Determination of Equivalent Pore Radius for Human Red Cells by Osmotic Pressure Measurement

A new method has been developed to measure the equivalent pore radius in cellular membranes, and has been applied to human red cells. When red cells are suddenly introduced into a non-isosmolar concentration of non-lipid-soluble non-electrolyte molecules, water will enter or leave the cell. The rate of cell swelling or shrinking is determined and extrapolated to zero time to give the initial rate of volume change. By suitable adjustment of the concentration of the external solution the initial rate may be brought to zero. The transient equilibrium concentration, determined by interpolation from experimental data, gives a measure of Staverman's reflection coefficient, σ. The zero time method has enabled us to determine σ for nine permeant molecules. σ is directly related to the equivalent pore radius; the experimental data lead to a value of 4.2 Å for the equivalent pore radius in man, in good agreement with the previous figure of 3.5 Å given by Paganelli and Solomon. The zero time method offers a number of advantages over previous methods for determination of this parameter. It requires no measurement of the rate of water entrance into the cell, and is essentially independent of the kinetics of cell swelling. It may be applied to a variety of living cells so that many additional membranes may now be characterized in terms of their equivalent pore radius.     

Kinetics of Diffusion and Convection in 3.2-Å Pores: Exact Solution by Computer Simulation

The kinetics of transport in pores the size postulated for cell membranes has been investigated by direct computer simulation (molecular dynamics). The simulated pore is 11 Å long and 3.2 Å in radius, and the water molecules are modeled by hard, smooth spheres, 1 Å in radius. The balls are given an initial set of positions and velocities (with an average temperature of 313° K) and the computer then calculates their exact paths through the pore. Two different conditions were used at the ends of the pore. In one, the ends are closed and the balls are completely isolated. In the other, the ball density in each end region is fixed so that a pressure difference can be established and a net convective flow produced. The following values were directly measured in the simulated experiments: net and diffusive (oneway) flux; pressure, temperature, and diffusion coefficients in the pore; area available for diffusion; probability distribution of ball positions in the pore; and the interaction between diffusion and convection. The density, viscosity, and diffusion coefficients in the bulk fluid were determined from the theory of hard sphere dense gases. From these values, the “equivalent” pore radius (determined by the same procedure that is used for cell membranes) was computed and compared with the physical pore radius of the simulated pore.     

Changes in the Permeability of the Salivary Gland Caused by Sympathetic Stimulation and by Catecholamines

The permeability of the submaxillary gland of cats and dogs has been tested by determining the rates at which non-electrolytes penetrate from the plasma into the saliva. Electrical stimulation of the cervical sympathetic trunk or administration of epinephrine or norepinephrine increases the permeability of the gland enabling glucose (molecular radius, MR = 3.5 Å), sucrose (MR = 4.4 Å), raffinose (MR = 5.6 Å), polyglycol 1000 (MR = 7.2 Å), and polyglycol 1540 (MR = 8.1 Å) to penetrate into the saliva from which they are otherwise excluded. Inulin (MR = 14.7 Å) does not enter the saliva under these circumstances. Analysis of the transfer rates suggests that the molecules diffuse through a pore structure permitting free diffusion for molecules with a radius less than 5.7 Å. Close intraarterial injection of C¹⁴-glucose demonstrates that at least part of this permeability is located in the duct system of the gland. Since epinephrine does not enable sucrose to enter the cells of the gland, it appears that penetration from the extracellular space into the saliva occurs by diffusion through intercellular gaps. The characteristics of the permeability allow conclusions as to the localisation and geometry of the ultrastructural change produced.     

Voltage-Driven Translocation of DNA through a High Throughput Conical Solid-State Nanopore

Nanopores have become an important tool for molecule detection at single molecular level. With the development of fabrication technology, synthesized solid-state membranes are promising candidate substrates in respect of their exceptional robustness and controllable size and shape. Here, a 30–60 (tip-base) nm conical nanopore fabricated in 100 nm thick silicon nitride (Si₃N₄) membrane by focused ion beam (FIB) has been employed for the analysis of λ-DNA translocations at different voltage biases from 200 to 450 mV. The distributions of translocation time and current blockage, as well as the events frequencies as a function of voltage are investigated. Similar to previously published work, the presence and configurations of λ-DNA molecules are characterized, also, we find that greater applied voltages markedly increase the events rate, and stretch the coiled λ-DNA molecules into linear form. However, compared to 6–30 nm ultrathin solid-state nanopores, a threshold voltage of 181 mV is found to be necessary to drive DNA molecules through the nanopore due to conical shape and length of the pore. The speed is slowed down ∼5 times, while the capture radius is ∼2 fold larger. The results show that the large nanopore in thick membrane with an improved stability and throughput also has the ability to detect the molecules at a single molecular level, as well as slows down the velocity of molecules passing through the pore. This work will provide more motivations for the development of nanopores as a Multi-functional sensor for a wide range of biopolymers and nano materials.     

Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin

Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ∼70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.     

Cat Heart Muscle in Vitro : III. The extracellular space

The "osmotic gradient" method, an intracellular microelectrode technique for determining whether an uncharged, water-soluble molecule enters cells or remains extracellular, is described. Using this method, a series of carbohydrates of graded molecular size were examined. In cat papillary muscles mannitol, molecular radius 4.0 Å, remained extracellular while arabinose, molecular radius 3.5 Å entered the cells. Measurement of the simultaneous uptake of H³-mannitol and C¹⁴-inulin showed that mannitol equilibrates with 40 per cent of total water in 1 hour, after which the mannitol space does not further increase. By contrast, inulin, molecular radius ~15 Å, equilibrates with 24 per cent of total water in 1 hour; thereafter the inulin space continues to increase very slowly. The intracellular K concentrations are significantly higher and the intracellular Na and Cl concentrations significantly lower when mannitol rather than inulin is used to measure the extracellular space. The intracellular Cl concentration determined with Cl³⁶ or Br⁸² is significantly higher than that calculated from the membrane potential assuming a passive Cl distribution. In addition, it is shown that choline enters and is probably metabolized by the cells of papillary muscle.     

Crystal structure of the avian reovirus inner capsid protein sigmaA

Avian reovirus, an important avian pathogen, expresses eight structural and four nonstructural proteins. The structural σA protein is a major component of the inner capsid, clamping together λA building blocks. σA has also been implicated in the resistance of avian reovirus to the antiviral action of interferon by strongly binding double-stranded RNA in the host cell cytoplasm and thus inhibiting activation of the double-stranded RNA-dependent protein kinase. We have solved the structure of bacterially expressed σA by molecular replacement and refined it using data to 2.3-Å resolution. Twelve σA molecules are present in the P1 unit cell, arranged as two short double helical hexamers. A positively charged patch is apparent on the surface of σA on the inside of this helix and mutation of either of two key arginine residues (Arg155 and Arg273) within this patch abolishes double-stranded RNA binding. The structural data, together with gel shift assay, electron microscopy, and sedimentation velocity centrifugation results, provide evidence for cooperative binding of σA to double-stranded RNA. The minimal length of double-stranded RNA required for σA binding was observed to be 14 to 18 bp.     

An X-Ray Scattering Investigation of Wild Cucumber Mosaic Virus and a Related Protein

X-ray scattering data are presented on solutions of wild cucumber mosaic virus and the associated “top component” particles which have little or no RNA. The radii of gyration are 112 Å and 135 Å for bottom and top component, respectively. The radial density distribution within each particle is calculated by Fourier inversion of the scattered amplitudes. The virus particle or bottom component has approximately uniform density with an outer radius of about 140 Å. The transform of the top component shows an almost hollow center extending out to 105 Å with a surrounding shell of high density about 35 Å thick. Thus the RNA would appear to occupy the region inside 105 Å and does not overlap appreciably the region occupied by protein. The virus has associated with it approximately 0.38 gm of water per gm of virus, resulting in an average electron density of 1.25 times that of water.     

Probing the Average Local Structure of Biomolecules Using Small-Angle Scattering and Scaling Laws

Small-angle neutron and x-ray scattering have become invaluable tools for probing the nanostructure of molecules in solution. It was recently shown that the definite integral of the scattering profile exhibits a scaling (power-law) behavior with respect to molecular mass. We derive the origin of this relationship, and discuss how the integrated scattering profile can be used to identify differing levels of disorder over local ≲30 Å length scales. We apply our analysis to globular and intrinsically disordered proteins.     

Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs

We have determined the crystal structure of the RNA octamer duplex r(guguuuac)/r(guaggcac) with a tandem wobble pair, G·G/U·U (motif III), to compare it with U·G/G·U (motif I) and G·U/U·G (motif II) and to better understand their relative stabilities. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 41.92 Å, c = 56.41 Å, and γ = 120°, with one duplex in the asymmetric unit. The structure was solved by the molecular replacement method at 1.9 Å resolution and refined to a final R factor of 19.9% and R_free of 23.3% for 2862 reflections in the resolution range 10.0–1.9 Å with F ≥ 2σ(F). The final model contains 335 atoms for the RNA duplex and 30 water molecules. The A-RNA stacks in the familiar head-to-tail fashion forming a pseudo-continuous helix. The uridine bases of the tandem U·G pairs have slipped towards the minor groove relative to the guanine bases and the uridine O2 atoms form bifurcated hydrogen bonds with the N1 and N2 of guanines. The N2 of guanine and O2 of uridine do not bridge the ‘locked’ water molecule in the minor groove, as in motifs I and II, but are bridged by water molecules in the major groove. A comparison of base stacking stabilities of motif III with motifs I and II confirms the result of thermodynamic studies, motif I > motif III > motif II.     

Monomeric Amyloid Beta Peptide in Hexafluoroisopropanol Detected by Small Angle Neutron Scattering

Small proteins like amyloid beta (Aβ) monomers are related to neurodegenerative disorders by aggregation to insoluble fibrils. Small angle neutron scattering (SANS) is a nondestructive method to observe the aggregation process in solution. We show that SANS is able to resolve monomers of small molecular weight like Aβ for aggregation studies. We examine Aβ monomers after prolonged storing in d-hexafluoroisopropanol (dHFIP) by using SANS and dynamic light scattering (DLS). We determined the radius of gyration from SANS as 1.0±0.1 nm for Aβ_1–40 and 1.6±0.1 nm for Aβ_1–42 in agreement with 3D NMR structures in similar solvents suggesting a solvent surface layer with 5% increased density. After initial dissolution in dHFIP Aβ aggregates sediment with a major component of pure monomers showing a hydrodynamic radius of 1.8±0.3 nm for Aβ_1–40 and 3.2±0.4 nm for Aβ_1–42 including a surface layer of dHFIP solvent molecules.     

Small Angle X-Ray Scattering of the Thylakoid Membranes of Rhodopseudomonas spheroides in Aqueous Suspensions

The diffraction patterns of particles which have the shape of hollow spheres, i.e. vesicles, can be satisfactorily analyzed by means of a new formula of Weick (1974). This formula is used for the small angle X-ray scattering analysis of aqueous suspensions of thylakoids of Rhodopseudomonas spheroides. Some essential results are: (a) The membrane has a rather asymmetric structure with one layer of low electron density at its inner side and two layers of high electron density near the outer surface of the thylakoids. (b) The distance of the electron density maxima of the latter two layers is 45 ± 5 Å. (c) Between the two maxima is a region of an electron density nearly equal to that of water. (d) The sequence of the peaks is - + 0 + with increasing radius. The peaks extend over an interval of 120 ± 10 Å. (e) The thylakoids are strikingly of the same size. Their diameters, if defined by the outmost layer, vary statistically by about 4% and have an average value of approximately 640 Å.     

THE AXOSTYLE OF SACCINOBACULUS : II. Motion of the Microtubule Bundle and a Structural Comparison of Straight and Bent Axostyles

Undulations of the flagellate Saccinobaculus result from motility in its axostyle, a bundle consisting of thousands of cross-bridged microtubules. In its resting state, the axostyle is a helix of large pitch and slowly varying radius. The active state as seen by light microscopy involves first a bending of the anterior end of the axostyle to a radius of about 8 µm with a circular arc ranging from 60° to 180°, and then the propagation of this bend without damping to the posterior end of the organism at speeds up to 100 µm/s. The cross section of an unbent axostyle is crescent shaped. This crescent flattens as the bend arrives and reappears as the bend passes by. Intertubule bridges impart to the axostyle tubules an axial periodicity of about 150 Å which can serve as a marker for the investigation of tubule sliding or contraction associated with bend formation. Optical diffraction measurements on electron micrographs of the bend demonstrate that the axostyle tubules slide over one another and that the tubules on the inside of a bend usually contract, sometimes by as much as 25%. Possible relationships between the contraction and sliding of the tubules are discussed.     

