Transport at the nanoscale: temperature dependence of ion conductance

Temperature dependent ion conductance in nanopores is measured in a wide range of electrolyte concentrations and compared with molecular modeling. Single outer membrane protein F (OmpF) channels from E. coli are reconstituted into planar lipid bilayers. In qualitative agreement with the experimental data, applied-field molecular dynamics unraveled atomistic details of the ion transport. Comparing the temperature dependence of the channel conductance with that of the bulk conductivity in the range from 0 to 90°C revealed that at low salt concentrations the transport is mainly driven along the pore surface. Increasing the salt concentration saturates the surface charge transport and induces ion transport in the center of the nanopore. The confinement of the nanopore then favors the formation of ion pairs. Stepping up the temperature reduces the life time of the ion pairs and increases the channel conductance more than expected from the bulk behavior.     

Partitioning of Differently Sized Poly(ethylene glycol)s into OmpF Porin

To understand the physics of polymer equilibrium and dynamics in the confines of ion channel pores, we study partitioning of poly(ethylene glycol)s (PEGs) of different molecular weights into the bacterial porin, OmpF. Thermodynamic and kinetic parameters of partitioning are deduced from the effects of polymer addition on ion currents through single OmpF channels reconstituted into planar lipid bilayer membranes. The equilibrium partition coefficient is inferred from the average reduction of channel conductance in the presence of PEG; rates of polymer exchange between the pore and the bulk are estimated from PEG-induced conductance noise. Partition coefficient as a function of polymer weight is best fitted by a “compressed exponential” with the compression factor of 1.65. This finding demonstrates that PEG partitioning into the OmpF channel pore has sharper dependence on polymer molecular weight than predictions of hard-sphere, random-flight, or scaling models. A 1360-Da polymer separates regimes of partitioning and exclusion. Comparison of its characteristic size with the size of a 2200-Da polymer previously found to separate these regimes for the α-toxin shows good agreement with the x-ray structural data for these channels. The PEG-induced conductance noise is compatible with the polymer mobility reduced inside the OmpF pore by an order of magnitude relatively to its value in bulk solution.     

Size and Dynamics of the Vibrio cholerae Porins OmpU and OmpT Probed by Polymer Exclusion

The trimeric OmpU and OmpT porins form large, triple-barrel hydrophilic channels in the outer membrane of the pathogen Vibrio cholerae. They have distinct pore properties, such as conductance, block by deoxycholic acid, and sensitivity to acidic pH. Their three-dimensional structures are unknown, but they share significant sequence homologies. To gain insight into the molecular basis for the distinct functional properties of these two similar porins, we carried out polymer exclusion experiments using planar lipid bilayer and patch-clamp electrophysiology. By studying the partitioning of polyethylene glycols (PEGs) of different molecular weights into each porin, we determined an effective radius of 0.55 nm and 0.43 nm for OmpU and OmpT respectively, and found an increased OmpU effective radius at acidic pH. PEGs or high buffer ionic strength promotes the appearance of single step closures in OmpU similar to the acidic-pH induced closures we documented previously. In addition, these closing events can be triggered by nonpenetrating PEGs applied asymmetrically. We believe our results support a model whereby acidic pH, high ionic strength, or exposure to PEGs stabilizes a less conductive state that corresponds to the appearance of an additional resistive element on one side of the OmpU protein and common to the three monomers.     

Effect of temperature on the escape of charged polymer chain from a repulsive nanopore

The effect of temperature on the escape of a charged polymer chain from a repulsive nanopore is studied by Langevin dynamics simulations. The conformation properties of the charged polymer chain are dependent on the temperature as it is in random coil state at high temperature and in compact globule state at low temperature. The scaling behaviour between the escape time and polymer length is independent of temperature, while the escape time decreases with increasing the temperature in an exponential way. Different temperature-dependent behaviours are observed for the escape time in three temperature regimes: low temperature where the polymer is in compact globule state, intermediate temperature around the coil-to-globule transition temperature, and high temperature where the polymer is in the random coil state. We further find that, with a decrease in the temperature, the total number of moving steps for the escape increases sharply in the low-temperature regime while the time duration for each moving step increases sharply in the intermediate temperature regime.     

