Carnevale, Vincenzo; Treptow, Werner; Klein, Michael L.
Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2504-2508, OCT 6 2011

Molecular dynamics (MD) calculations have been used to identify Na(+) binding sites in the lumen of a bacterial voltage-gated ion channel. MD trajectories have been carried out starting from the recently reported X-ray crystal structure of NavAb in a closed or inactivated conformation. The X-ray structure is stable on the time scale of the MD simulations when equilibrated in a fully hydrated lipid bilayer. Exposure to a 70 mM NaCl solution and a trajectory spanning similar to 0.15 mu s reveals two locations in the selectivity filter (SF) of the channel, with Na(+) coordinated to both water molecules and negatively charged protein residues. The nature of the Na(+) dynamic hydration environment has been explored, and surprisingly water seems to be able to permeate from bulk, via the SF, to the central cavity, whereas Na(+) ions remain near their primary SF locations, a finding that contrasts with the situation that obtains for potassium channels. SECTION: Biophysical Chemistry

DOI:10.1021/jz2011379

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