Use of 13Ca chemical-shifts in protein structure determination

Autores
Vila, Jorge Alberto; Ripoll, Daniel R.; Scheraga, Harold A.
Año de publicación
2007
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
A physics-based method aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid, all-α-helical protein; namely, the Bacillus subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank.
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados Unidos
Fil: Ripoll, Daniel R.. Cornell Theory Center; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Materia
PEPTIDES AND PROTEINS
MONOMERS
PROTEIN STRUCTURE
CHEMICAL STRUCTURE
CONFORMATION
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:11336/135117
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/135117
network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling Use of 13Ca chemical-shifts in protein structure determinationVila, Jorge AlbertoRipoll, Daniel R.Scheraga, Harold A.PEPTIDES AND PROTEINSMONOMERSPROTEIN STRUCTURECHEMICAL STRUCTURECONFORMATIONhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1A physics-based method aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid, all-α-helical protein; namely, the Bacillus subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank.Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados UnidosFil: Ripoll, Daniel R.. Cornell Theory Center; Estados UnidosFil: Scheraga, Harold A.. Cornell University; Estados UnidosAmerican Chemical Society2007-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/135117Vila, Jorge Alberto; Ripoll, Daniel R.; Scheraga, Harold A.; Use of 13Ca chemical-shifts in protein structure determination; American Chemical Society; Journal of Physical Chemistry B; 111; 23; 5-2007; 6577-65851520-6106CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1021/jp0683871info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/jp0683871info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:07:43Zoai:ri.conicet.gov.ar:11336/135117instacron: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 10:07:43.66CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Use of 13Ca chemical-shifts in protein structure determination
title Use of 13Ca chemical-shifts in protein structure determination
spellingShingle Use of 13Ca chemical-shifts in protein structure determination
Vila, Jorge Alberto
PEPTIDES AND PROTEINS
MONOMERS
PROTEIN STRUCTURE
CHEMICAL STRUCTURE
CONFORMATION
title_short Use of 13Ca chemical-shifts in protein structure determination
title_full Use of 13Ca chemical-shifts in protein structure determination
title_fullStr Use of 13Ca chemical-shifts in protein structure determination
title_full_unstemmed Use of 13Ca chemical-shifts in protein structure determination
title_sort Use of 13Ca chemical-shifts in protein structure determination
dc.creator.none.fl_str_mv Vila, Jorge Alberto
Ripoll, Daniel R.
Scheraga, Harold A.
author Vila, Jorge Alberto
author_facet Vila, Jorge Alberto
Ripoll, Daniel R.
Scheraga, Harold A.
author_role author
author2 Ripoll, Daniel R.
Scheraga, Harold A.
author2_role author
author
dc.subject.none.fl_str_mv PEPTIDES AND PROTEINS
MONOMERS
PROTEIN STRUCTURE
CHEMICAL STRUCTURE
CONFORMATION
topic PEPTIDES AND PROTEINS
MONOMERS
PROTEIN STRUCTURE
CHEMICAL STRUCTURE
CONFORMATION
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 physics-based method aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid, all-α-helical protein; namely, the Bacillus subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank.
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados Unidos
Fil: Ripoll, Daniel R.. Cornell Theory Center; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
description A physics-based method aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid, all-α-helical protein; namely, the Bacillus subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank.
publishDate 2007
dc.date.none.fl_str_mv 2007-05
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/11336/135117
Vila, Jorge Alberto; Ripoll, Daniel R.; Scheraga, Harold A.; Use of 13Ca chemical-shifts in protein structure determination; American Chemical Society; Journal of Physical Chemistry B; 111; 23; 5-2007; 6577-6585
1520-6106
CONICET Digital
CONICET
url http://hdl.handle.net/11336/135117
identifier_str_mv Vila, Jorge Alberto; Ripoll, Daniel R.; Scheraga, Harold A.; Use of 13Ca chemical-shifts in protein structure determination; American Chemical Society; Journal of Physical Chemistry B; 111; 23; 5-2007; 6577-6585
1520-6106
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1021/jp0683871
info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/jp0683871
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 American Chemical Society
publisher.none.fl_str_mv American Chemical Society
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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