The Structure of Mytilus Smooth Muscle and the Electrical Constants of the Resting Muscle

The individual muscle fibers of the anterior byssus retractor muscle (ABRM) of Mytilus edulis L. are uninucleate, 1.2–1.8 mm in length, 5 µm in diameter, and organized into bundles 100–200 µm in diameter, surrounded by connective tissue. Some bundles run the length of the whole muscle. Adjacent muscle cell membranes are interconnected by nexuses at frequent intervals. Specialized attachments exist between muscle fibers and connective tissue. Electrical constants of the resting muscle membrane were measured with intracellular recording electrodes and both extracellular and intracellular current-passing electrodes. With an intracellular current-passing electrode, the time constant τ, was 4.3 ± 1.5 ms. With current delivered via an extracellular electrode τ was 68.3 ± 15 ms. The space constant, λ, was 1.8 mm ± 0.4. The membrane input resistance, R_eff, ranged from 23 to 51 MΩ. The observations that values of τ depend on the method of passing current, and that the value of λ is large relative to fiber length and diameter are considered evidence that the individual muscle fibers are electrically interconnected within bundles in a three-dimensional network. Estimations are made of the membrane resistance, R_m, to compare the values to fast and slow striated muscle fibers and mammalian smooth muscles. The implications of this study in reinterpreting previous mechanical and electrical studies are discussed.     

KINETOPLAST DEOXYRIBONUCLEIC ACID OF THE HEMOFLAGELLATE TRYPANOSOMA LEWISI

Cesium chloride centrifugation of DNA extracted from cells of blood strain Trypanosoma lewisi revealed a main band, ρ = 1.707, a light satellite, ρ = 1.699, and a heavy satellite, ρ = 1.721. Culture strain T. lewisi DNA comprised only a main band, ρ = 1.711, and a light satellite, ρ = 1.699. DNA isolated from DNase-treated kinetoplast fractions of both the blood and culture strains consisted of only the light satellite DNA. Electron microscope examination of rotary shadowed preparations of lysates revealed that DNA from kinetoplast fractions was mainly in the form of single 0.4 µ circular molecules and large masses of 0.4 µ interlocked circles with which longer, often noncircular molecules were associated. The 0.4 µ circular molecules were mainly in the covalently closed form: they showed a high degree of resistance to thermal denaturation which was lost following sonication; and they banded at a greater density than linear DNA in cesium chloride-ethidium bromide gradients. Interpretation of the large masses of DNA as comprising interlocked covalently closed 0.4 µ circles was supported by the findings that they banded with single circular molecules in cesium chloride-ethidium bromide gradients, and following breakage of some circles by mild sonication, they disappeared and were replaced by molecules made up of low numbers of apparently interlocked 0.4 µ circles. When culture strain cells were grown in the presence of either ethidium bromide or acriflavin, there was a loss of stainable kinetoplast DNA in cytological preparations. There was a parallel loss of light satellite and of circular molecules from DNA extracted from these cells.     

Geometrical Membrane Curvature as an Allosteric Regulator of Membrane Protein Structure and Function

Transmembrane proteins are embedded in cellular membranes of varied lipid composition and geometrical curvature. Here, we studied for the first time the allosteric effect of geometrical membrane curvature on transmembrane protein structure and function. We used single-channel optical analysis of the prototypic transmembrane β-barrel α-hemolysin (α-HL) reconstituted on immobilized single small unilamellar liposomes of different diameter and therefore curvature. Our data demonstrate that physiologically abundant geometrical membrane curvatures can enforce a dramatic allosteric regulation (1000-fold inhibition) of α-HL permeability. High membrane curvatures (1/diameter ∼1/40 nm⁻¹) compressed the effective pore diameter of α-HL from 14.2 ± 0.8 Å to 11.4 ± 0.6 Å. This reduction in effective pore area (∼40%) when combined with the area compressibility of α-HL revealed an effective membrane tension of ∼50 mN/m and a curvature-imposed protein deformation energy of ∼7 k_BT. Such substantial energies have been shown to conformationally activate, or unfold, β-barrel and α-helical transmembrane proteins, suggesting that membrane curvature could likely regulate allosterically the structure and function of transmembrane proteins in general.     

A Physical Interpretation of the Phenomenological Coefficients of Membrane Permeability

A "translation" of the phenomenological permeability coefficients into friction and distribution coefficients amenable to physical interpretation is presented. Expressions are obtained for the solute permeability coefficient ω and the reflection coefficient σ for both non-electrolytic and electrolytic permeants. An analysis of the coefficients is given for loose membranes as well as for dense natural membranes where transport may go through capillaries or by solution in the lipoid parts of the membrane. Water diffusion and filtration and the relation between these and capillary pore radius of the membrane are discussed. For the permeation of ions through the charged membranes equations are developed for the case of zero electrical current in the membrane. The correlation of σ with ω and L_p for electrolytes resembles that for non-electrolytes. In this case ω and σ depend markedly on ion concentration and on the charge density of the membrane. The reflection coefficient may assume negative values indicating anomalous osmosis. An analysis of the phenomena of anomalous osmosis was carried out for the model of Teorell and Meyer and Sievers and the results agree with the experimental data of Loeb and of Grim and Sollner. A set of equations and reference curves are presented for the evaluation of ω and σ in the transport of polyvalent ions through charged membranes.     

