Design of minimally strained nucleic Acid nanotubes

A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double-helical domain is connected to each of its neighbors via two or more Holliday-junction-like reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a five-parameter characterization of the segmented double-helical structure. Once the constraint equations have been derived, the primary design problem for a minimally strained N-domain structure is reduced to solving three simultaneous equations in 2N+2 variables. Symmetry analysis and tube merging then allow for the design of a wide variety of tubes, which can be tailored to satisfy requirements such as specific inner and outer radii, or multiple lobed structures. The general form of the equations allows similar techniques to be applied to various nucleic acid helices: B-DNA, A-DNA, RNA, DNA-PNA, or others. Possible applications for such tubes include nanoscale scaffolding as well as custom-shaped enclosures for other nano-objects.     

Self-Organization of Recombinant Membrane Porin OmpF from Yersinia pseudotuberculosis in Aqueous Environments

Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation. In aqueous solutions, rOmpF undergoes conformational changes, reversible self-association, and aggregation. When transferred from 8M urea into water, PBS (containing 0.15 M NaCl, pH 7.4), or buffer containing 0.8 M urea (pH 8.0), fully unfolded rOmpF forms relatively compact monomeric intermediates prone to self-association with formation of multimers. The oligomeric intermediates have high content of native protein-like secondary structure and pronounced tertiary structure. In acidic media (pH 5.0, close to the protein isoelectric point), rOmpF undergoes rapid irreversible aggregation. Therefore, we found that medium composition significantly affects both porin folding and processes of its self-association and aggregation.     

HURP wraps microtubule ends with an additional tubulin sheet that has a novel conformation of tubulin

HURP is a newly discovered microtubule-associated protein (MAP) required for correct spindle formation both in vitro and in vivo. HURP protein is highly charged with few predicted secondary and tertiary folding domains. Here we explore the effect of HURP on pure tubulin, and describe its ability to induce a new conformation of tubulin sheets that wrap around the ends of intact microtubules, thereby forming two concentric tubes. The inner tube is a normal microtubule, while the outer one is a sheet composed of tubulin protofilaments that wind around the inner tube with a 42.5° inclination. We used cryo-electron microscopy and unidirectional surface shadowing to elucidate the structure and conformation of HURP-induced tubulin sheets and their interaction with the inner microtubule. These studies clarified that HURP-induced sheets are composed of anti-parallel protofilaments exhibiting P2 symmetry. HURP is a unique MAP that not only stabilizes and bundles microtubules, but also polymerizes free tubulin into a new configuration.     

Low resolution structure and dynamics of a colicin-receptor complex determined by neutron scattering

Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.     

An iterative Fourier-Bessel algorithm for reconstruction of helical structures with severe Bessel overlap

Classical Fourier-Bessel methodology fails when used to reconstruct helical structures with severe Bessel overlap on the layer lines. In the reconstruction of a peculiar type of double-layered helical tube of GDP-tubulin, we face the problem of Bessel overlap on all the layer lines due to the superposition of the Fourier components from the inner and outer layers of the tube. In order to decompose the Fourier terms of the inner and outer layers more than one image of the tubes must be combined and the orientations of their inner and outer layer helices must be determined. While there is no direct analytical method to determine these orientational parameters, we have devised an iterative Fourier-Bessel algorithm to calculate the correct orientations and thus allow us to obtain a reconstruction from multiple images of the double-layered tubes. The algorithm successfully works for the reconstruction of computer-modeled double-layered helical tubes as well as with real images obtained by cryo-electron microscopy. The algorithm has also been applied with very satisfactory results to the reconstruction of 13-protofilament microtubules, which is another helical structure that suffer Bessel overlap, suggesting its generality.     

Hydrogen adsorption capacities of multi-walled boron nitride nanotubes and nanotube arrays: a grand canonical Monte Carlo study

Hydrogen adsorption in multi-walled boron nitride nanotubes and their arrays was studied using grand canonical Monte Carlo simulation. The results show that hydrogen storage increases with tube diameter and the distance between the tubes in multi-walled boron nitride nanotube arrays. Also, triple-walled boron nitride nanotubes present the lowest level of hydrogen physisorption, double-walled boron nitride nanotubes adsorb hydrogen better when the diameter of the inner tube diameter is sufficiently large, and single-walled boron nitride nanotubes adsorb hydrogen well when the tube diameter is small enough. Boron nitride nanotube arrays adsorb hydrogen, but the percentage of adsorbed hydrogen (by weight) in boron nitride nanotube arrays is rather similar to that found in multi-walled boron nitride nanotubes. Also, when the Langmuir and Langmuir-Freundlich equations were fitted to the simulated data, it was found that multi-layer adsorptivity occurs more prominently as the number of walls and the tube diameter increase. However, in single-walled boron nitride nanotubes with a small diameter, the dominant mechanism is monolayer adsorptivity.     

