Structure and dynamics of ion transport through gramicidin A

Abstract

Molecular dynamics calculations in which all atoms were allowed to move were performed on a water-filled ion channel of the polypeptide dimer gramicidin A (approximately 600 atoms total) in the head-to-head Urry model conformation. Comparisons were made among nine simulations in which four different ions (lithium, sodium, potassium, and cesium) were each placed at two different locations in the channel as well as a reference simulation with only water present. Each simulation lasted for 5 ps and was carried out at approximately 300 K. The structure and dynamics of the peptide and interior waters were found to depend strongly on the ion tested and upon its location along the pore. Speculations on the solution and diffusion of ions in gramicidin are offered based on the observations in our model that smaller ions tended to lie off axis and to distort the positions of the carbonyl oxygens more to achieve proper solvation and that the monomer-monomer junction was more distortable than the center of the monomer. With the potential energy surface used, the unique properties of the linear chain of interior water molecules were found to be important for optimal solvation of the various ions. Strongly correlated motions persisting over 25 A among the waters in the interior single-file column were observed.