Article

Coupling between Protein and Reaction Dynamics in Enzymatic Processes:  Application of Grote−Hynes Theory to Catechol O-Methyltransferase

Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, 12071 Castellón, Spain, Departament de Química Física, Universidad de Valencia, 46100 Burjasot, Valencia, Spain, CNRS UMR 8640 PASTEUR, Departement de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
J. Am. Chem. Soc., 2006, 128 (18), pp 6186–6193
DOI: 10.1021/ja058826u
Publication Date (Web): April 18, 2006
Copyright © 2006 American Chemical Society

Abstract

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The generalized Langevin equation (GLE)-based Grote−Hynes (GH) theory is used to calculate the transmission coefficients, κ, for the methyl transfer from S-adenosylmethionine to catecholate both in aqueous solution and in the catechol O-methyltransferase active site. Values of κ, which measures the deviation of the rate constants from the Transition State Theory (TST) predictions, are obtained by means of rare event molecular dynamics simulations. The results are 0.62 ± 0.04 and 0.83 ± 0.03 for the aqueous and enzymatic environments, respectively, while the Grote−Hynes predictions are 0.58 ± 0.09 and 0.89 ± 0.03, respectively. The Kramers theory estimates are much smaller, about 0.01 and 0.1, respectively. Thus, the enzymatic transmission coefficient is closer to TST predictions than the value obtained in solution. In addition, our results show that the enzymatic coefficient is also closer to its nonadiabatic (or frozen environment) limit than is the solution coefficient. These findings can be understood considering that, during the passage over the barrier top, there is a smaller coupling between the reactive system and the environment in the enzyme than in solution, as well as a smaller reorganization suffered by the enzyme. Analysis of the transition state friction kernel leads to the identification of some key vibrational modes governing the coupling between the two different environments and the reacting solute in the transition state region and insights on their relevance for the reaction dynamics' influence on the transmission coefficient.

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Received 30 December 2005
Published online 18 April 2006
Published in print 1 May 2006
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