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We present simulation results for the effective diffusion coefficients of a sodium ion in a series of model ion channels of different diameters and hydrophobicities, including models of alamethicin, a leucine-serine peptide, and the M2 helix bundle of the nicotinic acetylcholine receptor. The diffusion coefficient, which in the simulations has a value of 0.15(2) A2ps-1 in bulk water, is found to be reduced to as little as 0.02(1) A2ps-1 in the narrower channels, and to about 0.10(5) A2ps-1 in wider channels such as the nicotinic acetylcholine receptor. It is anticipated that this work will be useful in connection with calculations of channel conductivity using such techniques as the Poisson-Nernst-Planck equation, Eyring rate theory, or Brownian dynamics.

Original publication




Journal article


Biophys J

Publication Date





2767 - 2782


Alamethicin, Amino Acid Sequence, Animals, Bayes Theorem, Biophysical Phenomena, Biophysics, Diffusion, In Vitro Techniques, Ion Channels, Models, Biological, Models, Molecular, Molecular Sequence Data, Peptides, Protein Conformation, Protein Structure, Secondary, Receptors, Nicotinic, Sodium, Static Electricity, Surface Properties, Thermodynamics