co *IP1(1).Co *1 
enddump
// End of dump

call /kinetics/MIPP/notes LOAD \
"Model for Multiple Inositol Polyphosphate Phosphatase. Primary refs:" \
"Nogimori et al, JBC 266, 1991: 16499-506; Chi et al, MCB 20, 2000:" \
"6496-507"
call /kinetics/MIPP/ip6_trp/notes LOAD \
"InsP6 ER-cytosol transport. Rate based on cytosolic levels of " \
"InsP6. ER-cytosol transport for other inositol phosphates are" \
"assigned the same rate as of now, as exact transport rates are " \
"not known."
call /kinetics/MIPP/ip5(12456)_trp/notes LOAD \
"Ins(12456)P5 ER-cytosol transport"
call /kinetics/MIPP/ip5(13456)_trp/notes LOAD \
"Ins(13456)P5 ER-cytosol transport"
call /kinetics/MIPP/ip4(1456)_trp/notes LOAD \
"Ins(1456)P4 ER-cytosol transport"
call /kinetics/MIPP/ip4(1345)_trp/notes LOAD \
"Ins(1345)P4 ER-cytosol transport"
call /kinetics/MIPP/ip3(145)_trp/notes LOAD \
"Ins(145)P3 ER-cytosol transport"
call /kinetics/MIPP/MIPP/notes LOAD \
"Multiple Inositol Polyphosphate Phosphatase" \
"from Nogimori et al, JBC 266(25); 1991: 16499-506" \
"" \
"MIPP clustered in ER. Distinct transporters present for cytosolic " \
"substrates. Accounts for 30-45% of total 3-phosphatase activity " \
"against substrates, hence cytosolic counterparts of this enzyme " \
"must be present (as per Chi et al, MCB 20; 2000: 6496-507)                                     "
call /kinetics/MIPP/MIPP/ip5_3pase/notes LOAD \
"Ins(13456)P5 3-phosphatase" \
"from Nogimori et al, JBC 266; 1991"
call /kinetics/MIPP/MIPP/ip4_3pase/notes LOAD \
"Ins(1345)P4 3-phosphatase" \
"from Nogimori et al, JBC 266; 1991"
call /kinetics/MIPP/MIPP/ip6_pase/notes LOAD \
"InsP6 2/3-phosphatase" \
"from Nogimori et al, JBC 266; 1991"
call /kinetics/MIPP/IP5(12456)/notes LOAD \
"Inositol(12456)pentakisphosphate" \
"Conc = 4% of total InsP5"
call /kinetics/CaMKII/notes LOAD \
"Main reference here is the review by Hanson and Schulman, Ann Rev Biochem" \
"1992 vol 61 pp 559-601. Most of the mechanistic details and a few constants" \
"are derived from there. Many kinetics are from Hanson and Schulman JBC" \
"267:24 17216-17224 1992." \
"The enzymes look a bit complicated." \
"Actually it is just 3 reactions for different sites," \
"by 4 states of CaMKII, defined by the phosphorylation state." \
"This model approximates the fact that the enzyme is actually present as" \
"a decamer/dodecamer. It does so by treating the autophosphorylation reactions" \
"as being independent of the concentration of CaMKII. Also the rates for" \
"the autophosphorylation steps have been scaled to fit this " \
"approximation. "
call /kinetics/CaMKII/CaMKII/notes LOAD \
"Huge concentration of CaMKII. In PSD it is 20-40% of protein," \
" so we assume it is around" \
"2.5% of protein in spine as a whole. This level is so high it is unlikely to" \
" matter much if we are off a bit. This comes to about 70 uM." \
"Seen the review:" \
"Hanson and Schulman 1992 Ann. Rev. Biuochem 60:559-601"
call /kinetics/CaMKII/CaMKII-CaM/notes LOAD \
"This is the regular, CaM-activated form of CaMKII." \
"See the review" \
"Hanson and Schulman 1992 Ann. Rev. Biochem 60:559-601"
call /kinetics/CaMKII/CaMKII-thr286*-CaM/notes LOAD \
"From Hanson and Schulman, the thr286 is responsible for autonomous activation" \
"of CaMKII."
call /kinetics/CaMKII/CaMKII***/notes LOAD \
"From Hanson and Schulman, the CaMKII does a lot of autophosphorylation" \
"just after the CaM is released. This prevents further CaM binding and renders" \
"the enzyme quite independent of Ca."
call /kinetics/CaMKII/CaMKII-bind-CaM/notes LOAD \
"This is tricky. There is some cooperativity here arising from interactions" \
"between the subunits of the CAMKII holoenzyme. However, the" \
"stoichiometry is 1. " \
"Kd = 0.1 uM. Rate is fast (see Hanson et al Neuron 12 943-956 1994)" \
"Hanson and Schulman 1992 AnnRev Biochem 61:559-601" \
"give tau for dissoc as 0.2 sec at low Ca, 0.4 at high." \
"Low Ca = 100 nM = physiol."
call /kinetics/CaMKII/CaMK-thr286-bind-CaM/notes LOAD \
"Affinity is up 1000X over the unphosphorylated CaMKII, which makes the" \
"Kd of 0.1 nM. See Hanson et al 1994 Neuron 12:943-956." \
"Time to release is about 20 sec, so the kb is OK at 0.1/sec." \
"as tested by a few runs." \
""
call /kinetics/CaMKII/CaMKII-thr286/notes LOAD \
"The threonine-286 phosphorylated form of CaMKII. It is likely" \
"to be a short-lived intermediate, since it will be phosphorylated further" \
"as soon as the CAM falls off."
call /kinetics/CaMKII/CaMK-thr306/notes LOAD \
"This forms due to basal autophosphorylation, but I think it has to be" \
"considered as a pathway even if some CaM is floating around. In either" \
"case it will tend to block further binding of CaM, and will not display any" \
"enzyme activity. See Hanson and Schulman JBC 267:24 pp17216-17224 1992"
call /kinetics/CaMKII/total-CaMKII/notes LOAD \
"This pool is purely here to provide a single, fixed number," \
"which is the total amount of CaMKII. This is used by the" \
"autophosphorylation steps to scale down the rates so that the" \
"autophosphorylation reactions are independent of CaMKII levels."
call /kinetics/CaMKII/basal-activity/notes LOAD \
"This reaction represents one of the unknowns in CaMK-II" \
"biochemistry: what maintains the basal level of phosphorylation" \
"on thr 286 ? See Hanson and Schulman Ann Rev Biochem 1992" \
"61:559-601, specially pg 580, for review. I have not been able to" \
"find any compelling mechanism in the literature, but fortunately" \
"the level of basal activity is well documented. " \
"Lisman et al propose that the levels of PP1 are very low in the " \
"postsynaptic density, and PP2A is excluded from the PSD, and this would" \
"lead to autophosphorylation at a sustained level."
call /kinetics/CaMKII/tot_CaM_CaMKII/notes LOAD \
"This pool sums the levels of the CaM-bound forms of CaMKII:" \
"CaMKII-CaM + CaMKII-thr286*-CaM. Although their phosphorylation states" \
"are different, the level of activity is about the same so it makes sense" \
"to sum the levels." \
"Hanson et al 1994 Neuron 12:943-956"
call /kinetics/CaMKII/tot_CaM_CaMKII/CaM_act_305/notes LOAD \
"Rates from autocamtide phosphorylation, from " \
"Hanson and Schulman JBC 267:24 17216-17224 1992. See especially Fig 5."
call /kinetics/CaMKII/tot_CaM_CaMKII/CaM_act_286/notes LOAD \
"See Hanson and Schulman 1992 JBC 267(24):17216-17224"
call /kinetics/CaMKII/tot_CaM_CaMKII/CaM-CaMK-phos/notes LOAD \
"rates referred from standard CaM-CaMKII phosphorylation rates"
call /kinetics/CaMKII/tot_CaM_CaMKII/CaM-CaMK-phos1/notes LOAD \
"rates referred from standard CaM-CaMKII phosphorylation rates"
call /kinetics/CaMKII/tot_autonomous_CaMKII/notes LOAD \
"This is the sum total of the various CaM-independent forms of the " \
"kinase. There are actually several possible states here, but I only" \
"consider the forms thr-286 phosphorylated form and the doubly/triply" \
"phosphorylated form including the thr305/306, represented here" \
"as CaMKII***" \
""
call /kinetics/CaMKII/tot_autonomous_CaMKII/auton_305/notes LOAD \
"See Hanson and Schulman 1992 JBC 267(24):17216-17224" \
"for afterburst rates of phosphorylation"
call /kinetics/CaMKII/tot_autonomous_CaMKII/auton_286/notes LOAD \
"The autonomous rate has a slightly higher Km than the CaM-bound rate," \
"but Vmax is the same." \
"Hanson and Schulman 1992 Ann Rev Biochem 61:559-601" \
"and " \
"Hanson and Schulman 1992 JBC 267(24):17216-17224"
call /kinetics/CaMKII/tot_autonomous_CaMKII/CaMK-phos/notes LOAD \
"rates referred from standard CaMKII phosphorylation rates"
call /kinetics/CaMKII/tot_autonomous_CaMKII/CaMK-phos1/notes LOAD \
"rates referred from standard CaMKII phosphorylation rates"
call /kinetics/CaMKII/PP1-active/notes LOAD \
"Cohen et al Meth Enz 159 390-408 is main source of info" \
"concentration of enzyme = 1.8 uM"
call /kinetics/CaMKII/PP1-active/Deph-thr286/notes LOAD \
"The rates are from Stralfors et al Eur J Biochem 149 295-303 giving" \
"Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14." \
"Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so" \
"k1 becomes 5.72e-6" \
"Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates" \
"are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10" \
"to 5.72e-7, 1.4, 0.35. " \
"This gives the final Km of 5.1, and Vmax of 0.35/sec."
