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dc.contributor.author
Vila, Jorge Alberto
dc.contributor.author
Baldoni, Hector Armando
dc.contributor.author
Scheraga, Harold A.
dc.date.available
2024-06-10T13:33:33Z
dc.date.issued
2009-12
dc.identifier.citation
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
dc.identifier.issn
0192-8651
dc.identifier.uri
http://hdl.handle.net/11336/237646
dc.description.abstract
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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
John Wiley & Sons
dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
COMPUTATIONAL CHEMISTRY
dc.subject
DENSITY FUNCTIONAL THEORY
dc.subject
DFT
dc.subject
CHEMICAL SHIFTS
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PROTEIN STRUCTURE DETERMINATION
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PROTEIN STRUCTURE VALIDATION
dc.subject.classification
Matemática Aplicada
dc.subject.classification
Matemáticas
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
dc.title
Performance of density functional models to reproduce observed 13 C α chemical shifts of proteins in solution
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2024-06-04T15:00:56Z
dc.journal.volume
30
dc.journal.number
6
dc.journal.pagination
884-892
dc.journal.pais
Estados Unidos
dc.description.fil
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
dc.description.fil
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
dc.description.fil
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
dc.journal.title
Journal of Computational Chemistry
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/https://doi.org/10.1002/jcc.21105
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/jcc.21105
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