Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 82, Issue 7, Pages 1387-1399Publisher
WILEY
DOI: 10.1002/prot.24506
Keywords
EVB; free energy calculations; serine hydrolase; mutation; stereoselective enzyme; enzyme design; transesterification
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Funding
- National Institutes of Health (NIH) [GM024492]
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The prospect for computer-aided refinement of stereoselective enzymes is further validated by simulating the ester hydrolysis by the wild-type and mutants of CalB, focusing on the challenge of dealing with strong steric effects and entropic contributions. This was done using the empirical valence bond (EVB) method in a quantitative screening of the enantioselectivity, considering both k(cat) and k(cat)/K-M of the R and S stereoisomers. Although the simulations require very extensive sampling for convergence they give encouraging results and major validation, indicating that our approach offers a powerful tool for computer-aided design of enantioselective enzymes. This is particularly true in cases with large changes in steric effects where alternative approaches may have difficulties in capturing the interplay between steric clashes with the reacting substrate and protein flexibility. Proteins 2014; 82:1387-1399. (c) 2014 Wiley Periodicals, Inc.
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