Secondary structure analysis of polypeptides based on an excitonic coupling model to describe the band profile of amide I′ of IR, Raman, and vibrational circular dichroism spectra

FTIR and, to a lesser extent, visible Raman spectroscopy are frequently used to determine the secondary structure composition of peptides and proteins in solution. This generally allows distinguishing between alpha-helices, beta-strand, and what is often called a random coil conformation. Thus, these vibrational spectroscopies generally appear as useful but low resolution techniques. We developed a novel approach, which allows a more precise structure analysis of short and intermediate sized peptides. It is based on exploiting the delocalization of amide I' over several peptide groups owing to excitonic coupling. The vibrational eigenfunctions obtained by diagonalizing the complete Hamiltonian of the interacting amide I' modes were used to calculate the amide I' band profile in the IR, isotropic, and anisotropic Raman and vibrational circular dichroism spectrum. A combined use of these profiles is a tool to distinguish between helical segments of different length and between different conformations adopted in what is inappropriately termed the random coil state. Our algorithm is particularly useful to identify the polyproline II conformation, which is adopted by many unfolded proteins at room temperature.