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dc.contributor.author
Vila, Jorge Alberto
dc.contributor.author
Villegas, Myriam E.
dc.contributor.author
Baldoni, Hector Armando
dc.contributor.author
Scheraga, Harold A.
dc.date.available
2021-06-30T12:04:10Z
dc.date.issued
2007-07
dc.identifier.citation
Vila, Jorge Alberto; Villegas, Myriam E.; Baldoni, Hector Armando; Scheraga, Harold A.; Predicting 13Ca chemical shifts for validation of protein structures; Springer; Journal Of Biomolecular Nmr; 38; 3; 7-2007; 221-235
dc.identifier.issn
0925-2738
dc.identifier.uri
http://hdl.handle.net/11336/135133
dc.description.abstract
The 13Ca chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initially, a validation test of this methodology was carried out by a detailed examination of the correlation between computed and observed 13Ca chemical shifts of 10,564 (of the 16,299) residues from 139 conformations of the human protein ubiquitin. The results of this validation test on ubiquitin show agreement with conclusions derived from computation of the chemical shifts at the ab initio Hartree-Fock level. Further, application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, namely the conformationally averaged root-mean-square-deviation, enables us to: (a) offer a criterion for an accurate assessment of the quality of NMRderived protein conformations; (b) examine whether X-ray or NMR-solved structures are better representations of the observed 13Ca chemical shifts in solution; (c) provide evidence indicating that the proposed methodology is more accurate than automated predictors for validation of protein structures; (d) shed light as to whether the agreement between computed and observed 13Ca chemical shifts is influenced by the identity of an amino acid residue or its location in the sequence; and (e) provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Springer
dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
13C CHEMICAL SHIFT PREDICTION
dc.subject
PROTEIN STRUCTURE VALIDATION
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SOLUTION STRUCTURE
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UBIQUITIN
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X-RAY AND NMR STRUCTURES
dc.subject.classification
Biofísica
dc.subject.classification
Ciencias Biológicas
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
dc.title
Predicting 13Ca chemical shifts for validation of protein structures
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2020-09-24T14:24:55Z
dc.journal.volume
38
dc.journal.number
3
dc.journal.pagination
221-235
dc.journal.pais
Alemania
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: Villegas, Myriam E.. 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: 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 Biomolecular Nmr
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1007/s10858-007-9162-x
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs10858-007-9162-x
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