Partitioning of differently sized poly(ethylene glycol)s into OmpF porin

Unique Properties of Nutrient Channels on Plasmodium-Infected Erythrocytes

Intracellular malaria parasites activate an ion and organic solute channel on their host erythrocyte membrane to acquire a broad range of essential nutrients. This plasmodial surface anion channel (PSAC) facilitates the uptake of sugars, amino acids, purines, some vitamins, and organic cations, but remarkably, it must exclude the small Na+ ion to preserve infected erythrocyte osmotic stability in plasma. Although molecular, biochemical, and structural studies have provided fundamental mechanistic insights about PSAC and advanced potent inhibitors as exciting antimalarial leads, important questions remain about how nutrients and ions are transported. Here, I review PSAC's unusual selectivity and conductance properties, which should guide future research into this important microbial ion channel.

Revealing the single-channel characteristics of OprD (OccAB1) porins from hospital strains of Acinetobacter baumannii

Nowadays, reports of antimicrobial resistance (AMR) against many antibiotics are increasing because of their misapplication. With this rise, there is a serious decrease in the discovery and development of new types of antibiotics amid an increase in multi-drug resistance. Unfermented Acinetobacter baumannii from gram-negative bacteria, which is one of the main causes of nosocomial infections and multi-drug resistance, has 4 main kinds of antibiotic resistance mechanism: inactivating antibiotics by enzymes, reduced numbers of porins and changing of their target or cellular functions due to mutations, and efflux pumps. In this study, characterization of the possible mutations in OprD (OccAB1) porins from hospital strains of A. baumannii were investigated using single channel electrophysiology and compared with the standard OprD isolated from wild type ATCC 19,606. For this aim, 5 A. baumannii bacteria samples were obtained from patients infected with A. baumannii, after which OprD porins were isolated from these A. baumannii strains. OprD porins were then inserted in an artificial lipid bilayer and the current-voltage curves were obtained using electrical recordings through a pair of Ag/AgCl electrodes. We observed that each porin has a characteristic conductance and single channel recording, which then leads to differences in channel diameter. Finally, the single channel data have been compared with the gene sequences of each porin. It was interesting to find out that each porin isolated has a unique porin diameter and decreased anion selectivity compared to the wild type.

DNA origami in the quest for membrane piercing

The tool kit for label-free single-molecule sensing, nucleic acid sequencing (DNA, RNA and protein) and other biotechnological applications has been significantly broadened due to the wide range of available nanopore-based technologies. Currently, various sources of nanopores, including biological, fabricated solid-state, hybrid and recently de novo chemically synthesized ion-like channels have put in use for rapid single-molecule sensing of biomolecules and other diagnostic applications. At length scales of hundreds of nanometers, DNA nanotechnology, particularly DNA origami-based devices, enables the assembly of complex and dynamic 3-dimensional nanostructures, including nanopores with precise control over the size/shape. DNA origami technology has enabled to construct nanopores by DNA alone or hybrid architects with solid-state nanopore devices or nanocapillaries. In this review, we briefly discuss the nanopore technique that uses DNA nanotechnology to construct such individual pores in lipid-based systems or coupled with other solid-state devices, nanocapillaries for enhanced biosensing function. We summarize various DNA-based design nanopores and explore the sensing properties of such DNA channels. Apart from DNA origami channels we also pointed the design principles of RNA nanopores for peptide sensing applications.

Probing Protein Nanopores with Poly(ethylene glycol)s

Neutral water-soluble poly(ethylene glycol)s (PEGs) have been extensively explored in protein nanopore research for the past several decades. The principal use of PEGs is to investigate the membrane protein ion channel physical characteristics and transport properties. In addition, protein nanopores are used to study polymer-protein interactions and polymer physicochemical properties. In this review, we focus on the biophysical studies on probing protein ion channels with PEGs, specifically on nanopore sizing by PEG partitioning. We discuss the fluctuation analysis of ion channel currents in response to the PEGs moving within their confined geometries. The advantages, limitations, and recent developments of the approach are also addressed. This article is protected by copyright. All rights reserved.

