Coupled Ion Movement Underlies Rectification in an Inward-Rectifier K+ Channel

We studied block of the internal pore of the ROMK1 inward-rectifier K⁺ channel by Mg²⁺ and five quaternary ammoniums (tetramethylammonium, tetraethylammonium, tetrapropylammonium, tetrabutylammonium, and tetrapentylammonium). The apparent affinity of these blockers varied as a function of membrane voltage. As a consequence, the channel conducted K⁺ current more efficiently in the inward than the outward direction; i.e., inward rectification. Although the size of some monovalent quaternary ammoniums is rather large, the zδ values (which measure voltage dependence of their binding to the pore) were near unity in symmetric 100 mM K⁺. Furthermore, we observed that not only the apparent affinities of the blockers themselves, but also their dependence on membrane voltage (or zδ), varied as a function of the concentration of extracellular K⁺. These results suggest that there is energetic coupling between the binding of blocking and permeating (K⁺) ions, and that the voltage dependence of channel blockade results, at least in part, from the movement of K⁺ ions in the electrical field. A further quantitative analysis of the results explains why the complex phenomenon of inward rectification depends on both membrane voltage and the equilibrium potential for K⁺.     

Effect of cell electroporation on the conductivity of a cell suspension

An increased permeability of a cell membrane during the application of high-voltage pulses results in increased transmembrane transport of molecules that otherwise cannot enter the cell. Increased permeability of a cell membrane is accompanied by increased membrane conductivity; thus, by measuring electric conductivity the extent of permeabilized tissue could be monitored in real time. In this article the effect of cell electroporation caused by high-voltage pulses on the conductivity of a cell suspension was studied by current-voltage measurements during and impedance measurement before and after the pulse application. At the same time the percentage of permeabilized and survived cells was determined and the extent of osmotic swelling measured. For a train of eight pulses a transient increase in conductivity of a cell suspension was obtained above permeabilization threshold in low- and high-conductive medium with complete relaxation in <1 s. Total conductivity changes and impedance measurements showed substantial changes in conductivity due to the ion efflux in low-conductive medium and colloid-osmotic swelling in both media. Our results show that by measuring electric conductivity during the pulses we can detect limit permeabilization threshold but not directly permeabilization level, whereas impedance measurements in seconds after the pulse application are not suitable.     

Soft perforation of planar bilayer lipid membranes of dipalmitoylphosphatidylcholine at the temperature of the phase transition from the liquid crystalline to the gel state

In contrast to the widely used method of electroporation, the method of soft perforation of lipid bilayers is proposed. It is based on the structural rearrangement of the lipid bilayer formed from disaturated phospholipids at the temperature of the phase transition from the liquid crystalline state to the gel state. This allows us to obtain a lipid pore population without the use of a strong electric field. It is shown that the planar lipid bilayer membrane (pBLM) formed from dipalmitoylphosphatidylcholine in 1 M LiCl aqueous solution exhibits the appearance of up to 50 lipid pores per 1 mm² of membrane surface, with an average single pore conductivity of 31±13 nS. The estimation of a single pore radius carried out with water-soluble poly(ethylene glycol)s (PEGs) showed that the average pore radius ranged between 1.0–1.7 nm. It was found experimentally that PEG-1450, PEG-2000, and PEG-3350 should be in a position to block the single pore conductivity completely, while PEG-6000 fully restored the ionic conductivity. The similarity of these PEG effects to ionic conductivity in protein pores makes it possible to suggest that the partition of the PEG molecules between the pore and the bulk solution does not depend on the nature of the chemical groups located in the pore wall.     

Lack of Negatively Charged Residues at the External Mouth of Kir2.2 Channels Enable the Voltage-Dependent Block by External Mg2+

