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Sample records for carbon-sulfur bond cleavage

  1. Characterization of carbon-sulfur bond cleavage by axenic and mixed cultures of Rhodococcus rhodochrous IGTS8

    Energy Technology Data Exchange (ETDEWEB)

    Kayser, K.J.; Bielaga, B.A.; Jackowski, K.; Oduson, O.; Kilbane, J. II

    1992-12-31

    Growth assays reveal that Rhodococcus rhodochrous IGTS8 can utilize a wide range of organosulfur compounds as the sole source of sulfur. Compounds that are utilized include thiophenes, sulfides, disulfides, mercaptans, sulfoxides, and sulfones. None of the organosulfur compounds tested can serve as a carbon source. A convenient spectrophotometric assay (Gibbs assay) based on the chromogenic reaction of 2,6-dichloroquinone-4-chloroimide with aromatic hydroxyl groups was developed and used in conjunction with GC/MS analysis to examine the kinetics of carbon-sulfur bond cleavage by axenic and mixed cell cultures of Rhodococcus rhodochrous IGTS8. The desulfurization trait is expressed at uniform levels during the mid-exponential phase, reaches a maximum during idiophase, and then declines in stationary-phase cells. Desulfurization rates for dibenzothiophene (DBT) range from 8 to 15 {mu}M of DBT/10{sup 12} cells/hour. Mixtures of genetically marked Rhodococcus rhodochrous IGTS8 and an organisms incapable of cleaning carbon-sulfur bonds in relevant test compounds, Enterobacter cloacae, were prepared in ratios that varied over six orders of magnitude. Growth studies revealed that Enterobacter cloacae was able to gain access to sulfur liberated from organosulfur compounds by IGTS8; however, cell-to-cell contact was required. These data also indicate that the desulfurization activity of IGTS8 cells in mixed cultures may be as much as 200-fold higher than in axenic cultures.

  2. Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.

    Science.gov (United States)

    Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C; Nicolet, Yvain

    2016-05-01

    Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate. PMID:27102684

  3. Can laccases catalyze bond cleavage in lignin?

    DEFF Research Database (Denmark)

    Munk, Line; Sitarz, Anna Katarzyna; Kalyani, Dayanand;

    2015-01-01

    these enzymes may help degrading lignin, using oxygen as the oxidant. Laccases can catalyze polymerization of lignin, but the question is whether and how laccases can directly catalyze modification of lignin via catalytic bond cleavage. Via a thorough review of the available literature and detailed...

  4. Regioselectivity in the Reductive Bond Cleavage of Diarylalkylsulfonium Salts

    DEFF Research Database (Denmark)

    Kampmeier, Jack; Mansurul Hoque, AKM; D. Saeva, Franklin;

    2009-01-01

    This investigation was stimulated by reports that one-electron reductions of monoaryldialkylsulfonium salts never give aryl bond cleavage whereas reductions of diarylmonoalkylsulfonium salts preferentially give aryl bond cleavage. We studied the product ratios from the reductive cleavage of di-4......- tolylethylsulfonium and di-4-tolyl-2-phenylethylsulfonium salts by a variety of one-electron reducing agents ranging in potential from -0.77 to +2.5 eV (vs SCE) and including thermal reductants, indirect electrolyses mediated by a series of cyanoaromatics, and excited singlet states. We report that the cleavage...... products vary from regiospecific alkyl cleavage to predominant aryl cleavage as a function of the potential of the reducing agent. We conclude that differences between the reductive cleavages of mono- and diarylsulfonium salts are direct consequences of the structures of the sulfuranyl radical...

  5. Microbial cleavage of organic C-S bonds

    Science.gov (United States)

    Kilbane, II, John J.

    1994-01-01

    A microbial process for selective cleavage of organic C--S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials, Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C--S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

  6. Reductive cleavage of the peptide bond

    Science.gov (United States)

    Holian, J.; Garrison, W. M.

    1973-01-01

    In many biological research efforts, long chain organic molecules are studied by breaking large molecules into smaller components. Cleavage technique of recent interest is the use of solvated electrons. These are formed when aqueous solutions are bombarded with gamma radiation. Solvated electron is very reactive and can reduce most any species present, even to form free radicals.

  7. Biotic and abiotic carbon to sulfur bond cleavage. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Frost, J.W.

    1994-05-01

    The microbial desulfurization of organosulfur compounds occurs by unprecedented and largely unexplored biochemical processes. A study of such biotic desulfurizations can be expected to give rise to new and useful chemistry and enzymology. The potential value of understanding and harnessing these processes is seen in relation to the need for methods for the removal of organically bound sulfur from coal and the degradation of organic sulfur-containing pollutants. This research effort has been directed towards an examination of desulfurization ability in well characterized microorganisms, the isolation of bacteria with desulfurization ability from natural sources, the characterization and mechanistic evaluation of the observed biocatalytic processes, the development of biomimetic synthetic organic chemistry based on biotic desulfurization mechanisms and the design and preparation of improved coal model compounds for use in microbial selection processes. A systematic approach to studying biodesulfurizations was undertaken in which organosulfur compounds have been broken down into classes based on the oxidation state of the sulfur atom and the structure of the rest of the organic material. Microbes have been evaluated in terms of ability to degrade organosulfur compounds with sulfur in its sulfonic acid oxidation state. These compounds are likely intermediates in coal desulfurization and are present in the environment as persistent pollutants in the form of detergents. It is known that oxygen bonded to sulfur lowers the carbon-sulfur bond energy, providing a thermodynamic basis for starting with this class of compounds.

  8. Rhodium-catalyzed C-C bond cleavage reactions

    Czech Academy of Sciences Publication Activity Database

    Nečas, D.; Kotora, Martin

    2007-01-01

    Roč. 11, č. 17 (2007), s. 1566-1591. ISSN 1385-2728 Institutional research plan: CEZ:AV0Z40550506 Keywords : rhodium * catalysis * C-C bond cleavage Subject RIV: CC - Organic Chemistry Impact factor: 3.961, year: 2007

  9. Cleavage of an amide bond by a ribozyme

    Science.gov (United States)

    Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)

    1995-01-01

    A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

  10. Cleavage enhancement of specific chemical bonds in DNA-Cisplatin complexes induced by X-rays

    International Nuclear Information System (INIS)

    The chemical bond transformation of cisplatin-DNA complexes can be probed efficiently by XPS which provides a concomitant X-ray irradiation source as well. The presence to Pt could considerably increase formation of the SE induced by X-ray and that the further interaction of these LEE with DNA leads to the enhancement of bond cleavages.

  11. O2 Protonation Controls Threshold Behavior for N-Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides.

    Science.gov (United States)

    Wu, R R; Rodgers, M T

    2016-06-01

    IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H](+) and [Cyd+H](+), have established that both N3 and O2 protonated conformers coexist in the gas phase. Threshold collision-induced dissociation (CID) of [dCyd+H](+) and [Cyd+H](+) is investigated here using guided ion beam tandem mass spectrometry techniques to elucidate the mechanisms and energetics for N-glycosidic bond cleavage. N-Glycosidic bond cleavage is observed as the major dissociation pathways resulting in competitive elimination of either protonated or neutral cytosine for both protonated cytosine nucleosides. Electronic structure calculations are performed to map the potential energy surfaces (PESs) for both N-glycosidic bond cleavage pathways observed. The molecular parameters derived from theoretical calculations are employed for thermochemical analysis of the energy-dependent CID data to determine the minimum energies required to cleave the N-glycosidic bond along each pathway. B3LYP and MP2(full) computed activation energies for N-glycosidic bond cleavage associated with elimination of protonated and neutral cytosine, respectively, are compared to measured values to evaluate the efficacy of these theoretical methods in describing the dissociation mechanisms and PESs for N-glycosidic bond cleavage. The 2'-hydroxyl of [Cyd+H](+) is found to enhance the stability of the N-glycosidic bond vs that of [dCyd+H](+). O2 protonation is found to control the threshold energies for N-glycosidic bond cleavage as loss of neutral cytosine from the O2 protonated conformers is found to require ∼25 kJ/mol less energy than the N3 protonated analogues, and the activation energies and reaction enthalpies computed using B3LYP exhibit excellent agreement with the measured thresholds for the O2 protonated conformers. PMID:27159774

  12. Reductive cleavage of dichalcogenide bonds. Communication 3. Selectivity of electron exchange in diaryldichalcogenide-bispyridinium systems

    International Nuclear Information System (INIS)

    The kinetics of reductive cleavage of the dichalcogenide bond in dimeric Schiff's bases ArEEAr (E = S, Te) induced by indirect electron transfer by the in situ generated bridged bispyridinium radical cations and biradicals was studied by cyclic voltammetry. It is found that the dependence between the apparent rate constants of intermolecular electron transfer and the electron-withdrawing properties of diaryldichalcogenides is violated. The mechanisms of homogeneous (chemical) and heterogeneous (electrochemical) reductive cleavage of diaryldichalcogenides are discussed

  13. Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II

    2005-10-01

    The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

  14. Structural dynamics effects on the ultrafast chemical bond cleavage of a photodissociation reaction

    OpenAIRE

    Corrales, Maria E.; Loriot, Vincent; Balerdi, Garikoitz; González-Vázquez, Jesús; de Nalda, Rebeca; Bañares, Luis; Zewail, Ahmed H.

    2014-01-01

    The correlation between chemical structure and dynamics has been explored in a series of molecules with increasing structural complexity in order to investigate its influence on bond cleavage reaction times in a photodissociation event. Femtosecond time-resolved velocity map imaging spectroscopy reveals specificity of the ultrafast carbon–iodine (C–I) bond breakage for a series of linear (unbranched) and branched alkyl iodides, due to the interplay between the pure reaction coordinate and the...

  15. Synthesis of sulfonamides via copper-catalyzed oxidative C-N bond cleavage of tertiary amines.

    Science.gov (United States)

    Ji, Jing; Liu, Zhengyi; Liu, Ping; Sun, Peipei

    2016-08-01

    A copper-catalyzed coupling reaction of sulfonyl chlorides with tertiary amines via the oxidative C-N bond cleavage of tertiary amines was developed. Sulfonamides were synthesized using this strategy in moderate to good yields. The reaction was applicable to various tertiary amines, as well as sulfonyl chlorides. PMID:27356858

  16. Rhodium-catalyzed C-C Bond Cleavage Reactions - An Update

    Czech Academy of Sciences Publication Activity Database

    Korotvička, A.; Nečas, D.; Kotora, Martin

    2012-01-01

    Roč. 16, č. 10 (2012), s. 1170-1214. ISSN 1385-2728 Grant ostatní: GA MŠk(CZ) LC06070 Institutional research plan: CEZ:AV0Z40550506 Keywords : rhodium * C-C bond cleavage * catalysis * synthesis Subject RIV: CC - Organic Chemistry Impact factor: 3.039, year: 2012

  17. Facile P-C/C-H Bond Cleavage Reactivity of Nickel Bis(diphosphine) Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shaoguang; Li, Haixia; Appel, Aaron M.; Hall, Michael B.; Bullock, R. Morris

    2016-07-04

    Unusual cleavage of P-C and C-H bonds of the P2N2 ligand in heteroleptic [Ni(P2N2)(diphosphine)]2+ complexes results in the formation of an iminium formyl nickelate featuring a C,P,P-tridentate coordination mode.

  18. Thermodynamic Strategies for C-O Bond Formation and Cleavage via Tandem Catalysis.

    Science.gov (United States)

    Lohr, Tracy L; Li, Zhi; Marks, Tobin J

    2016-05-17

    To reduce global reliance on fossil fuels, new renewable sources of energy that can be used with the current infrastructure are required. Biomass represents a major source of renewable carbon based fuel; however, the high oxygen content (∼40%) limits its use as a conventional fuel. To utilize biomass as an energy source, not only with current infrastructure, but for maximum energy return, the oxygen content must be reduced. One method to achieve this is to develop selective catalytic methods to cleave C-O bonds commonly found in biomass (aliphatic and aromatic ethers and esters) for the eventual removal of oxygen in the form of volatile H2O or carboxylic acids. Once selective methods of C-O cleavage are understood and perfected, application to processing real biomass feedstocks such as lignin can be undertaken. This Laboratory previously reported that recyclable "green" lanthanide triflates are excellent catalysts for C-O bond-forming hydroalkoxylation reactions. Based on the virtues of microscopic reversibility, the same lanthanide triflate catalyst should catalyze the reverse C-O cleavage process, retrohydroalkoxylation, to yield an alcohol and an alkene. However, ether C-O bond-forming (retrohydroalkoxylation) to form an alcohol and alkene is endothermic. Guided by quantum chemical analysis, our strategy is to couple endothermic, in tandem, ether C-O bond cleavage with exothermic alkene hydrogenation, thereby leveraging the combined catalytic cycles thermodynamically to form an overall energetically favorable C-O cleavage reaction. This Account reviews recent developments on thermodynamically leveraged tandem catalysis for ether and more recently, ester C-O bond cleavage undertaken at Northwestern University. First, the fundamentals of lanthanide-catalyzed hydroelementation are reviewed, with particular focus on ether C-O bond formation (hydroalkoxylation). Next, the reverse C-O cleavage/retrohydroalkoxylation processes enabled by tandem catalysis are

  19. Carbon-carbon bond cleavage and rearrangement of benzene by a trinuclear titanium hydride

    Science.gov (United States)

    Hu, Shaowei; Shima, Takanori; Hou, Zhaomin

    2014-08-01

    The cleavage of carbon-carbon (C-C) bonds by transition metals is of great interest, especially as this transformation can be used to produce fuels and other industrially important chemicals from natural resources such as petroleum and biomass. Carbon-carbon bonds are quite stable and are consequently unreactive under many reaction conditions. In the industrial naphtha hydrocracking process, the aromatic carbon skeleton of benzene can be transformed to methylcyclopentane and acyclic saturated hydrocarbons through C-C bond cleavage and rearrangement on the surfaces of solid catalysts. However, these chemical transformations usually require high temperatures and are fairly non-selective. Microorganisms can degrade aromatic compounds under ambient conditions, but the mechanistic details are not known and are difficult to mimic. Several transition metal complexes have been reported to cleave C-C bonds in a selective fashion in special circumstances, such as relief of ring strain, formation of an aromatic system, chelation-assisted cyclometallation and β-carbon elimination. However, the cleavage of benzene by a transition metal complex has not been reported. Here we report the C-C bond cleavage and rearrangement of benzene by a trinuclear titanium polyhydride complex. The benzene ring is transformed sequentially to a methylcyclopentenyl and a 2-methylpentenyl species through the cleavage of the aromatic carbon skeleton at the multi-titanium sites. Our results suggest that multinuclear titanium hydrides could serve as a unique platform for the activation of aromatic molecules, and may facilitate the design of new catalysts for the transformation of inactive aromatics.

  20. Reaction Pathways and Energetics of Etheric C–O Bond Cleavage Catalyzed by Lanthanide Triflates

    Energy Technology Data Exchange (ETDEWEB)

    Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.

    2013-09-06

    Efficient and selective cleavage of etheric C-O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C-O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C-O cleavage occurs via a C-H → O-H proton transfer in concert with weakening of the C-O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C-O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.

