Scaling Behavior of Ionic Transport in Membrane Nanochannels

Electrophysiological dissection of the ion channel activity of the Pseudomonas aeruginosa ionophore protein toxin Tse5

We present an in-depth electrophysiological analysis of Tse5, a pore-forming toxin (PFT) delivered by the type VI secretion system (T6SS) of Pseudomonas aeruginosa. The T6SS is a sophisticated bacterial secretion system that injects toxic effector proteins into competing bacteria or host cells, providing a competitive advantage by disabling other microbes and modulating their environment. Our findings highlight the dependency of Tse5 insertion on membrane charge and electrolyte concentration, suggesting an in vivo effect from the periplasmic space. Conductance and selectivity experiments reveal a predominant and reproducible pore architecture of Tse5, characterized by a weak cation selectivity without chemical specificity. pH titration experiments suggest a proteolipidic pore structure influenced by both protein and lipid charges, a hypothesis further supported by experiments involving engineered mutants of Tse5 with altered glycine zippers. These results significantly advance our understanding of Tse5's molecular mechanism of toxicity, paving the way for potential applications in biosensing and macromolecular delivery.

Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels

Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5-10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure-function correlations in these membrane pores.

Viroporins: discovery, methods of study, and mechanisms of host-membrane permeabilization

The 'Viroporin' family comprises a number of mostly small-sized, integral membrane proteins encoded by animal and plant viruses. Despite their sequence and structural diversity, viroporins share a common functional trend: their capacity to assemble transmembrane channels during the replication cycle of the virus. Their selectivity spectrum ranges from low-pH-activated, unidirectional proton transporters, to size-limited permeating pores allowing passive diffusion of metabolites. Through mechanisms not fully understood, expression of viroporins facilitates virion assembly/release from infected cells, and subverts the cell physiology, contributing to cytopathogenicity. Compounds that interact with viroporins and interfere with their membrane-permeabilizing activity in vitro, are known to inhibit virus production. Moreover, viroporin-defective viruses comprise a source of live attenuated vaccines that prevent infection by notorious human and livestock pathogens. This review dives into the origin and evolution of the viroporin concept, summarizes some of the methodologies used to characterize the structure-function relationships of these important virulence factors, and attempts to classify them on biophysical grounds attending to their mechanisms of ion/solute transport across membranes.

Supralinear scaling behavior of ionic transport in membrane nanochannels regulated by outer-surface charges

The peculiarity of ion transport at the nanoscale is revealed through electrophysiological studies of two biological ion channels: the cation-selective bacterial porin-OmpF and the mitochondrial voltage-dependent anion channel (VDAC). We provide evidence of an unprecedented scaling behavior in the power-law relationship between conductivity and concentration G ∼ c α with α > 1 when functional groups attached to the pore inner wall have opposite charges to those located in the nanochannel's outer surface. Indeed, we find α ∼ 1.4 both for OmpF in positively charged membranes and for VDAC in negatively charged ones. The experiments are analyzed using different levels of theoretical models, starting with an equivalent circuit where total electrical current is described as the sum of ionic currents. Subsequently, we show that electrical circuits incorporating simplifying assumptions such as local electroneutrality and Donnan equilibrium consistently account for the measured G-c relationships yielding extremely similar results to the numerical results of structure-based Poisson-Nernst-Planck equations computed without these assumptions. We demonstrate that unexpected scaling exponents do not correspond to deviations from these classical equilibrium/electroneutrality assumptions, but rather to the structural features of the pore that are not included in oversimplified models in terms of shape and/or charge distribution. In contrast to the predictions of widely accepted models, we demonstrate both experimentally and theoretically that the conductance of ion-selective nanochannels can be drastically reduced in dilute solutions through a mechanism in which membrane charges and pore charges do not compensate for each other but act as interacting sites of opposite charge. Our insights into the critical role of external surface charges aim to open new conceptual avenues for developing nanofluidic devices with enhanced capabilities for energy conversion and sensing properties.

Ion transport and ultra-efficient osmotic power generation in boron nitride nanotube porins

Nanotube porins form transmembrane nanomaterial-derived scaffolds that mimic the geometry and functionality of biological membrane channels. We report synthesis, transport properties, and osmotic energy harvesting performance of another member of the nanotube porin family: boron nitride nanotube porins (BNNTPs). Cryo-transmission electron microscopy imaging, liposome transport assays, and DNA translocation experiments show that BNNTPs reconstitute into lipid membranes to form functional channels of ~2-nm diameter. Ion transport studies reveal ion conductance characteristics of individual BNNTPs, which show an unusual C1/4 scaling with ion concentration and pronounced pH sensitivity. Reversal potential measurements indicate that BNNTPs have strong cation selectivity at neutral pH, attributable to the high negative charge on the channel. BNNTPs also deliver very large power density up to 12 kW/m2 in the osmotic gradient transport experiments at neutral pH, surpassing that of other BNNT-based devices by two orders of magnitude under similar conditions. Our results suggest that BNNTPs are a promising platform for mass transport and osmotic power generation.