Polymeric nonelectrolytes to probe pore geometry: application to the alpha-toxin transmembrane channel

Asymmetrical (one-sided) application of penetrating water-soluble polymers, polyethylene glycols (PEGs), to a well-defined channel formed by Staphylococcus aureus alpha-toxin is shown to probe channel pore geometry in more detail than their symmetrical (two-sided) application. Polymers added to the cis side of the planar lipid membrane (the side of protein addition) affect channel conductance differently than polymers added to the trans side. Because a satisfactory theory quantitatively describing PEG partitioning into a channel pore does not exist, we apply the simple empirical rules proposed previously (, J. Membr. Biol. 161:83-92) to gauge the size of pore openings as well as the size and position of constrictions along the pore axis. We estimate the radii of the two openings of the channel to be practically identical and equal to 1. 2-1.3 nm. Two apparent constrictions with radii of approximately 0. 9 nm and approximately 0.6-0.7 nm are inferred to be present in the channel lumen, the larger one being closer to the cis side. These structural findings agree well with crystallographic data on the channel structure (, Science. 274:1859-1866) and verify the practicality of polymer probing. The general features of PEG partitioning are examined using available theoretical considerations, assuming there is no attraction between PEG and the channel lumen. It is shown that the sharp dependence of the partition coefficient on polymer molecular weight found under both symmetrical and asymmetrical polymer application can be rationalized within a "hard sphere nonideal solution model." This finding is rather surprising because PEG forms highly flexible coils in water with a Kuhn length of only several Angstroms.     

Modifying the pH sensitivity of OmpG nanopore for improved detection at acidic pH

The outer membrane protein G (OmpG) nanopore is a monomeric β-barrel channel consisting of seven flexible extracellular loops. Its most flexible loop, loop 6, can be used to host high-affinity binding ligands for the capture of protein analytes, which induces characteristic current patterns for protein identification. At acidic pH, the ability of OmpG to detect protein analytes is hampered by its tendency toward the closed state, which renders the nanopore unable to reveal current signal changes induced by bound analytes. In this work, critical residues that control the pH-dependent gating of loop 6 were identified, and an OmpG nanopore that can stay predominantly open at a broad range of pHs was created by mutating these pH-sensitive residues. A short single-stranded DNA was chemically tethered to the pH-insensitive OmpG to demonstrate the utility of the OmpG nanopore for sensing complementary DNA and a DNA binding protein at an acidic pH.     

Developing synthetic conical nanopores for biosensing applications

In this review we bring together recent results from our group focused towards the development of biosensors from single conically-shaped artificial nanopores. The nanopores, used in the work presented here, were prepared using the track-etch process. The fabrication of track-etched conical nanopores has been optimized to allow for single nanopores with reproducible dimensions to be prepared. We have also demonstrated techniques that allow for easy and controllable manipulation of nanopore geometry (e.g., cone angle). We will consider the ion transport properties of the conical nanopores and factors that affect these properties. Methods for introducing functions that mimic biological ion channels, such as voltage-gating, into these nanopores will also be addressed. Three prototype sensors developed from single conical nanopores will be presented. In the first two sensors, the single conical nanopores function as resistive-pulse sensors and detect the presence of analytes as current-blockade events in the ion current. The third sensor functions in an on/off mode, much like a ligand-gated ion channel. In the presence of a target analyte, the ion current permanently shuts off.     

Multiscale simulation studies of geometrical effects on solution transport through nanopores

Due to intrinsic properties, solid-state nanopores are widely used in nanopore technology. Different geometries (cylindrical (CY), hourglass (HG) and conical (CO)) of artificial nanopores have been fabricated and studied. Each was found to promote different transport abilities experimentally. To explore such pore effects, the combination of finite element (FE) and molecular dynamics (MD) simulations with applied electric filed (150 mV) were performed. The dimension of anion-selective protein pore was used as a nanopore template. Different pore geometries with a narrowest diameter ranging from 1.8 to 1.8 μm were studied here. Firstly, we found that the narrowest regions at a pore orifice in CO and constriction site in HG maximise water velocity and consequently control a water flow rate. Secondly, CY triggers the highest water flux, but low ion selectivity, whilst the funnel-like geometries (HG and CO) enhance the ion selectivity significantly. Both HG and CO show similar degrees of permeant flux and selectivity. The orifice and constriction site in CO and HG are the main player for selectivity and permeation control. Thirdly, the transport properties are tuneable by changing the flow direction in asymmetric CO pore. The tip-to-base flow in CO obviously promotes stronger anion selectivity than the base-to-tip one.     

