//genesis // kkit Version 8 flat dumpfile // Saved on Tue Aug 27 16:57:20 2002 include kkit {argv 1} FASTDT = 0.0001 SIMDT = 0.001 CONTROLDT = 1 PLOTDT = 1 MAXTIME = 900 TRANSIENT_TIME = 10 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1.6667e-21 VERSION = 8.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump table input output alloced step_mode stepsize x y z simobjdump xtree path script namemode sizescale simobjdump xcoredraw xmin xmax ymin ymax simobjdump xtext editable simobjdump xgraph xmin xmax ymin ymax overlay simobjdump xplot pixflags script fg ysquish do_slope wy simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ link savename file version md5sum mod_save_flag x y z simobjdump kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \ xtree_fg_req xtree_textfg_req x y z simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ xtree_textfg_req x y z simobjdump proto x y z simobjdump linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z simobjdump uplink xtree_fg_req xtree_textfg_req x y z simobjdump downlink xtree_fg_req xtree_textfg_req x y z simobjdump mirror notes xtree_fg_req x y z simundump group /kinetics/GC 0 black black x 0 0 "" black \ /home2/bhalla/scripts/modules/black_0.g 0 0 0 -83 -747 0 simundump kpool /kinetics/GC/NO.sGCfast 0 0 0 0 0 0 0 0 1 0 "" 27 black -72 \ -748 0 simundump kpool /kinetics/GC/NO.SGC_6coord 0 0 0 0 0 0 0 0 1 0 "" 0 black -64 \ -747 0 simundump kpool /kinetics/GC/sGCfast 0 3 3 3 3 3 3 0 1 4 "" 15 black -80 -749 \ 0 simundump kreac /kinetics/GC/NO_bind_sGCfast 0 700 800 "" white black -76 \ -752 0 simundump kreac /kinetics/GC/form_6coord 0 850 0 "" white black -69 -751 0 simundump kreac /kinetics/GC/act_sGCfast 0 20 0.2 "" white black -61 -750 0 simundump kreac /kinetics/GC/act_sGCslow 0 1.6 0.02 "" white black -56 -757 0 simundump kreac /kinetics/GC/NObindnonheme 0 5 25 "" white black -61 -756 0 simundump kpool /kinetics/GC/nonhemebind_int 0 0 0 0 0 0 0 0 1 0 "" 7 black \ -65 -762 0 simundump kpool /kinetics/GC/NO.sGC6coord 0 0 0 0 0 0 0 0 1 0 "" 32 black -74 \ -760 0 simundump kreac /kinetics/GC/form6coord 0 850 0 "" white black -69 -755 0 simundump kreac /kinetics/GC/NO_bind_sGCslow 0 700 800 "" white black -76 \ -754 0 simundump kpool /kinetics/GC/NO.sGCslow 0 0 0 0 0 0 0 0 1 0 "" 47 black -80 \ -759 0 simundump kpool /kinetics/GC/sGCslow 0 3 3 3 3 3 3 0 1 4 "" 55 black -83 -757 \ 0 simundump kpool /kinetics/GC/NO 0 5 0.1 0.1 0.1 0.1 5 0 1 0 "" 0 black -59 \ -753 0 simundump kpool /kinetics/GC/sGCtot 0 0 0 0 0 0 0 0 1 0 "" 22 black -50 -754 \ 0 simundump kenz /kinetics/GC/sGCtot/sGC_act 0 0 0 0 0 1 3.675 88.2 22.05 0 1 \ "" black 22 "" -42 -754 0 simundump kpool /kinetics/GC/NO.sGC_5coord 0 0 0 0 0 0 0 0 1 0 "" 57 black \ -50 -749 0 simundump kreac /kinetics/GC/phosph_NO.sGC 0 0.25 0 "" white black -42 -746 0 simundump kpool /kinetics/GC/deph_NO.sGC 0 0 0 0 0 0 0 0 1 0 "" 25 black -35 \ -749 0 simundump kpool /kinetics/GC/NO2.sGC_5coord 0 0 0 0 0 0 0 0 1 0 "" 29 black \ -50 -759 0 simundump kpool /kinetics/GC/deph_NO2.sGC 0 0 0 0 0 0 0 0 1 0 "" 43 black -33 \ -759 0 simundump kreac /kinetics/GC/phosph_NO2.sGC 0 0.6 0 "" white black -42 -762 0 simundump kpool /kinetics/GC/GTP 0 1000 10 10 10 10 1000 0 1 4 "" 16 black \ -20 -756 0 simundump kpool /kinetics/GC/sGC-ppase 0 0.5 0.5 0.5 0.5 0.5 0.5 0 1 0 "" 56 \ black -25 -746 0 simundump kpool /kinetics/GC/sGC-ppase* 0 0 0 0 0 0 0 0 1 0 "" 46 black -24 \ -752 0 simundump kenz /kinetics/GC/sGC-ppase*/deph_NO2_sGC 0 0 0 0 0 1 1.8 7.2 1.8 0 \ 0 "" black 46 "" -42 -756 0 simundump kenz /kinetics/GC/sGC-ppase*/deph_NO_sGC 0 0 0 0 0 1 1.8 7.2 1.8 0 \ 0 "" black 46 "" -42 -752 0 simundump kreac /kinetics/GC/deph_sGC-ppase 0 20 0 "" white black -20 -749 0 simundump group /kinetics/PDE 0 black black x 0 0 "" PDE \ /home2/bhalla/scripts/modules/PDE_0.g 0 0 0 -13 -761 0 simundump kpool /kinetics/PDE/PDE 0 5 0.28 0.28 0.28 0.28 5 0 1 0 "" 57 black \ -10 -756 0 simundump kenz /kinetics/PDE/PDE/PDE_basal 0 0 0 0 0 1 12.245 9.6 2.4 0 1 "" \ black 57 "" -7 -759 0 simundump kpool /kinetics/PDE/cGK 0 14.6 1.1 1.1 1.1 1.1 14.6 0 1 0 "" 41 \ black 5 -744 0 simundump kpool /kinetics/PDE/cGMP.PDE 0 0 0 0 0 0 0 0 1 0 "" 32 black 4 -756 \ 0 simundump kenz /kinetics/PDE/cGMP.PDE/cGMP.PDE_basal 0 0 0 0 0 1 12.245 9.6 \ 2.4 0 0 "" black 32 "" 4 -759 0 simundump kpool /kinetics/PDE/5primeGMP 0 0 0 0 0 0 0 0 1 0 "" 22 black 2 \ -762 0 simundump kreac /kinetics/PDE/PDEbind_cGMP 0 10 13 "" white black -6 -751 0 simundump kreac /kinetics/PDE/cGMPbindcGK 0 10 81 "" white black 4 -747 0 simundump kpool /kinetics/PDE/cGMP_PDE* 0 0.5 0 0 0 0 0.5 0 1 0 "" 47 black \ 16 -756 0 simundump kenz /kinetics/PDE/cGMP_PDE*/PDE_active 0 0 0 0 0 1 33.362 15.48 \ 3.87 0 1 "" black 47 "" 16 -759 0 simundump kreac /kinetics/PDE/fast_site_bind 0 10 37 "" white black -10 -747 \ 0 simundump kpool /kinetics/PDE/Myo_phosphatase 0 0.5 0.5 0.5 0.5 0.5 0.5 0 1 0 \ "" 0 black 16 -750 0 simundump kenz /kinetics/PDE/Myo_phosphatase/PP1 0 0 0 0 0 1 0.99 7.92 1.98 0 \ 0 "" black 0 "" 16 -751 0 simundump kpool /kinetics/PDE/cGMP.PKG 0 0 0 0 0 0 0 0 1 0 "" 32 black -7 \ -744 0 simundump kpool /kinetics/PDE/cGMP2.PKG 0 7.3 0 0 0 0 7.3 0 1 0 "" 24 black 3 \ -750 0 simundump kenz /kinetics/PDE/cGMP2.PKG/PKG_act 0 0 0 0 0 1 0.3011 2.4088 \ 0.6022 0 0 "" black 24 "" 5 -751 0 simundump kenz /kinetics/PDE/cGMP2.PKG/sGCppase_act 0 0 0 0 0 1 123.1 49.24 \ 12.31 0 0 "" black 24 "" -8 -749 0 simundump kpool /kinetics/cGMP 0 10 0 0 0 0 10 0 1 0 "" 54 black -20 -753 0 simundump xgraph /graphs/conc1 0 0 900 0 0.0024221 0 simundump xgraph /graphs/conc2 0 0 900 0 10.023 0 simundump xplot /graphs/conc1/cGMP_PDE*.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xplot /graphs/conc2/5primeGMP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 22 0 0 1 simundump xgraph /moregraphs/conc3 0 0 1483 0 0.084449 0 simundump xgraph /moregraphs/conc4 0 0 1468 0.058788 0.28079 0 simundump xplot /moregraphs/conc3/cGMP2.PKG.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 24 0 0 1 simundump xplot /moregraphs/conc3/cGMP.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 54 0 0 1 simundump xcoredraw /edit/draw 0 -85 18 -764 -742 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "This model includes the cGMP dependent protein kinase, which is one" \ "of the important downstream molecules. This model features phosphorylation" \ "of PDE by cGMP_PKG, and the direct binding of cGMP with PDE and undergoing" \ "hydrolysis to 5primeGMP. Mechanism of cGMP binding to cGK as proposed by " \ "Taylor et al., 2000, JBC, 275(36):28053-28062. Kinetic parameters used" \ "from the literature cited in the model, as well as refs cited in those " \ "papers. Model was tested using Corbin et al., EJBiochem, 2000, 267:2760-2767." \ "Three plots for the phosphorylation pf PDE and PDE assay were replicated. Though" \ "the shape of the curves matched well, numbers could not be matched exactly, which" \ "might be due to the use of Vmax values of PKG and PDE which were from other" \ "literature sources, since Corbin et al., do not say much about the changes in Vmax." \ "Still we could see the 1.5 to 1.7 fold increase in activity as proposed by Corbin et al" \ "and other papers. A couple of inhibitors were used by Corbin et al., in their expts," \ "which we did not use in the model. So by bringing down the concentration of the PKG and PDe" \ "as do the inhibitors, we could match the numbers. But the values shown in this model are" \ "near physiological levels, and to match the plots we have to replicate the experimental" \ "conditions exactly." addmsg /kinetics/GC/NO_bind_sGCfast /kinetics/GC/NO.sGCfast REAC B A addmsg /kinetics/GC/form_6coord /kinetics/GC/NO.sGCfast REAC A B addmsg /kinetics/GC/form_6coord /kinetics/GC/NO.SGC_6coord REAC B A addmsg /kinetics/GC/act_sGCfast /kinetics/GC/NO.SGC_6coord REAC A B addmsg /kinetics/GC/NO_bind_sGCfast /kinetics/GC/sGCfast REAC A B addmsg /kinetics/GC/sGCfast /kinetics/GC/NO_bind_sGCfast SUBSTRATE n addmsg /kinetics/GC/NO.sGCfast /kinetics/GC/NO_bind_sGCfast PRODUCT n addmsg /kinetics/GC/NO /kinetics/GC/NO_bind_sGCfast SUBSTRATE n addmsg /kinetics/GC/NO.sGCfast /kinetics/GC/form_6coord SUBSTRATE n addmsg /kinetics/GC/NO.SGC_6coord /kinetics/GC/form_6coord PRODUCT n addmsg /kinetics/GC/NO.SGC_6coord /kinetics/GC/act_sGCfast SUBSTRATE n addmsg /kinetics/GC/NO.sGC_5coord /kinetics/GC/act_sGCfast PRODUCT n addmsg /kinetics/GC/nonhemebind_int /kinetics/GC/act_sGCslow SUBSTRATE n addmsg /kinetics/GC/NO2.sGC_5coord /kinetics/GC/act_sGCslow PRODUCT n addmsg /kinetics/GC/NO.sGC6coord /kinetics/GC/NObindnonheme SUBSTRATE n addmsg /kinetics/GC/nonhemebind_int /kinetics/GC/NObindnonheme PRODUCT n addmsg /kinetics/GC/NO /kinetics/GC/NObindnonheme SUBSTRATE n addmsg /kinetics/GC/NObindnonheme /kinetics/GC/nonhemebind_int REAC B A addmsg /kinetics/GC/act_sGCslow /kinetics/GC/nonhemebind_int REAC A B addmsg /kinetics/GC/form6coord /kinetics/GC/NO.sGC6coord REAC B A addmsg /kinetics/GC/NObindnonheme /kinetics/GC/NO.sGC6coord REAC A B addmsg /kinetics/GC/NO.sGCslow /kinetics/GC/form6coord SUBSTRATE n addmsg /kinetics/GC/NO.sGC6coord /kinetics/GC/form6coord PRODUCT n addmsg /kinetics/GC/sGCslow /kinetics/GC/NO_bind_sGCslow SUBSTRATE n addmsg /kinetics/GC/NO.sGCslow /kinetics/GC/NO_bind_sGCslow PRODUCT n addmsg /kinetics/GC/NO /kinetics/GC/NO_bind_sGCslow SUBSTRATE n addmsg /kinetics/GC/NO_bind_sGCslow /kinetics/GC/NO.sGCslow REAC B A addmsg /kinetics/GC/form6coord /kinetics/GC/NO.sGCslow REAC A B addmsg /kinetics/GC/NO_bind_sGCslow /kinetics/GC/sGCslow REAC A B addmsg /kinetics/GC/NO_bind_sGCfast /kinetics/GC/NO REAC A B addmsg /kinetics/GC/NO_bind_sGCslow /kinetics/GC/NO REAC A B addmsg /kinetics/GC/NObindnonheme /kinetics/GC/NO REAC A B addmsg /kinetics/GC/NO.sGC_5coord /kinetics/GC/sGCtot SUMTOTAL n nInit addmsg /kinetics/GC/NO2.sGC_5coord /kinetics/GC/sGCtot SUMTOTAL n nInit addmsg /kinetics/GC/sGCtot /kinetics/GC/sGCtot/sGC_act ENZYME n addmsg /kinetics/GC/GTP /kinetics/GC/sGCtot/sGC_act SUBSTRATE n addmsg /kinetics/GC/act_sGCfast /kinetics/GC/NO.sGC_5coord REAC B A addmsg /kinetics/GC/sGC-ppase*/deph_NO_sGC /kinetics/GC/NO.sGC_5coord REAC sA B addmsg /kinetics/GC/phosph_NO.sGC /kinetics/GC/NO.sGC_5coord REAC B A addmsg /kinetics/GC/deph_NO.sGC /kinetics/GC/phosph_NO.sGC SUBSTRATE n addmsg /kinetics/GC/NO.sGC_5coord /kinetics/GC/phosph_NO.sGC PRODUCT n addmsg /kinetics/GC/sGC-ppase*/deph_NO_sGC /kinetics/GC/deph_NO.sGC MM_PRD pA addmsg /kinetics/GC/phosph_NO.sGC /kinetics/GC/deph_NO.sGC REAC A B addmsg /kinetics/GC/act_sGCslow /kinetics/GC/NO2.sGC_5coord REAC B A addmsg /kinetics/GC/sGC-ppase*/deph_NO2_sGC /kinetics/GC/NO2.sGC_5coord REAC sA B addmsg /kinetics/GC/phosph_NO2.sGC /kinetics/GC/NO2.sGC_5coord REAC B A addmsg /kinetics/GC/sGC-ppase*/deph_NO2_sGC /kinetics/GC/deph_NO2.sGC MM_PRD pA addmsg /kinetics/GC/phosph_NO2.sGC /kinetics/GC/deph_NO2.sGC REAC A B addmsg /kinetics/GC/deph_NO2.sGC /kinetics/GC/phosph_NO2.sGC SUBSTRATE n addmsg /kinetics/GC/NO2.sGC_5coord /kinetics/GC/phosph_NO2.sGC PRODUCT n addmsg /kinetics/GC/sGCtot/sGC_act /kinetics/GC/GTP REAC sA B addmsg /kinetics/GC/deph_sGC-ppase /kinetics/GC/sGC-ppase REAC B A addmsg /kinetics/PDE/cGMP2.PKG/sGCppase_act /kinetics/GC/sGC-ppase REAC sA B addmsg /kinetics/GC/sGC-ppase*/deph_NO2_sGC /kinetics/GC/sGC-ppase* REAC eA B addmsg /kinetics/GC/sGC-ppase*/deph_NO_sGC /kinetics/GC/sGC-ppase* REAC