Scaling of ionic conductance in a fluctuating single-layer nanoporous membrane

Single-layer membranes have emerged as promising candidates for applications requiring high transport rates due to their low resistance to molecular transport. Owing to their atomically thin structure, these membranes experience significant microscopic fluctuations, emphasizing the need to explore their impact on ion transport processes. In this study, we investigate the effects of membrane fluctuations on the elementary scaling behavior of ion conductance [Formula: see text] as a function of ion concentration [Formula: see text], represented as [Formula: see text], using molecular dynamics simulations. Our findings reveal that membrane fluctuations not only alter the conductance coefficient [Formula: see text] but also the power-law exponent [Formula: see text]. We identify two distinct frequency regimes of membrane fluctuations, GHz-scale and THz-scale fluctuations, and examine their roles in conductance scaling. Furthermore, we demonstrate that the alteration of conductance scaling arises from the non-linearity between ion conductance and membrane shape. This work provides a fundamental understanding of ion transport in fluctuating membranes.

The Complex Proteolipidic Behavior of the SARS-CoV-2 Envelope Protein Channel: Weak Selectivity and Heterogeneous Oligomerization

The envelope (E) protein is a small polypeptide that can form ion channels in coronaviruses. In SARS coronavirus 2 (SARS-CoV-2), the agent that caused the recent COVID-19 pandemic, and its predecessor SARS-CoV-1, E protein is found in the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), where virion budding takes place. Several reports claim that E protein promotes the formation of "cation-selective channels". However, whether this term represents specificity to certain ions (e.g., potassium or calcium) or the partial or total exclusion of anions is debatable. Herein, we discuss this claim based on the available data for SARS-CoV-1 and -2 E and on new experiments performed using the untagged full-length E protein from SARS-CoV-2 in planar lipid membranes of different types, including those that closely mimic the ERGIC membrane composition. We provide evidence that the selectivity of the E-induced channels is very mild and depends strongly on lipid environment. Thus, despite past and recent claims, we found no indication that the E protein forms cation-selective channels that prevent anion transport, and even less that E protein forms bona fide specific calcium channels. In fact, the E channel maintains its multi-ionic non-specific neutral character even in concentrated solutions of Ca2+ ions. Also, in contrast to previous studies, we found no evidence that SARS-CoV-2 E channel activation requires a particular voltage, high calcium concentrations or low pH, in agreement with available data from SARS-CoV-1 E. In addition, sedimentation velocity experiments suggest that the E channel population is mostly pentameric, but very dynamic and probably heterogeneous, consistent with the broad distribution of conductance values typically found in electrophysiological experiments. The latter has been explained by the presence of proteolipidic channel structures.

Biphasic concentration patterns in ionic transport under nanoconfinement revealed in steady-state and time-dependent properties

Ion permeation across nanoscopic structures differs considerably from microfluidics because of strong steric constraints, transformed solvent properties, and charge-regulation effects revealed mostly in diluted solutions. However, little is known about nanofluidics in moderately concentrated solutions, which are critically important for industrial applications and living systems. Here, we show that nanoconfinement triggers general biphasic concentration patterns in a myriad of ion transport properties by using two contrasting systems: a biological ion channel and a much larger synthetic nanopore. Our findings show a low-concentration regime ruled by classical Debye screening and another one where ion-ion correlations and enhanced ion-surface interactions contribute differently to each electrophysiological property. Thus, different quantities (e.g., conductance vs noise) measured under the same conditions may appear contradictory because they belong to different concentration regimes. In addition, non-linear effects that are barely visible in bulk conductivity only in extremely concentrated solutions become apparent in nanochannels around physiological conditions.

The P. aeruginosa effector Tse5 forms membrane pores disrupting the membrane potential of intoxicated bacteria

The type VI secretion system (T6SS) of Pseudomonas aeruginosa injects effector proteins into neighbouring competitors and host cells, providing a fitness advantage that allows this opportunistic nosocomial pathogen to persist and prevail during the onset of infections. However, despite the high clinical relevance of P. aeruginosa, the identity and mode of action of most P. aeruginosa T6SS-dependent effectors remain to be discovered. Here, we report the molecular mechanism of Tse5-CT, the toxic auto-proteolytic product of the P. aeruginosa T6SS exported effector Tse5. Our results demonstrate that Tse5-CT is a pore-forming toxin that can transport ions across the membrane, causing membrane depolarisation and bacterial death. The membrane potential regulates a wide range of essential cellular functions; therefore, membrane depolarisation is an efficient strategy to compete with other microorganisms in polymicrobial environments.

