// DOQCS :http://doqcs.ncbs.res.in/ // Accession Name = CaMKII // Accession Number = 33 // Pathway Name = CaMKII // Pathway Number = 174 // Transcriber = Upinder S. Bhalla, NCBS // Developer = William R. Holmes // Species = Generic mammalian // Tissue = Brain - Neuronal // Cell Compartment = Synapse // Notes = This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in William R. Holmes J Comput Neurosci. (2000) 8(1):65-85. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original. //genesis // kkit Version 11 flat dumpfile // Saved on Fri Dec 9 17:22:53 2005 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 2e-05 CONTROLDT = 5 PLOTDT = 0.005 MAXTIME = 30 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 0 DEFAULT_VOL = 1.309e-19 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 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0 simundump kreac /kinetics/CaMKII/dephosph_T305 0 0.01 0 "" white 21 3 -23 0 simundump doqcsinfo /kinetics/doqcsinfo 0 pdb174.g CaMKII pathway \ "Upinder S. Bhalla, NCBS" " William R. Holmes" "citation here" \ "General Mammalian" "Brain - Neuronal" Synapse Qualitative \ "William R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication )" \ "Approximate implementation" "Approximates original data " 19 -13 0 simundump xgraph /graphs/conc1 0 0 30 0 5.3812 0 simundump xgraph /graphs/conc2 0 0 30 0 0.1415 0 simundump xplot /graphs/conc1/Tot-active-CaMKII.Co 3 524288 \ "delete_plot.w ; edit_plot.D " maroon 0 0 1 simundump xplot /graphs/conc1/CaN-CaMCa4.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 25 0 0 1 simundump xplot /graphs/conc1/CaMKII-CaMCa4.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 56 0 0 1 simundump xplot /graphs/conc1/Trapped-T286.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 61 0 0 1 simundump xplot /graphs/conc1/Autonomous.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 58 0 0 1 simundump xplot /graphs/conc1/Capped.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 51 0 0 1 simundump xplot /graphs/conc2/CaMCa4.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 18 0 0 1 simundump xplot /graphs/conc2/Ca.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 62 0 0 1 simundump xgraph /moregraphs/conc3 0 0 30 0 1 0 simundump xgraph /moregraphs/conc4 0 0 30 0 1 0 simundump xcoredraw /edit/draw 0 -2 21 -25 8 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 \ "Just the CaMKII part of the Holmes 2000 JCNS model" \ "" addmsg /kinetics/CaMKII/CaMKII-CaM-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaMKII/CaMKII-CaMCa-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaMKII/CaMKII-CaMCa2-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/CaMKII/CaMKII-CaMCa3-bind-Ca /kinetics/Ca REAC A B addmsg /kinetics/Ca_tab /kinetics/Ca SLAVE output addmsg /kinetics/CaMKII/CaMKII-bind-CaM /kinetics/CaM/CaM REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa /kinetics/CaM/CaMCa REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa2 /kinetics/CaM/CaMCa2 REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa3 /kinetics/CaM/CaMCa3 REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa4 /kinetics/CaM/CaMCa4 REAC A B addmsg /kinetics/CaMKII/Autonomous-bind-CaMCa4 /kinetics/CaM/CaMCa4 REAC A B addmsg /kinetics/CaMKII/Autonomous_lose_CaMCa4 /kinetics/CaM/CaMCa4 REAC B A addmsg /kinetics/CaMKII/CaMKII-CaM-bind-Ca /kinetics/CaMKII/CaMKII-CaM REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaM /kinetics/CaMKII/CaMKII-CaM REAC B A addmsg /kinetics/CaMKII/CaMKII-CaM /kinetics/CaMKII/CaMKII-CaM-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CAMKII-CaMCa /kinetics/CaMKII/CaMKII-CaM-bind-Ca PRODUCT n addmsg /kinetics/Ca /kinetics/CaMKII/CaMKII-CaM-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaM-bind-Ca /kinetics/CaMKII/CAMKII-CaMCa REAC B A addmsg /kinetics/CaMKII/CaMKII-CaMCa-bind-Ca /kinetics/CaMKII/CAMKII-CaMCa REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa /kinetics/CaMKII/CAMKII-CaMCa REAC B A addmsg /kinetics/CaMKII/CAMKII-CaMCa /kinetics/CaMKII/CaMKII-CaMCa-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa2 /kinetics/CaMKII/CaMKII-CaMCa-bind-Ca PRODUCT n addmsg /kinetics/Ca /kinetics/CaMKII/CaMKII-CaMCa-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa-bind-Ca /kinetics/CaMKII/CaMKII-CaMCa2 REAC B A addmsg /kinetics/CaMKII/CaMKII-CaMCa2-bind-Ca /kinetics/CaMKII/CaMKII-CaMCa2 REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa2 /kinetics/CaMKII/CaMKII-CaMCa2 REAC B A addmsg /kinetics/CaM/CaM /kinetics/CaMKII/CaMKII-bind-CaM SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaM /kinetics/CaMKII/CaMKII-bind-CaM PRODUCT n addmsg /kinetics/CaMKII/CaMKII /kinetics/CaMKII/CaMKII-bind-CaM SUBSTRATE n addmsg /kinetics/CaM/CaMCa /kinetics/CaMKII/CaMKII-bind-CaMCa SUBSTRATE n addmsg /kinetics/CaMKII/CAMKII-CaMCa /kinetics/CaMKII/CaMKII-bind-CaMCa PRODUCT n addmsg /kinetics/CaMKII/CaMKII /kinetics/CaMKII/CaMKII-bind-CaMCa SUBSTRATE n addmsg /kinetics/CaM/CaMCa2 /kinetics/CaMKII/CaMKII-bind-CaMCa2 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa2 /kinetics/CaMKII/CaMKII-bind-CaMCa2 PRODUCT n addmsg /kinetics/CaMKII/CaMKII /kinetics/CaMKII/CaMKII-bind-CaMCa2 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-bind-CaM /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa2 /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa3 /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa4 /kinetics/CaMKII/CaMKII REAC A B addmsg /kinetics/CaMKII/dephosph_T286 /kinetics/CaMKII/CaMKII REAC B A addmsg /kinetics/CaM/CaMCa3 /kinetics/CaMKII/CaMKII-bind-CaMCa3 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa3 /kinetics/CaMKII/CaMKII-bind-CaMCa3 PRODUCT n addmsg /kinetics/CaMKII/CaMKII /kinetics/CaMKII/CaMKII-bind-CaMCa3 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa2 /kinetics/CaMKII/CaMKII-CaMCa2-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa3 /kinetics/CaMKII/CaMKII-CaMCa2-bind-Ca PRODUCT n addmsg /kinetics/Ca /kinetics/CaMKII/CaMKII-CaMCa2-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa2-bind-Ca /kinetics/CaMKII/CaMKII-CaMCa3 REAC B A addmsg /kinetics/CaMKII/CaMKII-CaMCa3-bind-Ca /kinetics/CaMKII/CaMKII-CaMCa3 REAC A B addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa3 /kinetics/CaMKII/CaMKII-CaMCa3 REAC B A addmsg /kinetics/CaMKII/CaMKII-CaMCa3 /kinetics/CaMKII/CaMKII-CaMCa3-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa4 /kinetics/CaMKII/CaMKII-CaMCa3-bind-Ca PRODUCT n addmsg /kinetics/Ca /kinetics/CaMKII/CaMKII-CaMCa3-bind-Ca SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa3-bind-Ca /kinetics/CaMKII/CaMKII-CaMCa4 REAC B A addmsg /kinetics/CaMKII/CaMKII-bind-CaMCa4 /kinetics/CaMKII/CaMKII-CaMCa4 REAC B A addmsg /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286 /kinetics/CaMKII/CaMKII-CaMCa4 REAC sA B addmsg /kinetics/CaMKII/Dephosph_trapped_T286 /kinetics/CaMKII/CaMKII-CaMCa4 REAC B A addmsg /kinetics/CaM/CaMCa4 /kinetics/CaMKII/CaMKII-bind-CaMCa4 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa4 /kinetics/CaMKII/CaMKII-bind-CaMCa4 PRODUCT n addmsg /kinetics/CaMKII/CaMKII /kinetics/CaMKII/CaMKII-bind-CaMCa4 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa4 /kinetics/CaMKII/Tot-active-CaMKII SUMTOTAL n nInit addmsg /kinetics/CaMKII/Trapped-T286 /kinetics/CaMKII/Tot-active-CaMKII SUMTOTAL n nInit addmsg /kinetics/CaMKII/Capped /kinetics/CaMKII/Tot-active-CaMKII SUMTOTAL n nInit addmsg /kinetics/CaMKII/Autonomous /kinetics/CaMKII/Tot-active-CaMKII SUMTOTAL n nInit addmsg /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286 /kinetics/CaMKII/Tot-active-CaMKII REAC eA B addmsg /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305 /kinetics/CaMKII/Tot-active-CaMKII REAC eA B addmsg /kinetics/CaMKII/Tot-active-CaMKII /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286 ENZYME n addmsg /kinetics/CaMKII/CaMKII-CaMCa4 /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286 SUBSTRATE n addmsg /kinetics/CaMKII/Total_CaMKII /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286 INTRAMOL n addmsg /kinetics/CaMKII/Tot-active-CaMKII /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305 ENZYME n addmsg /kinetics/CaMKII/Autonomous /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305 SUBSTRATE n addmsg /kinetics/CaMKII/Total_CaMKII /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305 INTRAMOL n addmsg /kinetics/CaMKII/Trapped-T286 /kinetics/CaMKII/Dephosph_trapped_T286 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII-CaMCa4 /kinetics/CaMKII/Dephosph_trapped_T286 PRODUCT n addmsg /kinetics/CaMKII/Autonomous-bind-CaMCa4 /kinetics/CaMKII/Trapped-T286 REAC B A addmsg /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286 /kinetics/CaMKII/Trapped-T286 MM_PRD pA addmsg /kinetics/CaMKII/Autonomous_lose_CaMCa4 /kinetics/CaMKII/Trapped-T286 REAC A B addmsg /kinetics/CaMKII/Dephosph_trapped_T286 /kinetics/CaMKII/Trapped-T286 REAC A B addmsg /kinetics/CaMKII/Autonomous /kinetics/CaMKII/dephosph_T286 SUBSTRATE n addmsg /kinetics/CaMKII/CaMKII /kinetics/CaMKII/dephosph_T286 PRODUCT n addmsg /kinetics/CaMKII/Trapped-T286 /kinetics/CaMKII/Autonomous_lose_CaMCa4 SUBSTRATE n addmsg /kinetics/CaMKII/Autonomous /kinetics/CaMKII/Autonomous_lose_CaMCa4 PRODUCT n addmsg /kinetics/CaM/CaMCa4 /kinetics/CaMKII/Autonomous_lose_CaMCa4 PRODUCT n addmsg /kinetics/CaM/CaMCa4 /kinetics/CaMKII/Autonomous-bind-CaMCa4 SUBSTRATE n addmsg /kinetics/CaMKII/Autonomous /kinetics/CaMKII/Autonomous-bind-CaMCa4 SUBSTRATE n addmsg /kinetics/CaMKII/Trapped-T286 /kinetics/CaMKII/Autonomous-bind-CaMCa4 PRODUCT n addmsg /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305 /kinetics/CaMKII/Capped MM_PRD pA addmsg /kinetics/CaMKII/dephosph_T305 /kinetics/CaMKII/Capped REAC A B addmsg /kinetics/CaMKII/Autonomous-bind-CaMCa4 /kinetics/CaMKII/Autonomous REAC A B addmsg /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305 /kinetics/CaMKII/Autonomous REAC sA B addmsg /kinetics/CaMKII/Autonomous_lose_CaMCa4 /kinetics/CaMKII/Autonomous REAC B A addmsg /kinetics/CaMKII/dephosph_T286 /kinetics/CaMKII/Autonomous REAC A B addmsg /kinetics/CaMKII/dephosph_T305 /kinetics/CaMKII/Autonomous REAC B A addmsg /kinetics/CaMKII/Capped /kinetics/CaMKII/dephosph_T305 SUBSTRATE n addmsg /kinetics/CaMKII/Autonomous /kinetics/CaMKII/dephosph_T305 PRODUCT n addmsg /kinetics/CaMKII/Tot-active-CaMKII /graphs/conc1/Tot-active-CaMKII.Co PLOT Co *Tot-active-CaMKII.Co *maroon addmsg /kinetics/CaMKII/CaMKII-CaMCa4 /graphs/conc1/CaMKII-CaMCa4.Co PLOT Co *CaMKII-CaMCa4.Co *56 addmsg /kinetics/CaMKII/Trapped-T286 /graphs/conc1/Trapped-T286.Co PLOT Co *Trapped-T286.Co *61 addmsg /kinetics/CaMKII/Autonomous /graphs/conc1/Autonomous.Co PLOT Co *Autonomous.Co *58 addmsg /kinetics/CaMKII/Capped /graphs/conc1/Capped.Co PLOT