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The L-Ascorbate Pathway Model in LBS
directive sample 900.0 5000
// Compartments comp cytosol = new comp;
// Enzymes spec sub_GDP_D_mannose_epimerase = new{}; spec GDP_D_mannose_epimerase = new{}; spec GDP_L_Gal_phosphorylase = new{}; spec Gal_P_phosphatase = new{}; spec D_Ara_dehydrogenase = new{}; spec D_Ara_Lac_oxidase= new{}; spec GDP = new{};
// Metabolites spec GDP_D_Man = new{}; spec GDP_L_Gal = new{}; spec L_Gal_P = new{}; spec L_Gal = new{}; spec L_Gal_Lac = new{}; spec L_ascorbate = new{};
// Rate constants rate GDP_clearance = 1.0*10^-9; rate kb = 0.01; rate ku = 1.0*10^-4; rate GDP_D_mannose_epimerase_Km = 0.0045; rate GDP_D_mannose_epimerase_Kcat = 0.041; rate Ki = 5.0e-4; rate GDP_L_Gal_phosphorylase_Km = 0.01; rate GDP_L_Gal_phosphorylase_Kcat = 13.0; rate Gal_P_phosphatase_Km = 0.107; rate Gal_P_phosphatase_Kcat = 6.0; rate D_Ara_dehydrogenase_Km = 180.0; rate D_Ara_dehydrogenase_Kcat = 125.0; rate L_Gal_Lac_dehydrogenase_Km = 53.7; rate L_Gal_Lac_dehydrogenase_Kcat = 18.8;
module mmInhibitionRXN(spec sub, enz, prod, inhib; rate km, kcat, k) { rate rxn_rate = kcat*enz/(sub+km*(1+inhib/k)); sub + enz ->[rxn_rate] enz + prod };
module mmRXN(spec sub, enz, prod; rate km, kcat) { rate rxn_rate = kcat*enz/(sub+km); sub + enz ->[rxn_rate] enz + prod };
module mmTwoProductsRXN(spec sub, enz, prod1, prod2; rate km, kcat) { rate rxn_rate = kcat*enz/(sub+km); sub + enz ->[rxn_rate] enz + prod1 + prod2 };
cytosol[ sub_GDP_D_mannose_epimerase + sub_GDP_D_mannose_epimerase <->{kb}{ku} GDP_D_mannose_epimerase | mmInhibitionRXN(GDP_D_Man, GDP_D_mannose_epimerase, GDP_L_Gal, GDP, GDP_D_mannose_epimerase_Km, GDP_D_mannose_epimerase_Kcat, Ki) | mmTwoProductsRXN(GDP_L_Gal, GDP_L_Gal_phosphorylase, L_Gal_P, GDP, GDP_L_Gal_phosphorylase_Km, GDP_L_Gal_phosphorylase_Kcat) | mmRXN(L_Gal_P, Gal_P_phosphatase, L_Gal, Gal_P_phosphatase_Km, Gal_P_phosphatase_Kcat) | mmRXN(L_Gal, D_Ara_dehydrogenase, L_Gal_Lac, D_Ara_dehydrogenase_Km, D_Ara_dehydrogenase_Kcat) | mmRXN(L_Gal_Lac, D_Ara_Lac_oxidase, L_ascorbate, L_Gal_Lac_dehydrogenase_Km, L_Gal_Lac_dehydrogenase_Kcat) | ->{10} GDP_D_Man | GDP ->{GDP_clearance} | init sub_GDP_D_mannose_epimerase 1 | init GDP_D_mannose_epimerase 0 | init GDP_L_Gal_phosphorylase 1 | init Gal_P_phosphatase 1 | init D_Ara_dehydrogenase 1 | init D_Ara_Lac_oxidase 1 | init GDP 0 ] </pre>