  1. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

    Science.gov (United States)

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

  2. Carbon–carbon bond cleavage for Cu-mediated aromatic trifluoromethylations and pentafluoroethylations

    Directory of Open Access Journals (Sweden)

    Tsuyuka Sugiishi

    2015-12-01

    Full Text Available This short review highlights the copper-mediated fluoroalkylation using perfluoroalkylated carboxylic acid derivatives. Carbon–carbon bond cleavage of perfluoroalkylated carboxylic acid derivatives takes place in fluoroalkylation reactions at high temperature (150–200 °C or under basic conditions to generate fluoroalkyl anion sources for the formation of fluoroalkylcopper species. The fluoroalkylation reactions, which proceed through decarboxylation or tetrahedral intermediates, are useful protocols for the synthesis of fluoroalkylated aromatics.

  3. Carbon–carbon bond cleavage for Cu-mediated aromatic trifluoromethylations and pentafluoroethylations

    Science.gov (United States)

    Sugiishi, Tsuyuka; Aikawa, Kohsuke

    2015-01-01

    Summary This short review highlights the copper-mediated fluoroalkylation using perfluoroalkylated carboxylic acid derivatives. Carbon–carbon bond cleavage of perfluoroalkylated carboxylic acid derivatives takes place in fluoroalkylation reactions at high temperature (150–200 °C) or under basic conditions to generate fluoroalkyl anion sources for the formation of fluoroalkylcopper species. The fluoroalkylation reactions, which proceed through decarboxylation or tetrahedral intermediates, are useful protocols for the synthesis of fluoroalkylated aromatics. PMID:26734112

  4. D-β-aspartyl residue exhibiting uncommon high resistance to spontaneous peptide bond cleavage

    Science.gov (United States)

    Aki, Kenzo; Okamura, Emiko

    2016-02-01

    Although L-amino acids were selected as main constituents of peptides and proteins during chemical evolution, D-aspartyl (Asp) residue is found in a variety of living tissues. In particular, D-β-Asp is thought to be stable than any other Asp isomers, and this could be a reason for gradual accumulation in abnormal proteins and peptides to modify their structures and functions. It is predicted that D-β-Asp shows high resistance to biomolecular reactions. For instance, less reactivity of D-β-Asp is expected to bond cleavage, although such information has not been provided yet. In this work, the spontaneous peptide bond cleavage was compared between Asp isomers, by applying real-time solution-state NMR to eye lens αΑ-crystallin 51-60 fragment, S51LFRTVLD58SG60 and αΒ-crystallin 61-67 analog, F61D62TGLSG67 consisting of L-α- and D-β-Asp 58 and 62, respectively. Kinetic analysis showed how tough the uncommon D-β-Asp residue was against the peptide bond cleavage as compared to natural L-α-Asp. Differences in pKa and conformation between L-α- and D-β-Asp side chains were plausible factors to determine reactivity of Asp isomers. The present study, for the first time, provides a rationale to explain less reactivity of D-β-Asp to allow abnormal accumulation.

  5. Competition between Covalent and Noncovalent Bond Cleavages in Dissociation of Phosphopeptide-Amine Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Laskin, Julia; Yang, Zhibo; Woods, Amina S.

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A3pXA3-NH2 (X=S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. We demonstrate that covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel

  6. N-H bond cleavage of ammonia on graphene-like B36 borophene: DFT studies.

    Science.gov (United States)

    Rostami, Zahra; Soleymanabadi, Hamed

    2016-04-01

    Ammonia N-H bond cleavage at metal-free substrates has attracted great attention because of its industrial importance. Here, we investigate the dissociative adsorption of ammonia onto the surface of a B36 borophene sheet by means of density functional theory calculations. We show that the N-H bond may be broken at the edges of B36 even at room temperature, regarding the small energy barrier of 14.1-19.3 kcal mol(-1) at different levels of theory, and more negative Gibbs free energy change. Unlike basis set size, the kind of exchange correlation functional significantly affects the electronic properties of the studied systems. Also, by increasing the percentage of Hartree Fock (HF) exchange of density functionals, the activation and adsorption energies are lowered. A linear relationship between the highest occupied molecular orbital or lowest unoccupied molecular orbital of B36 borophene and the %HF exchange of functionals is predicted. Our work reveals that pure whole boron nanosheets may be promising metal-free materials in N-H bond cleavage, which would raise the potential application of these sheets. PMID:26969676

  7. Bond cleavages of adenosine 5'-triphosphate induced by monochromatic soft X-rays

    International Nuclear Information System (INIS)

    To investigate which type of bond is likely to be cleaved by soft X-ray exposure to an adenosine 5'-triphosphate (ATP), we observed spectral changes in X-ray absorption near edge structure (XANES) around nitrogen and oxygen K-edge of an ATP film by soft X-ray irradiation. Experiments were performed at a synchrotron soft X-ray beamline at SPring-8, Japan. The XANES spectra around the nitrogen and oxygen .K-edge slightly varied by exposure to 560 eV soft X-rays. These changes are originated from the cleavage of C-N bonds between a sugar and a nucleobase site and of C-O, P-O or O-H bond of sugar and phosphate site. From the comparison between the change in XANES intensity of σ* peak at nitrogen and that at oxygen K-edges, it is inferred that the C-O, P-O or O-H bond of sugar and phosphate is much efficiently cleaved than the C-N of N-glycoside bond by the exposure of 560 eV soft X-ray to ATP film.

  8. METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II

    2004-10-01

    The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will be to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the

  9. Molecular features in complex environment: Cooperative team players during excited state bond cleavage.

    Science.gov (United States)

    Thallmair, Sebastian; Roos, Matthias K; de Vivie-Riedle, Regina

    2016-07-01

    Photoinduced bond cleavage is often employed for the generation of highly reactive carbocations in solution and to study their reactivity. Diphenylmethyl derivatives are prominent precursors in polar and moderately polar solvents like acetonitrile or dichloromethane. Depending on the leaving group, the photoinduced bond cleavage occurs on a femtosecond to picosecond time scale and typically leads to two distinguishable products, the desired diphenylmethyl cations (Ph2CH(+)) and as competing by-product the diphenylmethyl radicals ([Formula: see text]). Conical intersections are the chief suspects for such ultrafast branching processes. We show for two typical examples, the neutral diphenylmethylchloride (Ph2CH-Cl) and the charged diphenylmethyltriphenylphosphonium ions ([Formula: see text]) that the role of the conical intersections depends not only on the molecular features but also on the interplay with the environment. It turns out to differ significantly for both precursors. Our analysis is based on quantum chemical and quantum dynamical calculations. For comparison, we use ultrafast transient absorption measurements. In case of Ph2CH-Cl, we can directly connect the observed signals to two early three-state and two-state conical intersections, both close to the Franck-Condon region. In case of the [Formula: see text], dynamic solvent effects are needed to activate a two-state conical intersection at larger distances along the reaction coordinate. PMID:26958588

  10. Cleavage of thymine N3-H bonds by low-energy electrons attached to base π* orbitals

    International Nuclear Information System (INIS)

    In this work, we extend our earlier studies on single strand break (SSB) formation in DNA to consider the possibility of cleaving a thymine N3-H bond to generate a nitrogen-centered anion and a hydrogen radical which might proceed to induce further bond cleavages. In earlier studies, we considered SSBs induced by low-energy electrons that attach to DNA bases' π* orbitals or to phosphate P=O π* orbitals to cleave sugar-phosphate C-O bonds or base-sugar N1-C bonds. We also studied the effects of base π-stacking on the rates of such bond cleavages. To date, our results suggest that sugar-phosphate C-O bonds have the lowest barriers to cleavage, that attachment of electrons with energies below 2 eV most likely occurs at the base π* orbitals, that electrons with energy above 2 eV can also attach to phosphate P=O π* orbitals, and that base π stacking has a modest but slowing effect on the rates of SSB formation. However, we had not yet examined the possibility that base N3-H bonds could rupture subsequent to base π* orbital capture. In the present work, the latter possibility is considered and it is found that the barrier to cleavage of the N3-H bond in thymine is considerably higher than for cleaving sugar-phosphate C-O bonds, so our prediction that SSB formation is dominated by C-O bond cleavage remains intact

  11. METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane III

    2003-12-01

    The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project will focus on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate amidase. The objective of the final phase of the project will be to develop derivative CN bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. The project is on schedule and no major difficulties have been encountered. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments have resulted in the isolation of promising cultures that may be capable of cleaving C-N bonds in aromatic amides, several amidase genes have been cloned and are currently undergoing directed evolution to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. Future research will address expression of these genes in Rhodococcus erythropolis. Enrichment culture experiments and directed evolution experiments continue to be a main focus of research activity and further work is required to obtain an appropriate amidase that will selectively cleave C-N bonds in aromatic substrates. Once an appropriate amidase gene is obtained it must be combined with genes encoding an enzyme capable of converting carbazole to 2'aminobiphenyl-2,3-diol: specifically carA genes. The carA genes from two sources have been cloned and are ready for construction of C-N bond cleavage

  12. The solvent effect on the electrocatalytic cleavage of carbon-halogen bonds on Ag and Au

    International Nuclear Information System (INIS)

    In recent years it has been shown in detail how the electrocatalytic cleavage of carbon-halogen bonds is modulated by (a) the stepwise or concerted nature of the dissociative electron-transfer mechanism, which is influenced by the nature of the electrode surface, the type of halogen atom and the molecular structure of RX as a whole, and (b) the double-layer structure (as a function of the nature and bulkiness of the supporting electrolyte ions). In order to both complete and support the interpretative scheme thus developed, this work is focused on the solvent role. When one compares aprotic with protic organic solvents after appropriate intersolvental normalization, interesting peculiarities emerge, especially concerning protic media. Solvent proticity deeply affects both the reaction mechanism (on both non-catalytic and catalytic electrodes) and the extent of the catalytic effects. These items are discussed on the basis of a complete investigation carried out with a carefully controlled experimental protocol on two chloride and bromide couples, one aromatic and one aliphatic, representative of stepwise and concerted mechanisms, respectively, in four aprotic and four protic solvents, on both non−catalytic GC and catalytic Ag and Au electrodes. The results are discussed in the framework of a recently developed interpretative scheme of the carbon-halogen cleavage mechanism

  13. ATP-Dependent C–F Bond Cleavage Allows the Complete Degradation of 4-Fluoroaromatics without Oxygen

    Science.gov (United States)

    Tiedt, Oliver; Mergelsberg, Mario; Boll, Kerstin; Müller, Michael; Adrian, Lorenz; Jehmlich, Nico; von Bergen, Martin

    2016-01-01

    ABSTRACT Complete biodegradation of the abundant and persistent fluoroaromatics requires enzymatic cleavage of an arylic C–F bond, probably the most stable single bond of a biodegradable organic molecule. While in aerobic microorganisms defluorination of fluoroaromatics is initiated by oxygenases, arylic C–F bond cleavage has never been observed in the absence of oxygen. Here, an oxygen-independent enzymatic aryl fluoride bond cleavage is described during the complete degradation of 4-fluorobenzoate or 4-fluorotoluene to CO2 and HF in the denitrifying Thauera aromatica: the ATP-dependent defluorination of 4-fluorobenzoyl-coenzyme A (4-F-BzCoA) to benzoyl-coenzyme A (BzCoA) and HF, catalyzed by class I BzCoA reductase (BCR). Adaptation to growth with the fluoroaromatics was accomplished by the downregulation of a promiscuous benzoate-CoA ligase and the concomitant upregulation of 4-F-BzCoA-defluorinating/dearomatizing BCR on the transcriptional level. We propose an unprecedented mechanism for reductive arylic C–F bond cleavage via a Birch reduction-like mechanism resulting in a formal nucleophilic aromatic substitution. In the proposed anionic 4-fluorodienoyl-CoA transition state, fluoride elimination to BzCoA is favored over protonation to a fluorinated cyclic dienoyl-CoA. PMID:27507824

  14. Efficient Synthesis of Functionalized Benzimidazoles and Perimidines: Ytterbium Chloride Catalyzed CmC Bond Cleavage%Efficient Synthesis of Functionalized Benzimidazoles and Perimidines: Ytterbium Chloride Catalyzed CmC Bond Cleavage

    Institute of Scientific and Technical Information of China (English)

    Cai, Lijian; Ji, Xiaofeng; Yao, Zhigang; Xu, Fan; Shen, Qi

    2011-01-01

    An efficient method is developed for the synthesis of functionalized benzimidazoles and perimidines by the condensation of aryl diamines with β-carbonyl compounds catalyzed by ytterbium chloride. The reactions give good yields under mild conditions. A mechanism involving a lanthanide activated C--C bond cleavage is proposed.

  15. Controllable synthesis of silver and silver sulfide nanocrystals via selective cleavage of chemical bonds

    International Nuclear Information System (INIS)

    A one-step colloidal process has been adopted to prepare silver (Ag) and silver sulfide (Ag2S) nanocrystals, thus avoiding presynthesis of an organometallic precursor and the injection of a toxic phosphine agent. During the reaction, a layered intermediate compound is first formed, which then acts as a precursor, decomposing into the nanocrystals. The composition of the as-obtained products can be controlled by selective cleavage of S–C bonds or Ag–S bonds. Pure Ag2S nanocrystals can be obtained by directly heating silver acetate (Ag(OAc)) and n-dodecanethiol (DDT) at 200 ° C without any surfactant, and pure Ag nanocrystals can be synthesized successfully if the reaction temperature is reduced to 190 ° C and the amount of DDT is decreased to 1 ml in the presence of a non-coordinating organic solvent (1-octadecene, ODE). Otherwise, the mixture of Ag and Ag2S is obtained by directly heating Ag(OAc) in DDT by increasing the reaction temperature or in a mixture of DDT and ODE at 200 ° C. The formation mechanism has been discussed in detail in terms of selective S–C and Ag–S bond dissociation due to the nucleophilic attack of DDT and the lower bonding energy of Ag–S. Interestingly, some products can easily self-assemble into two- or three-dimensional (2D or 3D) highly ordered superlattice structures on a copper grid without any additional steps. The excess DDT plays a key role in the superlattice structure due to the bundling and interdigitation of the thiolate molecules adsorbed on the as-obtained nanocrystals. (paper)

  16. Transition metal-catalyzed oxidative double bond cleavage of simple and bio-derived alkenes and unsaturated fatty acids

    NARCIS (Netherlands)

    Spannring, Peter; Bruijnincx, Pieter C. A.; Weckhuysen, Bert. M.; Klein Gebbink, Bert

    2014-01-01

    The oxidative cleavage of the C=C double bond in unsaturated fatty acids into aldehydes or carboxylic acids is a reaction of current interest in biomass valorization. The products of this reaction, which is currently being performed on an industrial scale by means of ozonolysis, can be applied for t

  17. Dihydrogen bond interactions as a result of H2 cleavage at Cu, Ag and Au centres.

    Science.gov (United States)

