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At least 1,009 records · Page 56Linked to original sources
PubMed2006

Nature of point defects on SiO2/Mo(112) thin films and their interaction with Au atoms.

We have studied by means of periodic DFT calculations the structure and properties of point defects at the surface of ultrathin silica films epitaxially grown on Mo(112) and their interaction with adsorbed Au atoms. For comparison, the same defects have been generated on an unsupported silica film with the same structure. Four defects have been considered: nonbridging oxygen (NBO, [triple bond]Si-O(*)), Si dangling bond (E' center, [triple bond]Si(*)), oxygen vacancy (V(O), [triple bond]Si-Si[triple bond]), and peroxo group ([triple bond]Si-O-O-Si[triple bond]), but only the NBO and the V(O) centers are likely to form on the SiO(2)/Mo(112) films under normal experimental conditions. The [triple bond]Si-O(*) center captures one electron from Mo forming a silanolate group, [triple bond]Si-O(-), sign of a direct interaction with the metal substrate. Apart from the peroxo group, which is unreactive, the other defects bind strongly the Au atom forming stable surface complexes, but their behavior may differ from that of the same centers generated on an unsupported silica film. This is true in particular for the two most likely defects considered, the nonbridging oxygen, [triple bond]Si-O(*), and the oxygen vacancy, [triple bond]Si-Si[triple bond].

Journal Article↗
PubMed2004

Monte Carlo molecular simulation of the hydration of K-montmorillonite at 353 K and 625 bar.

Monte Carlo molecular simulations of the hydration of K-saturated Wyoming-type montmorillonite at constant stress in the NPzzT ensemble and at constant chemical potential in the grand canonical muVT ensemble, under basin-like conditions of 353 K and 625 bar, show a strong tendency of the K+ ions to adhere to the siloxane surface, forming predominant inner-sphere complexes with tetrahedral oxygen atoms and adsorbed water molecules. Simulations in the grand canonical ensemble predict that none of the K-montmorillonite hydrates, the one-, two-, and three-layer hydrates, are stable in this environment of high depth, temperature, and pressure. The most nearly stable configuration corresponds to the one-layer hydrate, characterized by a d001 spacing of 12.75 A, the adsorbed water being 60 molecules/layer or 180.83 mg of H2O/g of clay, an internal energy of -22.73 kcal/mol, an interlayer density of 0.365 g/mL, and a pressure tensor, Pzz, of 1999.9 bar. The interlayer structure consists of two close layers of water molecules 0.50 A from the midplane, with broad shoulders on the sides, the protons oriented toward the midplane and the siloxane surfaces, and the K+ ions close to the clay surfaces and on the interlayer midplane.

Adsorption↗
PubMed2002

Synthesis and application of chiral phosphino-imidazoline ligands: Ir-catalyzed enantioselective hydrogenation.

[reaction: see text] A series of chiral phosphino-imidazolines (PHIM ligands) 1a-j with different substituents at the stereogenic center, the nitrogen atom of the imidazoline ring, and at the phosphorus atom were synthesized. Iridium complexes derived from these ligands have been evaluated as catalysts for the enantioselective hydrogenation of unfunctionalized olefins. In several cases, higher enantiomeric excesses were observed than with analogous phosphino-oxazoline ligands.

Journal Article↗
PubMed2004

Variable LH2 stoichiometry and core clustering in native membranes of Rhodospirillum photometricum.

The individual components of the photosynthetic unit (PSU), the light-harvesting complexes (LH2 and LH1) and the reaction center (RC), are structurally and functionally known in great detail. An important current challenge is the study of their assembly within native membranes. Here, we present AFM topographs at 12 A resolution of native membranes containing all constituents of the PSU from Rhodospirillum photometricum. Besides the major technical advance represented by the acquisition of such highly resolved data of a complex membrane, the images give new insights into the organization of this energy generating apparatus in Rsp. photometricum: (i) there is a variable stoichiometry of LH2, (ii) the RC is completely encircled by a closed LH1 assembly, (iii) the LH1 assembly around the RC forms an ellipse, (iv) the PSU proteins cluster together segregating out of protein free lipid bilayers, (v) core complexes cluster although enough LH2 are present to prevent core-core contacts, and (vi) there is no cytochrome bc1 complex visible in close proximity to the RCs. The functional significance of all these findings is discussed.

