Dynamics of unfolded protein transport through an aerolysin pore

Protein export is an essential mechanism in living cells and exported proteins are usually translocated through a protein-conducting channel in an unfolded state. Here we analyze, by electrical detection, the entry and transport of unfolded proteins, at the single molecule level, with different stabilities through an aerolysin pore, as a function of the applied voltage and protein concentration. The frequency of ionic current blockades varies exponentially as a function of the applied voltage and linearly as a function of protein concentration. The transport time of unfolded proteins decreases exponentially when the applied voltage increases. We prove that the ionic current blockade duration of a double-sized protein is longer than that assessed for a single protein supporting the transport phenomenon. Our results fit with the theory of confined polyelectrolyte and with some experimental results about DNA or synthetic polyelectrolyte translocation through protein channels as a function of applied voltage. We discuss the potential of the aerolysin nanopore as a tool for protein folding studies as it has already been done for α-hemolysin.     

An AC electroosmotic micropump for circular chromatographic applications

Flow rates of up to 50 microm s(-1) have been successfully achieved in a closed-loop channel using an AC electroosmotic pump. The AC electroosmotic pump is made of an interdigitated array of unequal width electrodes located at the bottom of a channel, with an AC voltage applied between the small and the large electrodes. The flow rate was found to increase linearly with the applied voltage and to decrease linearly with the applied frequency. The pump is expected to be suitable for circular chromatography for the following reasons: the driving forces are distributed over the channel length and the pumping direction is set by the direction of the interdigitated electrodes. Pumping in a closed-loop channel can be achieved by arranging the electrode pattern in a circle. In addition the inherent working principle of AC electroosmotic pumping enables the independent optimisation of the channel height or the flow velocity.     

Analytical theory of hysteresis in ion channels: two-state model

Channel-forming proteins in a lipid bilayer of a biological membrane usually respond to variation of external voltage by changing their conformations. Periodic voltages with frequency comparable with the inverse relaxation time of the protein produce hysteresis in the occupancies of the protein conformations. If the channel conductance changes when the protein jumps between these conformations, hysteresis in occupancies is observed as hysteresis in ion current through the channel. We develop an analytical theory of this phenomenon assuming that the channel conformational dynamics can be described in terms of a two-state model. The theory describes transient behavior of the channel after the periodic voltage is switched on as well as the shape and area of the hysteretic loop as functions of the frequency and amplitude of the applied voltage. The area vanishes as the voltage period T tends to zero and infinity. Asymptotic behaviors of the loop area A in the high- and low-frequency regimes, respectively, are A approximately T and A approximately T(-1).     

Microscopic effect of an applied voltage on the solvated gramicidin a transmembrane channel in the presence of Na+ and K+ cations

Using the previously reported ab initio interaction energies among K⁺, Na⁺, water, and Gramicidin A (GA), this report presents Monte Carlo simulations for the microscopic effect of an applied voltage (0.5 V/32 Å) on a solvated gramicidin. The reorientation of water molecules due to the applied voltage is found to be marginal for both cations. The energy contribution due to water dipoles was within 10% of the total energy contribution due to the applied voltage. Inside the channel the total energy contribution varied almost linearly along the channel axis; outside the channel the slope of the total energy contribution with respect to the channel axis decreased.     

Energy-resolved collisional activation of dimethyl phosphonate and dimethyl phosphite ions in a quadrupole ion trap and a triple quadrupole mass spectrometer

Collision-activated dissociation spectra of dimethyl phosphonate and dimethyl phosphite ions were measured as a function of the amplitude of a supplementary AC voltage applied across the end-caps of an ion-trap mass spectrometer. These spectra yield breakdown graphs which bear a close resemblance to those obtained by varying collision energy in a triple-quadrupole mass spectrometer operating under multiple-collision conditions. Variation in the time of excitation at the resonance frequency provides an alternative route to breakdown graphs. The results demonstrate that energy deposition occurs via multiple activating collisions in the ion trap. Maximum energy deposition observed is somewhat smaller under normal operating conditions in the ion trap than in the triple-quadrupole mass spectrometer.     

