The Shaping of Enzymatic Free Energy Barriers through the Creation of Rate-Promoting Vibrations via Inter-Residue Cross-Talk on Multiple Time Scales

Years ago, we identified a rapid vibrational motion─termed a rate-promoting vibration (RPV)─as central to the reaction coordinate of some enzymes. This study addresses two key questions for one example enzyme we have studied, lactate dehydrogenase (LDH): first, what is a lower bound on the RPV’s contribution to catalytic efficiency, and second, what is the mechanism of RPV formation via allosteric transmission. The goal is to understand how we can artificially create such a system. LDH catalyzes the interconversion of pyruvate and lactate via hydride and proton transfer. Altering the motion range between Val31 and Arg106, central residues in the promoting vibration, with a modest constraint reduces the reaction rate (through a raising of the free energy barrier) by over 3 orders of magnitude. Committor analysis shows that shorter distances in the constrained system shift the transition state toward proton transfer, while natural or longer distances favor a transition state formed in hydride transfer. PCA confirms the anticorrelated motion between Val31 and Arg106, aligning with vibrational modes to optimize the reaction path. Critically, we find that a breathing motion among alpha helices is used to create the necessary distance over which a rapid and short RPV can be effective. Network analysis reveals that Val31, Ala34, and Cys35 have higher eigenvector centrality in reactive trajectories, indicating enhanced inter-residue communication. These findings underscore RPVs as crucial modulators of enzymatic function through dynamic and allosteric mechanisms and suggest an approach to the generation of nonbiologic protein catalysts that include a promoting vibration.