Protein nanopores with covalently attached molecular adapters

Molecular adapters are crucial for the stochastic sensing of organic analytes with alpha-hemolysin (alphaHL) protein nanopores when direct interactions between analytes and the pore cannot readily be arranged by conventional protein engineering. In our earlier studies, cyclodextrin adapters were lodged noncovalently within the lumen of the alphaHL pore. In the present work, we have realized the controlled covalent attachment of a beta-cyclodextrin (betaCD) adapter in the two possible molecular orientations inside alphaHL pores prepared by genetic engineering. There are two advantages to such a covalent system. First, the adapter cannot dissociate, which means there are no gaps during stochastic detection, a crucial advance for single-molecule exonuclease DNA sequencing where the continuous presence of a molecular adapter will be essential for reading individual nucleotides. Second, the ability to orient the adapter allows analytes to bind through only one of the two entrances to the betaCD cavity. We demonstrate that the covalently attached adapters can be used to alter the ion selectivity of the alphaHL pore, examine binding events at elevated temperatures, and detect analytes with prolonged dwell times.     

Controlling a single protein in a nanopore through electrostatic traps

Protein-protein pore interaction is a fundamental and ubiquitous process in biology and medical biotechnology. Here, we employed high-resolution time-resolved single-channel electrical recording along with protein engineering to examine a protein-protein pore interaction at single-molecule resolution. The pore was formed by Staphylococcus aureus alpha-hemolysin (alphaHL) protein and contained electrostatic traps formed by rings of seven aspartic acid residues placed at two different positions within the pore lumen. The protein analytes were positively charged presequences (pb2) of varying length fused to the small ribonuclease barnase (Ba). The presence of the electrostatic traps greatly enhanced the interaction of the pb2-Ba protein with the alphaHL protein pore. This study demonstrates the high sensitivity of the nanopore technique to an array of factors that govern the protein-protein pore interaction, including the length of the pb2 presequence, the position of the electrostatic traps within the pore lumen, the ionic strength of the aqueous phase, and the transmembrane potential. Alterations in the functional properties of the pb2-Ba protein and the alphaHL protein pore and systematic changes of the experimental parameters revealed the balance between forces driving the pb2-Ba protein into the pore and forces driving it out.     

甲烷在中孔分子筛MCM-41中吸附的计算机模拟

采用巨正则系综Monte Carlo方法研究了甲烷在两个不同孔径的MCM-41中不同温度下的吸附等温线和其在孔中的相行为和排列方式.模拟结果显示,在较小孔径的MCM-41中,流体分子达到毛细凝聚所需的化学位较小,并且观察到两个孔径下计算机模拟得到的亚稳态区域都非常宽,使得层状转变（如果有的话）被包含在这个区域.通过比较两种孔径下达到毛细凝聚后的构型,可以看出,在3.5 nm的孔中流体的分子结构出现非常有序的排列,而在5.0 nm的孔中则没有.在常温300 K时甲烷的吸附的计算机模拟表明,孔壁对流体分子的作用仅仅影响较靠近壁面附近的流体分子的排列,而对孔中间的分子几乎没有影响.     

Single-molecule detection of nitrogen mustards by covalent reaction within a protein nanopore

Mustards, including sulfur mustards and nitrogen mustards, form a class of cytotoxic, vesicant chemical warfare agents. Mustards have also been used to treat cancer and played a vital role in the development of chemotherapy. Additionally, because of their destructive properties, ease of synthesis, and the lack of effective antidotes, mustards are unquestionably terrorist threats. Therefore, quick and convenient detection of mustards is a critical issue. In the present study, we achieved detection of various mustards on the basis of their chemical reactivity by using engineered alpha-hemolysin (alphaHL) protein pores as sensor elements. We describe four classes of reactions for detecting mustards. These reactions occur between mustards and thiol groups contributed by cysteine side-chains within the lumen of the alphaHL pore or on an internal molecular adapter. The approach is quick and straightforward. It can confirm the existence of mustards in as little as 10 min at 50 microM or lower.     

