(45c) A Monte Carlo Approach towards Understanding the Catalytic Mechanism of Methanol Dehydrogenase Enzyme Immobilized On 2-D Surfaces

Recently, studies on enzymes and their use as catalysts
in bio fuel cells¹ has been an active field of research due to the increasing
demand for novel clean energy sources. Methanol Dehydrogenase (MDH) is an
enzyme which can be used as an effective biocatalyst in fuel cells due to its
ability produce electrons by the oxidation of methanol². MDH is
found in the periplasm of Methylotropic bacteria and consists of an active site
containing a Pyrroloquinoline Quinone (PQQ) cofactor, a divalent calcium
cation, a catalytic base ASP 303 and twelve other amino acids with water
molecules². Several studies^3,4 predicted the various
reaction mechanisms at the active site of MDH for the oxidation of methanol to
formaldehyde. However the diffusion of methanol towards the active site in MDH
is one field which needs to be explored yet. In our work, we report a model for
the diffusion of methanol towards the active site in MDH using Monte Carlo
Modeling. For this purpose, we have considered MDH immobilized on nanowire
bundles prepared by template wetting method. Several properties like structure,
stability and affect of various parameters like temperature, pressure etc on
the immobilized enzyme have been investigated through Molecular Dynamics as
they have a direct impact on the electron collection efficiency. Once these
properties are obtained, an enzymatic reaction where the substrate molecules (S)
attach to the enzyme surface (E) and diffuse towards the active site (A)
is considered. The substrate molecules follow a random walk (or a Brownian
motion) in their process of diffusion and on reaching the active site they react
to form the product (P). In order to carry out these simulations, a 1024
× 1024 square lattice with periodic boundary conditions is used to represent
the enzyme surface and the excluded volume condition is maintained throughout
the simulation. Various amino acids in the enzyme which encounter the substrate
molecules during their random walk are assumed to be obstacles (O) on
the surface. These simulations give us a better understanding of the catalytic
mechanism in MDH immobilized on 2-D surfaces and thus help us to evaluate the
kinetics and their dependence on various factors like obstacle density,
substrate and active site concentrations, temperature and time.

1. Minteer, S. D.; Liaw, B. Y.;
Cooney, M. J., Enzyme-based biofuel cells. Current Opinion in Biotechnology 2007,
18, (3), 228-234.

2. 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.

3. Idupulapati, N. B.; Mainardi, D.
S., A DMol3 study of
the methanol addition-elimination oxidation mechanism by methanol dehydrogenase
enzyme. Molecular Simulation 2008, 34, (10-15), 1057-1064.

4. Andres, J.; Moliner, V.; Domingo, L.R.; Picher, M.T.;
Krechl, J., A
theoretical study of the molecular mechanism for the oxidation of methanol by
PQQ. Journal of the American Chemical Society, 1995,
117, (34), 8807-8815.