Angstroms In Diameter Research Articles

Natural-product-derived membranes for high-efficiency anionic dye removal

Nature possesses inexhaustible resources that inspire researchers to convert natural products into functional materials. Membranes with excellent permeability to balance the trade-off relationship between permeance and retention are highly desirable in the water-purification field. Herein, β-cyclodextrin (β-CD) and sodium ligninsulfonate (SLS) as derivatives of natural products were utilized to construct membranes with enhanced permeability via a facile molecularly engineered interfacial polymerization with 1,3,5-trimesoyl chloride. β-CD with an inner cavity of intrinsic 3D hollow bowls of several angstroms in diameter and hydrophilicity, it was utilized to reduce the permeation resistance of water. SLS endowed the newly designed SLS-CD-2 membrane with a highly negatively charged surface. Thus, the fabricated SLS-CD-2 membrane demonstrated a high permeance of 33.7 L m−2 h−1 bar−1 and a rejection rate of 99.8% for the filtration of Congo red solution. A 91.5% increase in permeance and a negligible change in retention were observed for the SLS-CD-2 membrane compared with those of the membrane without β-CD. The SLS-CD-2 membrane also exhibited excellent separation performance for the filtration of mixed-dye solution, high separation stability, and outstanding anti-pollution capacity. The results indicated the importance of the newly designed membrane in separation processes.

Engineering the Extracellular Loops of Outermembrane Protein G in Creating a Nanopore Sensing Platform

Outermembrane protein G (OmpG) is a 14-stranded beta barrel proin naturally found in the outermembrane of E. coli. It contains seven flexible extracellular loops that create a dynamic behavior in single channel recording termed gating. OmpG gating and its 8 Angstrom diameter make it unsuitable for sensing protein analytes that cannot enter its lumen, a process called translocation. Thus, we have taken advantage of its extracellular loops to facilitate binding of target analytes. We have seen that upon binding to loop 6, proteins cans be detected via the changes in OmpG gating. The changes in gating can be mediated by electrostatic interactions between the OmpG loops and the binding pocket of the protein analyte. We therefore extended our study to create OmpG nanopores with altered charged properties to understand the mechanism of detection and to enhance the binding signal of a specific target in a mixture. We also found that detection of proteins using OmpG can be achieved not only by using loop 6 but also with four other loops. With this knowledge we can engineer multiple binding sites into one nanopore to lower the limit of detection creating a more sensitive nanopore sensor. By gaining a fundamental understanding of OmpG and how it can interact with analytes will help in the building of a robust OmpG library for a plethora of target analytes.

Simulation BeSe Nanowires in Two Phasese Zinc-Blende and Wurtzite Using Density Functional Theory

In this work, we are reporting on the simulation of the beryllium selenide (BeSe) nanowires (NWs) by computational package Q-Espresso / PWSCF according to the ab-initio calculations. Structural and electronic properties, including cohesive energy and Density Of State (DOS) BeSe NWs in two phases on the zinc–blende (ZB) and wurtzite (WZ), using density functional theory based on pseudo-potential approximation and generalized gradient approximation (GGA) up to 20 angstrom in diameter has been calculated. Due to dangling bonds (DBs) in the side surface NWs, cohesive energy is obtained less than the amount of this energy in bulk state of this compound, but with increasing diameter of NWs, the amount of this energy will approach to the bulk state. Comparison of cohesive energy with beryllium selenide NWs in two phases, we find these NWs in WZ phase is more stable and have good compatibility for this result with other results in NWs of similar compounds. The value of energy gap in these NWs on various diameters is obtained less than the amount of the bulk state. It is observed that by increasing the diameter of NWs, the cohesive energy approaches to its value in bulk state.

