Channels In Biological Membranes Research Articles

(Invited) Nanofluidic Ion Transport in Carbon Nanotube Porin Channels

Extreme spatial confinement in narrow fluidic channels strongly influences their transport properties and enables unconventional selectivity mechanisms that can often mimic some of the selectivity and transport characteristics of biological membrane channels. More than any modern nanomaterial, carbon nanotubes have enabled experimental platforms that can recreate such extreme confinement in a channel with defined geometry and controllable electronic properties. I will discuss ion transport in canon nanotube porin channels and show how confinement phenomena, coupled with the different electronic effects in these channels can shape their transport properties and ion selectivity characteristics. Overall, these observations contribute to our understanding of nanoscale transport and pave the way for developing a new generation of precision separation platforms for biomedical and industrial use.

Zn-ion ultrafluidity via bioinspired ion channel for ultralong lifespan Zn-ion battery.

Rechargeable aqueous Zn-ion batteries have been deemed a promising energy storage device. However, the dendrite growth and side reactions have hindered their practical application. Herein, inspired by the ultrafluidic and K+ ion-sieving flux through enzyme-gated potassium channels (KcsA) in biological plasma membranes, a metal-organic-framework (MOF-5) grafted with -ClO4 groups (MOF-ClO4) as functional enzymes is fabricated to mimic the ultrafluidic lipid-bilayer structure for gating Zn2+ 'on' and anions 'off' states. The MOF-ClO4 achieved perfect Zn2+/SO4 2- selectivity (∼10), enhanced Zn2+ transfer number ([Formula: see text]) and the ultrafluidic Zn2+ flux (1.9×10-3 vs. 1.67mmol m-2 s-1 for KcsA). The symmetric cells based on MOF-ClO4 achieve a lifespan of over 5400h at 10mAcm-2/20mAhcm-2. Specifically, the performance of the PMCl-Zn//V2O5 pouch cell keeps 81% capacity after 2000 cycles at 1Ag-1. The regulated ion transport, by learning from a biological plasma membrane, opens a new avenue towards ultralong lifespan aqueous batteries.

α-Latrotoxin Tetramers Spontaneously Form Two-Dimensional Crystals in Solution and Coordinated Multi-Pore Assemblies in Biological Membranes.

α-Latrotoxin (α-LTX) was found to form two-dimensional (2D) monolayer arrays in solution at relatively low concentrations (0.1 mg/mL), with the toxin tetramer constituting a unit cell. The crystals were imaged using cryogenic electron microscopy (cryoEM), and image analysis yielded a ~12 Å projection map. At this resolution, no major conformational changes between the crystalline and solution states of α-LTX tetramers were observed. Electrophysiological studies showed that, under the conditions of crystallization, α-LTX simultaneously formed multiple channels in biological membranes that displayed coordinated gating. Two types of channels with conductance levels of 120 and 208 pS were identified. Furthermore, we observed two distinct tetramer conformations of tetramers both when observed as monodisperse single particles and within the 2D crystals, with pore diameters of 11 and 13.5 Å, suggestive of a flickering pore in the middle of the tetramer, which may correspond to the two states of toxin channels with different conductance levels. We discuss the structural changes that occur in α-LTX tetramers in solution and propose a mechanism of α-LTX insertion into the membrane. The propensity of α-LTX tetramers to form 2D crystals may explain many features of α-LTX toxicology and suggest that other pore-forming toxins may also form arrays of channels to exert maximal toxic effect.

Design of DNA-Based Artificial Transmembrane Channels for Biosensing and Biomedical Applications

Biomolecular channels on the cell membrane are essential for transporting substances across the membrane to maintain cell physiological activity. Artificial transmembrane channels used to mimic biological membrane channels can regulate intra/extracellular ionic and molecular homeostasis, and they elucidate cellular structures and functionalities. Due to their program design, facile preparation, and high biocompatibility, DNA nanostructures have been widely used as scaffolds for the design of artificial transmembrane channels and exploited for ionic and molecular transport and biomedical applications. DNA-based artificial channels can be designed from two structural modules: DNA nanotubes/nanopores as transport modules for mass transportation and hydrophobic segments as anchor modules for membrane immobilization. In this review, various lipophilic modification strategies for the design of DNA channels and membrane insertion are outlined. Several types of DNA transmembrane channels are systematically summarized, including DNA wireframe channels, DNA helix bundle channels, DNA tile channels, DNA origami channels, and so on. We then discuss efforts to exploit them in biosensor and biomedical applications. For example, ligand-gated and environmental stimuli-responsive artificial transmembrane channels have been designed for transmembrane signal transduction. DNA-based artificial channels have been developed for cell mimicry and the regulation of cell behaviors. Finally, we provide some perspectives on the challenges and future developments of artificial transmembrane channel research in biomimetic science and biomedical applications.

