# #Hynne2001_Glycolysis # modified by MRR into a model of glycerol metabolism pow(x,y)=x^y root(x,y)=y^(1/x) # Compartment: id = extracellular, name = extracellular, constant par extracell=1.0 # Compartment: id = cytosol, name = cytosol, constant par cytosol=1.0 # Reaction: id = vTIM, name = Triosephosphate isomerase # Local Parameter: # Parameter: id = V7f, name = V7f, constant par V7f=116.365 # Local Parameter: # Parameter: id = K7DHAP, name = K7DHAP, constant par K7DHAP=1.23 # Local Parameter: # Parameter: id = K7GAP, name = K7GAP, constant par K7GAP=1.27 # Local Parameter: # Parameter: id = V7r, name = V7r, constant par V7r=116.365 # Local Parameter: # Parameter: id = K7eq, name = K7eq, constant par K7eq=0.055 vTIM=cytosol * (V7f * DHAP / (K7DHAP + DHAP + K7DHAP / K7GAP * GAP) - V7r * (GAP / K7eq) / (K7DHAP + DHAP + K7DHAP / K7GAP * GAP)) # Reaction: id = vGAPDH, name = Glyceraldehyde 3-phosphate dehydrogenase # Local Parameter: # Parameter: id = V8f, name = V8f, constant par V8f=833.858 # Local Parameter: # Parameter: id = K8GAP, name = K8GAP, constant par K8GAP=0.6 # Local Parameter: # Parameter: id = K8NAD, name = K8NAD, constant par K8NAD=0.1 # Local Parameter: # Parameter: id = K8BPG, name = K8BPG, constant par K8BPG=0.01 # Local Parameter: # Parameter: id = K8NADH, name = K8NADH, constant par K8NADH=0.06 # Local Parameter: # Parameter: id = V8r, name = V8r, constant par V8r=833.858 # Local Parameter: # Parameter: id = K8eq, name = K8eq, constant par K8eq=0.0055 vGAPDH=cytosol * (V8f * GAP * NAD / K8GAP / K8NAD / ((1 + GAP / K8GAP + BPG / K8BPG) * (1 + NAD / K8NAD + NADH / K8NADH)) - V8r * BPG * NADH / K8eq / K8GAP / K8NAD / ((1 + GAP / K8GAP + BPG / K8BPG) * (1 + NAD / K8NAD + NADH / K8NADH))) # Reaction: id = vlpPEP, name = Phosphoenolpyruvate synthesis # Local Parameter: # Parameter: id = k9f, name = k9f, constant par k9f=443866.0 # Local Parameter: # Parameter: id = k9r, name = k9r, constant par k9r=1528.62 vlpPEP=cytosol * (k9f * BPG * ADP - k9r * PEP * ATP) # Reaction: id = vPK, name = Pyruvate kinase # Local Parameter: # Parameter: id = V10m, name = V10m, constant par V10m=343.096 # Local Parameter: # Parameter: id = K10PEP, name = K10PEP, constant par K10PEP=0.2 # Local Parameter: # Parameter: id = K10ADP, name = K10ADP, constant par K10ADP=0.17 vPK=cytosol * (V10m * ADP * PEP / ((K10PEP + PEP) * (K10ADP + ADP))) # Reaction: id = vdifGlyc, name = Glycerol out # Local Parameter: # Parameter: id = k16, name = k16, constant par k16=1.9 # Local Parameter: # Parameter: id = Yvol, name = Yvol, constant par Yvol_1_2=59.0 vdifGlyc=k16 / Yvol_1_2 * (cytosol * Glyc - extracell * GlycX) # Reaction added by MRR: glycerol kinase param vmaxgk=1000, Kgk=2 vgk=cytosol*vmaxgk*Glyc/(Kgk+Glyc) # Reaction added by MRR: glycerol 3-phosphate dehydrogenase param vmaxg3pd_p=1.4e-4, Kg3pdGol3P=34 param vmaxg3pd_m=1.9, Kg3pdDHAP=24 vg3pd=cytosol*(vmaxg3pd_p*Gol3P/Kg3pdGol3P - vmaxg3pd_m*DHAP/Kg3pdDHAP)/(1+Gol3P/Kg3pdGol3P+DHAP/Kg3pdDHAP) # Species: id = ATP, name = ATP, affected by kineticLaw param ATP=2.1 # Species: id = ADP, name = ADP, affected by kineticLaw param ADP=1.5 # Species: id = GAP, name = Glyceraldehyde 3-phosphate, affected by kineticLaw init GAP=0.115 dGAP/dt=(1/(cytosol))*(( 1 * vTIM) + (-1 * vGAPDH)) # Species: id = DHAP, name = Dihydroxyacetone phosphate, affected by kineticLaw init DHAP=2.95 dDHAP/dt=(1/(cytosol))*(-1 * vTIM + vg3pd) # Species: id = NAD, name = NAD, affected by kineticLaw param NAD=0.65 # Species: id = BPG, name = 1,3-Bisphosphoglycerate, affected by kineticLaw init BPG=2.7E-4 dBPG/dt=(1/(cytosol))*(( 1 * vGAPDH) + (-1 * vlpPEP)) # Species: id = NADH, name = NADH, affected by kineticLaw param NADH=0.33 # Species: id = PEP, name = Phosphoenolpyruvate, affected by kineticLaw init PEP=0.04 dPEP/dt=(1/(cytosol))*(( 1 * vlpPEP) + (-1 * vPK)) # Species: id = Glyc, name = Glycerol, affected by kineticLaw init Glyc=4.196 dGlyc/dt=(1/(cytosol))*((-1*vgk) + (-59.0 * vdifGlyc)) # Species: id = GlycX, name = Extracellular glycerol param GlycX=1.68478 # Species added by MRR: id = Gol3P, name = glycerol 3-phosphate init Gol3P=1 dGol3P/dt=(1/cytosol)*(vgk-vg3pd) aux flux=vPK @ meth=cvode, tol=1e-6, atol=1e-8 @ bound=40000, total=200 done