Kir channels display voltage-dependent block by cytosolic cations such as Mg²⁺ and polyamines that causes inward rectification. In fact, cations can regulate K channel activity from both the extracellular and intracellular sides. Previous studies have provided insight into the up-regulation of Kir channel activity by extracellular K⁺ concentration. In contrast, extracellular Mg²⁺ has been found to reduce the amplitude of the single-channel current at milimolar concentrations. However, little is known about the molecular mechanism of Kir channel blockade by external Mg²⁺ and the relationship between the Mg²⁺ blockade and activity potentiation by permeant K⁺ ions. In this study, we applied an interactive approach between theory and experiment. Electrophysiological recordings on Kir2.2 and its mutants were performed by heterologous expression in Xenopus laevis oocytes. Our results confirmed that extracellular Mg²⁺ could reduce heterologously expressed WT Kir2.2 currents in a voltage dependent manner. The kinetics of inhibition and recovery of Mg²⁺ exhibit a 3∼4s time constant. Molecular dynamics simulation results revealed a Mg²⁺ binding site located at the extracellular mouth of Kir2.2 that showed voltage-dependent Mg²⁺ binding. The mutants, G119D, Q126E and H128D, increased the number of permeant K⁺ ions and reduced the voltage-dependent blockade of Kir2.2 by extracellular Mg²⁺.     

Buffered diffusion around a spherical proton pumping cell: a theoretical analysis

H⁺ ions are a substrate of many active and passive membrane transporters in all cells. Absolute proton fluxes are often quantified using intracellular pH sensitive microelectrodes or pH sensitive dyes. These measurements, however, rely on a priori estimates of the intracellular buffer capacity and on the assumption of diffusive equilibrium inside the cell. Here, assuming local equilibrium of protons with a single mobile buffer, we model the diffusion of H⁺ in the extracellular medium around an H⁺ pumping cell to estimate the expected pH changes as a function of time, distance from the cell, extracellular buffer capacity, and the absolute proton flux across the membrane. In particular, using accurate numerical simulation, we gauge the range of validity of an explicit, analytical solution of the linearized, nonstationary diffusion equation. Our results provide a framework to quantify the absolute membrane proton flux, if spatiotemporal information about the extracellular pH change is available, e.g., using imaging of pH dependent fluorescent dyes.     

Interaction between the Pore and a Fast Gate of the Cardiac Sodium Channel

Permeant ions affect a fast gating process observed in human cardiac sodium channels (Townsend, C., H.A. Hartmann, and R. Horn. 1997. J. Gen. Physiol. 110:11–21). Removal of extracellular permeant ions causes a reduction of open probability at positive membrane potentials. These results suggest an intimate relationship between the ion-conducting pore and the gates of the channel. We tested this hypothesis by three sets of manipulations designed to affect the binding of cations within the pore: application of intracellular pore blockers, mutagenesis of residues known to contribute to permeation, and chemical modification of a native cysteine residue (C373) near the extracellular mouth of the pore. The coupling between extracellular permeant ions and this fast gating process is abolished both by pore blockers and by a mutation that severely affects selectivity. A more superficial pore mutation or chemical modification of C373 reduces single channel conductance while preserving both selectivity of the pore and the modulatory effects of extracellular cations. Our results demonstrate a modulatory gating role for a region deep within the pore and suggest that the structure of the permeation pathway is largely preserved when a channel is closed.     

The Third Sodium Binding Site of Na,K-ATPase Is Functionally Linked to Acidic pH-Activated Inward Current

Sodium- and potassium-activated adenosine triphosphatases (Na,K-ATPase) is the ubiquitous active transport system that maintains the Na⁺ and K⁺ gradients across the plasma membrane by exchanging three intracellular Na⁺ ions against two extracellular K⁺ ions. In addition to the two cation binding sites homologous to the calcium site of sarcoplasmic and endoplasmic reticulum calcium ATPase and which are alternatively occupied by Na⁺ and K⁺ ions, a third Na⁺-specific site is located close to transmembrane domains 5, 6 and 9, and mutations close to this site induce marked alterations of the voltage-dependent release of Na⁺ to the extracellular side. In the absence of extracellular Na⁺ and K⁺, Na,K-ATPase carries an acidic pH-activated, ouabain-sensitive “leak” current. We investigated the relationship between the third Na⁺ binding site and the pH-activated current. The decrease (in E961A, T814A and Y778F mutants) or the increase (in G813A mutant) of the voltage-dependent extracellular Na⁺ affinity was paralleled by a decrease or an increase in the pH-activated current, respectively. Moreover, replacing E961 with oxygen-containing side chain residues such as glutamine or aspartate had little effect on the voltage-dependent affinity for extracellular Na⁺ and produced only small effects on the pH-activated current. Our results suggest that extracellular protons and Na⁺ ions share a high field access channel between the extracellular solution and the third Na⁺ binding site.     

