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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/135138
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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 |
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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 |
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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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13.070432 |