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Fast and accurate computation of the 13 C chemical shifts for an alanine‐rich peptide
Author(s) -
Vila Jorge A.,
Baldoni Héctor A.,
Ripoll Daniel R.,
Scheraga Harold A.
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20177
Subject(s) - ramachandran plot , chemical shift , alanine , chemistry , computation , polyproline helix , quantum chemical , computational chemistry , crystallography , amino acid , peptide , stereochemistry , physics , molecule , protein structure , mathematics , organic chemistry , algorithm , biochemistry
The purpose of this work is, first, to present a fast and accurate technique to compute Boltzmann‐averaged values of the quantum‐chemical 13 C chemical shifts for each amino acid in oligopeptides, demonstrated here by an application to the peptide Ac‐XXOO‐NH 2 (where X denotes diaminobutyric acid, A is alanine, and O is ornithine) [XAO] and, second, to discuss the capability of the 13 C α and 13 C β chemical shifts to distinguish the PP II conformation from the α‐helix and statistical‐coil conformations. Use is made of a combination of approaches, summarized as follows: (1) derivation of an ensemble of conformations by using a molecular mechanics technique; (2) use of a clustering procedure to form families and build a reduced set of conformations consisting of the lowest‐energy conformations of each family, and (3) computation of the 13 C chemical shifts for the lowest‐energy conformations of each family, using a quantum‐chemical approach that treats a selected residue, or group of residues, with a 6‐311+G(2d,p) locally‐dense basis set, while the remaining residues in the sequence are treated with a 3‐21G basis set. The whole procedure is quite accurate and speeds up the computation of the Boltzmann‐averaged values of the 13 C‐chemical shifts by several orders of magnitude. The present application sheds some light on the conformational preference for alanine and non‐alanine residues to occupy the PP II helical region of the Ramachandran map. Proteins 2004. © 2004 Wiley‐Liss, Inc.