    Grabowski, Sławomir J; Ruipérez, Fernando

    2016-05-14

    A quantum chemical study of H2 activation at fluorides of coinage metals, MF (M = Cu, Ag and Au), and its splitting was performed. The following reaction path was analyzed: FMH2→ FHHM → HMFH, where both the molecular complexes and the corresponding transition states have been characterized at the CCSD(T)/aug-cc-pVQZ//MP2/aug-cc-pVQZ level of theory. Further single-point CASSCF/CASPT2 calculations, including spin-orbit coupling effects, were also performed to analyze the role of non-dynamic correlation. The scalar relativistic effects are included via aug-cc-pVQZ-PP basis sets used for the metals. The dihydrogen-bonded copper (FHHCu) and silver (FHHAg) complexes are observed as a result of H2 cleavage, while the corresponding FHHAu gold complex is not found but the HAuHF arrangement is observed, instead. The energetic and geometrical parameters of the complexes have been analyzed and both the Quantum Theory of Atoms in Molecules approach and the Natural Bond Orbitals method were additionally applied to analyze the intermolecular interactions. PMID:27101741

  18. Bond cleavage reactions in the tripeptide tri-alanine upon free electron capture

    International Nuclear Information System (INIS)

    In the present study we performed dissociative electron attachment (DEA) measurements with the tripeptide tri-alanine, C9H17N3O4, utilizing a crossed electron-molecular beam experiment with high electron energy resolution (about 100 meV). Anion efficiency yields as a function of the incident electron energy are obtained for the most abundant anions up to electron energies of ∼ eV. Quantum chemical calculations are performed to determine the thermochemical thresholds for the anions observed in the measurements. There is no evidence of a molecular anion with lifetime of mass spectrometric timescales. The dehydrogenated closed shell anion (M-H)- is one of the fragment anions observed for which the calculations show that H-loss is energetically possible from carboxyl, as well as amide groups. In contrast to the dipeptide di-alanine and monomer alanine the cleavage of the N-Cα bond in the peptide chain is already possible by attachment of electrons at ∼ 0 eV. (authors)

  19. Unexpected carbon-oxygen bond cleavage of THF promoted by guanidinate titanium complex/lithium diisopropylamide: Synthesis and crystal structure

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yong; WANG Mei; YAO Yingming; SHEN Qi

    2005-01-01

    An unexpected carbon-oxygen bond cleavage of THF (THF = tetrahydrofuran) promoted by guanidinate titanium complex was described. Guanidinate lithium [Pr2iNC(NCy)2]Li (Cy = cyclohexyl) formed in situ reacted with TiCl4(THF)2 in a 2:1 molar ratio to produce the guanidinate titanium chloride [Pr2iNC(NCy)2]2TiCl2 (1) in good yield. The reaction of [Pr2iNC(NCy)2]2TiCl2 with lithium diisopropylamide in THF afforded an unexpected [Pr2iNC(NCy)2]2Ti(OBun)2 (2), which was formed by the cleavage of carbon-oxygen bond of THF. Complexes 1 and 2 were fully characterized by elemental analysis, NMR and IR spectroscopies, and X-ray crystal structure determination for complex 2.

  20. Metal-catalyzed activation of ethers via C-O bond cleavage: a new strategy for molecular diversity.

    Science.gov (United States)

    Cornella, Josep; Zarate, Cayetana; Martin, Ruben

    2014-12-01

    In 1979, the seminal work of Wenkert set the standards for the utilization of aryl and vinyl ethers as coupling partners via C-O bond-cleavage. Although the topic remained dormant for almost three decades, the last few years have witnessed a renaissance in this area of expertise, experiencing an exponential growth and becoming a significant discipline within the cross-coupling arena. The means to utilize readily accessible aryl or vinyl ethers as counterparts does not only represent a practical, powerful and straightforward alternative to organic halides, but also constitutes an excellent opportunity to improve our chemical knowledge about a relatively unexplored area of expertise. This review summarizes the most significant developments in the area of C-O bond-cleavage when employing aryl or vinyl ethers, providing a detailed overview of the current state of the art and including future aspects, when applicable. PMID:25157613

  1. In vitro characterization of a phosphate starvation-independent carbon-phosphorus bond cleavage activity in Pseudomonas fluorescens 23F.

    OpenAIRE

    McMullan, G.; Quinn, J P

    1994-01-01

    A novel, metal-dependent, carbon-phosphorus bond cleavage activity, provisionally named phosphonoacetate hydrolase, was detected in crude extracts of Pseudomonas fluorescens 23F, an environmental isolate able to utilize phosphonoacetate as the sole carbon and phosphorus source. The activity showed unique specificity toward this substrate; its organic product, acetate, was apparently metabolized by the glyoxylate cycle enzymes of the host cell. Unlike phosphonatase, which was also detected in ...

  2. Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability.

    Science.gov (United States)

    Wu, R R; Rodgers, M T

    2016-06-21

    Our previous gas-phase infrared multiple photon dissociation action spectroscopy study of protonated 2'-deoxyadenosine and adenosine, [dAdo+H](+) and [Ado+H](+), found that both N3 and N1 protonated conformers are populated with the N3 protonated ground-state conformers predominant in the experiments. Therefore, N-glycosidic bond dissociation mechanisms of N3 and N1 protonated [dAdo+H](+) and [Ado+H](+) and the associated quantitative thermochemical values are investigated here using both experimental and theoretical approaches. Threshold collision-induced dissociation (TCID) of [dAdo+H](+) and [Ado+H](+) with Xe is studied using guided ion beam tandem mass spectrometry techniques. For both systems, N-glycosidic bond cleavage reactions are observed as the major dissociation pathways resulting in production of protonated adenine or elimination of neutral adenine. Electronic structure calculations are performed at the B3LYP/6-311+G(d,p) level of theory to probe the potential energy surfaces (PESs) for N-glycosidic bond cleavage of [dAdo+H](+) and [Ado+H](+). Relative energetics of the reactants, transition states, intermediates and products along the PESs for N-glycosidic bond cleavage are determined at the B3LYP/6-311+G(2d,2p), B3LYP-GD3BJ/6-311+G(2d,2p), and MP2(full)/6-311+G(2d,2p) levels of theory. The predicted N-glycosidic bond dissociation mechanisms for the N3 and N1 protonated species differ. Base rotation of the adenine residue enables formation of a strong N3H(+)O5' hydrogen-bonding interaction that stabilizes the N3 protonated species and its glycosidic bond. Comparison between experiment and theory indicates that the N3 protonated species determine the threshold energies, as excellent agreement between the measured and B3LYP computed activation energies (AEs) and reaction enthalpies (ΔHrxns) for N-glycosidic bond cleavage of the N3 protonated species is found. PMID:27240654

  3. Highly Efficient Oxidative Cleavage of Carbon-Carbon Double Bond over meso-Tetraphenyl Cobalt Porphyrin Catalyst in the Presence of Molecular Oxygen

    Institute of Scientific and Technical Information of China (English)

    周贤太; 纪红兵

    2012-01-01

    Highly efficient and selective carbon-carbon double bond aerobic cleavage of olefins catalyzed by metallopor- phyrins was investigated, and carbonyl compounds and epoxide were produced as the main products. CoTPP (co- balt meso-tetraphenyl porphyrin) showed excellent activity for the oxidative cleavage of carbon-carbon double bond by using styrene as model compound, in which the TOF (turnover frequency) and selectivity toward benzaldehyde was obtained with 2×10^4h-1 and 86%,respectively.

  4. Reductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study

    OpenAIRE

    Srnec, Martin; Ryde, Ulf; Rulisek, Lubomir

    2011-01-01

    The key step in the reaction mechanism of multicopper oxidases (MCOs)-the cleavage of the O-O bond in O-2-has been investigated using combined quantum mechanical and molecular mechanical (QM/MM) methods. This process represents a reaction pathway from the peroxy intermediate after it accepts one electron from the nearby type-1 Cu site to the experimentally-observed native intermediate, which is the only fully oxidised catalytically relevant state in MCOs. Scans of the QM(DFT)/MM potential ene...

  5. Selective Oxidative Decarbonylative Cleavage of Unstrained C(sp(3))-C(sp(2)) Bond: Synthesis of Substituted Benzoxazinones.

    Science.gov (United States)

    Verma, Ajay; Kumar, Sangit

    2016-09-01

    A transition metal (TM)-free practical synthesis of biologically relevant benzoxazinones has been established via a selective oxidative decarbonylative cleavage of an unstrained C(sp(3))-C(sp(2)) bond employing iodine, sodium bicarbonate, and (t)butyl hydroperoxide in DMSO at 95 °C. Control experiments and Density Functional Theory (DFT) calculations suggest that the reaction involves a [1,5]H shift and extrusion of CO gas as the key steps. The extrusion of CO has also been established using PMA-PdCl2. PMID:27549986

  6. Anaerobic DNA cleavage in red light by dicopper(II) complexes on disulphide bond activation

    Indian Academy of Sciences (India)

    Debojyoti Lahiri; Ritankar Majumdar; Ashis K Patra; Akhil R Chakravarty

    2010-05-01

    Binuclear complexes [Cu(-RSSR)]2 (1) and [M2(-PDS)(H2O)]2 (M = Cu(II), 2; Fe(II), 3), where H2RSSR is a reduced Schiff base derived from 2-(thioethyl)salicylaldimine having a disulphide moiety and H2PDS is derived from dimerization of D-penicillamine, have been prepared, structurally characterized, and their photo-induced DNA cleavage activity studied. The crystal structure of 1 shows the complex as a discrete binuclear species with each metal in a CuN2O2 square-planar geometry (Cu…Cu, 6.420 Å). The tetradentate RSSR2- acts as a bridging ligand. The sulphur atoms in the disulphide unit do not interact with the metal ions. Complexes 1-3 do not show any DNA cleavage activity in darkness. The copper(II) complexes exhibit chemical nuclease activity in the presence of 3-mercaptopropionic acid. Cleavage of supercoiled DNA has been observed in UV-A light of 365 nm for 1 and red light of 647.1 nm for both 1 and 2 in air. Mechanistic data reveal the involvement of the disulphide unit as photosensitizer generating hydroxyl radicals ($^{\\bullet}$OH) as the reactive species. Photo-induced DNA cleavage in red light seems to involve sulphide radicals in a type-I process and hydroxyl radicals. The dicopper(II) complexes show significant anaerobic photo-induced DNA cleavage activity in red light under argon following type-I pathway without involving any reactive oxygen species.

  7. Probing Electron-Induced Bond Cleavage at the Single-Molecule Level Using DNA Origami Templates

    DEFF Research Database (Denmark)

    Keller, Adrian Clemens; Bald, Ilko; Rotaru, Alexandru;

    2012-01-01

    nucleobases. Here we present a strategy that allows for the first time to visualize the electron-induced dissociation of single chemical bonds within complex, but well-defined self-assembled DNA nanostructures. We employ atomic force microscopy to image and quantify LEE-induced bond dissociations within...... chromatin, now becomes feasible....

  8. Investigations on organolead compounds V. Lead---lead bond cleavage reactions of hexaphenyldilead

    NARCIS (Netherlands)

    Willemsens, L.C.; Kerk, G.J.M. van der

    1968-01-01

    It has been shown that a number of nucleophilic and weakly electrophilic reagents (organolithium and organomagnesium compounds, metallic lithium, potassium permanganate, sodium ethoxide, diaryl disulphides, sulphur, ozone, hypochlorous acid and iodine/iodide) selectively cleave the lead---lead bond

  9. Mechanisms of Selective Cleavage of C-O Bonds in Di-aryl Ethers in Aqueous Phase

    Energy Technology Data Exchange (ETDEWEB)

    He, Jiayue; Zhao, Chen; Mei, Donghai; Lercher, Johannes A.

    2014-01-02

    A novel route for cleaving the C-O aryl ether bonds of p-substituted H-, CH3-, and OH- diphenyl ethers has been explored over Ni/SiO2 catalysts at very mild conditions. The C-O bond of diphenyl ether is cleaved by parallel hydrogenolysis and hydrolysis (hydrogenolysis combined with HO* addition) on Ni. The rates as a function of H2 pressure from 0 to 10 MPa indicate that the rate-determining step is the C-O bond cleavage on Ni. H* atoms compete with the organic reactant for adsorption leading to a maximum in the rate with increasing H2 pressure. In contrast to diphenyl ether, hydrogenolysis is the exclusive route for cleaving an ether C-O bond of di-p-tolyl ether to form p-cresol and toluene. 4,4'-dihydroxydiphenyl ether undergoes sequential surface hydrogenolysis, first to phenol and HOC6H4O* (adsorbed), which is then cleaved to phenol (C6H5O* with added H*) and H2O (O* with two added H*) in a second step. Density function theory supports the operation of this pathway. Notably, addition of H* to HOC6H4O* is less favorable than a further hydrogenolytic C-O bond cleavage. The TOFs of three aryl ethers with Ni/SiO2 in water followed the order 4,4'-dihydroxydiphenyl ether (69 h-1) > diphenyl ether (26 h-1) > di-p-tolyl ether (1.3 h-1), in line with the increasing apparent activation energies, ranging from 93 kJ∙mol-1 (4,4'-dihydroxydiphenyl ether) < diphenyl ether (98 kJ∙mol-1) to di-p-tolyl ether (105 kJ∙mol-1). D.M. thanks the support from the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the

  10. Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation.

    Science.gov (United States)

    Raich, L; Nin-Hill, A; Ardèvol, A; Rovira, C

    2016-01-01

    Carbohydrates play crucial roles in many biological processes, from cell-cell adhesion to chemical signaling. Their complexity and diversity, related to α/β anomeric configuration, ring substituents, and conformational variations, require a diverse set of enzymes for their processing. Among them, glycoside hydrolases (GHs) are responsible for the hydrolysis of one of the strongest bonds in nature: the glycosidic bond. These highly specialized biological catalysts select particular conformations their carbohydrate substrates to enhance catalysis. The evolution of this conformation during the reaction of glycosidic bond cleavage, known as the conformational catalytic itinerary, is of fundamental interest in glycobiology, with impact on inhibitor and drug design. Here we review some of the aspects and the main strategies one needs to take into account when simulating a reaction in a GH enzyme using QM/MM metadynamics. Several specific aspects are highlighted, from the importance of the distortion of the substrate at the Michaelis complex to the variable control during the metadynamics simulation or the analysis of the reaction mechanism and conformational itinerary. The increasing speed of computer power and methodological advances have added a vital tool to the study of GH mechanisms, as shown here and recent reviews. It is hoped that this chapter will serve as a first guide for those attempting to perform a metadynamics simulation of these relevant and fascinating enzymes. PMID:27498638

  11. Oxidative C-C bond cleavage of ketone enolates by nitrosation

    Czech Academy of Sciences Publication Activity Database

    Mašek, Tomáš; Champalet, Valentine; Jahn, Ullrich

    Lisboa : -, 2015 - (Rauter, A.; Martins, A.; Matos, A.; Dias, C.; Xavier, N.; Nunes, R.; Lucas, S.; Cachatra, V.; Paiva, A.; Batista, D.). s. 249 ISBN 978-989-8124-11-1. [ESOC 2015. European Symposium on Organic Chemistry /19./. 12.07.2015-16.07.2015, Lisboa] Institutional support: RVO:61388963 Keywords : ketone enolates * nitrosation * C-C bond Subject RIV: CC - Organic Chemistry

  12. Bond cleavage reactions of the bridge structure in coal in the presence of hydrogen donating compounds; Suiso kyoyosei kagobutsu sonzaika deno sekitanchu no kakyo kozo no kairetsu hanno

    Energy Technology Data Exchange (ETDEWEB)

    Bando, N.; Kidena, K.; Murata, S.; Nomura, M. [Osaka University, Osaka (Japan). Faculty of Engineering

    1996-10-28

    In this paper, bond cleavage reactions are discussed in relation to the softening and solubilization of coal. Were used 9,10-dihydroanthracene (DHA) and 9,10-dihydrophenanthrene (DHP) as models of hydrogen donating compounds in coal, and bibenzyl, 1,2-diethane, benzylphenylether, and 1,5-dibenzylnaphthalene were used as models of bridge structure compounds. They were compared mutually, as to reactivity of coal against DHA and DHP. For the homolytic cleavage of bridges, DHA with excellent radical supplement performance provided excellent hydrogen donating performance. While, for the ipso-position cleavage of bridges, it was found that DHP can act as an effective hydrogen donor. For the reaction between coal and hydrogenated aromatic compounds, cleavage of relatively weak bonds, such as ether linkage and dimethylene linkage, occurred at about 380{degree}C, and hydrogen from DHA or DHP was consumed. On the other hand, the results suggested that the cleavage reaction at ipso-position affected by hydrogen donating solvent is also important at temperature range around 420{degree}C. 2 refs., 3 figs., 1 tab.

