Bubbles, gating, and anesthetics in ion channels

Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction

The theoretical prediction of water drying transitions near nonpolar surfaces has stimulated an intensive search for biological processes exploiting this extreme form of hydrophobicity. Here we quantitatively demonstrate that drying of a hydrophobic constriction is the major determinant of ion conductance in the GLIC pentameric ion channel. Molecular-dynamics simulations show that in the closed state, the channel conductance is ∼12 orders-of-magnitude lower than in the open state. This large drop in conductance is remarkable because even in the functionally closed conformation the pore constriction remains wide enough for the passage of sodium ions, aided by a continuous bridge of ∼12 water molecules. However, we find that the free energy cost of hydrating the hydrophobic gate is large, accounting almost entirely for the energetic barrier blocking ion passage. The free energies of transferring a sodium ion into a prehydrated gate in functionally closed and open states differ by only 1.2 kcal/mol, compared to an 11 kcal/mol difference in the costs of hydrating the hydrophobic gate. Conversely, ion desolvation effects play only minor roles in GLIC ion channel gating. Our simulations help rationalize experiments probing the gating kinetics of the nicotinic acetylcholine receptor in response to mutations of pore-lining residues. The molecular character and phase behavior of water should thus be included in quantitative descriptions of ion channel gating.

Electric-field-induced wetting and dewetting in single hydrophobic nanopores

The behaviour of water in nanopores is very different from that of bulk water. Close to hydrophobic surfaces, the water density has been found to be lower than in the bulk, and if confined in a sufficiently narrow hydrophobic nanopore, water can spontaneously evaporate. Molecular dynamics simulations have suggested that a nanopore can be switched between dry and wet states by applying an electric potential across the nanopore membrane. Nanopores with hydrophobic walls could therefore create a gate system for water, and also for ionic and neutral species. Here, we show that single hydrophobic nanopores can undergo reversible wetting and dewetting due to condensation and evaporation of water inside the pores. The reversible process is observed as fluctuations between conducting and non-conducting ionic states and can be regulated by a transmembrane electric potential.

Voltage-gated hydrophobic nanopores

Hydrophobicity is a fundamental property that is responsible for numerous physical and biophysical aspects of molecular interactions in water. Peculiar behavior is expected for water in the vicinity of hydrophobic structures, such as nanopores. Indeed, hydrophobic nanopores can be found in two distinct states, dry and wet, even though the latter is thermodynamically unstable. Transitions between these two states are kinetically hindered in long pores but can be much faster in shorter pores. As it is demonstrated for the first time in this paper, these transitions can be induced by applying a voltage across a membrane with a single hydrophobic nanopore. Such voltage-induced gating in single nanopores can be realized in a reversible manner through electrowetting of inner walls of the nanopores. The resulting I-V curves of such artificial hydrophobic nanopores mimic biological voltage-gated channels.

Hydration properties of mechanosensitive channel pores define the energetics of gating

Opening of ion channels directly by tension in the surrounding membrane appears to be the most ancient and simple mechanism of gating. Bacterial mechanosensitive channels MscL and MscS are the best-studied tension-gated nanopores, yet the key physical factors that define their gating are still hotly debated. Here we present estimations, simulations and experimental results showing that hydration of the pore might be one of the major parameters defining the thermodynamics and kinetics of mechanosensitive channel gating. We associate closing of channel pores with complete dehydration of the hydrophobic gate (occlusion by 'vapor lock') and formation of two water-vapor interfaces above and below the constriction. The opening path is the expansion of these interfaces, ultimately leading to wetting of the hydrophobic pore, which does not appear to be the exact reverse of the closing path, thus producing hysteresis. We discuss specifically the role of polar groups (glycines) buried in narrow closed conformations but exposed in the open states that change the wetting characteristics of the pore lining and stabilize conductive states of the channels.

Ionic capillary evaporation in weakly charged nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.

New insights into the molecular mechanisms of general anaesthetics

This paper provides new insights of how general anaesthetic research should be carried out in the future by an analysis of what we know, what we do not know and what we would like to know. I describe previous hypotheses on the mechanism of action of general anaesthetics (GAs) involving membranes and protein receptors. I provide the reasons why the GABA type A receptor, the NMDA receptor and the glycine receptor are strong candidates for the sites of action of GAs. I follow with a review on attempts to provide a mechanism of action, and how future research should be conducted with the help of physical and chemical methods.

