Reassessing the exon–foldon correspondence using frustration analysis
- Autores
- Galpern, Ezequiel Alejandro; Jaafari, Hana; Bueno, Carlos; Wolynes, Peter G.; Ferreiro, Diego
- Año de publicación
- 2024
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon–intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon–foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them.
Fil: Galpern, Ezequiel Alejandro. 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; Argentina
Fil: Jaafari, Hana. Rice University; Estados Unidos
Fil: Bueno, Carlos. Rice University; Estados Unidos
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; Argentina - Materia
-
Protein evolution
Protein folding
Foldon - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/266911
Ver los metadatos del registro completo
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Reassessing the exon–foldon correspondence using frustration analysisGalpern, Ezequiel AlejandroJaafari, HanaBueno, CarlosWolynes, Peter G.Ferreiro, DiegoProtein evolutionProtein foldingFoldonhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon–intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon–foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them.Fil: Galpern, Ezequiel Alejandro. 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; ArgentinaFil: Jaafari, Hana. Rice University; Estados UnidosFil: Bueno, Carlos. Rice University; Estados UnidosFil: 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; ArgentinaNational Academy of Sciences2024-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/266911Galpern, Ezequiel Alejandro; Jaafari, Hana; Bueno, Carlos; Wolynes, Peter G.; Ferreiro, Diego; Reassessing the exon–foldon correspondence using frustration analysis; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 121; 28; 7-2024; 1-80027-8424CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pnas.org/doi/10.1073/pnas.2400151121info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.2400151121info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:15:19Zoai:ri.conicet.gov.ar:11336/266911instacron: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 10:15:19.501CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Reassessing the exon–foldon correspondence using frustration analysis |
title |
Reassessing the exon–foldon correspondence using frustration analysis |
spellingShingle |
Reassessing the exon–foldon correspondence using frustration analysis Galpern, Ezequiel Alejandro Protein evolution Protein folding Foldon |
title_short |
Reassessing the exon–foldon correspondence using frustration analysis |
title_full |
Reassessing the exon–foldon correspondence using frustration analysis |
title_fullStr |
Reassessing the exon–foldon correspondence using frustration analysis |
title_full_unstemmed |
Reassessing the exon–foldon correspondence using frustration analysis |
title_sort |
Reassessing the exon–foldon correspondence using frustration analysis |
dc.creator.none.fl_str_mv |
Galpern, Ezequiel Alejandro Jaafari, Hana Bueno, Carlos Wolynes, Peter G. Ferreiro, Diego |
author |
Galpern, Ezequiel Alejandro |
author_facet |
Galpern, Ezequiel Alejandro Jaafari, Hana Bueno, Carlos Wolynes, Peter G. Ferreiro, Diego |
author_role |
author |
author2 |
Jaafari, Hana Bueno, Carlos Wolynes, Peter G. Ferreiro, Diego |
author2_role |
author author author author |
dc.subject.none.fl_str_mv |
Protein evolution Protein folding Foldon |
topic |
Protein evolution Protein folding Foldon |
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 folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon–intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon–foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them. Fil: Galpern, Ezequiel Alejandro. 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; Argentina Fil: Jaafari, Hana. Rice University; Estados Unidos Fil: Bueno, Carlos. Rice University; Estados Unidos 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; Argentina |
description |
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon–intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon–foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them. |
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/11336/266911 Galpern, Ezequiel Alejandro; Jaafari, Hana; Bueno, Carlos; Wolynes, Peter G.; Ferreiro, Diego; Reassessing the exon–foldon correspondence using frustration analysis; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 121; 28; 7-2024; 1-8 0027-8424 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/266911 |
identifier_str_mv |
Galpern, Ezequiel Alejandro; Jaafari, Hana; Bueno, Carlos; Wolynes, Peter G.; Ferreiro, Diego; Reassessing the exon–foldon correspondence using frustration analysis; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 121; 28; 7-2024; 1-8 0027-8424 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://pnas.org/doi/10.1073/pnas.2400151121 info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.2400151121 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-nd/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
National Academy of Sciences |
publisher.none.fl_str_mv |
National Academy of Sciences |
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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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 |