Influence of cultivation conditions on mechanical and morphological properties of bacterial cellulose tubes

Bacterial cellulose (BC) was deposited in tubular form by fermenting Acetobacter xylinum on top of silicone tubes as an oxygenated support and by blowing different concentrations of oxygen, that is, 21% (air), 35%, 50%, and 100%. Mechanical properties such as burst pressure and tensile properties were evaluated for all tubes. The burst pressure of the tubes increased with an increase in oxygen ratio and reached a top value of 880 mmHg at 100% oxygen. The Young's modulus was approximately 5 MPa for all tubes, irrespective of the oxygen ratio. The elongation to break decreased from 30% to 10-20% when the oxygen ratio was increased. The morphology of the tubes was characterized by Scanning Electron Microscopy (SEM). All tubes had an even inner side and a more porous outer side. The cross section indicated that the tubes are composed of layers and that the amount of layers and the yield of cellulose increased with an increase in oxygen ratio. We propose that an internal vessel wall with high density is required for the tube to sustain a certain pressure. An increase in wall thickness by an increase in oxygen ratio might explain the increasing burst pressure with increasing oxygen ratio. The fermentation method used renders it possible to produce branched tubes, tubes with unlimited length and inner diameters. Endothelial cells (ECs) were grown onto the lumen of the tubes. The cells formed a confluent layer after 7 days. The tubes potential as a vascular graft is currently under investigation in a large animal model at the Centre of Vascular Engineering, Sahlgrenska University     

Light-scattering studies of the alpha-ketoglutarate dehydrogenase complex from escherichia coli. I. Characterization of the self-association of the complex

The self-association of Escherichia coli alpha-ketoglutarate dehydrogenase complex (KGDC) purified by a column Chromatographic technique, was characterized by light-scattering photometry. The complex adopts a solution conformation somewhat larger than that observed in the electron microscope. The evidence suggests a nonideal indefinite self-association model for KGDC in KCl, phosphate buffer. The KGDC monomer has a molecular charge of about -3 x 10(2) at neutral pH. The self-association is promoted by increasing KCl concentrations, pH (in the range from 6.3 to 7.4) and temperature (from 20 to 30 degrees C). The effects of pH changes suggest a release of protons during the self-association and a minor 'preferential' interaction of phosphate ions. For the association of one monomer to the aggregate at neutral pH and 25 degrees C. DeltaG degrees = -7.8 kcal mol(-1). DeltaH degrees = 24 kcal mol(-1) and DeltaS degrees = 1.1 x 10(2) cal mol(-1) K(-1). These data indicate that hydrophobic interactions drive the association. Thermodynamically, the self-association of KGDC is a complex phenomenon and may serve to stabilize the enzyme complex in solution.     

Neutron scattering analysis of bacterial lipopolysaccharide phase structure. Changes at high pH

The aggregate structure of lipopolysaccharide isolated from an Re strain of Escherichia coli was examined at different pH values using small angle neutron scattering. At pH values of 6 and 7.4, angle-averaged scattering of the sodium salt of this isolate was consistent with randomly coiled tubular micelles approximately 100 A in diameter. At pH 9.1, however, Kratky analysis of the scattering data was distinctly different and consistent with pairing of uniform tubular micelle sections of length 1440 and 110 A in diameter. Contrast variation measurements of the micelles yielded an average micellar weight of the sample at pH 9.1 of approximately 1.11 X 10(7) daltons and suggested that the aggregates were tubular micelles of size and length similar to that derived from the scattering intensity data. Anisotropic scattering patterns of samples under shear indicated a rigidification of the micelles as the pH was increased to 9.1 and the temperature decreased from 25 to 10 degrees C. The rotational diffusion constants deduced from the observed shear anisotropy indicate that the structure at pH 9.1 must have smallest and largest dimensions which differ by at least an order of magnitude, ruling out spherical or moderately ellipsoidal structures. Analysis of the shear rate needed to induce anisotropic scattering indicated that the stiffness length of the micelles at pH 9.1 was approximately 1000 A and decreased at higher and lower pH values.     