Photoisomerization of an individual azobenzene molecule in water: an on-off switch triggered by light at a fixed wavelength

The alpha-hemolysin (alphaHL) pore was used as a nanoreactor for the direct observation of the reversible photoisomerization of individual tethered azobenzene molecules in an aqueous environment. alphaHL pores, PAZO, were used that had been derivatized within the lumen at a single cysteine residue with 4-((4-(2-chloroethanoamido)phenyl)diazenyl)benzenesulfonate. Trans-cis isomerizations were monitored at the single-molecule level by observing the modulation of the current passing through PAZO by electrical recording in planar bilayers. When PAZO was irradiated at 330 nm, continuous interconversion between the trans and cis states was observed. Either the trans or the cis state was maintained in the dark, depending upon which was present when the light source was shuttered. The cis state of PAZO was surprisingly stable in the dark, and no cis --> trans transitions were seen over a total observation period of more than 8 h. Therefore, based on our findings, it might be possible to make fast digital nanoscale switches operated by light of a fixed wavelength.     

Effect of temperature on the adsorption of water in porous carbons

We report experimental and simulation studies to investigate the effect of temperature on the adsorption isotherms for water in carbons. Adsorption isotherms are measured by a gravimetric technique in carbon-fiber monoliths at 378 and 423 K and studied by molecular simulation in ideal carbon pores in the temperature range 298-600 K. Experimental adsorption isotherms show a gradual water uptake, as the pressure increases, and narrow adsorption-desorption hysteresis loops. In contrast, simulated adsorption isotherms at room temperature are characterized by negligible uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption-desorption hysteresis loops. As the temperature increases, the relative pressure at which pore filling occurs increases and the size of the hysteresis loop decreases. Experimental adsorption-desorption hysteresis loops are narrower than those from simulation. Discrepancies between simulation and experimental results are attributed to heterogeneities in chemical composition, pore connectivity, and nonuniform pore-size distribution, which are not accounted for in the simulation model. The hysteresis phase diagram for confined water is obtained by recording the pressure-density conditions that bound the simulated hysteresis loop at each temperature. We find that the hysteresis critical temperature, i.e., the lowest temperature at which no hysteresis is detected, can be hundreds of degrees lower than the vapor-liquid critical temperature for bulk model water. The properties of confined water are discussed with the aid of simulation snapshots and by analyzing the structure of the confined fluid.     

Catalyzing the translocation of polypeptides through attractive interactions

Facilitated translocation of polypeptides through a protein pore is a ubiquitous and fundamental process in biology. Several translocation systems possess various well-defined binding sites within the pore lumen, but a clear mechanistic understanding of how the interaction of the polypeptides with the binding site alters the underlying kinetics is still missing. Here, we employed rational protein design and single-channel electrical recordings to obtain detailed kinetic signatures of polypeptide translocation through the staphylococcal alpha-hemolysin (alphaHL) transmembrane pore, a robust, tractable, and versatile beta-barrel protein. Acidic binding sites composed of rings of negatively charged aspartic acid residues, engineered at strategic positions within the beta barrel, produced dramatic changes in the functional properties of the alphaHL protein, facilitating the transport of cationic polypeptides from one side of the membrane to the other. When two electrostatic binding sites were introduced, at the entry and exit of the beta barrel, both the rate constants of association and dissociation increased substantially, diminishing the free energy barrier for translocation. By contrast, more hydrophobic polypeptides exhibited a considerable decrease in the rate constant of association to the pore lumen, having to overcome a greater energetic barrier because of the hydrophilic nature of the pore interior.     

A storable encapsulated bilayer chip containing a single protein nanopore

A robust, portable chip containing a single protein nanopore would be a significant development in the practical application of stochastic sensing technology. Here, we describe a chip in which a single alpha-hemolysin (alphaHL) pore in a planar phospholipid bilayer is sandwiched between two layers of agarose gel. These encapsulated nanopore chips remain functional after storage for weeks. The detection of the second messenger inositol 1,4,5-trisphosphate (IP3) was demonstrated with a chip containing a genetically engineered alphaHL pore as the sensor element.     

On the hysteresis loop and equilibrium transition in slit-shaped ink-bottle pores

Bin grand canonical Monte Carlo simulations have been carried out to study adsorption–desorption of argon at 87.3 K in a model ink-bottle mesoporous solid in order to investigate the interplay between the pore blocking process, controlled by the evaporation through the pore mouth via the meniscus separating the adsorbate and the bulk gas surroundings, and the cavitation process, governed by the instability of the stretched fluid (with a decrease in pressure) in the cavity. The evaporation mechanism switches from pore blocking to cavitation when the size of the pore neck is decreased, and is relatively insensitive to the neck length under conditions where cavitation is the controlling mechanism. We have applied the recently-developed Mid-Density scheme to determine the equilibrium branch of the hysteresis loop, and have found that, unlike ideal simple pores of constant size and infinite length, where the equilibrium transition is vertical, the equilibrium branch of an ink-bottle pore has three distinct sub-branches within the hysteresis loop. The first sub-branch is steep but continuous and is close to the desorption branch (which is typical for a pore with two open ends); this is associated with the equilibrium state in the neck. The third sub-branch is much steeper and is close to the adsorption branch (which is typical for either a pore with one end closed or a closed pore), and is associated with the equilibrium state in the cavity. The second sub-branch, connecting the other two sub-branches, has a more gradual slope. The domains of these three sub-branches depend on the relative sizes of the cavity and the neck, and their respective lengths. Our investigation of the effects of changing neck length clearly demonstrates that cavitation depends, not only on fluid properties, as frequently stated, but also on pore geometry.     

