Biophysical Journal
Volume 78, Issue 2, February 2000, Pages 557-570
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Simulations of Ion Permeation Through a Potassium Channel: Molecular Dynamics of KcsA in a Phospholipid Bilayer

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Abstract

Potassium channels enable K+ ions to move passively across biological membranes. Multiple nanosecond-duration molecular dynamics simulations (total simulation time 5 ns) of a bacterial potassium channel (KcsA) embedded in a phospholipid bilayer reveal motions of ions, water, and protein. Comparison of simulations with and without K+ ions indicate that the absence of ions destabilizes the structure of the selectivity filter. Within the selectivity filter, K+ ions interact with the backbone (carbonyl) oxygens, and with the side-chain oxygen of T75. Concerted single-file motions of water molecules and K+ ions within the selectivity filter of the channel occur on a 100-ps time scale. In a simulation with three K+ ions (initially two in the filter and one in the cavity), the ion within the central cavity leaves the channel via its intracellular mouth after ∼900 ps; within the cavity this ion interacts with the Oγ atoms of two T107 side chains, revealing a favorable site within the otherwise hydrophobically lined cavity. Exit of this ion from the channel is enabled by a transient increase in the diameter of the intracellular mouth. Such “breathing” motions may form the molecular basis of channel gating.

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