Exploring the Origin of Amidase Substrate Promiscuity in CALB by a Computational Approach
| Autor: | Katarzyna Świderek, Eduardo García-Junceda, Miquel À Galmés, Vicent Moliner |
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| Přispěvatelé: | Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), Universidad Jaime I, National Institutes of Health (US), Agencia Estatal de Investigación (España), García-Junceda, Eduardo [0000-0002-2344-8743], García-Junceda, Eduardo |
| Rok vydání: | 2020 |
| Předmět: |
Computational chemistry
Free energy surfaces Stereochemistry Enzyme promiscuity Lipase b Molecular dynamics 010402 general chemistry 01 natural sciences enzyme catalysis QM/MM Catalysis Amidase Amidase activity biology enzyme promiscuity 010405 organic chemistry Chemistry Substrate (chemistry) Enzyme catalysis General Chemistry biology.organism_classification computational chemistry molecular dynamics 0104 chemical sciences Promiscuity biology.protein Candida antarctica free energy surfaces |
| Zdroj: | Repositori Universitat Jaume I Universitat Jaume I Digital.CSIC. Repositorio Institucional del CSIC instname |
| Popis: | Enzyme promiscuity attracts the interest of the industrial and academic sectors because of its application in the design of biocatalysts. The amidase activity of Candida antarctica lipase B (CALB) on two different substrates has been studied by theoretical quantum mechanics/molecular mechanics methods, supported by experimental kinetic measurements. The aim of the study is to understand the substrate promiscuity of CALB in this secondary reaction and the origin of its promiscuous catalytic activity. The computational results predict activation free energies in very good agreement with the kinetic data and confirm that the activity of CALB as an amidase, despite depending on the features of the amide substrate, is dictated by the electrostatic effects of the protein. The protein polarizes and activates the substrate as well as stabilizes the transition state, thus enhancing the rate constant. Our results can provide guides for future designs of biocatalysts based on electrostatic arguments. This work was supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (Grant PGC2018-094852-B-C21), the Spanish Ministerio de Economía y Competitividad (Grant MAT2015-65184-C2-2-R), Universitat Jaume I (project UJI·B2017- 31), and the National Institutes of Health (Ref no. NIH R01 GM065368). K.Ś. thanks the MINECO for a Juan de la Cierva—Incorporación (ref IJCI-2016-27503) contract. M.À.G. thanks Universitat Jaume I for a doctoral FPI grant (PREDOC/2017/23). |
| Databáze: | OpenAIRE |
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