Control of the Conductance of Engineered Protein Nanopores through Concerted Loop Motions

Protein nanopores have attracted much interest for nucleic acid sequencing, chemical sensing, and protein folding at the single molecule level. The outer membrane protein OmpG from E. coli stands out because it forms a nanopore from a single polypeptide chain. This property allows the separate engineering of each of the seven extracellular loops that control access to the pore. The longest of these loops, loop 6, has been recognized as the main gating loop that closes the pore at low pH values and opens it at high pH values. A method was devised to pin each of the loops to the embedding membrane and measure the single‐pore conductances of the resulting constructs. The electrophysiological and complementary NMR measurements show that the pinning of individual loops alters the structure and dynamics of neighboring and distant loops in a correlated fashion. Pinning loop 6 generates a constitutively open pore and patterns of concerted loop motions control access to the OmpG nanopore.     

Adsorption properties of ordered mesoporous silicas synthesized in the presence of block copolymer Pluronic F127 under microwave irradiation

Ordered mesoporous silicas (OMSs) were prepared at different temperatures by using tetraethyl orthosilicate (TEOS) as a silica source, poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer (Pluronic F127) as a structure directing agent and sodium chloride as an additive under acidic conditions and microwave irradiation. The small angle X-ray diffraction patterns of these samples indicate the presence of ordered mesopores, while adsorption studies show that they possess high volumes of pores, bimodal pore size distributions and large pore sizes. There is an interesting change in the hysteresis loop of nitrogen adsorption isotherms with increasing temperature of hydrothermal treatment; a delayed desorption characteristic for cage-like mesostructures is observed for the OMS samples treated at 100 and 120?°C, while the hydrothermal treatment at 140 and 160?°C leads to the samples having hysteresis loops characteristic for channel-like materials.     

Single-molecule electrophoresis of beta-hairpin peptides by electrical recordings and Langevin dynamics simulations

We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various beta-hairpin peptides across the staphylococcal alpha-hemolysin (alphaHL) protein pore at single-molecule resolution. The beta-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the beta-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded beta-hairpin peptides occurred more slowly. In this case, the beta-hairpin peptides traversed the alphaHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a beta-barrel protein pore is dependent on the folding features of the polypeptide.     

Molecular simulation of protein dynamics in nanopores. I. Stability and folding

Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of alpha-de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature T(f) and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with T(f) decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's walls with a negative potential energy. In such pores the energetic effects dominate the entropic effects. As a result, the unfolded state is stabilized, with a folding temperature T(f) which is lower than its value in the bulk and that, compared with the bulk, the folding rate decreases. The opposite is true in the presence of a repulsive interaction potential between the proteins and the walls. Moreover, for short proteins in very tight pores with attractive walls, there exists an unfolded state with only one alpha-helical hydrogen bond and an energy nearly equal to that of the folded state. The proteins have, however, high entropies, implying that they cannot fold onto their native structure, whereas in the presence of repulsive walls the proteins do attain their native structure. There is a pronounced asymmetry between the two termini of the protein with respect to their interaction with the pore walls. The effect of a variety of factors, including the pore size and the proteins' length, as well as the temperature, is studied in detail.     

Layering, condensation, and evaporation of short chains in narrow slit pores

The phase behavior of short-chain fluids in slit pores is investigated by using a nonlocal-density-functional theory that takes into account the effects of segment size, chain connectivity, and van der Waals attractions explicitly. The layering and capillary condensation/evaporation transitions are examined at different chain length, temperature, pore width, and surface energy. It is found that longer chains are more likely to show hysteresis loops and multilayer adsorptions along with the capillary condensation and evaporation. Decreasing temperature favors the inclusion of layering transitions into the condensation/evaporation hysteresis loops. For large pores, the surface energy has relatively small effect on the pressures of the capillary condensation and evaporation but affects significantly on the layering pressures. It is also observed that all phase transitions within the pore take place at pressures lower than the corresponding bulk saturation pressure. The critical temperature of condensation/evaporation is always smaller than that of the bulk fluid. All coexistence curves for confined phase transitions are contained within the corresponding bulk vapor-liquid coexistence curve. As in the bulk phase, the longer the chain length, the higher are the critical temperatures of phase transitions in the pore.     