Co *Capped.Co *51 addmsg /kinetics/CaM/CaMCa4 /graphs/conc2/CaMCa4.Co PLOT Co *CaMCa4.Co *18 addmsg /kinetics/Ca /graphs/conc2/Ca.Co PLOT Co *Ca.Co *62 enddump // End of dump setfield /kinetics/Ca_tab table->dx 0.0050063 setfield /kinetics/Ca_tab table->invdx 199.75 call /kinetics/Ca/notes LOAD \ "70 nM initial conc from Holmes." \ "" call /kinetics/CaM/CaM/notes LOAD \ "Init conc form model is 80 uM." call /kinetics/CaMKII/CaMKII/notes LOAD \ "Init level is 100 holoenzymes of 10 subunits each." call /kinetics/CaMKII/Tot-active-CaMKII/phosph_T286/notes LOAD \ "This enzyme represents an intra-holoenzyme reaction from one active" \ "subunit to its neighbor. k1 is now in units of 1/sec." \ "The Km, Ratio and Vmax terms are pretty meaningless. The " \ "enzyme really is there just to represent the forward rate of 0.5" \ "from CaMKII-CaMCa4 to Trapped-T285. We have a high k3 so that the " \ "reac is limited only by k1. The enzyme itself does not have much purpose" \ "other than to allow scaling of the overall rate by the proportion of" \ "adjacent molecules in the appropriate state." call /kinetics/CaMKII/Tot-active-CaMKII/phosph_T305/notes LOAD \ "This enzyme also represents an intra-holoenzyme reaction." \ "So it is not really treated as an enzyme in Holme's model, more like" \ "a probability of reaction that scales according to the number of" \ "active CaMKII neighboring subunits. Here we approximate it as an" \ "enzyme rate limited by the k1=0.1 step, no back reaction, and with a " \ "scaling from Total_CaMKII such that the effective forward rate will" \ "simply be the fraction of CaMKII that are active, times 1/10 for nearest" \ "neigbors, times k1." call /kinetics/CaMKII/Dephosph_trapped_T286/notes LOAD \ "This rate is for the back reaction for the step represented here as" \ "a separate enzyme, but by Holmes as a single reversible reaction. Here" \ "it is treated as separate because the forward reaction is dependent on" \ "activity levels of the CaMKII, whereas the back reaction is not." \ "Holmes tries a range of values for this back-reaction and says that" \ "it doesn't matter much." call /kinetics/CaMKII/Total_CaMKII/notes LOAD \ "This is not directly in the Holmes model. It is a trick used in " \ "GENESIS/Kinetikit to scale activity down for intramolecular reactions." \ "Here it is used to scale the autophosph reactions such that only" \ "neighboring subunits will phosphorylate each other. This is done by" \ "scaling down the actual conc (in the enzyme parent, Tot-active-CaMKII)" \ "by the total conc such that instead of a conc, we the fraction of " \ "nearby subunits that will be active. Note that this conc of" \ "10000 CaMKII subunits is 10 times" \ "the true conc, since only 1/10 of the molecules are neighboring molecules." call /kinetics/CaMKII/Autonomous_lose_CaMCa4/notes LOAD \ "Holmes says that this rate is variable, and depends on Ca conc." \ "It is 0.1 when [Ca] = 10 nM, and 0.00355/sec when [Ca] is 1.0" \ "For our purposes, we assume a good steady approx to this rate is" \ "0.02." call /kinetics/CaMKII/dephosph_T305/notes LOAD \ "This is treated as a separate reaction because it is independent of" \ "the CaMKII concentration or activation state, unlike the forward" \ "reaction in the Holmes paper. Holmes tries a range of rates for this" \ "step, and says it doesn't matter much." call /kinetics/doqcsinfo/notes LOAD \ " This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in William R. Holmes J Comput Neurosci. (2000) 8(1):65-85. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original. " complete_loading