Molecular Dynamics Simulated Annealing Study of Gramicidin A in Water and the Hydrophobic Environment

Gramicidin A is a hydrophobic 15-residue peptide with alternating {\scriptsize D}- and {\scriptsize L}-amino acids, and it forms various conformations depending on its environment. For example, gramicidin A adopts a random coil or helical conformations, such as $\beta^{4.4}$-helix, $\beta^{6.3}$-helix, and double-stranded helix in organic solvents. To investigate the structural and dynamical properties of gramicidin A in water and the hydrophobic environment, we performed molecular dynamics simulated annealing simulations with implicit solvent based on a generalized Born model. From the simulations, it was found that gramicidin A has a strong tendency to form a random-coil structure in water, while in the hydrophobic environment it becomes compact and can fold into right- and left-handed conformations of $\beta$-helix structures. We discuss the folding mechanism of the $\beta$-helix conformation of gramicidin A.