J Phys Chem B. 2015 Jan 22;119(3):873-82. doi: 10.1021/jp505746x. Epub 2014 Sep 10.

Linking electrostatic effects and protein motions in enzymatic catalysis. A theoretical analysis of catechol o-methyltransferase.

The journal of physical chemistry. B

Rafael García-Meseguer, Kirill Zinovjev, Maite Roca, Javier J Ruiz-Pernía, Iñaki Tuñón

PMID: 25159911 DOI: 10.1021/jp505746x

Abstract

The role of protein motions in enzymatic catalysis is the subject of a hot scientific debate. We here propose the use of an explicit solvent coordinate to analyze the impact of environmental motions during the reaction process. The example analyzed here is the reaction catalyzed by catechol O-methyltransferase, a methyl transfer reaction from S-adenosylmethionine (SAM) to the nucleophilic oxygen atom of catecholate. This reaction proceeds from a charged reactant to a neutral product, and then a large electrostatic coupling with the environment could be expected. By means of a two-dimensional free energy surface, we show that a large fraction of the environmental motions needed to attain the transition state happens during the first stages of the reaction because most of the environmental motions are slower than changes in the substrate. The incorporation of the solvent coordinate in the definition of the transition state improves the transmission coefficient and the committor histogram in solution, while the changes are much less significant in the enzyme. The equilibrium solvation approach seems then to work better in the enzyme than in aqueous solution because the enzyme provides a preorganized environment where the reaction takes place.

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• Journal Article