  13. Unified view of oxidative C-H bond cleavage and sulfoxidation by a nonheme iron(IV)-oxo complex via Lewis acid-promoted electron transfer.

    Science.gov (United States)

    Park, Jiyun; Morimoto, Yuma; Lee, Yong-Min; Nam, Wonwoo; Fukuzumi, Shunichi

    2014-04-01

    Oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by a nonheme iron(IV)-oxo complex, [(N4Py)Fe(IV)(O)](2+) (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), were remarkably enhanced by the presence of triflic acid (HOTf) and Sc(OTf)3 in acetonitrile at 298 K. All the logarithms of the observed second-order rate constants of both the oxidative C-H bond cleavage and sulfoxidation reactions exhibit remarkably unified correlations with the driving forces of proton-coupled electron transfer (PCET) and metal ion-coupled electron transfer (MCET) in light of the Marcus theory of electron transfer when the differences in the formation constants of precursor complexes between PCET and MCET were taken into account, respectively. Thus, the mechanisms of both the oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by [(N4Py)Fe(IV)(O)](2+) in the presence of HOTf and Sc(OTf)3 have been unified as the rate-determining electron transfer, which is coupled with binding of [(N4Py)Fe(IV)(O)](2+) by proton (PCET) and Sc(OTf)3 (MCET). There was no deuterium kinetic isotope effect (KIE) on the oxidative C-H bond cleavage of toluene via the PCET pathway, whereas a large KIE value was observed with Sc(OTf)3, which exhibited no acceleration of the oxidative C-H bond cleavage of toluene. When HOTf was replaced by DOTf, an inverse KIE (0.4) was observed for PCET from both toluene and [Ru(II)(bpy)3](2+) (bpy =2,2'-bipyridine) to [(N4Py)Fe(IV)(O)](2+). The PCET and MCET reactivities of [(N4Py)Fe(IV)(O)](2+) with Brønsted acids and various metal triflates have also been unified as a single correlation with a quantitative measure of the Lewis acidity. PMID:24605985

  14. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl- CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during à-oxidation of 3- methyl-branched fatty acids

    CERN Document Server

    Foulon, V; Croes, K; Waelkens, E

    1999-01-01

    Purification, molecular cloning, and expression of 2-hydroxyphytanoyl- CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during à-oxidation of 3- methyl-branched fatty acids

  15. Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

    International Nuclear Information System (INIS)

    Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π* shape resonance in energy region * orbital of the base to the σ* orbital of the glycosidic N–C bond. In addition, the metastable state formed after impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided

  16. Effect of copper-sulphur bond on the DNA photo-cleavage activity of 2-(methylthio)ethylpyridine-2-carbaldimine copper(II) complexes

    Indian Academy of Sciences (India)

    Tarkeshwar Gupta; Ashis K Patra; Shanta Dhar; Munirathinam Nethaji; Akhil R Chakravarty

    2005-03-01

    The binding and photo-induced DNA cleavage activity of a binary complex [CuL2](ClO4)2 (1) and the in situ generated ternary complexes [CuLB](ClO4)2 from 1 (B: 1,10-phenanthroline, phen, 2; dipyrido[3,2-: 2',3'-]quinoxaline, dpq, 3) are studied, where L is a N2S-donor tridentate Schiff base 2-(methylthio)ethylpyridine-2-carbaldimine. Complex 1, structurally characterized by X-ray diffraction study, has six-coordinate meridional geometry showing CuN4S2 coordination. The Cu-N bond lengths are in the range of 1.968(3) to 2.158(4) Å. The Cu-S bond lengths of 2.599(2) and 2.705(2) Å are significantly long indicating weak covalent interaction between copper and sulphur atoms. The thiomethyl groups are cis to each other giving S-Cu-S angle of 75.82(5)°. The Cu-N(pyridyl) bond distances are longer than the Cu-N(imine) bonds. The complexes are redox active and display a quasi-reversible cyclic voltammetric response assignable to the Cu(II)/Cu(I) couple near 0.0 V vs SCE in DMF-Tris buffer (1 : 4 /) using 0.1 M KCl as supporting electrolyte. Electronic spectra of the complexes show a - band in the range 630 to 700 nm in DMF along with higher energy charge transfer bands. While complex 1 is a poor binder to DNA, the ternary complexes show good DNA binding propensity. The photo-nuclease activity of 1-3 is studied using UV and visible wavelengths. The DNA cleavage activity at 365 nm follows the order: 3 > 2 > 1. The cleavage reaction involves the formation of singlet oxygen as the reactive species in a type-II process.

  17. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

    International Nuclear Information System (INIS)

    Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process. Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure

  18. Splitting a Substrate into Three Parts: Gold-Catalyzed Nitrogenation of Alkynes by C-C and C≡C Bond Cleavage.

    Science.gov (United States)

    Qin, Chong; Su, Yijin; Shen, Tao; Shi, Xiaodong; Jiao, Ning

    2016-01-01

    A gold-catalyzed nitrogenation of alkynes for the synthesis of carbamides and amino tetrazoles through C-C and C≡C bond cleavages is described. A diverse set of functionalized carbamide and amino tetrazole derivatives were selectively constructed under mild conditions. The chemoselectivity can be easily switched by the selection of the acid additives. The reaction is characterized by its broad substrate scope, direct construction of high value products, easy operation under air, and mild conditions at room temperature. This chemistry provides a way to transform alkynes by splitting the substrate into three parts. PMID:26494539

  19. Homolytic cleavage of the O-Cu(ii) bond: XAFS and EPR spectroscopy evidence for one electron reduction of Cu(ii) to Cu(i).

    Science.gov (United States)

    Yi, Hong; Zhang, Guanghui; Xin, Jie; Deng, Yi; Miller, Jeffrey T; Kropf, Arthur J; Bunel, Emilio E; Qi, Xiaotian; Lan, Yu; Lee, Jyh-Fu; Lei, Aiwen

    2016-05-25

    The investigation into the active copper(i) catalysts from copper(ii) precursors has become a fundamental and important task in copper catalysis. In this work, we demonstrate that the (t)BuO(-) anion serves not only as a base but also as a mediator to promote the reduction of Cu(ii) to Cu(i) in copper catalysis. XAFS and EPR spectroscopy evidence the [Cu(O(t)Bu)3](-) ate complex as the key intermediate which undergoes homolytic-cleavage of the O-Cu(ii) bond generating [Cu(O(t)Bu)2](-) ate complex. PMID:27145712

  20. Formation of a Six-Coordinate fac-[Re(Co)3]+ Complex by the N-C bond cleavage of a potentially tetradentate ligand

    International Nuclear Information System (INIS)

    The rhenium(I) compound fac-[Re(CO)3(daa)]. Hpab.H2O (Hpab N,N'-(l,2-phenylene)bis(2'-aminobenzamide); Hdaa 2-amino-N-(2-aminophenyl)benzamide) was synthesized from the reaction of [Re(CO)5,Br] with two equivalent of Hpab in toluene. The monoanionic tridentate ligand daa was formed by the rhenium-mediated cleavage of an amido N-C bond of the potentially tetradentate ligand Hpab. The compound was characterized by IR spectroscopy and X-ray crystallography, and daa is coordinated as a diamino amide via three nitrogen-donor atoms

  1. Catalytic diastereoselective tandem conjugate addition-elimination reaction of Morita-Baylis-Hillman C adducts by C-C bond cleavage

    KAUST Repository

    Yang, Wenguo

    2012-02-08

    Through the cleavage of the C-C bond, the first catalytic tandem conjugate addition-elimination reaction of Morita-Baylis-Hillman C adducts has been presented. Various S N2′-like C-, S-, and P-allylic compounds could be obtained with exclusive E configuration in good to excellent yields. The Michael product could also be easily prepared by tuning the β-C-substituent group of the α-methylene ester under the same reaction conditions. Calculated relative energies of various transition states by DFT methods strongly support the observed chemoselectivity and diastereoselectivity. © 2012 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim.

  2. Tomato carotenoid cleavage dioxygenases 1A and 1B: Relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles

    Directory of Open Access Journals (Sweden)

    Andrea Ilg

    2014-01-01

    Full Text Available The biosynthetic processes leading to many of the isoprenoid volatiles released by tomato fruits are still unknown, though previous reports suggested a clear correlation with the carotenoids contained within the fruit. In this study, we investigated the activity of the tomato (Solanum lycopersicum carotenoid cleavage dioxygenase (SlCCD1B, which is highly expressed in fruits, and of its homolog SlCCD1A. Using in vitro assays performed with purified recombinant enzymes and by analyzing products formed by the two enzymes in carotene-accumulating Escherichia coli strains, we demonstrate that SlCCD1A and, to a larger extent, SlCCD1B, have a very relaxed specificity for both substrate and cleavage site, mediating the oxidative cleavage of cis- and all-trans-carotenoids as well as of different apocarotenoids at many more double bonds than previously reported. This activity gives rise to a plenitude of volatiles, mono-apocarotenoids and dialdehyde products, including cis-pseudoionone, neral, geranial, and farnesylacetone. Our results provide a direct evidence for a carotenoid origin of these compounds and point to CCD1s as the enzymes catalyzing the formation of the vast majority of tomato isoprenoid volatiles, many of which are aroma constituents.

  3. Tomato carotenoid cleavage dioxygenases 1A and 1B: Relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles

    KAUST Repository

    Ilg, Andrea

    2014-06-25

    The biosynthetic processes leading to many of the isoprenoid volatiles released by tomato fruits are still unknown, though previous reports suggested a clear correlation with the carotenoids contained within the fruit. In this study, we investigated the activity of the tomato (Solanum lycopersicum) carotenoid cleavage dioxygenase (SlCCD1B), which is highly expressed in fruits, and of its homolog SlCCD1A. Using in vitro assays performed with purified recombinant enzymes and by analyzing products formed by the two enzymes in carotene-accumulating Escherichia coli strains, we demonstrate that SlCCD1A and, to a larger extent, SlCCD1B, have a very relaxed specificity for both substrate and cleavage site, mediating the oxidative cleavage of cis- and all-. trans-carotenoids as well as of different apocarotenoids at many more double bonds than previously reported. This activity gives rise to a plenitude of volatiles, mono-apocarotenoids and dialdehyde products, including cis-pseudoionone, neral, geranial, and farnesylacetone. Our results provide a direct evidence for a carotenoid origin of these compounds and point to CCD1s as the enzymes catalyzing the formation of the vast majority of tomato isoprenoid volatiles, many of which are aroma constituents. © 2014 The Authors.

  4. Aggregation of bovine serum albumin upon cleavage of its disulfide bonds, studied by the time-resolved small-angle X-ray scattering technique with synchrotron radiation

    International Nuclear Information System (INIS)

    A rapid mixing system of the stopped-flow type, used with small-angle X-ray scattering equipment using synchrotron radiation, is described. The process of aggregation of bovine serum albumin was traced with a time interval of 50 s, initiated upon cleavage of its disulfide bonds by reduction with dithiothreitol. The results indicate that a 218-fold molar excess of dithiothreitol over the number of moles of disulfide bonds in bovine serum albumin is sufficient to initiate the reaction immediately after mixing, which reaches equilibrium in about 15 min. On the other hand, half this amount is not sufficient to initiate the reaction, so that the reaction is delayed by about 150 s. Such a single-shot time-resolved experiment showed that experiments with a time interval of 100 ms are possible with repeated multi-shot runs. (Auth.)

  5. Mechanism of ribonucleotide reductase from Herpes simplex virus type 1. Evidence for 3' carbon-hydrogen bond cleavage and inactivation by nucleotide analogs

    International Nuclear Information System (INIS)

    Isotope effects of 2.5, 2.1, and 1.0 were measured on the conversion of [3'-3H]ADP, [3'-H]UDP, and [5-3H] UDP to the corresponding 2'-deoxynucleotides by herpes simplex virus type 1 ribonucleotide reductase. These results indicate that the reduction of either purine or pyrimidine nucleotides requires cleavage of the 3' carbon-hydrogen bond of the substrate. The substrate analogs 2'-chloro-2'-deoxyuridine 5'-diphosphate (ClUDP), 2'-deoxy-2'-fluorouridine 5'-diphosphate, and 2'-azido-2'-deoxyuridine 5'-diphosphate were time-dependent inactivators of the herpes simplex virus type 1 ribonucleotide reductase. Incubation of [3'-3H]ClUDP with the enzyme was accompanied by time-dependent release of 3H to the solvent. Reaction of [beta-32P]ClUDP with the reductase resulted in the production of inorganic pyrophosphate. These results are consistent with the enzyme-mediated cleavage of the 3' carbon-hydrogen bond of ClUDP and the subsequent conversion of the nucleotide to 2-methylene-3(2H)furanone, as previously reported with the Escherichia coli ribonucleotide reductase

  6. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Annual report, October 1, 1980-September 30, 1981

    Energy Technology Data Exchange (ETDEWEB)

    Hirschon, A.S.; Zevely, J.; Mayo, F.R.

    1981-11-12

    The objective of this project is to determine the structure of bituminous coal by determining the proportions of the various kinds of connecting bonds and how they can best be broken. Results obtained during the past quarter are presented for the following tasks: (1) extractions and fractionations of coal products which covers pyridine extraction, fractionation of TIPS fractions, EDA extraction of Illinois No. 6 coal and swelling ratios of coal samples; (2) experiments on breakable single bonds which cover reactions of ethylenediamine and model ethers, reaction of pyridine-extracted coal with Me/sub 3/SiI, Baeyer-Villiger oxidations, reaction to diphenylmethane with 15% HNO/sub 3/, cleavage of TIPS with ZnI/sub 2/, and cleavage of black acids; and (3) oxygen oxidation No. 18. Some of the highlights of these studies are: (1) some model ethers are not cleaved by EDA under extraction conditions; (2) oxidation of diaryl ketones with m-chloroperbenzoic acid and saponification of the resulting esters in promising for identifying ketones, (3) treatment of a black acid with pyridine hydroiodide reduced the acid's molecular weight and increased its solubility in pyridine, but treatment with ZnI/sub 2/ was ineffective; (4) in comparison with 0.1 M K/sub 2/S/sub 2/O/sub 8/, 0.01 M persulfate is relatively ineffective in accelerating oxidation of BnNH/sub 2/-extracted coal in water suspension. 2 figures, 3 tables.

