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Protein Science (2008), 17:950-954. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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FOR THE RECORD

Correlation between 13C {alpha} chemical shifts and helix content of peptide ensembles

Daniel S. Weinstock, Chitra Narayanan, Jean Baum, and Ronald M. Levy

BIOMAPS Institute, Rutgers University, Piscataway, New Jersey 08854-8087, USA
Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA

(RECEIVED November 21, 2007; FINAL REVISION February 28, 2008; ACCEPTED March 1, 2008)

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 13C{alpha} 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.

Keywords: chemical shift; peptide ensembles


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