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 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.

Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate

“…PM6 has been successfully applied to study reaction mechanisms involved in enzyme-catalyzed reactions. [92][93][94] Moreover, our preliminary results show that the energy barrier obtained at the PM6/ff14SB level of theory is in more reasonable agreement with the experimental activation free energy compared to PM3, AM1/d and SCC-DFTB results.…”

Inversion of cpADH5 Enantiopreference and Altered Chain Length Specificity for Methyl 3‐Hydroxyalkanoates

“…Docking of selected 3‐hydroxy fatty acid methyl ester substrates to cpADH5 WT and resulting variants have been performed in order to generate a first molecular understanding of the structure‐function relationships of cpADH5 ability to oxidize 3‐hydroxy fatty acid methyl ester. In the substrate docking protocol, the partial charge of the catalytic zinc environment including the zinc ion and its coordinating residues (C44, H65, D154 and water) have been re‐parameterized. In addition, the oxidation mechanism‐based distance criteria (distances D1, D2 and D3 shown in Figure S1 in Supporting Information) have been applied to extract the catalytically active pose from a pool of docking poses.…”

“…Furthermore, cpADH5 has been investigated in detail by employing computational approaches. Carbonyl reduction mechanism as well as structural determinants of substrate spectrum was determined by using quantum mechanichs/molecular mechanics (QM/MM) techniques . Natural substrates and thus, function of the cpADH5 were predicted through virtual screening and QM/MM calculations .…”

“…Carbonyl reduction mechanism as well as structurald eterminants of substrate spectrum was determined by using quantum mechanichs/molecularm echanics (QM/MM) techniques. [17,21] Natural substrates and thus, function of the cpADH5 were predicted through virtuals creening and QM/MM calculations. [16a] In addition, its substrate binding pocket was engineered throughs tructure guided design forr eduction of aryl ketones such as 2-bromo-4'-chloroacetophenone.…”

Bacteria on steroids: the enzymatic mechanism of an NADH-dependent dehydrogenase that regulates the conversion of cortisol to androgen in the gut microbiome

“…To investigate possible reaction mechanisms, we ran a 20 ps long QM/MM MD equilibration to prepare the system, and used a QM/MM steered MD (SMD) approach (66,(75)(76)(77)(78) to induce the reaction to occur according to the chosen mechanisms we describe below. These selected reaction mechanisms were designed to determine multiple aspects of this complex reaction, one being the participation of a water molecule to mediate the interaction between the Zn 2+ ion and substrates, as previously suggested for similar enzymes (79). Our QM/MM SMD only forced the initial steps of the reactions, allowing the remaining steps to occur freely in case they were energetically favorable.…”