Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer

The M2 protein of influenza A virus forms homotetrameric helix bundles, whi ch function as proton-selective channels. The native form of the protein is 97 residues long, although peptides representing the transmembrane section display ion channel activity, which (like the native channel) is blocked b y the antiviral drug amantadine. As a small ion channel, M2 may provide use ful insights into more complex channel systems. Models of tetrameric bundle s of helices containing either 18 or 22 residues have been simulated while embedded in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidy lcholine bilayer. Several different starting models have been used. These s uggest that the simulation results, at least on a nanosecond time scale, ar e sensitive to the exact starting structure. Electrostatics calculations ca rried out on a ring of four ionizable aspartate residues at the N-terminal mouth of the channel suggest that at any one time, only one will be in a ch arged state. Helix bundle models were mostly stable over the duration of th e simulation, and their helices remained tilted relative to the bilayer nor mal. The M2 helix bundles form closed channels that undergo breathing motio ns, alternating between a tetramer and a dimer-of-dimers structure. Under t hese conditions either the channel forms a pocket of trapped waters or it c ontains a column of waters broken predominantly at the C-terminal mouth of the pore. These waters exhibit restricted motion in the pore and are effect ively "frozen" in a way similar to those seen in previous simulations of a proton channel formed by a four-helix bundle of a synthetic leucine-serine peptide.