Principles of conduction and hydrophobic gating in K+ channels

We present the first atomic-resolution observations of permeation and gating in a K(+) channel, based on molecular dynamics simulations of the Kv1.2 pore domain. Analysis of hundreds of simulated permeation events revealed a detailed conduction mechanism, resembling the Hodgkin-Keynes "knock-on" model, in which translocation of two selectivity filter-bound ions is driven by a third ion; formation of this knock-on intermediate is rate determining. In addition, at reverse or zero voltages, we observed pore closure by a novel "hydrophobic gating" mechanism: A dewetting transition of the hydrophobic pore cavity-fastest when K(+) was not bound in selectivity filter sites nearest the cavity-caused the open, conducting pore to collapse into a closed, nonconducting conformation. Such pore closure corroborates the idea that voltage sensors can act to prevent pore collapse into the intrinsically more stable, closed conformation, and it further suggests that molecular-scale dewetting facilitates a specific biological function: K(+) channel gating. Existing experimental data support our hypothesis that hydrophobic gating may be a fundamental principle underlying the gating of voltage-sensitive K(+) channels. We suggest that hydrophobic gating explains, in part, why diverse ion channels conserve hydrophobic pore cavities, and we speculate that modulation of cavity hydration could enable structural determination of both open and closed channels.

Structural basis of activation of cys-loop receptors: the extracellular-transmembrane interface as a coupling region

Cys-loop receptors mediate rapid transmission throughout the nervous system by converting a chemical signal into an electric one. They are pentameric proteins with an extracellular domain that carries the transmitter binding sites and a transmembrane region that forms the ion pore. Their essential function is to couple the binding of the agonist at the extracellular domain to the opening of the ion pore. How the structural changes elicited by agonist binding are propagated through a distance of 50 A to the gate is therefore central for the understanding of the receptor function. A step forward toward the identification of the structures involved in gating has been given by the recently elucidated high-resolution structures of Cys-loop receptors and related proteins. The extracellular-transmembrane interface has attracted attention because it is a structural transition zone where beta-sheets from the extracellular domain merge with alpha-helices from the transmembrane domain. Within this zone, several regions form a network that relays structural changes from the binding site toward the pore, and therefore, this interface controls the beginning and duration of a synaptic response. In this review, the most recent findings on residues and pairwise interactions underlying channel gating are discussed, the main focus being on the extracellular-transmembrane interface.

Atypical mechanism of conduction in potassium channels

Potassium channels can conduct passively K+ ions with rates of up to approximately 10(8) ions per second at physiological conditions, and they are selective to these species by a factor of 10(4) over Na+ ions. Ion conduction has been proposed to involve transitions between 2 main states, with 2 or 3 K+ ions occupying the selectivity filter separated by an intervening water molecule. The largest free energy barrier of such a process was reported to be of the order of 2-3 kcal mol(-1). Here, we present an alternative mechanism for conduction of K+ in potassium channels where site vacancies are involved, and we propose that coexistence of several ion permeation mechanisms is energetically possible. Conduction can be described as a more anarchic phenomenon than previously characterized by the concerted translocations of K+-water-K+.

The effect of hydrogen bonding on the solvent-mediated interaction of composite plates

When two solute particles in water sufficiently approach each other, the disruption of water-water hydrogen bonds in their first hydration layers gives rise to an additional contribution to their overall interaction. Here we present a probabilistic approach to examining interactions between two identical parallel plates whereof the surfaces are covered with uniformly distributed hydrophobic and hydrophilic sites. The proposed approach allows one to determine the average number of hydrogen bonds per water molecule in the first hydration shell of a plate. Because of the constraint imposed by the proximity to the plate, a water molecule forms less hydrogen bond in this shell than in the bulk medium. As a result, the water molecules prefer the latter to the former, even though a bond is stronger in the former than in the latter. The interplay of these factors results in an additional contribution to the overall plate interaction which is attractive and naturally short-range, appearing only when the distance between the plates is smaller than five lengths of a hydrogen bond. At a given distance, it monotonically increases from 0 to its maximum value as the fraction of hydrophobic surface area on a plate increases from 0 to 1. When this fraction is 0.5, this contribution can be up to two orders of magnitude larger than the van der Waals interaction (depending on the water density in the vicinity of a plate).