Synthesis and Structure Determination of the Hierarchical Meso-Microporous Zeolite ITQ-43

The formation of mesopores in microporous zeolites is generally performed by postsynthesis acid, basic, and steam treatments. The hierarchical pore systems thus formed allow better adsorption, diffusion, and reactivity of these materials. By combining organic and inorganic structure-directing agents and high-throughput methodologies, we were able to synthesize a zeolite with a hierarchical system of micropores and mesopores, with channel openings delimited by 28 tetrahedral atoms. Its complex crystalline structure was solved with the use of automated diffraction tomography.

Nanoparticle-based ultra-sensitive assay for discovery and evaluation of cancer markers.

e21169 Background: Our aim was to develop ultra-sensitive nanoparticle based assay for discovery of new cancer markers and evaluation of diagnostic applications. Methods: The nanoparticle probe based assay format uses a multi-step deterministic robotic process, which relies on non-isotropically oriented antibodies on functionalized glass as multiplexed microarrays to capture protein or DNA markers from biological samples. Functionalized, 130 angstrom diameter gold-probes also bind to the markers through a molecular-scale complex containing antibodies or DNA hybridization. The marker-bound molecular complex is then quantified through silver enhancement of the functionalized gold. Results: We have demonstrated the feasibility for the detection of cancer markers including NQO1, uteroglobin, CLC-5, uroplakin, RSOR, p53, CA125, AFP, HE4, CA15-3, CA19-9, beta-hCG, CEA, and PSA. The high sensitivity (e.g., PSA LOD <0.1pg/mL, uteroglobin LOD <10pg/mL) and broad dynamic range were demonstrated by target titrations in both buffer and serum samples. The clinical application has been explored by testing 288 bladder cancer serum samples, 144 kidney cancer samples, and over 500 PSA serum samples. Conclusions: The ultra-sensitive gold nano-particle probe-based tumor marker assay could provide a powerful tool for evaluating novel tumor markers, validation and clinical applications, including early diagnosis.

Ultra-sensitive detection of biomarkers and applications in pharmaceutical discovery and development. Example application to rat cardiac troponin I assay via nanoparticle probes

e14594 Although specific to heart, rat cardiac troponin I (cTnI) is an example of an important biomarker for assessing drug-induced cardiotoxicity in animal models used in various phases of drug discovery and development. Current commercially available assays can only detect 10 ∼ 100 pg/mL in serum at the lowest limits. To improve the sensitivity of rat cTnI assay, we have developed a generically applicable, microarray based nano-probe test. Our rat cTnI assay algorithm uses a multi-step robotic process, which relies on non- isotropically oriented antibodies on functionalized glass as multiplexed microarrays to capture cTnI from serum. Functionalized, 130 angstrom diameter gold nano-probes (measured by static light scattering, 5 nm S.D.) also bind to the troponin through a molecular-scale complex containing antibodies. The troponin-bound molecular complex is then quantified through silver enhancement of the functionalized gold. Assays in this format can be rapidly configured and implemented for a wide array of potential biomarkers. For cTnI we have demonstrated a robust and ultra-sensitive assay with an LOD of less than 500 femtograms of rat cTnI per mL serum, and an overall CV of less than 20%. The assay also shows very low background, a broad dynamic range and over 3 logs of linear dose response. As an example of the potential of high sensitivity, the nanoparticle-based rat cTnI assay could significantly increase the effectiveness of measuring drug-induced heart damage at very low drug dosages and early times. Such sensitive and early measurements can improve examination of the safety of drug candidates while correspondingly reducing drug development time and cost. [Table: see text]

Three-dimensional Reconstruction of a Membrane-bending Complex: THE RC-LH1-PufX CORE DIMER OF RHODOBACTER SPHAEROIDES

