The transition path sampling method previously applied in our group to the reaction catalyzed by lactate dehydrogenase was used to generate a transition path ensemble for this reaction. Based on analysis of the reactive trajectories generated, important residues behind the active site were implicated in a compressional motion that brought the donor-acceptor atoms of the hydride closer together. In addition, residues behind the active site were implicated in a relaxational motion, locking the substrate in product formation. Although this suggested that the compressionrelaxation motions of these residues were important to catalysis, it remained unproven. In this work, we used committor distribution analysis to show that these motions are integral components of the reaction coordinate.protein dynamics ͉ catalysis T he relationship between enzymatic structure and function remains an area of intense research. Many studies have demonstrated that factors such as electrostatic and entropic effects are significant to enzyme function (1). The role of dynamics in catalysis, however, is less well understood. Protein motions such as conformational fluctuations on the millisecond timescale have been shown to influence substrate binding and the height of the barrier to reaction. The role of vibrational motions on the femtosecond to picosecond timescale and their connection to catalysis remain controversial. It has been suggested that the vibrational motions that exist within the protein are in equilibrium with the reaction and thermally averaged along the reaction coordinate (2, 3). But we and others have suggested that vibrational motions within the protein may in fact be coupled to the reaction coordinate (4). Previous work in our group has suggested the coupling of these vibrational motions to the reaction coordinate and has developed methods to study their effect on enzyme reactions (5).The search for these subpicosecond motions (''protein promoting vibrations'') was first applied to the enzyme horse liver alcohol dehydrogenase. This work suggested there existed motions, protein-promoting vibrations (PPVs), that coupled directly to the reaction coordinate and that were on the timescale of barrier crossing (6). The algorithm was then tested on another enzyme system lactate dehydrogenase (LDH), and similar PPVs were identified that, along with conformational fluctuations, helped explain the preference of the heart isoform to produce pyruvate and of muscle isoform to produce lactate (7).Further investigation into the mechanism of LDH was achieved with the transition path sampling (TPS) method (8). TPS is a computational method that can simulate rare events in complex systems. Using a Monte Carlo approach, a reactive path ensemble connecting reactants to products can be defined without prior knowledge of the reaction coordinate. This method allows mechanistic details to be identified from reactive paths generated with no bias (9). A reactive path ensemble was generated for LDH, and it was found that, in all reactive trajectori...

Transition Path Sampling is a well known technique that generates reactive paths ensembles. Due to the atomic detail of these reactive paths, information about chemical mechanisms can be obtained. We present here a comparative study of Bacillus stearothermophilus and human heart homologs of lactate dehydrogenase. A comparison of the transition path ensemble of both enzymes revealed that small differences in the active site reverses the order of the particle transfer of the chemical step. Whereas the hydride transfer preceded the proton transfer in the heart heart LDH, the order is reversed in the Bacillus stearothermophilis homolog (in the direction of pyruvate to lactate). In addition, transition state analysis revealed that the dividing region that separates reactants and products, the separatrix, is likely wider for BsLDH as compared to human heart LDH. This would indicate a more variable transition process in the Bacillus enzyme.