Structural, thermodynamic, and kinetic properties of gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics

Gramicidin S (GS) analogues belong to an important class of cyclic peptides, characterized by an antiparallel double-stranded β-sheet structure with Type II′ β-turns. Such compounds can be used as model systems to understand the folding/unfolding process of β-hairpins and more in general of β-structures. In the present study, we specifically investigate the folding/unfolding behavior of the hexameric Gramicidin S analogue GS6 by using all-atoms molecular dynamics (MD) simulations at different temperatures, coupled to a statistical mechanical model based on the Quasi Gaussian Entropy theory. Such an approach permits to describe the structural, thermodynamic, and kinetic properties of the peptide and to quantitatively characterize its folding/unfolding transitions. © 2009 Wiley Periodicals, Inc.