// DOQCS : http://doqcs.ncbs.res.in/ // Accession Name = fig3_CaMKII // Accession Number = 2 // Transcriber = Upinder S. Bhalla, NCBS // Developer = Upinder S. Bhalla, NCBS // Species = Generic mammalian // Tissue = Neuronal // Cell Compartment = Synapse // Notes = This is the model file for figure 3 from Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It is a model of the Ca activation of CaMKII and other CaM-activated enzymes. It includes the regulatory phosphatases PP1 and PP2B (Calcineurin) acting on CaMKII and also includes CaM-activated adenylyl cyclase and PKA in the synapse.
Demonstration script files for generating the figures in the paper, including figure 3, are available here. //genesis // kkit Version 11 flat dumpfile // Saved on Mon Aug 7 15:49:53 2006 include kkit {argv 1} FASTDT = 0.001 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 1 MAXTIME = 300 TRANSIENT_TIME = 2 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 kpool /kinetics/AC/cAMP-PDE* 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[2] green blue -1.5969 -18.025 0 simundump kenz /kinetics/AC/cAMP-PDE*/PDE* 1 0 0 0 0 6e+05 8.4e-06 80 20 0 0 \ "" red green "" -0.3498 -22.55 0 simundump kreac /kinetics/AC/dephosph-PDE 1 0.1 0 "" white blue -3.4985 \ -19.087 0 simundump kpool /kinetics/AC/PDE1 1 0 2 2 1.2e+06 1.2e+06 0 0 6e+05 0 \ /kinetics/geometry[2] green blue -5.4043 -12.36 0 simundump kenz /kinetics/AC/PDE1/PDE1 1 0 0 0 0 6e+05 3.5e-07 6.67 1.667 0 0 \ "" red green "" -2.3373 -22.314 0 simundump kpool /kinetics/AC/CaM.PDE1 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[2] green blue -5.4043 -15.095 0 simundump kenz /kinetics/AC/CaM.PDE1/CaM.PDE1 1 0 0 0 0 6e+05 2.1e-06 40 10 0 \ 0 "" red green "" -3.2447 -21.527 0 simundump kreac /kinetics/AC/CaM_bind_PDE1 1 0.0012 5 "" white blue -2.1917 \ -13.538 0 simundump kpool /kinetics/Gs-alpha 1 0 0 0 0 0 0 0 6e+05 2 \ /kinetics/geometry[2] red black 1.4111 -28.275 0 simundump kpool /kinetics/tot_PP1 1 0 0 1.8 1.08e+06 0 0 0 6e+05 0 \ /kinetics/geometry[2] blue black -4 5 0 simundump xtab /kinetics/Ca_tab 1 0 0 1 2 0 "" edit_xtab white red 0 0 0 3 \ -12.713 2.8136 0 loadtab /kinetics/Ca_tab table 1 100 0 100 \ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 simundump kpool /kinetics/tot_CaMKII-active 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[2] blue black -11.365 4.2863 0 simundump kpool /kinetics/tot_CaN-active 1 0 0 0 0 0 0 0 6e+05 0 \ /kinetics/geometry[2] red black -8.861 -8.5101 0 simundump doqcsinfo /kinetics/doqcsinfo 0 db2.g \ fig3_CaMKII network "Upinder S. Bhalla, NCBS" "Upinder S. Bhalla, NCBS" \ "citation here" "Generic Mammalian" Neuronal Synapse \ "Quantitative match to