Behavior of Tn3 resolvase in solution and its interaction with res

The solution properties of Tn3 resolvase (Tn3R) were studied by sedimentation equilibrium, sedimentation velocity analytical ultracentrifugation, and small-angle neutron scattering. Tn3R was found to be in a monomer-dimer self-association equilibrium, with a dissociation constant of K(D)(1-2)=50 microM. Sedimentation velocity and small-angle neutron scattering data are consistent with a solution structure of dimeric Tn3R similar to that of gammadelta resolvase in a co-crystal structure, but with the DNA-binding domains in a more extended conformation. The solution conformations of sites I, II, and III were studied with small angle x-ray scattering and modeled using rigid-body and ab initio techniques. The structures of these sites do not show any distortion, at low resolution, from B-DNA. The equilibrium binding properties of Tn3R to the individual binding sites in res were investigated by employing fluorescence anisotropy measurements. It was found that site II and site III have the highest affinity for Tn3R, followed by site I. Finally, the affinity of Tn3R for nonspecific DNA was assayed by competition experiments.     

Plasmatubules in the pollen tubes of Nicotiana sylvestris

Ultrastructural studies of the pollen tubes of Nicotiana sylvestris grown in the pistil revealed an extensive development of plasmatubules formed by evaginations of the plasma membrane. The plasmatubules occurred as twisted tubular structures in the periplasmic space along the tube wall and, in cross section, exhibited circular profiles with an outer diameter of 28±4 nm. They were also seen in deep, pocket-like invaginations of the plasma membrane and in this case the profiles had an outer diameter of 34±8 nm. In the pocket-like invaginations they were partially branched and often closely packed to form groups with obvious patterns. The enlargement of the plasma-membrane area resulting from plasmatubules formed along the tube wall was about six-to tenfold. Pollen tubes grown in vitro exhibited poorly developed plasmatubules. It is suggested that the large extension of the plasma membrane could enhance the uptake of nutrients, and thus might be responsible for the comparatively fast growth of pollen tubes in the pistil. Moreover, it is also assumed that the turnover rate of the Golgi apparatus must be higher in pollen tubes growing in vivo than in vitro, in order to provide a sufficient amount of membrane for the formation of the plasma membrane with its tubular modifications.     

Construction of biotinylated peptide nanotubes for arranging proteins

Three kinds of biotinylated peptides with different linkers between biotin and beta-sheet peptide were designed and synthesized. The transmission electron microscopy revealed that the biotinylated peptides self-assembled to form a tubular structure with external diameter of ca. 60 nm and inner diameter of ca. 30 nm in an aqueous solution. The anti-biotin antibody effectively bound to biotin groups in the peptide nanotubes. The binding of antibody was regulated by not only the concentration of the protein in the solution but also the properties of biotinylated peptides forming the tubes. The antibody preferentially bound to the biotinylated peptide tubes assembled from the peptide with the most hydrophilic linker, suggesting that the surface properties and functions of the tubular structure were modulated and engineered by the design of the peptides.     

Lipid membrane templates the ordering and induces the fibrillogenesis of Alzheimer's disease amyloid-beta peptide

The lipid membrane has been shown to mediate the fibrillogenesis and toxicity of Alzheimer's disease (AD) amyloid-beta (Abeta) peptide. Electrostatic interactions between Abeta40 and the phospholipid headgroup have been found to control the association and insertion of monomeric Abeta into lipid monolayers, where Abeta exhibited enhanced interactions with charged lipids compared with zwitterionic lipids. To elucidate the molecular-scale structural details of Abeta-membrane association, we have used complementary X-ray and neutron scattering techniques (grazing-incidence X-ray diffraction, X-ray reflectivity, and neutron reflectivity) in this study to investigate in situ the association of Abeta with lipid monolayers composed of either the anionic lipid 1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (DPPG), the zwitterionic lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), or the cationic lipid 1,2-dipalmitoyl 3-trimethylammonium propane (DPTAP) at the air-buffer interface. We found that the anionic lipid DPPG uniquely induced crystalline ordering of Abeta at the membrane surface that closely mimicked the beta-sheet structure in fibrils, revealing an intriguing templated ordering effect of DPPG on Abeta. Furthermore, incubating Abeta with lipid vesicles containing the anionic lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG) induced the formation of amyloid fibrils, confirming that the templated ordering of Abeta at the membrane surface seeded fibril formation. This study provides a detailed molecular-scale characterization of the early structural fluctuation and assembly events that may trigger the misfolding and aggregation of Abeta in vivo. Our results implicate that the adsorption of Abeta to anionic lipids, which could become exposed to the outer membrane leaflet by cell injury, may serve as an in vivo mechanism of templated-aggregation and drive the pathogenesis of AD.     