Parametrical studies of electroosmotic transport characteristics in submicrometer channels

Spatially two-dimensional nonequilibrium mathematical model describing electroosmotic flow through a submicrometer channel with an electric charge fixed on the channel walls is presented. This system is governed by the hydrodynamic, electrostatic, and mass transport phenomena. The model is based on the coupled mass balances, Poisson, Navier-Stokes, and Nernst-Planck equations. Nonslip boundary conditions are employed. The effect of an imposed electric field on the system behavior is studied by means of a numerical analysis of the model equations. We have obtained the following findings. If the channel width is comparable to the thickness of the electric double layer, the system behaves as an ion-exchange membrane and the dependence of the electric current passing through the channel on the applied voltage is strongly nonlinear. In the case of negatively (positively) charged walls, a narrow region of very low conductivity (so-called ionic gate) is formed in the free electrolyte near the channel entry facing the anode (cathode) side. For a wide channel, the electric current is proportional to the applied voltage and the velocity of electrokinetic flow is linearly proportional to the electric field strength. Complex hydrodynamics (eddy formation and existence of ionic gates) is the most interesting characteristics of the studied system. Hence, current-voltage and velocity-voltage curves and the corresponding spatial distributions of the model variables at selected points are studied and described in detail.     

聚苯乙炔的伏安特性

聚苯乙炔的伏安特性周淑琴（中国科学院化学研究所北京１０００８０）关键词聚苯乙炔，伏 安特性，欧姆电导，空间电荷限制电流，高斯分布陷阱能级，陷阱态密度聚苯乙炔（ＰＰＡ）是一种具有π电子的共轭高分子聚合物，它的光电导特性引起了同行的兴趣［１］．目前高分...     

Electroactive-paper actuator made with cellulose/NaOH/urea and sodium alginate

In an earlier work we reported the discovery of cellulose as a smart material that can be used in sensors and actuators. While the cellulose-based Electro-Active Paper (EAPap) actuator has many merits – lightweight, dry condition, biodegradability, sustainability, large displacement output and low actuation voltage – its performance is sensitive to humidity. We report here on an EAPap made with a cellulose and sodium alginate that produces its maximum displacement at a lower humidity level than the earlier one. To fabricate this EAPap, we dissolved cellulose fibers into a aqueous solution of NaOH/urea. Sodium alginate (0, 5 or 10% by weight) was then added to this cellulose solution. The solution was cast into a sheet and hydrolyzed to form a wet cellulose-sodium alginate blend film. After drying, a bending EAPap actuator was made by depositing thin gold electrodes on both sides of it. The performance of the EAPap actuator was then evaluated in terms of free displacement and blocked force with respect to the actuation frequency, activation voltage and content of sodium alginate. The actuation principle is also discussed.     

Chemisorption of HCl to the MgO(001) surface: a DFT study

We use plane wave and embedded cluster ab initio density functional calculations to study adsorption, dissociation and diffusion of the HCl molecule on the MgO(001) surface. The two methods yield comparable results for adsorption of an isolated HCl molecule and complement each other when considering charged species and coverage effects. We find dissociative chemisorption at a coverage smaller than 0.5 monolayer with a Cl(-) ion electrostatically coupled to the OH(-) ion at the surface oxygen site. The adsorption energy of the Cl(-)[dot dot dot](OH)(-) complex is 1.5 eV and the activation energy of Cl(-) diffusion away from OH(-) is 0.6 eV. There is no significant activation energy for rotation of Cl(-) around the adsorption site. At rising coverage, an increase in dipole-dipole repulsion between HCl molecules leads to a lowering of the adsorption energy per HCl and a change of binding towards hydrogen-bridge type as well as a lowering of the activation energy for Cl(-) diffusion. OH(-) formed in the surface due to HCl adsorption has a stretch frequency of 3,083 cm(-1) with Cl(-) associated and 3,648 cm(-1) with Cl(-) removed.     