  7. Effect of thermal denaturation, inhibition, and cleavage of disulfide bonds on the low-frequency Raman and FTIR spectra of chymotrypsin and albumin

    Science.gov (United States)

    Brandt, Nikolay N.; Chikishev, Andrey Yu; Mankova, Anna A.; Sakodynskaya, Inna K.

    2015-05-01

    The analysis of the structure-function relationship is extremely important in the study of proteins. The importance of function-related motions of large parts or subglobules of protein molecules stimulates the spectroscopic study in the low-frequency (terahertz) domain. However, only tentative assignments are available and the spectroscopic data are insufficiently discussed in terms of structural changes. This work is aimed at the analysis of regularities of changes in the low-frequency (100 to 600 cm-1) FTIR and Raman spectra of proteins related to their structural modifications. We study the spectra of two proteins with substantially different structures (albumin and chymotrypsin) and the spectra of samples in which the structures of protein molecules are modified using inhibition, thermal denaturation, and cleavage of disulfide bonds. The results indicate that the low-frequency spectral interval can be used to characterize protein conformations. Correlated variations in the intensities of several low-frequency bands are revealed in the spectra of the modified proteins. The strongest spectral changes are caused by thermal denaturation of proteins, and the effect of cleavage of disulfide bonds is generally weaker. It is demonstrated that the inhibitor binding in the active site causes spectral changes that can be compared to the changes induced by thermal denaturation.

  8. Sequence-Specific Ultrasonic Cleavage of DNA

    OpenAIRE

    Grokhovsky, Sergei L.; Il'icheva, Irina A.; Nechipurenko, Dmitry Yu.; Golovkin, Michail V.; Panchenko, Larisa A.; Polozov, Robert V.; Nechipurenko, Yury D.

    2011-01-01

    We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multiva...

  9. Catalysis and co-catalysis of bond cleavages in coal and coal analogs. Final report, August 1, 1990--January 31, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Miller, B.

    1994-05-01

    In work prior to the inception of this project, the authors observed that mixtures of phenolic materials and polyalkoxyaromatic molecules were appreciably more effective in catalyzing the decompositions of di-2-naphthyl ether and of di-1-naphthyl sulfide in tetralin solutions at 450{degrees}C than were the phenols by themselves, even though the polyalkoxyaromatic molecules, in the absence of phenolic co- catalysts, show essentially no catalytic activity. This was of appreciable interest in coal research because dinapthyl ether and dinapthyl sulfide have been employed as model compounds for coals in studies aimed at cleaving ether and sulfide bonds similar to those in coals. The authors proposed (R. K. Sharma, K. P. Raman, and B. Miller) that the mixed catalysts used in these studies catalyze cleavages of ether and sulfide bonds by means of a mechanism involving electron transfer from the polyalkoxyaromatics to the substrates, which are activated as electron acceptors by hydrogen bonding to phenols. Since phenols themselves are electron donors, they also proposed that the well known effects of phenols in catalyzing the conversion of coals are due to similar electron transfer mechanisms.

  10. Protolytic Cleavage of Hg–C Bonds Induced by 1-Methyl-1,3-dihydro-2H-benzimidazole-2-selone: Synthesis and Structural Characterization of Mercury Complexes

    Science.gov (United States)

    2016-01-01

    Multinuclear (1H, 77Se, and 199Hg) NMR spectroscopy demonstrates that 1-methyl-1,3-dihydro-2H-benzimidazole-2-selone, H(sebenzimMe), a structural analogue of the selenoamino acid, selenoneine, binds rapidly and reversibly to the mercury centers of HgX2 (X = Cl, Br, I), while X-ray diffraction studies provide evidence for the existence of adducts of composition [H(sebenzimMe)]xHgX2 (X = Cl, x = 2, 3, 4; X = I, x = 2) in the solid state. H(sebenzimMe) also reacts with methylmercury halides, but the reaction is accompanied by elimination of methane resulting from protolytic cleavage of the Hg–C bond, an observation that is of relevance to the report that selenoneine demethylates CysHgMe, thereby providing a mechanism for mercury detoxification. Interestingly, the structures of [H(sebenzimMe)]xHgX2 exhibit a variety of different hydrogen bonding patterns resulting from the ability of the N–H groups to form hydrogen bonds with chlorine, iodine, and selenium. PMID:25822075

  11. Mechanistic aspects of dinitrogen cleavage and hydrogenation to produce ammonia in catalysis and organometallic chemistry: relevance of metal hydride bonds and dihydrogen.

    Science.gov (United States)

    Jia, Hong-Peng; Quadrelli, Elsje Alessandra

    2014-01-21

    Dinitrogen cleavage and hydrogenation by transition-metal centers to produce ammonia is central in industry and in Nature. After an introductory section on the thermodynamic and kinetic challenges linked to N2 splitting, this tutorial review discusses three major classes of transition-metal systems (homogeneous, heterogeneous and biological) capable of achieving dissociation and hydrogenation of dinitrogen. Molecular complexes, solid-state Haber-Bosch catalytic systems, silica-supported tantalum hydrides and nitrogenase will be discussed. Emphasis is focused on the reaction mechanisms operating in the process of dissociation and hydrogenation of dinitrogen, and in particular on the key role played by metal hydride bonds and by dihydrogen in such reactions. PMID:24108246

  12. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 12, June 1-September 30, 1981

    Energy Technology Data Exchange (ETDEWEB)

    Hirschon, A.S.; Zevely, J.; Mayo, F.R.

    1981-11-12

    We assume that bituminous coal consists mostly of an aggregate of condensed aromatic and aliphatic rings, connected and made insoluble (but swellable) by crosslinks containing single bonds. The objective of this project is to determine the proportions of the various kinds of connecting links and how they can best be broken - in other words, to determine the structure of bituminous coal, with emphasis on the crosslinks and breakable single bonds. The program began with an investigation of the structure of the TIPS fraction of Illinois No. 6 coal, that is, the two-thirds of the 16% extracted by pyridine that is toluene-insoluble, pyridine-soluble, mostly through changes in molecular weight during cleavage reactions in pyridine solution. The most promising of these cleavage reactions are now being applied to the 84% of coal that is insoluble in pyridine and presents the main problem in coal liquefaction, following the progress of the reactions by formation of soluble material and swelling of the insoluble portion. We found that benzylamine (BnNH/sub 2/) would extract an additional 14% (of the original weight of coal) of material from pyridine-extracted coal, and later that an ethylenediamine/dimethyl sulfoxide (EDA/DMSO) mixture would dissolve another 21% of the original coal. The BnNH/sub 2/ extract is soluble in pyridine. Our best present guess is that the BnNH/sub 2/ extract cleaves most of the ester groups in coal and that EDA/DMSO cleaves the remaining ester and most of the ether groups.

  13. Synthesis of Biaryls through Nickel-Catalyzed Suzuki-Miyaura Coupling of Amides by Carbon-Nitrogen Bond Cleavage.

    Science.gov (United States)

    Shi, Shicheng; Meng, Guangrong; Szostak, Michal

    2016-06-01

    The first Ni-catalyzed Suzuki-Miyaura coupling of amides for the synthesis of widely occurring biaryl compounds through N-C amide bond activation is reported. The reaction tolerates a wide range of electron-withdrawing, electron-neutral, and electron-donating substituents on both coupling partners. The reaction constitutes the first example of the Ni-catalyzed generation of aryl electrophiles from bench-stable amides with potential applications for a broad range of organometallic reactions. PMID:27101428

  14. Rhodium(i)-catalysed skeletal reorganisation of benzofused spiro[3.3]heptanes via consecutive carbon-carbon bond cleavage.

    Science.gov (United States)

    Matsuda, Takanori; Yuihara, Itaru; Kondo, Kazuki

    2016-08-01

    Skeletal reorganisation of benzofused spiro[3.3]heptanes has been achieved using rhodium(i) catalysts. The reaction of benzofused 2-(2-pyridylmethylene)spiro[3.3]heptanes proceeds via sequential C-C bond oxidative addition and β-carbon elimination. On the other hand, benzofused spiro[3.3]heptan-2-ols undergo two consecutive β-carbon elimination processes. In both cases, substituted naphthalenes are obtained. PMID:27357097

  15. EFFECT OF SOLVENT ON THE BETA-O-4 BOND CLEAVAGE OF A LIGNIN MODEL COMPOUND BY TERT-BUTOXIDE UNDER MILD CONDITIONS

    Directory of Open Access Journals (Sweden)

    Yuji Matsumoto

    2011-11-01

    Full Text Available The beta-O-4 bond cleavage of a non-phenolic β-O-4 type dimeric lignin model compound, 2-(2-methoxyphenoxy-1-(3,4-dimethoxyphenyl-ethanol (III, was examined in systems using potassium tert-butoxide as a base (0.5 mol/l and tert-butanol (tBuOH, dimethylsulfoxide, 1,4-dioxane, or tetrahydrofuran as a solvent. The β-O-4 bond of compound III was cleaved in any system at 30°C, and 2-methoxyphenol (II was liberated. The amount of compound II liberated was close to the quantitative yield on the basis of the amount of compound III that disappeared, except for the treatment in the t-BuOH system. The reaction rate was dependent on what solvent was used. Half-life periods for these systems were roughly about 6.0, 3.0, 0.7, and 0.2h, respectively. It seemed that the rates were very high when the polarity of the solvents was low. Two reaction products generated from the aromatic ring with two methoxyl groups of compound III, 4-acetyl-1,2-dimethoxybenzene and 3,4-dimethoxybenzoic acid, were detected in all the systems. A peculiar reaction product, 1,2-dimethoxybenzene, was detected in a fairly large quantity, only when the latter two solvents with low polarities were applied.

  16. Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH2BrI

    International Nuclear Information System (INIS)

    It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (nX) to a carbon-halogen antibonding orbital (σ*C-X). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH2BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH2BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH2Br + I radical pairs, iso-CH2Br-I, and iso-CH2I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH2Br-I. Both iso-CH2Br-I and iso-CH2I-Br are observed in cyclohexane with a ratio of ∼2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH2I-Br photoproduct as well as iso-CH2Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH2Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ∼1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH2BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes

  17. Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe-H - - - H-N Dihydorgen Bond Characterized by Neutron Diffraction

    International Nuclear Information System (INIS)

    Use of hydrogen as a fuel by [FeFe]-hydrogenase enzymes in nature requires heterolytic cleavage of the H-H bond into a proton (H+) and hydride (H-), a reaction that is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. An understanding of the catalytic oxidation of H2 by hydrogenases provides insights into the design of synthetic catalysts that are sought as cost-effective alternatives to the use of the precious metal platinum in fuel cells. Crystallographic studies on the [FeFe]-hydrogenase enzyme were critical to understanding of its reactivity, but the key H-H cleavage step is not readily observed experimentally in natural hydrogenases. Synthetic biomimics have provided evidence for H2 cleavage leading to hydride transfer to the metal and proton transfer to an amine. Limitations on the precise location of hydrogen atoms by x-ray diffraction can be overcome by use of neutron diffraction, though its use is severely limited by the difficulty of obtaining suitable crystals and by the scarcity of neutron sources. Here we show that an iron complex with a pendant amine in the diphosphine ligand cleaves hydrogen heterolytically under mild conditions, leading to [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4-, [PtBu2NtBu2 = 1,5-di(tert-butyl)-3,7-di(tert-butyl)-1,5-diaza-3,7-diphosphacyclooctane; ArF = 3,5-bis(trifluoromethyl)phenyl]. The Fe-H- - - H-N moiety has a strong dihydrogen bond, with a remarkably short H··· H distance of 1.489(10) Angstrom between the protic N-Hδ+ and hydridic Fe-Hδ-. The structural data for [CpC5F4NFeH(PtBu2NtBu2H)]+ provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes, with the pendant amine playing a key role as a proton relay. The iron complex [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4- is an electrocatalyst for oxidation of H2 (1 atm) at 22 °C, so the structural data are obtained on a complex that is a functional model for catalysis by [FeFe]-hydrogenase enzymes. This research was supported

  18. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 1, October 1-December 31, 1978

    Energy Technology Data Exchange (ETDEWEB)

    Buchanan, D.H.; Mayo, F.R.

    1979-01-25

    Bituminous coal is assumed to consist mostly of an aggregate of condensed aromatic and aliphatic rings, connected and made insoluble (but swellable) by crosslinks containing only single bonds. These connecting links consist mainly, possibly entirely, of combinations of carbon-carbon single bonds and ether (possibly ester) groups. It is at these crosslinks that the most extensive cuts can be made in the coal structure (to make it soluble or liquid) under the mildest conditions and with the least loss in fuel values. The objective of this project is to determine the proportion of the various kinds of connecting links and how they can best be broken; in other words, to determine the structure of coal with emphasis on the crosslinks. At present, our attention is directed to five kinds of connecting links: single (Ar-CH/sub 2/-Ar) and multiple methylene groups (Ar-(CH/sub 2/)/sub 2/-Ar) and three kinds of ethers, Ar-O-Ar, Ar-O-R, and R-O-R (Ar represents an aromatic aggregate and R is attached to O through at least one aliphatic carbon.) The work described in this quarterly report deals mainly with the oxidation of pyridine-extracted coal by O/sub 2/ and the cleavage by sodium in liquid ammonia of aromatic ether linkages in a pyridine-soluble, toluene-insoluble fraction of coal extract. Products from the NaOCl oxidation of pyridine-extracted coal were also studied by nuclear magnetic resonance (NMR) and acid-base titrations. 7 references, 2 figures, 6 tables.

  19. Cleavage of peptide bonds bearing ionizable amino acids at P1 by serine proteases with hydrophobic S1 pocket

    International Nuclear Information System (INIS)

    Research highlights: → Large pK shifts in ionizable groups when buried in the protein interior. → Substrate dependent shifts in pH optimum for serine proteases. → Lys side chain is a stronger acid in serine protease S1 pocket than Asp side chain. -- Abstract: Enzymatic hydrolysis of the synthetic substrate succinyl-Ala-Ala-Pro-Xxx-pNA (where Xxx = Leu, Asp or Lys) catalyzed by bovine chymotrypsin (CHYM) or Streptomyces griseus protease B (SGPB) has been studied at different pH values in the pH range 3-11. The pH optima for substrates having Leu, Asp, and Lys have been found to be 7.5-8.0, 5.5-6.0, and ∼10, respectively. At the normally reported pH optimum (pH 7-8) of CHYM and SGPB, the substrate with Leu at the reactive site is more than 25,000-fold more reactive than that with Asp. However, when fully protonated, Asp is nearly as good a substrate as Leu. The pK values of the side chains of Asp and Lys in the hydrophobic S1 pocket of CHYM and SGPB have been calculated from pH-dependent hydrolysis data and have been found to be about 9 for Asp and 7.4 and 9.7 for Lys for CHYM and SGPB, respectively. The results presented in this communication suggest a possible application of CHYM like enzymes in cleaving peptide bonds contributed by acidic amino acids between pH 5 and 6.

