title: The binding site of sodium in the gramicidin A channel.
abstract: The available information concerning the structure and location of the main binding site for sodium in the gramicidin A channel is reviewed and discussed. Results from molecular dynamics simulations using an atomic model of the channel embedded in a lipid bilayer are compared with experimental observations. The combined information from experiment and simulation suggests that the main binding sites for sodium are near the channel's mouth, approximately 9.2 A from the centre of the dimer channel, although the motion along the axis could be as large as 1 to 2 A. In the binding site, the sodium ion is lying off axis, making contact with two carbonyl oxygens and two single-file water molecules. The main channel ligand is provided by the carbonyl group of the Leu10-Trp11 peptide linkage, which exhibits the largest deflection from the ion-free channel structure.
authors.affiliation: Department of Physics, Université de Montreal, Quebec, Canada.
authors.forename: B
authors.initials: B
authors.lastname: Roux
authors.forename: T B
authors.initials: TB
authors.lastname: Woolf
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001665:Binding Sites; D006096:Gramicidin / Q000737:chemistry*; D007473:Ion Channels; D009682:Magnetic Resonance Spectroscopy; D012964:Sodium / Q000737:chemistry*
chemical_list: D000900:Anti-Bacterial Agents; D007473:Ion Channels; D006096:Gramicidin; D012964:Sodium