The transitional isoelectric focusing process

The transitional isoelectric focusing (IEF) process (the course of pH gradient formation by carrier ampholytes (CAs) and the correlation of the focusing time with CA concentration) were investigated using a whole-column detection capillary isoelectric focusing (CIEF) system. The transitional double-peak phenomenon in IEF was explained as a result of migration of protons from the anodic end and hydroxyl ions from the cathodic end into the separation channel and the higher electric field at both acidic and basic sides of the separation channel. It was observed that focusing times increase logarithmically with CA concentration under a constant applied voltage. The correlation of focusing time with CA concentration was explained by the dependence of the charge-transfer rate on the amount of charged CAs within the separation channel during focusing.     

Differences between signal currents for both polarities of applied voltages on cavity ionization chambers

A difference between the surface potential of the charge collecting electrode and that of the guard electrode of an ionization chamber changes the charge collecting volume depending on the applied voltage. If the difference is large, the saturation curve of the signal current shows a maximum at a low applied voltage. Even when there is no electrical or mechanical defect, the signal current from a parallel plate ionization chamber irradiated with ⁶⁰Co γ-rays increases or decreases with the applied voltage beyond the recombination region depending on the polarity of the applied voltage. The variation in the signal current is explained as a result of the change in the stopping power of air due to the acceleration or deceleration of secondary electrons. These electrons are emitted from the polarizing electrode towards the collector as a result of Compton scattering. In a range of low applied voltages, the signal current from a cylindrical ionization chamber is expected to be smaller for a negative applied voltage than for a positive applied voltage. This is because epithermal electrons are expected to have a higher probability of being lost by back diffusion than positive ions which are originally produced in a thermal equilibrium condition. An experimental result, however, showed no difference in the polarities of the applied voltage. The result may be explained as a consequence of the fact that epithemal electrons do not drift for long distances and maintain their energies.     

Twist viscoelastic coefficient of novel thiol terminated alkoxy-cyanobiphenyl nematic liquid crystals

We report our studies on the refractive indices and twist viscoelastic coefficient of novel thiol terminated alkoxy-cyanobiphenyl nematic liquid crystals. Dynamic light scattering (DLS) was employed to measure the twist viscoelastic coefficient as a function of temperature and the length of alkoxy chain. Our studies show that the twist viscoelastic coefficient is about three times smaller than that of the ordinary alkoxy-cyanobiphenyl nematic liquid crystals. DLS experiments carried out on this system with applied electric field show that the director relaxation frequency increases. These measurements yield the ratio of dielectric anisotropy to twist viscosity. We have also estimated the activation energy corresponding to twist viscosity.     

Control of nonadiabatic dissociation dynamics with the use of laser-induced wave packet interferences

Based on wave packet interferences induced by a stationary laser field, a simple way of controlling nonadiabatic dissociation dynamics is proposed. We treat a simple two-state model of diatomic molecules. In this model, there exist two dissociative potential energy curves which cross and are strongly coupled at an internuclear distance, and thus dissociations into one channel are predominant. We propose a control scheme to selectively dissociate a molecule into any favorite channel by choosing the laser frequency and intensity appropriately. The semiclassical estimation of desirable laser parameters can be performed easily by regarding the dissociation processes as nonadiabatic transitions between the Floquet states. The agreement between the semiclassical estimation and the quantum wave packet calculation is found to be satisfactory in the high frequency region (> or =1000 cm(-1)) where the Floquet state picture is valid. In the low frequency region (<1000 cm(-1)), on the other hand, there are discrepancies between them due to the invalidity of the Floquet picture and the dissociation probability is sensitive to the laser phase. This control scheme is applied to the predissociation dynamics of NaI, NaI-->Na+I.     

