(94a) Ammonia Activated Methanol Oxidation by Methanol Dehydrogenase Enzyme: A Theoretical Study

Quinoprotein Methanol Dehydrogenase (MDH) is an enzyme that oxidizes methanol to formaldehyde. In the process it takes part in an electron transfer chain such that two electrons and protons are transferred one at a time to its natural electron mediator Cytochrome c_L (C_L). C_L gets oxidized by a cytochrome c_H which in turn gets oxidized by a membrane oxidase. This produces a proton motive force of almost one ATP, per methanol molecule oxidized. The functionality of enzyme MDH and C_L, when isolated from the bacteria reduces to a large extent. The possible reason can be change in physical and structural condition or absence of cofactors that may assist in the oxidation reaction [1]. In vitro the enzyme MDH and C_L gets activated in the presence of NH₃ at a ph of 9. It is assumed that the NH₃ helps in the initial abstraction of hydrogen from methanol which is also the rate limiting step [2]. Various mechanisms for oxidation of methanol in MDH have been proposed and one of them is Hydride-Transfer mechanism which is a four step mechanism. The first step involves transfer of proton and hydride from methanol to probable catalytic base Asp303 and PQQ, resulting in the formation of formaldehyde. The subsequent steps consists of transfer of protons between Asp303 and PQQ which finally reduces PQQ to PQQH₂ [2]. In this paper effect of NH₃ in the Hydride-Transfer mechanism of methanol oxidation is analyzed by classical transition state theory. It assumes that once a reaction passes though the reaction barrier it does not go back again. The optimized geometries of reactant, intermediates and final products are obtained for essential proton transfer. The trajectory files obtained from the reaction path are used as inputs to obtain corresponding transition state using linear synchronous (LST) and quadratic synchronous transit (QST) with conjugate gradient (CG) minimization. In order to confirm the reaction paths intrinsic reaction coordinate analysis is performed.

Reference 1. Williams, P. A.; Coates, L.; Mohammed, F.; Gill, R.; Erskine, P. T.; Coker, A.; Wood, S. P.; Anthony, C.; Cooper, J. B., The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallographica Section D: Biological Crystallography 2005, 61, (1), 75-79.

2. Anthony, C.; Williams, P., The structure and mechanism of methanol dehydrogenase. Biochimica et Biophysica Acta - Proteins and Proteomics 2003, 1647, (1-2), 18-23.