Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesing New Diels-Alderases

The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibil...

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Bibliographic Details
Published in:The Journal of Physical Chemistry B
Main Authors: Świderek, Katarzyna, Moliner, Vicent
Format: Article in Journal/Newspaper
Language:English
Published: American Chemical Society 2017
Subjects:
Diels-Alder
Candida Antarctica lipase B
CALB
enzyme promiscuity
M06-2X
QM/MM
Jaume
Antarc*
Antarctica
Online Access:http://hdl.handle.net/10234/167261
https://doi.org/10.1021/acs.jpcb.5b10527
Description
Summary:The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B (CALB) as a protein scaffold to re-design a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusion. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of reactant complex that, in turn, would reduce the energy barrier. This work was supported by the Spanish Ministerio de Economía y Competitividad (project CTQ2012-36253-C03), Universitat Jaume I (project P1•1B2014-26), Generalitat Valenciana (project PROMETEOII/2014/022), the Polish Ministry of Science and Higher Education ("Iuventus Plus" program project 0478/IP3/2015/73, 2015-2016) and the USA National Institute of Health (project NIH R01 GM065368). Authors acknowledge computational resources from the Servei d’Informàtica of Universitat Jaume I.

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