Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity

Figures

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  Fig 1. Schematic illustration of the Kv channel structure. (A) A cartoon model of a subunit of the Kv channel showing the voltage-sensing domains (VSDs) (S1–S4) in yellow, the S4–S5 helical linker in green, the S5 helix in cyan, the P-helix in pink, and the S6 helix in blue. (B) Two opposite subunits of the pore domain of the Kv channel are represented by ribbons. The other two subunits have been omitted. The selectivity filter is shown in purple, and the water cavity is located below the water cavity. The hinge region in S6 helix is highlighted in red.

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  Fig 2. pKa estimates of H418 and acidic residues and two key residues in the Kv1.2 channel. (A) The pKa estimates of H418 and the acidic residues in the pore domain of the closed Kv1.2 channels. (B) Multiple sequence alignment for the pore domains of the rat Kv1 subfamily. The cylinders above the sequences denote the secondary structural information of the four helical segments. The two key conserved residues E327 and H418 are highlighted in yellow and bold font. (C) Bottom and side views of the close pore domain of the Kv1.2 channel. The four subunits are represented by different colors in the ribbon diagram. The magnified view shows the key residues E327 and H418 and their neighbors in the inner helical bundle, which are represented by the licorice and Cα balls.

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  Fig 3. Pore closure due to protonation of the two key residues E327 and H418 in the Kv1.2 channel. (A) The structures of the open and closed Kv1.2 channel. Here, the ribbons represent the pore domain of Kv1.2 channels, the blue spheres denote water molecules, and the gray spheres denote potassium ions. The upper panel illustrates the bottom view of the open and closed conformations. The lower panel shows the wetted and dewetted water cavity in the channel. Both the two opposite subunits and lipid molecules have been omitted from the lower panel. (B) The time evolution of the number of water molecules in the water cavity of the WildUnP or Ep327/Hp418 states of the Kv1.2 channel. The five individual plots in each state represent the simulation results from each trajectory of our MD simulations. In addition, the red horizontal line separates the wetted state from the dewetted state of the water cavity. (C) The distributions of the number of water molecules in the water cavity. The left region with fewer water molecules corresponds to the dewetting condition, whereas the right region with many water molecules corresponds to the wetting condition.

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  Fig 4. Straightening of the S6 helix due to protonation of the two key residues E327 and H418 in the Kv1.2 channel. (A) The detailed structures of the open (left panels) and closed (right panels) Kv1.2 channels. The upper panel illustrates the distance between the R326 and H418 residues. For the open conformation of the pore, the distance between E327 and H418 is 7.6 Å, whereas it is 14.7 Å for the closed conformation. In addition, the lower panel shows the S6 helix when it is bent (black dotted line) or straight (solid red line). Here, two neighbor subunits are displayed using purple and cyan color, respectively, while the other subunits have been omitted. (B) The probability distribution curves for the inter-subunit distances between the R326 and H418 residues of the WildUnP and Ep327/Hp418 states. (C) The probability distribution of the dihedral angles, extended by the position of the Cα atoms in L393, L400, V408, and Y415, for each state. The left half region with the angle smaller than 180° corresponds to the bent S6 helix, whereas the right half and the secondary peak is the straight S6 helix. (D) Ensembles population of log scale for the R326–H418 distances and the dihedral…