Steric exclusion is the principal source of the preferential hydration of proteins in the presence of polyethylene glycols.

The preferential interactions of bovine serum albumin, lysozyme, chymotrypsinogen, ribonuclease A, and beta-lactoglobulin with polyethylene glycols (PEGs) of molecular weight 200-6,000 have been measured by dialysis equilibrium coupled with high precision densimetry. All the proteins were found to be preferentially hydrated in all the PEGs, and the magnitude of the preferential hydration increased with increasing PEG size for each protein. The change in the chemical potentials of the proteins with the addition of the PEGs had highly positive values, indicating a strong thermodynamic destabilization of the system by the PEGs. A viscosity study of the PEGs showed them to be randomly coiled polymers, as their radii of gyration were related to the molecular weight by Rg = aM0.55. The thickness of the effective shell impenetrable to PEG around protein molecules, calculated from the preferential hydration, was found to vary with PEG molecular weight in similar fashion as the PEG radius of gyration, supporting the proposal (Arakawa, T. & Timasheff, S.N., 1985a, Biochemistry 24, 6756-6762) that the preferential exclusion of PEGs from proteins is due principally to the steric exclusion of PEG from the protein domain, although favorable interactions with protein surface residues, in particular nonpolar ones, may compete with the exclusion. These thermodynamically unfavorable preferential exclusion interactions lead to the action of PEGs as precipitants, although they may destabilize protein structure at higher temperatures.     

Insights into the biophysical properties of GABA(A) ion channels: modulation of ion permeation by drugs and protein interactions

The fundamental properties of ion channels assure their selectivity for a particular ion, its rapid permeation through a central pore and that such electrical activity is modulated by factors that control the opening and closing (gating) of the channel. All cell types possess ion channels and their regulated flux of ions across the membrane play critical roles in all steps of life. An ion channel does not act alone to control cell excitability but rather forms part of larger protein complexes. The identification of protein interaction partners of ion channels and their influence on both the fundamental biophysical properties of the channel and its expression in the membrane are revealing the many ways in which electrical activity may be regulated. Highlighted here is the novel use of the patch clamp method to dissect out the influence of protein interactions on the activity of individual GABA(A) receptors. The studies demonstrate that ion conduction is a dynamic property of a channel and that protein interactions in a cytoplasmic domain underlie the channel's ability to alter ion permeation. A structural model describing a reorganisation of the conserved cytoplasmic gondola domain and the influence of drugs on this process are presented.     

Protein-protein association in polymer solutions: from dilute to semidilute to concentrated

In a typical cell, proteins function in the crowded cytoplasmic environment where 30% of the space is occupied by macromolecules of varying size and nature. This environment may be simulated in vitro using synthetic polymers. Here, we followed the association and diffusion rates of TEM1-beta-lactamase (TEM) and the beta-lactamase inhibitor protein (BLIP) in the presence of crowding agents of varying molecular mass, from monomers (ethylene glycol, glycerol, or sucrose) to polymeric agents such as different polyethylene glycols (PEGs, 0.2-8 kDa) and Ficoll. An inverse linear relation was found between translational diffusion of the proteins and viscosity in all solutions tested, in accordance with the Stokes-Einstein (SE) relation. Conversely, no simple relation was found between either rotational diffusion rates or association rates (k(on)) and viscosity. To assess the translational diffusion-independent steps along the association pathway, we introduced a new factor, alpha, which corrects the relative change in k(on) by the relative change in solution viscosity, thus measuring the deviations of the association rates from SE behavior. We found that these deviations were related to the three regimes of polymer solutions: dilute, semidilute, and concentrated. In the dilute regime PEGs interfere with TEM-BLIP association by introducing a repulsive force due to solvophobic preferential hydration, which results in slower association than predicted by the SE relation. Crossing over from the dilute to the semidilute regime results in positive deviations from SE behavior, i.e., relatively faster association rates. These can be attributed to the depletion interaction, which results in an effective attraction between the two proteins, winning over the repulsive force. In the concentrated regime, PEGs again dramatically slow down the association between TEM and BLIP, an effect that does not depend on the physical dimensions of PEGs, but rather on their mass concentration. This is probably a manifestation of the monomer-like repulsive depletion effect known to occur in concentrated polymer solutions. As a transition from moderate to high crowding agent concentration can occur in the cellular milieu, this behavior may modulate protein association in vivo, thereby modulating biological function.     