Current Fluctuations in Nanopores Reveal the Polymer-Wall Adsorption Potential

Modification of surface properties by polymer adsorption is a widely used technique to tune interactions in molecular experiments such as nanopore sensing. Here, we investigate how the ionic current noise through solid-state nanopores reflects the adsorption of short, neutral polymers to the pore surface. The power spectral density of the noise shows a characteristic change upon adsorption of polymer, the magnitude of which is strongly dependent on both polymer length and salt concentration. In particular, for short polymers at low salt concentrations no change is observed, despite the verification of comparable adsorption in these systems using quartz crystal microbalance measurements. We propose that the characteristic noise is generated by the movement of polymers on and off the surface and perform simulations to assess the feasibility of this model. Excellent agreement with experimental data is obtained using physically motivated simulation parameters, providing deep insight into the shape of the adsorption potential and underlying processes. This paves the way toward using noise spectral analysis for in situ characterization of functionalized nanopores.

PEG Equilibrium Partitioning in the α-Hemolysin Channel: Neutral Polymer Interaction with Channel Charges

We study the interaction of neutral polyethylene glycol (PEG) molecules of different molecular weights (MWs) with the charged residues of the α-hemolysin channel secreted by Staphylococcus aureus. Previously reported experiments of PEG equilibrium partitioning into this nanopore show that the charge state of the channel changes the ability of PEG entry in an MW-dependent manner. We explain such an effect by parameter-free calculations of the PEG self-energy from the channel 3D atomic structure that include repulsive dielectrophoretic and hydrostatic forces on the polymer. We found that the pH-induced shift in the measured free energy of partitioning ΔΔG_exp from single-channel conductance measurements agrees with calculated energy changes ΔΔE_calc. Our results show that the PEG-sizing technique may need corrections in the case of charged biological pores.

Bioactive Catalytic Nanocompartments Integrated into Cell Physiology and Their Amplification of a Native Signaling Cascade

Bioactive nanomaterials have the potential to overcome the limitations of classical pharmacological approaches by taking advantage of native pathways to influence cell behavior, interacting with them and eliciting responses. Herein, we propose a cascade system mediated by two catalytic nanocompartments (CNC) with biological activity. Activated by nitric oxide (NO) produced by inducible nitric oxidase synthase (iNOS), soluble guanylyl cyclase (sGC) produces cyclic guanosine monophosphate (cGMP), a second messenger that modulates a broad range of physiological functions. As alterations in cGMP signaling are implicated in a multitude of pathologies, its signaling cascade represents a viable target for therapeutic intervention. Following along this line, we encapsulated iNOS and sGC in two separate polymeric compartments that function in unison to produce NO and cGMP. Their action was tested in vitro by monitoring the derived changes in cytoplasmic calcium concentrations of HeLa and differentiated C2C12 myocytes, where the produced second messenger influenced the cellular homeostasis.

Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture

The high complexity of in situ ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of in situ environments.

Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes, including Synechococcus and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the Synechococcus-heterotroph coculture system and the interactions shaping the system.

Microelectrochemical cell arrays for whole-cell currents recording through ion channel proteins based on trans-electroporation approach

High electrostability and long life-time of planar chip technology are crucial for electrophysiological measurements such as ionic current recording through ion channel proteins embedded in biological cell membrane. In this paper, we propose a novel planar microchip integrated with microelectrochemical cell array toward to a feasible solution for ion channel screening with high resolution and long life-time. In order to reduce the interference from the leakage currents, a synthetic lipid bilayer is applied to form a high sealing resistance. The whole-cell electrical access can be constructed via electroporating the lipid bilayer in close proximity to the cell membrane. Parameters of electroporation including amplitude and time scale are firstly optimized by using parallel electroporation to the lipid bilayers. In this approach, individual cells can be trapped to the target positions by applying dielectrophoresis (DEP) manipulation. Poly(ethylene glycol) (PEG) is employed with low concentration to facilitate the closed contact between the cells and the lipid bilayer to increase the efficiency of the whole-cell mode construction. Through this chip based method, stable current recordings through inward rectifier potassium (Kir) ion channels embedded in rat basophilic leukemia (RBL-1) cell membrane are achieved with high electrical sealing resistance (over 1 GΩ). In addition, without need for complex fluidic connections, this method allows for an easy operation and further miniaturization of the measuring system.

Scaling Behavior of Ionic Transport in Membrane Nanochannels

Ionic conductance in membrane channels exhibits a power-law dependence on electrolyte concentration ( G ∼ c^α). The many scaling exponents, α, reported in the literature usually require detailed interpretations concerning each particular system under study. Here, we critically evaluate the predictive power of scaling exponents by analyzing conductance measurements in four biological channels with contrasting architectures. We show that scaling behavior depends on several interconnected effects whose contributions change with concentration so that the use of oversimplified models missing critical factors could be misleading. In fact, the presence of interfacial effects could give rise to an apparent universal scaling that hides the channel distinctive features. We complement our study with 3D structure-based Poisson-Nernst-Planck (PNP) calculations, giving results in line with experiments and validating scaling arguments. Our findings not only provide a unified framework for the study of ion transport in confined geometries but also highlight that scaling arguments are powerful and simple tools with which to offer a comprehensive perspective of complex systems, especially those in which the actual structure is unknown.

Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

Background

Corynebacterium urealyticum, a pathogenic, multidrug resistant member of the mycolata, is known as causative agent of urinary tract infections although it is a bacterium of the skin flora. This pathogenic bacterium shares with the mycolata the property of having an unusual cell envelope composition and architecture, typical for the genus Corynebacterium. The cell wall of members of the mycolata contains channel-forming proteins for the uptake of solutes.

Results

In this study, we provide novel information on the identification and characterization of a pore-forming protein in the cell wall of C. urealyticum DSM 7109. Detergent extracts of whole C. urealyticum cultures formed in lipid bilayer membranes slightly cation-selective pores with a single-channel conductance of 1.75 nS in 1 M KCl. Experiments with different salts and non-electrolytes suggested that the cell wall pore of C. urealyticum is wide and water-filled and has a diameter of about 1.8 nm. Molecular modelling and dynamics has been performed to obtain a model of the pore. For the search of the gene coding for the cell wall pore of C. urealyticum we looked in the known genome of C. urealyticum for a similar chromosomal localization of the porin gene to known porH and porA genes of other Corynebacterium strains. Three genes are located between the genes coding for GroEL2 and polyphosphate kinase (PKK2). Two of the genes (cur_1714 and cur_1715) were expressed in different constructs in C. glutamicum ΔporAΔporH and in porin-deficient BL21 DE3 Omp8 E. coli strains. The results suggested that the gene cur_1714 codes alone for the cell wall channel. The cell wall porin of C. urealyticum termed PorACur was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 4 kDa on tricine-containing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).

Conclusions

Biophysical characterization of the purified protein (PorACur) suggested indeed that cur_1714 is the gene coding for the pore-forming protein in C. urealyticum because the protein formed in lipid bilayer experiments the same pores as the detergent extract of whole cells. The study is the first report of a cell wall channel in the pathogenic C. urealyticum.

Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae

The outer membranes (OM) of many Gram-negative bacteria contain general porins, which form nonspecific, large-diameter channels for the diffusional uptake of small molecules required for cell growth and function. While the porins of Enterobacteriaceae (e.g., E. coli OmpF and OmpC) have been extensively characterized structurally and biochemically, much less is known about their counterparts in Vibrionaceae. Vibrio cholerae, the causative agent of cholera, has two major porins, OmpU and OmpT, for which no structural information is available despite their importance for the bacterium. Here we report high-resolution X-ray crystal structures of V. cholerae OmpU and OmpT complemented with molecular dynamics simulations. While similar overall to other general porins, the channels of OmpU and OmpT have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels. Together with electrophysiological and in vitro transport data, our results illuminate small-molecule uptake within the Vibrionaceae.

A novel of PEG-conjugated phthalocyanine and evaluation of its photocytotoxicity and antibacterial properties for photodynamic therapy

A poly(ethylene glycol) (PEG)-conjugated silicon(IV) phthalocyanine axially substituted with (PEG1000) chains (SiPc-PEG) was synthesized, and this novel phthalocyanine was characterized by [Formula: see text]H-NMR, FT-IR and UV-Vis spectrophotometric methods. Elemental analysis data were beneficial for the evaluation of the chemical structure of the new compound. The total number of (O–CH[Formula: see text]–CH[Formula: see text] units was calculated as 44 and the structure of the new PEG-conjugated silicon phthalocyanine was determined by the use of integral areas in [Formula: see text]H-NMR spectrum and the ratio of SiPc:PEG1000 was found as 1:2. The photophysical and photochemical properties were determined in both DMSO and aqueous solutions. In addition, the photocytotoxicity of the novel PEG-conjugated silicon(IV) phthalocyanine was also examined by testing against human cervical-carcinoma (HeLa) and hepato-carcinoma cells (HuH-7). The IC[Formula: see text] value for the SiPc-PEG compound was determined as 0.28 [Formula: see text]M for HeLa cells and 0.4 [Formula: see text]M for HuH-7 cells. These results imply that HeLa cells are apparently more responsive to photodynamic therapy (PDT) treatment by SiPc-PEG than HuH-7 cells at low concentrations (up to 0.5 [Formula: see text]M) of the studied photosensitizer. Additionally, SiPc-PEG showed antibacterial activity against Escherichia coli at 48 h of incubation, the viabilities of E.coli cultures exposed to 1000 [Formula: see text]g/mL and 2500 [Formula: see text]g/mL SiPc-PEG concentration were reduced by about 90%, and the additional growth inhibitory effect of photoactivation was also observed clearly at these efficient concentrations. To conclude, the novel compound may have a high potential for photodynamic therapy.

