Synthetic catalytic pores

Catalytic activity of a synthetic multifunctional pore is studied in large unilamellar vesicles under conditions where substrate and synthetic catalytic pore (SCP) approach the membrane either from the same side (cis catalysis) or from opposite sides (trans catalysis). A synthetic supramolecular rigid-rod beta-barrel with excellent ion channel characteristics is identified as SCP using 8-acetoxypyrene-1,3,6-trisulfonate (AcPTS) as model substrate. The key finding is that application of supportive membrane potentials increases the initial velocity of AcPTS esterolysis (v0). This results in an increase of Vmax beyond experimental error (+30%), whereas KM increases less significantly. Long-range electrostatic steering by the membrane potential, possibly guiding substrates into the transmembrane catalyst and, more importantly, accelerating product release (foff = 1.3) is discussed as one possible explanation of this global reduction of catalyst saturation. Control experiments show, inter alia, that similarly strong changes do not occur with opposing membrane potentials.     

Temperature-responsive protein pores

We describe temperature-responsive protein pores containing single elastin-like polypeptide (ELP) loops. The ELP loops were placed within the cavity of the lumen of the alpha-hemolysin (alphaHL) pore, a heptamer of known crystal structure. The cavity is roughly spherical with a molecular surface volume of about 39,500 A3. In an applied potential, the wild-type alphaHL pore remained open for long periods. In contrast, the ELP loop-containing alphaHL pores exhibited transient current blockades, the nature of which depended on the length and sequence of the inserted loop. Together with similar results obtained with poly(ethylene glycols) covalently attached within the cavity, the data suggest that the transient current blockades are caused by excursions of ELP into the transmembrane beta-barrel domain of the pore. Below its transition temperature, the ELP loop is fully expanded and blocks the pore completely, but reversibly. Above its transition temperature, the ELP is dehydrated and the structure collapses, enabling a substantial flow of ions. Potential applications of temperature-responsive protein pores in medical biotechnology are discussed.     

Synthetic pores with sticky pi-clamps

In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore. This breakthrough is important for the application of synthetic pores as multianalyte sensors.     

Some considerations concerning the technical use of narrow pores

Carrier transport and diffusion through narrow pores (single-file diffusion) are basic transport mechanisms that have been proposed to explain the specific passive permeation properties of biological membranes. Unlike carrier diffusion, the concept of single-file diffusion has been scarcely considered in connection with technical purposes. Taking into account, however, that extensive studies have been made in recent years on artificial lipid membranes with single-file pores and that cylindrical pores with a very narrow diameter distribution can be produced in thin plates by etching nuclear tracks, it seems useful to discuss more carefully the specific properties and conceivable applications of the single-file pore. As properties of obvious technical interest one finds high permselectivity and high transport rate. In addition, the voltage-dependent block of narrow pores provides an intriguing possibility of ionic flux control. A therapeutic system functioning as an artificial suprarenal gland is briefly outlined as an example.     

Adhesive pi-clamping within synthetic multifunctional pores

We report the design, synthesis, and evaluation of synthetic multifunctional pores with adhesive, that is, electron-deficient naphthalenediimide (NDI) pi-clamps at their inner surface. We find that, in lipid bilayer membranes, comparable synthetic pores with and without pi-clamps have similar, nanomolar activity. Functional relevance of adhesive pi-clamping within synthetic pores is demonstrated by means of an innovative in situ blocker screening method. The obtained line of experimental evidence includes (a) different blockage efficiency with and without pi-clamps (quantified as clamping factors), (b) increasing clamping factors with increasing blocker charge (supportive ion pairing), and, most importantly, (c) increasing clamping factors with increasing aromatic electron donor-acceptor interactions. The availability of advanced synthetic multifunctional pores with refined active sites is important for practical applications in domains such as drug discovery (enzyme inhibitor screening) and diagnostics (multianalyte sensing).     

