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 -lysyl- l -alanine- l -alanine, and l -seryl- l -alanine- l -alanine in D 2 O. Additionally, we recorded spectra of N -acetyl- l -alanyl- l -alanine in D 2 O 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 a β-helix or extended polyproline II conformation, while a two-conformer model yields coexisting polyproline II and extended β-type conformers. Acetyl- l -alanyl- l -alanine in DMSO- d 6 adopts a β-sheet-like structure. Its amide I bands are significantly less broadened than those observed with D 2 O 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.