QM/MM Calculations Revealing the Resting and Catalytic States in Zinc-Dependent Medium-Chain Dehydrogenases/Reductases

Abstract

Oxido-reductases from medium-chain dehydrogenase/reductase (MDR) family are excellent biocatalysts for the generation of optically pure alcohols from prochiral ketones. The mechanism of hydride and proton transfer steps in zinc-catalyzed carbonyl reduction has been investigated by quantum mechanical/molecular mechanical (QM/MM) calculations. The recent X-ray structure of zinc-dependent carbonyl reductase from Candida parapsilosis (CPCR2; PDB ID 4C4O) shows two different conformers of Glu66 and two positions of the catalytic zinc ion. Starting from four different hypothetical states, we obtained only two minima, so-called Znrest–Gluin and Zncat–Gluout of zinc ion and Glu66, indicating a coupled movement. We analyzed the dependence of barriers for the hydride transfer for these two states in the reduction of carbonyl substrate using QM/MM steered molecular dynamics (SMD) simulations. Our calculations show that the catalytic state (Zncat–Gluout) has a ∼20 kcal/mol lower reaction barrier in comparison to the resting state (Znrest–Gluin). This indicates that the coupled movement of zinc ion and Glu influences not only the ligand exchange but also the catalytic process of MDRs.