Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations

J Chem Inf Model. 2024 May 13;64(9):3953-3958. doi: 10.1021/acs.jcim.4c00475. Epub 2024 Apr 12.

Abstract

The rate constants of enzyme-catalyzed reactions (kcat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, without introducing the transition-state theory assumptions, and takes into account the dynamical equilibrium between the reactive and non-reactive conformations of the enzyme/substrate complex. Our computed kcat values are in order-of-magnitude agreement with the experimental data for two representative enzymatic reactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biocatalysis*
  • Enzymes / chemistry
  • Enzymes / metabolism
  • Kinetics
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Quantum Theory*

Substances

  • Enzymes