Conformational analysis of tetrapeptides by exploiting the excitonic coupling between amide I modes
Article first published online: 28 JUN 2004
Copyright © 2004 John Wiley & Sons, Ltd.
Journal of Raman Spectroscopy
Volume 35, Issue 7, pages 586–591, July 2004
How to Cite
Huang, Q. and Schweitzer-Stenner, R. (2004), Conformational analysis of tetrapeptides by exploiting the excitonic coupling between amide I modes. J. Raman Spectrosc., 35: 586–591. doi: 10.1002/jrs.1201
- Issue published online: 28 JUN 2004
- Article first published online: 28 JUN 2004
- Manuscript Accepted: 13 MAR 2004
- Manuscript Received: 23 DEC 2003
- NIH. Grant Number: P20 RR16439-01.
- peptide structure analysis;
- excitonic coupling;
- amide I;
- Raman and IR spectroscopy
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.