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 ε=4r. The lowest energy conformation presents a secondary structure constituted by an α-helix at the N-terminal end followed by two γ-turns in the central region. The rest of the accessible minima found present also a high tendency to form γ-turns. Finally, a 100 ps MD trajectory calculation at 298 K suggest a stability of the secondary structure elements of the lowest energy conformation.