Ion leakage through transient water pores in protein-free lipid membranes driven by transmembrane ionic charge imbalance

We have employed atomic-scale molecular dynamics simulations to address ion leakage through transient water pores in protein-free phospholipid membranes. Our results for phospholipid membranes in aqueous solution with NaCl and KCl salts show that the formation of transient water pores and the consequent ion leakage can be induced and be driven by a transmembrane ionic charge imbalance, an inherent feature in living cells. These processes take place if the gradient is large enough to develop a sufficiently significant potential difference across the membrane. The transport of cations and anions through the water pores is then seen; it discharges the transmembrane potential, considerably reduces the size of a water pore, and makes the water pore metastable, leading eventually to its sealing. The ion transport is found to be sensitive to the type of ions. It turns out that Na(+) and Cl(-) ions leak through a membrane at approximately the same ratio despite the fact that Na(+) ions are expected to experience a lower potential barrier for the permeation through the pore. This is because of strong interactions of sodium ions with the carbonyl region of a phospholipid membrane as well as with lipid headgroups forming pore "walls," considerably slowing down the permeation of sodium ions. In contrast, we observed a pronounced selectivity of a phospholipid membrane to the permeation of potassium ions as compared to chloride ions: Potassium ions, being larger than sodium ions, interact only weakly with phospholipid headgroups, so that these interactions are not able to compensate for a large difference in free-energy barriers for permeation of K(+) and Cl(-) ions. These findings are found to be robust to a choice of force-field parameters for ions (tested by Gromacs and Charmm force-fields for ions). What is more, a potassium ion is found to be able to permeate a membrane along an alternate, "water-defect-mediated" pathway without actual formation of a pore. The "water-defect-mediated" leakage involves formation of a single water defect only and is found to be at least one order of magnitude faster than the pore-mediated ion leakage.     

Molecular dynamics simulations of hydrophilic pores in lipid bilayers

Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the existence of such meta-stable hydrophilic pores. To study the properties of these structures and understand the mechanism by which pore expansion leads to membrane rupture, a series of molecular dynamics simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer have been conducted. The system was simulated in two different states; first, as a bilayer containing a meta-stable pore and second, as an equilibrated bilayer without a pore. Surface tension in both cases was applied to study the formation and stability of hydrophilic pores inside the bilayers. It is observed that below a critical threshold tension of approximately 38 mN/m the pores are stabilized. The minimum radius at which a pore can be stabilized is 0.7 nm. Based on the critical threshold tension the line tension of the bilayer was estimated to be approximately 3 x 10(-11) N, in good agreement with experimental measurements. The flux of water molecules through these stabilized pores was analyzed, and the structure and size of the pores characterized. When the lateral pressure exceeds the threshold tension, the pores become unstable and start to expand causing the rupture of the membrane. In the simulations the mechanical threshold tension necessary to cause rupture of the membrane on a nanosecond timescale is much higher in the case of the equilibrated bilayers, as compared with membranes containing preexisting pores.     

Glutamate, water and ion transport through a charged nanosize pore

The transport of transmitter, ions and water through a positively-charged nanopore was investigated through computer simulations. The physics of the problem is described by a coupled set of Poisson-Nernst-Planck and Navier-Stokes equations in a computational domain consisting a cylindrical pore, whose radius ranged from 1 to 8 nm and which was flanked by two compartments representing the vesicular interior and extra-cellular space. The concentration of co-ions is suppressed and of counter-ions enhanced, especially near the pore wall owing to electrostatic interactions. Glutamate (i.e. the transmitter considered) is negatively charged and is simulated as a counter-ion. The electro-kinetically induced pressure due to the movement of ions is negative and very pronounced near the pore wall where the concentration and flux of counter-ions is very high. The water velocity peaks in the pore center, diminishes to zero at the pore wall, but is constant along the pore axis. The mean velocity of the water/fluid is proportional to the vesicular pressure and pore cross-sectional area. Interestingly it is inversely related to the vesicular glutamate concentration. The factors determining the glutamate flux are complex. The diffusive flux generally predominates for narrow pore, and convective flux may dominate for wide pore if the vesicular pressure is high. Surprisingly at low vesicular pressure the mean total glutamate flux per unit cross-sectional pore area is higher for narrow pores. Higher flux is probably due to the rise of glutamate concentration in the nanopore, which is much more pronounced for narrow nanopores, due to the maintenance of approximate neutrality of charges in the pore and on the pore wall. In conclusion intra-vesicular pressure helps ‘flushing-out’ the transmitter, but the induced pressure ‘drags-out’ the water into the extra-cellular space.     

