Why are the low-energy protein normal modes evolutionarily conserved?

Autores
Echave, Julian
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Proteins fluctuate, and such fluctuations are functionally important. As with any functionally relevant trait, it is interesting to study how fluctuations change during evolution. In contrast with sequence and structure, the study of the evolution of protein motions is much more recent. Yet, it has been shown that the overall fluctuation pattern is evolutionarily conserved. Moreover, the lowest-energy normal modes have been found to be the most conserved. The reasons behind such a differential conservation have not been explicitly studied. There are two limiting explanations. A "biological"explanation is that because such modes are functional, there is natural selection pressure against their variation. An alternative "physical" explanation is that the lowest-energy normal modes may be more conserved because they are just more robust with respect to random mutations. To investigate this issue, I studied a set of globin-like proteins using a perturbed elastic network model (ENM) of the effect of random mutations on normal modes. I show that the conservation predicted by the model is in excellent agreement with observations. These results support the physical explanation: the lowest normal modes are more conserved because they are more robust.
Fil: Echave, Julian. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
CHEMICAL PHYSICS
COMPUTER MODELING
MOLECULAR DYNAMICS
NORMAL MODES
PROTEIN DYNAMICS
PROTEIN EVOLUTION
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:11336/195117
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/195117
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network_name_str CONICET Digital (CONICET)
spelling Why are the low-energy protein normal modes evolutionarily conserved?Echave, JulianCHEMICAL PHYSICSCOMPUTER MODELINGMOLECULAR DYNAMICSNORMAL MODESPROTEIN DYNAMICSPROTEIN EVOLUTIONhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1Proteins fluctuate, and such fluctuations are functionally important. As with any functionally relevant trait, it is interesting to study how fluctuations change during evolution. In contrast with sequence and structure, the study of the evolution of protein motions is much more recent. Yet, it has been shown that the overall fluctuation pattern is evolutionarily conserved. Moreover, the lowest-energy normal modes have been found to be the most conserved. The reasons behind such a differential conservation have not been explicitly studied. There are two limiting explanations. A "biological"explanation is that because such modes are functional, there is natural selection pressure against their variation. An alternative "physical" explanation is that the lowest-energy normal modes may be more conserved because they are just more robust with respect to random mutations. To investigate this issue, I studied a set of globin-like proteins using a perturbed elastic network model (ENM) of the effect of random mutations on normal modes. I show that the conservation predicted by the model is in excellent agreement with observations. These results support the physical explanation: the lowest normal modes are more conserved because they are more robust.Fil: Echave, Julian. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaInt Union Pure Applied Chemistry2012-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/195117Echave, Julian; Why are the low-energy protein normal modes evolutionarily conserved?; Int Union Pure Applied Chemistry; Pure and Applied Chemistry; 84; 9; 2-2012; 1931-19370033-4545CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1351/PAC-CON-12-02-15info:eu-repo/semantics/altIdentifier/url/https://www.degruyter.com/document/doi/10.1351/PAC-CON-12-02-15/htmlinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:28:26Zoai:ri.conicet.gov.ar:11336/195117instacron: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 10:28:26.522CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Why are the low-energy protein normal modes evolutionarily conserved?
title Why are the low-energy protein normal modes evolutionarily conserved?
spellingShingle Why are the low-energy protein normal modes evolutionarily conserved?
Echave, Julian
CHEMICAL PHYSICS
COMPUTER MODELING
MOLECULAR DYNAMICS
NORMAL MODES
PROTEIN DYNAMICS
PROTEIN EVOLUTION
title_short Why are the low-energy protein normal modes evolutionarily conserved?
title_full Why are the low-energy protein normal modes evolutionarily conserved?
title_fullStr Why are the low-energy protein normal modes evolutionarily conserved?
title_full_unstemmed Why are the low-energy protein normal modes evolutionarily conserved?
title_sort Why are the low-energy protein normal modes evolutionarily conserved?
dc.creator.none.fl_str_mv Echave, Julian
author Echave, Julian
author_facet Echave, Julian
author_role author
dc.subject.none.fl_str_mv CHEMICAL PHYSICS
COMPUTER MODELING
MOLECULAR DYNAMICS
NORMAL MODES
PROTEIN DYNAMICS
PROTEIN EVOLUTION
topic CHEMICAL PHYSICS
COMPUTER MODELING
MOLECULAR DYNAMICS
NORMAL MODES
PROTEIN DYNAMICS
PROTEIN EVOLUTION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Proteins fluctuate, and such fluctuations are functionally important. As with any functionally relevant trait, it is interesting to study how fluctuations change during evolution. In contrast with sequence and structure, the study of the evolution of protein motions is much more recent. Yet, it has been shown that the overall fluctuation pattern is evolutionarily conserved. Moreover, the lowest-energy normal modes have been found to be the most conserved. The reasons behind such a differential conservation have not been explicitly studied. There are two limiting explanations. A "biological"explanation is that because such modes are functional, there is natural selection pressure against their variation. An alternative "physical" explanation is that the lowest-energy normal modes may be more conserved because they are just more robust with respect to random mutations. To investigate this issue, I studied a set of globin-like proteins using a perturbed elastic network model (ENM) of the effect of random mutations on normal modes. I show that the conservation predicted by the model is in excellent agreement with observations. These results support the physical explanation: the lowest normal modes are more conserved because they are more robust.
Fil: Echave, Julian. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Proteins fluctuate, and such fluctuations are functionally important. As with any functionally relevant trait, it is interesting to study how fluctuations change during evolution. In contrast with sequence and structure, the study of the evolution of protein motions is much more recent. Yet, it has been shown that the overall fluctuation pattern is evolutionarily conserved. Moreover, the lowest-energy normal modes have been found to be the most conserved. The reasons behind such a differential conservation have not been explicitly studied. There are two limiting explanations. A "biological"explanation is that because such modes are functional, there is natural selection pressure against their variation. An alternative "physical" explanation is that the lowest-energy normal modes may be more conserved because they are just more robust with respect to random mutations. To investigate this issue, I studied a set of globin-like proteins using a perturbed elastic network model (ENM) of the effect of random mutations on normal modes. I show that the conservation predicted by the model is in excellent agreement with observations. These results support the physical explanation: the lowest normal modes are more conserved because they are more robust.
publishDate 2012
dc.date.none.fl_str_mv 2012-02
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/11336/195117
Echave, Julian; Why are the low-energy protein normal modes evolutionarily conserved?; Int Union Pure Applied Chemistry; Pure and Applied Chemistry; 84; 9; 2-2012; 1931-1937
0033-4545
CONICET Digital
CONICET
url http://hdl.handle.net/11336/195117
identifier_str_mv Echave, Julian; Why are the low-energy protein normal modes evolutionarily conserved?; Int Union Pure Applied Chemistry; Pure and Applied Chemistry; 84; 9; 2-2012; 1931-1937
0033-4545
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1351/PAC-CON-12-02-15
info:eu-repo/semantics/altIdentifier/url/https://www.degruyter.com/document/doi/10.1351/PAC-CON-12-02-15/html
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 Int Union Pure Applied Chemistry
publisher.none.fl_str_mv Int Union Pure Applied Chemistry
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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