Light scattering and transmission electron microscopy studies reveal a mechanism for calcium/calmodulin-dependent protein kinase II self-association

Calmodulin (CaM)-kinase II holoenzymes composed of either alpha or beta subunits were analyzed using light scattering to determine a mechanism for self-association. Under identical reaction conditions, only alphaCaM-kinase II holoenzymes self-associated. Self-association was detected at a remarkably low enzyme concentration (0.14 microM or 7 microg/mL). Light scattering revealed two phases of self-association: a rapid rise that peaked, followed by a slower decrease that stabilized after 2-3 min. Electron microscopy identified that the rapid rise in scattering was due to the formation of loosely packed clusters of holoenzymes that undergo further association into large complexes of several microns in diameter over time. Self-association required activation by Ca(2+)/CaM and was strongly dependent on pH. Self-association was not detected at pH 7.5, however, the extent of this process increased as reaction pH decreased below 7.0. A peptide substrate (autocamtide-2) and inhibitor (AIP) designed from the autoregulatory domain of CaM-kinase II potently prevented self-association, whereas the peptide substrate syntide-2 did not. Thus, CaM-kinase II self-association is isoform specific, regulated by the conditions of activation, and is inhibited by peptides that bind to the catalytic domain likely via their autoregulatory-like sequence. A model for CaM-kinase II self-association is presented whereby catalytic domains in one holoenzyme interact with the regulatory domains in neighboring holoenzymes. These intersubunit-interholoenzyme autoinhibitory interactions could contribute to both the translocation and inactivation of CaM-kinase II previously reported in models of ischemia.     

Detection and localization of pectin methylesterase isoforms in pollen tubes of Nicotiana tabacum L.

Pectin methylesterases (PMEs) were detected in tobacco ( Nicotiana tabacum) pollen tubes grown in vitro. Seven PME isoforms exhibiting a wide isoelectric-point (pI) range (5.3-9.1) were found in crude extracts of pollen tubes. These isoforms were mainly retrieved in supernatants after low- and high-speed separation of the crude extract. Two isoforms, with pIs 5.5 and 7.3 and molecular weight about 158 kDa, were detected by immunoblotting with anti-flax PME antiserum. Localization of pectins and PME isoforms in pollen tubes was investigated by immunogold labelling with JIM5 monoclonal antibodies and anti-flax PME antiserum, respectively. In germinated pollen grains, two PME isoforms were mainly detected in the exine, Golgi apparatus and secretory vesicles. In pollen tubes the same two PME isoforms were distributed along the outer face of the plasma membrane in the vicinity of the inner layer of the cell wall, in the Golgi and around secretory vesicles. In pollen grains, PME isoforms were, in some cases, mixed with acidic pectins in proximity to the outer surface of the plasma membrane. In pollen tubes the presence of PMEs inside secretory vesicles carrying esterified pectins supports the hypothesis that, during pollen tube growth, PMEs could be transferred by secretory vesicles in a precursor form and be activated at the tip where exocytosis takes place.     

Vinculin tail conformation and self-association is independent of pH and H906 protonation

Vinculin is a highly conserved cytoskeletal protein that localizes to sites of cell adhesion. The tail domain of vinculin (Vt) forms tight autoinhibitory interactions with the head domain and down-regulates vinculin function by obscuring ligand binding sites. Ligand binding is required for both vinculin activation and function, and one of vinculin's primary roles as a cell adhesion protein involves its ability to link the Actin cytoskeleton to the cell membrane. Vt can bind F-Actin and phosphoinositol 4,5-bisphosphate, and association with these ligands has been reported to cause a conformational change in Vt. Moreover, a single histidine residue, H906, was reported to be critical for both a pH dependent conformational change and pH dependent self-association. In this study, we investigate the role of pH on Vt structure and self-association. In contrast to earlier observations, our studies do not support a significant alteration in Vt conformation over this pH range. Moreover, while we identify a site of Vt dimerization, similar to that observed previously by X-ray crystallography, the weak K(d) (approximately 300 microM) determined for Vt self-association does not differ significantly between pH 5.5 and pH 7.5.     