Bacterial Proteins↗
PubMed1986

Inhibition of prolyl 4-hydroxylase by hydroxyanthraquinones.

Prolyl 4-hydroxylase (EC 1.14.11.2) is an essential enzyme in the post-translational modification of collagen. Inhibitors of this enzyme are of potential interest for the treatment of diseases involving excessive deposition of collagen. We have found that anthraquinones with at least two hydroxy groups ortho to each other are potent inhibitors of this enzyme. Kinetic studies revealed that 2,7,8-trihydroxyanthraquinone (THA) competitively inhibited the co-substrate, 2-oxoglutarate, but was non-competitive with regard to ascorbate and was tentatively considered to be uncompetitive with regard to protocollagen. The inhibition by THA was greatly enhanced in the absence of added Fe2+ and was partially reversed by the addition of concentrations of Fe2+ in excess of the optimum for the enzymic reaction. Binding studies indicated that THA is an effective chelating agent for Fe2+. Several non-quinoidal compounds bearing the catechol moiety also inhibited the enzyme. The results suggest that THA inhibited prolyl 4-hydroxylase by binding to the enzyme at the site for 2-oxoglutarate possibly involving the Fe2+ atom, rather than by complexing with Fe2+ in free solution. The inhibition of prolyl 4-hydroxylase by THA exhibited strong positive co-operativity and may involve three distinct but non-independent binding sites.

Animals↗
PubMed2004

Electronic photodissociation spectroscopy of Aun- x Xe (n = 7-11) versus time-dependent density functional theory prediction.

Electronic (one-photon) photodepletion spectra were recorded for gold cluster anions complexed with one xenon atom over the photon energy range 2.1-3.4 eV. Clusters were generated by pulsed laser vaporization and probed under collisionless molecular beam conditions. The spectra obtained are highly structured with the narrowest features--assigned to individual electronic transitions--having bandwidths of less than 40 meV. Time-dependent density functional theory predictions of optically allowed transitions for the most stable--planar--isomers of the corresponding bare metal cluster anions are generally consistent with the experimental observation.

Journal Article↗
PubMed2002

Simulating materials failure by using up to one billion atoms and the world's fastest computer: Work-hardening.

We describe the second of two large-scale atomic simulation projects on materials failure performed on the 12-teraflop ASCI (Accelerated Strategic Computing Initiative) White computer at the Lawrence Livermore National Laboratory. This investigation simulates ductile failure by using more than one billion atoms where the true complexity of the creation and interaction of hundreds of dislocations are revealed.

Journal Article↗
PubMed2003

Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum.

The cap at the growing end of the bacterial flagellum is essential for its growth, remaining stably attached while permitting the insertion of flagellin transported from the cytoplasm through the narrow central channel. We analyzed the structure of the isolated cap in its frozen hydrated state by electron cryomicroscopy. The 3D density map now shows detailed features of domains and their connections, giving reliable volumes and masses, making assignment of the domains to the amino acid sequence possible. A model of the cap-filament complex built with an atomic model of the filament allows a quantitative analysis of the cap domain movements on cap binding and rotation that promotes the efficient self assembly of flagellin during the filament growth process.

Bacterial Proteins↗
PubMed1992

Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study.

