Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels

Abstract

Molecular dynamics simulations are carried out to obtain estimates of diffusion coefficients of biologically important Na +, K +, Ca 2+ and Cl − ions in hydrophobic cylindrical channels with varying radii and large reservoirs. Calculations for the cylindrical channels are compared to those for the KcsA potassium channel, for which the protein structure has recently been determined from X-ray diffraction experiments. Our results show that ion diffusion is maintained at reasonably high levels even within narrow channels, and does not support the very small diffusion coefficients used in some continuum models in order to fit experimental data. The present estimates of ion diffusion coefficients are useful in the calculation of channel conductance using the Poisson–Nernst–Planck theory, or Brownian dynamics.