A three-dimensional model of the dimeric reaction center-light harvesting I-PufX (RC-LH1-PufX) complex from Rhodobacter sphaeroides, calculated from electron microscope single particle analysis of negatively stained complexes, shows that the two halves of the dimer molecule incline toward each other on the periplasmic side, creating a remarkable V-shaped structure. The distribution of negative stain is consistent with loose packing of the LH1 ring near the 14th LH1 alpha/beta pair, which could facilitate the migration of quinone and quinol molecules across the LH1 boundary. The three-dimensional model encloses a space near the reaction center Q(B) site and the 14th LH1 alpha/beta pair, which is approximately 20 angstroms in diameter, sufficient to sequester a quinone pool. Helical arrays of dimers were used to construct a three-dimensional membrane model, which matches the packing lattice deduced from electron microscope analysis of the tubular dimer-only membranes found in mutants of Rba. sphaeroides lacking the LH2 complex. The intrinsic curvature of the dimer explains the shape and approximately 70-nm diameter of these membrane tubules, and at least partially accounts for the spherical membrane invaginations found in wild-type Rba. sphaeroides. A model of dimer aggregation and membrane curvature in these spherical membrane invaginations is presented.

Atomic-Level Models of the Bacterial Carboxysome Shell

The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.

Ultrastructural organization and development cycle of soil ultramicrobacteria belonging to the class Alphaproteobacteria

Gram-negative chemoorganotrophic soil ultramicrobacteria (UMB), strains NF1 and NF3, have been isolated. In their development cycle, the strains formed small coccoid cells of 400-800 nm and ultrasmall cells of 200-300 nm. Phylogenetically, the strains NF1 and NF3 belong to Alphaproteobacteria and are close to the type strain of the recently described species Kaistia adipata. The ultrastructure of UMB cells has been studied using ultrathin sections and freeze-fracturing. It has been shown that the structure of UMB cell walls is of the gram-negative type; the outer membrane and peptidoglycan layer are well differentiated. The cell surface has numerous protrusions (prosthecae) of conical or spherical shape filled with the contents of the periplasm. The formation of unusual cellular structures (not occurring in known free-living bacteria) is a feature of UMB: these include the following: (a) piles of rod-like subunits, ca. 30 A in diameter and 150-250 angstroms in length: (b) long bunches (up to 300-400 angstroms) comprised of filamentous subunits; and (c) large electron-dense spherical bodies (up to 200-300 angstroms in diameter) localized in the periplasm. A distinctive feature of UMB is their ability to grow as facultative parasites on living cyanobacterial (CB) cells. In this case, three types of interaction between UMB and CB have been revealed: (1) adsorption of UMB cells on the surface of CB cells; (2) penetration of UMB into polysaccharide sheathes; and (3) penetration of UMB into CB eytoplasm. UMB cells have been shown to reproduce by budding, with buds (up to 2-3) located directly on the mother cell, without formation of intennediate hyphae.

Characterization of Palladium Nanoparticles by Using X-ray Reflectivity, EXAFS, and Electron Microscopy

We compared the characteristics of dodecanethiolate palladium nanoparticles synthesized by two different techniques, a one-phase method and a two-phase method. From transmission electron microscopy (TEM), we determined that the particle sizes were 46 +/- 10 angstroms and 20 +/- 5 angstroms for the one- and two-phase particles, respectively. Electron diffraction confirmed that their structure was face-centered cubic (fcc). The lattice constant a0 was 3.98 +/- 0.01 angstroms and 3.90 +/- 0.01 angstroms for the one- and two-phase particles, respectively. High-resolution TEM (HRTEM) showed that the one-phase particles had an ordered core surrounded by a disordered shell structure, while the two-phase particles appeared to be crystalline throughout. The particles were also analyzed with extended X-ray absorption fine structure (EXAFS). A cuboctahedral fcc model was used to fit the data, which implied particle sizes of less than 10 angstroms for both the one- and two-phase particles. The discrepancy between the two techniques was attributed to the presence of a disordered phase, which we presumed was composed of Pd-S compounds. Compared with the bulk palladium, lattice expansion was observed in both one- and two-phase particles by electron diffraction, HRTEM, and EXAFS. At the air/water interface, a uniform film that produced surface pressure/area isotherms could only be obtained from the two-phase particles. The one-phase particles did not wet the water surface. X-ray reflectivity data indicated that the Langmuir monolayer of the two-phase particles was only 13 angstroms thick. TEM revealed the diameter of the particles in this layer to be 23 angstroms; hence the particles assumed an oblate structure after spreading. EXAFS examination of a stack of 750 Langmuir monolayers indicated far fewer Pd-S compounds, which may have dissolved in the water. The data were consistent with a model of a monolayer of truncated cuboctahedron Pd particles that were 7 angstroms thick and 19 angstroms in diameter.