Laser Techniques on Acoustically Levitated Droplets

This work reports the results of an experimental study where laser techniques are applied to acoustically levitated droplets of trehalose aqueous solutions in order to perform spectroscopic analyses as a function of concentration and to test the theoretical diameter law. The study of such systems is important in order to better understand the behaviour of trehalose-synthesizing extremophiles that live in extreme environments. In particular, it will be shown how acoustic levitation, combined with optical spectroscopic instruments allows to explore a wide concentration range and to test the validity of the diameter law as a function of levitation lag time, i.e. the D2 vs t law. On this purpose a direct diameter monitoring by a video camera and a laser pointer was first performed; then the diameter was also evaluated by an indirect measure through an OH/CH band area ratio analysis of collected Raman and Infrared spectra. It clearly emerges that D2 vs t follows a linear trend for about 20 minutes, reaching then a plateau at longer time. This result shows how trehalose is able to avoid total water evaporation, this property being essential for the surviving of organisms under extreme environmental conditions.

Engineering Enhanced Pore Sizes Using FhuA Δ1-160 from E. coli Outer Membrane as Template

Biological membranes are the perfect example of a molecular filter using membrane channels to control the permeability of small water-soluble molecules. To allow filtering of larger hydrophilic molecules we started from the known mutant channel FhuA Δ1-160 in which the cork domain closing the channel had been removed. Here we further expand the pore diameter by copying the amino acid sequence of two β-strands in a stepwise manner increasing the total number of β-strands from 22 to 34. The pore size of the respective expanded channel protein was characterized by single-channel conductance. Insertion of additional β-strands increased the pore conductance but also induced more ion current flickering on the millisecond scale. Further, polymer exclusion measurements were performed by analyzing single-channel conductance in the presence of differently sized polyethylene glycol of known polymer random coil radii. The conclusion from channel conductance of small channel penetrating polymers versus larger excluded ones suggested an increase in pore radii from 1.6 nm for FhuA Δ1-160 up to a maximum of about 2.7 nm for +8 β insertion. Integration of more β-strand caused instability of the channel and exclusion of smaller sized polymer. FhuA Δ1-160 + 10 β and FhuA Δ1-160 + 12 β effective radius decreased to 1.4 and 1.3 nm, respectively, showing the limitations of this approach.

Ion Transport in Confined Geometries below the Nanoscale: Access Resistance Dominates Protein Channel Conductance in Diluted Solutions

Synthetic nanopores and mesoscopic protein channels have common traits like the importance of electrostatic interactions between the permeating ions and the nanochannel. Ion transport at the nanoscale occurs under confinement conditions so that the usual assumptions made in microfluidics are challenged, among others, by interfacial effects such as access resistance (AR). Here, we show that a sound interpretation of electrophysiological measurements in terms of channel ion selective properties requires the consideration of interfacial effects, up to the point that they dominate protein channel conductance in diluted solutions. We measure AR in a large ion channel, the bacterial porin OmpF, by means of single-channel conductance measurements in electrolyte solutions containing varying concentrations of high molecular weight PEG, sterically excluded from the pore. Comparison of experiments performed in charged and neutral planar membranes shows that lipid surface charges modify the ion distribution and determine the value of AR, indicating that lipid molecules are more than passive scaffolds even in the case of large transmembrane proteins. We also found that AR may reach up to 80% of the total channel conductance in diluted solutions, where electrophysiological recordings register essentially the AR of the system and depend marginally on the pore characteristics. These findings may have implications for several low aspect ratio biological channels that perform their physiological function in a low ionic strength and macromolecule crowded environment, just the two conditions enhancing the AR contribution.