DNA nanopores as artificial membrane channels for bioprotonics

Biological membrane channels mediate information exchange between cells and facilitate molecular recognition. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout, which results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces. Here we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioprotonic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin and the cardiac biomarker B-type natriuretic peptide, without modifying the biomolecules. We anticipate this robust interface will allow facile electronic measurement and quantification of biomolecules in a multiplexed manner.

Cation-Gated Ion Transport at Nanometer Scale for Tunable Power Generation.

Gated ion channels in biological cell membranes allow efficient tuning of cross-membrane ion transport with enhanced permeation and selectivity, converting ionic signals into various forms of electrical signals and energies on demands, which functionalities though are still difficult to achieve in artificial membranes. Here, we report cation-gated ion transport through synthesized porous aromatic films containing nanometer-scale ionic channels together with -NH2 groups at interiors. Ion selectivity and permeability is greatly tuned by gating cations, up to 2 orders of magnitude, and as a consequence, the membrane efficiently produces switchable electricity output from salinity gradients. The results are attributed to positively charged cations binding at -NH2 groups, which screens the intrinsic negative surface charge at channels' interiors and inverts charge polarity there. Our work adds understanding to ion gating effects at nanoscale and offers strategies of developing smart membranes and their heterostructures for separation, energy conversion, cell membrane mimics, and related technologies.

Acylated and alkylated benzo(crown-ethers) form ion-dependent ion channels in biological membranes

Synthetic ion channels based on benzo(crown-ether) compounds have been previously reported to function as ion-selective channels in planar lipid bilayers, with hydrogen bonding networks implicated in the formation of self-aggregated complexes. Herein, we report the synthesis and characterization of two new families of benzo(crown-ether) compounds, termed monoacylated and monoalkylated benzo(crown-ethers) (MABCE), both of which lack hydrogen bond donors. Depending on the length of alkyl chain substituent and the size of macrocycle, MABCE compounds inhibit bacterial growth and transport ions across biological membranes. Single-channel recordings show that the activity is higher in the presence of K+ as compared with Na+; however, under bionic conditions, open channels do not exhibit any preference between the two ions. These findings reveal that the ionic preference of benzo(crown-ether) compounds is either due to the regulation of assembly of ion-conducting supramolecular complexes or its membrane insertion by cations, as opposed to ion-selective transport through these scaffolds. Furthermore, our data show that the H-bonding network is not needed to form these assemblies in the membrane.

Ion Transport, Selectivity and Charge Formation Mechanisms in Carbon Nanotube Porins: An Ab Initio Study

Narrow carbon nanotubes (CNTs) desalinate water, mimicking water channels of biological membranes, yet the physics behind selectivity, especially, relative roles of water and ion interactions within CNT and with surrounding matrix, is still unclear. Here we report ab initio (DFT) inverstigation of the energies involved in transfer of water and ions from bulk solution into bare and water-filled (5,5) nanotubes of diameter 0.68 nm and (6,6) nanotubes of diameter 0.8 nm, more common in experimental studies.In the first part, we will clarify the effect of the medium surrounding CNT, defined by its dielectric constant ε. Since nanotubes need to be embedded in an insulating matrix, ε may have a direct impact on water and ion transfer, yet its effect has not been previously investigated. The transfer energies computed ab initio in the full range 1 < ε < ∞ permit a transparent breakdown to three main contributions: binding to CNT, intra-CNT hydration, and dielectric energy. The results for (5,5) and (6,6) tubes indicate that dielectric energy is small in the case of water transfer. It is however very significant in the case of ions and scales linearly with 1/ε, reminiscent of the Born solvation model, with the slope in the range 75-130 kJ/mol for all analyzed ions and CNTs. This suggests that the dielectric energy is of the order of several tens kJ/mol for CNTs embedded in lipid bilayers (e ~2) and may easily turn ion transfer form preferential uptake to strong exclusion, as observed for K+. In contrast, Cl- appear to be strongly excluded for all ε, thus dielectric energy only enhances the exclusion. Curiously, opposite of conclusions previously drawn from classical MD simulations, ab initio simulations demonstrate that water and ion arrange in a single file in (5,5) tubes, yet it is strongly distorted in (6,6) tubes. Figure below displays most favorable arrangement of water (A) and ions (B,C) in (6,6) tubes. As a result, some species are solvated by more than two water molecules, which significantly affects their overall ion transfer energies, but not as mush its dielectric part.In the second on-going study, we carry out full thermodynamic analysis (including both enthalpy and entropy) of the effect of OH- and H3O+ ions, inherently present in water, on transfer of salt (KCl) and ionic conductance within CNTs. Its main purpose is to rationalize data on ion conductance and its dependence on KCl concentration and pH. Published experimental results indicate that (6,6) channels strongly exclude chloride in neutral conditions thereby conductance predominantly occurs as simultaneous uptake and migration of K+ and OH- ions. This suggests that the energy associated with OH- transfer is several tens kJ/mol lower than for Cl-, however, simulations show no such difference, and cannot explain the abnormally high contribution of OH- to CNT conductance. Based on simulations results, we also reject ion pairing (that may explain recent anion transfer data) and recently proposed electroneutrality breakdown in narrow channels as plausible explanations of the unusually high OH- contribution. However, simulations, currently on-going, point to possibility of some unorthodox transport regimes that might reasonably explain these and other experimental findings. Figure 1

Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport

Reproducing the structure and function of biological membrane channels, synthetic nanopores have been developed for applications in membrane filtration technologies and biomolecular sensing. Stable stand-alone synthetic nanopores have been created from a variety of materials, including peptides, nucleic acids, synthetic polymers, and solid-state membranes. In contrast to biological nanopores, however, furnishing such synthetic nanopores with an atomically defined shape, including deliberate placement of each and every chemical group, remains a major challenge. Here, we introduce a chemosynthetic macromolecule-extended pillararene macrocycle (EPM)-as a chemically defined transmembrane nanopore that exhibits selective transmembrane transport. Our ionic current measurements reveal stable insertion of individual EPM nanopores into a lipid bilayer membrane and remarkable cation type-selective transport, with up to a 21-fold selectivity for potassium over sodium ions. Taken together, direct chemical synthesis offers a path to de novo design of a new class of synthetic nanopores with custom transport functionality imprinted in their atomically defined chemical structure.

Interactions of Surfactants with Biomimetic Membranes. 1. Ionic Surfactants

AbstractWhen impregnated with esters of fatty acids, nitrocellulose filters can be used as a biomimetic membrane. They are easy to make, cheap, and may be used not only as an imitation of biological membranes but also as a sensor to characterize surfactant interactions with dirty fabric. These impregnated filters when fixed in a thermostatically controlled chamber separated into two compartments that contain stirred aqueous solutions by the filter, may be considered as a simple model of a laundry machine. The results revealed that the addition of ionic surfactants into one of the solutions led to the formation of transmembrane electrical potential that is proportional to the logarithm of surfactant concentration. Thus, our biomimetic membranes can be used as electrochemical sensors to detect and measure surfactant concentration. When concentration is near the critical micelle concentration (CMC), a new phenomenon was observed, i.e., spontaneous oscillations of both transmembrane potential and transmembrane current, which mimics the opening and closing of aqueous channels in biological membranes. A further increase of surfactant concentration les to a sharp 100‐fold decrease of transmembrane electrical resistance and the disappearance of any transmembrane voltage. This effect, explained by the washing out of fatty acids from the pores, may be used for screening and development of new detergents.

Differential regulation of drought stress by biological membrane transporters and channels.

Stress arising due to abiotic factors affects the plant's growth and productivity. Among several existing abiotic stressors like cold, drought, heat, salinity, heavy metal, etc., drought condition tends to affect the plant's growth by inducing two-point effect, i.e., it disturbs the water balance as well as induces toxicity by disturbing the ion homeostasis, thus hindering the growth and productivity of plants, and to survive under this condition, plants have evolved several transportation systems that are involved in regulating the drought stress. The role of membrane transporters has gained interest since genetic engineering came into existence, and they were found to be the important modulators for tolerance, avoidance, ion movements, stomatal movements, etc. Here in this comprehensive review, we have discussed the role of transporters (ABA, protein, carbohydrates, etc.) and channels that aids in withstanding the drought stress as well as the regulatory role of transporters involved in osmotic adjustments arising due to drought stress. This review also provides a gist of hydraulic conductivity by roots that are involved in regulating the drought stress.