Nanopore cheminformatics

A cheminformatics method is described for classification, and biophysical examination, of individual molecules. A novel molecular detector is used--one based on current blockade measurements through a nanometer-scale ion channel (alpha-hemolysin). Classification results are described for blockades caused by DNA molecules in the alpha-hemolysin nanopore detector, with signal analysis and pattern recognition performed using a combination of methods from bioinformatics and machine learning. Due to the size of the alpha-hemolysin protein channel, the blockade events report on one DNA molecule at a time, which enables a variety of reproducible, single-molecule biophysical experiments. To capture the full sensitivity of the nanopore detector's blockade signal, Hidden Markov Models (HMMs) were used with Expectation/Maximization for denoising and for associating a feature vector with the ionic current blockade of each captured DNA molecule. Support Vector Machines (SVMs) that employ novel kernel designs were then used as discriminators. With SVM training performed off-line, and economical HMM processing on-line, blockade classification was possible during capture. HMMs were also used in conjunction with a time-domain finite state automaton (off-line) for feature discovery and kinetics analysis. Analysis of the DNA data indicates a variety of binding (DNA-protein), fraying, and conformational shifts that are consistent with data obtained from thermodynamic analyses (melting curves), X-ray crystallography, and NMR studies. The software tools are designed for analysis of generic blockades in ionic channels, including those in other biological pore-forming toxins, other biological channels in general, and semiconductor-based channels.     

Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel

RNA and DNA strands produce ionic current signatures when driven through an alpha-hemolysin channel by an applied voltage. Here we combine this nanopore detector with a support vector machine (SVM) to analyze DNA hairpin molecules on the millisecond time scale. Measurable properties include duplex stem length, base pair mismatches, and loop length. This nanopore instrument can discriminate between individual DNA hairpins that differ by one base pair or by one nucleotide.     

Probing alamethicin channels with water-soluble polymers. Size-modulated osmotic action.

Contrary to expectations based on heightened solution viscosity, alamethicin channels appear to speed up in the presence of water soluble polyethylene glycols (PEGs) and dextrans. Specifically, added polymers reduce the probabilities of transition to higher-conductance states but do not change channel lifetimes. They thereby shorten the duration of current "bursts." These modified probabilities and kinetics reveal the action of polymer osmotic stress to suppress channel formation. The osmotic action of large, fully excluded polymers shows that some 3,000 A3 of water are taken up by the channel from the solution upon each transition to an adjacent higher-conductance state. The partial osmotic action of incompletely excluded polymers reveals the extent of exclusion for different-size polymers. The partial exclusion thus measured agrees remarkably well with estimates using data on reduction of single-channel conductance by current-impeding polymers. One can relate the degree of each polymer's exclusion to its size and to the radius of the channel pore.     

Improved 3D continuum calculations of ion flux through membrane channels

A continuum model, based on the Poisson–Nernst–Planck (PNP) theory, is applied to simulate steady-state ion flux through protein channels. The PNP equations are modified to explicitly account (1) for the desolvation of mobile ions in the membrane pore and (2) for effects related to ion sizes. The proposed algorithm for a three-dimensional self-consistent solution of PNP equations, in which final results are refined by a focusing technique, is shown to be suitable for arbitrary channel geometry and arbitrary protein charge distribution. The role of the pore shape and protein charge distribution in formation of basic electrodiffusion properties, such as channel conductivity and selectivity, as well as concentration distributions of mobile ions in the pore region, are illustrated by simulations on model channels. The influence of the ionic strength in the bulk solution and of the externally applied electric field on channel properties are also discussed.     

