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Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases

✍ Scribed by Nikolaj Otte; Marco Bocola; Walter Thiel

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
626 KB
Volume
30
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

CHARMM force‐field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6‐31G*) interaction energies of complexes between water and the model compound 1,1‐dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6‐311+G*//B3LYP/6‐31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6‐31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

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