Reaction mechanism of the mandelate anion racemization catalyzed by mandelate racemase enzyme: A QM/MM molecular dynamics free energy study

The present work studies the reaction mechanism of the racemization of mandelate substrate by mandelate racemase enzyme. The reaction has some intriguing aspects such as the deprotonation of a nonacid hydrogen and the achievement of the pseudosymmetry necessary to obtain the racemic mixture. We will make use of a QM/MM potential energy surface to compute the free energy profiles associated with the reaction. The most favorable reaction mechanism consists of two proton transfers and the configuration inversion of the stereogenic carbon taking place in a concerted manner. We have also designed a suitable reaction coordinate to compute the free energy profiles for this rather complicated reaction. In addition, analysis of the electrostatic effects and bond distances along the reaction will explain how the enzyme accomplishes the catalysis. Finally, the enzymatic reaction will be compared to a model of the uncatalyzed reaction and the catalytic effect of mandelate racemase will be evaluated.