Electrical Conductance of Charged Nanopores

A nanopore's response to an electrical potential drop is characterized by its electrical conductance, . For the last two decades, it has been thought that at low electrolyte concentrations, , the conductance is concentration-independent such that . It has been recently demonstrated that surface charge regulation changes the dependency to , whereby the slope typically takes the values α = 1/3 or 1/2. However, experiments have observed slopes of 2/3 and 1 suggesting that additional mechanisms, such as convection and slip-lengths, appear. Here, we elucidate the interplay between three mechanisms: surface charge regulation, convection, and slip lengths. We show that the inclusion of convection does not change the slope, and when the effects of hydrodynamic slip are included, the slope is doubled. We show that when all effects are accounted for, α can take any value between 0 and 1 where the exact value of the slope depends on the material properties. This result is of utmost importance in designing any electro-kinetically driven nanofluidic system characterized by its conductance.

Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

Biological nanochannels which can regulate ionic transport across cell membranes intelligently play a significant role in physiological functions. Inspired by these nanochannels, numerous artificial nanochannels have been developed during recent years. The exploration of smart solid-state nanochannels can lay a solid foundation, not only for fundamental studies of biological systems but also practical applications in various fields. The basic fabrication principles, functional materials, and diverse applications based on artificial nanochannels are summarized in this review. In addition, theoretical insights into transport mechanisms and structure-function relationships are discussed. Meanwhile, it is believed that improvements will be made via computer-guided strategy in designing more efficient devices with upgrading accuracy. Finally, some remaining challenges and perspectives for developments in both novel conceptions and technology of this inspiring research field are stated.

Dynorphin A induces membrane permeabilization by formation of proteolipidic pores. Insights from electrophysiology and computational simulations

Dynorphins are endogenous neuropeptides that function as ligands for the κ-opioid receptor. In addition to opioid activity, dynorphins can induce several pathological effects such as neurological dysfunctions and cell death. Previous studies have suggested that Dynorphin A (DynA) mediates some pathogenic actions through formation of transient pores in lipid domains of the plasma membrane. Here, we use planar bilayer electrophysiology to show that DynA induces pore formation in negatively charged membranes. We find a large variability in pore conformations showing equilibrium conductance fluctuations, what disregards electroporation as the dominant mechanism of pore formation. Ion selectivity measurements showing cationic selectivity indicate that positive protein charges of DynA are stabilized by phosphatidyl serine negative charges in the formation of combined structures. We complement our study with computational simulations that assess the stability of diverse peptide arrangements in the hydrophobic core of the bilayer. We show that DynA is capable of assembling in charged membranes to form water-filled pores that conduct ions.

Rational ion transport management mediated through membrane structures

Unique membrane structures endow membranes with controlled ion transport properties in both biological and artificial systems, and they have shown broad application prospects from industrial production to biological interfaces. Herein, current advances in nanochannel-structured membranes for manipulating ion transport are reviewed from the perspective of membrane structures. First, the controllability of ion transport through ion selectivity, ion gating, ion rectification, and ion storage is introduced. Second, nanochannel-structured membranes are highlighted according to the nanochannel dimensions, including single-dimensional nanochannels (i.e., 1D, 2D, and 3D) functioning by the controllable geometrical parameters of 1D nanochannels, the adjustable interlayer spacing of 2D nanochannels, and the interconnected ion diffusion pathways of 3D nanochannels, and mixed-dimensional nanochannels (i.e., 1D/1D, 1D/2D, 1D/3D, 2D/2D, 2D/3D, and 3D/3D) tuned through asymmetric factors (e.g., components, geometric parameters, and interface properties). Then, ultrathin membranes with short ion transport distances and sandwich-like membranes with more delicate nanochannels and combination structures are reviewed, and stimulus-responsive nanochannels are discussed. Construction methods for nanochannel-structured membranes are briefly introduced, and a variety of applications of these membranes are summarized. Finally, future perspectives to developing nanochannel-structured membranes with unique structures (e.g., combinations of external macro/micro/nanostructures and the internal nanochannel arrangement) for mediating ion transport are presented.

