Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.

Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Research Abstract Details 

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Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Abstract Text:

Myriam E Villegas,Jorge A Vila,Harold A Scheraga,

The dependence of the (13)C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel beta-sheet model peptide represented by the amino acid sequence Ac-(Ala)(3)-X-(Ala)(12)-NH(2) where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel beta-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the (13)C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel beta-sheet, there is (i) good agreement between computed and observed (13)C(alpha) and (13)C(beta) chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed (13)C(alpha) and (13)C(beta) chemical shifts as a function of chi(1) for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed (13)C(alpha) chemical shifts on chi(xi) (with xi > or = 2) compared to chi(1) for eleven out of seventeen residues. Our results suggest that predicted (13)C(alpha) and (13)C(beta) chemical shifts, based only on backbone (phi,psi) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into account.

Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Publishing Authors By Initials

ME Villegas,JA Vila,HA Scheraga,

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Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Journal of biomolecular NMR

VOLUME: 37

Page Numbers: 137-46

Journal Abbreviation: J. Biomol. NMR

ISSN: 0925-2738

DAY: 19

MONTH: 12

YEAR: 2006

Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Information

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LANGUAGE: eng

NlmUniqueID: 9110829

Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: chemistry

Chemical & Substance for Abstract: Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.

AFFILIATION: Facultad de Ciencias Físico Matemáticas y Naturales, Instituto de Matemática Aplicada San Luis, Universidad Nacional de San Luis, CONICET, Ejército de Los Andes, San Luis, 950-5700, Argentina.

Country: Netherlands

AGENCY: United States FIC

GRANT: TW-6335

ACRONYM: TW

MEDLINETA: J Biomol NMR

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