Reactive Quantum-Mechanical Molecular Dynamics Simulations to Reveal Mechanisms of Enzyme Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but tradeoffs between accuracy and computational cost have limited their use. Here, we develop a reactive QMD approach to investigate mechanisms of isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenol isocyanide, forming a thioimidate intermediate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation. X-ray crystallography and functional assays of ICH mutants suggest this order of events might occur during enzyme catalysis. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate reactions relevant to enzyme catalysis involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.