Simulation and optimization of metabolic pathways

Abstract

A program to simulate metabolic pathways on the basis of either kinetic data or data on the steady-state levels and fluxes using Biochemical Systems Theory is presented. Having established such a model it is possible to determine the rate-controlling enzymes and metabolites for the system. While this in itself yields extremely valuable information pinpointing the limiting fluxes through the system, a more usual objective is to maximize a production rate or flux or to minimize byproducts or toxic intermediates. For this reason the problem is posed as a constrained optimization problem. While we recognize that the optimum thus found may be unachievable in practical terms due to limitations in the extent to which cells can be manipulated, it is important in that it: (a) gives an upper or lower bound to the production rate or flux; and (b) indicates the ideal combination of variables which should be aimed at. The model system used to test the software is a pathway for the degradation of toluene encoded by the TOL plasmid from Pseudomonas putida transformed into Escherichia coli. Kinetic data has been obtained, partly from the literature and partly by approximation, and realistic metabolite and enzyme concentrations are chosen.