Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels

Abstract

Water is at the heart of almost all biological phenomena, without which no life that we know of would have been possible. It is a misleadingly complex liquid that exists in near coexistence with the vapor phase under ambient conditions. Confinement within a hydrophobic cavity can tip this balance enough to drive a cooperative dewetting transition. For a nanometer-scale pore, the dewetting transition leads to a stable dry state that is physically open but impermeable to ions. This phenomenon is often referred to as hydrophobic gating. Numerous transmembrane protein ion channels have now been observed to utilize hydrophobic gating in their activation and regulation. Here, we review recent theoretical, simulation, and experimental studies that together have started to establish the principles of hydrophobic gating and discuss how channels of various sizes, topologies, and biological functions can utilize these principles to control the thermodynamic properties of water within their interior pores for gating and regulation. Exciting opportunities remain in multiple areas, particularly on direct experimental detection of hydrophobic dewetting in biological channels and on understanding how the cell may control the hydrophobic gating in regulation of ion channels.

FIG. 1.

Hydration and ion permeability of nanopores. (a) Intermittent water fluctuation within cylindrical hydrophobic nanopores of different diameter. (b) Levels of hydration of hydrophobic, semi-hydrophobic, and hydrophilic pores of different diameter. (c) Illustration of hydrophobic gating in a model nanopore. The dashed squared box shows the dewetted region that blocks the permeation of ions (blue and red spheres). (d) Dewetting transitions (top panel) block ion permeation (lower panels). Figures are obtained with permission from P. Aryal, M. S. P. Sansom, and S. J. Tucker, J. Mol. Biol. 427, 121 (2015). Copyright 2015 Author(s), licensed under a Creative Commons Attribution 3.0 Unported License; O. Beckstein and M. S. P. Sansom, Phys. Biol. 1, 42 (2004). Copyright 2004 IOP Publishing; and Rao et al., Proc. Natl. Acad. Sci. U. S. A. 116, 13989 (2019). Copyright 2019 Author(s), licensed under a Creative Commons Attribution 4.0 license.

FIG. 2.

Ion conduction pathways in four different potassium channels. Shown is a longitudinal section of the pore central region with carbon and sulfur atoms in yellow and the hydrophilic atoms in red. The position of the channel within the membrane has been pinpointed by dotted lines. The selectivity filters are located at narrowest portions, below which are nm-scale interior pore cavities (circled). The figure is obtained with permission from P. Aryal, M. S. P. Sansom, and S. J. Tucker, J. Mol. Biol. 427, 121 (2015). Copyright 2015 Author(s), licensed under a Creative Commons Attribution 3.0 Unported License.

FIG. 3.

Hydrophobic gating of the 5-HT3 receptor. (a) Cross section of the staring structure emphasizing the hydrated state of the pore region (red circle) (PDB ID: 4PIR). Protein (gray surface) is embedded in the membrane lipid, and only two subunits are shown for visual clarity. Water oxygen atoms are shown as blue spheres and lipid in liquorice. Only the TM domain has been shown. (b) Snapshots of the dewetted pore observed during the MD simulation showing lack of physical constriction. (c) Density of water in the pore region during the MD simulation showing the persistent and fast depletion of water in a ∼2-nm region marked by the red arrow. The figure is obtained with permission from Klesse et al., J. Mol. Biol. 431, 3353 (2019). Copyright 2019 Author(s), licensed under a Creative Commons Attribution 4.0 license.

FIG. 4.

Conformational transitions of the pore control the hydrophobic gating. (a) Rotation of the Asn side chain in the TRPV1 channel can modulate the hydrophobicity of the pore to trigger the dewetting with limited changes in the pore shape and geometry. (b) Extracellular view of the GLIC iris-like motion of the M2 helices from open to closed states. Three Cα atoms from each subunit are shown as spheres and colored according to their position (top: red, middle: blue, and bottom: green), and the pentagon formed by these atoms is colored accordingly. The numbers indicate each pentagon edge’s length, and the bold green and red arrows show the direction of motion. These figures are obtained with permission from F. Zhu, G. Hummer, and J.-P. Changeux, Proc. Natl. Acad. Sci. U. S. A. 107, 19814 (2010). Copyright 2010 National Academy of Sciences and Kasimova et al., J. Phys. Chem. Lett. 9, 1260 (2018). Copyright 2018 American Chemical Society.

FIG. 5.

Pore conformational transition and hydrophobic gating of BK channels. (a) Packing of the neighboring helices in the metal-bound (open) and metal-free (putative closed) states with key residues shown in licorice. The location of the helix in the metal-free state has been shown as a transparent trace in the structure of the metal-bound state to illustrate the rotation (red arrow) of the helix upon metal-removal. (b) Longitudinal sections through the center of the TM domain illustrating the water exposed surfaces of the pore cavity. Nonpolar hydrocarbons, nitrogen, and charged oxygen atoms are colored in silver, blue, and red, respectively. Key hydrophobic and charged residues with drastically different pore exposures in the two states are marked with green arrows. (c) Numbers of pore water molecules during the simulation of the metal-free and metal-bound states of the human BK channel. (d) Correlation of the hydrophobicity of residue 316 (Ala in the wild-type) and gating voltage of the human BK channel. Residue 316 locates in the middle of the pore region. While hydrophobic mutations favor the closed state (increase in V_1/2), charged/polar mutants favor the open state (decrease in V_1/2). This figure is obtained with permission from Jia et al., Nat. Commun. 9, 3408 (2018). Copyright 2018 Author(s), licensed under a Creative Commons Attribution 4.0 license.

FIG. 6.

A simulation-free heuristic model for rapid identification of hydrophobic gates in channel structures. The hydration free energy (G), largely a function of the minimal pore radius and overall pore hydrophobicity, predicts the likely existence of hydrophobic gates. The figure is obtained with permission from Rao et al., Proc. Natl. Acad. Sci. U. S. A. 116, 13989 (2019). Copyright 2019 Author(s), licensed under a Creative Commons Attribution 4.0 license.

FIG. 7.

Probing the gas meniscus between a superhydrophobic surface and a hydrophobic microsphere under water using AFM. The figure is obtained with permission form Eriksson et al., ACS Nano 13, 2246 (2019). Copyright 2019 American Chemical Society.