THE FORM AND STRUCTURE OF KINETOPLAST DNA OF CRITHIDIA

Cesium chloride centrifugation of each of the DNAs extracted from eight strains of Crithidia revealed a main band at ρ = 1.717 g/cm³ and a satellite band varying from ρ = 1.701 to 1.705 g/cm³ for the different strains By electron microscopy each DNA was shown to include circular molecules, 0.69–0.80 µ in mean contour length, and large, topologically two-dimensional masses of DNA in which the molecules appeared in the form of rosettes. DNA isolated from kinetoplast fractions of Crithidia acanthocephali was shown to consist of light satellite DNA and to be mainly in the form of large masses, 0.8 µ (mol wt = 1.54 x 10⁶ daltons) circular molecules, and a few long, linear molecules. The results of experiments involving ultracentrifugation, heating, and quenching, sonication, and endodeoxyribonuclease digestion, combined with electron microscopy, are consistent with the following hypothesis. The large DNA masses are associations of 0.8 µ circles which are mainly covalently closed. The circles are held together in groups (the rosettes) of up to 46 by the topological interlocking of each circle with many other circles in the group. A group of circles is attached to an adjacent group by one or more circles, each interlocking with many circles of both groups. Each of the associations comprises, on the average, about 27,000 circles (total mol wt 41 x 10⁹ daltons). A model is proposed for the in situ arrangement of the associations which takes into consideration their form and structure, and appearance in thin sections     

Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import

Several in vitro studies have shown the presence of an affinity gradient in nuclear pore complex proteins for the import receptor Importinβ, at least partially contributing to nucleocytoplasmic transport, while others have historically argued against the presence of such a gradient. Nonetheless, the existence of an affinity gradient has remained an uncharacterized contributing factor. To shed light on the affinity gradient theory and better characterize how the existence of such an affinity gradient between the nuclear pore and the import receptor may influence the nucleocytoplasmic traffic, we have developed a general-purpose agent based modeling (ABM) framework that features a new method for relating rate constants to molecular binding and unbinding probabilities, and used our ABM approach to quantify the effects of a wide range of forward and reverse nucleoporin-Importinβ affinity gradients. Our results indicate that transport through the nuclear pore complex is maximized with an effective macroscopic affinity gradient of 2000 µM, 200 µM and 10 µM in the cytoplasmic, central channel and nuclear basket respectively. The transport rate at this gradient is approximately 10% higher than the transport rate for a comparable pore lacking any affinity gradient, which has a peak transport rate when all nucleoporins have an affinity of 200 µM for Importinβ. Furthermore, this optimal ratio of affinity gradients is representative of the ratio of affinities reported for the yeast nuclear pore complex – suggesting that the affinity gradient seen in vitro is highly optimized.     

The Structure of the Karrikin-Insensitive Protein (KAI2) in Arabidopsis thaliana

KARRIKIN INSENSITIVE 2 (KAI2) is an α/β hydrolase involved in seed germination and seedling development. It is essential for plant responses to karrikins, a class of butenolide compounds derived from burnt plant material that are structurally similar to strigolactone plant hormones. The mechanistic basis for the function of KAI2 in plant development remains unclear. We have determined the crystal structure of Arabidopsis thaliana KAI2 in space groups P2₁ 2₁ 2₁ (a  = 63.57 Å, b  = 66.26 Å, c  = 78.25 Å) and P2₁ (a  = 50.20 Å, b  = 56.04 Å, c  = 52.43 Å, β  = 116.12°) to 1.55 and 2.11 Å respectively. The catalytic residues are positioned within a large hydrophobic pocket similar to that of DAD2, a protein required for strigolactone response in Petunia hybrida. KAI2 possesses a second solvent-accessible pocket, adjacent to the active site cavity, which offers the possibility of allosteric regulation. The structure of KAI2 is consistent with its designation as a serine hydrolase, as well as previous data implicating the protein in karrikin and strigolactone signalling.