Reversible electrical breakdown of lipid bilayers: formation and evolution of pores

The mechanism of reversible electric breakdown of lipid membranes is studied. The following stages of the process of pore development are substantiated. Hydrophobic pores are formed in the lipid bilayer by spontaneous fluctuations. If these water-filled defects extend to a radius of 0.3 to 0.5 nm, a hydrophilic pore is formed by reorientation of the lipid molecules. This process is favoured by a potential difference across the membrane. The conductivity of the pores depends on membrane voltage, and the type of this dependence changes with the radius of the pore. Hydrophilic pores of an effective radius of 0.6 up to more than 1 nm are formed, which account for the membrane conductivity increase observed. The characteristic times of changes in average radius and number of pores during the voltage pulse and after it are investigated.     

Reversible electrical breakdown of lipid bilayers: formation and evolution of pores

The mechanism of reversible electric breakdown of lipid membranes is studied. The following stages of the process of pore development are substantiated. Hydrophobic pores are formed in the lipid bilayer by spontaneous fluctuations. If these water-filled defects extend to a radius of 0.3 to 0.5 nm, a hydrophilic pore is formed by reorientation of the lipid molecules. This process is favoured by a potential difference across the membrane. The conductivity of the pores depends on membrane voltage, and the type of this dependence changes with the radius of the pore. Hydrophilic pores of an effective radius of 0.6 up to more than 1 nm are formed, which account for the membrane conductivity increase observed. The characteristic times of changes in average radius and number of pores during the voltage pulse and after it are investigated.     

Molecular Dynamics Simulation Analysis of Membrane Defects and Pore Propensity of Hemifusion Diaphragms

Membrane fusion often exhibits slow dynamics in electrophysiological experiments, involving prespike foot and fusion pore-flickering, but the structural basis of such phenomena remains unclear. Hemifusion intermediates have been implicated in the early phase of membrane fusion. To elucidate the dynamics of formation of membrane defects and pores within the hemifusion diaphragm (HD), atomistic and coarse-grained models of hemifusion intermediates were constructed using dipalmitoylphosphatidylcholine or dioleoylphosphatidylcholine membranes. The work necessary to displace a lipid molecule to the hydrophobic core of the bilayer was measured. For a lipid within the HD with radius of 4 nm, the work was ∼80 kJ/mol, similar to that in a planar bilayer. The work was much less (∼40 kJ/mol) when the HD was surrounded by a steep stalk, i.e., stalk wings forming a large angle at the junction of three bilayers. In the latter case, the lipid displacement engendered formation of a pore contacting the HD rim. The work was similarly small (40 kJ/mol) for a small HD of 1.5 nm radius, where a pore formed and grew rapidly, quickly generating a toroidal structure (<40 ns). Combining the steep stalk and the small HD decreased the work further, although quantitative analysis was difficult because the latter system was not in a stable equilibrium state. Results suggest that fine tuning of fusion dynamics requires strict control of the HD size and the angle between the expanded stalk and HD. In additional free simulations, the steep stalk facilitated widening of a preformed pore contacting the HD rim.     

