(37d) A Multi-Scale Modeling Study of MDH-Catalyzed Methanol Oxidation: The Effect of the Ion In the Enzyme Active Site

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. Ca²⁺ ion in the active site holds the PQQ in place and also acts as a Lewis acid during the oxidation mechanism[5]. From previous studies, it was observed that the energy barrier for the oxidation of methanol was influenced by the atomic size of the ion in the active site of MDH[5]. Thus, the various studies on ion-modified enzymes indicate that ions play a vital and diverse role in enzyme catalysis.

From the possible mechanisms for methanol oxidation by MDH proposed in the literature, the Hydride Transfer (H-T) mechanism [1] seems, to the best of our knowledge, to be the preferred one under normal conditions. So far, no information was reported in the literature concerning methanol oxidation by Mg²⁺-containing MDH. Hence, in this work the naturally occurring Ca²⁺ ion in the active site of MDH enzyme was replaced with Mg²⁺ ion and H-T methanol oxidation mechanism for the Mg²⁺-containing MDH was tested.

A MDH active site model was considered to test the H-T 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. It has been observed that the free energy barrier for the rate determining step of the H-T mechanism with the Mg²⁺-MDH active site model is 1.5kcal/mol greater than that of the Ca²⁺-MDH active site model. Information regarding energy barriers and pre-exponential factors thus obtained determine the reaction rates involved in each step of the methanol oxidation mechanism by MDH. These microscopic reaction rates are then provided as inputs in a Kinetic Monte Carlo (kMC) program, and the methanol oxidation process is modeled. These simulations give a better understanding of the catalytic methanol oxidation mechanism by MDH, helping evaluate the kinetics and their dependence on various factors like obstacle density, substrate and active site concentrations, temperature and time, and the nature of the ion in the MDH active site.

References:

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 C_L. 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.

5.   Idupulapati, N.B., Mainardi, D.S., “Coordination and binding of ions in Ca2+- and Ba2+-containing methanol dehydrogenase and interactions with methanol”, Journal of Molecular Structure: THEOCHEM, 901 (1-3), 2009.