PKA PKC. Reactions: Kf and Kb are in units of um and sec.
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1 Notes on output: Molecules: Only non-zero intial concentrations are shown. All other values are generated in the course of the simulation. A value of 1 for Buffering indicates that the molecular concentration is held fixed at the initial concentration throughout the simulation run Reactions: Kf and Kb are in units of um and sec. Enzymes: Km and Vmax are in units of um and sec. The ratio term is the ratio between k2 and k3 in the. expanded Michaelis-Menten formulation: E + S <==k2====k1==> E.S ---k3---> E + P The Classical column is zero when the explicit Michaelis-. Menten formulation (above) is used, where there is an explicit representation of a molecule for E.S In some cases the classical Michaelis-Menten form is used where rate = [E][S].k3/([S] + Km) Here the Classical column value is 1. This implies that the entire concentration of enzyme is available for other interactions even when it is involved in one or more catalytic steps. PKA Initial concentrations for PKA pathway AC AMP ATP E camp-pde GDP.Gabc L PKA-inhibitor R R2C L.R.GDP.Gabc <=====> Gbg + L.R + GTP.Ga camp2.r2c2 + camp <=====> camp3.r2c camp + camp3.r2c2 <=====> camp4.r2c R2C2 + camp <=====> camp.r2c camp.r2c2 + camp <=====> camp2.r2c camp-pde* <=====> camp-pde AC + GTP.Ga <=====> Gs.AC GTP.Ga <=====> GDP.Ga PKA-active + PKA-inhibitor <=====> inhibited-pka 60 1 R + L <=====> L.R L + R.GDP.Gabc <=====> L.R.GDP.Gabc GDP.Gabc + L.R <=====> L.R.GDP.Gabc GDP.Gabc + R <=====> R.GDP.Gabc camp4.r2c2 <=====> PKA-active + camp4.r2c camp4.r2c <=====> PKA-active + camp4.r GDP.Ga + Gbg <=====> GDP.Gabc 6 0 camp ==== camp-pde ====> AMP camp ==== camp-pde* ====> AMP ATP ==== Gs.AC ====> camp camp-pde ==== PKA-active ====> camp-pde* PKC AA DAG
2 PKC-basal* PKC-cytosolic AA + PKC-cytosolic <=====> PKC-AA* PKC-cytosolic + Ca <=====> PKC-Ca PKC-Ca + AA <=====> PKC-Ca-AA* DAG + PKC-Ca <=====> PKC-Ca-DAG PKC-DAG-AA <=====> PKC-DAG-AA* PKC-cytosolic <=====> PKC-basal* 1 50 PKC-Ca <=====> PKC-Ca-memb* PKC-Ca-DAG <=====> PKC-DAG-memb* PKC-cytosolic + DAG <=====> PKC-DAG PKC-DAG + AA <=====> PKC-DAG-AA PKC-active = PKC-basal* + PKC-AA* + PKC-Ca_memb* + PKC-DAG-memb* + PKC-Ca-AA* + PKC-DAG-AA* CaMKII CaM CaMKII CaNAB I I1* neurogranin PKA-active PKC-active PP1-active PP2A CaMKII <=====> CaMKII-thr CaNAB + Ca + Ca <=====> CaNAB-Ca Ca + Ca + CaNAB-Ca2 <=====> CaNAB-Ca CaNAB-Ca4 + CaM-TR2-Ca2 <=====> CaMCa2-CANAB CaM-Ca3 + Ca <=====> CaM-Ca CaM + Ca + Ca <=====> CaM-TR2-Ca CaM-TR2-Ca2 + Ca <=====> CaM-Ca CaM-Ca3 + CaNAB-Ca4 <=====> CaMCa3-CaNAB CaM-Ca4 + CaNAB-Ca4 <=====> CaMCa4-CaNAB CaMKII-thr286 + CaM-Ca4 <=====> CaMKII-thr286*-CaM CaM-Ca4 + CaMKII <=====> CaMKII-CaM 50 5 neurogranin* <=====> neurogranin PP1-I1 <=====> PP1-active + I1 1 0 I1* + PP1-active <=====> PP1-I1* neurogranin + CaM <=====> neurogranin-cam CaM(Ca)n-CaNAB = CaMCa2-CaNAB + CaMCa3-CaNAB + CaMCa4-NAB neurogranin* ==== CaM(Ca)n-CaNAB ====> neurogranin