Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions
- Autores
- Rossi, María Agustina; Palzkill, Timothy; Almeida, Fabio C L; Vila, Alejandro Jose
- Año de publicación
- 2022
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution.
Fil: Rossi, María Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Palzkill, Timothy. Baylor College Of Medicine (baylor College Of Medicine);
Fil: Almeida, Fabio C L. Universidade Federal do Rio de Janeiro; Brasil
Fil: Vila, Alejandro Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina - Materia
-
ALTERNATIVE CONFORMATIONS
EPISTASIS
PROTEIN EVOLUTION
Β-LACTAMASE - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/213372
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Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic InteractionsRossi, María AgustinaPalzkill, TimothyAlmeida, Fabio C LVila, Alejandro JoseALTERNATIVE CONFORMATIONSEPISTASISPROTEIN EVOLUTIONΒ-LACTAMASEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution.Fil: Rossi, María Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Palzkill, Timothy. Baylor College Of Medicine (baylor College Of Medicine);Fil: Almeida, Fabio C L. Universidade Federal do Rio de Janeiro; BrasilFil: Vila, Alejandro Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaOxford University Press2022-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/213372Rossi, María Agustina; Palzkill, Timothy; Almeida, Fabio C L; Vila, Alejandro Jose; Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions; Oxford University Press; Molecular Biology and Evolution; 39; 10; 10-2022; 1-120737-4038CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/mbe/article/doi/10.1093/molbev/msac194/6711538info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/msac194info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:20:33Zoai:ri.conicet.gov.ar:11336/213372instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:20:33.312CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
title |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
spellingShingle |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions Rossi, María Agustina ALTERNATIVE CONFORMATIONS EPISTASIS PROTEIN EVOLUTION Β-LACTAMASE |
title_short |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
title_full |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
title_fullStr |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
title_full_unstemmed |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
title_sort |
Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions |
dc.creator.none.fl_str_mv |
Rossi, María Agustina Palzkill, Timothy Almeida, Fabio C L Vila, Alejandro Jose |
author |
Rossi, María Agustina |
author_facet |
Rossi, María Agustina Palzkill, Timothy Almeida, Fabio C L Vila, Alejandro Jose |
author_role |
author |
author2 |
Palzkill, Timothy Almeida, Fabio C L Vila, Alejandro Jose |
author2_role |
author author author |
dc.subject.none.fl_str_mv |
ALTERNATIVE CONFORMATIONS EPISTASIS PROTEIN EVOLUTION Β-LACTAMASE |
topic |
ALTERNATIVE CONFORMATIONS EPISTASIS PROTEIN EVOLUTION Β-LACTAMASE |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution. Fil: Rossi, María Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina Fil: Palzkill, Timothy. Baylor College Of Medicine (baylor College Of Medicine); Fil: Almeida, Fabio C L. Universidade Federal do Rio de Janeiro; Brasil Fil: Vila, Alejandro Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina |
description |
Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-10 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/213372 Rossi, María Agustina; Palzkill, Timothy; Almeida, Fabio C L; Vila, Alejandro Jose; Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions; Oxford University Press; Molecular Biology and Evolution; 39; 10; 10-2022; 1-12 0737-4038 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/213372 |
identifier_str_mv |
Rossi, María Agustina; Palzkill, Timothy; Almeida, Fabio C L; Vila, Alejandro Jose; Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions; Oxford University Press; Molecular Biology and Evolution; 39; 10; 10-2022; 1-12 0737-4038 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/mbe/article/doi/10.1093/molbev/msac194/6711538 info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/msac194 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Oxford University Press |
publisher.none.fl_str_mv |
Oxford University Press |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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13.070432 |