Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

摘要: The ability to characterize biological dynamics is important for understanding the integrated molecular processes that underlie normal and abnormal cellular states. availability of metabolomic data, in addition new developments formal description dynamic states networks, has enabled a data integration approach building large-scale kinetic networks. We show network models can be constructed scalable manner using mapped onto stoichiometric models, resulting mass action simulation (MASS) models. Enzymes their various functional are represented explicitly as compounds, or nodes network, within this formalism. Analyses simulations MASS regulatory enzymes control networks part by binding numerous metabolites at multiple sites. Thus, reflected fractional enzyme, such fraction total enzyme concentration catalytically active versus inactive state. feasible construction represents practical means increase size, scope, predictive capabilities cell biology.