Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction

Abstract

The mechanism of ion conduction by potassium channels is one of the central issues in physiology. In particular, it is still unclear how the ion concentration and the membrane voltage drive ion conduction. We have investigated the dynamics of the ion conduction processes in the Kv1.2 pore domain, by molecular dynamics (MD) simulations with several different voltages and ion concentrations. By focusing on the detailed ion movements through the pore including selectivity filter (SF) and cavity, we found two major conduction mechanisms, called the III-IV-III and III-II-III mechanisms, and the balance between the ion concentration and the voltage determines the mechanism preference. In the III-IV-III mechanism, the outermost ion in the pore is pushed out by a new ion coming from the intracellular fluid, and four-ion states were transiently observed. In the III-II-III mechanism, the outermost ion is pulled out first, without pushing by incoming ions. Increases in the ion concentration and voltage accelerated ion conductions, but their mechanisms were different. The increase in the ion concentrations facilitated the III-IV-III conductions, while the higher voltages increased the III-II-III conductions, indicating that the pore domain of potassium channels permeates ions by using two different driving forces: a push by intracellular ions and a pull by voltage.

Fig 1. The simulation system and the definitions of the ion-binding sites in the pore.

(A) The entire structure of our simulation system. The cyan ribbons represent the pore domain of homo-tetrameric Kv1.2 (part of the structure PDB-ID: 2r9r), and only two of the four subunits are shown for clarity. Green and gray balls are K⁺ and Cl⁻ ions, respectively. Cyan dots are atoms composing the POPE lipid bilayer. The oxygen and hydrogen atoms of the water molecules are shown as red and white dots, respectively. In the figure, the bottom and top correspond to the intra- and extra-cellular sides across the membrane, respectively. During the simulations, a constant electric field was applied along the direction from the intra- to extracellular side. (B) The structure of the SF and the definition of the ion-binding sites. The sticks indicate the structure of the signature sequence (TVGYG) of two of the four subunits. The ion-binding sites were defined by certain threshold values along the pore axis coordinates (see the main text). (C) Density plot of K⁺ ions (the green line) and water molecules (the blue line) under the +1,226 mV conditions.

Fig 2. The ion-binding state graphs at (A) +460 mV and (B) + 1,073 mV.

The nodes indicate the ion-binding states of the pore, and the edges indicate the transitions between them. These figures summarize the ion-binding states observed during the simulations.

Fig 3. Motions of K⁺ ions in the pore axis at (A) +460 mV and (B) +1,073 mV.

The colors of the plots indicate the identity of each K⁺ ion.

Fig 4. Ion conduction processes under negative (-1,380 mV) voltage.

(A) Ion-binding state graph. (B and C) Snapshots of the K:0:2:4 and K:0:2:5 states, respectively. (D) The trajectory of K⁺ ions in the pore axis.

Fig 5. The ratios of the ion conduction mechanisms observed during the simulations.

The orange and cyan bars indicate the ratios of the III-IV-III and III-II-III conductions, respectively. The orange and cyan values along with each bar indicate observed number of ion conduction events in each mechanism (note that the length of the simulation trajectories are not the same among the trajectories; the two trajectories, 150 mM with +920 mV and 600 mM with +920 mV, are 1.0 μs and others are 0.5 μs). The error bars show the bootstrap errors of the ion current (black) and the ratio of the mechanisms (green). (A) The dependency of the ion conduction mechanisms on the membrane voltage. (B) The dependency of the ion conduction mechanisms on the ion concentrations, taken from our previous study [28].