Structural and Kinetic Characterization of a β-hairpin Peptide in Solution: A Molecular Dynamics Study of a Synthetic Analog of Gramicidin S

Abstract

In the present study we have performed MD simulations to characterize the kinetics and dynamics of the folding process of a Synthetic Analog of Gramicidin S. A 6-meric peptide was chosen because of its shortness and the consequent reduced computational power required. Unfortunately, the structural data obtained by NMR experiments are not deposited in any data bank: the starting atomic coordinates in the simulation were thus reconstructed starting from the primary sequence of the peptide [cyclo(Lys-dTyr-Pro)2]. The 6 amino acids were arranged as an extended linear structure. This extended structure was then made cyclic and equilibrated before the productive MD simulation.