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Correlation between 13 C α chemical shifts and helix content of peptide ensembles
Author(s) -
Weinstock Daniel S.,
Narayanan Chitra,
Baum Jean,
Levy Ronald M.
Publication year - 2008
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.073365408
Subject(s) - helicity , ramachandran plot , conformational isomerism , physics , peptide , crystallography , torsion (gastropod) , random coil , chemistry , dihedral angle , nuclear magnetic resonance , protein structure , molecule , circular dichroism , quantum mechanics , medicine , hydrogen bond , surgery
Replica exchange molecular dynamics simulations are used to generate three ensembles of an S‐peptide analog (AETAAAKFLREHMDS). Percent helicity of the peptide ensembles calculated using STRIDE is compared to percent helicity calculated from 13 C α chemical shift deviations (CSD) from random coil in order to test the assumption that CSD can be correlated to percent helicity. The two estimates of helicity, one based on structure and the other on CSD, are in close to quantitative agreement, except at the edges of helical stretches where disagreements of as much as 50% can be found. These disagreements can occur by CSDs both as an under‐ and an overestimate of peptide helicity. We show that underestimation arises due to ensemble averaging of positive CSDs from conformers with torsion angles in the helical region of Ramachandran space with negative CSDs corresponding to conformers of the peptide in the extended region. In contrast, overestimation comes about due to the fact that a large number of conformations with torsion angles in the helical region are not counted as helical by STRIDE due to a lack of correlated helical torsion angles in neighboring residues.