title: Conformational study of a nine residue fragment of the antigenic loop of foot-and-mouth disease virus.
abstract: The nine-residue peptide Ac-TASARGDLA-NHMe was selected as model peptide in order to understand the conformational features of the antigenic loop of foot-and-mouth disease virus (FMDV). A throughout exploration of the conformational space has been carried out by means of molecular dynamics (MD) and energy minimization. The calculations have been carried out using the AMBER force field. Solvent effects have been included by an effective dielectric constant of epsilon = 4r. The lowest energy conformation presents a secondary structure constituted by an alpha-helix at the N-terminal end followed by two gamma-turns in the central region. The rest of the accessible minima found present also a high tendency to form gamma-turns. Finally, a 100 ps MD trajectory calculation at 298 K suggest a stability of the secondary structure elements of the lowest energy conformation.
authors.affiliation: Dept. d'Enginyeria Química, UPC ETS d'Enginyers Industrials, Barcelona, Spain.
authors.forename: M C
authors.initials: MC
authors.lastname: Vega
authors.forename: C
authors.initials: C
authors.lastname: Aleman
authors.forename: E
authors.initials: E
authors.lastname: Giralt
authors.forename: J J
authors.initials: JJ
authors.lastname: Perez
mesh_terms: D000595:Amino Acid Sequence; D000956:Antigens, Viral / Q000737:chemistry*; D005537:Aphthovirus / Q000276:immunology*; D002213:Capsid / Q000737:chemistry* / Q000276:immunology; D036022:Capsid Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D010446:Peptide Fragments; C442501:VP1 protein, Foot-and-mouth disease virus