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.

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

“…We note, however, that both Val and Leu side chains used in this study can affect vibrational spectral features in the amide I and II regions indirectly, i.e., through their influence on the backbone conformation. 30 Water-soluble variants of the original model peptides necessarily include hydrophilic side chains, 44 which may contain chromophores that contribute directly to the vibrational spectra in the amide I and II regions. For hydrophilic peptides designed to fold into the same ␤…”

“…A complementary technique, vibrational CD ͑VCD͒, uses circularly polarized IR light and provides spectra with detailed "fingerprints" analogous to standard IR spectra. VCD measurements in the amide I and II regions have been widely used to study conformations of small peptides, including small cyclic peptides and turns [28][29][30][31][32] that resemble the peptides analyzed in this work. These measurements can be challenging because VCD bands tend to be weaker than IR absorbance bands by a factor of 10 4 -10 5 ; however, the vibrational transitions probed by VCD are typically more localized to specific chromophores or normal modes and are sensitive to dipole coupling of nearby residues.…”

Monitoring the Backbone Conformation of Valinomycin by Raman Optical Activity

“…The ROA peaks of the amide I band are usually observed in the spectra of proteins [10] and also in small flexible peptides. [43,58,59] We explain the absence of this band by the internal achirality (planarity) of the amide and ester chromophores, weak interaction among the carbonyl groups, and by the molecular flexibility.…”

“…This methodology has been successfully applied to simulations of both vibrational circular dichroism (VCD) [39,40] and ROA [12,19] spectra, including ROA of flexible molecules. [41][42][43] A database of characteristic fragments can be used for many conformers with a similar structure. [41] The B3LYP [44] functional was previously used to calculate accurate force field and polarizability tensors of valinomycin.…”

“…Combining MD and quantum mechanical calculations was found to be beneficial for small molecules in solution which exhibit similar flexible structure to valinomycin. [19,41,43] The ROA and Raman tensors and the force field of the P1 conformer were transferred to 17 MD geometries of the propeller Figure 4. Calculated ROA (top) and Raman (bottom) spectra of the bracelet conformers of free valinomycin (sB1, sB2, asB1, and asB2; see Supporting Information for structural details) and the experimental spectra in dioxane.…”