Conformation of Single and Interacting Lipopolysaccharide Surfaces Bearing O-Side Chains

The outer surfaces of Gram-negative bacteria are composed of lipopolysaccharide (LPS) molecules exposing oligo- and polysaccharides to the aqueous environment. This unique, structurally complex biological interface is of great scientific interest as it mediates the interaction of bacteria with antimicrobial agents as well as with neighboring bacteria in colonies and biofilms. Structural studies on LPS surfaces, however, have so far dealt almost exclusively with rough mutant LPS of reduced molecular complexity and limited biological relevance. Here, by using neutron reflectometry, we structurally characterize planar monolayers of wild-type LPS from Escherichia coli O55:B5 featuring strain-specific O-side chains in the presence and absence of divalent cations and under controlled interaction conditions. The model used for the reflectivity analysis is self-consistent and based on the volume fraction profiles of all chemical components. The saccharide profiles are found to be bimodal, with dense inner oligosaccharides and more dilute, extended O-side chains. For interacting LPS monolayers, we establish the pressure-distance curve and determine the distance-dependent saccharide conformation.     

The fine structure and function of the tentacle in Tokophrya infusionum

The feeding apparatus of Suctoria consists of long, thin, stiff tubes called tentacles. When a swimming prey attaches to the tip of the tentacle a number of events follow in rapid succession. The tentacle broadens, a stream of tiny granules starts to move upward at its periphery to the tip, the prey becomes immobilized and shortly thereafter the cytoplasm of the still living prey begins to flow through the center of the tentacle to the body of the predator. An electron microscope study of the tentacle in Tokophrya infusionum, a protozoan of the subclass Suctoria, has disclosed a number of structural details which help to clarify some of the mechanisms involved in this unusual way of feeding. Each tentacle is composed of two concentric tubes. The lumen of the inner tube is surrounded by 49 tubular fibrils most probably of contractile nature. In the inner tube the cytoplasm of the prey is present during feeding, and in the outer tube are small dense bodies. It was found that the dense bodies originate in the cytoplasm of Tokophrya. They have an elongate, missile-like appearance, pointed at one end, rounded at the other, and are composed of several distinct segments. At the tip of the tentacle they penetrate the plasma membrane, with their pointed ends sticking out. It is assumed that the missile-like bodies play a major role in the feeding process. Their composite structure suggests that they might contain a number of enzymes which most probably are responsible for the various events preceding the actual food intake.     

A new sampler for extracting undisturbed surface peat cores for growth pot experiments

The sampler extracts uncompressed cores of 13·3 cm in diameter, up to 70 cm long, from the surface layers of peat. It has two close-fitting concentric cylindrical tubes, the outer one acting as a cutter and the inner one as a collector. As the outer tube is introduced by rotation into the peat, the cut core is collected in the inner tube which is maintained in a fixed position during the rotation phase and then pushed down stepwise. This limits friction between the peat core and the wall of the corer and prevents compression or distortion of the peat. These problems are also reduced by means of three skew cutters allowing the peat to be supported during the slicing action. Air can penetrate between the tubes to the lower end of the core, suppressing any suction effect during withdrawal. The sampler has been tested and has worked satisfactorily in many different peat types.     

Charged multivesicular body protein 2B (CHMP2B) of the endosomal sorting complex required for transport-III (ESCRT-III) polymerizes into helical structures deforming the plasma membrane

The endosomal sorting complexes required for transport (ESCRT-0-III) allow membrane budding and fission away from the cytosol. This machinery is used during multivesicular endosome biogenesis, cytokinesis, and budding of some enveloped viruses. Membrane fission is catalyzed by ESCRT-III complexes made of polymers of charged multivesicular body proteins (CHMPs) and by the AAA-type ATPase VPS4. How and which of the ESCRT-III subunits sustain membrane fission from the cytoplasmic surface remain uncertain. In vitro, CHMP2 and CHMP3 recombinant proteins polymerize into tubular helical structures, which were hypothesized to drive vesicle fission. However, this model awaits the demonstration that such structures exist and can deform membranes in cellulo. Here, we show that depletion of VPS4 induces specific accumulation of endogenous CHMP2B at the plasma membrane. Unlike other CHMPs, overexpressed full-length CHMP2B polymerizes into long, rigid tubes that protrude out of the cell. CHMP4s relocalize at the base of the tubes, the formation of which depends on VPS4. Cryo-EM of the CHMP2B membrane tubes demonstrates that CHMP2B polymerizes into a tightly packed helical lattice, in close association with the inner leaflet of the membrane tube. This association is tight enough to deform the lipid bilayer in cases where the tubular CHMP2B helix varies in diameter or is closed by domes. Thus, our observation that CHMP2B polymerization scaffolds membranes in vivo represents a first step toward demonstrating its structural role during outward membrane deformation.