title: Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B.
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.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California, 90089.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schopf
authors.forename: Arieh
authors.initials: A
authors.lastname: Warshel
mesh_terms: D000438:Alcohols / Q000737:chemistry / Q000378:metabolism; D002384:Catalysis; D003198:Computer Simulation; D004951:Esterification; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism*; D008049:Lipase / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D011485:Protein Binding; D015203:Reproducibility of Results; D013237:Stereoisomerism; D013816:Thermodynamics
chemical_list: D000438:Alcohols; D005656:Fungal Proteins; D008049:Lipase; C431349:lipase B, Candida antarctica
keywords: EVB; enzyme design; free energy calculations; mutation; serine hydrolase; stereoselective enzyme; transesterification