(188cw) Identifying the Atomistic Features That Enhance the Rate of Methyl-Transfer Catalysis of Ketol-Acid Reductoisomerase

Considerable advances in the theoretical understanding of enzyme structure and function have been made in the past, yet the design of a protein capable of refined function remains a very difficult feat. In the following work, we investigate the atomistic drivers of reactivity for the rate-limiting step of ketol-acid reductoisomerase (KARI), an enzyme that catalyzes a methyl transfer of a substrate relevant to biofuel precursors. Prior work by Bonk, Weis, et al. employed the use of quantum mechanical/molecular mechanical (QM/MM) simulations to identify the conformational features near the active-site of the enzyme that differentiate between dynamic trajectories that successfully transfer the methyl group, versus those that fail. Moreover, these conformational features are identified in the reactant well of the enzyme, before the enzyme begins to catalyze the reaction and climb the activation barrier. This collective set of conformational features leads to significant increase in reactivity, when sampled more frequently before the reaction. We perform quantum mechanical (QM) calculations on frames of dynamic trajectories to identify the origin of reactivity, and why these conformational features are predictive before the reaction occurs. We employ the use of Natural Bonding Orbital (NBO) analysis to trace the electronic density through the methyl transfer, and identify how these structural features lead to increases in reactivity from a mechanistic point-of-view. The study of these features potentially provides for unique, chemical insight towards engineering targets for enzyme design.