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Biophys J, December 1998, p. 2767-2782, Vol. 75, No. 6

Dynamic Properties of Na+ Ions in Models of Ion Channels: A Molecular Dynamics Study

G. R. Smith and M. S. P. Sansom

Laboratory of Molecular Biophysics, University of Oxford, Oxford OX1 3QU, United Kingdom

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) Å2ps-1 in bulk water, is found to be reduced to as little as 0.02(1) Å2ps-1 in the narrower channels, and to about 0.10(5) Å2ps-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.

Biophys J, December 1998, p. 2767-2782, Vol. 75, No. 6
© 1998 by the Biophysical Society   0006-3495/98/12/2767/16  $2.00


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