call /kinetics/CaMKII/PP1-active/Deph-thr305/notes LOAD \
"Dephosphorylation tempkin are assumed to be the same for all" \
"phosphorylation sites on CaMKII. " \
"The rates are from Stralfors et al Eur J Biochem 149 295-303 giving" \
"Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14." \
"Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so" \
"k1 becomes 5.72e-6" \
"Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates" \
"are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10" \
"to 5.72e-7, 1.4, 0.35. " \
"This gives the final Km of 5.1, and Vmax of 0.35/sec."
call /kinetics/CaMKII/PP1-active/Deph-thr306/notes LOAD \
"Dephosphorylation tempkin are assumed to be the same for all" \
"phosphorylation sites on CaMKII. " \
"The rates are from Stralfors et al Eur J Biochem 149 295-303 giving" \
"Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14." \
"Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so" \
"k1 becomes 5.72e-6" \
"Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates" \
"are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10" \
"to 5.72e-7, 1.4, 0.35. " \
"This gives the final Km of 5.1, and Vmax of 0.35/sec."
call /kinetics/CaMKII/PP1-active/Deph-thr286c/notes LOAD \
"Dephosphorylation tempkin are assumed to be the same for all" \
"phosphorylation sites on CaMKII. " \
"The rates are from Stralfors et al Eur J Biochem 149 295-303 giving" \
"Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14." \
"Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so" \
"k1 becomes 5.72e-6" \
"Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates" \
"are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10" \
"to 5.72e-7, 1.4, 0.35. " \
"This gives the final Km of 5.1, and Vmax of 0.35/sec."
call /kinetics/CaMKII/PP1-active/Deph_thr286b/notes LOAD \
"Rates are assumed to be the same for all phosphorylation sites" \
"on CaMKII. " \
"The rates are from Stralfors et al Eur J Biochem 149 295-303 giving" \
"Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14." \
"Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so" \
"k1 becomes 5.72e-6" \
"Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates" \
"are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10" \
"to 5.72e-7, 1.4, 0.35. " \
"This gives the final Km of 5.1, and Vmax of 0.35/sec."
call /kinetics/CaM/notes LOAD \
"This is the basic Ca-binding-to-CaM model." \
"Main data sources are " \
"Forsen et al 1986 Calcium and Cell funciton VI 113_157" \
"Drabikowski and Brzeska 1982 JBC 257(19):11584-11590" \
"Martin et al 1985 Eur J Biochem 151(3):543-550" \
"Stemmer and Klee 1994 Biochem 33:6859-6866" \
"Data is pretty thorough."
call /kinetics/CaM/CaM/notes LOAD \
"LOT of this present in the cell: upto 1% of total protein mass. " \
"(Alberts et al, Mol Biol of the Cell, Garland Publishers) says " \
"25 uM. Meyer et al, Science 256; 1992: 1199-1202 refer to " \
"studies saying it is comparable to CaMK levels." \
"(Kakiuchi et al, J Biochem 92; 1982; 1041-48) say conc in " \
"cerebral cortex & cerebellum homogenates: 20-30uM" \
"Lower conc in other tissues: lung, adrenal gland, liver, " \
"kidney, spleen = 6,5,5,3,2 uM respectively"
call /kinetics/CaM/CaM-TR2-bind-Ca/notes LOAD \
"We use the Martin et al 1985 Eur J Biochem 151(3):543-550 rates here, " \
"plus the Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 binding consts." \
"All are scaled by 3X to cell temperature." \
"kf = 2e-10 kb = 72" \
"Stemmer & Klee 1994 Biochem 33:6859-6866 have values of : K1=.9, K2=1.1." \
"Assume 1.0uM for both" \
""
call /kinetics/CaM/CaM-TR2-Ca2-bind-Ca/notes LOAD \
"Stemmer and Klee 1994 Biochem 33:6859-6866" \
"K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get" \
"kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10" \
""
call /kinetics/CaM/CaM-Ca3-bind-Ca/notes LOAD \
"Use K3 = 21.5 uM here from Stemmer and Klee table 3." \
"Stemmer and Klee 1994 Biochem 33:6859-6866" \
"kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10"
call /kinetics/CaM/CaM-Ca4/notes LOAD \
"The four-calcium-bound form of CaM. It is the active form for most" \
"reactions."
call /kinetics/CaM/CaM-Ca3/notes LOAD \
"The TR1 end now begins to bind Ca. This form has 2 Ca's on the" \
"TR2 end, and one on the TR1."
call /kinetics/CaM/CaM-TR2-Ca2/notes LOAD \
"This is the intermediate where the TR2 end (the high-affinity end) has" \
"bound the Ca but the TR1 end has not."
call /kinetics/PKC/notes LOAD \
"Protein Kinase C. This module represents a weighted average of" \
"the alpha, beta and gamma isoforms. It takes inputs from" \
"Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid)." \
"Regulation parameters are largely from Schaechter and Benowitz" \
"1993 J Neurosci 13(10):4361 who use synaptosomes from" \
"mammalian brain and in one paper look at all three inputs." \
"Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source" \
"of data and helps to tighten the DAG inputs. " \
"General reviews include Azzi et al 1992 Eur J Bioch 208:541" \
"and Nishizuka 1988, Nature 334:661" \
"Concentration info from Kikkawa et al 1982 JBC 257(22):13341" \
"The process of parameterization is described in detail" \
"in several places. See Supplementary notes to " \
"Bhalla and Iyengar 1999 Science 284:92-96, available at the site" \
"http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html" \
"The parameterization is also described in a book chapter:" \
"Bhalla, 2000: Simulations of Biochemical Signaling in" \
"Computational Neuroscience: Realistic Modeling for Experimentalists." \
"Ed. E. De Schutter. CRC Press." \
""
call /kinetics/PKC/PKC-act-by-Ca/notes LOAD \
"This Kd is a straightforward result from the Schaechter and Benowitz" \
"1993 J Neurosci 13(10):4361 curves. The time-course is based on the" \
"known rapid activation of PKC and also the fact that Ca association" \
"with proteins is typically quite fast. My guess is that this tau of" \
"2 sec is quite conservative and the actualy rate may be much faster." \
"The parameter is quite insensitive for most stimuli." \
"" \
""
call /kinetics/PKC/PKC-act-by-DAG/notes LOAD \
"Ca.PKC interaction with DAG is modeled by this reaction." \
"Kf based on Shinomura et al PNAS 88 5149-5153 1991 and" \
"Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and uses" \
"the constraining procedure referred to in the general" \
"notes for PKC."
call /kinetics/PKC/PKC-Ca-to-memb/notes LOAD \
"Membrane translocation is a standard step in PKC activation." \
"It also turns out to be necessary to replicate the curves" \
"from Schaechter and Benowitz 1993 J Neurosci 13(10):4361" \
"and Shonomura et al 1991 PNAS 88:5149-5153. These rates" \
"are constrained by matching the curves in the above papers and" \
"by fixing a rather fast (sub-second) tau for PKC activation."
call /kinetics/PKC/PKC-DAG-to-memb/notes LOAD \
"membrane translocation step for Ca.DAG.PKC complex." \
"Rates constrained from Shinomura et al 1991 PNAS 88:5149-5153" \
" and Schaechter and Benowitz 1993 J Neurosci 13(10):4361" \
"as derived in the references cited in PKC general notes."
call /kinetics/PKC/PKC-act-by-Ca-AA/notes LOAD \
"Ca-dependent AA activation of PKC." \
"Note that this step combines the AA activation and also the " \
"membrane translocation." \
"From Schaechter and Benowitz 1993 J Neurosci 13(10):4361"
call /kinetics/PKC/PKC-act-by-DAG-AA/notes LOAD \
"Membrane translocation step for PKC-DAG-AA complex." \
"Rates from matching concentration-effect data in our" \
"two main references:" \
"Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and" \
"Shinomura et al 1988 PNAS 88: 5149-5153"
call /kinetics/PKC/PKC-DAG-AA*/notes LOAD \
"Membrane translocated form of PKC-DAG-AA complex."
call /kinetics/PKC/PKC-Ca-AA*/notes LOAD \
"Membrane bound and active complex of PKC, Ca and AA."
call /kinetics/PKC/PKC-Ca-memb*/notes LOAD \
"This is the direct Ca-stimulated activity of PKC."
call /kinetics/PKC/PKC-DAG-memb*/notes LOAD \
"Active, membrane attached form of Ca.DAG.PKC complex."
call /kinetics/PKC/PKC-basal*/notes LOAD \
"This is the basal PKC activity which contributes about" \
"2% to the maximum."
call /kinetics/PKC/PKC-basal-act/notes LOAD \
"Basal activity of PKC is quite high, about 10% of max." \
"See Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and" \
"Shinomura et al 1991 PNAS 88:5149-5153. This is partly due to" \
"basal levels of DAG, AA and Ca, but even when these are taken" \
"into account (see the derivations as per the PKC general notes)" \
"there is a small basal activity still to be accounted for. This" \
"reaction handles it by giving a 2% activity at baseline."