Functional Characterization of Cell-Free Expressed OprF Porin from Pseudomonas aeruginosa Stably Incorporated in Tethered Lipid Bilayers

OprF has a central role in Pseudomonas aeruginosa virulence and thus provides a putative target for either vaccines or antibiotic cofactors that could overcome the bacterium's natural resistance to antibiotics. Here we describe a procedure to optimize the production of highly pure and functional OprF porins that are then incorporated into a tethered lipid bilayer. This is a stable biomimetic system that provides the capability to investigate structural aspects and function of OprF using and neutron reflectometry and electrical impedance spectroscopy. The recombinant OprF produced using the optimized cell-free procedure yielded a quantity of between 0.5 to 1.0 mg/mL with a purity ranging from 85 to 91% in the proteoliposomes. The recombinant OprF is capable of binding IFN-γ and is correctly folded in the proteoliposomes. Because OprF proteins form pores the biomimetic system allowed the measurement of OprF conductance using impedance spectroscopy. The neutron reflectometry measurements showed that the OprF protein is incorporated into the lipid bilayer but with parts of the protein in both the regions above and below the lipid bilayer. Those structural aspects are coherent with the current assumed structure of a transmembrane N-terminal domain composed by eight stranded beta-barrels and a globular C-terminal domain located in the periplasm. Currently there are no crystal structures available for OprF. The experimental model system that we describe provides a basis for further fundamental studies of OprF and particularly for the ongoing biotechnological development of OprF as a target for antibacterial drugs.

Poly(ethylene glycol)s in Semidilute Regime: Radius of Gyration in the Bulk and Partitioning into a Nanopore

Using two approaches, small-angle neutron scattering (SANS) from bulk solutions and nanopore conductance-fluctuation analysis, we studied structural and dynamic features of poly(ethylene glycol) (PEG) water/salt solutions in the dilute and semidilute regimes. SANS measurements on PEG 3400 at the zero-average contrast yielded the single chain radius of gyration (R_g) over 1-30 wt %. We observed a small but statistically reliable decrease in R_g with increasing PEG concentration: at 30 wt % the chain contracts by a factor of 0.94. Analyzing conductance fluctuations of the α-hemolysin nanopore in the mixtures of PEG 200 with PEG 3400, we demonstrated that polymer partitioning into the nanopore is mostly due to PEG 200. Specifically, for a 1:1 wt/wt mixture the smaller polymer dominates to the extent that only about 1/25 of the nanopore volume is taken by the larger polymer. These findings advance our conceptual and quantitative understanding of nanopore polymer partitioning; they also support the main assumptions of the recent "polymers-pushing-polymers" model.

Orientation of the OmpF Porin in Planar Lipid Bilayers

The outer-membrane protein OmpF is an abundant trimeric general diffusion porin that plays a central role in the transport of antibiotics and colicins across the outer membrane of E. coli. Individual OmpF trimers in planar lipid bilayers (PLBs) show one of two current-voltage asymmetries, thus implying that insertion occurs with either the periplasmic or the extracellular end first. A method for establishing the orientation of OmpF in PLB was developed, based on targeted covalent modification with membrane-impermeant reagents of peripheral cysteine residues introduced near the periplasmic or the extracellular entrance. By correlating the results of the modification experiments with measurements of current asymmetry or the sidedness of binding of the antibiotic enrofloxacin, OmpF orientation could be quickly determined in subsequent experiments under a variety of conditions. Our work will allow the precise interpretation of past and future studies of antibiotic permeation and protein translocation through OmpF and related porins.

Size-dependent forced PEG partitioning into channels: VDAC, OmpC, and α-hemolysin

Nonideal polymer mixtures of PEGs of different molecular weights partition differently into nanosize protein channels. Here, we assess the validity of the recently proposed theoretical approach of forced partitioning for three structurally different β-barrel channels: voltage-dependent anion channel from outer mitochondrial membrane VDAC, bacterial porin OmpC (outer membrane protein C), and bacterial channel-forming toxin α-hemolysin. Our interpretation is based on the idea that relatively less-penetrating polymers push the more easily penetrating ones into nanosize channels in excess of their bath concentration. Comparison of the theory with experiments is excellent for VDAC. Polymer partitioning data for the other two channels are consistent with theory if additional assumptions regarding the energy penalty of pore penetration are included. The obtained results demonstrate that the general concept of "polymers pushing polymers" is helpful in understanding and quantification of concrete examples of size-dependent forced partitioning of polymers into protein nanopores.

In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms.

Single channel activity of OmpF-like porin from Yersinia pseudotuberculosis

To gain a mechanistic insight in the functioning of the OmpF-like porin from Yersinia pseudotuberculosis (YOmpF), we compared the effect of pH variation on the ion channel activity of the protein in planar lipid bilayers and its binding to lipid membranes. The behavior of YOmpF channels upon acidification was similar to that previously described for Escherichia coli OmpF. In particular, a decrease in pH of the bathing solution resulted in a substantial reduction of YOmpF single channel conductance, accompanied by the emergence of subconductance states. Similar subconductance substates were elicited by the addition of lysophosphatidylcholine. This observation, made with porin channels for the first time, pointed to the relevance of lipid-protein interactions, in particular, the lipid curvature stress, to the appearance of subconductance states at acidic pH. Binding of YOmpF to membranes displayed rather modest dependence on pH, whereas the channel-forming potency of the protein tremendously decreased upon acidification.

