RC: The estimation of kinetic parameters in Systems Biology by comparing molecular interaction fields of enzymes

The kinetic modelling of biochemical pathways requires a consistent set of enzymatic kinetic parameters. We report results from software development to assist the user in systems biology, allowing the retrie-val of heterogeneous protein sequence, structural and kinetic data. For the simulation of biological networks, missing enzymatic kinetic para-meters can be calculated using a similarity analysis of the enzymes’ molecular interaction fields. The quantitative PIPSA (qPIPSA) meth-odology relates changes in the molecular interaction fields of the enzymes with variations in the enzymatic rate constants or binding affinities. As an illustrative example, this approach is used to predict kinetic parameters for glucokinases from Escherichia coli based on experimental values for a test set of enzymes. The best correlation of the electrostatic potentials with kinetic parameters is found for the open form of the glucokinases. The similarity analysis was extended to a large set of glucokinases from various organisms