Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation

Autores
Vila, Jorge Alberto; Aramini. James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.
Año de publicación
2008
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.
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: Aramini. James M.. State University of New Jersey; Estados Unidos
Fil: Rossi, Paolo. State University of New Jersey; Estados Unidos
Fil: Kuzin, Alexandre. Columbia University; Estados Unidos
Fil: Su, Min. Columbia University; Estados Unidos
Fil: Seetharaman, Jayaraman. Columbia University; Estados Unidos
Fil: Xiao, Rong. State University of New Jersey; Estados Unidos
Fil: Tong, Liang. Columbia University; Estados Unidos
Fil: Montelione, Gaetano T.. State University of New Jersey; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Materia
PROTEIN DETERMINATION
PROTEIN VALIDATION
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:11336/135138

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network_name_str CONICET Digital (CONICET)
spelling Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validationVila, Jorge AlbertoAramini. James M.Rossi, PaoloKuzin, AlexandreSu, MinSeetharaman, JayaramanXiao, RongTong, LiangMontelione, Gaetano T.Scheraga, Harold A.PROTEIN DETERMINATIONPROTEIN VALIDATIONhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.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: Aramini. James M.. State University of New Jersey; Estados UnidosFil: Rossi, Paolo. State University of New Jersey; Estados UnidosFil: Kuzin, Alexandre. Columbia University; Estados UnidosFil: Su, Min. Columbia University; Estados UnidosFil: Seetharaman, Jayaraman. Columbia University; Estados UnidosFil: Xiao, Rong. State University of New Jersey; Estados UnidosFil: Tong, Liang. Columbia University; Estados UnidosFil: Montelione, Gaetano T.. State University of New Jersey; Estados UnidosFil: Scheraga, Harold A.. Cornell University; Estados UnidosNational Academy of Sciences2008-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/135138Vila, Jorge Alberto; Aramini. James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; et al.; Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 105; 38; 7-2008; 14389-143940027-8424CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.0807105105info:eu-repo/semantics/altIdentifier/url/https://www.pnas.org/content/105/38/14389info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:20:27Zoai:ri.conicet.gov.ar:11336/135138instacron: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 10:20:27.637CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
title Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
spellingShingle Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
Vila, Jorge Alberto
PROTEIN DETERMINATION
PROTEIN VALIDATION
title_short Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
title_full Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
title_fullStr Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
title_full_unstemmed Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
title_sort Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation
dc.creator.none.fl_str_mv Vila, Jorge Alberto
Aramini. James M.
Rossi, Paolo
Kuzin, Alexandre
Su, Min
Seetharaman, Jayaraman
Xiao, Rong
Tong, Liang
Montelione, Gaetano T.
Scheraga, Harold A.
author Vila, Jorge Alberto
author_facet Vila, Jorge Alberto
Aramini. James M.
Rossi, Paolo
Kuzin, Alexandre
Su, Min
Seetharaman, Jayaraman
Xiao, Rong
Tong, Liang
Montelione, Gaetano T.
Scheraga, Harold A.
author_role author
author2 Aramini. James M.
Rossi, Paolo
Kuzin, Alexandre
Su, Min
Seetharaman, Jayaraman
Xiao, Rong
Tong, Liang
Montelione, Gaetano T.
Scheraga, Harold A.
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv PROTEIN DETERMINATION
PROTEIN VALIDATION
topic PROTEIN DETERMINATION
PROTEIN VALIDATION
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 recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.
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: Aramini. James M.. State University of New Jersey; Estados Unidos
Fil: Rossi, Paolo. State University of New Jersey; Estados Unidos
Fil: Kuzin, Alexandre. Columbia University; Estados Unidos
Fil: Su, Min. Columbia University; Estados Unidos
Fil: Seetharaman, Jayaraman. Columbia University; Estados Unidos
Fil: Xiao, Rong. State University of New Jersey; Estados Unidos
Fil: Tong, Liang. Columbia University; Estados Unidos
Fil: Montelione, Gaetano T.. State University of New Jersey; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
description A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.
publishDate 2008
dc.date.none.fl_str_mv 2008-07
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/11336/135138
Vila, Jorge Alberto; Aramini. James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; et al.; Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 105; 38; 7-2008; 14389-14394
0027-8424
CONICET Digital
CONICET
url http://hdl.handle.net/11336/135138
identifier_str_mv Vila, Jorge Alberto; Aramini. James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; et al.; Quantum chemical 13Ca chemical shift calculations for protein NMR structure determination, refinement, and validation; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 105; 38; 7-2008; 14389-14394
0027-8424
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.0807105105
info:eu-repo/semantics/altIdentifier/url/https://www.pnas.org/content/105/38/14389
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 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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