Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families

Autores
Parra, Rodrigo Gonzalo; Freiberger, Maria Ines; Poley Gil, Miriam; Fernandez Martin, Miguel; Radusky, Leandro Gabriel; Ruiz Serra, Victoria; Wolynes, Peter G.; Ferreiro, Diego; Valencia, Alfonso
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.
Fil: Parra, Rodrigo Gonzalo. Barcelona Supercomputing Center; España
Fil: Freiberger, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Laboratorio de Fisiología de Proteínas; Argentina
Fil: Poley Gil, Miriam. Barcelona Supercomputing Center; España
Fil: Fernandez Martin, Miguel. Barcelona Supercomputing Center; España
Fil: Radusky, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ruiz Serra, Victoria. Barcelona Supercomputing Center; España
Fil: Wolynes, Peter G.. Rice University; Estados Unidos
Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Laboratorio de Fisiología de Proteínas; Argentina
Fil: Valencia, Alfonso. Barcelona Supercomputing Center; España. Institució Catalana de Recerca i Estudis Avancats; España
Materia
Protein evolution
Local frustration
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/265246
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein familiesParra, Rodrigo GonzaloFreiberger, Maria InesPoley Gil, MiriamFernandez Martin, MiguelRadusky, Leandro GabrielRuiz Serra, VictoriaWolynes, Peter G.Ferreiro, DiegoValencia, AlfonsoProtein evolutionLocal frustrationhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.Fil: Parra, Rodrigo Gonzalo. Barcelona Supercomputing Center; EspañaFil: Freiberger, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Laboratorio de Fisiología de Proteínas; ArgentinaFil: Poley Gil, Miriam. Barcelona Supercomputing Center; EspañaFil: Fernandez Martin, Miguel. Barcelona Supercomputing Center; EspañaFil: Radusky, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ruiz Serra, Victoria. Barcelona Supercomputing Center; EspañaFil: Wolynes, Peter G.. Rice University; Estados UnidosFil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Laboratorio de Fisiología de Proteínas; ArgentinaFil: Valencia, Alfonso. Barcelona Supercomputing Center; España. Institució Catalana de Recerca i Estudis Avancats; EspañaOxford University Press2024-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/265246Parra, Rodrigo Gonzalo; Freiberger, Maria Ines; Poley Gil, Miriam; Fernandez Martin, Miguel; Radusky, Leandro Gabriel; et al.; Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families; Oxford University Press; Nucleic Acids Research; 52; W1; 7-2024; W233-W2370305-10481362-4962CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae244/7642057info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkae244info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:20:37Zoai:ri.conicet.gov.ar:11336/265246instacron: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 10:20:37.333CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
title Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
spellingShingle Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
Parra, Rodrigo Gonzalo
Protein evolution
Local frustration
title_short Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
title_full Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
title_fullStr Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
title_full_unstemmed Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
title_sort Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
dc.creator.none.fl_str_mv Parra, Rodrigo Gonzalo
Freiberger, Maria Ines
Poley Gil, Miriam
Fernandez Martin, Miguel
Radusky, Leandro Gabriel
Ruiz Serra, Victoria
Wolynes, Peter G.
Ferreiro, Diego
Valencia, Alfonso
author Parra, Rodrigo Gonzalo
author_facet Parra, Rodrigo Gonzalo
Freiberger, Maria Ines
Poley Gil, Miriam
Fernandez Martin, Miguel
Radusky, Leandro Gabriel
Ruiz Serra, Victoria
Wolynes, Peter G.
Ferreiro, Diego
Valencia, Alfonso
author_role author
author2 Freiberger, Maria Ines
Poley Gil, Miriam
Fernandez Martin, Miguel
Radusky, Leandro Gabriel
Ruiz Serra, Victoria
Wolynes, Peter G.
Ferreiro, Diego
Valencia, Alfonso
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Protein evolution
Local frustration
topic Protein evolution
Local frustration
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.
Fil: Parra, Rodrigo Gonzalo. Barcelona Supercomputing Center; España
Fil: Freiberger, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Laboratorio de Fisiología de Proteínas; Argentina
Fil: Poley Gil, Miriam. Barcelona Supercomputing Center; España
Fil: Fernandez Martin, Miguel. Barcelona Supercomputing Center; España
Fil: Radusky, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ruiz Serra, Victoria. Barcelona Supercomputing Center; España
Fil: Wolynes, Peter G.. Rice University; Estados Unidos
Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica. Laboratorio de Fisiología de Proteínas; Argentina
Fil: Valencia, Alfonso. Barcelona Supercomputing Center; España. Institució Catalana de Recerca i Estudis Avancats; España
description According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.
publishDate 2024
dc.date.none.fl_str_mv 2024-07
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/11336/265246
Parra, Rodrigo Gonzalo; Freiberger, Maria Ines; Poley Gil, Miriam; Fernandez Martin, Miguel; Radusky, Leandro Gabriel; et al.; Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families; Oxford University Press; Nucleic Acids Research; 52; W1; 7-2024; W233-W237
0305-1048
1362-4962
CONICET Digital
CONICET
url http://hdl.handle.net/11336/265246
identifier_str_mv Parra, Rodrigo Gonzalo; Freiberger, Maria Ines; Poley Gil, Miriam; Fernandez Martin, Miguel; Radusky, Leandro Gabriel; et al.; Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families; Oxford University Press; Nucleic Acids Research; 52; W1; 7-2024; W233-W237
0305-1048
1362-4962
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/nar/advance-article/doi/10.1093/nar/gkae244/7642057
info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkae244
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc/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
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv 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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score 13.070432

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