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

Abstract

The 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.