Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure

Autores
Yeh, So Wei; Liu, Jen Wei; Yu, Sung Huan; Yih, Chien Hua; Hwang, Jenn Kang; Echave, Julián
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.
Fil: Yeh, So Wei. National Chiao Tung University; China
Fil: Liu, Jen Wei. National Chiao Tung University; China
Fil: Yu, Sung Huan. National Chiao Tung University; China
Fil: Yih, Chien Hua. National Chiao Tung University; China
Fil: Hwang, Jenn Kang. National Chiao Tung University; China
Fil: Echave, Julián. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
Protein Evolution
Local Packing Density
Relative Solvent Accessibility
Evolutionary Rate
Weighted Contact Number
Contact Number
Protein Structure
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:11336/32948
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/32948
network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent ExposureYeh, So WeiLiu, Jen WeiYu, Sung HuanYih, Chien HuaHwang, Jenn KangEchave, JuliánProtein EvolutionLocal Packing DensityRelative Solvent AccessibilityEvolutionary RateWeighted Contact NumberContact NumberProtein Structurehttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.Fil: Yeh, So Wei. National Chiao Tung University; ChinaFil: Liu, Jen Wei. National Chiao Tung University; ChinaFil: Yu, Sung Huan. National Chiao Tung University; ChinaFil: Yih, Chien Hua. National Chiao Tung University; ChinaFil: Hwang, Jenn Kang. National Chiao Tung University; ChinaFil: Echave, Julián. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaOxford University Press2013-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/32948Yeh, So Wei; Liu, Jen Wei; Yu, Sung Huan; Yih, Chien Hua; Hwang, Jenn Kang; et al.; Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure; Oxford University Press; Molecular Biology and Evolution; 31; 1; 10-2013; 135-1390737-40381537-1719CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/mbe/article/31/1/135/1048166info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/mst178info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:16:54Zoai:ri.conicet.gov.ar:11336/32948instacron: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:34982025-10-15 15:16:55.167CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
title Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
spellingShingle Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
Yeh, So Wei
Protein Evolution
Local Packing Density
Relative Solvent Accessibility
Evolutionary Rate
Weighted Contact Number
Contact Number
Protein Structure
title_short Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
title_full Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
title_fullStr Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
title_full_unstemmed Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
title_sort Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
dc.creator.none.fl_str_mv Yeh, So Wei
Liu, Jen Wei
Yu, Sung Huan
Yih, Chien Hua
Hwang, Jenn Kang
Echave, Julián
author Yeh, So Wei
author_facet Yeh, So Wei
Liu, Jen Wei
Yu, Sung Huan
Yih, Chien Hua
Hwang, Jenn Kang
Echave, Julián
author_role author
author2 Liu, Jen Wei
Yu, Sung Huan
Yih, Chien Hua
Hwang, Jenn Kang
Echave, Julián
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Protein Evolution
Local Packing Density
Relative Solvent Accessibility
Evolutionary Rate
Weighted Contact Number
Contact Number
Protein Structure
topic Protein Evolution
Local Packing Density
Relative Solvent Accessibility
Evolutionary Rate
Weighted Contact Number
Contact Number
Protein Structure
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.
Fil: Yeh, So Wei. National Chiao Tung University; China
Fil: Liu, Jen Wei. National Chiao Tung University; China
Fil: Yu, Sung Huan. National Chiao Tung University; China
Fil: Yih, Chien Hua. National Chiao Tung University; China
Fil: Hwang, Jenn Kang. National Chiao Tung University; China
Fil: Echave, Julián. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.
publishDate 2013
dc.date.none.fl_str_mv 2013-10
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/11336/32948
Yeh, So Wei; Liu, Jen Wei; Yu, Sung Huan; Yih, Chien Hua; Hwang, Jenn Kang; et al.; Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure; Oxford University Press; Molecular Biology and Evolution; 31; 1; 10-2013; 135-139
0737-4038
1537-1719
CONICET Digital
CONICET
url http://hdl.handle.net/11336/32948
identifier_str_mv Yeh, So Wei; Liu, Jen Wei; Yu, Sung Huan; Yih, Chien Hua; Hwang, Jenn Kang; et al.; Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure; Oxford University Press; Molecular Biology and Evolution; 31; 1; 10-2013; 135-139
0737-4038
1537-1719
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/31/1/135/1048166
info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/mst178
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
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 13.22299

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