Methanol Dehydrogenase (MDH) is a water-soluble quinoprotein that oxidizes methanol and other primary alcohols to their corresponding aldehydes. The crystal structure of MDH from Methlylobacterium extorquens [1, 2] and from Methylophilus W3A1 [3, 4] has been characterized and it has been determined that the enzyme active center contains a Ca2+ ion, pyrroloquinoline quinone (PQQ) and amino acids. Two possible mechanisms for methanol oxidation by MDH have been proposed in the literature, the Addition-Elimination (A-E) and the Hydride Transfer (H-T) mechanisms [1]; however, to the best of our knowledge, no clear evidence exists in the literature regarding what methanol oxidation mechanism operates in nature by MDH.

In this work, two MDH active site models are considered to test possible methanol oxidation mechanisms based on the exposed residues methanol molecules face upon approaching the MDH active site through the enzyme binding pocket. Density Functional Theory calculations are performed using the DMOL3 module of the Materials Studio software to investigate reaction pathways. Energy barriers are calculated in gas as well as implicit and explicit solvent (water) phases. Additionally, the effects of enzyme environment on methanol oxidation are explored by adding representative portions of cytochrome cL, the MDH natural electron mediator, to the MDH active site models.

1. Ghosh, M., C. Anthony, K. Harlas, M.G. Goodwin, and C.C.F. Blake, The Refined Structure of the Quinoprotein Methanol Dehydrogenase from Methylobacterium Extorquens at 1.94 Å. Structure (London), 1995. 3: p. 1771-1787.

2. Afolabi, P.R., M. F., K. Amaratunga, O. Majekodunmi, S.L. Dales, R. Gill, D. Thompson, J.B. Cooper, S.P. Wood, P.M. Goodwin, and C. Anthony, Site-Directed Mutagenesis and X-Ray Crystallography of the PQQ-Containing Quinoprotein Methanol Dehydrogenase and Its Electron Acceptor, Cytochrome CL. Biochem., 2001. 40: p. 9799-9809.

3. Xia, Z.X., Y.N. He, W.W. Dai, S. White, G. Boyd, and F.S. Mathews, Detailed Active Site Configuration of a New Crystal Form of Methanol Dehydrogenase from Methylophilus W3A1 at 1.9 Å Resolution. Biochem., 1999. 38: p. 1214-1220.

4. Xia, Z.X., W.W. Dai, Y.S. Zhang, S. White, G. Boyd, and F.S. Mathews, Determination of the Gene Sequence and the Three-dimensional Structure at 2.4 Å Resolution of Methanol Dehydrogenase fromMethylophilusW3A1. J. Mol. Biol., 1996. 259: p. 480-501.