Application of OmpF nanochannel forming protein in polynucleotide sequence recognition

Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.

Bilayer-spanning DNA nanopores with voltage-switching between open and closed state

Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology.

VCA1008: An Anion-Selective Porin of Vibrio Cholerae

A putative porin function has been assigned to VCA1008 of Vibrio cholerae. Its coding gene, vca1008, is expressed upon colonization of the small intestine in infant mice and human volunteers, and is essential for infection. In vitro, vca1008 is expressed under inorganic phosphate limitation and, in this condition, VCA1008 is the major outer membrane protein of the bacterium. Here, we provide the first functional characterization of VCA1008 reconstituted into planar lipid bilayers. Our main findings were: 1) VCA1008 forms an ion channel that, at high voltage (~±100 mV), presents a voltage-dependent activity and displays closures typical of trimeric porins, with a conductance of 4.28±0.04 nS (n=164) in 1M KCl; 2) It has a preferred selectivity for anions over cations; 3) Its conductance saturates with increasing inorganic phosphate concentration, suggesting VCA1008 contains binding site(s) for this anion; 4) Its ion selectivity is controlled by both fixed charged residues within the channel and diffusion along the pore; 5) Partitioning of poly (ethylene glycol)s (PEGs) of different molecular mass suggests that VCA1008 channel has a pore exclusion limit of 0.9 nm.

Discovery of a cell wall porin in the mycolic-acid-containing actinomycete Dietzia maris DSM 43672

The cell wall of the Gram-positive mycolic-acid-containing actinomycete Dietzia maris DSM 43672 was found to contain a pore-forming protein, as observed from reconstitution experiments with artificial lipid bilayer experiments in the presence of cell wall extracts. The cell wall porin was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 120 kDa on tricine-containing SDS/PAGE. The 120 kDa protein dissociated into subunits with a molecular mass of about 35 kDa when it was heated to 100 °C in 8 m urea. The 120 kDa protein, here named PorADm , formed ion-permeable channels in lipid bilayer membranes with a high single-channel conductance of about 5.8 nS in 1 m KCl. Asymmetric addition of PorADm to lipid bilayer membranes resulted in an asymmetric voltage dependence. Zero-current membrane potential measurements with different salt solutions suggested that the porin of D. maris is cation-selective because of negative charges localized at the channel mouth. Analysis of the single-channel conductance using non-electrolytes with known hydrodynamic radii indicated that the diameter of the cell wall channel is about 2 nm. The channel characteristics of the cell wall porin of D. maris are compared with those of other members of the mycolata. They share some common features because they are composed of small molecular mass subunits and form large and water-filled channels. The porin was subjected to protein analysis by mass spectrometry but its sequence had no significant homology to any known porin sequences.

Use of nonelectrolytes reveals the channel size and oligomeric constitution of the Borrelia burgdorferi P66 porin

In the Lyme disease spirochete Borrelia burgdorferi, the outer membrane protein P66 is capable of pore formation with an atypical high single-channel conductance of 11 nS in 1 M KCl, which suggested that it could have a larger diameter than 'normal' Gram-negative bacterial porins. We studied the diameter of the P66 channel by analyzing its single-channel conductance in black lipid bilayers in the presence of different nonelectrolytes with known hydrodynamic radii. We calculated the filling of the channel with these nonelectrolytes and the results suggested that nonelectrolytes (NEs) with hydrodynamic radii of 0.34 nm or smaller pass through the pore, whereas neutral molecules with greater radii only partially filled the channel or were not able to enter it at all. The diameter of the entrance of the P66 channel was determined to be ≤1.9 nm and the channel has a central constriction of about 0.8 nm. The size of the channel appeared to be symmetrical as judged from one-sidedness of addition of NEs. Furthermore, the P66-induced membrane conductance could be blocked by 80-90% by the addition of the nonelectrolytes PEG 400, PEG 600 and maltohexaose to the aqueous phase in the low millimolar range. The analysis of the power density spectra of ion current through P66 after blockage with these NEs revealed no chemical reaction responsible for channel block. Interestingly, the blockage of the single-channel conductance of P66 by these NEs occurred in about eight subconductance states, indicating that the P66 channel could be an oligomer of about eight individual channels. The organization of P66 as a possible octamer was confirmed by Blue Native PAGE and immunoblot analysis, which both demonstrated that P66 forms a complex with a mass of approximately 460 kDa. Two dimension SDS PAGE revealed that P66 is the only polypeptide in the complex.