The coupling between electron transfer and protein structure and dynamics in the photosynthetic reaction center of Rhodopseudomonas viridis is investigated. For this purpose molecular dynamics simulations of the essential portions (a segment of 5797 atoms) of this protein complex have been carried out. Electron transfer in the primary event is modeled by altering the charge distributions of the chromophores according to quantum chemical calculations. The simulations show (i) that fluctuations of the protein matrix, which are coupled electrostatically to electron transfer, play an important role in controlling the electron transfer rates and (ii) that the protein matrix stabilizes the separated electron pair state through rapid (200 fs) and temperature-independent dielectric relaxation. The photosynthetic reaction center resembles a polar liquid in that the internal motions of the whole protein complex, rather than only those of specific side groups, contribute to i and ii. The solvent reorganization energy is about 4.5 kcal/mol. The simulations indicate that rather small structural rearrangements and changes in motional amplitudes accompany the primary electron transfer.

Bacterial Chromatophores↗
PubMed2001

Mutations in both sides of the photosystem I reaction center identify the phylloquinone observed by electron paramagnetic resonance spectroscopy.

The core of photosystem I (PS1) is composed of the two related integral membrane polypeptides, PsaA and PsaB, which bind two symmetrical branches of cofactors, each consisting of two chlorophylls and a phylloquinone, that potentially link the primary electron donor and the tertiary acceptor. In an effort to identify amino acid residues near the phylloquinone binding sites, all tryptophans and histidines that are conserved between PsaA and PsaB in the region of the 10th and 11th transmembrane alpha-helices were mutated in Chlamydomonas reinhardtii. The mutant PS1 reaction centers appear to assemble normally and possess photochemical activity. An electron paramagnetic resonance (EPR) signal attributed to the phylloquinone anion radical (A(1)(-)) can be observed either transiently or after illumination of reaction centers with pre-reduced iron-sulfur clusters. Mutation of PsaA-Trp(693) to Phe resulted in an inability to photo-accumulate A(1)(-), whereas mutation of the analogous tryptophan in PsaB (PsaB-Trp(673)) did not produce this effect. The PsaA-W693F mutation also produced spectral changes in the time-resolved EPR spectrum of the P(700)(+) A(1)(-) radical pair, whereas the analogous mutation in PsaB had no observable effect. These observations indicate that the A(1)(-) phylloquinone radical observed by EPR occupies the phylloquinone-binding site containing PsaA-Trp(693). However, mutation of either tryptophan accelerated charge recombination from the terminal Fe-S clusters.

Animals↗
PubMed2004

Atomic resolution structures and solution behavior of enzyme-substrate complexes of Enterobacter cloacae PB2 pentaerythritol tetranitrate reductase. Multiple conformational states and implications for the mechanism of nitroaromatic explosive degradation.

The structure of pentaerythritol tetranitrate (PETN) reductase in complex with the nitroaromatic substrate picric acid determined previously at 1.55 A resolution indicated additional electron density between the indole ring of residue Trp-102 and the nitro group at C-6 of picrate. The data suggested the presence of an unusual bond between substrate and the tryptophan side chain. Herein, we have extended the resolution of the PETN reductase-picric acid complex to 0.9 A. This high-resolution analysis indicates that the active site is partially occupied with picric acid and that the anomalous density seen in the original study is attributed to the population of multiple conformational states of Trp-102 and not a formal covalent bond between the indole ring of Trp-102 and picric acid. The significance of any interaction between Trp-102 and nitroaromatic substrates was probed further in solution and crystal complexes with wild-type and mutant (W102Y and W102F) enzymes. Unlike with wild-type enzyme, in the crystalline form picric acid was bound at full occupancy in the mutant enzymes, and there was no evidence for multiple conformations of active site residues. Solution studies indicate tighter binding of picric acid in the active sites of the W102Y and W102F enzymes. Mutation of Trp-102 does not impair significantly enzyme reduction by NADPH, but the kinetics of decay of the hydride-Meisenheimer complex are accelerated in the mutant enzymes. The data reveal that decay of the hydride-Meisenheimer complex is enzyme catalyzed and that the final distribution of reaction products for the mutant enzymes is substantially different from wild-type enzyme. Implications for the mechanism of high explosive degradation by PETN reductase are discussed.

2,4-Dinitrophenol↗
PubMed2004

Three-dimensional model of the pore form of anthrax protective antigen. Structure and biological implications.

