Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements.

Extensive conformational sampling and calculations of vibrational coupling provide a quantitative basis for the structurally inhomogeneous spectra of the amide unit in aqueous solutions containing folded and unfolded state distributions of helices. Replica exchange molecular dynamics simulations of the capped helical peptide, AA(AAKAA)(3)AAY, is carried out over a range of temperatures, where the system populates the folded and unfolded states. This sampling defines a set of ensembles that characterizes the conformational variability for configurations identified by their fraction of helical content. The effects of hydrogen bonding, both internal and external (with water), and the coupling between amide-I modes are computed as a function of temperature and helical content. End-to-end distance and coupling distributions are also computed. The solvent H-bonding, which is present at all temperatures, shifts the amide-I band toward lower frequency compared with the unsolvated band. Upon thermal denaturation of the peptide, the amide-I band shifts to higher frequency because the increase in solvent H-bonding fails to compensate for the loss in internal (helical) H-bonds. The loss of uniformity of the mode coupling along the helix at higher temperatures accounts for the well-known thermal broadening of the amide IR spectrum. The calculated inhomogeneities of segments of the peptide predict experimental properties of isotope-edited helices.