Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential

Citations Over TimeTop 17% of 2010 papers

Abstract

Long-range electrostatic interactions are important in simulations of enzymatic reactions. They can be divided into the effects due to bulk solvent and those due to the electrostatic potential of the outer macromolecule. We study and quantify the importance of these two effects for two test systems by application of the solvated macromolecule boundary potential (SMBP) [J. Chem. Theory Comput. 2009, 5, 3114-3128]. We validate the accuracy of the SMBP for these test systems and present a transferable protocol for determination of optimal SMBP parameters as well as recommended default values for these parameters. Two enzymatic reactions with different characteristics are studied: the intramolecular Claisen rearrangement in chorismate mutase that is associated with little charge transfer and the hydroxylation reaction in p-hydroxybenzoate hydroxylase that corresponds to a formal "OH(+)" transfer and thus involves significant charge transfer. It is found that the effects of the electrostatic potential of the outer macromolecule and of bulk solvent are only important in the latter case, where their neglect causes deviations in the computed barriers on the order of 1-2 kcal/mol, respectively. Even larger deviations on the order of several kilocalories per mole are observed for the reaction energies in p-hydroxybenzoate hydroxylase if the electrostatic potential of the outer macromolecule is neglected.

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