Single polypeptide detection using a translocon EXP2 nanopore

DNA sequencing using nanopores has already been achieved and commercialized; the next step in advancing nanopore technology is towards protein sequencing. Although trials have been reported for discriminating the 20 amino acids using biological nanopores and short peptide carriers, it remains challenging. The size compatibility between nanopores and peptides is one of the issues to be addressed. Therefore, exploring biological nanopores that are suitable for peptide sensing is key in achieving amino acid sequence determination. Here, we focus on EXP2, the transmembrane protein of a translocon from malaria parasites, and describe its pore-forming properties in the lipid bilayer. EXP2 mainly formed a nanopore with a diameter of 2.5 nm assembled from 7 monomers. Using the EXP2 nanopore allowed us to detect poly-L-lysine (PLL) at a single-molecule level. Furthermore, the EXP2 nanopore has sufficient resolution to distinguish the difference in molecular weight between two individual PLL, long PLL (Mw: 30,000–70,000) and short PLL (Mw: 10,000). Our results contribute to the accumulation of information for peptide-detectable nanopores.     

Single-molecule analysis of DNA-protein complexes using nanopores

We present a method for rapid measurement of DNA-protein interactions using voltage-driven threading of single DNA molecules through a protein nanopore. Electrical force applied to individual ssDNA-exonuclease I complexes pulls the two molecules apart, while ion current probes the dissociation rate of the complex. Nanopore force spectroscopy (NFS) reveals energy barriers affecting complex dissociation. This method can be applied to other nucleic acid-protein complexes, using protein or solid-state nanopore devices.     

Correction

Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into account inter- and intramolecular interactions, as well as the finite size of the NTRs (∼20% of the NPC channel diameter). It reproduces various proposed scenarios for the channel structure, ranging from a central polymer condensate (selective phase) to brushlike polymer arrangements localized at the channel wall (virtual gate, reduction of dimensionality), with the transport receptors lining the polymer surface. In addition, it predicts a new structure in which NTRs become an integral part of the transport barrier by forming a cross-linked network with the unstructured proteins stretching across the pore. The model provides specific and distinctive predictions for the equilibrium spatial distributions of NTRs for these different scenarios that can be experimentally verified by, e.g., superresolution fluorescence microscopy. Moreover, it suggests mechanisms by which globular macromolecules (colloidal particles) can cause polymer-coated nanopores to switch between open and closed configurations, a possible explanation of the biological function of the NPC, and suggests potential technological applications for filtration and single-molecule sensing.     

Model Inspired by Nuclear Pore Complex Suggests Possible Roles for Nuclear Transport Receptors in Determining Its Structure

Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into account inter- and intramolecular interactions, as well as the finite size of the NTRs (∼20% of the NPC channel diameter). It reproduces various proposed scenarios for the channel structure, ranging from a central polymer condensate (selective phase) to brushlike polymer arrangements localized at the channel wall (virtual gate, reduction of dimensionality), with the transport receptors lining the polymer surface. In addition, it predicts a new structure in which NTRs become an integral part of the transport barrier by forming a cross-linked network with the unstructured proteins stretching across the pore. The model provides specific and distinctive predictions for the equilibrium spatial distributions of NTRs for these different scenarios that can be experimentally verified by, e.g., superresolution fluorescence microscopy. Moreover, it suggests mechanisms by which globular macromolecules (colloidal particles) can cause polymer-coated nanopores to switch between open and closed configurations, a possible explanation of the biological function of the NPC, and suggests potential technological applications for filtration and single-molecule sensing.     

Simultaneously Enhancing the Thermal Stability,Mechanical Modulus,and Electrochemical Performance of Solid Polymer Electrolytes by Incorporating 2D Sheets

Solid state electrolytes are the key components for high energy density lithium ion batteries and especially for lithium metal batteries where lithium dendrite growth is an inevitable obstacle in liquid electrolytes. Solid polymer electrolytes based on a complex of polymers and lithium salts are intrinsically advantageous over inorganic electrolytes in terms of processability and film‐forming properties. But other properties such as ionic conductivity, thermal stability, mechanical modulus, and electrochemical stability need to be improved. Herein, for the first time, 2D additives using few‐layer vermiculite clay sheets as an example to comprehensively upgrade poly(ethylene oxide)‐based solid polymer electrolyte are introduced. With clay sheet additives, the polymer electrolyte exhibits improved thermal stability, mechanical modulus, ionic conductivity, and electrochemical stability along with reduced flammability and interface resistance. The composite polymer electrolyte can suppress the formation and growth of lithium dendrites in lithium metal batteries. It is anticipated that the clay sheets upgraded solid polymer electrolyte can be integrated to construct high performance solid state lithium ion and lithium metal batteries with higher energy and safety.