Effective diffusion coefficients of K+ and Cl- ions in ion channel models

We have used molecular dynamics simulations, corresponding to a total simul ation time of 11 ns, to investigate the effective short-time local diffusio n coefficient of potassium and chloride ions in a series of model ion chann els. These models, which include channels formed by the fungal peptide alam ethicin, by a synthetic leucine-serine peptide, and by the pore-lining M2 h elix bundle of the nicotinic acetylcholine receptor, have a range of differ ent secondary structures, diameters and hydrophobicities. We find that the diffusion coefficients of both ions are appreciably reduced in the narrower channels, the extent of the reduction being similar for both the anionic a nd cationic species. This suggests that a difference in mobility cannot be the source of the ion selectivity exhibited by some of the channels (for ex ample, the leucine-serine peptide). We find no evidence for a reduction in mobility of either ion in the nAChR model. These results are broadly in lin e with a previous similar study of Na+ ions, and may be useful in Poisson-N ernst-Planck, Eyring rate theory or Brownian dynamics calculations of chann el conductance. (C) 1999 Elsevier Science B.V. All rights reserved.