Efficient, Positive, and Energy Stable Schemes for Multi-D Poisson–Nernst–Planck Systems

In this paper, we design, analyze, and numerically validate positive and energy-dissipating schemes for solving the time-dependent multi-dimensional system of Poisson–Nernst–Planck equations, which has found much use in the modeling of biological membrane channels and semiconductor devices. The semi-implicit time discretization based on a reformulation of the system gives a well-posed elliptic system, which is shown to preserve solution positivity for arbitrary time steps. The first order (in time) fully-discrete scheme is shown to preserve solution positivity and mass conservation unconditionally, and energy dissipation with only a mild O(1) time step restriction. The scheme is also shown to preserve the steady-states. For the fully second order (in both time and space) scheme with large time steps, solution positivity is restored by a local scaling limiter, which is shown to maintain the spatial accuracy. These schemes are easy to implement. Several three-dimensional numerical examples verify our theoretical findings and demonstrate the accuracy, efficiency, and robustness of the proposed schemes, as well as the fast approach to steady-states.

On Local Activity and Edge of Chaos in a NaMLab Memristor.

Local activity is the capability of a system to amplify infinitesimal fluctuations in energy. Complex phenomena, including the generation of action potentials in neuronal axon membranes, may never emerge in an open system unless some of its constitutive elements operate in a locally active regime. As a result, the recent discovery of solid-state volatile memory devices, which, biased through appropriate DC sources, may enter a local activity domain, and, most importantly, the associated stable yet excitable sub-domain, referred to as edge of chaos, which is where the seed of complexity is actually planted, is of great appeal to the neuromorphic engineering community. This paper applies fundamentals from the theory of local activity to an accurate model of a niobium oxide volatile resistance switching memory to derive the conditions necessary to bias the device in the local activity regime. This allows to partition the entire design parameter space into three domains, where the threshold switch is locally passive (LP), locally active but unstable, and both locally active and stable, respectively. The final part of the article is devoted to point out the extent by which the response of the volatile memristor to quasi-static excitations may differ from its dynamics under DC stress. Reporting experimental measurements, which validate the theoretical predictions, this work clearly demonstrates how invaluable is non-linear system theory for the acquirement of a comprehensive picture of the dynamics of highly non-linear devices, which is an essential prerequisite for a conscious and systematic approach to the design of robust neuromorphic electronics. Given that, as recently proved, the potassium and sodium ion channels in biological axon membranes are locally active memristors, the physical realization of novel artificial neural networks, capable to reproduce the functionalities of the human brain more closely than state-of-the-art purely CMOS hardware architectures, should not leave aside the adoption of resistance switching memories, which, under the appropriate provision of energy, are capable to amplify the small signal, such as the niobium dioxide micro-scale device from NaMLab, chosen as object of theoretical and experimental study in this work.

The Bionic Water Channel of Ultra-Short, High Affinity Carbon Nanotubes with High Water Permeability and Proton Selectivity

The development of the bionic water channel aims to replace the possible use of natural aquaporins (AQPs) for water purification, while retaining the ability of natural AQPs to carry out ultra-fast water transport and repel ions. Carbon nanotube channels (CNTCs) are a convenient membrane-based model system for studying nano-fluidic transport that replicates a number of key structural features of biological membrane channels. In this report, we describe protocols for CNTCs synthesis by ultrasound-assisted cutting of long CNTs in the presence of lipid amphiphiles. CNTCs have a similar thickness to the lipid membrane and high affinity for it. The ultra-short high-affinity CNTCs have high permeability and ion selectivity. The water permeability of the CNTCs is 1936 ± 123 μm/s, which is 2.3 times that of natural AQPs, and completely rejects salt ions. In general, carbon nanotubes represent a multifunctional nanopore building module for creating high-ranking functional bionic materials. This study has reference significance for the design of new bionic water channel and the actual development of bionic membrane based on CNTs.

Water and Ion Transfer to Narrow Carbon Nanotubes: Roles of Exterior and Interior.

Narrow carbon nanotubes (CNTs) desalinate water, mimicking water channels of biological membranes, yet the physics behind selectivity, especially the effect of the membrane embedding CNTs on water and ion transfer, is still unclear. Here, we report ab initio analysis of the energies involved in transfer of water and K+ and Cl- ions from solution to empty and water-filled 0.68 nm CNTs for different dielectric constants (ϵ) of the surrounding matrix. The transfer energies computed for 1 ≤ ϵ < ∞ permit a transparent breakdown of the transfer energy to three main contributions: binding to CNT, intra-CNT hydration, and dielectric polarization of the matrix. The latter scales inversely with ϵ and is of the order 102/ϵ kJ/mol for both ions, which may change ion transfer from favorable to unfavorable, depending on ion, ϵ, and CNT diameter. This may have broad implications for designing and tuning selectivity of nanochannel-based devices.