Structure of the Dodecahedral Penton Particle from Human Adenovirus Type 3

The sub-viral dodecahedral particle of human adenovirus type 3, composed of the viral penton base and fiber proteins, shares an important characteristic of the entire virus: it can attach to cells and penetrate them. Structure determination of the fiberless dodecahedron by cryo-electron microscopy to 9 Angstroms resolution reveals tightly bound pentamer subunits, with only minimal interfaces between penton bases stabilizing the fragile dodecahedron. The internal cavity of the dodecahedron is approximately 80 Angstroms in diameter, and the interior surface is accessible to solvent through perforations of approximately 20 Angstroms diameter between the pentamer towers. We observe weak density beneath pentamers that we attribute to a penton base peptide including residues 38-48. The intact amino-terminal domain appears to interfere with pentamer-pentamer interactions and its absence by mutation or proteolysis is essential for dodecamer assembly. Differences between the 9 Angstroms dodecahedron structure and the adenovirus serotype 2 (Ad2) crystallographic model correlate closely with differences in sequence. The 3D structure of the dodecahedron including fibers at 16 Angstroms resolution reveals extra density on the top of the penton base that can be attributed to the fiber N terminus. The fiber itself exhibits striations that correlate with features of the atomic structure of the partial Ad2 fiber and that represent a repeat motif present in the amino acid sequence. These new observations offer important insights into particle assembly and stability, as well as the practicality of using the dodecahedron in targeted drug delivery. The structural work provides a sound basis for manipulating the properties of this particle and thereby enhancing its value for such therapeutic use.

Molecular Structure of fd (f1, M13) Filamentous Bacteriophage Refined with Respect to X-ray Fibre Diffraction and Solid-state NMR Data Supports Specific Models of Phage Assembly at the Bacterial Membrane

Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 angstroms in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific transport of nucleoprotein assemblages across membranes. The Ff group (fd, f1 and M13) has been especially widely studied. Models of virion assembly have been proposed based on a molecular model of the fd virion derived by X-ray fibre diffraction. A somewhat different model of the fd virion using solid-state NMR data has been proposed, not consistent with these models of assembly nor with the X-ray diffraction data. Here we show that reinterpreted NMR data are also consistent with the model derived from X-ray fibre diffraction studies, and discuss models of virion assembly.

Gas Adsorption Sites in a Large-Pore Metal-Organic Framework

The primary adsorption sites for Ar and N2 within metal-organic framework-5, a cubic structure composed of Zn4O(CO2)6 units and phenylene links defining large pores 12 and 15 angstroms in diameter, have been identified by single-crystal x-ray diffraction. Refinement of data collected between 293 and 30 kelvin revealed a total of eight symmetry-independent adsorption sites. Five of these are sites on the zinc oxide unit and the organic link; the remaining three sites form a second layer in the pores. The structural integrity and high symmetry of the framework are retained throughout, with negligible changes resulting from gas adsorption.