Threading synthetic polyelectrolytes through protein pores

We have measured the ionic current signatures of sodium poly(styrene sulfonate) as its single molecules translocate through an alpha-hemolysin pore embedded into a bilayer in a salty aqueous medium under an externally applied electric field. As in the previous experiments involving DNA and RNA, the pore current, which is a measure of the ionic conductivity of the low molar mass electrolyte ions, is significantly reduced when the polymer molecule translocates through the pore. The magnitude and the duration of the reduction in the pore current are measured for each of the translocation events. By studying thousands of events of reduction in the ionic current, we have constructed distribution functions for the extent of the reduced current and for the translocation time. The details of these distribution functions are significantly different from those for DNA and RNA. By investigating over two orders of magnitude in the molecular weight of the polymer, the average translocation time is found to be proportional to the molecular weight and inversely proportional to the applied voltage. This demonstration of threading a synthetic polyelectrolyte through a protein pore opens up many opportunities to systematically explore the fundamental physical principles behind translocation of single macromolecules, by resorting to the wide variety of synthetically available polymers without the complexities arising from the sequences of biological polymers. In addition, the present experiments suggest yet another experimental protocol for separation of polymer molecules directly in aqueous media.     

Sugar sensing with synthetic multifunctional pores

Recently, synthetic multifunctional pores have been identified as "universal" detectors of chemical reactions. In this report, we show that with the assistance of enzymes as variable co-sensors, synthetic multifunctional pores can serve as similar universal sensors of variable components in mixed analytes. Sugar sensing in soft drinks is used to exemplify this new concept. This is achieved using invertase and hexokinase as co-sensors and a new synthetic multifunctional pore capable of discriminating between ATP and ADP in an "on-off" manner as sensor. The on-off discrimination between ATP as good and ADP as poor pore blocker is shown to be reasonably tolerant of changing experimental conditions. These results identify universal sensing with synthetic multifunctional pores as a robust, sensitive, and noninvasive method with appreciable promise for practical applications.     

Modeling molecular transport in slit pores

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1-1 nm(-3). Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid-fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation.     

Calculations of the distribution of trace impurities in cylindrical pores

The equilibrium distribution of a trace impurity and the self-diffusion coefficients of molecules of the base component and the trace impurity in narrow cylindrical pores were calculated using the lattice-gas model. Two types of lattice structures with six and eight closest neighbors were considered. The sizes of the base component and impurity molecules were taken to be identical. Lateral interactions were taken into account in the quasi-chemical approximation. The equilibrium distributions of the trace impurity across a pore section in the gas and liquid phases of the base component and at the interface for the case of capillary condensation were considered. The probability of existence of isolated dimeric clusters was estimated and the self-diffusion coefficients of the base component and trace impurity for a single-phase distribution of the base component were calculated. The effects of the energy of interaction of impurities with the pore walls and the concentration of the base component on the diffusion mobility of the impurities were analyzed. The concentration dependences of the partition coefficient for the trace impurity between the pore center and the pore wall and the concentration dependences of the self-diffusion coefficients for the trace impurity molecules become nonmonotonic with an increase in the base component concentration. These effects are due to the displacement of the impurity from the near-surface area to the bulk of a pore following an increase in the pore coverage by the base component and to higher mobility of the impurity in the free bulk of the pore. Further filling of the pore bulk reduces the mobility of all molecules. The energetics of intermolecular interactions also plays a certain role. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 605–615, April, 2000.     

Electrokinetic effects in membrane pores and the determination of zeta-potential

The surface charge or electrical potential properties of microfiltration, ultrafiltration and nanofiltration membranes can have a very significant influence on their separation performance. Such properties are most commonly quantified in terms of zeta-potentials obtained by calculation following experimental measurement of streaming potentials. Such calculation requires numerical solution of the equations governing fluid flow and electrical-potential distribution in the pores. A method for such calculations is presented, which includes a numerical solution of the non-linear Poisson–Boltzmann equation and allows for the mobilities of anions and cations to be individually specified. By expressing the results of such calculations in terms of a factor to be applied to a classical analytical result, it is shown to be very important to use proper numerical calculations in the interpretation of electrokinetic data for membranes. Use of a classical analytical analysis to calculate ‘relative', ‘apparent', ‘equivalent' or ‘nominal' zeta-potentials is likely to lead to substantial underestimation of the true zeta-potential and possible serious error even in the interpretation of relative changes in membrane properties. The calculations needed to avoid such difficulties may be readily carried out on a PC. It is also important to account for the individual mobilities of the anions and cations in the electrolyte used for measurements.     