Glutamate, water and ion transport through a charged nanosize pore

The transport of transmitter, ions and water through a positively-charged nanopore was investigated through computer simulations. The physics of the problem is described by a coupled set of Poisson-Nernst-Planck and Navier-Stokes equations in a computational domain consisting a cylindrical pore, whose radius ranged from 1 to 8 nm and which was flanked by two compartments representing the vesicular interior and extra-cellular space. The concentration of co-ions is suppressed and of counter-ions enhanced, especially near the pore wall owing to electrostatic interactions. Glutamate (i.e. the transmitter considered) is negatively charged and is simulated as a counter-ion. The electro-kinetically induced pressure due to the movement of ions is negative and very pronounced near the pore wall where the concentration and flux of counter-ions is very high. The water velocity peaks in the pore center, diminishes to zero at the pore wall, but is constant along the pore axis. The mean velocity of the water/fluid is proportional to the vesicular pressure and pore cross-sectional area. Interestingly it is inversely related to the vesicular glutamate concentration. The factors determining the glutamate flux are complex. The diffusive flux generally predominates for narrow pore, and convective flux may dominate for wide pore if the vesicular pressure is high. Surprisingly at low vesicular pressure the mean total glutamate flux per unit cross-sectional pore area is higher for narrow pores. Higher flux is probably due to the rise of glutamate concentration in the nanopore, which is much more pronounced for narrow nanopores, due to the maintenance of approximate neutrality of charges in the pore and on the pore wall. In conclusion intra-vesicular pressure helps 'flushing-out' the transmitter, but the induced pressure 'drags-out' the water into the extra-cellular space.     

Heteropore populations of bullfrog alveolar epithelium

Diffusional fluxes of a large number of hydrophilic solutes and water across bullfrog (Rana catesbeiana) alveolar epithelium were measured in the Ussing-type flux chamber. Lungs were isolated from double-pithed animals and studied as flat sheets. Radioactive solutes and water were added to the upstream reservoir, and the rate of change of downstream reservoir radioactivity was monitored. A permeability coefficient was estimated for each substance from a linear relationship between radiotracer concentration in the downstream reservoir and time. These permeability data were used to analyze the equivalent water-filled pore characteristics of the alveolar epithelial barrier. The data reveal that the alveolar epithelium is best characterized by two distinct pore populations rather than by a single homogeneous pore population. The large-pore population consists of pores with a radius of about 5 nm and occupies 4% of the available pore area. The small-pore population consists of pores with a radius of about 0.5 nm and occupies 96% of the available pore area. The number of small pores to large pores is 2.68 X 10(3). After the alveolar surface was damaged by acid, a large-pore population with a radius of about 27 nm was seen, allowing nearly free diffusion of solutes. A major implication of the presence of two populations of pores in the alveolar epithelium is that hydrostatically driven bulk water flow occurs predominantly through the large pores, while osmotically driven bulk water flow takes place predominantly through the small pores. As a result, in general, hydrostatic and osmotic gradients may not be equally effective driving forces for water flow across this tissue.     

Imaging the Lipid-Phase-Dependent Pore Formation of Equinatoxin II in Droplet Interface Bilayers

Using phase-separated droplet interface bilayers, we observe membrane binding and pore formation of a eukaryotic cytolysin, Equinatoxin II (EqtII). EqtII activity is known to depend on the presence of sphingomyelin in the target membrane and is enhanced by lipid phase separation. By imaging the ionic flux through individual pores in vitro, we observe that EqtII pores form predominantly within the liquid-disordered phase. We observe preferential binding of labeled EqtII at liquid-ordered/liquid-disordered domain boundaries before it accumulates in the liquid-disordered phase.     

