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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/32948
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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 Técnicas2025-09-29T10:19:44Zoai: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:34982025-09-29 10:19:45.235CONICET 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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1844614171995406336 |
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13.070432 |