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Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer
L R Forrest1, A Kukol, I T Arkin
1Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England.
Abstract:
The M2 protein of influenza A virus forms homotetrameric helix bundles, which 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 by the antiviral drug amantadine. As a small ion channel, M2 may provide useful insights into more complex channel systems. Models of tetrameric bundles of helices containing either 18 or 22 residues have been simulated while embedded in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylcholine bilayer. Several different starting models have been used. These suggest that the simulation results, at least on a nanosecond time scale, are sensitive to the exact starting structure. Electrostatics calculations carried 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 charged state. Helix bundle models were mostly stable over the duration of the simulation, and their helices remained tilted relative to the bilayer normal. The M2 helix bundles form closed channels that undergo breathing motions, alternating between a tetramer and a dimer-of-dimers structure. Under these conditions either the channel forms a pocket of trapped waters or it contains a column of waters broken predominantly at the C-terminal mouth of the pore. These waters exhibit restricted motion in the pore and are effectively "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 (, Biophys. J. 77:2400-2410).
Insights
Influenza A virus M2 protein forms proton channels. Simulations reveal these channels are mostly closed, with water molecules restricted within, offering insights into ion channel function.
Area of Science:
- Biophysics
- Structural Biology
- Virology
Background:
- The M2 protein of influenza A virus is a proton-selective channel crucial for viral replication.
- Its transmembrane domain forms homotetrameric helix bundles, and its structure provides insights into complex ion channel systems.
- The channel activity is inhibited by amantadine, an antiviral drug.
Purpose of the Study:
- To simulate and analyze the structural dynamics of M2 protein helix bundle models embedded in a lipid bilayer.
- To investigate the channel's water content and proton transport mechanism at a molecular level.
Main Methods:
- Molecular dynamics simulations of 18- and 22-residue M2 helix bundle models in a POPC lipid bilayer.
- Electrostatics calculations to analyze ionizable residues at the channel's N-terminal mouth.
- Analysis of helix bundle stability, orientation, and water dynamics within the channel.
Main Results:
- M2 helix bundles remained stable and tilted relative to the bilayer normal during simulations.
- Simulated channels were predominantly closed, exhibiting breathing motions between tetrameric and dimer-of-dimers states.
- Water molecules within the pore showed restricted motion, either forming trapped pockets or a broken column, suggesting a mechanism for proton selectivity.
Conclusions:
- The M2 protein forms a dynamic, mostly closed ion channel with restricted water movement.
- These findings contribute to understanding the molecular basis of proton transport in viral ion channels.
- The simulation results are sensitive to initial structural configurations, highlighting the importance of starting models.