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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/5809
Ver los metadatos del registro completo
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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 Técnicas2025-09-29T10:02:35Zoai: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:34982025-09-29 10:02:35.704CONICET 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 |
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CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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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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1844613831761854464 |
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13.070432 |