DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

Abstract

The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, (S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2′ ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log K eq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.Electronic supplementary materialThe online version of this article (doi:10.1007/s10822-017-0026-5) contains supplementary material, which is available to authorized users.

Computational mechanistic study of human liver glycerol 3‐phosphate dehydrogenase using ONIOM method

“…ONIOM calculations have provided complementary mechanistic insights to the existing experimental studies for a variety of enzyme reactions, and as a result, invaluable information were obtained. [14][15][16][17][18][19] Out of a variety of DFT functionals, M06-2X and B3LYP functionals with 6-31G basis set produced mechanistic results in accordance with the experimental results for a variety of enzyme reactions involving hydride transfer processes in choline oxidase, [13] and monoamine oxidase, [20,21] alcohol dehydrogenase, [22] cholesterol oxidase, [23] and HMG-CoA reductase. [12] By using ONIOM calculations, we investigated the role of Lys120, Lys204, and protonated-Asp260 (Figure 1) in the hydride transfer process as potential general acid candidates.…”

Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate

“…A reaction coordinate featuring overlapped timing of proton and hydride transfer is characteristic of metal-independent enzyme catalysis to alcohol oxidation. 91 − 93 It differs from the stepwise catalysis of Zn 2+ -dependent ADHs. 94 In these ADHs, lowering of the p K a in the Zn 2+ -bound alcohol strongly activates the substrate for C–H bond cleavage already in the ground-state complex.…”

“…The chemical step of transient oxidation presumably involves coordinated (i.e., concerted but likely asynchronous ,− ) abstraction of the hydride from the C2 and the proton of the 2-OH of the reactive alcohol group, as shown in Scheme . A reaction coordinate featuring overlapped timing of proton and hydride transfer is characteristic of metal-independent enzyme catalysis to alcohol oxidation. − It differs from the stepwise catalysis of Zn 2+ -dependent ADHs . In these ADHs, lowering of the p K a in the Zn 2+ -bound alcohol strongly activates the substrate for C–H bond cleavage already in the ground-state complex .…”