Visualization and analysis of apolipoprotein A-I interaction with binary phospholipid bilayers

Apolipoprotein A-I (apoA-I) interaction with specific cell lipid domains was suggested to trigger cholesterol and phospholipid efflux. We analyzed here apoA-I interaction with dimyristoylphosphatidylcholine/distearoylphosphatidylcholine (DMPC/DSPC) bilayers at a temperature showing phase coexistence. Solid and liquid-crystalline domains were visualized by two-photon fluorescence microscopy on giant unilamellar vesicles (GUVs) labeled with 6-dodecanoyl-2-dimethyl-amino-naphthalene (Laurdan). A decrease of vesicle size was detected as long as they were incubated with lipid-free apoA-I, together with a shape deformation and a relative enrichment in DSPC. Selective lipid removal mediated by apoA-I from different domains was followed in real time by changes in the Laurdan generalized polarization. The data show a selective interaction of apoA-I with liquid-crystalline domains, from which it removes lipids, at a molar ratio similar to the domain compositions. Next, apoA-I was incubated with DMPC/DSPC small unilamellar vesicles, and products were isolated and quantified. Protein solubilized both lipids but formed complexes relatively enriched in the liquid component. We also show changes in the GUV morphology when cooling down. Our results suggest that the most efficient reaction between apoA-I and DMPC/DSPC occurs in particular bilayer conditions, probably when small fluid domains are nucleated within a continuous gel phase and interfacial packing defects are maximal.

The Birnavirus Crystal Structure Reveals Structural Relationships among Icosahedral Viruses

Double-stranded RNA virions are transcriptionally competent icosahedral particles that must translocate across a lipid bilayer to function within the cytoplasm of the target cell. Birnaviruses are unique among dsRNA viruses as they have a single T = 13 icosahedral shell, lacking the characteristic inner capsid observed in the others. We determined the crystal structures of the T = 1 subviral particle (260 angstroms in diameter) and of the T = 13 intact virus particle (700 angstroms in diameter) of an avian birnavirus to 3 angstroms and 7 angstroms resolution, respectively. Our results show that VP2, the only component of the virus icosahedral capsid, is homologous both to the capsid protein of positive-strand RNA viruses, like the T = 3 nodaviruses, and to the T = 13 capsid protein of members of the Reoviridae family of dsRNA viruses. Together, these results provide important insights into the multiple functions of the birnavirus capsid and reveal unexpected structural relationships among icosahedral viruses.

Study of the low-temperature reaction between CO and O2 over Pd and Pt surfaces

Field electron microscopy (FEM), high-resolution electron energy loss spectroscopy (HREELS), molecular beams (MB) and temperature-programmed reaction (TPR) have been applied to the study of the kinetics of CO oxidation at low temperature, and to determine the roles of subsurface atomic oxygen (Osub) and surface reconstruction in self-oscillatory phenomena, on Pd(111), Pd(110) and Pt(100) single crystals and on Pd and Pt tip surfaces. It was found that high local concentrations of adsorbed CO during the transition from a Pt(100)-hex reconstructed surface to the unreconstructed 1×1 phase apparently prevents oxygen atoms from occupying hollow sites on the surface, and leads to the appearance of a weakly bound active adsorbed atomic oxygen (Oads) state in an on-top or bridge position. It was also inferred that subsurface oxygen Osub on the Pd(110) surface may play an important role in the formation of new active sites for the weakly bound Oads atoms. Experiments with 18O isotope labeling clearly show that the weakly bound atomic oxygen is the active form of oxygen that reacts with CO to form CO2 at T ∼140–160 K. Sharp tips of Pd and Pt, several hundreds angstroms in diameter, were used to perform in situ investigations of dynamic surface processes. The principal conclusion from those studies was that non–linear reaction kinetics is not restricted to macroscopic planes since: (i) planes as small as ∼200 A in diameter show the same non-linear kinetics as larger flat surfaces; (ii) regular waves appear under conditions leading to reaction rate oscillations; (iii) the propagation of reaction–diffusion waves involves the participation of different crystal nanoplanes via an effective coupling between adjacent planes.

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes. The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix-hairpin-helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30-35 angstroms diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding.