eA B addmsg /kinetics/GC/deph_sGC-ppase /kinetics/GC/sGC-ppase* REAC A B addmsg /kinetics/PDE/cGMP2.PKG/sGCppase_act /kinetics/GC/sGC-ppase* MM_PRD pA addmsg /kinetics/GC/sGC-ppase* /kinetics/GC/sGC-ppase*/deph_NO2_sGC ENZYME n addmsg /kinetics/GC/NO2.sGC_5coord /kinetics/GC/sGC-ppase*/deph_NO2_sGC SUBSTRATE n addmsg /kinetics/GC/sGC-ppase* /kinetics/GC/sGC-ppase*/deph_NO_sGC ENZYME n addmsg /kinetics/GC/NO.sGC_5coord /kinetics/GC/sGC-ppase*/deph_NO_sGC SUBSTRATE n addmsg /kinetics/GC/sGC-ppase* /kinetics/GC/deph_sGC-ppase SUBSTRATE n addmsg /kinetics/GC/sGC-ppase /kinetics/GC/deph_sGC-ppase PRODUCT n addmsg /kinetics/PDE/PDE /kinetics/PDE/PDE/PDE_basal ENZYME n addmsg /kinetics/cGMP /kinetics/PDE/PDE/PDE_basal SUBSTRATE n addmsg /kinetics/PDE/cGMPbindcGK /kinetics/PDE/cGK REAC A B addmsg /kinetics/PDE/PDEbind_cGMP /kinetics/PDE/cGMP.PDE REAC B A addmsg /kinetics/PDE/cGMP2.PKG/PKG_act /kinetics/PDE/cGMP.PDE REAC sA B addmsg /kinetics/PDE/Myo_phosphatase/PP1 /kinetics/PDE/cGMP.PDE MM_PRD pA addmsg /kinetics/PDE/cGMP.PDE/cGMP.PDE_basal /kinetics/PDE/cGMP.PDE REAC eA B addmsg /kinetics/PDE/cGMP.PDE /kinetics/PDE/cGMP.PDE/cGMP.PDE_basal ENZYME n addmsg /kinetics/cGMP /kinetics/PDE/cGMP.PDE/cGMP.PDE_basal SUBSTRATE n addmsg /kinetics/PDE/cGMP_PDE*/PDE_active /kinetics/PDE/5primeGMP MM_PRD pA addmsg /kinetics/PDE/PDE/PDE_basal /kinetics/PDE/5primeGMP MM_PRD pA addmsg /kinetics/PDE/cGMP.PDE/cGMP.PDE_basal /kinetics/PDE/5primeGMP MM_PRD pA addmsg /kinetics/PDE/cGMP.PDE /kinetics/PDE/PDEbind_cGMP PRODUCT n addmsg /kinetics/cGMP /kinetics/PDE/PDEbind_cGMP SUBSTRATE n addmsg /kinetics/PDE/PDE /kinetics/PDE/PDEbind_cGMP SUBSTRATE n addmsg /kinetics/cGMP /kinetics/PDE/cGMPbindcGK SUBSTRATE n addmsg /kinetics/PDE/cGK /kinetics/PDE/cGMPbindcGK SUBSTRATE n addmsg /kinetics/PDE/cGMP.PKG /kinetics/PDE/cGMPbindcGK PRODUCT n addmsg /kinetics/PDE/cGMP2.PKG/PKG_act /kinetics/PDE/cGMP_PDE* MM_PRD pA addmsg /kinetics/PDE/Myo_phosphatase/PP1 /kinetics/PDE/cGMP_PDE* REAC sA B addmsg /kinetics/PDE/cGMP_PDE* /kinetics/PDE/cGMP_PDE*/PDE_active ENZYME n addmsg /kinetics/cGMP /kinetics/PDE/cGMP_PDE*/PDE_active SUBSTRATE n addmsg /kinetics/PDE/cGMP.PKG /kinetics/PDE/fast_site_bind SUBSTRATE n addmsg /kinetics/PDE/cGMP2.PKG /kinetics/PDE/fast_site_bind PRODUCT n addmsg /kinetics/cGMP /kinetics/PDE/fast_site_bind SUBSTRATE n addmsg /kinetics/PDE/Myo_phosphatase/PP1 /kinetics/PDE/Myo_phosphatase REAC eA B addmsg /kinetics/PDE/Myo_phosphatase /kinetics/PDE/Myo_phosphatase/PP1 ENZYME n addmsg /kinetics/PDE/cGMP_PDE* /kinetics/PDE/Myo_phosphatase/PP1 SUBSTRATE n addmsg /kinetics/PDE/cGMPbindcGK /kinetics/PDE/cGMP.PKG REAC B A addmsg /kinetics/PDE/fast_site_bind /kinetics/PDE/cGMP.PKG REAC A B addmsg /kinetics/PDE/fast_site_bind /kinetics/PDE/cGMP2.PKG REAC B A addmsg /kinetics/PDE/cGMP2.PKG/PKG_act /kinetics/PDE/cGMP2.PKG REAC eA B addmsg /kinetics/PDE/cGMP2.PKG/sGCppase_act /kinetics/PDE/cGMP2.PKG REAC eA B addmsg /kinetics/PDE/cGMP2.PKG /kinetics/PDE/cGMP2.PKG/PKG_act ENZYME n addmsg /kinetics/PDE/cGMP.PDE /kinetics/PDE/cGMP2.PKG/PKG_act SUBSTRATE n addmsg /kinetics/PDE/cGMP2.PKG /kinetics/PDE/cGMP2.PKG/sGCppase_act ENZYME n addmsg /kinetics/GC/sGC-ppase /kinetics/PDE/cGMP2.PKG/sGCppase_act SUBSTRATE n addmsg /kinetics/PDE/PDEbind_cGMP /kinetics/cGMP REAC A B addmsg /kinetics/PDE/cGMPbindcGK /kinetics/cGMP REAC A B addmsg /kinetics/PDE/fast_site_bind /kinetics/cGMP REAC A B addmsg /kinetics/GC/sGCtot/sGC_act /kinetics/cGMP MM_PRD pA addmsg /kinetics/PDE/cGMP_PDE*/PDE_active /kinetics/cGMP REAC sA B addmsg /kinetics/PDE/PDE/PDE_basal /kinetics/cGMP REAC sA B addmsg /kinetics/PDE/cGMP.PDE/cGMP.PDE_basal /kinetics/cGMP REAC sA B addmsg /kinetics/PDE/cGMP_PDE* /graphs/conc1/cGMP_PDE*.Co PLOT Co *cGMP_PDE*.Co *47 addmsg /kinetics/PDE/5primeGMP /graphs/conc2/5primeGMP.Co