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

Abstract

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) Å 2 ps −1 in bulk water, is found to be reduced to as little as 0.02(1) Å 2 ps −1 in the narrower channels, and to about 0.10(5) Å 2 ps −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.