Binding of kappa-conotoxin PVIIA to Shaker K+ channels reveals different K+ and Rb+ occupancies within the ion channel pore

The x-ray structure of the KcsA channel at different [K(+)] and [Rb(+)] provided insight into how K(+) channels might achieve high selectivity and high K(+) transit rates and showed marked differences between the occupancies of the two ions within the ion channel pore. In this study, the binding of kappa-conotoxin PVIIA (kappa-PVIIA) to Shaker K(+) channel in the presence of K(+) and Rb(+) was investigated. It is demonstrated that the complex results obtained were largely rationalized by differences in selectivity filter occupancy of this 6TM channels as predicted from the structural work on KcsA. kappa-PVIIA inhibition of the Shaker K(+) channel differs in the closed and open state. When K(+) is the only permeant ion, increasing extracellular [K(+)] decreases kappa-PVIIA affinity for closed channels by decreasing the "on" binding rate, but has no effect on the block of open channels, which is influenced only by the intracellular [K(+)]. In contrast, extracellular [Rb(+)] affects both closed- and open-channel binding. As extracellular [Rb(+)] increases, (a) binding to the closed channel is slightly destabilized and acquires faster kinetics, and (b) open channel block is also destabilized and the lowest block seems to occur when the pore is likely filled only by Rb(+). These results suggest that the nature of the permeant ions determines both the occupancy and the location of the pore site from which they interact with kappa-PVIIA binding. Thus, our results suggest that the permeant ion(s) within a channel pore can determine its functional and pharmacological properties.     

Interactions between Impermeant Blocking Ions in the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel Pore: Evidence for Anion-Induced Conformational Changes

It is well known that extracellular Cl⁻ ions can weaken the inhibitory effects of intracellular open channel blockers in the cystic fibrosis transmembrane conductance regulator (CFTR) Cl⁻ channel pore. This effect is frequently attributed to repulsive ion-ion interactions inside the pore. However, since Cl⁻ ions are permeant in CFTR, it is also possible that extracellular Cl⁻ ions are directly competing with intracellular blocking ions for a common binding site; thus, this does not provide direct evidence for multiple, independent anion binding sites in the pore. To test for the possible through-space nature of ion-ion interactions inside the CFTR pore, we investigated the interaction between impermeant anions applied to either end of the pore. We found that inclusion of low concentrations of impermeant Pt(NO₂)₄²⁻ ions in the extracellular solution weaken the blocking effects of three different intracellular blockers [Pt(NO₂)₄²⁻, glibenclamide and 5-nitro-2-(3-phenylpropylamino)benzoic acid] without affecting their apparent voltage dependence. However, the effects of extracellular Pt(NO₂)₄²⁻ ions are too strong to be accounted for by simple competitive models of ion binding inside the pore. In addition, extracellular Fe(CN)₆³⁻ ions, which do not appear to enter the pore, also weaken the blocking effects of intracellular Pt(NO₂)₄²⁻ ions. In contrast to previous models that invoked interactions between anions bound concurrently inside the pore, we propose that Pt(NO₂)₄²⁻ and Fe(CN)₆³⁻ binding to an extracellularly accessible site outside of the channel permeation pathway alters the structure of an intracellular anion binding site, leading to weakened binding of intracellular blocking ions.     

Self-electroporation as a Model for Fusion Pore Formation

Abstract

The creation of a small opening called the fusion pore is a necessary prerequisite for neurotransmitter release from synaptic vesicles. It is known that high intensity electric fields can create pores in vesicles by a process called electroporation. Due to the presence of charged phosphatidylserine (PS) molecules on the inner leaflet of the cell membrane, an electric field that is strong enough to cause electroporation of a synaptic vesicle might be present. It was shown by K. Rosenheck [K. Rosenheck. Biophys J 75, 1237–1243 (1998)] that in a planar geometry, fields sufficient to cause electroporation can occur at intermembrane separations of less than ～3 nm. It is frequently found, however, that the cell membrane is not planar but caves inward at the locations where a vesicle is close to it. Indentation of the cell membrane in the fusion region was modelled as a hemisphere and a theoretical study of the electric field in the vicinity of the cell membrane taking into account the screening effect of dissolved ions in the cytoplasm was performed. It was discovered that fields crossing the electroporation threshold occurred at a distance of 2 nm or less, supporting the claim that electroporation could be a possible mechanism for fusion pore formation.     