Inspection of the engineered FhuA ΔC/Δ4L protein nanopore by polymer exclusion

Extensive engineering of protein nanopores for biotechnological applications using native scaffolds requires further inspection of their internal geometry and size. Recently, we redesigned ferric hydroxamate uptake component A (FhuA), a 22-β-stranded protein containing an N-terminal 160-residue cork domain (C). The cork domain and four large extracellular loops (4L) were deleted to obtain an unusually stiff engineered FhuA ΔC/Δ4L nanopore. We employed water-soluble poly(ethylene glycols) and dextran polymers to examine the interior of FhuA ΔC/Δ4L. When this nanopore was reconstituted into a synthetic planar lipid bilayer, addition of poly(ethylene glycols) produced modifications in the single-channel conductance, allowing for the evaluation of the nanopore diameter. Here, we report that FhuA ΔC/Δ4L features an approximate conical internal geometry with the cis entrance smaller than the trans entrance, in accord with the asymmetric nature of the crystal structure of the wild-type FhuA protein. Further experiments with impermeable dextran polymers indicated an average internal diameter of ~2.4 nm, a conclusion we arrived at based upon the polymer-induced alteration of the access resistance contribution to the nanopore's total resistance. Molecular insights inferred from this work represent a platform for future protein engineering of FhuA that will be employed for specific tasks in biotechnological applications.

Polymers pushing Polymers: Polymer Mixtures in Thermodynamic Equilibrium with a Pore

We investigate polymer partitioning from polymer mixtures into nanometer size cavities by formulating an equation of state for a binary polymer mixture assuming that only one (smaller) of the two polymer components can penetrate the cavity. Deriving the partitioning equilibrium equations and solving them numerically allows us to introduce the concept of "polymers-pushing-polymers" for the action of non-penetrating polymers on the partitioning of the penetrating polymers. Polymer partitioning into a pore even within a very simple model of a binary polymer mixture is shown to depend in a complicated way on the composition of the polymer mixture and/or the pore-penetration penalty. This can lead to enhanced as well as diminished partitioning, due to two separate energy scales that we analyse in detail.

Transport of long neutral polymers in the semidilute regime through a protein nanopore

We investigate the entrance of single poly(ethylene glycol) chains into an α-hemolysin channel. We detect the frequency and duration of the current blockades induced by large neutral polymers, where chain radius is larger than pore diameter. In the semidilute regime, these chains pass only if the monomer concentration is larger than a well-defined threshold. Experiments are performed in a very large domain of concentration and molecular mass, up to 35% and 200 kDa, respectively, which was previously unexplored. The variation of the dwell time as a function of molecular mass shows that the chains are extracted from the semidilute solution in contact with the pore by a reptation mechanism.

Electric-field-driven polymer entry into asymmetric nanoscale channels

The electric-field-driven entry process of flexible charged polymers such as single-stranded DNA (ssDNA) into asymmetric nanoscale channels such as the α-hemolysin protein channel is studied theoretically and using molecular dynamics simulations. Dependence of the height of the free-energy barrier on the polymer length, the strength of the applied electric field, and the channel entrance geometry is investigated. It is shown that the squeezing effect of the driving field on the polymer and the lateral confinement of the polymer before its entry to the channel crucially affect the barrier height and its dependence on the system parameters. The attempt frequency of the polymer for passing the channel is also discussed. Our theoretical and simulation results support each other and describe related data sets of polymer translocation experiments through the α-hemolysin protein channel reasonably well.

Free-energy barrier for electric-field-driven polymer entry into nanoscale channels

Free-energy barrier for entry of a charged polymer into a nanoscale channel by a driving electric field is studied theoretically and using molecular dynamics simulations. Dependence of the barrier height on the polymer length, the driving field strength, and the channel entrance geometry is investigated. Squeezing effect of the electric field on the polymer before its entry to the channel is taken into account. It is shown that lateral confinement of the polymer prior to its entry changes the polymer length dependence of the barrier height noticeably. Our theory and simulation results are in good agreement and reasonably describe related experimental data.

First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin

We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force F(eff) can be obtained after appropriate subdivision of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson-Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.

