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

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 Zn_rest–Glu_in and Zn_cat–Glu_out 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 (Zn_cat–Glu_out) has a ∼20 kcal/mol lower reaction barrier in comparison to the resting state (Zn_rest–Glu_in). This indicates that the coupled movement of zinc ion and Glu influences not only the ligand exchange but also the catalytic process of MDRs