Transport mechanisms of SARS-CoV-E viroporin in calcium solutions: Lipid-dependent Anomalous Mole Fraction Effect and regulation of pore conductance

The envelope protein E of the SARS-CoV coronavirus is an archetype of viroporin. It is a small hydrophobic protein displaying ion channel activity that has proven highly relevant in virus-host interaction and virulence. Ion transport through E channel was shown to alter Ca²⁺ homeostasis in the cell and trigger inflammation processes. Here, we study transport properties of the E viroporin in mixed solutions of potassium and calcium chloride that contain a fixed total concentration (mole fraction experiments). The channel is reconstituted in planar membranes of different lipid compositions, including a lipid mixture that mimics the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane where the virus localizes within the cell. We find that the E ion conductance changes non-monotonically with the total ionic concentration displaying an Anomalous Mole Fraction Effect (AMFE) only when charged lipids are present in the membrane. We also observe that E channel insertion in ERGIC-mimic membranes – including lipid with intrinsic negative curvature – enhances ion permeation at physiological concentrations of pure CaCl₂ or KCl solutions, with a preferential transport of Ca²⁺ in mixed KCl-CaCl₂ solutions. Altogether, our findings demonstrate that the presence of calcium modulates the transport properties of the E channel by interacting preferentially with charged lipids through different mechanisms including direct Coulombic interactions and possibly inducing changes in membrane morphology.

Specific adsorption of trivalent cations in biological nanopores determines conductance dynamics and reverses ionic selectivity

Adsorption processes are central to ionic transport in industrial and biological membrane systems. Multivalent cations modulate the conductive properties of nanofluidic devices through interactions with charged surfaces that depend principally on the ion charge number. Considering that ion channels are specialized valves that demand a sharp specificity in ion discrimination, we investigate the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores. We consider here OmpF from Escherichia coli, an archetypical protein nanopore, to probe the specificity of biological nanopores to multivalent cations. We systematically compare the effect of three trivalent electrolytes on OmpF current-voltage relationships and characterize the degree of rectification induced by each ion. We also analyze the open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption and evaluate the extent of charge inversion through selectivity measurements. We show that the interaction of trivalent electrolytes with biological nanopores occurs via ion-specific adsorption yielding differential modulation of ion conduction and selectivity inversion. We also demonstrate the existence of non-equilibrium fluctuations likely related to ion-dependent trapping-detrapping processes. Our study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.

Electric control of ionic transport in sub-nm nanopores

The ion transport behavior through sub-nm nanopores (length (L) ≈ radius (R)) on a film is different from that in nanochannels (L ≫ R), and even more different from the bulk behavior. The many intriguing phenomena in ionic transport are the key to the design and fabrication of solid-state nanofluidic devices. However, ion transport through sub-nm nanopores is not yet clearly understood. We investigate the ionic transport behavior of sub-nm nanopores from the perspective of conductance via molecular dynamics (MD) and experimental methods. Under the action of surface charge, the average ion concentration inside the nanopore is much higher than the bulk value. It is found that 100 mM is the transition point between the surface-charge-governed and the bulk behavior regimes, which is different from the transition point for nanochannels (10 mM). Moreover, by investigating the access, pores, surface charge, electroosmosis and potential leakage conductance, it is found that the conductive properties of the nanopore at low bulk concentration are determined by the surface charge potential leaks into the reservoir. Specifically, there is a huge increase in cation mobility through a cylindrical nanopore, which implies potential applications for the fast charging of supercapacitors and batteries. Sub-nm nanopores also show a strong selectivity toward Na⁺, and a strong repellence toward Cl⁻. These conclusions presented here will be useful not only in understanding the behavior of ion transport, but also in the design of nanofluidic devices.

The ion transport behavior through sub-nm nanopores (length (L) ≈ radius (R)) on a film is different from that in nanochannels (L ≫ R), and even more different from the bulk behavior.

Ion Transport in Electrically Imperfect Nanopores

Ionic transport through a charged nanopore at low ion concentration is governed by the surface conductance. Several experiments have reported various power-law relations between the surface conductance and ion concentration, i.e., G_surf ∝ c₀^α. However, the physical origin of the varying exponent, α, is not yet clearly understood. By performing extensive coarse-grained Molecular Dynamics simulations for various pore diameters, lengths, and surface charge densities, we observe varying power-law exponents even with a constant surface charge and show that α depends on how electrically "perfect" the nanopore is. Specifically, when the net charge of the solution in the pore is insufficient to ensure electroneutrality, the pore is electrically "imperfect" and such nanopores can exhibit varying α depending on the degree of "imperfectness". We present an ionic conductance theory for electrically "imperfect" nanopores that not only explains the various power-law relationships but also describes most of the experimental data available in the literature.

