(562f) Cost Efficiency Model for the Network-Wide Quantitative Determination of Enzyme Activities

Flux Balance Analysis (FBA) has become the most commonly applied method to evaluate internal fluxes from extracellular flux measurements and an inferred objective function that is thought to be enforced by evolution. However, FBA results in a high-dimensional solution space instead of a unique flux distribution. Kinetic models on the other hand do return a unique flux solution, but their development has been hindered by difficulties in collecting adequate enzyme activity data. We present an enzyme cost efficiency model designed to simultaneously determine all enzyme activities from enzyme concentration measurements. The premise of this model is the economical usage of enzymes, which implies a minimal investment in protein cost for a given flux demand. The cost efficiency model corresponds to a constrained optimization problem that minimizes the distance between measured and simulated enzyme concentrations and maximizes the biomass production. A bidirectional mass action model links enzyme activities and concentrations to the flux distribution. The forward and reverse rate constants were constrained by the equilibrium rate constants which reduces the number of activity variables by a factor of two, whilst enforcing thermodynamic consistency. The parameter fitting was solved as a double non-linear inverse problem. Enzyme activities were fitted in an outer loop and enzyme concentrations were optimized in an inner loop. This cost efficiency model presents a novel optimization framework that enables the formulation of kinetic models for large metabolic networks suitable for rational design of metabolism.