Mechanism of ion transport and gating in gramicidin nanotubes

The crystal structures of monovalent ion complexes of gramicidin provide information concerning the nature of the interactions of ions with the peptide backbone and water in the channel. There are between 1 and 2 cations per channel distributed in partial occupancy over subsets of seven sites. Analysis reveals unexpected chemical features including coordination of the cations with the π orbitals of carbonyl groups and peptide bonds that form the walls of the channel, asymmetry in the positions of water molecules on either side of the cations in the channel, and ion specific distribution in the seven sites within the channel. In most cases each ion makes three or four contacts to the π clouds of the carbonyl or peptide groups. The peptide bond angle ω(Cα_n-C₁- N₁-Cα_n+1) of residues involved in ion coordination exhibits significant non-planarity. ¹³C NMR chemical shift measurements attributed to Na⁺ ion interactions with leucine residues in gramicidin channels in lipid bilayers correlate with these observations. The majority of the water molecules in the asymmetric gramicidin channel have their dipoles aligned parallel to one another suggesting that there is an overall dipole in the channel compatible with unidirectional ion movement. The ethanol amine residues at either end of the channel appear to play a role in channel gating.