  20. The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions.

    Science.gov (United States)

    Hartmann, Tobias; Schrapers, Peer; Utesch, Tillmann; Nimtz, Manfred; Rippers, Yvonne; Dau, Holger; Mroginski, Maria Andrea; Haumann, Michael; Leimkühler, Silke

    2016-04-26

    Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal-containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pKa of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase. PMID:27054466

  1. Unusual C-C bond cleavage in the formation of amine-bis(phenoxy) group 4 benzyl complexes: Mechanism of formation and application to stereospecific polymerization

    KAUST Repository

    Gowda, Ravikumar R.

    2014-08-11

    Group 4 tetrabenzyl compounds MBn4 (M = Zr, Ti), upon protonolysis with an equimolar amount of the tetradentate amine-tris(phenol) ligand N[(2,4-tBu2C6H2(CH 2)OH]3 in toluene from -30 to 25 °C, unexpectedly lead to amine-bis(phenoxy) dibenzyl complexes, BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn2 (M = Zr (1), Ti (2)) in 80% (1) and 75% (2) yields. This reaction involves an apparent cleavage of the >NCH2-ArOH bond (loss of the phenol in the ligand) and formation of the >NCH 2-CH2Bn bond (gain of the benzyl group in the ligand). Structural characterization of 1 by X-ray diffraction analysis confirms that the complex formed is a bis(benzyl) complex of Zr coordinated by a newly derived tridentate amine-bis(phenoxy) ligand arranged in a mer configuration in the solid state. The abstractive activation of 1 and 2 with B(C6F 5)3·THF in CD2Cl2 at room temperature generates the corresponding benzyl cations {BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn(THF)}+[BnB(C6F5) 3]- (M = Zr (3), Ti, (4)). These cationic complexes, along with their analogues derived from (imino)phenoxy tri- and dibenzyl complexes, [(2,6-iPr2C6H3)N=C(3,5- tBu2C6H2)O]ZrBn3 (5) and [2,4-Br2C6H2(O)(6-CH2(NC 5H9))CH2N=CH(2-adamantyl-4-MeC 6H2O)]ZrBn2 (6), have been found to effectively polymerize the biomass-derived renewable β-methyl-α-methylene- γ-butyrolactone (βMMBL) at room temperature into the highly stereoregular polymer PβMMBL with an isotacticity up to 99% mm. A combined experimental and DFT study has yielded a mechanistic pathway for the observed unusual C-C bond cleavage in the present protonolysis reaction between ZrBn4 and N[(2,4-tBu2C 6H2(CH2)OH]3 for the formation of complex 1, which involves the benzyl radical and the Zr(III) species, resulting from thermal and photochemical decomposition of ZrBn4, followed by a series of reaction sequences consisting of protonolysis, tautomerization, H-transfer, oxidation, elimination, and radical coupling. © 2014 American Chemical Society.

  2. Aza-Quaternary Scaffolds from Selective Bond Cleavage of Bridgehead-Substituted 7-Azabicyclo[2.2.1]heptane: Total Synthesis of (+)-Cylindricines C-E and (-)-Lepadiformine A.

    Science.gov (United States)

    Pandey, Ganesh; Janakiram, Vaitla

    2015-09-01

    A novel bridgehead-substituted aza-bicyclic framework has been designed and developed in both enantiomeric forms through an asymmetric desymmetrization reaction. Strategic exploitation of the ring strain in the aza-bicyclic framework has been utilized for the construction of the chiral aza-quaterenary scaffolds by selective bond fragmentation processes. Furthermore, a strategically designed precursor is employed for selective bond cleavage to initiate a cascade rearrangement for the total synthesis of the 1-azaspirotricyclic marine alkaloids (+)-cylindricines C, D, and E, as well as (-)-lepadiformine A. An oxidation/retro-aldol/aza-Michael sequence generated three new chiral centers with the required configuration in one pot. PMID:26220441

  3. Formation of a dinuclear copper(II) complex through the cleavage of CN bond of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole

    International Nuclear Information System (INIS)

    A simple mononuclear octahedral copper(II) complex was attempted from the reaction of three moles of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole and one mole of copper(II) perchlorate hexahydrate in methanol. However, the product of the reaction was confirmed to be a dinuclear copper(II) complex with μ-(3-(pyridin-2-yl)-pyrazolato) and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the CbenzoylN bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the (3-(pyridin-2-yl)-pyrazolato)(3-(pyridin-2-yl)-1H-pyrazole)Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and β = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (ε = 116 dm3 mol−1 cm−1) supports the presence of Cu(II) centres

  4. A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex.

    Science.gov (United States)

    Borowski, Tomasz; Bassan, Arianna; Siegbahn, Per E M

    2004-05-17

    Density functional calculations using the B3LYP functional have been used to study the reaction mechanism of [Fe(Tp(Ph2))BF] (Tp(Ph2) = hydrotris(3,5-diphenylpyrazol-1-yl)borate; BF = benzoylformate) with dioxygen. This mononuclear non-heme iron(II) complex was recently synthesized, and it proved to be the first biomimetic complex reproducing the dioxygenase activity of alpha-ketoglutarate-dependent enzymes. Moreover, the enthalpy and entropy of activation for this biologically interesting process were derived from kinetic experiments offering a unique possibility for direct comparison of theoretical and experimental data. The results reported here support a mechanism in which oxidative decarboxylation of the keto acid is the rate-limiting step. This oxygen activation process proceeds on the septet potential energy surface through a transition state for a concerted O-O and C-C bond cleavage. In the next step, a high-valent iron-oxo species performs electrophilic attack on the phenyl ring of the Tp(Ph2) ligand leading to an iron(III)-radical sigma-complex. Subsequent proton-coupled electron-transfer yields an iron(II)-phenol intermediate, which can bind dioxygen and reduce it to a superoxide radical. Finally, the protonated superoxide radical leaves the first coordination sphere of the iron(III)-phenolate complex and dismutates to dioxygen and hydrogen peroxide. The calculated activation barrier (enthalpy and entropy) and the overall reaction energy profile agree well with experimental data. A comparison to the enzymatic process, which is suggested to occur on the quintet surface, has been made. PMID:15132638

  5. Recent Progress in the Research of Transition-Metal-Catalyzed C-CN Bond Cleavage%过渡金属催化的C—CN键断裂的研究进展

    Institute of Scientific and Technical Information of China (English)

    寇学振; 范佳骏; 童晓峰; 沈增明

    2013-01-01

    有机氰化物是一种重要的合成中间体,在药物、农药、染料和活性物质中都有应用.使用廉价、简单、低毒的氰基化合物在过渡金属的催化下通过C-CN键断裂生成复杂的氰化物是合成有机氰化物的重要手段之一.综述了不同过渡金属(如Ni,Pd,Rh,Cu,Ru,Fe,Mo,Co等)催化不同种类的氰基化合物C-CN键断裂的最新研究进展,如含C(sp1)-CN键化合物、C(sp2)-CN键化合物以及C(sp3)-CN键化合物,并对有关的反应机理及C-CN键断裂机理的进展进行了探讨.%Nitriles are an important class of organic compounds which can be found in pharmaceuticals,agrochemicals,dyes,and bioactive compounds.Transition-metal-catalyzed C-CN bond cleavage using inexpensive,simple and less toxic nitriles is one of the most attractive modem methods for the synthesis of complicated organic cyanides.Research progress of transition-metal-catalyzed (Ni,Pd,Rh,Cu,Ru,Fe,Mo,Co) different types of C-CN bond cleavage is reviewed,which includes some organic cyanides containing C(sp1)—CN bond,C(sp2)—CN bond and C(sp3)—CN bond.The C-CN cleavage mechanisms are also discussed in this review.

  6. Formation of a dinuclear copper(II) complex through the cleavage of CBond' name='Single-Bond' value='Single-Bond'/>N bond of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole

    Energy Technology Data Exchange (ETDEWEB)

    Shardin, Rosidah; Pui, Law Kung; Yamin, Bohari M. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia); Kassim, Mohammad B. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor, Malaysia and Fuel Cell Institute, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia)

    2014-09-03

    A simple mononuclear octahedral copper(II) complex was attempted from the reaction of three moles of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole and one mole of copper(II) perchlorate hexahydrate in methanol. However, the product of the reaction was confirmed to be a dinuclear copper(II) complex with μ-(3-(pyridin-2-yl)-pyrazolato) and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the C{sub benzoyl}Bond' name='Single-Bond' value='Single-Bond'/>N bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the (3-(pyridin-2-yl)-pyrazolato)(3-(pyridin-2-yl)-1H-pyrazole)Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and β = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (ε = 116 dm{sup 3} mol{sup −1} cm{sup −1}) supports the presence of Cu(II) centres.

  7. A Carbon-Sulfur Hybrid with Pomegranate-like Structure for Lithium-Sulfur Batteries.

    Science.gov (United States)

    Shi, Yanting; Lv, Wei; Niu, Shuzhang; He, Yanbing; Zhou, Guangmin; Chen, Guohua; Li, Baohua; Yang, Quan-Hong; Kang, Feiyu

    2016-05-01

    A carbon-sulfur hybrid with pomegranate-like core-shell structure, which demonstrates a high rate performance and relatively high cyclic stability, is obtained through carbonization of a carbon precursor in the presence of a sulfur precursor (FeS2 ) and a following oxidation of FeS2 to sulfur by HNO3 . Such a structure effectively protects the sulfur and leaves enough buffer space after Fe(3+) removal and, at the same time, has an interconnected conductive network. The capacity of the obtained hybrid is 450 mA h g(-1) under the current density of 5 C. This work provides a simple strategy to design and prepare various high-performance carbon-sulfur hybrids for lithium-sulfur batteries. PMID:26918663

  8. Diversification of ortho-Fused Cycloocta-2,5-dien-1-one Cores and Eight- to Six-Ring Conversion by σ Bond C-C Cleavage.

    Science.gov (United States)

    Eccleshare, Lee; Lozada-Rodríguez, Leticia; Cooper, Phillippa; Burroughs, Laurence; Ritchie, John; Lewis, William; Woodward, Simon

    2016-08-22

    Sequential treatment of 2-C6 H4 Br(CHO) with LiC≡CR(1) (R(1) =SiMe3 , tBu), nBuLi, CuBr⋅SMe2 and HC≡CCHClR(2) [R(2) =Ph, 4-CF3 Ph, 3-CNPh, 4-(MeO2 C)Ph] at -50 °C leads to formation of an intermediate carbanion (Z)-1,2-C6 H4 {CA (=O)C≡CB R(1) }{CH=CH(CH(-) )R(2) } (4). Low temperatures (-50 °C) favour attack at CB leading to kinetic formation of 6,8-bicycles containing non-classical C-carbanion enolates (5). Higher temperatures (-10 °C to ambient) and electron-deficient R(2) favour retro σ-bond C-C cleavage regenerating 4, which subsequently closes on CA providing 6,6-bicyclic alkoxides (6). Computational modelling (CBS-QB3) indicated that both pathways are viable and of similar energies. Reaction of 6 with H(+) gave 1,2-dihydronaphthalen-1-ols, or under dehydrating conditions, 2-aryl-1-alkynylnaphthlenes. Enolates 5 react in situ with: H2 O, D2 O, I2 , allylbromide, S2 Me2 , CO2 and lead to the expected C-E derivatives (E=H, D, I, allyl, SMe, CO2 H) in 49-64 % yield directly from intermediate 5. The parents (E=H; R(1) =SiMe3 , tBu; R(2) =Ph) are versatile starting materials for NaBH4 and Grignard C=O additions, desilylation (when R(1) =SiMe) and oxime formation. The latter allows formation of 6,9-bicyclics via Beckmann rearrangement. The 6,8-ring iodides are suitable Suzuki precursors for Pd-catalysed C-C coupling (81-87 %), whereas the carboxylic acids readily form amides under T3P® conditions (71-95 %). PMID:27452351

  9. Efficient and facile Ar-Si bond cleavage by montmorillonite KSF: synthetic and mechanistic aspects of solvent-free protodesilylation studied by solution and solid-state MAS NMR.

    Science.gov (United States)

    Zafrani, Yossi; Gershonov, Eytan; Columbus, Ishay

    2007-08-31

    A facile and efficient method for the cleavage of the Ar-Si bond of various aryl trimethyl silanes is described. When adsorbed on montmorillonite KSF (mont KSF), these arylsilanes readily undergo a solvent-free protodesilylation to the corresponding arenes at room temperature in excellent yields. This approach seems to be superior to the traditional mild methods (i.e., desilylation by TFA, TBAF, CsF), in terms of reaction yield, rate, and environmentally benign conditions. Some mechanistic studies using both solution and solid-state magic-angle spinning (SS MAS) (1)H NMR are also presented. PMID:17676903

  10. 硅胶担载的高锰酸钾对烯烃碳碳双键的氧化%Carbon-Carbon Double Bond Cleavage by Silica-supported Potassium Permanganate under Conditions Free of Organic Solvent

    Institute of Scientific and Technical Information of China (English)

    王文军; 戴乾圜

    2002-01-01

    An improved simple method for carbon-carbon double bond cleavage by silica-supported potassium permanganate was described and a possible mechanism was proposed.%在无有机溶剂做介质的条件下,用硅胶吸附的高锰酸钾氧化6种难溶于水的液态烯烃,得到了双键发生断裂的氧化产物.该反应操作简便,反应快,收率好.此外,对硅胶的活化作用机制进行了浅析.