PLOT Co *5primeGMP.Co *22 addmsg /kinetics/PDE/cGMP2.PKG /moregraphs/conc3/cGMP2.PKG.Co PLOT Co *cGMP2.PKG.Co *24 addmsg /kinetics/cGMP /moregraphs/conc3/cGMP.Co PLOT Co *cGMP.Co *54 enddump // End of dump call /kinetics/GC/notes LOAD \ "This group features the binding reaction scheme as proposed by" \ "Stone and Marletta,1996, Biochemistry, 35(4):1093-1099. They" \ "report a two step binding step for the activation of sGC by NO." \ "Rates shown in the model are used directly from their experiments" \ "on stopped flow kinetics. " call /kinetics/GC/sGCfast/notes LOAD \ "Stone and Marletta, Biochemistry,35(4), 1996," \ "" \ "They have reported that the binding of sGC with NO occurs through two" \ "phases;a slow process and a fast process. 30% of the sGC binds " \ "quickly to NO; but the rest 70% goes through a slow process which" \ "involves the binding of another NO to an unidentified non-heme " \ "site on the protein, which seems to be not necessarily the same " \ "site used in the initial two step binding to the heme." \ "" \ "Stone and Marletta,1995,34;14668-14674;-- report that the native" \ "heme stoichiometry is 2 per heterodimer. spectrally only one" \ "type of heme is observed, indicating that both hemes are in " \ "similar environment. they conclude that each subunit of the " \ "heterodimer binds 1 equiv of heme at a site conserved between" \ "the two subunits." \ "" \ "Concentration 3 uM assumed on the basis of reported data" \ "(Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ;" \ "Ariano et al., PNAS, 1982, 79:1316-1320)" \ "" \ "" \ "" \ "" call /kinetics/GC/NO_bind_sGCfast/notes LOAD \ "This is the fast binding of NO to sGC, subsequently activating" \ "it, as proposed by Stone and Marletta." \ "" \ "Rates of these binding reactions used directly from Stone and" \ "Marletta,1996, Biochemistry, 35(4):1093-1099, " \ "based on whose paper this model is made. Rates obtained from" \ "stopped flow kinetics detailed in their paper." call /kinetics/GC/form_6coord/notes LOAD \ "Rates used directly from Stone and Marletta,1996,Biochemistry," \ "35(4):1093-1099." call /kinetics/GC/act_sGCfast/notes LOAD \ "Rates used directly from Stone and Marletta,1996,Biochemistry," \ "35(4):1093-1099." call /kinetics/GC/act_sGCslow/notes LOAD \ "Rates used directly from Stone and Marletta,1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/GC/NObindnonheme/notes LOAD \ "This step is the one that differs from the fast reaction scheme," \ "as reported by Stone and Marletta. Here the reaction is dependent " \ "upon the binding of NO to an unidentified non-heme site on the" \ "protein." \ "" \ "Rates used directly from Stone and Marletta,1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/GC/nonhemebind_int/notes LOAD \ "here the new NO has bound to the unidentified non-heme site on" \ "the 6-coordinate complex, and this will convert to the" \ "5-coordinate complex. this binding of a new NO to the non-heme " \ "site on the 6-coordinate complex is characteristic of the slow " \ "binding process of NO to sGC." call /kinetics/GC/NO.sGC6coord/notes LOAD \ "this compoud, a 6-coordinate complex will be bound by another NO" \ "to an unidentified non-heme site in the next reaction step." call /kinetics/GC/form6coord/notes LOAD \ "Rates used directly from Stone and Marletta,1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/GC/NO_bind_sGCslow/notes LOAD \ "This is the slow binding of NO to sGC, as reported by Stone and " \ "Marletta,1996, Biochemistry, 35(4):1093-1099. " \ "The rates shown have been used directly from their data from" \ "stopped flow kinetics." call /kinetics/GC/sGCslow/notes LOAD \ "This is the slow reaction process of the binding of NO to sGC." \ "we can notice the binding of another NO in the third reaction " \ "step to a non-heme site, which then converts to the 5-coordinate" \ "complex. this binding of another NO to an non-heme site is" \ "characteristic of the slow binding process of NO to sGC.