Gold nanomaterials based pseudostationary phases in capillary electrophoresis: A brand‐new attempt at chondroitin sulfate isomers separation

In this work, a CE method with bare gold nanorods (GNRs) based pseudostationary phase was developed and applied for the separation of chondroitin sulfate (CS) isomers, CS, and dermatan sulfate (DS). The separation efficiency was investigated by varying the experimental parameters such as concentration and pH of the BGE, separation voltage, internal diameter of capillary, different size, and morphology of gold nanomaterials. Results showed that different size and morphology of gold nanomaterials had different effects on the separation of CS and DS. The best separation of CS and DS was achieved in the BGE composed of aqueous 150 mmol/L (mM) ethylenediamine + 20 mM sodium dihydrogen phosphate + 30% v/v GNRs, pH 4.5, at the separation voltage of ?10 kV. Capillary was 59.2 cm in length (effective length 49 cm), 50 μm id capillary thermostated at 25°C. CE with bare GNRs used as pseudostationary phase was shown to be a suitable technique for the separation of CS and DS mixtures with wider peaks. RSD of migration time and peak area of CS and DS were 0.13, 0.14 and 0.86, 1.07%, respectively.     

A model for interfacial resistance observed during solubilization with micellar solution

The quantitative behavior of interfacial resistance to mass transfer at an oil-water interface in presence of a surfactant, which occurs in addition to the diffusional resistance, is modeled. Successive approximations are used to simplify the detailed behavior to show that the experimentally determined quantitative behavior of solubilization kinetics, is also theoretically justified. The solubility of oil, the frequency of collision of micelles with the oil-water interface, and the resistance to the entry of the solubilizate into the micelle (activation energy) are identified as the key quantities governing this resistance.     

Voltage dependence of a stochastic model of activation of an alpha helical S4 sensor in a K channel membrane

The voltage dependence of the ionic and gating currents of a K channel is dependent on the activation barriers of a voltage sensor with a potential function which may be derived from the principal electrostatic forces on an S4 segment in an inhomogeneous dielectric medium. By variation of the parameters of a voltage-sensing domain model, consistent with x-ray structures and biophysical data, the lowest frequency of the survival probability of each stationary state derived from a solution of the Smoluchowski equation provides a good fit to the voltage dependence of the slowest time constant of the ionic current in a depolarized membrane, and the gating current exhibits a rising phase that precedes an exponential relaxation. For each depolarizing potential, the calculated time dependence of the survival probabilities of the closed states of an alpha helical S4 sensor are in accord with an empirical model of the ionic and gating currents recorded during the activation process.     

The Optimal Control of Geometry and Voltage Parameters on Electrokinetic Transport to Avoid Sample Leakage in Microfluidic Chips

Computer simulation is used to investigate sample transport phenomena of cross microfluidic chips. In this study, Kirchhoff circuit theory is employed to calculate the electric field strength and approximate electroosmotic flow. It is apparent from the results that both the simulation and the theoretical data show similar trends in the electroosmosis of cross microchips. The main target in this study is to summarize the optimal controlling parameter values for avoiding sample leakage in the transport process. The effects of the applied voltage ratio, the geometry ratio and the zeta potential were simulated using a computational fluid dynamics and multiphysics solver software package (CFD-ACE+). Under our designed conditions, two major conclusions were reached: (1) for high-voltage ratios, the sample leakage can be avoided as the geometry ratio is large enough at 0.5 or greater, and (2) for small geometries, maintaining a smaller voltage ratio, 0.3 or less, is essential for avoiding sample leakage. The key is to govern the sample velocity in the upstream faster than that in the downstream. Although real experimental conditions can be further fine tuned under microscopy monitoring, these conclusions are helpful to design the proper channel geometry and set up suitable voltage parameters to avoid sample leakages in one cross-channel chip.     