I1* ==== CaM(Ca)n-CaNAB ====> I PP1-I1* ==== CaM(Ca)n-CaNAB ====> PP1-I I1* ==== CaNAB-Ca4 ====> I I1 ==== PKA-active ====> I1* ==== PKA-active ====> neurogranin ==== PKC-active ====> neurogranin* neurogranin-cam ==== PKC-active ====> CaM + neurogranin* CaMKII-thr286*-CaM ==== PP1-active ====> CaMKII-CaM CaMKII*** ==== PP1-active ====> CaMKII-thr CaMK-thr306 ==== PP1-active ====> CaMKII CaMKII*** ==== PP1-active ====> CaMK-thr CaMKII-thr286 ==== PP1-active ====> CaMKII I1* ==== PP2A ====> I PP1-I1* ==== PP2A ====> PP1-I CaMKII-thr286 ==== tot_autonomous_camkii ====> CaMKII*** CaMKII-CaM ==== tot_autonomous_camkii ====> CaMKII-thr286*-CaM CaMKII-thr286 ==== tot_cam_camkii ====> CaMKII***
3 CaMKII-CaM ==== tot_cam_camkii ====> CaMKII-thr286*-CaM MAPK and Entire network AC AC AMP E APC ATP E CaM CaMKII camp-pde CaNAB craf EGF EGFR G-GDP GAP GDP-Ras Glu Grb I I1* inact-gef Inositol IP MAPK MAPKK mglur mglurantag MKP neurogranin PC PDE PIP PKA-inhibitor PKC-cytosolic PLA2-cytosolic PLC PLC_g PP1-active PP2A PPhosphatase2A R2C SHC Sos temp-pip G*GTP + PLC-Ca <=====> PLC-Ca-Gq Ca + PLC <=====> PLC-Ca 3 1 Rec-Glu-Gq <=====> G*GTP + BetaGamma + Rec-Glu EGFR + EGF <=====> L.EGFR Rec-Gq + mglurantag <=====> Blocked-rec-Gq G-GDP <=====> G*GTP + BetaGamma CaMKII <=====> CaMKII-thr BetaGamma + inact-gef <=====> GEF-Gprot-bg 6 1 CaNAB + Ca + Ca <=====> CaNAB-Ca Ca + Ca + CaNAB-Ca2 <=====> CaNAB-Ca CaM-Ca4 + AC1 <=====> AC1-CaM 50 1 inact-gef + CaM-Ca4 <=====> CaM-GEF 60 1 CaNAB-Ca4 + CaM-TR2-Ca2 <=====> CaMCa2-CANAB CaM-Ca3 + Ca <=====> CaM-Ca CaM + Ca + Ca <=====> CaM-TR2-Ca CaM-TR2-Ca2 + Ca <=====> CaM-Ca
4 CaM-Ca3 + CaNAB-Ca4 <=====> CaMCa3-CaNAB CaM-Ca4 + CaNAB-Ca4 <=====> CaMCa4-CaNAB CaMKII-thr286 + CaM-Ca4 <=====> CaMKII-thr286*-CaM CaM-Ca4 + CaMKII <=====> CaMKII-CaM 50 5 R2C2-cAMP2 + camp <=====> R2C2-cAMP camp + R2C2-cAMP3 <=====> R2C2-cAMP R2C2 + camp <=====> R2C2-cAMP R2C2-cAMP + camp <=====> R2C2-cAMP PDE1 + CaM-Ca4 <=====> CaM.PDE PLC_g + Ca <=====> Ca.PLC_g Ca + PLC_G* <=====> Ca.PLC_g* DAG + PLA2-Ca* <=====> DAG-Ca-PLA2* AA <=====> APC DAG <=====> PC IP3 <=====> Inositol AC2* <=====> AC GAP* <=====> GAP GEF* <=====> inact-gef 1 0 inact-gef* <=====> inact-gef 1 0 neurogranin* <=====> neurogranin camp-pde* <=====> camp-pde PLA2* <=====> PLA2-cytosolic Ca.PLC_g* <=====> Ca.PLC_g SHC* <=====> SHC Sos* <=====> Sos PP1-I1 <=====> PP1-active + I1 1 0 Glu + Rec-Gq <=====> Rec-Glu-Gq Grb2 + Sos <=====> Sos.Grb Sos* + Grb2 <=====> Sos*.Grb Gs-alpha + AC1 <=====> AC1-Gs AC2 + Gs-alpha <=====> AC2-Gs Gs-alpha + AC2* <=====> AC2*-Gs G*GTP <=====> G*GDP PLC-Ca-Gq <=====> G*GDP + PLC-Ca I1* + PP1-active <=====> PP1-I1* PKA-active + PKA-inhibitor <=====> inhibited-pka 60 1 L.EGFR <=====> Internal_L.EGFR neurogranin + CaM <=====> neurogranin-cam temp-pip2 + PLA2-Ca* <=====> PIP2-Ca-PLA2* temp-pip2 + PLA2-cytosolic <=====> PIP2-PLA2* AA + PKC-cytosolic <=====> PKC-AA* PKC-cytosolic + Ca <=====> PKC-Ca PKC-Ca + AA <=====> PKC-Ca-AA* DAG + PKC-Ca <=====> PKC-Ca-DAG PKC-DAG-AA <=====> PKC-DAG-AA* PKC-cytosolic <=====> PKC-basal* 1 50 PKC-Ca <=====> PKC-Ca-memb* PKC-Ca-DAG <=====> PKC-DAG-memb* PKC-cytosolic + DAG <=====> PKC-DAG PKC-DAG + AA <=====> PKC-DAG-AA PLA2* + Ca <=====> PLA2*-Ca PLA2-cytosolic + Ca <=====> PLA2-Ca* PLC + G*GTP <=====> PLC-Gq Ca + PLC-Gq <=====> PLC-Ca-Gq 30 1 craf-1* + GTP-Ras <=====> Raf-GTP-Ras* GTP-Ras <=====> GDP-Ras G-GDP + mglur <=====> Rec-Gq G-GDP + Rec-Glu <=====> Rec-Glu-Gq mglur + Glu <=====> Rec-Glu R2C2-cAMP4 <=====> PKA-active + R2C-cAMP R2C-cAMP4 <=====> PKA-active + R2-cAMP Sos.Grb2 + SHC* <=====> Shc*.Sos.Grb G*GDP + BetaGamma <=====> G-GDP 6 0 PKC-active = PKC-basal* + PKC-AA* + PKC-Ca_memb* + PKC-DAG-memb* + PKC-Ca-AA* + PKC-DAG-AA* CaM(Ca)n-CaNAB = CaMCa2-CaNAB + CaMCa3-CaNAB + CaMCa4-NAB ATP ==== AC1-CaM ====> camp
5 ATP ==== AC1-Gs ====> camp ATP ==== AC2* ====> camp ATP ==== AC2*-Gs ====> camp ATP ==== AC2-Gs ====> camp PIP2 ==== Ca.PLC_g ====> DAG + IP PIP2 ==== Ca.PLC_g* ====> DAG + IP neurogranin* ==== CaM(Ca)n-CaNAB ====> neurogranin I1* ==== CaM(Ca)n-CaNAB ====> I PP1-I1* ==== CaM(Ca)n-CaNAB ====> PP1-I GDP-Ras ==== CaM-GEF ====> GTP-Ras camp ==== CaM.PDE1 ====> AMP camp ==== camp-pde ====> AMP camp ==== camp-pde* ====> AMP I1* ==== CaNAB-Ca4 ====> I APC ==== DAG-Ca-PLA2* ====> AA GTP-Ras ==== GAP ====> GDP-Ras GDP-Ras ==== GEF* ====> GTP-Ras GDP-Ras ==== GEF-Gprot-bg ====> GTP-Ras Ca.PLC_g ==== L.EGFR ====> Ca.PLC_g* SHC ==== L.EGFR ====> SHC* PLA2-cytosolic ==== MAPK* ====> PLA2* craf-1* ==== MAPK* ====> craf-1** Sos ==== MAPK* ====> Sos* MAPK ==== MAPKK* ====> MAPK-tyr MAPK-tyr ==== MAPKK* ====> MAPK* MAPK-tyr ==== MKP-1 ====> MAPK MAPK* ==== MKP-1 ====> MAPK-tyr camp ==== PDE1 ====> AMP APC ==== PIP2-Ca-PLA2* ====> AA APC ==== PIP2-PLA2* ====> AA inact-gef ==== PKA-active ====> inact-gef* I1 ==== PKA-active ====> I1* camp-pde ==== PKA-active ====> camp-pde* craf-1 ==== PKC-active ====> craf-1* GAP ==== PKC-active ====> GAP* inact-gef ==== PKC-active ====> GEF* neurogranin ==== PKC-active ====> neurogranin* neurogranin-cam ==== PKC-active ====> CaM + neurogranin* AC2 ==== PKC-active ====> AC2* APC ==== PLA2*-Ca ====> AA APC ==== PLA2-Ca* ====> AA PIP2 ==== PLC-Ca ====> DAG + IP PIP2 ==== PLC-Ca-Gq ====> DAG + IP CaMKII-thr286*-CaM ==== PP1-active ====> CaMKII-CaM CaMKII*** ==== PP1-active ====> CaMKII-thr CaMK-thr306 ==== PP1-active ====> CaMKII CaMKII*** ==== PP1-active ====> CaMK-thr CaMKII-thr286 ==== PP1-active ====> CaMKII I1* ==== PP2A ====> I PP1-I1* ==== PP2A ====> PP1-I craf-1* ==== PPhosphatase2A ====> craf MAPKK* ==== PPhosphatase2A ====> MAPKK-ser MAPKK-ser ==== PPhosphatase2A ====> MAPKK craf-1** ==== PPhosphatase2A ====> craf-1* MAPKK ==== Raf-GTP-Ras* ====> MAPKK-ser MAPKK-ser ==== Raf-GTP-Ras* ====> MAPKK* GDP-Ras ==== Shc*.Sos.Grb2 ====> GTP-Ras CaMKII-thr286 ==== tot_autonomous_camkii ====> CaMKII*** CaMKII-CaM ==== tot_autonomous_camkii ====> CaMKII-thr286*-CaM CaMKII-thr286 ==== tot_cam_camkii ====> CaMKII*** CaMKII-CaM ==== tot_cam_camkii ====> CaMKII-thr286*-CaM
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