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Advances in Physical Chemistry
Volume 2012 (2012), Article ID 867409, 15 pages
http://dx.doi.org/10.1155/2012/867409
Review Article

Applications of Potential Energy Surfaces in the Study of Enzymatic Reactions

Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada N9B 3P4

Received 26 June 2011; Revised 23 August 2011; Accepted 29 August 2011

Academic Editor: Laimutis Bytautas

Copyright © 2012 Eric A. C. Bushnell et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

From a generated PES, one can determine the relative energies of species involved, the sequence in which they occur, and the activation barrier(s) associated with individual steps or the overall mechanism. Furthermore, they can provide more insights than a simple indication of a path of sequential mechanistic structures and their energetic relationships. The investigation into the activation of O2 by alpha-ketoglutarate-dependent dioxygenase (AlkB) clearly shows the opportunity for spin inversion, where one can see that the lowest energy product may be formed via several possible routes. In the investigation of uroporphyrinogen decarboxylase III (UROD), the use of QM/MM methods allowed for the inclusion of the anisotropic protein environment providing greater insight into the rate-limiting barrier. Lastly, the mechanism of 6-phospho-α-glucosidase (GlvA) was discussed using different active site models. In particular, a continuum model PES was compared to the gas-phase PES.