AC conductance of transmembrane protein channels. The number of ionized residue mobile counterions at infinite dilution

Simultaneous measurements of the AC and DC conductances of alpha-hemolysin (alphaHL) ion channels and outer membrane protein F (OmpF) porins in dilute ionic solutions is described. AC conductance measurements were performed by applying a 10 mV rms AC voltage across a suspended planar bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine in the absence and presence of the protein and detecting the AC current response using phase-sensitive lock-in techniques. The conductances of individual alphaHL channels and OmpF porins were measured in symmetric KCl solutions containing between 5 and 1000 mM KCl. The AC and DC conductances of each protein were in agreement for all solution conditions, demonstrating the reliability of the AC method in single-channel recordings. Linear plots of conductance versus bulk KCl concentration for both proteins extrapolate to significant nonzero conductances (0.150 +/- 0.050 nS and 0.028 +/- 0.008 nS for OmpF and alphaHL, respectively) at infinite KCl dilution. The infinite dilution conductances are ascribed to mobile counterions of the ionizable residues within the protein lumens. A method of analyzing the plots of conductance vs KCl concentration is introduced that allows the determination of the concentration of mobile counterions associated with ionizable groups without knowledge of either the protein geometry or the ion mobilities. At neutral pH, an equivalent of 3 mobile counterions (K+ or Cl-) is estimated to contribute to the conductivity of the alphaHL channel.     

Confinement in nanopores can destabilize α-helix folding proteins and stabilize the β structures

Protein folding in confined media has attracted wide attention over the past decade due to its importance in both in vivo and in vitro applications. Currently, it is generally believed that protein stability increases by decreasing the size of the confining medium, if its interaction with the confining walls is repulsive, and that the maximum folding temperature in confinement occurs for a pore size only slightly larger than the smallest dimension of the folded state of a protein. Protein stability in pore sizes, very close to the size of the folded state, has not however received the attention that it deserves. Using detailed, 0.3-ms-long molecular dynamics simulations, we show that proteins with an α-helix native state can have an optimal folding temperature in pore sizes that do not affect the folded-state structure. In contradiction to the current theoretical explanations, we find that the maximum folding temperature occurs in larger pores for smaller α-helices. In highly confined pores the free energy surface becomes rough, and a new barrier for protein folding may appear close to the unfolded state. In addition, in small nanopores the protein states that contain the β structures are entropically stabilized, in contrast to the bulk. As a consequence, folding rates decrease notably and the free energy surface becomes rougher. The results shed light on many recent experimental observations that cannot be explained by the current theories, and demonstrate the importance of entropic effects on proteins' misfolded states in highly confined environments. They also support the concept of passive effect of chaperonin GroEL on protein folding by preventing it from aggregation in crowded environment of biological cells, and provide deeper clues to the α → β conformational transition, believed to contribute to Alzheimer's and Parkinson's diseases. The strategy of protein and enzyme stabilization in confined media may also have to be revisited in the case of tight confinement. For in silico studies of protein folding in confined media, use of non-Go potentials may be more appropriate.     

Behavior of a thermotropic nematic liquid crystal confined to controlled pore glasses as studied by 129Xe NMR spectroscopy

