Understanding the dynamic responses of living cells upon genetic and environmental perturbations is crucial to decipher the metabolic functions of organisms. Mathematical models are essential to provide a large and coherent picture of these complex systems. They can guide the metabolic engineering of organisms to produce desired chemicals and fuels from renewable sources. Building these models requires a comprehensive understanding of the enzyme kinetics as metabolic fluxes are limited by enzymatic activity. The enzymes, acting as biocatalysts in living organisms are an outcome of natural selection. For a global understanding of their design and evolution, they should be studied along with the underlying optimality principles.<br/><br/>In this work, we investigate the optimal modes of operations for enzymes, under the premise that the evolutionary pressure drives enzyme kinetics towards increased catalytic activity. We thereby assumed that the enzyme usage is optimized for each reaction, such that the minimal amount of enzyme is used to generate the required flux under the given reactant concentrations and thermodynamic constraints. We formulated an optimization framework that maximizes the reaction rate at the elementary reaction level with a fixed total enzyme concentration. While theoretical studies using this approach exist, these studies use approximate rate laws and only investigate simple enzyme mechanisms. Our study formulates a mixed-integer linear problem (MILP) enabling an efficient estimation of the optimal catalytic properties of complex enzyme mechanisms. The framework further allows to assess the distribution of the thermodynamic forces and enzyme states, providing detailed insight into the mode of operation. Our results confirm earlier theoretical studies on optimal kinetic design, using a reversible Michaelis-Menten mechanism. We further explored the optimal modes of operation for a random-ordered multi-substrate mechanism. Our algorithm estimates an optimal objective for the reaction rate, which is achieved by unique or alternative modes of operation depending on the concentrations of the reactants.<br/><br/>Our formulation can be applied to all types of enzyme mechanisms with known elementary reactions, exploring the kinetic and thermodynamic landscape of optimal enzyme utilization. The proposed framework can be used to guide and evaluate directed evolution studies, and it can be used to estimate the limits of the direct evolution of enzymes.

Optimal enzyme utilization suggests condition-specific saturations and binding mechanisms

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.