Physics-based method to validate and repair flaws in protein structures

Autores
Martín, Osvaldo Antonio; Arnautova, Yelena A.; Icazatti Zuñiga, Alejandro Ariel; Scheraga, Harold A.; Vila, Jorge Alberto
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.
Fil: Martín, Osvaldo Antonio. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Arnautova, Yelena A.. Molsoft LLC.; Estados Unidos
Fil: Icazatti Zuñiga, Alejandro Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Fil: Vila, Jorge Alberto. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Materia
Chemical Shifts
Proteins
Validation
Repair
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:11336/5809
Acceder
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spelling Physics-based method to validate and repair flaws in protein structuresMartín, Osvaldo AntonioArnautova, Yelena A.Icazatti Zuñiga, Alejandro ArielScheraga, Harold A.Vila, Jorge AlbertoChemical ShiftsProteinsValidationRepairhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.Fil: Martín, Osvaldo Antonio. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaFil: Arnautova, Yelena A.. Molsoft LLC.; Estados UnidosFil: Icazatti Zuñiga, Alejandro Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaFil: Scheraga, Harold A.. Cornell University; Estados UnidosFil: Vila, Jorge Alberto. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaNational Academy of Sciences2013-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/5809Martín, Osvaldo Antonio; Arnautova, Yelena A.; Icazatti Zuñiga, Alejandro Ariel; Scheraga, Harold A.; Vila, Jorge Alberto; Physics-based method to validate and repair flaws in protein structures; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 110; 42; 10-2013; 16826-168310027-8424enginfo:eu-repo/semantics/altIdentifier/url/http://www.pnas.org/content/110/42/16826.abstractinfo:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.1315525110info:eu-repo/semantics/altIdentifier/doi/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:32:02Zoai:ri.conicet.gov.ar:11336/5809instacron: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:34982025-10-22 11:32:03.199CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Physics-based method to validate and repair flaws in protein structures
title Physics-based method to validate and repair flaws in protein structures
spellingShingle Physics-based method to validate and repair flaws in protein structures
Martín, Osvaldo Antonio
Chemical Shifts
Proteins
Validation
Repair
title_short Physics-based method to validate and repair flaws in protein structures
title_full Physics-based method to validate and repair flaws in protein structures
title_fullStr Physics-based method to validate and repair flaws in protein structures
title_full_unstemmed Physics-based method to validate and repair flaws in protein structures
title_sort Physics-based method to validate and repair flaws in protein structures
dc.creator.none.fl_str_mv Martín, Osvaldo Antonio
Arnautova, Yelena A.
Icazatti Zuñiga, Alejandro Ariel
Scheraga, Harold A.
Vila, Jorge Alberto
author Martín, Osvaldo Antonio
author_facet Martín, Osvaldo Antonio
Arnautova, Yelena A.
Icazatti Zuñiga, Alejandro Ariel
Scheraga, Harold A.
Vila, Jorge Alberto
author_role author
author2 Arnautova, Yelena A.
Icazatti Zuñiga, Alejandro Ariel
Scheraga, Harold A.
Vila, Jorge Alberto
author2_role author
author
author
author
dc.subject.none.fl_str_mv Chemical Shifts
Proteins
Validation
Repair
topic Chemical Shifts
Proteins
Validation
Repair
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.
Fil: Martín, Osvaldo Antonio. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Arnautova, Yelena A.. Molsoft LLC.; Estados Unidos
Fil: Icazatti Zuñiga, Alejandro Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Fil: Vila, Jorge Alberto. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
description A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.
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/11336/5809
Martín, Osvaldo Antonio; Arnautova, Yelena A.; Icazatti Zuñiga, Alejandro Ariel; Scheraga, Harold A.; Vila, Jorge Alberto; Physics-based method to validate and repair flaws in protein structures; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 110; 42; 10-2013; 16826-16831
0027-8424
url http://hdl.handle.net/11336/5809
identifier_str_mv Martín, Osvaldo Antonio; Arnautova, Yelena A.; Icazatti Zuñiga, Alejandro Ariel; Scheraga, Harold A.; Vila, Jorge Alberto; Physics-based method to validate and repair flaws in protein structures; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 110; 42; 10-2013; 16826-16831
0027-8424
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.pnas.org/content/110/42/16826.abstract
info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.1315525110
info:eu-repo/semantics/altIdentifier/doi/
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
application/pdf
application/pdf
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
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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