Dimpled vesicles: the interplay between energetics and transient pores

The familiar biconcave shape of the red-blood cell (RBC) deforms as the cell travels through capillaries. Its dimpled configurations are unique cell shapes and display malleability to form echinocytes, discocytes and stomatocytes, in response to external perturbations. Sheetz and Singer introduced intercalating species to the exterior lipid leaflet of the membrane to promote cup-shaped stomatocytes, and observed that additives to the interior had the opposite effect. Shape transformations appear to be controlled via the RBC bilayer and the asymmetric surface areas of the two leaflets [Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 4457]. Our system promotes area-difference between the lipid bilayer leaflets from a fully symmetrical system and has mimicked the RBC discoid. In our analysis, we explore the system energetic and geometric confinements, which points to transient pores as enablers for the vesicles to deflate and thereby to assume lower profiles.     

Theoretical description of pores in the simulation of composite materials

The influence of porosity on the electric conductivity and the dielectric constants of composite materials was studied using computer simulation (the Monte Carlo method). A new approach to the simulation of porous systems that treats pores as a component equivalent to the solid phase components was proposed. Within the framework of this approach, an analysis of the influence of the micro- and macroporosity on the electric conductivity was carried out. It was established that the concept of a barrier-disordered system is also valid for pores. It was shown for the first time that pores can serve as one of the factors that forms the contact barrier distribution function. The proposed theoretical models were in good agreement with the experimental data.     

Adsorption of water molecules in slit pores

We report molecular dynamics (MD) simulations on the adsorption of water in attractive and repulsive slit pores, where the slit and a bulk region are in contact with each other. Water structure, surface force and adsorption behavior are investigated as a function of the overall density in the bulk region. The gas–liquid transition in both types of pores occurs at similar densities of the bulk region.     

Self-assembled peptide tubelets with 7 A pores

Here we report the preparation and structural characteristics of self-assembling peptide tubelets composed of 32-membered rings formed of alternating alpha-amino acids and cis-3-aminocyclohexanecarboxylic acids. The tubelets possess a partial hydrophobic core environment, provided by the projection of the cyclohexane C2 methylene moiety into the lumen, and a Van der Waals pore diameter of about 7 A.     

On the cavitation and pore blocking in slit-shaped ink-bottle pores

We present GCMC simulations of argon adsorption in slit pores of different channel geometry. We show that the isotherm for an ink-bottle pore can be reconstructed as a linear combination of the local isotherms of appropriately chosen independent unit cells. Second, depending on the system parameters and operating conditions, the phenomena of cavitation and pore blocking can occur for a given configuration of the ink-bottle pore by varying the geometrical aspect ratio. Although it has been argued in the literature that the geometrical aspects of the system govern the evaporation mechanism (either cavitation or pore blocking), we here put forward an argument that the local compressibility in different parts of the ink-bottle pore is the deciding factor for evaporation. When the fluid in the small neck is strongly bound, cavitation is the governing process, and molecules in the cavity evaporate to the surrounding bulk gas via a mass transfer mechanism through the pore neck. When the pore neck is sufficiently large, the system of neck and cavity evaporates at the same pressure, which is a consequence of the comparable compressibility between the fluid in the neck and that in the cavity. This suggests that local compressibility is the measure of cohesiveness of the fluid prior to evaporation. One consequence that we derive from the analysis of isotherms of a number of connected pores is that by analyzing the adsorption branch or the desorption branch of an experimental isotherm may not lead to the correct pore sizes and the correct pore volume distribution.     

Macroporous oxide materials with three-dimensionally interconnected pores

Ordered mesoscale hollow spheres (1000 nm diameter) of binary oxides such as TiO₂ and ZrO₂ as well as of ternary oxides such as ferroelectric PbTiO₃ and Pb(ZrTi)O₃ have been prepared by templating against colloidal crystals of polystyrene, by adopting different procedures.