Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation
Autor(a) principal: | |
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Data de Publicação: | 2011 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | https://doi.org/10.1016/j.jbiotec.2011.09.007 http://www.locus.ufv.br/handle/123456789/21712 |
Resumo: | A combined docking and molecular dynamics protocol was applied to investigate quercetin binding modes within the catalytic cavity of Candida antarctica lipase B (CALB) and Pseudomonas cepacia lipase (PCL), aiming to explain the difference of specificity of these enzymes in acetylation reaction. For both lipases, docking of quercetin yielded two families of conformers with either the quercetin A or B-ring pointing towards the catalytic residues. Molecular dynamics (MD) calculations were subsequently performed on several complexes of each family. MD trajectories were analyzed focusing on the orientation of the acyl donor bound to the catalytic serine towards the oxyanion hole residues and the proximity of quercetin hydroxyl groups to the catalytic residues. Results showed that with CALB, the acetate was not correctly positioned within the oxyanion hole whatever the orientation of quercetin, suggesting that no product could be obtained. With PCL, the acetate remained within the oxyanion hole during all MD trajectories. Depending on quercetin orientation, either the 7-OH group or the 3, 5, 3′, 4′-OH groups came alternatively near the catalytic residues, suggesting that all of them could be acylated. The capacity of models to explain the regioselectivity of the reaction was discussed. Key residues and interactions involved in quercetin binding modes were identified and related to the reaction feasibility. |
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Eduardo, Basilio De OliveiraChristelle, BidouilLatifa, ChebilElaine-Rose, MaiaBernard, MaigretEvelyne, Ronat-HeidtMohamed, GhoulJean-Marc, EngasserCatherine, Humeau2018-09-09T22:59:18Z2018-09-09T22:59:18Z2011-12-1001681656https://doi.org/10.1016/j.jbiotec.2011.09.007http://www.locus.ufv.br/handle/123456789/21712A combined docking and molecular dynamics protocol was applied to investigate quercetin binding modes within the catalytic cavity of Candida antarctica lipase B (CALB) and Pseudomonas cepacia lipase (PCL), aiming to explain the difference of specificity of these enzymes in acetylation reaction. For both lipases, docking of quercetin yielded two families of conformers with either the quercetin A or B-ring pointing towards the catalytic residues. Molecular dynamics (MD) calculations were subsequently performed on several complexes of each family. MD trajectories were analyzed focusing on the orientation of the acyl donor bound to the catalytic serine towards the oxyanion hole residues and the proximity of quercetin hydroxyl groups to the catalytic residues. Results showed that with CALB, the acetate was not correctly positioned within the oxyanion hole whatever the orientation of quercetin, suggesting that no product could be obtained. With PCL, the acetate remained within the oxyanion hole during all MD trajectories. Depending on quercetin orientation, either the 7-OH group or the 3, 5, 3′, 4′-OH groups came alternatively near the catalytic residues, suggesting that all of them could be acylated. The capacity of models to explain the regioselectivity of the reaction was discussed. Key residues and interactions involved in quercetin binding modes were identified and related to the reaction feasibility.engJournal of Biotechnologyv. 156, n. 3, p. 203- 210, dez. 2011Elsevier B.V.info:eu-repo/semantics/openAccessLipase specificityFlavonoidAcylationDockingMolecular dynamicsCombined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylationinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALartigo.pdfartigo.pdftexto completoapplication/pdf883187https://locus.ufv.br//bitstream/123456789/21712/1/artigo.pdf0cf366618e09d405840abd00cefecd27MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/21712/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILartigo.pdf.jpgartigo.pdf.jpgIM Thumbnailimage/jpeg5229https://locus.ufv.br//bitstream/123456789/21712/3/artigo.pdf.jpg06205f8a52c3fd7b08465442d164c7dcMD53123456789/217122018-09-09 23:00:38.227oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452018-09-10T02:00:38LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.en.fl_str_mv |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
title |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
spellingShingle |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation Eduardo, Basilio De Oliveira Lipase specificity Flavonoid Acylation Docking Molecular dynamics |
title_short |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
title_full |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
title_fullStr |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
title_full_unstemmed |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
title_sort |
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation |
author |
Eduardo, Basilio De Oliveira |
author_facet |
Eduardo, Basilio De Oliveira Christelle, Bidouil Latifa, Chebil Elaine-Rose, Maia Bernard, Maigret Evelyne, Ronat-Heidt Mohamed, Ghoul Jean-Marc, Engasser Catherine, Humeau |
author_role |
author |
author2 |
Christelle, Bidouil Latifa, Chebil Elaine-Rose, Maia Bernard, Maigret Evelyne, Ronat-Heidt Mohamed, Ghoul Jean-Marc, Engasser Catherine, Humeau |
author2_role |
author author author author author author author author |
dc.contributor.author.fl_str_mv |
Eduardo, Basilio De Oliveira Christelle, Bidouil Latifa, Chebil Elaine-Rose, Maia Bernard, Maigret Evelyne, Ronat-Heidt Mohamed, Ghoul Jean-Marc, Engasser Catherine, Humeau |
dc.subject.pt-BR.fl_str_mv |
Lipase specificity Flavonoid Acylation Docking Molecular dynamics |
topic |
Lipase specificity Flavonoid Acylation Docking Molecular dynamics |
description |
A combined docking and molecular dynamics protocol was applied to investigate quercetin binding modes within the catalytic cavity of Candida antarctica lipase B (CALB) and Pseudomonas cepacia lipase (PCL), aiming to explain the difference of specificity of these enzymes in acetylation reaction. For both lipases, docking of quercetin yielded two families of conformers with either the quercetin A or B-ring pointing towards the catalytic residues. Molecular dynamics (MD) calculations were subsequently performed on several complexes of each family. MD trajectories were analyzed focusing on the orientation of the acyl donor bound to the catalytic serine towards the oxyanion hole residues and the proximity of quercetin hydroxyl groups to the catalytic residues. Results showed that with CALB, the acetate was not correctly positioned within the oxyanion hole whatever the orientation of quercetin, suggesting that no product could be obtained. With PCL, the acetate remained within the oxyanion hole during all MD trajectories. Depending on quercetin orientation, either the 7-OH group or the 3, 5, 3′, 4′-OH groups came alternatively near the catalytic residues, suggesting that all of them could be acylated. The capacity of models to explain the regioselectivity of the reaction was discussed. Key residues and interactions involved in quercetin binding modes were identified and related to the reaction feasibility. |
publishDate |
2011 |
dc.date.issued.fl_str_mv |
2011-12-10 |
dc.date.accessioned.fl_str_mv |
2018-09-09T22:59:18Z |
dc.date.available.fl_str_mv |
2018-09-09T22:59:18Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.1016/j.jbiotec.2011.09.007 http://www.locus.ufv.br/handle/123456789/21712 |
dc.identifier.issn.none.fl_str_mv |
01681656 |
identifier_str_mv |
01681656 |
url |
https://doi.org/10.1016/j.jbiotec.2011.09.007 http://www.locus.ufv.br/handle/123456789/21712 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofseries.pt-BR.fl_str_mv |
v. 156, n. 3, p. 203- 210, dez. 2011 |
dc.rights.driver.fl_str_mv |
Elsevier B.V. info:eu-repo/semantics/openAccess |
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Elsevier B.V. |
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openAccess |
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application/pdf |
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Journal of Biotechnology |
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Journal of Biotechnology |
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