QM-FE Calculations of Aliphatic Hydrogen Abstraction in Citrate Synthase and in Solution:  Reproduction of the Effect of Enzyme Catalysis and Demonstration that an Enolate Rather than an Enol Is Formed

Mechanistic enzymologists have long debated how enzymes catalyze the abstraction of an unactivated C−H group. Citrate synthase, due to its ability to catalyze this abstraction and its central role in the respiratory cycle, has been extensively studied both experimentally and theoretically. Despite this scrutiny, the question remains as to whether the initial aliphatic hydrogen abstraction step of the mechanism is stabilized by the formation of an enol-imidazolate intermediate through “short, strong” hydrogen bonds, as opposed to the more traditional enolate-imidazole complex. In an attempt to present a definitive answer to this question, quantum mechanical-free energy (QM-FE) calculations were performed for the formation of the enolate-imidazole complex from the reactants, as well as for the further formation of the enol-imidazolate system. These reactions were found to be extremely sensitive to the use of nonbonded cutoffs, and reliable results were only obtained with the use of particle mesh Ewald (PME) to treat the electrostatic interactions. Because of the length of these simulations, we also used a coarse-grained parallel approach to free energy calculations. The results indicate that the enolate-imidazole complex is the more stable one within the enzyme by approximately 13 kcal/mol. The calculated barrier to the formation of the enolate is in good quantitative agreement with the k_cat for this enzyme.