ION-TRANSPORT THROUGH GRAMICIDIN-A - WATER-STRUCTURE AND FUNCTIONALITY

Molecular Dynamics (MD) simulations were performed on a gramicidin A d imer model representing a transmembrane channel. Different from previo us simulations the peptide was in contact with bulk water at both ends of the dimer to guarantee a realistic description of the hydration of the biomolecule. The flexible BJH model for water was employed in the simulations and the gramicidin-water, gramicidin-ion and ion-water po tentials used are based on molecular orbital calculations. The water s tructure near the gramicidin was investigated first by a simulation wi thout ions, while for the energy profiles of the ion transport through the channel a potassium or a sodium ion was added. These investigatio ns provide a detailed and conclusive picture on a molecular level of t he role of water in the ion transport through a gramicidin A channel a nd can explain the experimental results on the selectivity between alk ali ions, their double or even triple occupancy, the exclusion or perm eability of anions depending upon cation concentration and the consequ ences of differences in the ionic charge. The investigation demonstrat e that the water molecules around the gramicidin behave as an integral part of the peptide and the functionality is the result of the whole complex biomolecule-water.