experiments, Qualitative" \ "Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 ( Peer-reviewed publication )" \ "Exact GENESIS implementation" \ "Approximates original data , Quantitatively predicts new data" 12 4 0 simundump xgraph /graphs/conc1 0 0 10000 0 35 0 simundump xgraph /graphs/conc2 0 0 10000 0 1.2 0 simundump xplot /graphs/conc1/Ca.Co 3 524288 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xplot /graphs/conc1/tot_CaMKII-active.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc2/tot_CaN-active.Co 3 524288 \ "delete_plot.w ; edit_plot.D " red 0 0 1 simundump xgraph /moregraphs/conc3 0 0 10000 0 0.3 0 simundump xgraph /moregraphs/conc4 0 0 10000 0 1.6 0 simundump xplot /moregraphs/conc3/PKA-active.Co 3 524288 \ "delete_plot.w ; edit_plot.D " yellow 0 0 1 simundump xplot /moregraphs/conc4/tot_PP1.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xcoredraw /edit/draw 0 -12.24 2.2387 -6.9655 5.3066 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 \ "Merged in ac19.g on top of" \ "allcam35.g to add in" \ "CaM-dependent PDE" \ "Added in a few plots and a stimulus" \ "table to allcam36.g" \ "Eliminated notes for portability." addmsg /kinetics/CaMKII/CaMKII-bind-CaM /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/PP1-active/Deph-thr306 /kinetics/CaMKII/CaMKII MM_PRD pA addmsg /kinetics/PP1-active/Deph_thr286b /kinetics/CaMKII/CaMKII MM_PRD pA addmsg /kinetics/CaMKII/basal-activity /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaM /kinetics/CaMKII/CaMKII-CaM REAC B A addmsg /kinetics/PP1-active/Deph-thr286 /kinetics/CaMKII/CaMKII-CaM MM_PRD pA addmsg /kinetics/CaMKII/tot_CaM_CaMKII/CaM_act_286 /kinetics/CaMKII/CaMKII-CaM REAC sA B addmsg /kinetics/CaMKII/tot_autonomous_CaMKII/auton_286 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/kinetics/Ca REAC A B addmsg /kinetics/PP2B/Ca-bind-CaNAB-Ca2 /kinetics/Ca REAC A B addmsg /kinetics/PP2B/Ca-bind-CaNAB-Ca2 /kinetics/Ca REAC A B addmsg /kinetics/PP2B/Ca-bind-CaNAB /kinetics/Ca REAC A B addmsg /kinetics/PP2B/Ca-bind-CaNAB /kinetics/Ca REAC A B addmsg /kinetics/Ca_tab /kinetics/Ca SLAVE output addmsg /kinetics/PKC-active/PKC-phosph-neurogranin /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active/PKC-phosph-ng-CaM /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active/phosph-AC2 /kinetics/PKC-active REAC eA B addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-phosph-neurogranin ENZYME n addmsg /kinetics/CaM/neurogranin /kinetics/PKC-active/PKC-phosph-neurogranin SUBSTRATE n addmsg /kinetics/PKC-active /kinetics/PKC-active/PKC-phosph-ng-CaM ENZYME n addmsg /kinetics/CaM/neurogranin-CaM /kinetics/PKC-active/PKC-phosph-ng-CaM SUBSTRATE n addmsg /kinetics/PKC-active /kinetics/PKC-active/phosph-AC2 ENZYME n addmsg /kinetics/AC/AC2 /kinetics/PKC-active/phosph-AC2 SUBSTRATE n addmsg /kinetics/CaM/CaM-TR2-Ca2-bind-Ca /kinetics/CaM-Ca3 REAC B A addmsg /kinetics/CaM/CaM-Ca3-bind-Ca /kinetics/CaM-Ca3 REAC A B addmsg /kinetics/PP2B/CaMCa3-bind-CaNAB /kinetics/CaM-Ca3 REAC A B addmsg /kinetics/CaM/CaM-TR2-bind-Ca /kinetics/CaM-TR2-Ca2 REAC B A addmsg /kinetics/CaM/CaM-TR2-Ca2-bind-Ca /kinetics/CaM-TR2-Ca2 REAC A B addmsg /kinetics/PP2B/CaM-Ca2-bind-CaNAB /kinetics/CaM-TR2-Ca2 REAC A B addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph_neurogranin /kinetics/CaM(Ca)n-CaNAB REAC eA B addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph_inhib1 /kinetics/CaM(Ca)n-CaNAB REAC eA B addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph-PP1-I* /kinetics/CaM(Ca)n-CaNAB REAC eA B addmsg /kinetics/PP2B/CaMCa4-CaNAB /kinetics/CaM(Ca)n-CaNAB SUMTOTAL n nInit addmsg /kinetics/PP2B/CaMCa3-CaNAB /kinetics/CaM(Ca)n-CaNAB SUMTOTAL n nInit addmsg /kinetics/PP2B/CaMCa2-CANAB /kinetics/CaM(Ca)n-CaNAB SUMTOTAL n nInit addmsg /kinetics/CaM(Ca)n-CaNAB /kinetics/CaM(Ca)n-CaNAB/dephosph_neurogranin ENZYME n addmsg /kinetics/CaM/neurogranin* /kinetics/CaM(Ca)n-CaNAB/dephosph_neurogranin SUBSTRATE n addmsg /kinetics/CaM(Ca)n-CaNAB /kinetics/CaM(Ca)n-CaNAB/dephosph_inhib1 ENZYME n addmsg /kinetics/PP1/I1* /kinetics/CaM(Ca)n-CaNAB/dephosph_inhib1 SUBSTRATE n addmsg /kinetics/CaM(Ca)n-CaNAB /kinetics/CaM(Ca)n-CaNAB/dephosph-PP1-I* ENZYME n addmsg /kinetics/PP1/PP1-I1* /kinetics/CaM(Ca)n-CaNAB/dephosph-PP1-I* SUBSTRATE n addmsg /kinetics/PKA-active/PKA-phosph-I1 /kinetics/PP1/I1 REAC sA B addmsg /kinetics/CaNAB-Ca4/dephosph_inhib1_noCaM /kinetics/PP1/I1 MM_PRD pA addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph_inhib1 /kinetics/PP1/I1 MM_PRD pA addmsg /kinetics/PP2A/PP2A-dephosph-I1 /kinetics/PP1/I1 MM_PRD pA addmsg /kinetics/PP1/dissoc-PP1-I1 /kinetics/PP1/I1 REAC B A addmsg /kinetics/PP1/Inact-PP1 /kinetics/PP1/I1* REAC A B addmsg /kinetics/PKA-active/PKA-phosph-I1 /kinetics/PP1/I1* MM_PRD pA addmsg /kinetics/CaNAB-Ca4/dephosph_inhib1_noCaM /kinetics/PP1/I1* REAC sA B addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph_inhib1 /kinetics/PP1/I1* REAC sA B addmsg /kinetics/PP2A/PP2A-dephosph-I1 /kinetics/PP1/I1* REAC sA B addmsg /kinetics/PP1/PP1-I1* /kinetics/PP1/Inact-PP1 PRODUCT n addmsg /kinetics/PP1/I1* /kinetics/PP1/Inact-PP1 SUBSTRATE n addmsg /kinetics/PP1-active /kinetics/PP1/Inact-PP1 SUBSTRATE n addmsg /kinetics/PP1/Inact-PP1 /kinetics/PP1/PP1-I1* REAC B A addmsg /kinetics/PP2A/PP2A-dephosph-PP1-I* /kinetics/PP1/PP1-I1* REAC sA B addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph-PP1-I* /kinetics/PP1/PP1-I1* REAC