(301g) Ammonia-Assisted Methanol Oxidation by Methanol Dehydrogenase Enzyme

Methanol Dehydrogenase (MDH) is an enzyme found in the periplasm of methylotropic bacteria that oxidizes methanol to formaldehyde by releasing two protons and two electrons one at a time. The active site of MDH consists of Pyrroloquinoline Quinone (PQQ) which is the cofactor, a divalent calcium cation, a catalytic base Asp303 and twelve other amino acids along with few water molecules. The natural mediator for the MDH is Cytochrome c_L (C_L). Methanol oxidation by MDH is believed to take place via an Addition-Elimination mechanism that involves transfer of protons from methanol to the MDH active site base Asp303.The catalytic base abstracts a proton from methanol and forms a hemiketal intermediate, and the rest of the methanol molecule binds to PQQ. The next step involves elimination of a proton from Asp303 that binds to PQQ, and in the final step a second proton transfer from methanol takes place to PQQ resulting in the formation of formaldehyde [1]. In vivo, MDH does not need any activator for that oxidation process to take place; however in vitro it is believed that apart from MDH there are other cofactors involved in the oxidation of methanol and therefore NH₃ as an activator is needed [2].

In this paper the surface interaction between MDH and C_L is investigated using Monte Carlo searches of the substrate-adsorbate system. The effect of NH₃ in the methanol Addition-Elimination mechanism is theoretically investigated by classical transition state theory. Initially optimized geometries of both reactants and products are found for defining atom pairing. The trajectory files obtained from the reaction path are used as inputs to obtain corresponding transition state using linear synchronous and quadratic synchronous transit (QST) with conjugate gradient (CG) minimization. In order to confirm the reaction paths intrinsic reaction coordinate analysis is then performed. References 1. Reddy, S. Y., et al., ?Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase?, Protein Science, vol 13, p. 1965-1978, 2004

2. Anthony, C. et al., ?The structure and mechanism of methanol dehydrogenase?, Biochemica et Biophysica Acta, vol 1647, p. 18-23, 2003