Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution

Autores
Vila, Jorge Alberto; Baldoni, Hector Armando; Scheraga, Harold A.
Año de publicación
2009
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional.
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: Baldoni, Hector Armando. 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
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Materia
COMPUTATIONAL CHEMISTRY
DENSITY FUNCTIONAL THEORY
DFT
CHEMICAL SHIFTS
PROTEIN STRUCTURE DETERMINATION
PROTEIN STRUCTURE 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:11336/237646
Acceder
id CONICETDig_c6c964efbf1062a80773fd16994c3673
oai_identifier_str oai:ri.conicet.gov.ar:11336/237646
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solutionVila, Jorge AlbertoBaldoni, Hector ArmandoScheraga, Harold A.COMPUTATIONAL CHEMISTRYDENSITY FUNCTIONAL THEORYDFTCHEMICAL SHIFTSPROTEIN STRUCTURE DETERMINATIONPROTEIN STRUCTURE VALIDATIONhttps://purl.org/becyt/ford/1.1https://purl.org/becyt/ford/1The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional.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: Baldoni, Hector Armando. 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"; ArgentinaFil: Scheraga, Harold A.. Cornell University; Estados UnidosJohn Wiley & Sons2009-12info: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/11336/237646Vila, Jorge Alberto; Baldoni, Hector Armando; Scheraga, Harold A.; Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution; John Wiley & Sons; Journal of Computational Chemistry; 30; 6; 12-2009; 884-8920192-8651CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.21105info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/jcc.21105info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:47:15Zoai:ri.conicet.gov.ar:11336/237646instacron: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 10:47:15.546CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
title Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
spellingShingle Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
Vila, Jorge Alberto
COMPUTATIONAL CHEMISTRY
DENSITY FUNCTIONAL THEORY
DFT
CHEMICAL SHIFTS
PROTEIN STRUCTURE DETERMINATION
PROTEIN STRUCTURE VALIDATION
title_short Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
title_full Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
title_fullStr Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
title_full_unstemmed Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
title_sort Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
dc.creator.none.fl_str_mv Vila, Jorge Alberto
Baldoni, Hector Armando
Scheraga, Harold A.
author Vila, Jorge Alberto
author_facet Vila, Jorge Alberto
Baldoni, Hector Armando
Scheraga, Harold A.
author_role author
author2 Baldoni, Hector Armando
Scheraga, Harold A.
author2_role author
author
dc.subject.none.fl_str_mv COMPUTATIONAL CHEMISTRY
DENSITY FUNCTIONAL THEORY
DFT
CHEMICAL SHIFTS
PROTEIN STRUCTURE DETERMINATION
PROTEIN STRUCTURE VALIDATION
topic COMPUTATIONAL CHEMISTRY
DENSITY FUNCTIONAL THEORY
DFT
CHEMICAL SHIFTS
PROTEIN STRUCTURE DETERMINATION
PROTEIN STRUCTURE VALIDATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.1
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional.
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: Baldoni, Hector Armando. 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
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
description The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional.
publishDate 2009
dc.date.none.fl_str_mv 2009-12
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/11336/237646
Vila, Jorge Alberto; Baldoni, Hector Armando; Scheraga, Harold A.; Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution; John Wiley & Sons; Journal of Computational Chemistry; 30; 6; 12-2009; 884-892
0192-8651
CONICET Digital
CONICET
url http://hdl.handle.net/11336/237646
identifier_str_mv Vila, Jorge Alberto; Baldoni, Hector Armando; Scheraga, Harold A.; Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution; John Wiley & Sons; Journal of Computational Chemistry; 30; 6; 12-2009; 884-892
0192-8651
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.21105
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/jcc.21105
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 John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
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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