A Novel Biosensor Based on Molybdenum Disulfide (MoS2 ) Modified Porous Anodic Aluminum Oxide Nanochannels for Ultrasensitive microRNA-155 Detection

Artificial photoresponsive nanochannels have attracted widespread attention because of their capacity to achieve ion transport through light modulation. Herein, a biosensor for ultrasensitive miRNA-155 detection is devised based on molybdenum disulfide (MoS₂ ) modified porous anodic aluminum oxide (AAO) photoresponsive nanochannels by atomic layer deposition (ALD). According to the optimized experimental results, when the cycles of ALD, the wavelength, and the power of the excitation laser are 70 cycles, 450 nm, and 80 mW, respectively, the most supreme photocurrent performance of these photoresponsive nanochannels are obtained. AAO nanochannels modified with MoS₂ can work as a photoelectrochemical (PEC) biosensor by generating photoexcitation current; what is more, the high channel density in AAO can magnify the ion current signal response effectively by aggrandizing the flux of electroactive species. By using AAO photoresponsive nanochannels with an average diameter of 150 nm as PEC biosensor, an ultrasensitive detection record ranging from 0.01 fM to 0.01 nM with a detection limit of 3 aM can be achieved. This work not only proposes a simple method for manufacturing semiconductor photoresponsive nanochannels, but also exhibits great potential in the ultrasensitive detection of biomolecules.

Transitions between nanomechanical and continuum mechanical contacts: new insights from liquid structure

The use of continuum mechanics to describe contacts involving nanoscale and atomic interactions has been one of the key controversies in nanoscience, tribology, and petrophysical and geological studies. By applying a novel nonequilibrium molecular dynamics scheme to wet quartz contacts, this study revealed the key transitions between continuum electrostatic, nanomechanical and Hertzian contact behaviors at around one nm of surface separation, which results in critical contact pressure fluctuations between -30 and 100 MPa. Using a novel liquid-structure analysis scheme based on the spatial distribution of water molecules, the nanomechanical behavior was found to originate from the collapse and localization of layers of water molecules. Moreover, the role of surface curvature on this effect was also quantified and explained based on a new topological descriptor. The findings of this study enrich our understanding of wet contacts and have a wide range of applications from the nanoscale to macroscale.

Measurements of the size and correlations between ions using an electrolytic point contact

The size of an ion affects everything from the structure of water to life itself. In this report, to gauge their size, ions dissolved in water are forced electrically through a sub-nanometer-diameter pore spanning a thin membrane and the current is measured. The measurements reveal an ion-selective conductance that vanishes in pores <0.24 nm in diameter-the size of a water molecule-indicating that permeating ions have a grossly distorted hydration shell. Analysis of the current noise power spectral density exposes a threshold, below which the noise is independent of current, and beyond which it increases quadratically. This dependence proves that the spectral density, which is uncorrelated below threshold, becomes correlated above it. The onset of correlations for Li+, Mg2+, Na+ and K+-ions extrapolates to pore diameters of 0.13 ± 0.11 nm, 0.16 ± 0.11 nm, 0.22 ± 0.11 nm and 0.25 ± 0.11 nm, respectively-consonant with diameters at which the conductance vanishes and consistent with ions moving through the sub-nanopore with distorted hydration shells in a correlated way.

Lipid Headgroup Charge and Acyl Chain Composition Modulate Closure of Bacterial β-Barrel Channels

The outer membrane of Gram-negative bacteria contains β-barrel proteins that form high-conducting ion channels providing a path for hydrophilic molecules, including antibiotics. Traditionally, these proteins have been considered to exist only in an open state so that regulation of outer membrane permeability was accomplished via protein expression. However, electrophysiological recordings show that β-barrel channels respond to transmembrane voltages by characteristically switching from a high-conducting, open state, to a so-called 'closed' state, with reduced permeability and possibly exclusion of large metabolites. Here, we use the bacterial porin OmpF from E. coli as a model system to gain insight on the control of outer membrane permeability by bacterial porins through the modulation of their open state. Using planar bilayer electrophysiology, we perform an extensive study of the role of membrane lipids in the OmpF channel closure by voltage. We pay attention not only to the effects of charges in the hydrophilic lipid heads but also to the contribution of the hydrophobic tails in the lipid-protein interactions. Our results show that gating kinetics is governed by lipid characteristics so that each stage of a sequential closure is different from the previous one, probably because of intra- or intermonomeric rearrangements.