Ab initio explorative survey of the mechanism catalyzed by mandelate racemase

There is chemical and kinetic evidence that the mechanism of action of mandelate racemase occurs via two acid/base catalysts, one to abstract a proton from the alpha-carbon and the second to deliver it back to the opposite face of the chiral center. Since the mechanistic details are not known, a few hypotheses have been put forward. Therefore we examine the viability of both concerted and sequential mechanisms on proton abstraction from the or-carbon of mandelate, either without taking into account environmental effects or with the addition to the model system of several functional groups of the residues belonging to the active site, in order to restrain the partners to particular positions without actually imposing arbitrary constraints. The importance of the environment in screening the most highly charged groups in the substrate and in facilitating the alpha-carbon-bound proton abstraction is evident. From the perusal of the geometries of the system along the reaction energy profile, it seems that there is no tendency toward a concerted mechanism: the proton delivery from mandelate to Lys occurs and subsequently the extra proton on protonated histidine is in turn delivered to mandelate.