title: Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: a molecular dynamics study.
abstract: In this study, molecular dynamics simulations were carried out on Lys- and Arg-containing Ala-based peptides (i.e. Ace-(AAAAK)(n)A-NH(2) and Ace-(AAAAR)(n)A-NH(2), where n=1-4), in order to explore and characterize their folding processes. For the oligopeptides, the evolution of α-helical structure with regard to the whole conformation, as well as to each residue was investigated, and the helix-forming propensities were characterized. On the basis of the helicity curves, representing the alteration of average helicity as a function of time, the typical time values describing the folding processes and subprocesses were identified. In the case of each peptide, the evolution and role of helix-stabilizing, non-local and side-chain-to-backbone H-bonds were examined. The appearing i←i+4 H-bonds pointed out the role of these interactions in the stabilization of α-helical conformations, while the occurring i←i+3 H-bonds indicated the presence of β-turn or 3(10)-helical structures. Studying the formation and role of non-local and side-chain-to-backbone H-bonds led to the observation that these types of interactions produced an effect on the evolution of helical conformations, as well as on the folding processes.
authors.affiliation: Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.
authors.forename: Gábor
authors.initials: G
authors.lastname: Janzsó
authors.forename: Ferenc
authors.initials: F
authors.lastname: Bogár
authors.forename: Liza
authors.initials: L
authors.lastname: Hudoba
authors.forename: Botond
authors.initials: B
authors.lastname: Penke
authors.forename: Gábor
authors.initials: G
authors.lastname: Rákhely
authors.forename: Balázs
authors.initials: B
authors.lastname: Leitgeb
mesh_terms: D000409:Alanine / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry*; D008239:Lysine / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides; D001120:Arginine; D008239:Lysine; D000409:Alanine