Conformational analysis of tetrapeptides by exploiting the excitonic coupling between amide I modes

Abstract

AbstractThe amide I band of the IR and to a lesser extent also of the corresponding visible Raman spectra of peptides and proteins are frequently used to determine their secondary structure composition. Thus far, however, this analytical approach is generally a low‐resolution technique, particularly because it mostly discriminates only between α‐helical, β‐sheet (parallel and antiparallel) and so‐called random coil conformations. This study shows that for tetrapeptides the combined use of the IR and Raman amide I band profiles allows one to discriminate currently known secondary structure motifs. To exploit the spectral information to its fullest extent, we developed an algorithm which calculates the amide I intensity profiles of IR, isotropic and anisotropic Raman scattering and also the depolarization ratios of the Raman bands as a function of the dihedral angles of the two central amino acid resides. The approach is based on a quantum mechanical treatment of the vibrational coupling between the amide I modes of the three peptide groups in the framework of a coupled oscillator model. We calculated the band profiles of a representative set of secondary structures, i.e. a right‐handed α‐helix, a 310‐helix, β‐sheets and a polyproline II (PPII)‐type 31‐helix and β‐turns. Our results unambiguously show that all these secondary structure motifs can be identified by comparing experimentally observed IR and Raman amide I bands with their respective calculated intensity distributions. Copyright © 2004 John Wiley & Sons, Ltd.