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

• Published in: Proteins: Structure, Function, and Bioinformatics
• Main Authors: Schopf, Patrick, Warshel, Arieh
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2014
• Subjects: Antarc*; Antarctica
• Online Access: http://dx.doi.org/10.1002/prot.24506; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.24506; https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.24506

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 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. © 2014 Wiley Periodicals, Inc.