Regiodivergent catalytic mechanism of cellular membrane-bound dehydrogenase for the high selective bio-oxidation of primary diols

Abstract

Gluconobacter oxydans demonstrated a distinct selective divergence in biocatalysis of primary diols with varying carbon chain lengths for hydroxyl acids production. Therefore, molecular docking and molecular dynamics simulation were employed to investigate the binding mode between membrane-bound alcohol dehydrogenase with primary diols and hydroxyl acids. The molecular docking results revealed that as carbon chain length of hydroxyl acids increased, the van der Waals interactions, which plays important binding role, significantly diminished from −8.31 to −25.75 kcal/mol, which suggesting that an increase in carbon chain length enhanced the binding affinity. The movement trajectory and dehydrogenase structural further confirmed that primary diols with C ≥ 5 could eventually convert to diacids, which elucidating the mechanism of region-selective biocatalysis. The simulation results of systems with varying protonation states constructed by constant pH method demonstrated that as pH increased to 6, the binding free energy of 5-hydroxyvaleric acid and dehydrogenase shifted from −18.48 to 10.84 kcal/mol, indicating a significant reduction in binding affinity. Moreover, by integrating multi-scale simulation indexes, it was determined that the critical pH regulatory points for the highly selective conversion of pentanol and hexanediol to hydroxyl acids, which were 5.5 and 7. The rational strategy of microsimulation guided macroscopic biocatalysis, which selectively converted 20 g/L pentadiol and hexanediol into 20.4 g/L and 19.2 g/L hydroxyl acids, thereby resulting in selective preparation of hydroxyl acids with C2-C6 by G. oxydans respectively. Importantly, the selective production technology effectively prevented the formation of diacid and enabled in situ separation and purification of hydroxyl acids from by-product.