Although pore formation by protective antigen (PA) is critical to cell intoxication by anthrax toxin (AT), the structure of the pore form of PA (the PA63 pore) has not been determined. Hence, in this study, the PA63 pore was modeled using the X-ray structures of monomeric PA and heptameric alpha-hemolysin (alpha-HL) as templates. The PA63 pore model consists of two weakly associated domains, namely the cap and stem domains. The ring-like cap domain has a length of 80 A and an outside diameter of 120 A, while the cylinder-like stem domain has a length of 100 A and outside diameter of approximately 28 A. This provides the PA63 pore model with a length of 180 A. Based on experimental results, the channel in the PA63 pore model was built to have a minimum diameter of ~12 A, depending on side chain conformations. Because of its large size and structural complexity, the all-atom model of the PA63 pore is the end-stage construction of four separate modeling projects described herein. The final model is consistent with published experimental results, including mutational analysis and channel conductance experiments. In addition, the model was energetically and hydropathically refined to optimize molecular packing within the protomers and at the protomer-protomer interfaces. By providing atomic detail to biochemical and biophysical data, the PA63 pore model may afford new insights into the binding mode of PA on the membrane surface, the prepore-pore transition, and the mechanism of cell entry by anthrax toxin.

Antigens, Bacterial↗
PubMed1992

The five-level model: a new approach to organizing body-composition research.

Body-composition research is a branch of human biology that has three interconnecting areas: body-composition levels and their organizational rules, measurement techniques, and biological factors that influence body composition. In the first area, which is inadequately formulated at present, five levels of increasing complexity are proposed: I, atomic; II, molecular; III, cellular; IV, tissue-system; and V, whole body. Although each level and its multiple compartments are distinct, biochemical and physiological connections exist such that the model is consistent and functions as a whole. The model also provides the opportunity to clearly define the concept of a body composition steady state in which quantitative associations exist over a specified time interval between compartments at the same or different levels. Finally, the five-level model provides a matrix for creating explicit body-composition equations, reveals gaps in the study of human body composition, and suggests important new research areas.

Adipose Tissue↗
PubMed1993

A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide.

An oligodeoxynucleotide that readily flips to the Z-DNA conformation in 10mM MgCl2 was produced by using Klenow enzyme to incorporate 5-bromodeoxycytosine and deoxyguanosine into a (dC-dG)22 template. During synthesis the oligomer can be labeled with 32P to high specific activity. The labeled oligodeoxynucleotide can be used in bandshift experiment to detect proteins that bind Z-DNA. This allows the binding specificity of such proteins to be determined with high reliability using unlabeled linear and supercoiled DNA competitors. In addition, because the radioactive oligodeoxynucleotide contains bromine atoms, DNA-protein complexes can be readily crosslinked using UV light. This allows an estimate to be made of the molecular weight of the proteins that bind to the radioactive probe. Both techniques are demonstrated using a goat polyclonal anti-Z-DNA antiserum.

Animals↗
PubMed1997

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.

Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here we describe a program called NUCPLOT which can automatically identify these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows all the interactions in a schematic manner. The program produces a PostScript output file representing hydrogen, van der Waals and covalent bonds between the protein and the DNA. The resulting diagram is both clear and simple and allows immediate identification of important interactions within the structure. It also facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which can be used for any protein-DNA complex and will also work for certain protein-RNA structures.

Computer Graphics↗
PubMed2004

Observation of dynamical instability for a Bose-Einstein condensate in a moving 1D optical lattice.

We have experimentally studied the unstable dynamics of a harmonically trapped Bose-Einstein condensate loaded into a 1D moving optical lattice. The lifetime of the condensate in such a potential exhibits a dramatic dependence on the quasimomentum state. This is unambiguously attributed to the onset of dynamical instability, after a comparison with the predictions of the Gross-Pitaevskii theory. Deeply in the unstable region we observe the rapid appearance of complex structures in the atomic density profile, as a consequence of the condensate phase uniformity breakdown.

Journal Article↗