Ion solvation and structural stability in a sodium channel

The stability and ion binding properties of the homo-tetrameric pore domain of a prokaryotic, voltage-gated sodium channel are studied by extensive all-atom molecular dynamics simulations, with the channel protein being embedded in a fully hydrated lipid bilayer. It is found that Na+ ion presents in a mostly hydrated state inside the wide pore of the selectivity filter of the sodium channel, in sharp contrast to the nearly fully dehydrated state for K+ ions in potassium channels. Our results also indicate that Na+ ions make contact with only one or two out of the four polypeptide chains forming the selectivity filter, and surprisingly, the selectivity filter exhibits robust stability for various initial ion configurations even in the absence of ions. These findings are quite different from those in potassium channels. Furthermore, an electric field above 0.5 V/nm is suggested to be able to induce Na+ permeation through the selectivity filter.

Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations

Hu Qiu, Rong Shen, Wanlin Guo

State Key Laboratory of Mechanics and Control of Mechanical Structures, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China

Received 18 November 2011. Revised 23 May 2012. Accepted 4 June 2012. Available online 11 June 2012.

► We study the stability and ion binding properties of a sodium ion channel (NavAb). ► Sodium ions in the selectivity filter are highly hydrated. ► Sodium ions bind with the channel protein in an asymmetric manner. ► Robust stability of the NavAb channel ► Ion permeation through NavAb can be induced by an electric field above 0.5 V/nm.

Sodium channels; Molecular dynamics; Structural stability; Ion hydration

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