Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer

Integral membrane proteins containing at least one transmembrane (TM) alpha -helix are believed to account for between 20% and 30% of most genomes. The re are several algorithms that accurately predict the number and position o f TM helices within,a membrane protein sequence. However, these methods ten d to disagree over the beginning and end residues of TM helices, posing pro blems for subsequent modeling and simulation studies. Molecular dynamics (M D) simulations in an explicit lipid and water environment are used to help define the TM helix of the M2 protein from influenza A virus. Based on: a c omparison of the results of five different secondary structure prediction a lgorithms, three different helix lengths (an 18mer, a 26mer, and a 34mer) w ere simulated. Each simulation system contained 127 POPC molecules plus sim ilar to 3500 -4700 waters, giving a total, of similar to 18,000-21,000 atom s. Two simulations, each of 2 ns duration, were run for the 18mer and 26mer , and five separate simulations were run for the 34mer, using different sta rting models generated by restrained in vacuo MD simulations. The total sim ulation time amounted to 11 ns. Analysis of the time-dependent secondary st ructure of the TM segments was used to define the regions that adopted a st able alpha-helical confirmation throughout the simulation. This analysis in dicates a core TM region of similar to 20 residues (from residue 22 to resi due 43) that remained in an alpha-helical conformation, Analysis of atomic density profiles suggested that the 18mer helix revealed a local perturbati on of the lipid bilayer. Polar side chains on either side of this region fo rm relatively long-lived H-bonds to lipid headgroups and water molecules.