  11. Leukemogenic membrane glycoprotein encoded by Friend spleen focus-forming virus: Transport to cell surfaces and shedding are controlled by disulfide-bonded dimerization and by cleavage of a hydrophobic membrane anchor

    International Nuclear Information System (INIS)

    The leukemogenic glycoprotein (gp55) encoded by Friend spleen focus-forming virus is predominantly retained in the rough endoplasmic reticulum (RER). However, a small proportion (ca. 5%) is processed to form a derivative that occurs on plasma membranes and causes mitosis of infected erythroblasts. The authors have now found that gp55 folds heterogeneously in the RER to form components with different disulfide bonds and that this difference may determine their processing fates. RER gp55 consists predominantly of monomers with intrachain disulfide bonds. In contrast, the processed molecules are disulfide-bonded dimers. These dimers are extensively modified in transit to cell surfaces by conversion of four N-linked high-mannose oligosaccharides to complex derivatives and by attachment of a sialylated O-linked oligosaccharide. The plasma membrane dimers are then slowly shed into the medium by a mechanism that involves proteolytic cleavage of approximately 25 membrane-anchoring hydrophobic amino acids from the carboxyl termini of the glycoproteins. Consequently, shed molecules have shorter polypeptide chains than cell-associated gp55. They conclude that gp55 folds into different disulfide-bonded components that do not substantially isomerize, and that only one specific dimer is competent for export from the RER. Mitogenic activity of gp55 could be caused by the cell surface dimers, by the shed derivative, or by the carboxyl-terminal hydrophobic anchors that remain in the membranes after the shedding reaction

  12. Characterization of carbon, sulfur and volatile compounds in nuclear fuel U3SI2-AL

    International Nuclear Information System (INIS)

    The scope of this work is to describe the characterization of Carbon, Sulfur and Volatile Compounds in nuclear fuel U3Si2-Al used in a research pool type reactor with 5 KW power capacities, located in Sao Paulo, Brazil. This reactor produces a large range of radioisotopes for radiopharmaceutical needed in Brazil nuclear medicine. The fabrication of the fuel U3Si2-Al plate is the key of the whole assembly production and its quality directly affects the safety and reliability of the fuel assembly performance. For this reason, it is very necessary to analyze the Carbon, Sulfur and Volatile Compounds to avoid damage in the fuel plate. The Carbon and Sulfur are characterized by the method of radio frequency furnace gas extraction system coupled with infrared cell detector. The Volatile Compounds are characterized by the method of heat gas extraction coupled with gravimetric technique. These methods are recommended by American Society for Testing Materials ASTM for nuclear materials. The average carbon and sulfur analyzed are 30 μg/g and 3 μg/g, respectively. The average for Volatile Compounds is 40 μg/g. These results represent satisfactory performance of the fuel inside the nuclear reactor. A statistical laboratory program has been set to validate the data generated in the nuclear fuel material to specify any agreement with the recommended ASTM methods. (author)

  13. PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond

    DEFF Research Database (Denmark)

    McSorley, Fern R.; Wyatt, Peter W.; Martinez, Ascuncion;

    2012-01-01

    The sequential activities of PhnY, an α-ketoglutarate/Fe(II)-dependent dioxygenase, and PhnZ, a Fe(II)-dependent enzyme of the histidine-aspartate motif hydrolase family, cleave the carbon-phosphorus bond of the organophosphonate natural product 2-aminoethylphosphonic acid. PhnY adds a hydroxyl...

  14. Applications of bis(1-R-imidazol-2-yl)disulfides and diselenides as ligands for main-group and transition metals: kappa2-(N,N) coordination, S-S bond cleavage, and S-S/E-E (E = S, Se) bond metathesis reactions.

    Science.gov (United States)

    Figueroa, Joshua S; Yurkerwich, Kevin; Melnick, Jonathan; Buccella, Daniela; Parkin, Gerard

    2007-10-29

    Bis(1-R-imidazol-2-yl)disulfides, (mim(R))2 (R = Ph, Bu(t)), and diselenides, (seim(Mes))2, serve as bidentate N,N-donor ligands for main-group and transition metals. For example, [kappa2-(mim(Bu)(t))2]MCl2 (M = Fe, Co, Ni, Zn), [kappa2-(mim(Ph))2]MCl2 (M = Co, Zn), [kappa2-(mim(Bu)(t))2]CuX (X = Cl, I), and [kappa2-(seim(Mes))2]MCl2 (M = Fe, Co, Ni) are obtained by treatment of (mim(Bu)(t))2 or (seim(Mes))2 with the respective metal halide and have been structurally characterized by X-ray diffraction. On the other hand, the zerovalent nickel complex Ni(PMe3)4 effects cleavage of the disulfide bond of (mim(Bu)(t))2 to give square-planar trans-Ni(PMe3)2(mim(Bu)(t))2 in which the (mim(Bu)(t)) ligands coordinate via nitrogen rather than sulfur, a most uncommon coordination mode for this class of ligands. Although [kappa2-(mim(R))2]MCl2 (M = Fe, Co, Ni, Zn) are not subject to homolytic cleavage of the S-S bond because the tetravalent state is not readily accessible, the observation that [kappa2-(mimPh)2]CoCl2 and [kappa2-(mim(Bu)(t))2]CoCl2 form an equilibrium mixture with the asymmetric disulfide [kappa2-(mim(Ph))(mim(Bu)(t))]CoCl2 indicates that S-S bond cleavage via another mechanism is possible. Likewise, metathesis between disulfide and diselenide ligands is observed in the formation of [kappa2-(mim(Bu)(t))(seim(Mes))]CoCl2 upon treatment of [kappa2-(mim(Bu)(t))2]CoCl2 with [kappa2-(seim(Mes))2]CoCl2. PMID:17900186

  15. Applications of Bis(1-R-imidazol-2-yl)disulfides and Diselenides as Ligands for Main Group and Transition Metals: κ2-[N,N] Coordination, S-S Bond Cleavage and S-S/E-E (E = S, Se) Bond Metathesis Reactions

    Science.gov (United States)

    Figueroa, Joshua S.; Yurkerwich, Kevin; Melnick, Jonathan; Buccella, Daniela; Parkin, Gerard

    2008-01-01

    Bis(1-R-imidazol-2-yl)disulfides, (mimR)2 (R = Ph, But), and diselenides, (seimMes)2, serve as bidentate [N,N]-donor ligands for main group and transition metals. For example, [κ2-(mimBut)2]MCl2 (M = Fe, Co, Ni, Zn), [κ2-(mimPh)2]MCl2 (M = Co, Zn), [κ2-(mimBut)2]CuX (X = Cl, I) and [κ2-(seimMes)2]MCl2 (M = Fe, Co, Ni) are obtained by treatment of (mimBut)2 or (seimMes)2 with the respective metal halide, and have been structurally characterized by X-ray diffraction. On the other hand, the zerovalent nickel complex Ni(PMe3)4 effects cleavage of the disulfide bond of (mimBut)2 to give square planar trans-Ni(PMe3)2(mimBut)2 in which the (mimBut) ligands coordinate via nitrogen rather than sulfur, a most uncommon coordination mode for this class of ligands. Although [κ2-(mimR)2]MCl2 (M = Fe, Co, Ni, Zn) are not subject to homolytic cleavage of the S-S bond because the tetravalent state is not readily accessible, the observation that [κ2-(mimPh)2]CoCl2 and [κ2-(mimBut)2]CoCl2 form an equilibrium mixture with the asymmetric disulfide [κ2-(mimPh)(mimBut)]CoCl2 indicates that S-S bond cleavage via another mechanism is possible. Likewise, metathesis between disulfide and diselenide ligands is observed in the formation of [κ2-(mimBut)(seimMes)]CoCl2 upon treatment of [κ2-(mimBut)2]CoCl2 with [κ2-(seimMes)2]CoCl2. PMID:17900186

  16. Hydrodenitrogenation chemistry. I. Cleavage of alkylcarbon-nitrogen bonds, methane and ammonia formation in the HDN reaction of 1,2,3,4-tetrahydroquinoline with a nickel oxide catalyst supported on silica/alumina

    Energy Technology Data Exchange (ETDEWEB)

    Fish, R.H.; Thormodsen, A.D.; Moore, R.S.; Perry, D.L.; Heinemann, H.

    1986-11-01

    The hydrodenitrogenation reaction (HDN) is one of the most important industrial processes used in the refining of petroleum feedstocks and involves the removal of the nitrogen atom, as ammonia, from polynuclear heteroaromatic nitrogen compounds at high temperatures and high pressures of hydrogen gas (350-500/sup 0/C and 2000 psi). It is interesting to note that most of the reported heterogeneous catalysts require the complete hydrogenation of both the nitrogen heterocyclic ring and the aromatic ring before carbon-nitrogen bond cleavage can occur. A major breakthrough in the technical and economic aspects of the HDN reaction would take place if, in fact a catalyst could be found that would selectively cleave the C-N bond din the saturated nitrogen ring and subsequently produce ammonia, without substantial reduction of the aromatic rings, at lower temperatures as well as lower pressures of hydrogen gas. In this note, the authors report on a highly loaded nickel oxide catalyst (50% by weight Ni), supported on silica/alumina, that will effectively provide some of the criteria for an ideal HDN catalyst. 8 references.

  17. Ordered mesoporous carbon/sulfur nanocomposite of high performances as cathode for lithium-sulfur battery

    Energy Technology Data Exchange (ETDEWEB)

    Chen Shuru [State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, School of Energy Research, Xiamen University, Xiamen 361005 (China); Zhai Yunpu [Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, and Advanced Materials Laboratory, Fudan University, Shanghai 200433 (China); Xu Guiliang; Jiang Yanxia [State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, School of Energy Research, Xiamen University, Xiamen 361005 (China); Zhao Dongyuan, E-mail: dyzhao@fudan.edu.cn [Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, and Advanced Materials Laboratory, Fudan University, Shanghai 200433 (China); Li Juntao; Huang Ling [State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, School of Energy Research, Xiamen University, Xiamen 361005 (China); Sun Shigang, E-mail: sgsun@xmu.edu.cn [State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, School of Energy Research, Xiamen University, Xiamen 361005 (China)

    2011-11-01

    Ordered mesoporous carbon/sulfur (OMC/S) nanocomposites with hierarchically structured sulfur loading, ranging from 50 to 75 wt%, were synthesized via a simple melt-diffusion strategy. The OMC with a BET surface area of 2102 m{sup 2} g{sup -1}, a pore volume of 2.0 cm{sup 3} g{sup -1} and unique bimodal mesoporous (5.6/2.3 nm) structure, was prepared from a triconstituent co-assembly method. The resulting OMC/S nanocomposite material served as cathode of rechargeable lithium-sulfur (Li-S) battery. It has been tested that the novel OMC/S cathode can deliver a superior reversible capacity and cyclability. In particular, the nanocomposite with a loading of 60 wt% sulfur (OMC/S-60) presents the highest sulfur utilization ca. 70%, an excellent high rate capability ca. 6 C and a good cycling stability for up to 400 full charge-discharge cycles. The exceptional electrochemical performances are exclusively attributed to the large internal surface area and high porosity of the ordered mesoporous carbon, which favorites both electron and Li-ion transportations.

  18. Temperature dependent structural variation from 2D supramolecular network to 3D interpenetrated metal–organic framework: In situ cleavage of S–S and C–S bonds

    Energy Technology Data Exchange (ETDEWEB)

    Ugale, Bharat; Singh, Divyendu; Nagaraja, C.M., E-mail: cmnraja@iitrpr.ac.in

    2015-03-15

    Two new Zn(II)–organic compounds, [Zn(muco)(dbds){sub 2}(H{sub 2}O){sub 2}] (1) and [Zn(muco)(dbs)] (2) (where, muco=trans, trans-muconate dianion, dbds=4,4′-dipyridyldisulfide and dbs=4,4′-dipyridylsulfide) have been synthesized from same precursors but at two different temperatures. Both the compounds have been characterized by single-crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, IR spectroscopy, thermal analysis and photoluminescence studies. Compound 1 prepared at room temperature possesses a molecular structure extended to 2D supramolecular network through (H–O…H) hydrogen-bonding interactions. Compound 2, obtained at high temperature (100 °C) shows a 3-fold interpenetrating 3D framework constituted by an in situ generated dbs linker by the cleavage of S–S and C–S bonds of dbds linker. Thus, the influence of reaction temperature on the formation of two structural phases has been demonstrated. Both 1 and 2 exhibit ligand based luminescence emission owing to n→π⁎ and π→π⁎ transitions and also high thermal stabilities. - Graphical abstract: The influence of temperature on the formation of two structural phases, a 2D supramolecular network and a 3D 3-fold interpenetrating framework has been demonstrated and their luminescence emission is measured. - Highlights: • Two new Zn(II)–organic compounds were synthesized by tuning reaction temperatures. • Temperature induced in situ generation of dbs linker has been observed. • The compounds exhibit high thermal stability and luminescence emission properties. • The effect of temperature on structure, dimension and topology has been presented.

  19. Temperature dependent structural variation from 2D supramolecular network to 3D interpenetrated metal–organic framework: In situ cleavage of S–S and C–S bonds

    International Nuclear Information System (INIS)

    Two new Zn(II)–organic compounds, [Zn(muco)(dbds)2(H2O)2] (1) and [Zn(muco)(dbs)] (2) (where, muco=trans, trans-muconate dianion, dbds=4,4′-dipyridyldisulfide and dbs=4,4′-dipyridylsulfide) have been synthesized from same precursors but at two different temperatures. Both the compounds have been characterized by single-crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, IR spectroscopy, thermal analysis and photoluminescence studies. Compound 1 prepared at room temperature possesses a molecular structure extended to 2D supramolecular network through (H–O…H) hydrogen-bonding interactions. Compound 2, obtained at high temperature (100 °C) shows a 3-fold interpenetrating 3D framework constituted by an in situ generated dbs linker by the cleavage of S–S and C–S bonds of dbds linker. Thus, the influence of reaction temperature on the formation of two structural phases has been demonstrated. Both 1 and 2 exhibit ligand based luminescence emission owing to n→π⁎ and π→π⁎ transitions and also high thermal stabilities. - Graphical abstract: The influence of temperature on the formation of two structural phases, a 2D supramolecular network and a 3D 3-fold interpenetrating framework has been demonstrated and their luminescence emission is measured. - Highlights: • Two new Zn(II)–organic compounds were synthesized by tuning reaction temperatures. • Temperature induced in situ generation of dbs linker has been observed. • The compounds exhibit high thermal stability and luminescence emission properties. • The effect of temperature on structure, dimension and topology has been presented

  20. Synthesis and characterization of ethylbis(2-pyridylethyl)amineruthenium complexes and two different types of C-H bond cleavage at an ethylene arm.

    Science.gov (United States)

    Fukui, Sohei; Kajihara, Akari; Hirano, Toshiyuki; Sato, Fumitoshi; Suzuki, Noriyuki; Nagao, Hirotaka

    2011-06-01

    Ruthenium complexes bearing ethylbis(2-pyridylethyl)amine (ebpea), which has flexible -C(2)H(4)- arms between the amine and the pyridyl groups and coordinates to a metal center in facial and meridional modes, have been synthesized and characterized. Three trichloro complexes, fac-[Ru(III)Cl(3)(ebpea)] (fac-[1]), mer-[Ru(III)Cl(3)(ebpea)] (mer-[1]), and mer-[Ru(II)Cl(3){η(2)-N(C(2)H(5))(C(2)H(4)py)═CH-CH(2)py}] (mer-[2]), were synthesized using the Ru blue solution. Formation of mer-[2] proceeded via a C-H activation of the CH(2) group next to the amine nitrogen atom of the ethylene arm. Reduction reactions of fac- and mer-[1] afforded a triacetonitrile complex mer-[Ru(II)(CH(3)CN)(3)(ebpea)](PF(6))(2) (mer-[3](PF(6))(2)). Five nitrosyl complexes fac-[RuX(2)(NO)(ebpea)]PF(6) (X = Cl for fac-[4]PF(6); X = ONO(2) for fac-[5]PF(6)) and mer-[RuXY(NO)(ebpea)]PF(6) (X = Cl, Y = Cl for mer-[4]PF(6); X = Cl, Y = CH(3)O for mer-[6]PF(6); X = Cl, Y = OH for mer-[7]PF(6)) were synthesized and characterized by X-ray crystallography. A reaction of mer-[2] in H(2)O-C(2)H(5)OH at room temperature afforded mer-[1]. Oxidation of C(2)H(5)OH in H(2)O-C(2)H(5)OH and i-C(3)H(7)OH in H(2)O-i-C(3)H(7)OH to acetaldehyde and acetone by mer-[2] under stirring at room temperature occurred with formation of mer-[1]. Alternative C-H activation of the CH(2) group occurred next to the pyridyl group, and formation of a C-N bond between the CH moiety and the nitrosyl ligand afforded a nitroso complex [Ru(II)(N(3))(2){N(O)CH(py)CH(2)N(C(2)H(5))C(2)H(4)py}] ([8]) in reactions of nitrosyl complexes with sodium azide in methanol, and reaction of [8] with hydrochloric acid afforded a corresponding chloronitroso complex [Ru(II)Cl(2){N(O)CH(py)CH(2)N(C(2)H(5))C(2)H(4)py}] ([9]). PMID:21517051

  1. Si(111) cleavage and the (2 x 1) reconstruction process

    Science.gov (United States)

    Pearson, E. M.; Halicioglu, T.; Tiller, W. A.