Nanoporous silica-water interfaces studied by sum-frequency vibrational spectroscopy

Using sum-frequency vibrational spectroscopy, we found that water structure at nanoporous silica/water interfaces depended on the nanoporous film structure. For a periodic, self-assembled nanoporous film with monosized 2 nm pores occupying 20% of the top surface area, the surface vibrational spectrum was dominated by water in contact with silica, bare or covered by silane, at the top surface. It resembled the spectral characteristic of the hydrophilic water/silica or the hydrophobic water/silane interface. For a fractal nanoporous film with pores ranging from 5 to 50 nm in size occupying 90% of the top surface, the spectrum for a trimethyl silane-coated superhydrophobic porous film resembled largely that of a water/air interface. Only when the silane was completely removed would the spectrum revert to that characteristic of a hydrophilic water/silica interface. The surface charging behaviors of the bare nanoporous films in water with different pH were monitored by spectroscopic measurements and atomic force microscopy force measurements. The point of zero charge for the periodic porous film is around pH 2, similar to that of the flat silica surface. The point of zero charge could only be determined to be pH<6 for the fractal porous film because the thin fractal solid network limited the amount of surface charge and therefore, the accuracy of the measurements.

Synthetic proton-gated ion channels via single solid-state nanochannels modified with responsive polymer brushes

The creation of switchable and tunable nanodevices displaying transport properties similar to those observed in biological pores poses a major challenge in molecular nanotechnology. Here, we describe the construction of a fully "abiotic" nanodevice whose transport properties can be accurately controlled by manipulating the proton concentration in the surrounding environment. The ionic current switching characteristics displayed by the nanochannels resemble the typical behavior observed in many biological channels that fulfill key pH-dependent transport functions in living organisms, that is, the nanochannel can be switched from an "off" state to an "on" state in response to a pH drop. The construction of such a chemical nanoarchitecture required the integration of stable and ductile macromolecular building blocks constituted of pH-responsive poly(4-vinyl pyridine) brushes into solid state nanopores that could act as gate-keepers managing and constraining the flow of ionic species through the confined environment. In this context, we envision that the integration of environmental stimuli-responsive brushes into solid-state nanochannels would provide a plethora of new chemical alternatives for molecularly design robust signal-responsive "abiotic" devices mimicking the function of proton-gated ion channels commonly encountered in biological membranes.

Dewetting and hydrophobic interaction in physical and biological systems

Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations, and experiments pertaining to large-scale hydrophobicity in physical and biomolecular systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we cannot review all the significant and interesting work in this active field.

Ion channel gates: comparative analysis of energy barriers

The energetic profile of an ion translated along the axis of an ion channel should reveal whether the structure corresponds to a functionally open or closed state of the channel. In this study, we explore the combined use of Poisson-Boltzmann electrostatic calculations and evaluation of van der Waals interactions between ion and pore to provide an initial appraisal of the gating state of a channel. This approach is exemplified by its application to the bacterial inward rectifier potassium channel KirBac3.1, where it reveals the closed gate to be formed by a ring of leucine (L124) side chains. We have extended this analysis to a comparative survey of gating profiles, including model hydrophobic nanopores, the nicotinic acetylcholine receptor, and a number of potassium channel structures and models. This enables us to identify three gating regimes, and to show the limitation of this computationally inexpensive method. For a (closed) gate radius of 0.4 nm < R < 0.8 nm, a hydrophobic gate may be present. For a gate radius of 0.2 nm < R < 0.4 nm, both electrostatic and van der Waals interactions will contribute to the barrier height. Below R = 0.2 nm, repulsive van der Waals interactions are likely to dominate, resulting in a sterically occluded gate. In general, the method is more useful when the channel is wider; for narrower channels, the flexibility of the protein may allow otherwise-unsurmountable energetic barriers to be overcome.

Is a new paradigm needed to explain how inhaled anesthetics produce immobility?

A paradox arises from present information concerning the mechanism(s) by which inhaled anesthetics produce immobility in the face of noxious stimulation. Several findings, such as additivity, suggest a common site at which inhaled anesthetics act to produce immobility. However, two decades of focused investigation have not identified a ligand- or voltage-gated channel that alone is sufficient to mediate immobility. Indeed, most putative targets provide minimal or no mediation. For example, opioid, 5-HT3, gamma-aminobutyric acid type A and glutamate receptors, and potassium and calcium channels appear to be irrelevant or play only minor roles. Furthermore, no combination of actions on ligand- or voltage-gated channels seems sufficient. A few plausible targets (e.g., sodium channels) merit further study, but there remains the possibility that immobilization results from a nonspecific mechanism.