The structure of alanine based tripeptides in water and dimethyl sulfoxide probed by vibrational Spectroscopy

We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of cationic L-alanyl-D-alanyl-L-alanine, L-alanyl-alanine-L-alanine, and L-seryl-L-alanine-L-alanine in D2O. Additionally, we recorded spectra of N-acetyl-L-alanyl-L-alanine in D2O and in DMSO-d(6). The respective intensity ratios of the two amide I bands depend on excitonic coupling between the amide I modes of the two peptides. These intensity ratios were obtained from a spectral decomposition and then used to determine the dihedral angles between the peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, Biophys. J., 83, 83, 523, 2002). The validity of the obtained structures was checked by measuring the vibrational circular dichroism of the amide I bands. L-Lysyl-L-alanyl-L-alanine, L-seryl-L-alanyl-L-alanine, and acetyl-L-alanyl-L-alanine adopt structures similar to that observed for L-alanyl-L-alanyl-L-alanine. This suggests that the N-terminal residues do not significantly influence the dihedral angles between the two peptide groups. If one assumes a single dominant conformer, one obtains beta-helix or extended polyproline II conformation, while a two-conformer model yields coexisting polyproline II and extended beta-type conformers. Acetyl-L-alanyl-L-alanine in DMSO-d(6) adopts a beta-sheet-like structure. Its amide I bands are significantly less broadened than those observed with D2O solvent. Our results show that hydrogen bonding between the peptide and water molecules contributes significantly to the inhomogeneous broadening of amide I bands and stabilizes the polyproline II conformation.