call /kinetics/PKC/PKC-AA*/notes LOAD \
"This is the membrane-bound and active form of the PKC-AA complex." \
""
call /kinetics/PKC/PKC-act-by-AA/notes LOAD \
"AA stimulates PKC activity even at rather low Ca." \
"Schaechter and Benowitz 1993 J Neurosci 13(10):4361" \
"Note that this one reaction combines the initial interaction" \
"and also membrane translocation."
call /kinetics/PKC/PKC-Ca-DAG/notes LOAD \
"This is the active PKC form involving Ca and DAG." \
"It has to translocate to the membrane."
call /kinetics/PKC/PKC-n-DAG/notes LOAD \
"Binding of PKC to DAG, non-Ca dependent." \
"" \
"Kf based on Shinomura et al PNAS 88 5149-5153 1991" \
"Tau estimated as fast and here it is about the same time-course" \
"as the formation of DAG so it will not be rate-limiting."
call /kinetics/PKC/PKC-DAG/notes LOAD \
"This is a DAG-bound intermediate used in synergistic activation" \
"of PKC by DAG and AA."
call /kinetics/PKC/PKC-n-DAG-AA/notes LOAD \
"This is one of the more interesting steps. Mechanistically" \
"it does not seem necessary at first glance. Turns out that" \
"one needs this step to quantitatively match the curves" \
"in Schaechter and Benowitz 1993 J Neurosci 13(10):4361" \
"and Shinomura et al 1991 PNAS 88:5149-5153. There is" \
"a synergy between DAG and AA activation even at low" \
"Ca levels, which is most simply represented by this reaction." \
"Tau is assumed to be fast." \
"Kd comes from matching the experimental curves."
call /kinetics/PKC/PKC-DAG-AA/notes LOAD \
"Complex of PKC, DAG and AA giving rise to synergistic" \
"activation of PKC by DAG and AA at resting Ca." \
""
call /kinetics/PKC/PKC-cytosolic/notes LOAD \
"Marquez et al J. Immun 149,2560(92) est 1e6/cell for chromaffin cells" \
"" \
"Kikkawa et al 1982 JBC 257(22):13341 have PKC levels in brain at " \
"about 1 uM." \
"" \
"The cytosolic form is the inactive PKC. This is really a composite" \
"of three isoforms: alpha, beta and gamma which have slightly" \
"different properties and respond to different combinations of" \
"Ca, AA and DAG."
call /kinetics/PKC/AA/notes LOAD \
"Arachidonic Acid. This messenger diffuses through membranes" \
"as well as cytosolically, has been suggested as a possible" \
"retrograde messenger at synapses. "
call /kinetics/PKC/PKC-Ca/notes LOAD \
"This intermediate is strongly indicated by the synergistic" \
"activation of PKC by combinations of DAG and Ca, as well" \
"as AA and Ca. PKC by definition also has a direct Ca-activation," \
"to which this also contributes."
call /kinetics/PKC/PKC-active/notes LOAD \
"This is the total active PKC. It is the sum of the respective" \
"activities of " \
"PKC-basal*" \
"PKC-Ca-memb*" \
"PKC-DAG-memb*" \
"PKC-Ca-AA*" \
"PKC-DAG-AA*" \
"PKC-AA*" \
"I treat PKC here in a two-state manner: Either it is in an active" \
"state (any one of the above list) or it is inactive. No matter what " \
"combination of stimuli activate the PKC, I treat it as having the same" \
"activity. The scaling comes in through the relative amounts of PKC" \
"which bind to the respecive stimuli." \
"The justification for this is the mode of action of PKC, which like" \
"most Ser/Thr kinases has a kinase domain normally bound to and blocked" \
"by a regulatory domain. I assume that all the activators simply free" \
"up the kinase domain." \
"A more general model would incorporate a different enzyme activity for" \
"each combination of activating inputs, as well as for each substrate." \
"The current model seems to be a decent and much simpler approximation" \
"for the available data." \
"One caveat of this way of representing PKC is that the summation" \
"procedure assumes that PKC does not saturate with its substrates. " \
"If this assumption fails, then the contributing PKC complexes would" \
"experience changes in availability which would affect their " \
"balance. Given the relatively low percentage of PKC usually activated," \
"and its high throughput as an enzyme, this is a safe assumption under" \
"physiological conditions." \
""
call /kinetics/PKC/PKC-active/PKC-phos/notes LOAD \
"rates referred from standard PKC phosphorylation rates"
call /kinetics/IP3-3K/notes LOAD \
"Model for Ins(145)P3 3-kinase. This includes enzyme activation by Ca-CaM" \
"and CaMKII and inactivation by PKC. We dont include PKA phosphorylation" \
"or enzyme dimerization effects. Primary refs: Johanson et al, JBC 263, 1988:" \
"7465-71; Communi et al, EMBOJ 16, 1997: 1943-52; Erneux et al, Biochem 214, " \
"1993: 497-501; Sim et al, JBC 265, 1990: 10367-72 "
call /kinetics/IP3-3K/IP3_3K/notes LOAD \
"from Johanson et al, JBC, 1988, Vol. 263, No.16, pp 7465-7471" \
"" \
"this is the predominant isoform in brain ie IP3-3kinaseA:" \
"BiochemJ, 1995, 306, 429-435"
call /kinetics/IP3-3K/IP3_3K/ip3-3k/notes LOAD \
"from Johanson et al, JBC 263; 1988" \
"Original Vmax scaled up by 50% to obtain value at 37C, as " \
"enzyme assay was done at 30C" \
"Km increased from 0.2 to 1.4 as per various other reports " \
"(Shears Review, BiochemJ 260; 1989)"
call /kinetics/IP3-3K/IP3_3K*1/notes LOAD \
"Sim et al; JBC 265(18) June 25; 1990: pp 10367-10372" \
"Phos. at 2 major sites = Ser109 & Ser 175; but there is a possibility " \
"that inactivation is due to combined effect of multiple phosphorylations" \
"activity suppressed by 75%" \
""
call /kinetics/IP3-3K/IP3_3K*1/ip3-3k*1/notes LOAD \
"from Sim et al, JBC 265; 1990"
call /kinetics/IP3-3K/IP3_3K*/notes LOAD \
"phosphorylation at thr311" \
"" \
"Communi et al, EMBO J 16; 1997"
call /kinetics/IP3-3K/IP3_3K*/ip3-3k*/notes LOAD \
"from Communi et al, EMBO J 16; 1997" \
"" \
"In absence of CaM binding, activity same as that of " \
"non-phosphorylated enzyme"
call /kinetics/IP3-3K/IP3_3K_CaM*/notes LOAD \
"8-10 fold activation with both CaM bound and CaMKII phosphorylation" \
"(phos at thr311)" \
"" \
"Communi et al; EMBO J 16 (8), pp 1943-1952, 1997"
call /kinetics/IP3-3K/IP3_3K_CaM/notes LOAD \
"2-2.5 fold increase in enzyme activity due to CaM binding" \
"CaM binding involves Trp165" \
"" \
"Erneux et al; Biochem 214, 497-501 (1993)"
call /kinetics/IP3-3K/3K-bind-CaM/notes LOAD \
"Communi et al, EMBO J 16; 1997" \
"" \
"non-phosphorylated 3kinase with low sensitivity to CaM binding" \
"(Kd = 52nM)"
call /kinetics/IP3-3K/3K*-bind-CaM/notes LOAD \
"Communi et al, EMBO J 16; 1997" \
"" \
"phosphorylated 3kinase has 25 fold greater sensitivity to CaM" \
"binding than the non-phosphorylated enzyme (Kd of 2nM)"
call /kinetics/IP3-3K/IP3(145)/notes LOAD \
"Inositol (145)trisphosphate"
call /kinetics/IP3-3K/3k-CaM*-on/notes LOAD \
"Rates from Km of enzyme" \
"Communi et al, EMBO J 16(8)"
call /kinetics/IP3-3K/3k-CaM*-off/notes LOAD \
"Kf = Vmax for enzyme (Communi et al, EMBO J 16(8)) " \
"Vmax is such that enzyme activity is 9 fold above basal." \
"Kb derived from Keq value when reaction free energy = " \
"-10 kJ/mol"
call /kinetics/IP3-3K/3kCaM*_ip3_cmplx/notes LOAD \
"Enzyme complex exclusively modeled as M-M kinetics do not hold." \
"Enzyme is reversible as per free energy calculations that yield a" \
"a significant back flux."
call /kinetics/IP3-3K/3kCaM_ip3_cmplx/notes LOAD \
"Enzyme complex exclusively modeled because enzymes is reversible," \
"unlike M-M enzymes. Reversibility determined from dG " \
"calculations."