A New Proposal for the Action of Vasopressin, Based on Studies of a Complex Synthetic Membrane

The total osmotic flow of water across cell membranes generally exceeds diffusional flow measured with labeled water. The ratio of osmotic to diffusional flow has been widely used as a basis for the calculation of the radius of pores in the membrane, assuming Poiseuille flow of water through the pores. An important assumption underlying this calculation is that both osmotic and diffusional flow are rate-limited by the same barrier in the membrane. Studies employing a complex synthetic membrane show, however, that osmotic flow can be limited by one barrier (thin, dense barrier), and the rate of diffusion of isotopic water by a second (thick, porous) barrier in series with the first. Calculation of a pore radius is meaningless under these conditions, greatly overestimating the size of the pores determining osmotic flow. On the basis of these results, the estimation of pore radius in biological membranes is reassessed. It is proposed that vasopressin acts by greatly increasing the rate of diffusion of water across an outer barrier of the membrane, with little or no accompanying increase in pore size.     

Fluid mechanical and electrostatic study on the osmotic flow through cylindrical pores

When two solutions differing in solute concentration are separated by a porous membrane, the osmotic pressure will generate a net volume flux of the suspending fluid across the membrane; this is termed osmotic flow. We consider the osmotic flow across a membrane with circular cylindrical pores when the solute and the pore walls are electrically charged, and the suspending fluid is an electrolytic solution containing small cations and anions. Under the condition in which the radius of the pores and that of the solute molecules greatly exceed those of the solvent as well as the ions, a fluid mechanical and electrostatic theory is introduced to describe the osmotic flow in the presence of electric charge. The interaction energy, including the electrostatic interaction between the solute and the pore wall, plays a key role in determining the osmotic flow. We examine the electrostatic effect on the osmotic flow and discuss the difference in the interaction energy determined from the nonlinear Poisson-Boltzmann equation and from its linearized equation (the Debye-Hückel equation).     

Mechanism of electroporative dye uptake by mouse B cells.

The color change of electroporated intact immunoglobulin G receptor (Fc gammaR-) mouse B cells (line IIA1.6) after direct electroporative transfer of the dye SERVA blue G (Mr 854) into the cell interior is shown to be dominantly due to diffusion of the dye after the electric field pulse. Hence the dye transport is described by Fick's first law, where, as a novelty, time-integrated flow coefficients are introduced. The chemical-kinetic analysis uses three different pore states (P) in the reaction cascade (C <==> P1 <==> P2 <==> P3), to model the sigmoid kinetics of pore formation as well as the biphasic pore resealing. The rate coefficient for pore formation k(p) is dependent on the external electric field strength E and pulse duration tE. At E = 2.1 kV cm(-1) and tE = 200 micros, k(p) = (2.4 +/- 0.2) x 10(3) s(-1) at T = 293 K; the respective (field-dependent) flow coefficient and permeability coefficient are k(f)0 = (1.0 +/- 0.1) x 10(-2) s(-1) and P0 = 2 cm s(-1), respectively. The maximum value of the fractional surface area of the dye-conductive pores is 0.035 +/- 0.003%, and the maximum pore number is Np = (1.5 +/- 0.1) x 10(5) per average cell. The diffusion coefficient for SERVA blue G, D = 10(-6) cm2 s(-1), is slightly smaller than that of free dye diffusion, indicating transient interaction of the dye with the pore lipids during translocation. The mean radii of the three pore states are r(P1) = 0.7 +/- 0.1 nm, r(P2) = 1.0 +/- 0.1 nm, and r(P3) = 1.2 +/- 0.1 nm, respectively. The resealing rate coefficients are k(-2) = (4.0 +/- 0.5) x 10(-2) s(-1) and k(-3) = (4.5 +/- 0.5) x 10)(-3) s(-1), independent of E. At zero field, the equilibrium constant of the pore states (P) relative to closed membrane states (C) is K(p)0 = [(P)]/[C] = 0.02 +/- 0.002, indicating 2.0 +/- 0.2% water associated with the lipid membrane. Finally, the results of SERVA blue G cell coloring and the new analytical framework may also serve as a guideline for the optimization of the electroporative delivery of drugs that are similar in structure to SERVA blue G, for instance, bleomycin, which has been used successfully in the new discipline of electrochemotherapy.     

