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Biophys J, November 1999, p. 2502-2516, Vol. 77, No. 5

Molecular Dynamics Study of the KcsA Potassium Channel

Toby W. Allen,* Serdar Kuyucak,# and Shin-Ho Chung*

 *Protein Dynamics Unit, Department of Chemistry, and  #Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, A.C.T. 0200, Australia

The structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions. Self-diffusion of water within the narrow selectivity filter is found to be reduced by an order of magnitude from bulk levels, whereas the wider hydrophobic section of the pore maintains near-bulk self-diffusion. Simulations examining multiple ion configurations suggest a two-ion channel. Ion diffusion is found to be reduced to ~<FR><NU>1</NU><DE>3</DE></FR> of bulk diffusion within the selectivity filter. The reduced ion mobility does not hinder the passage of ions, as permeation appears to be driven by Coulomb repulsion within this multiple ion channel.

Biophys J, November 1999, p. 2502-2516, Vol. 77, No. 5
© 1999 by the Biophysical Society   0006-3495/99/11/2502/15  $2.00


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