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Multiple nanosecond duration molecular dynamics simulations were performed on the transmembrane region of the Torpedo nicotinic acetylcholine receptor embedded within a bilayer mimetic octane slab. The M2 helices and M2-M3 loop regions were free to move, whereas the outer (M1, M3, M4) helix bundle was backbone restrained. The M2 helices largely retain their hydrogen-bonding pattern throughout the simulation, with some distortions in the helical end and loop regions. All of the M2 helices exhibit bending motions, with the hinge point in the vicinity of the central hydrophobic gate region (corresponding to residues alphaL251 and alphaV255). The bending motions of the M2 helices lead to a degree of dynamic narrowing of the pore in the region of the proposed hydrophobic gate. Calculations of Born energy profiles for various structures along the simulation trajectory suggest that the conformations of the M2 bundle sampled correspond to a closed conformation of the channel. Principal components analyses of each of the M2 helices, and of the five-helix M2 bundle, reveal concerted motions that may be relevant to channel function. Normal mode analyses using the anisotropic network model reveal collective motions similar to those identified by principal components analyses.

Original publication




Journal article


Biophys J

Publication Date





3321 - 3333


Amino Acid Sequence, Animals, Anisotropy, Biophysics, Cell Membrane, Computer Simulation, Databases, Protein, Hydrogen Bonding, Ions, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Principal Component Analysis, Protein Binding, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Receptors, Nicotinic, Sequence Homology, Amino Acid, Sodium, Software, Time Factors, Torpedo, Water