(Stone" \ "and Marletta, 1996,35(4);1093-1099)" \ "" \ "Concentration 3 uM assumed on the basis of reported data " \ "(Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ; " \ "Ariano et al., PNAS, 1982, 79:1316-1320.)" call /kinetics/GC/NO/notes LOAD \ "Endogenously produced NO concentrations in the course of" \ "signal transduction processes are < 100 nM. (Varner et al.," \ "Nitric oxide in the nervous system, Academic press, London, UK," \ "pp.191-206.)" call /kinetics/GC/sGCtot/notes LOAD \ "This is the sumtotal of the sGC activated via two binding " \ "mecanisms as reported by Stone and Marletta, 1996, Biochemistry," \ "35(4):1093-1099." call /kinetics/GC/sGCtot/sGC_act/notes LOAD \ "The range of estimates found in the literature are:" \ "Km -> 40 - 150 uM (without NO)" \ " 20 - 40 uM (with NO)" \ "Vmax -> 10 - 100 nmol/mg/min (wihtout NO)" \ " 10 - 40 umol/mg/min (with NO)." \ "----- thru personal correspondence from T. Bellamy, Wolfson " \ "Ins. for Biomedical Sciences, UK." \ "NO increases the Vmax of sGC by 100-200 fold, and it has been " \ "proposed that this activation occurs subsequent to the binding " \ "of NO toa heme moiety on the enzyme. (Stone and Marletta,1995," \ "Biochemistry,34:14668-14674). " call /kinetics/GC/NO.sGC_5coord/notes LOAD \ "This is the active sGC, a 5-coordinate complex formed after a " \ "series of reaction steps, involving the formation of a " \ "6 coordinate complex which converted to a 5-coordinate complex." call /kinetics/GC/phosph_NO.sGC/notes LOAD \ "Rates fixed based on teh ratio of active and inactive forms." call /kinetics/GC/NO2.sGC_5coord/notes LOAD \ "This is the 5-coordinate complex of the enzyme sGC. This is" \ "also the active form of the enzyme." call /kinetics/GC/phosph_NO2.sGC/notes LOAD \ "Rates fixed based on the ratio of active and inactive forms." call /kinetics/GC/sGC-ppase*/deph_NO2_sGC/notes LOAD \ "similar to deph_NO_sGC.." call /kinetics/GC/sGC-ppase*/deph_NO_sGC/notes LOAD \ "Km and Vmax used from Ferrero et al., J Neurochem, 2000, 75:" \ "2029-2039, and other refs cited in their paper. Though there" \ "are no plots in this paper, the rates look ok when the model " \ "is being run. Still this part can be improved further based " \ "on more experimental observations, since at the moment, there" \ "is not much information on the rates and kinetic details" \ "of the phosphatase mediated sGC regulation." call /kinetics/GC/deph_sGC-ppase/notes LOAD \ "Rates fixed from the ratio of the inactive and active (phos) " \ "form of sGC-ppase." call /kinetics/PDE/notes LOAD \ "This model features the hydrolysis of cGMP by PDE. (The " \ "PDE taken into consideration is PDE 5, a hgihly cGMP specific " \ "PDE, and is considered to be the main enzyme responsible for " \ "terminating the action of cGMP generated following the release " \ "of NO from Nitrergic nerves, or from vascular endothelial cells." \ "(Gibson, Eur J Biochem,2001,411:1-10). PDE is phosphorylated by" \ "PKG. (Corbin et al., Eur J Biochem,2000,267:2760-2767). And" \ "occupation of the allosteric binding sites on PDE by cGMP is " \ "necessary for phosphorylation by PKG. (Gibson, Eur J Biochem," \ "2001,411:1-10)." \ "Three plots in the paper by Corbin et al., were replicated with this" \ "model. Though the shape of the curves matched well, the numbers could not be" \ "matched due to the differences in Vmax values used from different literature " \ "sources apart from Corbin et al. Various inhibitors were used by Corbin et al., " \ "in their expts and so to match the numbers in the plots we have to replicate the " \ "experimental