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Protein Science (2004), 13:3092-3103. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Specificity in lipases: A computational study of transesterification of sucrose

Gloria Fuentes1,2,3, Anthonio Ballesteros1 and Chandra S. Verma2,4

1 Departamento de Biocatálisis, Instituto de Catálisis, CSIC, Cantoblanco, 28049 Madrid, Spain
2 Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom

(RECEIVED March 16, 2004; FINAL REVISION August 20, 2004; ACCEPTED August 26, 2004)

Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational variability of the various substates of the substrates by small, local adjustments within the binding pocket. In contrast, the more constrained pocket of the lipase from Thermomyces adapts by adjusting through concerted global motions between subdomains. This leads to the identification of one large pocket in Candida that accommodates both the sucrose and the lauroyl moieties of the transition state, whereas in Thermomyces the binding pocket is smaller, leading to the localization of the two moieties in two distinct pockets; this partly rationalizes the broader specificity of the former relative to the latter. Mutations have been suggested to exploit the differences towards changing the observed selectivities.

Keywords: lipases; transesterification; sucrose; specificity; computational methods

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04724504.

Reprint requests to: C.S. Verma, Bioinformatics Institute, 30 Biopolis Way, #07–01 Matrix, Singapore-138671; e-mail: chandra{at}bii.a-start.edu.sg; fax: +0065-6478-9047.


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