Polymer partitioning and ion selectivity suggest asymmetrical shape for the membrane pore formed by epsilon toxin

Using poly-(ethylene glycol)s of different molecular weights, we probe the channels formed in planar lipid bilayers by epsilon toxin secreted by the anaerobic bacterium Clostridium perfringens. We find that the pore is highly asymmetric. The cutoff size of polymers entering the pore through its opening from the cis side, the side of toxin addition, is approximately 500 Da, whereas the cutoff size for the polymers entering from the trans side is approximately 2300 Da. Comparing these characteristic molecular weights with those reported earlier for OmpF porin and the alpha-Hemolysin channel, we estimate the radii of cis and trans openings as 0.4 nm and 1.0 nm, respectively. The simplest geometry corresponding to these findings is that of a truncated cone. The asymmetry of the pore is also confirmed by measurements of the reversal potential at oppositely directed salt gradients. The moderate anionic selectivity of the channel is salted-out more efficiently when the salt concentration is higher at the trans side of the pore.

The prediction and characterization of YshA, an unknown outer-membrane protein from Salmonella typhimurium

We have developed an effective pathway for the prediction and characterization of novel transmembrane β-barrel proteins. The Freeman-Wimley algorithm, which is a highly accurate prediction method based on the physicochemical properties of experimentally characterized transmembrane β barrel (TMBB) structures, was used to predict TMBBs in the genome of Salmonella typhimurium LT2. The previously uncharacterized product of gene yshA was tested as a model for validating the algorithm. YshA is a highly conserved 230-residue protein that is predicted to have 10 transmembrane β-strands and an N-terminal signal sequence. All of the physicochemical and spectroscopic properties exhibited by YshA are consistent with the prediction that it is a TMBB. Specifically, recombinant YshA localizes to the outer membrane when expressed in Escherichia coli; YshA has a β-sheet-rich secondary structure with stable tertiary contacts in the presence of detergent micelles or when reconstituted into a lipid bilayer. When in a lipid bilayer, YshA forms a membrane-spanning pore with an effective radius of ~0.7nm. Taken together, these data substantiate the predictions made by the Freeman-Wimley algorithm by showing that YshA is a TMBB protein.

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.

Molecular basis of enrofloxacin translocation through OmpF, an outer membrane channel of Escherichia coli--when binding does not imply translocation

The molecular pathway of enrofloxacin, a fluoroquinolone antibiotic, through the outer membrane channel OmpF of Escherichia coli is investigated. High-resolution ion current fluctuation analysis reveals a strong affinity for enrofloxacin to OmpF, the highest value ever recorded for an antibiotic-channel interaction. A single point mutation in the constriction zone of OmpF, replacing aspartic acid at the 113 position with asparagine (D113N), lowers the affinity to a level comparable to other antibiotics. All-atom molecular dynamics simulations allow rationalizing the translocation pathways: wild-type OmpF has two symmetric binding sites for enrofloxacin located at each channel entry separated by a large energy barrier in the center, which inhibits antibiotic translocation. In this particular case, our simulations suggest that the ion current blockages are caused by molecules occupying either one of these peripheral binding sites. Removal of the negative charge on position 113 removes the central barrier and shifts the two peripheral binding sites to a unique central site, which facilitates translocation. Fluorescence steady-state measurements agree with the different location of binding sites for wild-type OmpF and the mutant. Our results demonstrate how a single-point mutation of the porin, and the resulting intrachannel shift of the affinity site, may substantially modify translocation.

Bridging timescales and length scales: from macroscopic flux to the molecular mechanism of antibiotic diffusion through porins

Our aim in this study was to provide an atomic description of ampicillin translocation through OmpF, the major outer membrane channel in Escherichia coli and main entry point for beta-lactam antibiotics. By applying metadynamics simulations, we also obtained the energy barriers along the diffusion pathway. We then studied the effect of mutations that affect the charge and size at the channel constriction zone, and found that in comparison to the wild-type, much lower energy barriers are required for translocation. The expected higher translocation rates were confirmed on the macroscopic scale by liposome-swelling assays. A microscopic view on the millisecond timescale was obtained by analysis of temperature-dependent ion current fluctuations in the presence of ampicillin and provide the enthalpic part of the energy barrier. By studying antibiotic translocation over various timescales and length scales, we were able to discern its molecular mechanism and rate-limiting interactions, and draw biologically relevant conclusions that may help in the design of drugs with enhanced permeation rates.

Probing single nanometer-scale pores with polymeric molecular rulers

We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the alpha-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.