call /kinetics/IP3-3K/3k-CaM-on/notes LOAD \
"rates from Km for enzyme: Erneux et al, Biochem 214; 1993" \
"Enzyme is 2-2.5 fold more active than ip3-3k, but Km is " \
"doubled." \
""
call /kinetics/IP3-3K/3k-CaM-off/notes LOAD \
"Kf = Vmax for enzyme: Erneux et al, Biochem 214; 1993" \
"Enzyme is 2-2.5 fold more active than basal enzyme." \
"Kb derived from equilibrium conditions for dG = -10 kJ/mol"
call /kinetics/IP3-3K/IP4(1345)/notes LOAD \
"Inositol(1345)tetrakisphosphate"
call /kinetics/CaRegulation/notes LOAD \
"Ca Regulation model used for the IP3metabolism network. It includes 3 " \
"compartments: extracellular, intracellular and the Ca stores. Ca pumps " \
"that pump out Ca from cytoplasm to extracellular space and into stores, " \
"are balanced by leak channels from the stores and extracellular space." \
"The IP3 receptor and capacitative entry channels drive Ca under influence of" \
"different stimuli. Model includes the Ca buffer - Calsequestrin in the stores." \
"The model is a little artificial on IP3R kinetics, and does not include the " \
"influence of Ca on IP3R." \
""
call /kinetics/CaRegulation/CaTraspATPase/notes LOAD \
"kCa3 = 2 * Ca transporter rate since each step has 2 Ca++. " \
"= 0.5 uM/sec from Lauffenburger and Linderman 1993 Receptors pg200" \
"The amount of the activated transporter is about 0.01 uM = 6e3#. " \
"from runs. So 0.01uM * kf * 2 = 0.5 uM/sec (no back reaction) so " \
"kf = 25, kb = 0" \
"Alternatively, 6e3 * kf = 0.25 * 6e5, giving the same kf"
call /kinetics/CaRegulation/Ca-sequester/notes LOAD \
"Sequestered Ca pool" \
"The vol is 0.16 * the vol of the cell as a whole. "
call /kinetics/CaRegulation/Ca-leak-to-cytoplasm/notes LOAD \
"represents the channels that leak Ca into the cytoplasm. Effects " \
"of membrane potential are not considered. The amount and total " \
"flux are constrained by the need to balance Ca flux and keep " \
"basal Ca around 80 nM."
call /kinetics/CaRegulation/Ca-leak-to-cytoplasm/Ca-leak-chan/notes LOAD \
"The permeability is low to keep the Ca flow rate reasonable"
call /kinetics/CaRegulation/CaTransp-2Ca/notes LOAD \
"equivalent to the enzyme-substrate complex. 2 Ca are bound to " \
"the transporter. ATP is ignored."
call /kinetics/CaRegulation/CaTransp/notes LOAD \
"The calcium transporter levels are constrained by the resting " \
"levels of Ca in the cell. The rate of Ca sequestration depends " \
"on the amount of this pool. "
call /kinetics/CaRegulation/Ca-bind-to-Transp/notes LOAD \
"Rates from Lauffenburger abd Linderman 1993 Receptors pg 200. " \
"Kd = KCa2 = 0.2 uM"
call /kinetics/CaRegulation/IP3R/notes LOAD \
"The number of the IP3Rs in the cell is present only implicitly in the" \
"model, and is lumped in with the total permeability of the IP3R pool." \
"The latter is constrained by the height of the Ca transient."
call /kinetics/CaRegulation/IP3Rbind/notes LOAD \
"Based on Lauffenburger and Linderman 1993 Receptors pg 200. The " \
"binding of IP3 on this reaction had a Hill coeff of 3. The eqns of " \
"Mahama and Linderman (cited in the book as 1993 a) are equivalent " \
"to the binding all occurring in a single step, so that is how I do " \
"it in this version. Their Ki1 is 0.07 uM. Lots of other data sources: " \
"Ramos-Franco et al, Biophys J 75, 1998: 834-39 have Ca sensitivity " \
"curves. At 250 nM free Ca, the EC50 for type1 is 58 nM and type 2 is " \
"194 nM. Type 3 would be about 2 uM according to Newton et al, JBC " \
"268(46), 1994: 28613-19. For the purposes of this model we use a " \
"Kd of 2.7 uM which is high but maybe OK at low calcium. The details " \
"of Ca interaction with the IP3R are not included in this model."
call /kinetics/CaRegulation/IP3R*/notes LOAD \
"This is the ligand-bound form of the IP3R."
call /kinetics/CaRegulation/CaEPump/notes LOAD \
"The calcium electrogenic pump: Mc Burney and Neering, TINS 10(4), 1987, " \
"164-169. We treat the pump as a simple Michaelis-Menten enzyme. Levels " \
"are constrained tightly by the need to keep resting Ca levels at 80 nM."
call /kinetics/CaRegulation/CaEPump/Ca-pump-out/notes LOAD \
"From McBurney and Neering, TINS 10(4), 1987, 164-169 1987. We " \
"are using the high-affinity pump here. Their numbers exceed M&L " \
"so I am reducing the rates by 10X. Need to check. k1 = 3e-3, " \
"k2 = 288, k3 = 72, n = 1000. This comes to a Km of 0.2 for Ca, " \
"and a Vmax of 72." \
""
call /kinetics/CaRegulation/Ca-ext/notes LOAD \
"Extracell Ca conc = 4 mM Extracell vol assumed 100 X cell vol. It is anyway " \
"kept buffered for the purposes of the model, so the concentration won't change." \
""
call /kinetics/CaRegulation/Ca-leak-from-extracell/notes LOAD \
"This represents the pool of Ca leak channels. The conc gradient is so " \
"large that this pool needs only a small number of molecules." \
"For an equilibrium at 0.1 uM we need flow of 36e3/sec. With a permeability " \
"of 0.01 and a conc gradient of 4mM->0.1 uM (4e4) we get flux = N * perm * " \
"grad => N = 36e3 / (1e-2 * 4e3) = 900 if flux = 20e3, N =500, which is what we " \
"use. This works out to a concentration of 0.83 nM."
call /kinetics/CaRegulation/Ca-leak-from-extracell/Ca-leak-chan/notes LOAD \
"The permeability is low to keep the Ca flow rate reasonable"
call /kinetics/CaRegulation/capacitive_Ca_entry*/notes LOAD \
"This mechanism has taken a while to be more tightly confirmed as probably being " \
"the TRP channel. In this model the channel is implemented  to match experimental " \
"observations about capacitative Ca entry. Levels are set by two constraints: " \
"the resting Ca levels, and the height of the response to IP3."
call /kinetics/CaRegulation/inactivate_cap_Ca/notes LOAD \
"The Kd is set at about 3 uM so that at resting Ca the capacitative Ca " \
"entry is almost blocked. A 2nd order response makes the response steep."
call /kinetics/CaRegulation/inact_cap_entry/notes LOAD \
"represents the portion of the capacitative-Ca entry channel which is blocked " \
"when there is lots of Ca sequestered in the stores"
call /kinetics/CaRegulation/IP3/notes LOAD \
"Inositol(145)trisphosphate"
call /kinetics/CaRegulation/Ca/notes LOAD \
"This pool represents intracellular calcium. Resting levels are around 80 nM, " \
"but this is subject to all sorts of influxes and pumps."
call /kinetics/CaRegulation/Calseq/notes LOAD \
"This is Calsequestrin or the calcium buffer in the ER. " \
"from Cala & Jones, JBC 258(19), 1983: 11932-36" \
"Calseq is present as 4mg/g of membrane protein; membrane protein = 2% of cell " \
"mass = 0.02 * 1g/cc * (1e-9)cc = (2e-11) g" \
"Hence Calseq = 8e-14/55000 moles per (1.6e-13)l = 9.091uM " \
"As per Guidebook to the calcium-binding proteins by Celio; and Mitchell et al, JBC 263, " \
"1988: 1376-81; 1 mol of Calsequestrin binds 40 mol of Ca. This is the stoichiometry we " \
"use. System limitations do not allow us to create a 40th order reaction. Hence Calseq " \
"binding to Ca has been modeled in eight consecutive steps of 5th order each. The affinity " \
"of Calsequestrin for Ca in our model is constrained by the levels of free Ca in the stores " \
"(Ca-sequester). We use a Kd such that Ca-sequester levels remain similar to levels in the " \
"CaRegulation model without Ca buffering."
call /kinetics/CaRegulation/Ca5-Cal/notes LOAD \
"Calsequestrin with 5 Ca molecules bound"
call /kinetics/CaRegulation/Ca10-Cal/notes LOAD \
"Calsequestrin with 10 Ca molecules bound"
call /kinetics/CaRegulation/Ca15-Cal/notes LOAD \
"Calsequestrin with 15 Ca molecules bound"
call /kinetics/CaRegulation/Ca25-Cal/notes LOAD \
"Calsequestrin with 25 Ca molecules bound"
call /kinetics/CaRegulation/Ca30-Cal/notes LOAD \
"Calsequestrin with 30 Ca molecules bound"
call /kinetics/CaRegulation/Ca35-Cal/notes LOAD \
"Calsequestrin with 35 Ca molecules bound"
call /kinetics/CaRegulation/Ca40-Cal/notes LOAD \
"Calsequestrin with 40 Ca molecules bound"
call /kinetics/CaRegulation/Ca20-Cal/notes LOAD \
"Calsequestrin with 20 Ca molecules bound"
call /kinetics/Gq/notes LOAD \
"The model for the Gq pathway plus its activators, here represented" \
"by the metabotropic glutamate receptor. " \
"We assume GTP is present in fixed amounts, so we leave it out" \
"of the explicit equations in this model. Normally we would expect it" \
"to associate along with the G-Receptor-ligand complex." \
"Most info is from Berstein et al JBC 267:12 8081-8088 1992" \
"Structure of receptor activation of Gq from " \
"Fay et al Biochem 30 5066-5075 1991" \
"This mGluR/Gq model lacks a mechanism for receptor desensitization. "
call /kinetics/Gq/RecLigandBinding/notes LOAD \
"" \
"From Martin et al FEBS Lett 316:2 191-196 1993 we have Kd = 600 nM" \
"Assuming kb = 10/sec, we get kf = 10/(0.6 uM * 6e5) = 2.8e-5 1/sec/#" \
"The off time for Glu seems pretty slow:" \
"Nicoletti et al 1986 PNAS 83:1931-1935 and" \
"Schoepp and Johnson 1989 J Neurochem 53 1865-1870" \
"indicate it is at least 30 sec. Here we are a little faster because" \
"this is only a small part of the off rate, the rest coming from the" \
"Rec-Gq complex."
