Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach

Autores
Martín, Osvaldo Antonio; Villegas, Myriam E.; Vila, Jorge Alberto; Scheraga, Harold A.
Año de publicación
2010
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the 13Cα13Cα and 13Cβ13Cβ chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed 13Cα13Cα chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed 13Cα13Cα chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced −SH 13Cβ13Cβ , but not for the 13Cα13Cα , chemical shifts, in good agreement with the observation of 375 13Cα13Cα and 337 13Cβ13Cβ resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of 13Cα13Cα and 13Cβ13Cβ chemical shifts of cysteines in cystines.
Fil: Martín, Osvaldo Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Villegas, Myriam E.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina. Cornell University; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Materia
13c Chemical Shift Prediction
Cysteine Residue
Protein Structure Validation
X-Ray And Nmr Structures
Cysteine Redox State
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:11336/15428
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/15428
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approachMartín, Osvaldo AntonioVillegas, Myriam E.Vila, Jorge AlbertoScheraga, Harold A.13c Chemical Shift PredictionCysteine ResidueProtein Structure ValidationX-Ray And Nmr StructuresCysteine Redox Statehttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the 13Cα13Cα and 13Cβ13Cβ chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed 13Cα13Cα chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed 13Cα13Cα chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced −SH 13Cβ13Cβ , but not for the 13Cα13Cα , chemical shifts, in good agreement with the observation of 375 13Cα13Cα and 337 13Cβ13Cβ resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of 13Cα13Cα and 13Cβ13Cβ chemical shifts of cysteines in cystines.Fil: Martín, Osvaldo Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaFil: Villegas, Myriam E.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaFil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina. Cornell University; Estados UnidosFil: Scheraga, Harold A.. Cornell University; Estados UnidosSpringer2010-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/15428Martín, Osvaldo Antonio; Villegas, Myriam E.; Vila, Jorge Alberto; Scheraga, Harold A.; Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach; Springer; Journal Of Biomolecular Nmr; 46; 3; 3-2010; 217-2250925-27381573-5001enginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s10858-010-9396-xinfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs10858-010-9396-xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:43:09Zoai:ri.conicet.gov.ar:11336/15428instacron: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 09:43:09.559CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
title Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
spellingShingle Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
Martín, Osvaldo Antonio
13c Chemical Shift Prediction
Cysteine Residue
Protein Structure Validation
X-Ray And Nmr Structures
Cysteine Redox State
title_short Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
title_full Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
title_fullStr Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
title_full_unstemmed Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
title_sort Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach
dc.creator.none.fl_str_mv Martín, Osvaldo Antonio
Villegas, Myriam E.
Vila, Jorge Alberto
Scheraga, Harold A.
author Martín, Osvaldo Antonio
author_facet Martín, Osvaldo Antonio
Villegas, Myriam E.
Vila, Jorge Alberto
Scheraga, Harold A.
author_role author
author2 Villegas, Myriam E.
Vila, Jorge Alberto
Scheraga, Harold A.
author2_role author
author
author
dc.subject.none.fl_str_mv 13c Chemical Shift Prediction
Cysteine Residue
Protein Structure Validation
X-Ray And Nmr Structures
Cysteine Redox State
topic 13c Chemical Shift Prediction
Cysteine Residue
Protein Structure Validation
X-Ray And Nmr Structures
Cysteine Redox State
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the 13Cα13Cα and 13Cβ13Cβ chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed 13Cα13Cα chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed 13Cα13Cα chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced −SH 13Cβ13Cβ , but not for the 13Cα13Cα , chemical shifts, in good agreement with the observation of 375 13Cα13Cα and 337 13Cβ13Cβ resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of 13Cα13Cα and 13Cβ13Cβ chemical shifts of cysteines in cystines.
Fil: Martín, Osvaldo Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Villegas, Myriam E.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina. Cornell University; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
description Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the 13Cα13Cα and 13Cβ13Cβ chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed 13Cα13Cα chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed 13Cα13Cα chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced −SH 13Cβ13Cβ , but not for the 13Cα13Cα , chemical shifts, in good agreement with the observation of 375 13Cα13Cα and 337 13Cβ13Cβ resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of 13Cα13Cα and 13Cβ13Cβ chemical shifts of cysteines in cystines.
publishDate 2010
dc.date.none.fl_str_mv 2010-03
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/11336/15428
Martín, Osvaldo Antonio; Villegas, Myriam E.; Vila, Jorge Alberto; Scheraga, Harold A.; Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach; Springer; Journal Of Biomolecular Nmr; 46; 3; 3-2010; 217-225
0925-2738
1573-5001
url http://hdl.handle.net/11336/15428
identifier_str_mv Martín, Osvaldo Antonio; Villegas, Myriam E.; Vila, Jorge Alberto; Scheraga, Harold A.; Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach; Springer; Journal Of Biomolecular Nmr; 46; 3; 3-2010; 217-225
0925-2738
1573-5001
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1007/s10858-010-9396-x
info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs10858-010-9396-x
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
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
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 13.069144

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