Multi-Ion Mechanism for Ion Permeation and Block in the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel

The mechanism of Cl⁻ ion permeation through single cystic fibrosis transmembrane conductance regulator (CFTR) channels was studied using the channel-blocking ion gluconate. High concentrations of intracellular gluconate ions cause a rapid, voltage-dependent block of CFTR Cl⁻ channels by binding to a site ∼40% of the way through the transmembrane electric field. The affinity of gluconate block was influenced by both intracellular and extracellular Cl⁻ concentration. Increasing extracellular Cl⁻ concentration reduced intracellular gluconate affinity, suggesting that a repulsive interaction occurs between Cl⁻ and gluconate ions within the channel pore, an effect that would require the pore to be capable of holding more than one ion simultaneously. This effect of extracellular Cl⁻ is not shared by extracellular gluconate ions, suggesting that gluconate is unable to enter the pore from the outside. Increasing the intracellular Cl⁻ concentration also reduced the affinity of intracellular gluconate block, consistent with competition between intracellular Cl⁻ and gluconate ions for a common binding site in the pore. Based on this evidence that CFTR is a multi-ion pore, we have analyzed Cl⁻ permeation and gluconate block using discrete-state models with multiple occupancy. Both two- and three-site models were able to reproduce all of the experimental data with similar accuracy, including the dependence of blocker affinity on external Cl⁻ (but not gluconate) ions and the dependence of channel conductance on Cl⁻ concentration. The three-site model was also able to predict block by internal and external thiocyanate (SCN⁻) ions and anomalous mole fraction behavior seen in Cl⁻/SCN⁻ mixtures.     

Ion Channel Selectivity through Stepwise Changes in Binding Affinity

Voltage-gated Ca²⁺ channels select Ca²⁺ over competing, more abundant ions by means of a high affinity binding site in the pore. The maximum off rate from this site is ∼1,000× slower than observed Ca²⁺ current. Various theories that explain how high Ca²⁺ current can pass through such a sticky pore all assume that flux occurs from a condition in which the pore''s affinity for Ca²⁺ transiently decreases because of ion interactions. Here, we use rate theory calculations to demonstrate a different mechanism that requires no transient changes in affinity to quantitatively reproduce observed Ca²⁺ channel behavior. The model pore has a single high affinity Ca²⁺ binding site flanked by a low affinity site on either side; ions permeate in single file without repulsive interactions. The low affinity sites provide steps of potential energy that speed the exit of a Ca²⁺ ion off the selectivity site, just as potential energy steps accelerate other chemical reactions. The steps could be provided by weak binding in the nonselective vestibules that appear to be a general feature of ion channels, by specific protein structures in a long pore, or by stepwise rehydration of a permeating ion. The previous ion-interaction models and this stepwise permeation model demonstrate two general mechanisms, which might well work together, to simultaneously generate high flux and high selectivity in single file pores.     

Electroporative deformation of salt filled lipid vesicles

Membrane electroporation, vesicle shape deformation and aggregation of small, NaCl-filled lipid vesicles (of radius a = 50 nm) in DC electric fields was characterized using conductometric and turbidimetrical data. At pulse durations t_E≤ 55 ± 5 ms the increase in the conductivity of the vesicle suspension is due to the field-induced efflux of electrolyte through membrane electropores. Membrane electroporation and Maxwell stress on the vesicle membrane lead to vesicle elongation concomitant with small volume reduction (up to 0.6% in an electric field of E = 1 MV m^–1). At t_E > 55 ± 5 ms, further increases in the conductivity and the optical density suggest electroaggregation and electrofusion of vesicles. The conductivity changes after the electric pulse termination reflect salt ion efflux through slowly resealing electropores. The analysis of the volume reduction kinetics yields the bending rigidity κ = (4.1 ± 0.3) ⋅ 10^–20 J of the vesicle membrane. If the flow of Na⁺ and Cl^– ions from the vesicle interior is treated in terms of Hagen-Poiseuille's equation, the number of permeable electropores is N = 39 per vesicle with mean pore radius r_p = 0.85 ± 0.05 nm at E = 1 MVm^–1 and t_E≤ 55 ± 5 ms. The turbidimetric and conductometric data suggest that small lipid vesicles (a ≤ 50 nm) are not associated with extensive membrane thermal undulations or superstructures. In particular with respect to membrane curvature, the vesicle results are suggestive for the design and optimization of electroporative delivery of drugs and genes to cell tissue at small field strengths (≤1 MVm^–1) and large pulse durations (≤100 ms). Received: 8 July 1997 / Accepted: 15 September 1997     

