title: Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.
abstract: The alanine-based peptide Ac-XX(A)7OO-NH2, referred to as XAO (where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively), has recently been proposed to possess a well defined polyproline II (P(II)) conformation at low temperatures. Based on the results of extensive NMR and CD investigations combined with theoretical calculations, reported here, we present evidence that, on the contrary, this peptide does not have any significant amount of organized P(II) structure but exists in an ensemble of conformations with a distorted bend in the N- and C-terminal regions. The conformational ensemble was obtained by molecular dynamics/simulated annealing calculations using the amber suite of programs with time-averaged distance and dihedral-angle restraints obtained from rotating-frame nuclear Overhauser effect (ROE) volumes and vicinal coupling constants 3J(HN Eta alpha), respectively. The computed ensemble-averaged radius of gyration Rg (7.4 +/- 1.0) A is in excellent agreement with that measured by small-angle x-ray scattering (SAXS) whereas, if the XAO peptide were in the P(II) conformation, Rg would be 11.6 A. Depending on the pH, peptide concentration, and temperature, the CD spectra of XAO do or do not possess the maximum with positive ellipticity in the 217-nm region, which is characteristic of the P(II) structure, reflecting a shifting conformational equilibrium rather than an all-or-none transition. The "P(II) conformation" should, therefore, be considered as one of the accessible conformational states of individual amino acid residues in peptides and proteins rather than as a structure of most of the chain in the early stage of folding.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.
authors.forename: Joanna
authors.initials: J
authors.lastname: Makowska
authors.forename: Sylwia
authors.initials: S
authors.lastname: Rodziewicz-Motowidło
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Bagińska
authors.forename: Jorge A
authors.initials: JA
authors.lastname: Vila
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
authors.forename: Lech
authors.initials: L
authors.lastname: Chmurzyński
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000409:Alanine / Q000737:chemistry; D000613:Aminobutyrates / Q000737:chemistry; D002942:Circular Dichroism; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D009952:Ornithine / Q000737:chemistry; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013997:Time Factors
chemical_list: D000613:Aminobutyrates; D010455:Peptides; D011506:Proteins; C011083:polyproline; D009952:Ornithine; D000409:Alanine