title: Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature.
abstract: The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To characterize helical and unfolded states adopted by water-soluble Aib-containing peptides, the conformational preference of Ac-Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Tyr-NH(2) was determined by CD, NMR and MD simulations as a function of temperature. Temperature-dependent CD data indicated the contribution of two major components, each an admixture of helical and extended/polyproline II structures. Both right- and left-handed helical conformations were detected from deconvolution of CD data and (13)C NMR experiments. The presence of a helical backbone, more pronounced at the N-terminal, and a temperature-induced shift in alpha-helix/3(10)-helix equilibrium, more pronounced at the C-terminal, emerged from NMR data. Starting from polyproline II, the N-terminal of the peptide folded into a helical backbone in MD simulations within 5 ns at 60 degrees C. Longer simulations showed a mixed-helical backbone to be stable over the entire peptide at 5 degrees C while at 60 degrees C the mixed-helix was either stable at the N-terminus or occurred in short stretches through out the peptide, along with a significant population of polyproline II. Our results point towards conformational heterogeneity of water-soluble Aib-based peptide helices and the associated subtleties. The problem of analyzing CD and NMR data of both left- and right-handed helices are discussed, especially the validity of the ellipticity ratio [theta](222)/[theta](207), as a reporter of alpha-/3(10)- population ratio, in right- and left-handed helical mixtures.
authors.affiliation: Department of Biotechnology, West Bengal University of Technology, Kolkata 700064, India. ban_raja@yahoo.com
authors.forename: Raja
authors.initials: R
authors.lastname: Banerjee
authors.forename: Sarbani
authors.initials: S
authors.lastname: Chattopadhyay
authors.forename: Gautam
authors.initials: G
authors.lastname: Basu
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000595:Amino Acid Sequence; D000621:Aminoisobutyric Acids / Q000737:chemistry*; D002942:Circular Dichroism; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012995:Solubility; D013696:Temperature; D014867:Water / Q000737:chemistry*
chemical_list: D000621:Aminoisobutyric Acids; D010455:Peptides; D014867:Water; C100049:2-aminoisobutyric acid; D000409:Alanine