Molecular Transport through a Biomimetic DNA Channel on Live Cell Membranes.

Biological membrane channels, considered as molecular gatekeepers, control the transportation of molecules and ions across live cell membranes. Developing synthetic passable channels with predictable structures, high transport efficiency, and low cytotoxicity on live cells is of great interest for replicating the functions of endogenous protein channels, but remains challenging. The development of DNA nanotechnology provides possible solutions for making synthetic channels with precise structures and controllable functionalization. Therefore, in this work, we constructed a phosphorothioate-modified DNA nanopore able to structurally mimic biological channels for molecular transport across live cell membranes. With its stable structure with small hollow size (<2 nm) and the ability to interact with the lipid molecules, this DNA nanopore could show stable insertion into the plasma membrane. We further proved that this membrane-spanning channel could transport ions and antitumor drugs to neurons and cancer cells, respectively, and do so within a certain time window. We expect that this live cell membrane-spanning synthetic DNA nanopore will provide a tool for studying cellular communication, building synthetic cells, and achieving controlled transmembrane transport to cells.

Carbon nanotube porin diffusion in mixed composition supported lipid bilayers

Carbon nanotube porins (CNTPs), short pieces of carbon nanotubes capable of self-inserting into a lipid bilayer, represent a simplified model of biological membrane channels. We have used high-speed atomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavior of CNTPs in a mixed lipid membrane consisting of DOPC lipid with a variable percentage of DMPC lipid added to it. HS-AFM data reveal that the CNTPs undergo diffusive motion in the bilayer plane. Motion trajectories extracted from the HS-AFM movies indicate that CNTPs exhibit diffusion coefficient values broadly similar to values reported for membrane proteins in supported lipid bilayers. The data also indicate that increasing the percentage of DMPC leads to a marked slowing of CNTP diffusion. MD simulations reveal a CNTP-lipid assembly that diffuses in the membrane and show trends that are consistent with the experimental observations.

Effect of stochastic gating on channel-facilitated transport of non-interacting and strongly repelling solutes.

Ligand- or voltage-driven stochastic gating-the structural rearrangements by which the channel switches between its open and closed states-is a fundamental property of biological membrane channels. Gating underlies the channel's ability to respond to different stimuli and, therefore, to be functionally regulated by the changing environment. The accepted understanding of the gating effect on the solute flux through the channel is that the mean flux is the product of the flux through the open channel and the probability of finding the channel in the open state. Here, using a diffusion model of channel-facilitated transport, we show that this is true only when the gating is much slower than the dynamics of solute translocation through the channel. If this condition breaks, the mean flux could differ from this simple estimate by orders of magnitude.

Gated Water Transport through Graphene Nanochannels: From Ionic Coulomb Blockade to Electroosmotic Pump

Understanding and controlling water or ion transport in nanochannels plays an important role in further unravelling the transport mechanism of biological membrane channels and designing functional nanofluidic devices. Molecular dynamics simulations were conducted to investigate water and ion transport in graphene nanochannels. Similar to electron coulomb blockade phenomenon observed in quantum dots, we discovered an ionic coulomb blockade phenomenon in our graphene nanochannels, and another two ion transport modes were also proposed to rationalize the observed phenomena under different electric-field intensities. Furthermore, on the basis of this blockade phenomenon we found that the Open and Closed states of the graphene nanochannels for water transport could be switched according to external electric-field intensities, and electroosmotic flow could further enhance the water transport. These findings might have potential applications in designing and fabricating controllable valves in lab-on-chip nanodev...

High-Yield Synthesis and Optical Properties of Carbon Nanotube Porins

Carbon nanotube porins (CNTPs) are a convenient membrane-based model system for studying nanofluidic transport that replicates a number of key structural features of biological membrane channels. We present a generalized approach for CNTP synthesis using sonochemistry-assisted segmenting of carbon nanotubes. Prolonged tip sonication in the presence of lipid molecules debundles and fragments long carbon nanotube aggregates into stable and water-soluble individual CNTPs with lengths in the range 5–20 nm. We discuss the main parameters that determine the efficiency and the yield of this process, describe the optimized conditions for high-yield CNTP synthesis, and demonstrate that this methodology can be adapted for synthesis of CNTPs of different diameters. We also present the optical properties of CNTPs and show that a combination of Raman and UV–vis–NIR spectroscopy can be used to monitor the quality of the CNTP synthesis. Overall, CNTPs represent a versatile nanopore building block for creating higher-ord...