Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases
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...
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ftpubmed:oai:pubmedcentral.nih.gov:9067594 2023-05-15T13:44:11+02:00 Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases Galmés, Miquel À. Nödling, Alexander R. He, Kaining Luk, Louis Y. P. Świderek, Katarzyna Moliner, Vicent 2022-03-15 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9067594/ https://doi.org/10.1039/d2sc00778a en eng The Royal Society of Chemistry http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9067594/ http://dx.doi.org/10.1039/d2sc00778a This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/ CC-BY-NC Chem Sci Chemistry Text 2022 ftpubmed https://doi.org/10.1039/d2sc00778a 2022-06-05T00:42:18Z 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 pK(a) 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. Text Antarc* Antarctica PubMed Central (PMC) Chemical Science 13 17 4779 4787 |
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Chemistry |
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Chemistry Galmés, Miquel À. Nödling, Alexander R. He, Kaining Luk, Louis Y. P. Świderek, Katarzyna Moliner, Vicent Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
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Chemistry |
description |
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 pK(a) 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. |
format |
Text |
author |
Galmés, Miquel À. Nödling, Alexander R. He, Kaining Luk, Louis Y. P. Świderek, Katarzyna Moliner, Vicent |
author_facet |
Galmés, Miquel À. Nödling, Alexander R. He, Kaining Luk, Louis Y. P. Świderek, Katarzyna Moliner, Vicent |
author_sort |
Galmés, Miquel À. |
title |
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
title_short |
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
title_full |
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
title_fullStr |
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
title_full_unstemmed |
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
title_sort |
computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases |
publisher |
The Royal Society of Chemistry |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9067594/ https://doi.org/10.1039/d2sc00778a |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Chem Sci |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9067594/ http://dx.doi.org/10.1039/d2sc00778a |
op_rights |
This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/ |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1039/d2sc00778a |
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Chemical Science |
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13 |
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17 |
container_start_page |
4779 |
op_container_end_page |
4787 |
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1766198493636984832 |