call /kinetics/Gq/G-GDP/notes LOAD \
"This is the G-alpha-beta-gamma trimer in association with GDP." \
"" \
"From Pang and Sternweis JBC 265:30 18707-12 1990 we get concentration" \
"estimate of  1.6 uM to 0.8 uM. I use 1 uM which is well within this" \
"range." \
""
call /kinetics/Gq/Basal-Act-G/notes LOAD \
"This is the basal exchange of GTP for GDP. So slow as to be" \
"nearly negligible."
call /kinetics/Gq/Trimerize-G/notes LOAD \
"kf == kg3 = 1e-5 /cell/sec. As usual, there is no back-reaction" \
"kb = 0"
call /kinetics/Gq/Inact-G/notes LOAD \
"From Berstein et al JBC 267:12 8081-8088 1992, kcat for GTPase activity" \
"of Gq is only 0.8/min."
call /kinetics/Gq/mGluR/notes LOAD \
"From Mahama and Linderman, Total # of receptors/cell = 1900" \
"However, the density is likely to be very" \
"high at the synapse." \
"Fay et al Biochem 30 5066-5075 1991 have a value of 60K receptors per" \
"cell for neutrophils which comes to 0.1 uM." \
"Here we have a situation where trying to represent the synapse by" \
"a 10 micron cube gives awkward results. I will scale up to 0.3 uM since" \
"synaptic receptor density is likely to be higher, with the caveat that I" \
"should really be using a more geometrically realistic model."
call /kinetics/Gq/Rec-Glu/notes LOAD \
"Glu-Receptor complex."
call /kinetics/Gq/Rec-Gq/notes LOAD \
"Turns out that a large fraction of the the receptor binds to the G-protein" \
"even in the absence of ligand. This pool represents this step." \
"Fraction of Rec-Gq is 44%  of receptor, from " \
"Fay et al 1991 Biochem 30:5066-5075" \
"Since this is not the same receptor, this value is a bit doubtful. Still," \
"we adjust the rate consts in Rec-bind-Gq to match."
call /kinetics/Gq/Rec-Glu-bind-Gq/notes LOAD \
"This is the k1-k2 equivalent for enzyme complex formation in the" \
"binding of Rec-Glu to Gq." \
"See Fay et al Biochem 30 5066-5075 1991." \
"Closer reading of Fay et al suggests that " \
"kb <= 0.0001, so kf = 1e-8 by detailed balance. This" \
"reaction appears to be neglible."
call /kinetics/Gq/Glu-bind-Rec-Gq/notes LOAD \
"From Fay et al" \
"kb3 = kb = 1.06e-3 which is rather slow." \
"k+1 = kf = 2.8e7 /M/sec= 4.67e-5/sec use 5e-5." \
"However, the Kd from Martin et al may be more appropriate, as this" \
"is Glu not the system from Fay." \
"kf = 2.8e-5, kb = 10" \
"Let us compromise. since we have the Fay model, keep kf = k+1 = 2.8e-5." \
"But kb (k-3) is .01 * k-1 from Fay. Scaling by .01, kb = .01 * 10 = 0.1"
call /kinetics/Gq/Rec-Glu-Gq/notes LOAD \
"This is the ternary complex of receptor, ligand and G protein." \
""
call /kinetics/Gq/Activate-Gq/notes LOAD \
"This reaction is the critical one for activation of Gq. It probably" \
"encapsulates multiple steps. In this approximation the receptor-ligand-" \
"Gprotein complex splits up into GTP.Galpha, rec.ligand complex, and " \
"Gbetagamma. There is a hidden step of exchange of GDP for GTP. The" \
"reaction does not take these into account since it is assumed that" \
"both GTP and GDP levels are tightly regulated by metabolic control." \
"" \
"This is the kcat==k3 stage of the Rec-Glu ezymatic activation of Gq." \
"From Berstein et al actiation is at .35 - 0.7/min" \
"From Fay et al Biochem 30 5066-5075 1991 kf = .01/sec" \
"From Nakamura et al J physiol Lond 474:1 35-41 1994 see time courses." \
"Also (Berstein) 15-40% of gprot is in GTP-bound form on stim."
call /kinetics/Gq/Rec-bind-Gq/notes LOAD \
"From Berstein et al 1992 JBC 267(12):8081-8088 we know that 15-40%" \
"of Gq binds, GTP_gamma_S. Also about 20-30% of Gq is bound to GTP." \
"To get to these values the receptor-Gq amount should be similar. These" \
"rates are designed to give that steady state with a fast tau of 1 sec." \
""
call /kinetics/Gq/mGluRAntag/notes LOAD \
"I implement this as acting only on the Rec-Gq complex, based on" \
"a more complete model PLC_Gq48.g" \
"which showed that the binding to the receptor" \
"alone contributed only a small amount."
call /kinetics/Gq/Antag-bind-Rec-Gq/notes LOAD \
"The rate consts give a total binding affinity of under 0.2 nM, good" \
"for a strong antagonist."
call /kinetics/Gq/Blocked-rec-Gq/notes LOAD \
"This represents the blocked state of the receptor when bound" \
"to a competitive antagonist. Note that this is in the Gq bound form." \
"Simulations had shown that with the available rates, the blocking" \
"was minimal if only the unbound receptor could bind the antagonist."
call /kinetics/Gq/G*GDP/notes LOAD \
"This should correctly be called GDP.G_alpha. The name is preserved for" \
"backward compatibility reasons."
call /kinetics/Gq/G*GTP/notes LOAD \
"Activated G protein. Berstein et al indicate that about 20-40% of the total" \
"Gq alpha should bind GTP at steady stimulus."
call /kinetics/Gq/BetaGamma/notes LOAD \
"The betagamma subunits of Gq. This is an approximation to the possible" \
"combinations of betagamma subunits. Here they are all treated as a " \
"single pool. "
call /kinetics/Gq/Glu/notes LOAD \
"Varying the amount of (steady state) glu between .01 uM and up, the" \
"final amount of G*GTP complex does not change much. This means that" \
"the system should be reasonably robust wr to the amount of glu in the" \
"synaptic cleft. It would be nice to know how fast it is removed." \
"Schoepp et al 1990 TIPS 11:508-515 give a range of Glu EC50 from rat" \
"brain in the range 120 to 1000 uM." \
"Nicoletti 1986 PNAS 83:1931-1935 and" \
"Schoepp and Johnson 1989 J Neurochem 53:1865-1870 " \
"give an off time of at least 30 sec."
call /kinetics/PLCbeta/notes LOAD \
"PhospholipaseC beta. This model incorporates Ca and Gq regulation of " \
"PLCbeta that generates four separate active forms of the enzyme: " \
"PLC, PLC-Gq, PLC-Ca and PLC-Ca-Gq. GAP activity of  PLC has been included. " \
"Primary refs: Sternweis et al 1992 Phil Trans R Soc Lond, Smrcka et al 1991 " \
"Science 251:804-807, Biddlecome et al 1996 JBC 271: 7999-8007" \
" "
call /kinetics/PLCbeta/PLC-Gq/notes LOAD \
"from Smrcka et al, 1991 Science 251: 804-807"
call /kinetics/PLCbeta/PLC-Gq/PLC-Gq/notes LOAD \
"from Smrcka et al, 1991 Science 251: 804-807"
call /kinetics/PLCbeta/PLC-Ca/notes LOAD \
"From Sternweis et al Phil Trans R Soc Lond 1992, also matched by Homma et al." \
"k1 = 1.5e-5, now 4.2e-6" \
"k2 = 70/sec; now 40/sec" \
"k3 = 17.5/sec; now 10/sec" \
"Note that the wording in Sternweis et al is" \
"ambiguous re the Km." \
"Also Smrcka et al; Science 251, 15.2.1991, pp804-807"
call /kinetics/PLCbeta/PLC-Ca/PLC-Ca/notes LOAD \
"From Sternweis et al Phil Trans R Soc Lond 1992, also matched by Homma et al." \
"k1 = 1.5e-5, now 4.2e-6" \
"k2 = 70/sec; now 40/sec" \
"k3 = 17.5/sec; now 10/sec" \
"Note that the wording in Sternweis et al is" \
"ambiguous re the Km." \
"Also Smrcka et al; Science 251, 15.2.1991, pp804-807"
call /kinetics/PLCbeta/PC/notes LOAD \
"Phosphatidylcholine is the main (around 55%) metabolic product of DAG," \
"follwed by PE (around 25%). Ref is Welsh and Cabot, JCB35:231-245(1987)"
call /kinetics/PLCbeta/PLC-Ca-Gq/notes LOAD \
"This should really be labelled PLC-Ca-GTP.Gq_alpha" \
"This is the most active form of the enzyme. "
call /kinetics/PLCbeta/PLC-Ca-Gq/PLCb-Ca-Gq/notes LOAD \
"Km: Sternweis et al, Phil Trans R Soc Lond 1992" \
"Vmax: Smrcka et al, Science 1991"
call /kinetics/PLCbeta/PLC/notes LOAD \
"Smrcka et al; Science 251, 15.2.1991, pp804-807"
call /kinetics/PLCbeta/PLC/PLC/notes LOAD \
"Smrcka et al; Science 251, 15.2.1991, pp804-807"
call /kinetics/PLCbeta/Act-PLC-Ca/notes LOAD \
"Affinity for Ca = 1uM without AlF, 0.1 with:" \
" from Smrcka et al science 251 pp 804-807 1991" \
"so [Ca].kf = kb so kb/kf = 1 * 6e5 = 1/1.66e-6" \
"Assigned affinity to a Kd of 0.333 to maintain balance."
