Kinetic Modeling of E. coli Enzymes: Integration of in vitro Experimental Data

The metabolic network of E. coli is one of the most well studied biochemical systems, with an abundance of in vitro and in vivo data available for quantitative estimation of its kinetic parameters. In this chapter, we present our approach to developing mathematical description of individual enzymatic reactions within bacterial metabolic networks. This description is based on the detailed consideration of enzyme catalytic mechanisms and includes several stages: reconstruction of the enzyme catalytic cycle, derivation of the reaction rate equation, and validation of its parameters on the basis of available in vitro experimental data. We illustrate our strategy with the models developed for three E. coli enzymes with rather complicated regulatory mechanisms: allosteric tetramer phosphofructokinase-1, citrate synthase with its regulation by ATP and pH, and β-galactosidase validated against time dependencies of its substrates. The modeling results clearly demonstrate that developing detailed enzyme kinetic models is essential to capture key regulatory properties of enzymes. The kinetic models allow to integrate large sets of in vitro experimental data available for E. coli enzymes and to get insight into important regulatory features of their catalytic mechanism.