/* */ /* GLYCOLYSIS MODEL */ /* */ /* Model description for CHEM */ /* Sune Danø (sdd@kiku.dk), July 9, 2002. */ /* */ /* For details of the model, please refer to: */ /* Finn Hynne, Sune Danø and Preben Graae Sørensen, */ /* "Full-scale model of glycolysis in Saccharomyces */ /* cerevisiae", Biophysical Chemistry 94:1221-163, 2001. */ /* */ /* Units in min and mM. */ /* */ /* INTEGRATOR SETTINGS */ datafile = "p"; /* modejacobian = 0; */ /* modestif = 1; */ /* modesimp = 0; */ stime = 0; dtime = 0.1; etime = 500; epsr = 1.0E-10; epsa = 1.0E-18; /* INTRINSIC PARAMETERS */ Yvol = 5.90000E+1; /* NOTE: in order to change Yvol, change this parameter AND */ /* the stoichiometry of reactions 2, 13, 16 and 18. */ Atot = 3.93000E+0; Ntot = 9.80000E-1; /* GlcTrans */ K2Glc = 1.70000E+0; K2IG6P = 1.20000E+0; K2IIG6P = 7.20000E+0; P2 = 1.00000E+0; /* HK */ K3ATP = 1.00000E-1; K3Glc = 0; K3DGlc = 3.70000E-1; /* PGI */ K4G6P = 8.00000E-1; K4F6P = 1.50000E-1; K4eq = 1.30000E-1; /* PFK */ K5 = 2.10000E-2; kappa5 = 1.50000E-1; /* ALD */ ratio6 = 5.00000E+0; K6eq = 8.10000E-2; K6FBP = 3.00000E-1; K6GAP = 4.00000E+0; K6DHAP = 2.00000E+0; K6IGAP = 1.00000E+1; /* TIM */ K7DHAP = 1.23000E+0; K7GAP = 1.27000E+0; K7eq = 5.50000E-2; /* GAPDH */ K8GAP = 6.00000E-1; K8BPG = 1.00000E-2; K8NAD = 1.00000E-1; K8NADH = 6.00000E-2; K8eq = 5.50000E-3; /* PK */ K10ADP = 1.70000E-1; K10PEP = 2.00000E-1; /* PDC */ K11 = 3.00000E-1; /* ADH */ K12ACA = 7.10000E-1; K12NADH = 1.00000E-1; /* lpGlyc */ K15NADH = 1.30000E-1; K15DHAP = 2.50000E+1; K15INADH = 3.40000E-2; K15INAD = 1.30000E-1; /* VELOCITY PARAMETERS */ /* specific flow rate */ k0 = 0.048; /* GlcTrans */ V2f = 1.01496E+3; V2r = 1.01496E+3; /* HK */ V3m = 5.17547E+1; /* PGI */ V4f = 4.96042E+2; V4r = 4.96042E+2; /* PFK */ V5m = 4.54327E+1; /* ALD */ V6f = 2.20782E+3; V6r = V6f * ratio6; /* TIM */ V7f = 1.16365E+2; V7r = 1.16365E+2; /* GAPDH */ V8f = 8.33858E+2; V8r = 8.33858E+2; /* lpPEP */ k9f = 4.43866E+5; k9r = 1.52862E+3; /* PK */ V10m = 3.43096E+2; /* PDC */ V11m = 5.31328E+1; /* ADH */ V12m = 8.98023E+1; /* difEtOH: see below */ /* lpGlyc */ V15m = 8.14797E+1; /* difGlyc */ k16 = 1.90000E+0; /* difEtOH */ k13 = k16 * 8.8; /* difACA */ k18 = k16 * 13; /* lacto */ k20 = 2.83828E-3; /* storage */ k22 = 2.25932E+0; /* consum */ k23 = 3.20760E+0; /* AK */ k24f = 4.32900E+2; k24r = 1.33333E+2; /* REACTIONS */ inGlc: GlcX0 <=> GlcX; k> = k0; k< = k0; GlcTrans: GlcX <=> 59Glc; v> = V2f/Yvol*(([GlcX]/K2Glc)/(1+([GlcX]/K2Glc)+((P2*([GlcX]/K2Glc)+1) /(P2*([Glc]/K2Glc)+1)*(1+([Glc]/K2Glc)+([G6P]/K2IG6P) +([Glc]*[G6P]/(K2Glc*K2IIG6P)))))); v< = V2r/Yvol*(([Glc]/K2Glc)/(1+([Glc]/K2Glc)+((P2*([Glc]/K2Glc)+1) /(P2*([GlcX]/K2Glc)+1)*(1+([GlcX]/K2Glc))+([G6P]/K2IG6P) +([Glc]*[G6P]/(K2Glc*K2IIG6P))))); HK: