Electrostatics studies and molecular dynamics simulations of a homology model of the Shaker K⁺ channel pore

A homology model of the pore domain of the Shaker K⁺ channel has been constructed using a bacterial K⁺ channel, KcsA, as a template structure. The model is in agreement with mutagenesis and sequence variability data. A number of structural features are conserved between the two channels, including a ring of tryptophan sidechains on the outer surface of the pore domain at the extracellular end of the helix bundle, and rings of acidic sidechains close to the extracellular mouth of the channel. One of these rings, that formed by four Asp447 sidechains at the mouth of the Shaker pore, is shown by pK_A calculations to be incompletely ionized at neutral pH. The potential energy profile for a K⁺ ion moved along the central axis of the Shaker pore domain model selectivity filter reveals a shallow well, the depth of which is modulated by the ionization state of the Asp447 ring. This is more consistent with the high cation flux exhibited by the channel in its conductance value of 19 pS.