Effects of conformational degrees of freedom on catalytic efficiency studied by lattice model Monte Carlo simulations

Catalysis refers to the acceleration of chemical reactions by way of molecules that are not altered or consumed. Enzymes are proteins that act as catalysts in biochemical reactions and are well-known to facilitate catalytic efficiency far beyond the levels of artificial catalysts for reasons still debated. One of the origins of this behavior may be the ability for enzymes to undergo conformational changes during catalysis, which contrasts with the rigidity of typical artificial catalysts. [1] In the study of enzymatic catalysis, computational modeling and simulations have proven to play an instrumental role in furthering our understanding of these effects. In this work, we explore the splitting of a dimer into its two component monomers by modeling three types of processes with Monte Carlo simulations of a simple lattice model. The first is a spontaneous reaction with no catalyst present, the second consists of heterogeneous catalysis induced by a rigid catalyst, and the third considers a catalyst with internal degrees of freedom as a simple model of an enzyme. [1] To validate our simulations, we measure equilibrium properties and compare them with exact enumerations. We then determine transition probabilities to characterize the efficiency of the different types of processes. In addition, we investigate the effect of energy levels on reaction rates to test the so-called Sabatier principle. Finally, we extend the model to gain a better understanding of the role of conformational change on non-rigid catalysts like enzymes.

[1] O. Rivoire. How Flexibility Can Enhance Catalysis. Phys. Rev. Lett. 131, 088401 (2023)