Glc + ATP -> G6P + ADP; v> = V3m*[ATP]*[Glc]/(K3DGlc*K3ATP+K3Glc*[ATP]+K3ATP*[Glc]+[Glc]*[ATP]); PGI: G6P <=> F6P; v> = V4f*[G6P]/(K4G6P+[G6P]+(K4G6P/K4F6P)*[F6P]); v< = V4r*([F6P]/K4eq)/(K4G6P+[G6P]+(K4G6P/K4F6P)*[F6P]); PFK: F6P + ATP -> FBP + ADP; v> = V5m*([F6P]*[F6P])/(K5*(1+kappa5*([ATP]/[AMP])*([ATP]/[AMP])) +[F6P]*[F6P]); ALD: FBP <=> GAP + DHAP; v> = V6f*[FBP]/(K6FBP+[FBP]+[GAP]*K6DHAP*V6f/(K6eq*V6r)+[DHAP]*K6GAP*V6f /(K6eq*V6r)+[FBP]*[GAP]/K6IGAP+[GAP]*[DHAP]*V6f/(K6eq*V6r)); v< = (V6f*[GAP]*[DHAP]/K6eq)/(K6FBP+[FBP]+[GAP]*K6DHAP*V6f/(K6eq*V6r) +[DHAP]*K6GAP*V6f/(K6eq*V6r) +[FBP]*[GAP]/K6IGAP+[GAP]*[DHAP]*V6f/(K6eq*V6r)); TIM: DHAP <=> GAP; v> = V7f*[DHAP]/(K7DHAP+[DHAP]+(K7DHAP/K7GAP)*[GAP]); v< = V7r*([GAP]/K7eq)/(K7DHAP+[DHAP]+(K7DHAP/K7GAP)*[GAP]); GAPDH: GAP + NAD <=> BPG + NADH; v> = V8f*[GAP]*[NAD]/K8GAP/K8NAD /((1+[GAP]/K8GAP+[BPG]/K8BPG)*(1+[NAD]/K8NAD+[NADH]/K8NADH)); v< = V8r*[BPG]*[NADH]/K8eq/K8GAP/K8NAD /((1+[GAP]/K8GAP+[BPG]/K8BPG)*(1+[NAD]/K8NAD+[NADH]/K8NADH)); lpPEP: BPG + ADP <=> PEP + ATP; k> = k9f; k< = k9r; PK: PEP + ADP -> Pyr + ATP; v> = V10m*[ADP]*[PEP]/((K10PEP+[PEP])*(K10ADP+[ADP])); PDC: Pyr -> ACA; v> = V11m*[Pyr]/(K11+[Pyr]); ADH: ACA + NADH -> EtOH + NAD; v> = V12m*[ACA]*[NADH]/((K12NADH+[NADH])*(K12ACA+[ACA])); difEtOH: 59EtOH <=> EtOHX; v> = k13/Yvol*[EtOH]; v< = k13/Yvol*[EtOHX]; outEtOH: EtOHX -> P; k> = k0; lpGlyc: DHAP + NADH -> Glyc + NAD; v> = V15m*[DHAP]/(K15DHAP*(1+(K15INADH/[NADH])*(1+([NAD]/K15INAD))) +[DHAP]*(1+(K15NADH/[NADH])*(1+([NAD]/K15INAD)))); difGlyc: 59Glyc <=> GlycX; v> = k16/Yvol*[Glyc]; v< = k16/Yvol*[GlycX]; outGlyc: GlycX -> P; k> = k0; difACA: 59ACA <=> ACAX; v> = k18/Yvol*[ACA]; v< = k18/Yvol*[ACAX]; outACA: ACAX -> P; k> = k0; lacto: ACAX + CNX -> P; k> = k20; inCN: CNX0 <=> CNX; k> = k0; k< = k0; storage: ATP + G6P -> ADP; k> = k22; consum: ATP -> ADP; k> = k23; AK: AMP + ATP <=> 2ADP; k> = k24f; k< = k24r; /* conservation equations */ [AMP] = Atot - [ADP] - [ATP]; [NAD] = Ntot - [NADH]; /* mixed flow concentrations */ /* (the Hopf bifurcation point of the optimization) */ [GlcX0] = 18.5; [CNX0] = 5.6; /* dummy variable */ [P] = 0; /* INITIAL CONCENTRATIONS */ /* (the Hopf bifurcation point of the optimization) */ [GlcX](0) = 1.55307E+0; [Glc](0) = 5.73074E-1; [G6P](0) = 4.20000E+0; [F6P](0) = 4.90000E-1; [FBP](0) = 4.64000E+0; [GAP](0) = 1.15000E-1; [DHAP](0) = 2.95000E+0; [BPG](0) = 2.70000E-4; [PEP](0) = 4.00000E-2; [Pyr](0) = 8.70000E+0; [ACA](0) = 1.48153E+0; [EtOH](0) = 1.92379E+1; [EtOHX](0) = 1.64514E+1; [Glyc](0) = 4.19600E+0; [GlycX](0) = 1.68478E+0; [ACAX](0) = 1.28836E+0; [CNX](0) = 5.20358E+0; [ATP](0) = 2.10000E+0; [ADP](0) = 1.50000E+0; [NADH](0) = 3.30000E-1;