Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations

Abstract

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N′- methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (αR) and left-handed (αL) helical conformations. The computed ROA spectra based on MC-sampled αR and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the αL- and β-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the αL and PPII conformations but no substantial population of αL- or β-structures, despite sampling αL- and β-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach. © 2008 by the Biophysical Society.