Colloid-osmotic lysis is a general feature of the mechanism of action of Bacillus thuringiensis δ-endotoxins with different insect specificity

The mechanism of action of Bacillus thuringiensis insecticidal δ-endotoxins has long been the subject of controversy. As our working hypothesis we propose a two-step model in which, after binding a specific plasma membrane receptor, the action of all the δ-endotoxins studied here is to generate small pores in the plasma membrane, either directly by inserting into the membrane, or indirectly by perturbing resident plasma membrane molecules. The creation of these pores will lead to colloid-osmotic lysis, i.e., an equilibration of ions through the pore resulting in a net inflow of ions, an accompanying influx of water, cell swelling and eventual lysis. Our observations that cell swelling precedes lysis, that small molecules leak out of the cell before large ones, that osmotic protectants inhibit or delay cytolysis, and that the toxin-induced pore of 0.5–1.0 nm radius will allow equilibration of ions but not leakage of cytoplasmic macromolecules, are in full agreement with the predictions of this hypothesis. To explain the specificity of the δ-endotoxin-induced lytic pore formation, we propose that prior interaction between the toxin and cell-specific plasma membrane recpetors is necessary before these toxins can insert into, or interact with, the membrane.     

Functional size of complement and perforin pores compared by confocal laser scanning microscopy and fluorescence microphotolysis

Confocal laser scanning microscopy and fluorescence microphotolysis (also referred to as fluorescence photobleaching recovery) were employed to study the transport of hydrophilic fluorescent tracers through complement and perforin pores. By optimizing the confocal effect it was possible to determine the exclusion limit of the pores in situ, i.e. without separation of cells and tracer solution. Single-cell flux measurements by fluorescence microphotolysis yielded information on the sample population distribution of flux rates. By these means a direct comparison of complement and perforin pores was made in sheep erythrocyte membranes. In accordance with previous studies employing a variety of different techniques complement pores were found to have a functional radius of approx. 50 A when generated at high complement concentrations. The flux rate distribution indicated that pore size heterogeneity was rather small under these conditions. Perforin pores, generated in sheep erythrocyte membranes at high perforin concentrations, were found to have a functional size very similar to complement pores. Furthermore, the functional size of the perforin pore seemed to be relatively independent of the dynamic properties of the target membrane since in two cell membranes which are very different in this regard, the human erythrocyte membrane and the plasma membrane of erythroleukemic cells, the functional radius of the perforin pore was also close to 50 A. A perforin-specific antibody reduced the functional radius of perforin pores to 45 A.     

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.     

Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses

Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (∼16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules.     

Smooth DNA Transport through a Narrowed Pore Geometry

Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35–20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.     

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.     

Kinetics of Diffusion and Convection in 3.2-Å Pores: Exact Solution by Computer Simulation

The kinetics of transport in pores the size postulated for cell membranes has been investigated by direct computer simulation (molecular dynamics). The simulated pore is 11 Å long and 3.2 Å in radius, and the water molecules are modeled by hard, smooth spheres, 1 Å in radius. The balls are given an initial set of positions and velocities (with an average temperature of 313° K) and the computer then calculates their exact paths through the pore. Two different conditions were used at the ends of the pore. In one, the ends are closed and the balls are completely isolated. In the other, the ball density in each end region is fixed so that a pressure difference can be established and a net convective flow produced. The following values were directly measured in the simulated experiments: net and diffusive (oneway) flux; pressure, temperature, and diffusion coefficients in the pore; area available for diffusion; probability distribution of ball positions in the pore; and the interaction between diffusion and convection. The density, viscosity, and diffusion coefficients in the bulk fluid were determined from the theory of hard sphere dense gases. From these values, the “equivalent” pore radius (determined by the same procedure that is used for cell membranes) was computed and compared with the physical pore radius of the simulated pore.