Self-electroporation as a model for fusion pore formation

The creation of a small opening called the fusion pore is a necessary prerequisite for neurotransmitter release from synaptic vesicles. It is known that high intensity electric fields can create pores in vesicles by a process called electroporation. Due to the presence of charged phosphatidylserine (PS) molecules on the inner leaflet of the cell membrane, an electric field that is strong enough to cause electroporation of a synaptic vesicle might be present. It was shown by K. Rosenheck [K. Rosenheck. Biophys J 75, 1237-1243 (1998)] that in a planar geometry, fields sufficient to cause electroporation can occur at intermembrane separations of less than approximately 3 nm. It is frequently found, however, that the cell membrane is not planar but caves inward at the locations where a vesicle is close to it. Indentation of the cell membrane in the fusion region was modelled as a hemisphere and a theoretical study of the electric field in the vicinity of the cell membrane taking into account the screening effect of dissolved ions in the cytoplasm was performed. It was discovered that fields crossing the electroporation threshold occurred at a distance of 2 nm or less, supporting the claim that electroporation could be a possible mechanism for fusion pore formation.     

Ion binding properties and structure stability of the NaK channel

Ion distribution in the selectivity filter and ion-water and ion-protein interactions of NaK channel are systematically investigated by all-atom molecular dynamics simulations, with the tetramer channel protein being embedded in a solvated phospholipid bilayer. Analysis of the simulation results indicates that K⁺ ions prefer to bind within the sites formed by two adjacent planes of oxygen atoms from the selectivity filter, while Na⁺ ions are inclined to bind to a single plane of four oxygen atoms. At the same time, both K⁺ and Na⁺ ions can diffuse in the vestibule, accompanying with movements of the water molecules confined in a complex formed by the vestibule together with four small grottos connecting to it. As a result, K⁺ ions show a wide range of coordination numbers (6-8), while Na⁺ ions display a constant coordination number of ∼ 6 in the selectivity filter, which may result in the loss of selectivity of NaK. It is also found that a Ca²⁺ can bind at the extracellular site as reported in the crystal structure in a partially hydrated state, or at a higher site in a full hydration state. Furthermore, the carbonyl group of Asp66 can reorient to point towards the center pore when an ion exists in the vestibule, while that of Gly65 always aligns tangentially to the channel axis, as in the crystallographic structures.     

Functional Architecture of the Cytoplasmic Entrance to the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel Pore

As an ion channel, the cystic fibrosis transmembrane conductance regulator must form a continuous pathway for the movement of Cl⁻ and other anions between the cytoplasm and the extracellular solution. Both the structure and the function of the membrane-spanning part of this pathway are well defined. In contrast, the structure of the pathway that connects the cytoplasm to the membrane-spanning regions is unknown, and functional roles for different parts of the protein forming this pathway have not been described. We used patch clamp recording and substituted cysteine accessibility mutagenesis to identify positively charged amino acid side chains that attract cytoplasmic Cl⁻ ions to the inner mouth of the pore. Our results indicate that the side chains of Lys-190, Arg-248, Arg-303, Lys-370, Lys-1041, and Arg-1048, located in different intracellular loops of the protein, play important roles in the electrostatic attraction of Cl⁻ ions. Mutation and covalent modification of these residues have charge-dependent effects on the rate of Cl⁻ permeation, demonstrating their functional role in maximization of Cl⁻ flux. Other nearby positively charged side chains were not involved in electrostatic interactions with Cl⁻. The location of these Cl⁻-attractive residues suggests that cytoplasmic Cl⁻ ions enter the pore via a lateral portal located between the cytoplasmic extensions to the fourth and sixth transmembrane helices; a secondary, functionally less relevant portal might exist between the extensions to the 10th and 12th transmembrane helices. These results define the cytoplasmic mouth of the pore and show how it attracts Cl⁻ ions from the cytoplasm.     

