Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases
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Title
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolasesAuthor (s)
Date
2022-03-15Publisher
The Royal Society of ChemistryBibliographic citation
GALMÉS, Miquel À., et al. Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. Chemical Science, 2022, vol. 13, no 17, p. 4779-4787.Type
info:eu-repo/semantics/articleVersion
info:eu-repo/semantics/publishedVersionSubject
Abstract
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular ... [+]
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics strategy based on combining the best electrostatic properties of enzymes with activity in a common reaction is presented. The computational protocol has been applied to the re-design of the protein scaffold of an existing promiscuous esterase from Bacillus subtilis Bs2 to enhance its secondary amidase activity. After the alignment of Bs2 with a non-homologous amidase Candida antarctica lipase B (CALB) within rotation quaternions, a relevant spatial aspartate residue of the latter was transferred to the former as a means to favor the electrostatics of transition state formation, where a clear separation of charges takes place. Deep computational insights, however, revealed a significant conformational change caused by the amino acid replacement, provoking a shift in the pKa of the inserted aspartate and counteracting the anticipated catalytic effect. This prediction was experimentally confirmed with a 1.3-fold increase in activity. The good agreement between theoretical and experimental results, as well as the linear correlation between the electrostatic properties and the activation energy barriers, suggest that the presented computational-based investigation can transform in an enzyme engineering approach. [-]
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Chem. Sci., 2022,13Funder Name
Ministerio de Ciencia, Innovación y Universidades (Spain) | Generalitat Valenciana | Universitat Jaume I | Cardiff University | BBSRC | Leverhulme Trust | Royal Society of Chemistry
Project code
PGC2018-094852-B-C21 | PID2019-107098RJ-I00 | AICO/2019/195 | SEJI/2020/007 | UJI-A2019-04 | UJI-B2020-03 | BB/T015799/1 | RPG-2017-195 | RG170187 | RYC2020-030596-I | PREDOC/2017/23
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© 2022 The Author(s). Published by the Royal Society of Chemistry
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