call /kinetics/PLCbeta/PLC-bind-Gq/notes LOAD \
"this binding does not produce active PLC. This step was needed to" \
"implement the described (Smrcka et al) increase in affinity for Ca" \
"by PLC once Gq was bound." \
"The tempkin are the same as the binding step for Ca-PLC to Gq." \
"Kd is constrained by detailed balance."
call /kinetics/PLCbeta/PLC-Gq-bind-Ca/notes LOAD \
"this step has a high affinity for Ca, from Smrcka et al. 0.1uM" \
"so kf /kb = 1/6e4 = 1.666e-5:1. See the Act-PLC-by-Gq reaction." \
"Raised kf to 5e-5 based on match to conc-eff curves from " \
"Smrcka et al."
call /kinetics/PLCbeta/Inact-PLC-Gq/notes LOAD \
"Rate of 100/min to account for GAP activity of PLC:" \
"Biddlecome et al, JBC, 271, 14, 7999-8007, 1996"
call /kinetics/PLCbeta/Act-PLC-by-Gq/notes LOAD \
"Affinity for Gq is > 20 nM (Smrcka et al Science251 804-807 1991)" \
"so [Gq].kf = kb so 40nM * 6e5 = kb/kf = 24e3 so kf = 4.2e-5, kb =1" \
""
call /kinetics/PLCbeta/Degrade-DAG/notes LOAD \
"Rate based on basal and activated levels of DAG"
call /kinetics/PLCbeta/basal/notes LOAD \
"accounts for other PLC isoforms that contribute to basal levels of " \
"IP3"
call /kinetics/PLCbeta/DAG/notes LOAD \
"Basal levels of Diacylglycerol in model are 5.06 uM." \
"DAG is pretty nasty to estimate. Data sources are many and" \
"varied and sometimes difficult to reconcile. " \
"Welsh and Cabot 1987 JCB 35:231-245: DAG degradation" \
"Bocckino et al JBC 260(26):14201-14207: " \
"     hepatocytes stim with vasopressin: 190 uM." \
"Bocckino et al 1987 JBC 262(31):15309-15315:" \
"     DAG rises from 70 to 200 ng/mg wet weight, approx 150 to 450 uM." \
"Prescott and Majerus 1983 JBC 258:764-769: Platelets: 6 uM." \
"     Also see Rittenhouse-Simmons 1979 J Clin Invest 63." \
"Sano et al JBC 258(3):2010-2013: Report a nearly 10 fold rise." \
"Habenicht et al 1981 JBC 256(23)12329-12335: " \
"     3T3 cells with PDGF stim: 27 uM" \
"Cornell and Vance 1987 BBA 919:23-36: 10x rise from 10 to 100 uM" \
"" \
"" \
""
call /kinetics/PLCbeta/PIP2/notes LOAD \
"PIP2 conc: Willars et al; JBC 273 (9) 27.2.98; pp 5037-5046"
call /kinetics/134_dephos/notes LOAD \
"Model for Ins(134)P3 dephosphorylation. Two bisphosphate intermediates" \
"[Ins(13)P2 and Ins(34)P2] and two monophosphate intermediates [Ins(1)P1 " \
"and Ins(3)P1] are formed. Primary refs: Norris et al, JBC 269, 1994:8716-20;" \
"Caldwell et al, JBC 266, 1991:18378-86, Inhorn et al, JBC 262, 1987:15946-" \
"52; Gee et al, Biochem J 249, 1988:883-89" \
""
call /kinetics/134_dephos/IP2_3pase2/notes LOAD \
"from Caldwell et al, JBC 266(27); 1991: 18378-86" \
"" \
"enzyme is a heterodimer with one catalystic subunit and one regulatory" \
"78 kDa subunit"
call /kinetics/134_dephos/IP2_3pase2/ip2_3pase2/notes LOAD \
"from Caldwell et al, JBC 266; 1991"
call /kinetics/134_dephos/IP1(3)_deg/notes LOAD \
"Kf and Kb based on levels of Ins(3)P1." \
"Kb necessary as energetics calculations show backflow from " \
"inositol to be significant." \
""
call /kinetics/134_dephos/IP1(3)/notes LOAD \
"Inositol (3)monophosphate = 11% of Ins(1)P1 ~ 4.8uM " \
"Ackermann et al, Biochem J 242(2), 1987: 517"
call /kinetics/134_dephos/IP2_3pase1/notes LOAD \
"from Caldwell et al, JBC 266(27); 1991: 18378-86" \
"" \
"Enzyme is a homodimer with two catalytic subunits. Conc of enzyme " \
"increased 2 times from 1.9 nM to account for two monomeric subunit " \
"pools " \
""
call /kinetics/134_dephos/IP2_3pase1/ip2_3pase1/notes LOAD \
"from Caldwell et al, JBC 266; 1991" \
"enzyme activity was assayed for the monomeric form of the " \
"enzyme"
call /kinetics/134_dephos/IP2(34)/notes LOAD \
"Inositol (34)bisphosphate"
call /kinetics/134_dephos/IP_4pase-inact/notes LOAD \
"from Norris et al, JBC 269; 1994"
call /kinetics/134_dephos/IP_4pase/notes LOAD \
"from Norris et al, JBC 269(12); 1994: 8716-20" \
"Enzyme conc increased from 9 nM to 0.9 uM to obtain appreciable enzyme " \
"activity" \
"has two 4-phosphatase activities: against Ins(134)P3 and Ins(34)P2" \
"respectively"
call /kinetics/134_dephos/IP_4pase/ip3_4pase/notes LOAD \
"Ins(134)P3 4-phosphatase activity of InsP 4-phosphatase" \
"from Norris et al, JBC 269; 1994. Vmax reduced from 55/sec to " \
"20/sec to maintain relative levels of Ins(134)P3 and Ins(13)P2"
call /kinetics/134_dephos/IP_4pase/ip2_4pase/notes LOAD \
"Ins(34)P2 4-phosphatase activity of InsP 4-phosphatase" \
"from Norris et al, JBC 269; 1994"
call /kinetics/134_dephos/IP2(13)/notes LOAD \
"Inositol (13)bisphosphate"
call /kinetics/134_dephos/IP1(1)/notes LOAD \
"Inositol (1)monophsophate" \
"Basal Conc ~ 44uM : Ackermann et al, BiochemJ 1987, 242(2):" \
"517-24" \
"IP metabolism maintains only a tenth of this level while the " \
"rest is generated from PtdIns metabolism."
call /kinetics/134_dephos/ip1_1pase_cmplx/notes LOAD \
"Enzyme complex exclusively modeled to accomodate enzyme " \
"reversibility as calculated from dG calculations for -5 kJ/mol."
call /kinetics/134_dephos/1pase-on/notes LOAD \
"Rates derived from Km for Ins(1)P1-1phosphatase:" \
"Gee et al, Biochem J 249; 1988."
call /kinetics/134_dephos/1pase-off/notes LOAD \
"Kf = Vmax for Ins(1)P1-1phosphatase: Gee et al, Biochem J 249," \
"1988." \
"Kb necessary as estimated from percent inositol backflux " \
"calculations. This contributes to maintain Ins(1)P1 at 10% of" \
"its actual pool."
call /kinetics/134_dephos/ip1_syn/notes LOAD \
"This rxn. maintains levels of Ins(1)P1 at 44 uM basal. Actually, " \
"90% of Ins(1)P1 is generated from PtdIns degradation (Ackermann " \
"et al, Biochem J 242(2), 1987: 517-24) but for simplicity we " \
"use a back rxn. from Inositol to generate this conc."
