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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/213372

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spelling 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
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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/
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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
reponame_str CONICET Digital (CONICET)
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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