Electronic Polarization Leads to a Drier Dewetted State for Hydrophobic Gating in the Big Potassium Channel

Abstract

In the hydrophobic gating mechanism proposed for some ion channels, ion permeation is not blocked by the physical dimension of the channel pore but by its dewetted state which constitutes the energetic bottleneck. A major source of uncertainty in the mechanism is that the dewetted state was not observed in experiments and only probed in simulations using nonpolarizable force fields, which do not accurately represent the properties of confined water. Here we analyze hydration of the central cavity in the pore-gate domain of the Big Potassium channel using molecular dynamics and grand canonical Monte Carlo simulations with enhanced sampling techniques. Including polarization leads to a much drier dewetted state and a higher barrier for the transition to the wet state, suggesting more effective hydrophobic gating. The simulations also identify two backbone carbonyls at the bottom of the selectivity filter as good candidates for characterizing the dewetted state using infrared spectroscopies.

Figure 1:

The human big potassium (BK) ion channel. (a) The truncated BK structural model without the cytosolic-tail domain for the closed state from Ref. 5 embedded in a POPC bilayer for the simulation setup. (b) Illustration of the central cavity in the pore-gate domain (residues 275 to 295, and residues 310 to 326). Phosphorus atoms in POPC are shown as blue spheres, and potassium ions in the selectivity filter are shown as purple spheres.

Figure 2:

Results of molecular dynamics simulations using the CHARMM-Drude force field for the hydration level in the central cavity of the human BK channel starting from the dewetted state of the closed structural model. (a) Instantaneous number of water molecules in the cavity; (b) distribution of the number of cavity water; (c) running average for the number of cavity water. For results obtained with CHARMM36m, see Fig. S1.

Figure 3:

Binding free energy of water in the dewetted state of the central cavity in the human BK channel from grand canonical integration. (a-b) Results with the CHARMM36m force field. (c-d) Results with the CHARMM-Drude force field. For the binding free energy curves (b,d), the solid line and the shaded area represent the mean and the 95% confidence interval, respectively. For the average numbers of water in different B windows, see Fig. S5.

Figure 4:

Results of metadynamics simulations using the CHARMM-Drude force field for the hydration level in the central cavity of the human BK channel. Potential of mean force of cavity water numbers from multiple walkers metadynamics simulations is shown as the solid line and the shaded area represents the 95% confidence interval. As shown in Fig. S4, the statistical error from block average is on the order of 0.1 k_BT.

Figure 5:

Snapshots of the selectivity filter region in the (a) dewetted and (b) wet states to illustrate the distinct structural features. In the dewetted state, the backbone carbonyl groups of Met285 and Ser286 (shown in CPK) are dehydrated. An additional potassium ion (in yellow) is observed to reside in the selectivity filter to interact weakly (with distances ~5 Å) with the backbone carbonyls of Ser286. In the wet state, the carbonyl groups of Met285 and Ser286 are constantly in contact with water molecules in the cavity (those within 5 Å are shown in the licorice form). Radial distribution functions of water oxygen around backbone carbonyl groups (Met285 and Ser286), g(r), illustrate the distinct levels of solvation of these backbone groups in the dewetted (c, e) and wet (d, f) states from CHARMM-Drude simulations. The dashed lines indicate the integrated radial distribution functions, N(r). For comparison with the CHARMM36m results, see Figs. S14–S15.