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The M2delta peptide self-assembles to form a pentameric bundle of transmembrane alpha-helices that is a model of the pore-lining region of the nicotinic acetylcholine receptor. Long (>15 ns) molecular dynamics simulations of a model of the M2delta(5) bundle in a POPC bilayer have been used to explore the conformational dynamics of the channel assembly. On the timescale of the simulation, the bundle remains relatively stable, with the polar pore-lining side chains remaining exposed to the lumen of the channel. Fluctuations at the helix termini, and in the helix curvature, result in closing/opening transitions at both mouths of the channel, on a timescale of approximately 10 ns. On average, water within the pore lumen diffuses approximately 4x more slowly than water outside the channel. Examination of pore water trajectories reveals both single-file and path-crossing regimes to occur at different times within the simulation.

Original publication




Journal article


Biophys J

Publication Date





14 - 27


Amino Acid Sequence, Cell Membrane, Cell Membrane Permeability, Computer Simulation, Diffusion, Ion Channels, Lipid Bilayers, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Motion, Peptides, Porosity, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Receptors, Nicotinic, Sensitivity and Specificity, Water