sA B addmsg /kinetics/PP1/dissoc-PP1-I1 /kinetics/PP1/PP1-I1 REAC A B addmsg /kinetics/PP2A/PP2A-dephosph-PP1-I* /kinetics/PP1/PP1-I1 MM_PRD pA addmsg /kinetics/CaM(Ca)n-CaNAB/dephosph-PP1-I* /kinetics/PP1/PP1-I1 MM_PRD pA addmsg /kinetics/PP1/PP1-I1 /kinetics/PP1/dissoc-PP1-I1 SUBSTRATE n addmsg /kinetics/PP1-active /kinetics/PP1/dissoc-PP1-I1 PRODUCT n addmsg /kinetics/PP1/I1 /kinetics/PP1/dissoc-PP1-I1 PRODUCT n addmsg /kinetics/PKA-active/PKA-phosph-I1 /kinetics/PKA-active REAC eA B addmsg /kinetics/PKA/Release-C1 /kinetics/PKA-active REAC B A addmsg /kinetics/PKA/Release-C2 /kinetics/PKA-active REAC B A addmsg /kinetics/PKA/inhib-PKA /kinetics/PKA-active REAC A B addmsg /kinetics/PKA-active/PKA-phosph-GAP /kinetics/PKA-active REAC eA B addmsg /kinetics/PKA-active/phosph-PDE /kinetics/PKA-active REAC eA B addmsg /kinetics/PKA-active /kinetics/PKA-active/PKA-phosph-I1 ENZYME n addmsg /kinetics/PP1/I1 /kinetics/PKA-active/PKA-phosph-I1 SUBSTRATE n addmsg /kinetics/PKA-active /kinetics/PKA-active/PKA-phosph-GAP ENZYME n addmsg /kinetics/PKA-active /kinetics/PKA-active/phosph-PDE ENZYME n addmsg /kinetics/AC/cAMP-PDE /kinetics/PKA-active/phosph-PDE SUBSTRATE n addmsg /kinetics/PP2A/PP2A-dephosph-I1 /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A/PP2A-dephosph-PP1-I* /kinetics/PP2A REAC eA B addmsg /kinetics/PP2A /kinetics/PP2A/PP2A-dephosph-I1 ENZYME n addmsg /kinetics/PP1/I1* /kinetics/PP2A/PP2A-dephosph-I1 SUBSTRATE n addmsg /kinetics/PP2A /kinetics/PP2A/PP2A-dephosph-PP1-I* ENZYME n addmsg /kinetics/PP1/PP1-I1* /kinetics/PP2A/PP2A-dephosph-PP1-I* SUBSTRATE n addmsg /kinetics/CaNAB-Ca4/dephosph_inhib1_noCaM /kinetics/CaNAB-Ca4 REAC eA B addmsg /kinetics/PP2B/Ca-bind-CaNAB-Ca2 /kinetics/CaNAB-Ca4 REAC B A addmsg /kinetics/PP2B/CaM-Ca2-bind-CaNAB /kinetics/CaNAB-Ca4 REAC A B addmsg /kinetics/PP2B/CaMCa4-bind-CaNAB /kinetics/CaNAB-Ca4 REAC A B addmsg /kinetics/PP2B/CaMCa3-bind-CaNAB /kinetics/CaNAB-Ca4 REAC A B addmsg /kinetics/CaNAB-Ca4 /kinetics/CaNAB-Ca4/dephosph_inhib1_noCaM ENZYME n addmsg /kinetics/PP1/I1* /kinetics/CaNAB-Ca4/dephosph_inhib1_noCaM SUBSTRATE n addmsg /kinetics/PP2B/Ca-bind-CaNAB /kinetics/PP2B/CaNAB REAC A B addmsg /kinetics/PP2B/Ca-bind-CaNAB /kinetics/PP2B/CaNAB-Ca2 REAC B A addmsg /kinetics/PP2B/Ca-bind-CaNAB-Ca2 /kinetics/PP2B/CaNAB-Ca2 REAC A B addmsg /kinetics/CaNAB-Ca4 /kinetics/PP2B/Ca-bind-CaNAB-Ca2 PRODUCT n addmsg /kinetics/Ca /kinetics/PP2B/Ca-bind-CaNAB-Ca2 SUBSTRATE n addmsg /kinetics/Ca /kinetics/PP2B/Ca-bind-CaNAB-Ca2 SUBSTRATE n addmsg /kinetics/PP2B/CaNAB-Ca2 /kinetics/PP2B/Ca-bind-CaNAB-Ca2 SUBSTRATE n addmsg /kinetics/PP2B/CaNAB /kinetics/PP2B/Ca-bind-CaNAB SUBSTRATE n addmsg /kinetics/PP2B/CaNAB-Ca2 /kinetics/PP2B/Ca-bind-CaNAB PRODUCT n addmsg /kinetics/Ca /kinetics/PP2B/Ca-bind-CaNAB SUBSTRATE n addmsg /kinetics/Ca /kinetics/PP2B/Ca-bind-CaNAB SUBSTRATE n addmsg /kinetics/CaNAB-Ca4 /kinetics/PP2B/CaM-Ca2-bind-CaNAB SUBSTRATE n addmsg /kinetics/CaM-TR2-Ca2 /kinetics/PP2B/CaM-Ca2-bind-CaNAB SUBSTRATE n addmsg /kinetics/PP2B/CaMCa2-CANAB /kinetics/PP2B/CaM-Ca2-bind-CaNAB PRODUCT n addmsg /kinetics/PP2B/CaMCa3-bind-CaNAB /kinetics/PP2B/CaMCa3-CaNAB REAC B A addmsg /kinetics/PP2B/CaM-Ca2-bind-CaNAB /kinetics/PP2B/CaMCa2-CANAB REAC B A addmsg /kinetics/PP2B/CaMCa4-bind-CaNAB /kinetics/PP2B/CaMCa4-CaNAB REAC B A addmsg /kinetics/PP2B/CaMCa3-CaNAB /kinetics/PP2B/CaMCa3-bind-CaNAB PRODUCT n addmsg /kinetics/CaM-Ca3 /kinetics/PP2B/CaMCa3-bind-CaNAB SUBSTRATE n addmsg /kinetics/CaNAB-Ca4 /kinetics/PP2B/CaMCa3-bind-CaNAB SUBSTRATE n addmsg /kinetics/PP2B/CaMCa4-CaNAB /kinetics/PP2B/CaMCa4-bind-CaNAB PRODUCT n addmsg /kinetics/CaM-Ca4 /kinetics/PP2B/CaMCa4-bind-CaNAB SUBSTRATE n addmsg /kinetics/CaNAB-Ca4 /kinetics/PP2B/CaMCa4-bind-CaNAB SUBSTRATE n addmsg /kinetics/PKA/cAMP-bind-site-B1 /kinetics/PKA/R2C2 REAC A B addmsg /kinetics/PKA/cAMP-bind-site-B1 /kinetics/PKA/R2C2-cAMP REAC B A addmsg /kinetics/PKA/cAMP-bind-site-B2 /kinetics/PKA/R2C2-cAMP REAC A B addmsg /kinetics/PKA/R2C2 /kinetics/PKA/cAMP-bind-site-B1 SUBSTRATE n addmsg /kinetics/PKA/R2C2-cAMP /kinetics/PKA/cAMP-bind-site-B1 PRODUCT n addmsg /kinetics/cAMP /kinetics/PKA/cAMP-bind-site-B1 SUBSTRATE n addmsg /kinetics/PKA/R2C2-cAMP /kinetics/PKA/cAMP-bind-site-B2 SUBSTRATE n addmsg /kinetics/cAMP /kinetics/PKA/cAMP-bind-site-B2 SUBSTRATE n addmsg /kinetics/PKA/R2C2-cAMP2 /kinetics/PKA/cAMP-bind-site-B2 PRODUCT n addmsg /kinetics/PKA/R2C2-cAMP2 /kinetics/PKA/cAMP-bind-site-A1 SUBSTRATE n addmsg /kinetics/cAMP /kinetics/PKA/cAMP-bind-site-A1 SUBSTRATE n addmsg /kinetics/PKA/R2C2-cAMP3 /kinetics/PKA/cAMP-bind-site-A1 PRODUCT n addmsg /kinetics/cAMP /kinetics/PKA/cAMP-bind-site-A2 SUBSTRATE n addmsg /kinetics/PKA/R2C2-cAMP3 /kinetics/PKA/cAMP-bind-site-A2 SUBSTRATE n addmsg /kinetics/PKA/R2C2-cAMP4 /kinetics/PKA/cAMP-bind-site-A2 PRODUCT n addmsg /kinetics/PKA/cAMP-bind-site-B2 /kinetics/PKA/R2C2-cAMP2 REAC B A addmsg /kinetics/PKA/cAMP-bind-site-A1 /kinetics/PKA/R2C2-cAMP2 REAC A B addmsg /kinetics/PKA/cAMP-bind-site-A1 /kinetics/PKA/R2C2-cAMP3 REAC B A addmsg /kinetics/PKA/cAMP-bind-site-A2 /kinetics/PKA/R2C2-cAMP3 REAC A B addmsg /kinetics/PKA/cAMP-bind-site-A2 /kinetics/PKA/R2C2-cAMP4 REAC B A addmsg /kinetics/PKA/Release-C1 /kinetics/PKA/R2C2-cAMP4 REAC A B addmsg /kinetics/PKA/Release-C1 /kinetics/PKA/R2C-cAMP4 REAC B A addmsg /kinetics/PKA/Release-C2 /kinetics/PKA/R2C-cAMP4 REAC A B addmsg /kinetics/PKA/Release-C2 /kinetics/PKA/R2-cAMP4 REAC B A addmsg /kinetics/PKA/R2C2-cAMP4 /kinetics/PKA/Release-C1 SUBSTRATE n addmsg /kinetics/PKA-active /kinetics/PKA/Release-C1 PRODUCT n addmsg /kinetics/PKA/R2C-cAMP4 /kinetics/PKA/Release-C1 PRODUCT n addmsg /kinetics/PKA/R2C-cAMP4 /kinetics/PKA/Release-C2 SUBSTRATE n addmsg /kinetics/PKA-active /kinetics/PKA/Release-C2 PRODUCT n addmsg /kinetics/PKA/R2-cAMP4 /kinetics/PKA/Release-C2 PRODUCT n addmsg /kinetics/PKA/inhib-PKA /kinetics/PKA/PKA-inhibitor REAC A B addmsg /kinetics/PKA-active /kinetics/PKA/inhib-PKA SUBSTRATE n addmsg /kinetics/PKA/PKA-inhibitor /kinetics/PKA/inhib-PKA SUBSTRATE n addmsg /kinetics/PKA/inhibited-PKA /kinetics/PKA/inhib-PKA PRODUCT n addmsg /kinetics/PKA/inhib-PKA /kinetics/PKA/inhibited-PKA REAC B A addmsg /kinetics/PKA/cAMP-bind-site-B1 /kinetics/cAMP REAC A B addmsg /kinetics/PKA/cAMP-bind-site-B2 /kinetics/cAMP REAC A B addmsg /kinetics/PKA/cAMP-bind-site-A1 /kinetics/cAMP REAC A B addmsg /kinetics/PKA/cAMP-bind-site-A2 /kinetics/cAMP REAC A B addmsg /kinetics/AC/AC2*/kenz /kinetics/cAMP MM_PRD pA addmsg /kinetics/AC/AC2-Gs/kenz /kinetics/cAMP MM_PRD pA addmsg /kinetics/AC/AC1-CaM/kenz /kinetics/cAMP MM_PRD pA addmsg /kinetics/AC/AC1-Gs/kenz /kinetics/cAMP MM_PRD pA addmsg /kinetics/AC/AC2*-Gs/kenz /kinetics/cAMP MM_PRD pA addmsg /kinetics/AC/cAMP-PDE*/PDE* /kinetics/cAMP REAC sA B addmsg /kinetics/AC/cAMP-PDE/PDE /kinetics/cAMP REAC sA B addmsg /kinetics/AC/PDE1/PDE1 /kinetics/cAMP REAC sA B addmsg /kinetics/AC/CaM.PDE1/CaM.PDE1 /kinetics/cAMP REAC sA B addmsg /kinetics/AC/AC2*/kenz /kinetics/AC/ATP REAC sA B addmsg /kinetics/AC/AC2-Gs/kenz /kinetics/AC/ATP REAC sA B addmsg /kinetics/AC/AC1-CaM/kenz /kinetics/AC/ATP REAC sA B addmsg /kinetics/AC/AC1-Gs/kenz /kinetics/AC/ATP REAC sA B addmsg /kinetics/AC/AC2*-Gs/kenz /kinetics/AC/ATP REAC sA B addmsg /kinetics/AC/CaM-bind-AC1 /kinetics/AC/AC1-CaM REAC B A addmsg /kinetics/AC/AC1-CaM /kinetics/AC/AC1-CaM/kenz ENZYME n addmsg /kinetics/AC/ATP /kinetics/AC/AC1-CaM/kenz SUBSTRATE n addmsg /kinetics/AC/CaM-bind-AC1 /kinetics/AC/AC1 REAC A B addmsg /kinetics/AC/Gs-bind-AC1 /kinetics/AC/AC1 REAC A B addmsg /kinetics/CaM-Ca4 /kinetics/AC/CaM-bind-AC1 SUBSTRATE n addmsg /kinetics/AC/AC1-CaM /kinetics/AC/CaM-bind-AC1 PRODUCT n addmsg /kinetics/AC/AC1 /kinetics/AC/CaM-bind-AC1 SUBSTRATE n addmsg /kinetics/PKC-active/phosph-AC2 /kinetics/AC/AC2* MM_PRD pA addmsg /kinetics/AC/dephosph-AC2 /kinetics/AC/AC2* REAC A B addmsg /kinetics/AC/Gs-bind-AC2* /kinetics/AC/AC2* REAC A B addmsg /kinetics/AC/AC2* /kinetics/AC/AC2*/kenz ENZYME n addmsg /kinetics/AC/ATP /kinetics/AC/AC2*/kenz SUBSTRATE n addmsg /kinetics/AC/Gs-bind-AC2 /kinetics/AC/AC2-Gs REAC B A addmsg /kinetics/AC/AC2-Gs /kinetics/AC/AC2-Gs/kenz ENZYME n addmsg /kinetics/AC/ATP /kinetics/AC/AC2-Gs/kenz SUBSTRATE n addmsg /kinetics/AC/Gs-bind-AC2 /kinetics/AC/AC2 REAC A B addmsg /kinetics/PKC-active/phosph-AC2 /kinetics/AC/AC2 REAC sA B addmsg /kinetics/AC/dephosph-AC2 /kinetics/AC/AC2 REAC B A addmsg /kinetics/AC/AC2* /kinetics/AC/dephosph-AC2 SUBSTRATE n addmsg /kinetics/AC/AC2 /kinetics/AC/dephosph-AC2 PRODUCT n addmsg /kinetics/AC/Gs-bind-AC1 /kinetics/AC/AC1-Gs REAC B A addmsg /kinetics/AC/AC1-Gs /kinetics/AC/AC1-Gs/kenz ENZYME n addmsg /kinetics/AC/ATP /kinetics/AC/AC1-Gs/kenz SUBSTRATE n addmsg /kinetics/AC/AC2 /kinetics/AC/Gs-bind-AC2 SUBSTRATE n addmsg /kinetics/AC/AC2-Gs /kinetics/AC/Gs-bind-AC2 PRODUCT n addmsg /kinetics/Gs-alpha /kinetics/AC/Gs-bind-AC2 SUBSTRATE n addmsg /kinetics/Gs-alpha /kinetics/AC/Gs-bind-AC1 SUBSTRATE n addmsg /kinetics/AC/AC1 /kinetics/AC/Gs-bind-AC1 SUBSTRATE n addmsg /kinetics/AC/AC1-Gs /kinetics/AC/Gs-bind-AC1 PRODUCT n addmsg /kinetics/AC/cAMP-PDE*/PDE* /kinetics/AC/AMP MM_PRD pA addmsg /kinetics/AC/cAMP-PDE/PDE /kinetics/AC/AMP MM_PRD pA addmsg /kinetics/AC/CaM.PDE1/CaM.PDE1 /kinetics/AC/AMP MM_PRD pA addmsg /kinetics/AC/PDE1/PDE1 /kinetics/AC/AMP MM_PRD pA addmsg /kinetics/AC/Gs-bind-AC2* /kinetics/AC/AC2*-Gs REAC B A addmsg /kinetics/AC/AC2*-Gs /kinetics/AC/AC2*-Gs/kenz ENZYME n addmsg /kinetics/AC/ATP /kinetics/AC/AC2*-Gs/kenz SUBSTRATE n addmsg /kinetics/Gs-alpha /kinetics/AC/Gs-bind-AC2* SUBSTRATE n addmsg /kinetics/AC/AC2*-Gs /kinetics/AC/Gs-bind-AC2* PRODUCT n addmsg /kinetics/AC/AC2* /kinetics/AC/Gs-bind-AC2* SUBSTRATE n addmsg /kinetics/AC/cAMP-PDE/PDE /kinetics/AC/cAMP-PDE REAC eA B addmsg /kinetics/AC/dephosph-PDE /kinetics/AC/cAMP-PDE REAC B A addmsg /kinetics/PKA-active/phosph-PDE /kinetics/AC/cAMP-PDE REAC sA B addmsg /kinetics/AC/cAMP-PDE /kinetics/AC/cAMP-PDE/PDE ENZYME n addmsg /kinetics/cAMP /kinetics/AC/cAMP-PDE/PDE SUBSTRATE n addmsg /kinetics/AC/cAMP-PDE*/PDE* /kinetics/AC/cAMP-PDE* REAC eA B addmsg /kinetics/AC/dephosph-PDE /kinetics/AC/cAMP-PDE* REAC A B addmsg /kinetics/PKA-active/phosph-PDE /kinetics/AC/cAMP-PDE* MM_PRD pA addmsg /kinetics/AC/cAMP-PDE* /kinetics/AC/cAMP-PDE*/PDE* ENZYME n addmsg /kinetics/cAMP /kinetics/AC/cAMP-PDE*/PDE* SUBSTRATE n addmsg /kinetics/AC/cAMP-PDE* /kinetics/AC/dephosph-PDE SUBSTRATE n addmsg /kinetics/AC/cAMP-PDE /kinetics/AC/dephosph-PDE PRODUCT n addmsg /kinetics/AC/PDE1/PDE1 /kinetics/AC/PDE1 REAC eA B addmsg /kinetics/AC/CaM_bind_PDE1 /kinetics/AC/PDE1 REAC A B addmsg /kinetics/AC/PDE1 /kinetics/AC/PDE1/PDE1 ENZYME n addmsg /kinetics/cAMP /kinetics/AC/PDE1/PDE1 SUBSTRATE n addmsg /kinetics/AC/CaM.PDE1/CaM.PDE1 /kinetics/AC/CaM.PDE1 REAC eA B addmsg /kinetics/AC/CaM_bind_PDE1 /kinetics/AC/CaM.PDE1 REAC B A addmsg /kinetics/AC/CaM.PDE1 /kinetics/AC/CaM.PDE1/CaM.PDE1 ENZYME n addmsg /kinetics/cAMP /kinetics/AC/CaM.PDE1/CaM.PDE1 SUBSTRATE n addmsg /kinetics/AC/PDE1 /kinetics/AC/CaM_bind_PDE1 SUBSTRATE n addmsg /kinetics/AC/CaM.PDE1 /kinetics/AC/CaM_bind_PDE1 PRODUCT n addmsg /kinetics/CaM-Ca4 /kinetics/AC/CaM_bind_PDE1 SUBSTRATE n addmsg /kinetics/AC/Gs-bind-AC2 /kinetics/Gs-alpha REAC A B addmsg /kinetics/AC/Gs-bind-AC1 /kinetics/Gs-alpha REAC A B addmsg /kinetics/AC/Gs-bind-AC2* /kinetics/Gs-alpha REAC A B addmsg /kinetics/PP1-active /kinetics/tot_PP1 SUMTOTAL n nInit addmsg /kinetics/PP1-active/Deph-thr286 /kinetics/tot_PP1 SUMTOTAL nComplex nComplexInit addmsg /kinetics/PP1-active/Deph-thr305 /kinetics/tot_PP1 SUMTOTAL nComplex nComplexInit addmsg /kinetics/PP1-active/Deph-thr286c /kinetics/tot_PP1 SUMTOTAL nComplex nComplexInit addmsg /kinetics/PP1-active/Deph_thr286b /kinetics/tot_PP1 SUMTOTAL nComplex nComplexInit addmsg /kinetics/PP1-active/Deph-thr306 /kinetics/tot_PP1 SUMTOTAL nComplex nComplexInit addmsg /kinetics/CaMKII/tot_CaM_CaMKII /kinetics/tot_CaMKII-active SUMTOTAL n nInit addmsg /kinetics/CaMKII/tot_autonomous_CaMKII /kinetics/tot_CaMKII-active SUMTOTAL n nInit addmsg /kinetics/CaM(Ca)n-CaNAB /kinetics/tot_CaN-active SUMTOTAL n nInit addmsg /kinetics/CaNAB-Ca4 /kinetics/tot_CaN-active SUMTOTAL n nInit addmsg /kinetics/Ca /graphs/conc1/Ca.Co PLOT Co *Ca.Co *red addmsg /kinetics/tot_CaMKII-active /graphs/conc1/tot_CaMKII-active.Co PLOT Co *tot_CaMKII-active.Co *blue addmsg /kinetics/tot_CaN-active /graphs/conc2/tot_CaN-active.Co PLOT Co *tot_CaN-active.Co *red addmsg /kinetics/PKA-active /moregraphs/conc3/PKA-active.Co PLOT Co *PKA-active.Co *yellow addmsg /kinetics/tot_PP1 /moregraphs/conc4/tot_PP1.Co PLOT Co *tot_PP1.Co *blue enddump // End of dump setfield /kinetics/Ca_tab table->dx 1 setfield /kinetics/Ca_tab table->invdx 1 call /kinetics/tot_PP1/notes LOAD \ " tot_PP1 has inputs from Deph-thr286, PP1-active, Deph-thr305, Deph-thr286c, Deph-thr286b,Deph-thr305. except PP1-active all other inputs are enzyme-substrate complex which is not currently supported by doqcs." \ "But can be accessed from GENESIS file." call /kinetics/doqcsinfo/notes LOAD \ "This is the model file for figure 3 from Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It is a model of the Ca activation of CaMKII and other CaM-activated enzymes. It includes the regulatory phosphatases PP1 and PP2B (Calcineurin) acting on CaMKII and also includes CaM-activated adenylyl cyclase and PKA in the synapse.
Demonstration script files for generating the figures in the paper, including figure 3, are available here." complete_loading