conditions exactly. So by bringing down the concentration of PKG and PDE" \ "we could match the numbers as well. But the values shown in this model are near " \ "physiological levels, as thats what we intend to do basically -- Building models of" \ "signaling pathways whose behaviour is similar to what happens invivo." call /kinetics/PDE/PDE/notes LOAD \ "Phophosdiesterase. Degrades cGMP to 5primeGMP. " \ "Concentration used by Kuroda et al.,(J Neurosci, 2001,21(15):" \ "5693-5702) and initially from Kotera et al., " \ "(1997, Eur J Biochem, 249:434-442). PDE 5 is highly specific " \ "for cGMP and is considered to be the main enzyme responsible " \ "for terminating the action of cGMP generated following the release" \ "of NO from nitrergic nerves, or from vascular endothelial cells." \ "(Gibson,Eur J Pharmacol, 2001, 411:1-10). Occupation of the " \ "allosteric binding sites by cGMP is neessary for phosphorylation" \ "by PKG. In Corbinet al., EJBiochem, 2000, 267:2760-2767, " \ "Phosphorylation of PDE and PDE activity are measured, but" \ "as mentioned, due to the different sources of Vmax values" \ "the numbers could not be matched exactly with respect to the plots" \ "in the paper, and they were either more or less by a factor" \ "of two. To match the numbers exactly we have to replicate the" \ "experimental conditions exactly. " \ "" call /kinetics/PDE/cGK/notes LOAD \ "cGMP dependent protein kinase (also cGKI and cGKII)" \ "They are both present in the brain. While cGKI is selectively" \ "present only in the Purkinje cells of the cerebellum, cGKII" \ "is widely expressed in the brain tissue and may be a neuronal" \ "target of cGMP. (El-Husseini et al., J Neurochem, 1995;64:2814;" \ "Hofmann et al., 2000, J Cell Sci, 113:1671-1676; Lohmann et al.," \ "1997, Trends Biochem Sci, 22:307-312). PKG is a dimer, though " \ "the function of dimerization is not known, with some reports" \ "indicating that dimerization may not play a vital role in the" \ "activity of the enzyme. This is the inactive form, which on being " \ "bound by cGMP becomes active. The binding sites are described by their" \ "distinct rates of dissociation of bound cyclic nucleotide " \ "(fast and slow). - Taylor et al., 2000,JBC, 275(36):28053-28062. " \ "Intracellular concentration of PKG estimated to be present in " \ "vascular smooth muscle cells is around 0.3 - 0.5 uM. " \ "(Corbin et al., 2000, Eur J Biochem,267:2760-2767) " \ "" call /kinetics/PDE/cGMP.PDE/notes LOAD \ "cGMP bound PDE. Binding of cGMP to the allosteric cGMP-binding" \ "sites has been reported to be required for phosphorylation by" \ "cGMP-dep protein Kinase, and the elements contributing to the" \ "dimerization of this protein are located in or near the " \ "allosteric cGMP-binding sites, though the function of " \ "dimerization is unknown. " \ "(Fink et al., JBC, 1999, 274(49):34613-34620)" \ " " call /kinetics/PDE/5primeGMP/notes LOAD \ "5primeGMP - The hydrolysed product from cGMP, by the catalytic" \ "activity of PDE's. In this case the cGMP specific PDE, PDE5." call /kinetics/PDE/PDEbind_cGMP/notes LOAD \ "Kd ~1.3 uM. " \ "(Turko et al., JBC, 1996, 271(36):22240-22244, and " \ "Corbin et al., Eur J Biochem, 2000,267:2760-2767)" \ "" call /kinetics/PDE/cGMPbindcGK/notes LOAD \ "Kinase activation in both the isoforms of cGK depends on " \ "cyclic nucleotide occupation of the two cyclic nucleotide " \ "binding sites in the regulatory domain. This event is supposed " \ "to reduce the affinity of the auto-inhibition region of the " \ "regulatory domain for the catalytic domain. Investigations" \ "revealed that cGMP binds to a slowly dissociating cyclic " \ "nucleotide binding site and induces a conformational change" \ "resulting in a partially active kinase. Subsequent occupation" \ "of the