call /kinetics/145_dephos/notes LOAD \
"Model for Ins(145)P3 dephosphorylation. InsP3 degrades via Ins(14)P2 " \
"and Ins(4)P2 to inositol. Model incorporates enzyme inhibition from " \
"higher phosphates: InsP5 and InsP6. Primary refs: Hansen et al, JBC " \
"262, 1987: 17319-26; Hoer and Oberdisse, BiochemJ 278, 1991: 219-24;" \
"Inhorn and Majerus, JBC 262, 1987: 15946-52; Gee et al, BiochemJ 249," \
"1988: 883-89"
call /kinetics/145_dephos/IP3_5pase2/notes LOAD \
"from Hansen et al, JBC 262(36), Dec 25 1987: 17319-17326                           "
call /kinetics/145_dephos/IP3_5pase2/ip3_5pase2/notes LOAD \
"from Hansen et al, JBC 262, 1987" \
"activity determined from pH curve. Value scaled 1.5 times to obtain " \
"activity at 37C as original experiment was performed at 30C"
call /kinetics/145_dephos/IP_5pase1/notes LOAD \
"from Hansen et al, JBC 262(36); Dec 25 1987: 17319-26" \
"" \
"InsP 5phosphatase1 has two 5-phosphatase activities: against Ins(145)P3" \
"and Ins(1345)P4 respectively"
call /kinetics/145_dephos/IP_5pase1/ip3_5pase1/notes LOAD \
"Ins(145)P3 5-phosphatase  activity of InsP-5-phosphatase from" \
"Hansen et al, JBC 262; 1987"
call /kinetics/145_dephos/IP_5pase1/ip4_5pase/notes LOAD \
"Ins(1345)P4 5-phosphatase activity of InsP 5-phosphatase1" \
"from Hansen et al, JBC 262; 1987" \
"vmax for IP4 substrate is approx 0.1 times vmax for IP3" \
""
call /kinetics/145_dephos/IP2(14)/notes LOAD \
"Inositol(1,4) bisphosphate"
call /kinetics/145_dephos/IP5-inhib-5pase/notes LOAD \
"from Hoer and Oberdisse, Biochem J 278; 1991: 219-224"
call /kinetics/145_dephos/IP6-inhib-5pase/notes LOAD \
"from Hoer and Oberdisse, Biochem J 278; 1991: 219-224"
call /kinetics/145_dephos/IP_1pase/notes LOAD \
"from Inhorn and Majerus; JBC 262(33), 1987 pp 15946-15952" \
"InsP-1-phosphatase has two enzyme activities against Ins(14)P2 and " \
"Ins(134)P3 respectively"
call /kinetics/145_dephos/IP_1pase/ip2_1pase/notes LOAD \
"from Inhorn and Majerus, JBC 1987" \
"Vmax reduced from 5.625 to 2 to maintain levels of IP2(14)"
call /kinetics/145_dephos/IP_1pase/ip3_1pase/notes LOAD \
"Ins(134) 1-phosphatase activity of InsP 1-phosphatase" \
"from Inhorn and Majerus, JBC 262; 1987"
call /kinetics/145_dephos/IP1(4)/notes LOAD \
"Inositol 4-monophosphate" \
"Basal levels = 10% of Ins(1)P1 ~ 4uM" \
"Ackermann et al, BiochemJ 242, 1987(2): 517"
call /kinetics/145_dephos/IP1_pase/notes LOAD \
"from Gee et al, Biochem J. 1988, 249, 883-889" \
"Inositol monophosphate phosphatase; has two enzyme activities against" \
"Ins(4)P1 and Ins(1)P1 respectively"
call /kinetics/145_dephos/Ca-inhib-1pase/notes LOAD \
"Ki from Inhorn & Majerus, BiochemJ 262(33); 1987: 15946-52" \
""
call /kinetics/145_dephos/ip1_4pase_cmplx/notes LOAD \
"Enzyme complex exclusively modeled to accomodate enzyme " \
"reversibility as obtained from dG = -5 kJ/mol calculations."
call /kinetics/145_dephos/4pase-on/notes LOAD \
"Rates derived from Ins(4)P1 4-phosphatase Km: Gee et al, " \
"Biochem J 249; 1988"
call /kinetics/145_dephos/4pase-off/notes LOAD \
"Kf = Vmax for Ins(4)P1 4-phosphatase: Gee et al, Biochem J " \
"249, 1988." \
"Kb adjusted to generate reported basal levels of Ins(4)P1 = " \
"10% of Ins(1)P1 ~ 4uM"
call /kinetics/IP4-system/notes LOAD \
"This model depicts detailed dynamics of InsP4s: Ins(1456)P4, Ins(3456)P4" \
"and Ins(1346)P4. Interactions with InsP3s and InsP5 are included." \
"Ins(1345)P4 synthesis from Ins(134)P3 is also shown." \
""
call /kinetics/IP4-system/IP4(1346)/notes LOAD \
"Inositol (1346)tetrakisphosphate"
call /kinetics/IP4-system/IP4(3456)/notes LOAD \
"Inositol (3456)tetrakisphosphate" \
"basal levels ~ 1.4uM"
call /kinetics/IP4-system/IP4(1456)/notes LOAD \
"Inositol(1456)tetrakisphosphate"
call /kinetics/IP4-system/ip4-6pase/notes LOAD \
"this step is essential to maintain flux around the network," \
"rate adjusted accordingly"
call /kinetics/IP4-system/ip5_3pase/notes LOAD \
"Ins(13456)P5 3-phosphatase" \
"from Nogimori et al, JBC 266; 1991" \
"Backflux from the reversible InsP4 3-kinase is not sufficient " \
"to maintain Ins(1456)P4 levels. Hence this reaction is " \
"necessary. This reaction also maintains the flux in the " \
"network."
call /kinetics/IP4-system/IP3-Kcmplx-on/notes LOAD \
"Kf and Kb are equivalent to k1 and k2 for InsP3 56-K," \
"calculated from enzyme Km and Vmax: Yang and Shears, BiochemJ" \
"2000, 351: 551-555"
call /kinetics/IP4-system/6kinase/notes LOAD \
"Kf = Vmax for IP3 56-K " \
"from Yang and Shears, Biochem J 2000; 351:551-555" \
"Enzyme reversibility reported in Ho et al, Curr Biol 2002, 12:" \
"1-20. But backflow calculations do not show that Kb needs to be" \
"incorporated"
call /kinetics/IP4-system/5kinase/notes LOAD \
"Kf = 0.274 times Vmax of IP3 56-K as product ratio of " \
"Ins(1345)P4 : Ins(1346)P4 is 1 : 2.3-5" \
"from Wilson and Majerus, JBC 271; 1996" \
"Kb ascertained from dG calculations for equilibrium conditions.," \
"for a dG = -10 kJ/mol" \
"Also enzyme reversibility reported in Ho et al, Curr Biol 2002," \
"12: 1-20"
call /kinetics/IP4-system/ip4-5K/notes LOAD \
"Kf based on basal levels of Ins(1346)P4" \
"Kb obtained from dG calculations for equilibrium product " \
"substrate conditions."
call /kinetics/IP4-system/IP4-3K/notes LOAD \
"Ins(1456)P4 3kinase" \
"from Stephens et al, Biochem J 249; 1988: 283-92" \
""
call /kinetics/IP4-system/IP3-56Kcmplx/notes LOAD \
"enzyme substrate complex of IP3 56-K and Ins(134)P3. Complex " \
"exclusively modeled as reaction generates ratio of products," \
"and because 5-kinase is reversible due to large Ins(1345)P4 " \
"backflux"
call /kinetics/IP4-system/IP5(13456)/notes LOAD \
"Inositol(13456)pentakisphosphate" \
"Conc from Voglmaier et al, PNAS 93; 1996"
call /kinetics/IP4-system/ip4_3k_cmplx/notes LOAD \
"Enzyme complex exclusively modeled to include reversible " \
"kinetics, as the back flux is significant for dG = -10 kJ/mol"
call /kinetics/IP4-system/ip4-3k-on/notes LOAD \
"Rates derived from Km for enzyme: Stephens et al, Biochem J " \
"249; 1988."
call /kinetics/IP4-system/ip4-3k-off/notes LOAD \
"Kf = Vmax for enzyme: Stephens et al, Biochem J 249; 1988." \
"Kb ascertained from dG calculations for equilibrium conditions."
call /kinetics/IP4-system/ip4_1k_cmplx/notes LOAD \
"Enzyme complex exclusively modeled to accomodate reversible " \
"kinetics as opposed to M-M kinetics. Enzyme reversibility " \
"ascertained from dG calculations at -10 kJ/mol that yield a " \
"significant back flux from IP5." \
"Also IP4-1K is experimentally reversible: Ho et al, Curr Biol," \
"Mar 2002, 12: 1-20"
call /kinetics/IP4-system/ip4-1k-on/notes LOAD \
"Rates derives from enzyme Km and Vmax values:" \
"Yang and Shears, Biochem J 2000, 351: 551-555."
call /kinetics/IP4-system/ip4-1k-off/notes LOAD \
"Kf = enzyme Vmax : Yang and Shears, Biochem J 2000, 351, 551-5." \
"Kb ascertained from dG calculations for equilibrium product " \
"substrate conditions." \
"Ho et al, Curr Biol 2002, 12: 1-20 report a Vmax for reverse " \
"reaction of 0.0656 /sec. But this cannot be exactly incorporated " \
"unless Km for InsP5 is also known." \
"Simulations show that incorporation of this reverse reaction " \
"can maintain basal InsP4 levels but cannot achieve the " \
"stimulated InsP4 levels shown in Ho et al." \
"Hence the separate InsP5 1pase is retained."
