title: Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study.
abstract: We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of L-alanyl-D-alanyl-L-alanine, acetyl-L-alanyl-L-alanine, L-vanyl-L-vanyl-L-valine, L-seryl-L-seryl-L-serine, and L-lysyl-L-lysyl-L-lysine at acid, neutral, and alkaline pD. The respective intensity ratios of the two amide I bands depend on the excitonic coupling between the amide I modes of the peptide group. These intensity ratios were obtained from a self-consistent spectral decomposition and then were used to determine the dihedral angles between the two peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523-532). The validity of the obtained structures were checked by measuring and analyzing the vibrational circular dichroism of the two amide I bands. Thus, we found two solutions for all protonation states of trialanine. Assuming a single conformer, one obtains a very extended beta-helix-like structure. Alternatively, the data can be explained by the coexistence of a 3(1)(PII) and a beta-sheet-like structure. Acetyl-L-alanyl-L-alanine exhibits a structure which is very similar to that obtained for trialanine. The tripeptide with the central D-alanine adopts an extended structure with a negative psi and a positive phi angle. Trivaline and triserine adopt single beta(2)-like structures such as that identified in the energy landscape of the alanine dipeptide. Trilysine appears different from the other investigated homopeptides in that it adopts a left-handed helix which at acid pD is in part stabilized by hydrogen bonding between the protonated carboxylate (donor) and the N-terminal peptide carbonyl. Our result provides compelling evidence for the capability of short peptides to adopt stable structures in an aqueous solution, which at least to some extent reflect the intrinsic structural propensity of the respective amino acids in proteins. Furthermore, this paper convincingly demonstrates that the combination of different vibrational spectroscopies provides a powerful tool for the determination of the secondary structure of peptides in solution.
authors.affiliation: Department of Biology and Chemistry, University of Puerto Rico, Río Piedras Campus, P.O. Box 23346, San Juan, PR 00931, USA.
authors.forename: Fatma
authors.initials: F
authors.lastname: Eker
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Cao
authors.forename: Laurence
authors.initials: L
authors.lastname: Nafie
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schweitzer-Stenner
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry; D002942:Circular Dichroism; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D012694:Serine / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared; D013059:Spectrum Analysis, Raman; D014867:Water / Q000737:chemistry*
chemical_list: D000577:Amides; D009842:Oligopeptides; C104329:valyl-valyl-valine; D014867:Water; D012694:Serine; C039944:alanyl-alanyl-alanine; D008239:Lysine