Fullerene Coalescence in Nanopeapods: A Path to Novel Tubular Carbon

A fascinating structural transformation occurring inside single-walled carbon nanotubes (SWNTs) is the fullerene coalescence, which is responsible for forming stable zeppelinlike carbon molecules. We report in situ transmission electron microscope (TEM) observations revealing sequences of fullerene coalescence induced by electron irradiation on pristine nanotube peapods, together with extensive theoretical investigations of the microscopic mechanism underlying this process. TEM images indicate that the merging of fullerenes results in stable but corrugated tubules (5 to 7 Angstrom in diameter) confined within SWNTs. These observations have been confirmed using a combination of theoretical approaches based on molecular dynamics, empirical potentials, tight-binding methods, Monte Carlo techniques, and first principles calculations. We have fully elucidated the coalescence mechanism of fullerenes inside SWNTs under electron irradiation and thermal annealing. The process occurs via the polymerization Of C-60 molecules followed by surface reconstruction, which can be triggered either by the formation of vacancies (created under electron irradiation) or by surface-energy minimization activated by thermal annealing. These novel tubular forms of carbon contain hexagons, pentagons, heptagons, and octagons. The stability, electronic properties, and electron conductance of the novel tubules are strongly affected by the final geometry of the coalesced fullerene complex. The possibility of forming highly conducting and semiconducting tubular structures suggests new avenues in designing carbon nanowires with specific electronic characteristics.

Spin dynamics in semiconductor nanocrystals

Time-resolved Faraday rotation is used to study both transverse and longitudinal spin relaxation in chemically-synthesized CdSe nanocrystals (NCs) 22-80 Angstroms in diameter. The precession of optically-injected spins in a transverse magnetic field occurs at distinct frequencies whose assignment to electron and exciton spins is developed through systematic studies of the size-dependence and theoretical calculations. It is shown that the transverse spin lifetime is limited by inhomogeneous dephasing to a degree that cannot be accounted for by the NC size distribution alone. Longitudinal spin relaxation in these NCs occurs on several distinct timescales ranging from 100 ps-10 microseconds and exhibits markedly different dependencies on temperature and field in comparison to transverse spin relaxation.

Structure and Bonding of Gold Metal Clusters, Colloids, and Nanowires Studied by EXAFS, XANES, and WAXS

The structure and bonding of a series of gold clusters and gold nanomaterials stabilized by ligands or confined within nanoporous alumina have been investigated using EXAFS, XANES, and WAXS. Two gold clusters stabilized by two different ligands, Au-55(PPh3)(12)Cl-6 and AU(55)(T-8-OSS - SH)(12)Cl-6 were confirmed to be of face-centered cubic structure type with metal-metal distances of 2.785 and 2.794 Angstrom, respectively, shorter than in bulk gold. Colloidal gold of 180 Angstrom diameter stabilized by sulfonated phosphine ligands had structural and electronic properties very similar to those of bulk gold but smaller Debye-Waller factors. The cluster Au-55(PPh3)(12)Cl-6 adsorbed into nanoporous alumina membrane was found to retain its integrity inside the membrane but with slightly longer Au-Au bonds due to some aggregation. The same cluster thermally transformed into colloidal gold within the alumina membrane was found to be almost identical structurally and electronically to the bulk. Gold nanowires electrochemically grown within the nanoporous alumina were found to be composed on average of 120 Angstrom diameter crystallites. These have the same structure as the bulk, but with smaller Debye-Waller factors, indicating either a better crystallinity or that the gold atoms are more tightly held than in the bulk. The difference of area method L-3 - kL(2) was used to quantify the d orbital occupancy. The two ligand-stabilized Au-55 clusters both had a smaller value (2.7) than the bulk material (4.1). The nanomaterials inside the membrane also showed smaller L-3 - kL(2) values. The geometrical and electronic structures of these gold materials how a very clear pattern of buildup as the number of gold atoms increases from Au-55 clusters through Au colloids and nanowires to the bulk metal.