call /kinetics/IP4-system/IP3(134)/notes LOAD \
"Inositol (134)trisphosphate" \
""
call /kinetics/IP4-system/IP3-56K_IP4-1K/notes LOAD \
"Combined Ins(134)P3 5,6-kinase and Ins(3456)P4 1-kinase:" \
"from Yang and Shears, Biochem J 2000, 351: 551-555." \
"Conc from Wilson and Majerus, JBC 271(20); 1996: 11904-10" \
"5,6K Reaction products Ins(1346)P4 and Ins(1345)P4 are generated in" \
"a ratio of 2.3-5 : 1" \
"Enzyme inhibition by products, as depicted in previous versions " \
"of the model, removed because it is now shown that enzyme is " \
"multi-tasking and reversible with respect to these products:" \
"Ho et al, Curr Biol 2002, 12: 1-20. This non M-M ability has " \
"been incorporated." \
"But cycling to Ins(346)P3 by this enzyme not included because " \
"rest of Ins(346)P3 network biology is unknown in mammals."
call /kinetics/IP4-system/ip5_1pase/notes LOAD \
"InsP5 1-phosphatase" \
"Reaction is necessary to generate the flux of Ins(3456)P4 seen" \
"physiologically (Ho et al Curr Biol 2002, 12:1-20), although " \
"the IP4-1K/pase can maintain basal levels of this InsP4."
call /kinetics/IHP-system/notes LOAD \
"Model for interactions between Inositol High Polyphosphates. Primary " \
"refs: Voglmaier et al, PNAS 93, 1996: 4305-10; Huang et al, Biochem " \
"37, 1998: 14998-15004; Safrany et al, EMBO J 17, 1998: 6599-607;" \
"Saiardi et al, Curr Biol 9, 1999: 1323-26; Saiardi et al, JBC 275, " \
"2000: 24686-92 "
call /kinetics/IHP-system/dipp_ip6/notes LOAD \
"rate based on basal levels of PP-InsP4"
call /kinetics/IHP-system/PP-IP4/notes LOAD \
"Diphosphoinositol tetrakisphosphate" \
"Conc from Saiardi et al, JBC 275; 2000"
call /kinetics/IHP-system/IP6_K2/notes LOAD \
"from Saiardi et al, Curr Biol 9; 1999: 1323-26" \
"" \
"has InsP5 kinase/ PP-InsP4 synthase and PP-InsP4 kinase activity " \
"apart from InsP6 kinase activity (Saiardi et al, JBC 275(32); 2000: " \
"24686-92)" \
"" \
"also referred to as PiUS (Pi Uptake Stimulator)" \
"" \
""
call /kinetics/IHP-system/IP6_K2/ip6_k2/notes LOAD \
"from Saiardi et al, Curr Biol 9; 1999"
call /kinetics/IHP-system/IP6_K2/ip5_k2/notes LOAD \
"from Saiardi et al, JBC 275(32); 2000: 24686-92 "
call /kinetics/IHP-system/IP6_K2/pp-ip4-k2/notes LOAD \
"from Saiardi et al, JBC 275; 2000" \
"approx Km and Vmax calculated from first order rate constants"
call /kinetics/IHP-system/bisPP-IP3/notes LOAD \
"Bis(diphospho)inositol trisphosphate" \
"from Saiardi et al, JBC 275(32); 2000: 24686-92"
call /kinetics/IHP-system/ATP/notes LOAD \
"Conc for mammalian brain from Huang et al, Biochem 37; 1998"
call /kinetics/IHP-system/ADP/notes LOAD \
"Conc for mammaliam brain from Huang et al, Biochem 37; 1998"
call /kinetics/IHP-system/IP6/notes LOAD \
"Inositol hexakisphosphate " \
"Conc from Voglmaier et al, PNAS 93; 1996"
call /kinetics/IHP-system/ip5-kinase-pase/notes LOAD \
"Kf represents InsP5 2-kinase and Kb represents InsP6 2-phosphatase" \
"Although InsP5 2-kinases in yeast and plant systems have been " \
"characterized (Ives et al, JBC 275; 2000: 36575-83), the mammalian" \
"counterpart is still to be worked out." \
"Rates  calculated to maintain InsP5 and InsP6 levels"
call /kinetics/IHP-system/PP-IP5/notes LOAD \
"Diphosphoinositol pentakisphosphate" \
"Conc from Huang et al, Biochem 37; 1998"
call /kinetics/IHP-system/bisPP-IP4/notes LOAD \
"Bis(diphospho)inositol tetrakisphosphate" \
"Conc from Huang et al, Biochem 37; 1998"
call /kinetics/IHP-system/DIPP1/notes LOAD \
"Diphosphoinositol-Polyphosphate Phosphohydrolase" \
"from Safrany et al, EMBO J 17(22); 1998: 6599-607" \
""
call /kinetics/IHP-system/DIPP1/dipp_ip8/notes LOAD \
"from Safrany et al, EMBO J 17(22); 1998" \
"Vmax represents activity of human recombinant protein, which is" \
"20-50 fold greater than activity of the purified rat enzyme"
call /kinetics/IHP-system/DIPP1/dipp_ip7/notes LOAD \
"from Safrany et al, EMBO J 17(22); 1998" \
"Vmax represents activity of recombinant human protein which" \
"is 20-50 fold greater than activity of the purified rat enzyme"
call /kinetics/IHP-system/IP5-dipp-inhib/notes LOAD \
"IC50=1.6uM from  Safrany et al, EMBO J 17(22); 1998 "
call /kinetics/IHP-system/IP6-dipp-inhib/notes LOAD \
"IC50=0.2uM from Safrany et al, EMBO J 17(22); 1998"
call /kinetics/IHP-system/PP-IP5cmplx-on/notes LOAD \
"from Huang et al, Biochem 37; 1998" \
"Kf calculated using Km for PP-InsP5 and ATP, and Vmax of forward and " \
"backward reactions. " \
"Kb = Vmax of backward reaction " \
""
call /kinetics/IHP-system/PP-IP5cmplx-off/notes LOAD \
"from Huang et al, Biochem 37; 1998" \
"Kf = Vmax of forward reaction" \
"Kb calculated using Km for PP-InsP5 and ATP, and Vmax of forward and " \
"backward reactions"
call /kinetics/IHP-system/PP-IP5-K-complex/notes LOAD \
"enzyme substrate complex of PP-InsP5 kinase and PP-InsP5"
call /kinetics/IHP-system/IP6-K-complex/notes LOAD \
"enzyme substrate complex of InsP6 kinase and InsP6"
call /kinetics/IHP-system/IP6cmplx-off/notes LOAD \
"from Voglmaier et al, PNAS 93; 1996" \
"Kf = Vmax of forward reaction" \
"Kb calculated from Km for InsP6 and ATP, and Vmax of forward and " \
"backward  reactions"
call /kinetics/IHP-system/IP6cmplx-on/notes LOAD \
"from Voglmaier et al, PNAS 93; 1996" \
"Kf calculated from Km for InsP6 and ATP, and Vmax for forward and " \
"backward reactions" \
"Kb = Vmax of backward reaction"
call /kinetics/IHP-system/PP-IP5-K/notes LOAD \
"from Huang et al, Biochem 37; 1998: 14998-15004"
call /kinetics/IHP-system/IP6-K/notes LOAD \
"from Voglmaier et al, PNAS 93; 1996: 4305-10 " \
"" \
"has InsP5 kinase/ PP-InsP4 synthase and PP-InsP4 kinase apart from InsP6 " \
"kinase activity (Saiardi et al, JBC 275(32); 2000: 24686-92)"
call /kinetics/IHP-system/IP6-K/ip5_k1/notes LOAD \
"from Saiardi et al, JBC 275(32); 2000: 24686-92"
call /kinetics/IHP-system/IP6-K/pp-ip4-k1/notes LOAD \
"from Saiardi et al, JBC 275; 2000" \
"approx Km and Vmax calculated from first order rate constants"
call /kinetics/1345_dephos/notes LOAD \
"Model for Ins(1345)P4 dephosphorylation by InsP4 3-phosphatase and" \
"InsP 5-phosphatase1. Primary refs: Hoer et al, Biochem J 270, 1990:" \
"715-19; Hoer and Oberdisse, Biochem J 278, 1991: 219-24; Hansen et al," \
"JBC 262, 1987: 17319-26"
call /kinetics/1345_dephos/IP5-inhib-3pase/notes LOAD \
"from Hoer and Oberdisse, Biochem J 278; 1991: 219-224"
call /kinetics/1345_dephos/IP6-inhib-3pase/notes LOAD \
"from Hoer and Oberdisse, Biochem J 278; 1991: 219-224"
call /kinetics/1345_dephos/145-inhib-3pase/notes LOAD \
"from Hoer et al, Biochem J 270; 1990"
call /kinetics/1345_dephos/IP4-inhib-3pase/notes LOAD \
"from Hoer et al, Biochem J 270; 1990"
call /kinetics/1345_dephos/134-inhib-3pase/notes LOAD \
"from Hoer et al, Biochem J 270; 1990"
call /kinetics/1345_dephos/1345_3pase/notes LOAD \
"from Hoer et al, BiochemJ 270; 1990: 715-719"
call /kinetics/1345_dephos/1345_3pase/ip4_3pase/notes LOAD \
"Ins(1345)P4 3-phosphatase" \
"from Nogimori et al, JBC 266; 1991"
call /kinetics/doqcsinfo/notes LOAD \
"This network models detailed metabolism of Ins(145)P3, integrated with GPCR mediated PLCbeta activation and Ca release by the InsP3 receptor in the neuron. It is similar to the NonOsc_Ca_IP3metab model (accession 23) except that some enzymes have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. These modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12202356&query_hl=5> Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316</a>"
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