Sodium silicate based sol–gel structures for generating pressure-driven flow in microfluidic channels

In this article, we report the design of a microchip based hydraulic pump that employs a sodium silicate derived sol–gel structure for generating pressure-driven flow within a microfluidic network. The reported sol–gel structure was fabricated in a chosen location of our device by selectively retaining sodium silicate solution within a sub-micrometer deep segment via capillary forces, and then providing the precursor material appropriate thermal treatment. It was shown that while the molecular weight cut-off for these membranes is at least an order of magnitude smaller than their photo-polymerized counterparts, their electrical conductance is significant. Moreover, unlike their polymeric counterparts these structures were found to be capable of blocking electroosmotic flow, thereby generating a pressure-gradient around their interface with an open microchannel upon application of an electric field across the microchannel–membrane junction. In this work, a fraction of the resulting hydrodynamic flow was successfully guided to an electric field-free analysis channel to implement a pressure-driven assay. Our experiments show that the pressure-driven velocity produced in the analysis channel of our device varied linearly with the voltage applied across the sol–gel membrane and was nearly independent of the cross-sectional dimensions of the membrane and the microfluidic channels. With our current design pressure-driven velocities up to 1.7 mm/s were generated for an applied voltage of 2 kV, which easily covers the range of flow speeds that can minimize the plate height in most microfluidic separations. Finally, the functionality of our device was demonstrated by implementing a reverse phase chromatographic separation in the analysis channel of our device using the pressure-driven flow generated on-chip.     

Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments

A striking feature of the alpha-hemolysin channel-a prime candidate for biotechnological applications-is the dependence of its ionic conductance on the magnitude and direction of the applied bias. Through a combination of lipid bilayer single-channel recording and molecular dynamics (MD) simulations, we characterized the current-voltage relationship of alpha-hemolysin for all alkali chloride salts at neutral pH. The rectification of the ionic current was found to depend on the type of cations and increase from Li(+) to Cs(+). Analysis of the MD trajectories yielded a simple quantitative model that related the ionic current to the electrostatic potential, the concentration and effective mobility of ions in the channel. MD simulations reveal that the major contribution to the current asymmetry and rectification properties originates from the cationic contribution to the current that is significantly reduced in a cationic dependent way when the membrane polarity is reversed. The variation of chloride current was found to be less important. We report that the differential affinity of cations for the charged residues positioned at the channel's end modulates the number of ions inside the channel stem thus affecting the current properties. Through direct comparison of simulation and experiment, this study evaluates the accuracy of the MD method for prediction of the asymmetric, voltage dependent conductances of a membrane channel.     

Sequence-specific single-molecule analysis of 8-oxo-7,8-dihydroguanine lesions in DNA based on unzipping kinetics of complementary probes in ion channel recordings

Translocation measurements of intact DNA strands with the ion channel α-hemolysin (α-HL) are limited to single-stranded DNA (ssDNA) experiments as the dimensions of the channel prevent double-stranded DNA (dsDNA) translocation; however, if a short oligodeoxynucleotide is used to interrogate a longer ssDNA strand, it is possible to unzip the duplex region when it is captured in the α-HL vestibule, allowing the longer strand to translocate through the α-HL channel. This unzipping process has a characteristic duration based on the stability of the duplex. Here, ion channel recordings are used to detect the presence and relative location of the oxidized damage site 8-oxo-7,8-dihydroguanine (OG) in a sequence-specific manner. OG engages in base pairing to C or A with unique stabilities relative to native base Watson-Crick pairings, and this phenomenon is used here to engineer probe sequences (10-15mers) that, when base-paired with a 65mer sequence of interest, containing either G or OG at a single site, produce characteristic unzipping times that correspond well with the duplex melting temperature (T(m)). Unzipping times also depend on the direction from which the duplex enters the vestibule if the stabilities of leading base pairs at the ends of the duplex are significantly different. It is shown here that the presence of a single DNA lesion can be distinguished from an undamaged sequence and that the relative location of the damage site can be determined based on the duration of duplex unzipping.