The behavior of nematic liquid crystal (LC) Merck Phase 4 confined to controlled pore glass (CPG) materials was investigated using 129Xe nuclear magnetic resonance (NMR) spectroscopy of xenon gas dissolved in the LC. The average pore diameters of the materials varied from 81 to 2917 A, and the measurements were carried out within a wide temperature range (approximately 185-370 K). The spectra contain lots of information about the effect of confinement on the phase of the LC. The theoretical model of shielding of noble gases dissolved in liquid crystals on the basis of pairwise additivity approximation was applied to the analysis of the spectra. When pore diameter is small, smaller than approximately 150 A, xenon experiences on average an isotropic environment inside the pore, and no nematic-isotropic phase transition is observed. When the size is larger than approximately 150 A, nematic phase is observed, and the LC molecules are oriented along pore axis. The orientational order parameter of the LC, S, increases with increasing pore size. In the largest pores, the orientation of the molecules deviates from the pore axis direction to magnetic field direction, which implies that the size of the pores (approximately 3000 A) is close to magnetic coherence length. The decrease of magnetic coherence length with increasing temperature is clearly seen from the spectra. When the sample is cooled rapidly by immersing it in liquid nitrogen, xenon atoms do not squeeze out from the solid, as they do during gradual freezing, but they are occluded inside the solid lattice, and their chemical shift is very sensitive to crystal structure. This makes it possible to study the effect of confinement on the solid phases. According to the measured 129Xe NMR spectra, possibly three different solid phases are observed from bulk liquid crystal in the used temperature region. The same is also seen from the samples containing larger pores (pore size larger than approximately 500 A), and the solid-solid phase-transition temperatures are the same. However, no first-order solid-solid phase transitions are observed from the smaller pores. Melting point depression, that is, the depression of solid-nematic transition temperature observed from the pores as compared with that in bulk LC, is seen to be very sensitive to the pore size, and it can be used for the determination of pore size of an unknown material.     

Computer-aided simulation of the cathodic active layer in fuel cells with solid polymer electrolyte: the nature of overall current transient

Total computer-aided simulation of the structure and current-generation processes in the cathodic active layer of a fuel cell with solid polymer electrolyte is carried out. Not only the transport structure of the active layer but also the structure of support grains (agglomerates of carbon particles with platinum-covered surface) are modeled. The process of active layer functioning under potentiostatic conditions is studied. It is demonstrated for the first time how the moisture exchange in the pores of support grains affects the cathode overall characteristics. The time variations of the overall current, the average temperature of the active layer, and the total degree of water-flooding of support-grain pores within the active layer are calculated by numerical methods. It is shown that for the fuel cell voltage of 0.6 V and its working temperature of 80°C, the flooding process dominates over the process of drying of pores in support grains. In 10–15 s, all support-grain pores turn out to be entirely filled with water. Then they begin functioning not in the kinetic mode (in the moment of switching-on the current, the Knudsen diffusion of oxygen in the support grains is observed) but in the inner-diffusion mode. As a result, the overall cathodic current decreases from its initial value of 4.323 A/cm² to its final value of 0.526 A/cm² and the active layer temperature decreases from the initial value of 102°C to the final value of 82.5°C. The overall current transient is studied also experimentally, the qualitative coincidence of theoretical and experimental data is demonstrated.     

Capillary condensation in porous materials. Hysteresis and interaction mechanism without pore blocking/percolation process

We have performed measurements of boundary hysteresis loops, reversal curves, and subloops in p+-type porous silicon, a porous material composed of straight non-interconnected pores. These data show that a strong interaction mechanism exists between the pores. The pores of porous silicon are non-independent, whereas they are not interconnected. This hysteretic behavior is very similar to that observed in porous glass, which consists of cavities connected to each other by constrictions. This questions the so-called pore blocking/percolation model developed to explain the behavior of fluid in porous glass. More generally, if we disregard the shape of the boundary hysteresis loops which depends on the porous material (H1 for MCM-41 and SBA-15, H2 for porous glass and p+-type porous silicon), the hysteretic features inside the main loop are qualitatively the same for all these porous systems. This shows that none of these systems are composed of independent pores. A coupling between the pores is always present whether they are interconnected or not and whatever the shape of the main loop is.     

Density minimum of confined water at low temperatures: a combined study by small-angle scattering of X-rays and neutrons

A simple explanation is given for the low-temperature density minimum of water confined within cylindrical pores of ordered nanoporous materials of different pore size. The experimental evidence is based on combined data from in-situ small-angle scattering of X-rays (SAXS) and neutrons (SANS), corroborated by additional wide-angle X-ray scattering (WAXS). The combined scattering data cannot be described by a homogeneous density distribution of water within the pores, as was originally suggested from SANS data alone. A two-step density model reveals a wall layer covering approximately two layers of water molecules with higher density than the residual core water in the central part of the pores. The temperature-induced changes of the scattering signal from both X-rays and neutrons are consistent with a minimum of the average water density. We show that the temperature at which this minimum occurs depends monotonically on the pore size. Therefore we attribute this minimum to a liquid-solid transition of water influenced by confinement. For water confined in the smallest pores of only 2 nm in diameter, the density minimum is explained in terms of a structural transition of the surface water layer closest to the hydrophilic pore walls.