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Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B

Authors

  • Patrick Schopf,

    1. Department of Chemistry, University of Southern California, Los Angeles, California
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  • Arieh Warshel

    Corresponding author
    1. Department of Chemistry, University of Southern California, Los Angeles, California
    • Correspondence to: Arieh Warshel, Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, United States. E-mail: warshel@usc.edu

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ABSTRACT

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 kcat and kcat/KM 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. © 2014 Wiley Periodicals, Inc.

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