Structure of the ion channel peptide antibiotic gramicidin A

Abstract

The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 0.86 A resolution. The polypeptide crystallizes from ethanol as a left-handed, double-stranded, antiparallel beta 5.6-helical dimer that is 31 A long and an average of 4.8 A in diameter. The uncomplexed channel does not contain ions or solvent molecules, and its diameter is not uniform but varies from a minimum of 3.85 A to a maximum of 5.47 A. There are three empty cavities in the channel that have a diameter exceeding 5.25 A and appear to be large enough to accommodate water molecules or potassium ions in a chemically reasonable coordination environment. The observed crystal structure does not offer any obvious clues as to why an antiparallel beta 5.6-helix cannot function as an ion channel in lipid bilayers.