Calcium and Phosphatidylserine Inhibit Lipid Electropore Formation and Reduce Pore Lifetime

Molecular dynamics simulations of electroporation of homogeneous phospholipid bilayers show that the pore creation time is strongly dependent on the magnitude of the applied electric field. Here, we investigated whether heterogeneous bilayers containing phospholipids with zwitterionic and anionic headgroups exhibit a similar dependence. To facilitate this analysis we divide the life cycle of an electropore into several stages, marking the sequence of steps for pore creation and pore annihilation (restoration of the bilayer after removal of the electric field). We also report simulations of calcium binding isotherms and the effects of calcium ions on the electroporation of heterogeneous lipid bilayers. Calcium binding simulations are consistent with experimental data using a 1:2 Langmuir binding isotherm. We find that calcium ions and phosphatidylserine increase pore creation time and decrease pore annihilation time. For all systems tested, pore creation time was inversely proportional to the bilayer internal electric field.     

Zwitterionic polymers functionalised nanoporous graphene for water desalination: a molecular dynamics study

In this paper, one nanoporous graphene grafting several zwitterionic polymer chains was designed as the osmosis membrane for seawater desalination. Using molecular dynamics simulation, the efficiency and mechanism of salt rejection were discussed. The simulated results showed that the zwitterionic polymer chains on nanoporous graphene can form the charge channel to block Na⁺ and Cl^? ions pass through, and the slat rejection efficiency of functionalised graphene can reach to about 90%. In the simulation, the steric hindrance and electrostatic interaction are the main factors for the salt rejection. With time evolution, the charge channel formed by the soft polymer chains can decrease the effective pore area of membrane, leading to the increase of steric hindrance; the positive and negative centres of polymer chains can adsorb Na⁺ and Cl^? ions under electrostatic interaction in the solution, contributing into the increase of charge density above the membrane. These conclusions are consistent with experimental report. Our designed osmosis membrane about the graphene is helpful for improving the potential application of defect graphene in water desalination and reducing the trouble of obtaining appropriate graphene sheet with small aperture.     

Roles of Ca2+ in hyphal and yeast-form growth inCandida albicans. Growth regulation by altered extracellular and intracellular free Ca2+ concentrations

The dimorphic fungusCandida albicans has both a yeast form and a hyphal form. When yeast-form cells were starved and then transferred to aN-acetylglucosamine medium, the formation of true hyphae from the unbudded yeast-form cells was induced. Removal of Ca²⁺ from the medium with EGTA inhibited hyphal formation by 50%, resulting in only thin and short hyphae. Externally applied excess Ca²⁺ (>10⁻²M) also affected the hyphal formation, resulting in formation of pseudohyphae. This effect required a high concentration of Ca²⁺ but was Ca²⁺-specific. Deprivation of Ca²⁺ also inhibited yeast-form growth. Interestingly, such cells had abnormally wide bud necks and became defective in cell separation. To measure cytosolic free Ca²⁺, fura-2 was introduced into hyphal cells by electroporation. Its normal value was estimated to be about 100 nM. The electroporation caused transient elevation of cytosolic free Ca²⁺ concentration and transient cessation of hyphal growth. There was a close correlation between the timing of recovery of Ca²⁺ concentration and that of the resumption of hyphal growth. Our results demonstrate the importance of extracellular and intracellular free Ca²⁺ for the growth ofC. albicans.     

Secondary Water Pore Formation for Proton Transport in a ClC Exchanger Revealed by an Atomistic Molecular-Dynamics Simulation

Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger, and how the protein brings about the coupled movement of both ions are still unknown. In this work, we use an atomistic molecular dynamics (MD) simulation to demonstrate that a previously unknown secondary water pore is formed inside an Escherichia coli ClC exchanger. The secondary water pore is bifurcated from the chloride ion pathway at E148. From the systematic simulations, we determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore, and that the highly conserved tyrosine residue Y445 functions as a barrier that separates the proton from the chloride ion pathways. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore, and we propose a new mechanism for the coupled transport of chloride ions and protons. It has been reported that several members of ClC proteins are not just channels that simply transport chloride ions across lipid bilayers; rather, they are exchangers that transport both the chloride ion and proton in opposite directions. However, the ion transit pathways and the mechanism of the coupled movement of these two ions have not yet been unveiled. In this article, we report a new finding (to our knowledge) of a water pore inside a prokaryotic ClC protein as revealed by computer simulation. This water pore is bifurcated from the putative chloride ion, and water molecules inside the new pore connect two glutamate residues that are known to be key residues for proton transport. On the basis of our simulation results, we conclude that the water wire that is formed inside the newly found pore acts as a proton pathway, which enables us to resolve many problems that could not be addressed by previous experimental studies.