second, rapid dissociation site imparts additional " \ "conformational change until it forms the elongated shape " \ "that is reported to be associated with the fully active enzyme." \ "(Taylor et al., 2000, JBC, 275(36):28053-28062)" \ "Dissociation rates for cGKII binding sites from " \ "Taylor et al., 2000, and other refs cited in their paper." \ "cGMP dissociation from slow site -- 8.1/s (Smith et al., " \ "JBC,1995, 271(34):20756-20762)" \ "" call /kinetics/PDE/cGMP_PDE*/notes LOAD \ "Phosphorylated PDE. Phosphorylated by PKG, which requires cGMP" \ "to be bound to the allosteric binding sites on PDE. Hence there " \ "are more than one molecule of cGMP bound to the active enzyme" \ "complex, since initially, cGMP binding to the allosteric " \ "binding sites is necessary for phosphorylation of PDE by PKG." \ "" call /kinetics/PDE/cGMP_PDE*/PDE_active/notes LOAD \ "In this cGMP_PDE* enzyme complex, there are more than one cGMP" \ "molecule bound, since initially, cGMP binding to the allosteric" \ "binding sites is essential for phosphorylation by PKG. " \ "Vmax initially from Turko et al., 1998, Biochem J, " \ "329:505-510 and Kuroda et al., 2001, J Neurosci,21(15):5693-5702." \ "PDE has a high catalytic rate for cGMP hydrolysis. " \ "Km values reported are ~1-2 uM in various studies, including" \ "studies with purified enzyme preparations.(Fink et al., JBC," \ "1999, 274(49):34613-34620 and cited refs in their paper)." \ "Value used here from Mehats et al., Trends in Endocrinology &" \ "Metabolism, 2002, 13(1):29-35. Values similar to those used " \ "by Kuroda et al.,J Neurosci, 2001, 21(15):5693-5702." \ "Km for cGMP decreased from 0.98 to 0.58 uM and Vmax was " \ "reported to be slightly increased by phosphorylation." \ "(Corbin et al., Eur J Biochem, 2000)" call /kinetics/PDE/Myo_phosphatase/notes LOAD \ "Rybalkin et al., JBC, 2002, 277(5):3310-3317." \ "Myosin phosphatase reported to be involved in " \ "dephosphorylation of PDE5." \ "Rates from Rybalkin et al., 2002." call /kinetics/PDE/cGMP.PKG/notes LOAD \ "cGK bound by cGMP to the amino terminal slow site, which " \ "is subsequently bound to the fast site in the next step by " \ "another cGMP molecule. (Taylor et al., JBC, 2000, 275(36):" \ "28053-28062). Rates from Taylor et al., 2000." \ "" call /kinetics/PDE/cGMP2.PKG/notes LOAD \ "Phosphorylated cGMP-dependent protein kinase. cGMP binding to" \ "the inactive cGK activates it, making it participate in " \ "further downstream regulatory processes, mostly through " \ "phosphorylation regulation of its substrates. Here it " \ "phosphorylates PDE, which hydrolyses cGMP to 5primeGMP, thus" \ "maintaining the intracellular nucleotide levels. The activity " \ "of PDE is supposed to be enhanced following phosphorylation by" \ "PKG." call /kinetics/PDE/cGMP2.PKG/PKG_act/notes LOAD \ "Phosphorylation of PDE actually increases the enzyme activity." \ "And occupation of the allosteric binding sites by cGMP is " \ "necessary for phosphorylation by PKG. Phosphorylation following" \ "the occupation of the allosteric sites by cGMP." \ "(Gibson, Eur J Pharmacol,2001,411:1-10, Corbin et al., 2000," \ "Eur J Biochem, 267:2760-2767). Phosphorylation resulted in " \ "increases in phosphate content up to 0.6 mol per PDE5 subunit." \ "(Corbin et al., 2000), and since PKG is known to catalyze" \ "autophosphorylation, it was found to incorporate 2 mol per PDE5" \ "subunit in 60 mins." call /kinetics/cGMP/notes LOAD \ "cGMP takes part in various reactions downstream. One of the " \ "interesting schemes are the binding of cGMP to the allosteric " \ "cGMP binding sites, which is supposed to be essential for the" \ "phosphorylation of PDE by PKG. So in the cGMP_PDE* enzyme " \ "complex, there is more then one cGMP molecule bound. " complete_loading