Condensed Matter Physics, 2015, vol. 18, No. 1, p. 13601:1-14
DOI:10.5488/CMP.18.13601           arXiv:1504.00814

Title: Energetics of ion competition in the DEKA selectivity filter of neuronal sodium channels
  D. Boda (Department of Physical Chemistry, University of Pannonia, P. O. Box 158, Veszprém, H-8201, Hungary) ,
  G. Leaf (Mathematics and Computer Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA) ,
  J. Fonseca (The Network for Computational Nanotechnology, Purdue University, 1205 West State Street, West Lafayette, IN 47907, USA) ,
  B. Eisenberg (Department of Molecular Biophysics and Physiology, Rush University Medical Center, 1750 West Harrison St., Chicago, IL 60612 USA)

The energetics of ionic selectivity in the neuronal sodium channels is studied. A simple model constructed for the selectivity filter of the channel is used. The selectivity filter of this channel type contains aspartate (D), glutamate (E), lysine (K), and alanine (A) residues (the DEKA locus). We use Grand Canonical Monte Carlo simulations to compute equilibrium binding selectivity in the selectivity filter and to obtain various terms of the excess chemical potential from a particle insertion procedure based on Widom's method. We show that K+ ions in competition with Na+ are efficiently excluded from the selectivity filter due to entropic hard sphere exclusion. The dielectric constant of protein has no effect on this selectivity. Ca2+ ions, on the other hand, are excluded from the filter due to a free energetic penalty which is enhanced by the low dielectric constant of protein.

Key words: Monte Carlo, primitive model electrolytes, ion channel, selectivity
PACS: 61.20.Qg, 68.03.-g, 81.05.Rm, 61.20.Ja, 07.05.Tp

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