title: Tripeptides with ionizable side chains adopt a perturbed polyproline II structure in water.
abstract: The present paper reports the conformations of the acidic and basic homotripeptides triglutamate, triaspartate, and trilysine in aqueous solution to better understand their relevance for the structure of disordered proteins and protein segments and for a variety of protein binding processes. The determination of the dihedral angles of the central amino acid residue was achieved by analyzing the amide I band profile of the respective polarized visible Raman, Fourier transform infrared (FT-IR), and vibrational circular dichroism (VCD) spectra by means of recently developed algorithms [Schweitzer-Stenner, R. (2002) Biophys. J. 83, 523-532; Eker et al. (2002) J. Am. Chem. Soc. 124, 523-532]. The results were validated by measuring the UV electronic circular dichroism (ECD) spectra of the peptides. The analyses revealed that a polyproline II-like conformation is predominant at room temperature. For triaspartate and triglutamate the dihedral angles of phi = -70 degrees, psi = 165 degrees and phi = -60 degrees, psi = 160 degrees were obtained, respectively. A similar conformation, i.e., phi = -50 degrees, psi = 170 degrees, was obtained for trilysine, which is at variance with the earlier reported left-handed turn structure. The ECD spectrum of charged tripeptides displayed symmetric negative and positive couplets at 190 and 210 nm, which are interpreted as indicating a somewhat, perturbed polyproline II conformation, in agreement with the obtained dihedral angles. Comparison with literature data shows that the investigated tripeptides are ideal model systems for understanding the local conformation of functionally relevant K3, K2X, E3, and D3 segments in a variety of different proteins.
authors.affiliation: Departments of Chemistry and Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00931, USA.
authors.forename: Fatma
authors.initials: F
authors.lastname: Eker
authors.forename: Kai
authors.initials: K
authors.lastname: Griebenow
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Cao
authors.forename: Laurence A
authors.initials: LA
authors.lastname: Nafie
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schweitzer-Stenner
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D001665:Binding Sites; D002942:Circular Dichroism; D007477:Ions; D008024:Ligands; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012996:Solutions; D017550:Spectroscopy, Fourier Transform Infrared; D013059:Spectrum Analysis, Raman; D014867:Water
chemical_list: D007477:Ions; D008024:Ligands; D009842:Oligopeptides; D010455:Peptides; D012996:Solutions; D014867:Water; C011083:polyproline