title: Side chain and flexibility contributions to the Raman optical activity spectra of a model cyclic hexapeptide.
abstract: A model peptide, cyclo-(Phe-d-Pro-Gly-Arg-Gly-Asp), with a distinct folded structure containing short beta-hairpin and beta-sheet patterns was studied by Raman and Raman optical activity (ROA) spectroscopies. Unlike for previously analyzed vibrational circular dichroism of the same compound (Chirality 2008, 20, 1104), the Raman spectrum is dominated by side chain contributions and is more sensitive to their geometry fluctuations. The spectra and molecular motion were analyzed with the aid of the density functional theory simulations combined with molecular dynamics (MD). The side chain geometry fluctuations were found to significantly contribute to the broadening of the spectral bands, while dynamics of the backbone is rather restricted. According to our MD results, the side chains do not move freely but largely oscillate around preferred conformations. Averaging of computed spectra for many structures derived from the MD trajectories provided better spectral profiles than did a fixed geometry. The Raman and ROA scattering is dominated by the more polarizable phenylalanine and proline groups, as could be verified both by the computations and by comparison to experiments with a model Phe-d-Pro dipeptide. Computational analyses suggest that the ROA spectrum mostly senses local side chain conformation, whereas a vibrational coupling between different side chains contributes less. The coupling is mostly mediated by the peptide backbone and is restricted to specific vibrational region. The ROA spectroscopic technique thus provides important local structural information that needs, however, to be extracted by multiscale (QM/MM) simulation techniques.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Hudecová
authors.forename: Josef
authors.initials: J
authors.lastname: Kapitán
authors.forename: Vladimír
authors.initials: V
authors.lastname: Baumruk
authors.forename: Robert P
authors.initials: RP
authors.lastname: Hammer
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Keiderling
authors.forename: Petr
authors.initials: P
authors.lastname: Bour
mesh_terms: D008956:Models, Chemical; D015394:Molecular Structure; D009842:Oligopeptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D011789:Quantum Theory; D013059:Spectrum Analysis, Raman
chemical_list: D009842:Oligopeptides; D010456:Peptides, Cyclic; C064597:glycyl-arginyl-glycyl-aspartic acid