    1987-01-01

    Using a computer simulation technique with a semiempirical potential, a Si crystal was cleaved along the (111) plane. The pi-bonded chain structural features of the Si(111) cleavage surface are observed and found to be a consequence of the dynamics of this cleavage process and seem not to be influenced by the final energetics.

  2. Aspergillus flavus Conidia-derived Carbon/Sulfur Composite as a Cathode Material for High Performance Lithium–Sulfur Battery

    OpenAIRE

    Maowen Xu; Min Jia; Cuiping Mao; Sangui Liu; Shujuan Bao; Jian Jiang; Yang Liu; Zhisong Lu

    2016-01-01

    A novel approach was developed to prepare porous carbon materials with an extremely high surface area of 2459.6 m2g−1 by using Aspergillus flavus conidia as precursors. The porous carbon serves as a superior cathode material to anchor sulfur due to its uniform and tortuous morphology, enabling high capacity and good cycle lifetime in lithium sulfur-batteries. Under a current rate of 0.2 C, the carbon-sulfur composites with 56.7 wt% sulfur loading deliver an initial capacity of 1625 mAh g−1, w...

  3. Chemical bond cleavage induced by electron heating

    International Nuclear Information System (INIS)

    Gas emissions from titanium-metalloid compounds (titanium nitride and oxide) have been investigated to understand the effects of a microwave field on chemical reactions. We employed a high vacuum system (PO2 = 10−6 Pa) to observe in situ reductions. For titanium oxides, H-field heating significantly differed from conventional one in terms of oxygen emissions. For titanium nitride, the emissions were also induced by microwave heating. These tendencies were observed at temperatures above 1000 °C. A quantum chemical interpretation is provided to explain the emissions of the gases, and the experimental data is in good agreement with results predicted using the electronic energy band structure.

  4. Cleavage of nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor L. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2007-12-11

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  5. Cleavage of nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Waunakee, WI); Lyamichev, Victor I. (Madison, WI); Brow; Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2010-11-09

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  6. Cleavage of nucleic acids

    Science.gov (United States)

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    2000-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  7. A study on hydrogen, oxygen, carbon, sulfur and lead isotopes in the rich uranium deposit No.201

    International Nuclear Information System (INIS)

    The uranium deposit No.201 located in Indonesian granite is one of the richest uranium deposits of granite type in China. An attempt is made to investigate the sources of ore-forming solutions and ore-forming materials, and to presume the environment of ore formation in the light of the study on composition of stable isotopes such as hydrogen, oxygen, carbon, sulfur and lead. The research results indicate that the ore-forming fluids in the deposit is mainly composed of meteoric water, the ore-forming materials principally came from pre-Yanshanian granite Massif and possibly, partly from the lower crust, and metallogenesis was undertaken under relatively stable physicochemical conditions

  8. Doped carbon-sulfur species nanocomposite cathode for Li--S batteries

    Science.gov (United States)

    Wang, Donghai; Xu, Tianren; Song, Jiangxuan

    2015-12-29

    We report a heteroatom-doped carbon framework that acts both as conductive network and polysulfide immobilizer for lithium-sulfur cathodes. The doped carbon forms chemical bonding with elemental sulfur and/or sulfur compound. This can significantly inhibit the diffusion of lithium polysulfides in the electrolyte, leading to high capacity retention and high coulombic efficiency.

  9. Photochemical Degradation of Lignin through αC—O Bond Cleavage of Non Phenolic Benzyl Aryl Ether Units. A Study of the Photochemistry of a(2',4',6'-Trimethyl-Phenoxy)-3,4 Dimethoxy Toluene

    International Nuclear Information System (INIS)

    The results of this study show that, even in the case of a complete chemical group protection (phenolic groups as aliphatic ethers, carbonyl groups reduced to CH2), the UV part of the sunlight near 300 nm can initiate a benzylic cleavage responsible for a subsequent yellowing of the lignin materials

  10. Photocatalytic splitting of CS2 to S8 and a carbon-sulfur polymer catalyzed by a bimetallic ruthenium(II) compound with a tertiary amine binding site: toward photocatalytic splitting of CO2?

    Science.gov (United States)

    Livanov, Konstantin; Madhu, Vedichi; Balaraman, Ekambaram; Shimon, Linda J W; Diskin-Posner, Yael; Neumann, Ronny

    2011-11-21

    The catalytic photocleavage of CS(2) to S(8) and a (C(x)S(y))(n) polymer with visible light using a dinuclear ruthenium(II) compound with a bipyridine units for photoactivity and a vicinal tertiary amine binding site for CS(2) activation was studied. The catalyst was characterized by X-ray diffraction, (1)H NMR, and (13)C NMR, ESI-MS and elemental analysis. CS(2) photocleavage was significant (240 turnovers, 20 h) to yield isolable S(8) and a (C(x)S(y))(n) polymer. A mononuclear catalyst or one without an amine binding site showed significantly less activity. XPS of the (C(x)S(y))(n) polymer showed a carbon/sulfur ratio ∼1.5-1.6 indicating that in part both C-S bonds of CS(2) had been cleaved. Catalyst was also included within the polymer. The absence of peaks in the (1)H NMR verified the (C(x)S(y))(n) nature of the polymer, while (13)C NMR and IR indicated that the polymer had multiple types of C-S and C-C bonds. PMID:22029376

  11. Ratcheting of the substrate from the zymogen to proteinase conformations directs the sequential cleavage of prothrombin by prothrombinase

    OpenAIRE

    Bianchini, Elsa P.; Orcutt, Steven J.; Panizzi, Peter; Bock, Paul E.; Krishnaswamy, Sriram

    2005-01-01

    Prothrombinase catalyzes thrombin formation by the ordered cleavage of two peptide bonds in prothrombin. Although these bonds are likely ≈36 Å apart, sequential cleavage of prothrombin at Arg-320 to produce meizothrombin, followed by its cleavage at Arg-271, are both accomplished by equivalent exosite interactions that tether each substrate to the enzyme and facilitate presentation of the scissile bond to the active site of the catalyst. We show that impairing the conformational transition fr...

  12. Selective cleavage of pepsin by molybdenum metallopeptidase

    Energy Technology Data Exchange (ETDEWEB)

    Yenjai, Sudarat; Malaikaew, Pinpinat; Liwporncharoenvong, Teerayuth [Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110 (Thailand); Buranaprapuk, Apinya, E-mail: apinyac@swu.ac.th [Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110 (Thailand)

    2012-03-02

    Graphical abstract: Molybdenum metallopeptidase: the Mo(VI) cluster with six molybdenum cations has the ability to cleave protein under mild conditions (37 Degree-Sign C, pH 7) without reducing agents. The reaction required only low concentration of ammonium heptamolybdatetetrahydrate ((NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}{center_dot}4H{sub 2}O) (0.125 mM). The reaction undergoes possibly via a hydrolytic mechanism. This is the first demonstration of protein cleavage by a molybdenum cluster. Highlights: Black-Right-Pointing-Pointer This is the first demonstration of protein cleavage by a Mo(VI) cluster with six molybdenum cations. Black-Right-Pointing-Pointer The cleavage reaction undergoes at mild conditions. Black-Right-Pointing-Pointer No need of reducing agents. Black-Right-Pointing-Pointer Only low concentration of Mo(VI) cluster and short time of incubation are needed. -- Abstract: In this study, the cleavage of protein by molybdenum cluster is reported for the first time. The protein target used is porcine pepsin. The data presented in this study show that pepsin is cleaved to at least three fragments with molecular weights of {approx}23, {approx}19 and {approx}16 kDa when the mixture of the protein and ammonium heptamolybdate tetrahydrate ((NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}{center_dot}4H{sub 2}O) was incubated at 37 Degree-Sign C for 24 h. No self cleavage of pepsin occurs at 37 Degree-Sign C, 24 h indicating that the reaction is mediated by the metal ions. N-terminal sequencing of the peptide fragments indicated three cleavage sites of pepsin between Leu 112-Tyr 113, Leu 166-Leu 167 and Leu 178-Asn 179. The cleavage reaction occurs after incubation of the mixture of pepsin and (NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}{center_dot}4H{sub 2}O) only for 2 h. However, the specificity of the cleavage decreases when incubation time is longer than 48 h. The mechanism for cleavage of pepsin is expected to be hydrolytic chemistry of the amide bonds in the protein

  13. Selective cleavage of pepsin by molybdenum metallopeptidase

    International Nuclear Information System (INIS)

    Graphical abstract: Molybdenum metallopeptidase: the Mo(VI) cluster with six molybdenum cations has the ability to cleave protein under mild conditions (37 °C, pH 7) without reducing agents. The reaction required only low concentration of ammonium heptamolybdatetetrahydrate ((NH4)6Mo7O24·4H2O) (0.125 mM). The reaction undergoes possibly via a hydrolytic mechanism. This is the first demonstration of protein cleavage by a molybdenum cluster. Highlights: ► This is the first demonstration of protein cleavage by a Mo(VI) cluster with six molybdenum cations. ► The cleavage reaction undergoes at mild conditions. ► No need of reducing agents. ► Only low concentration of Mo(VI) cluster and short time of incubation are needed. -- Abstract: In this study, the cleavage of protein by molybdenum cluster is reported for the first time. The protein target used is porcine pepsin. The data presented in this study show that pepsin is cleaved to at least three fragments with molecular weights of ∼23, ∼19 and ∼16 kDa when the mixture of the protein and ammonium heptamolybdate tetrahydrate ((NH4)6Mo7O24·4H2O) was incubated at 37 °C for 24 h. No self cleavage of pepsin occurs at 37 °C, 24 h indicating that the reaction is mediated by the metal ions. N-terminal sequencing of the peptide fragments indicated three cleavage sites of pepsin between Leu 112-Tyr 113, Leu 166-Leu 167 and Leu 178-Asn 179. The cleavage reaction occurs after incubation of the mixture of pepsin and (NH4)6Mo7O24·4H2O) only for 2 h. However, the specificity of the cleavage decreases when incubation time is longer than 48 h. The mechanism for cleavage of pepsin is expected to be hydrolytic chemistry of the amide bonds in the protein backbone.

  14. The First Example of Cation Radical Induced Ether Cleavage of Benzyl Phenyl Ether

    International Nuclear Information System (INIS)

    A thermally stable benzyl phenyl ether has been shown to cleavage under mild conditions. The new reaction described herein further expands the chemistry of the ether cleavage by cation radicals. Over the last several years, our lab has discovered cation radical-induced oxidative C-O bond cleavages such as carbonates (eq 1), carbamates (eq 2), peroxides (eq 3), and alcohols (eq 4), where R is either tert-butyl or benzyl. It was recognized from those reactions that carbocationic chemistry with C-O bond cleavages was predominant, with a 2:1 stoichiometry of Th+·:oxidized molecules

  15. Aspergillus flavus Conidia-derived Carbon/Sulfur Composite as a Cathode Material for High Performance Lithium-Sulfur Battery

    Science.gov (United States)

    Xu, Maowen; Jia, Min; Mao, Cuiping; Liu, Sangui; Bao, Shujuan; Jiang, Jian; Liu, Yang; Lu, Zhisong

    2016-01-01

    A novel approach was developed to prepare porous carbon materials with an extremely high surface area of 2459.6 m2g-1 by using Aspergillus flavus conidia as precursors. The porous carbon serves as a superior cathode material to anchor sulfur due to its uniform and tortuous morphology, enabling high capacity and good cycle lifetime in lithium sulfur-batteries. Under a current rate of 0.2 C, the carbon-sulfur composites with 56.7 wt% sulfur loading deliver an initial capacity of 1625 mAh g-1, which is almost equal to the theoretical capacity of sulfur. The good performance may be ascribed to excellent electronic networks constructed by the high-surface-area carbon species. Moreover, the semi-closed architecture of derived carbons can effectively retard the polysulfides dissolution during charge/discharge, resulting in a capacity of 940 mAh g-1 after 120 charge/discharge cycles.

  16. A Size-Dependent Thermodynamic Model for Coke Crystallites: The Carbon-Sulfur System Up to 2500 K (2227 °C)

    Science.gov (United States)

    Ouzilleau, Philippe; Gheribi, Aïmen E.; Lindberg, Daniel K.; Chartrand, Patrice

    2016-06-01

    A model is presented for the development of the thermodynamic functions of enthalpy, entropy, and Gibbs energy for the elements carbon and sulfur in coke crystallites. The crystallites of various degrees of graphitization may be described by crystallite length L a and crystallite height L c. This carbon/sulfur model has been developed using concepts similar to those in the carbon/hydrogen model for coke crystallites. The major model parameters are derived from reported thermodynamic properties. Approximately 75 pct of the model parameters for the carbon/hydrogen and carbon/sulfur system are parameters common to both systems. The resulting crystallite size ( L a) constrained in the carbon/sulfur phase diagram, computed by a Gibbs energy minimization technique, is presented for 1 atm and temperatures between 1500 K and 2500 K (1227 °C and 2227 °C). A very good agreement is obtained between the predicted thermal desulfurization of petroleum cokes and critically assessed experimental data. The removal of sulfur from coke crystallites is predicted to occur mostly between 1600 K and 1850 K (1327 °C and 1577 °C) at 1 atm, depending on the L a value. The precision in the predictive calculations and the transferability of the model parameters are two aspects that tend to support the usefulness and the theoretical basis of the entire approach.

  17. A Size-Dependent Thermodynamic Model for Coke Crystallites: The Carbon-Sulfur System Up to 2500 K (2227 °C)

    Science.gov (United States)

    Ouzilleau, Philippe; Gheribi, Aïmen E.; Lindberg, Daniel K.; Chartrand, Patrice

    2016-03-01

    A model is presented for the development of the thermodynamic functions of enthalpy, entropy, and Gibbs energy for the elements carbon and sulfur in coke crystallites. The crystallites of various degrees of graphitization may be described by crystallite length L a and crystallite height L c. This carbon/sulfur model has been developed using concepts similar to those in the carbon/hydrogen model for coke crystallites. The major model parameters are derived from reported thermodynamic properties. Approximately 75 pct of the model parameters for the carbon/hydrogen and carbon/sulfur system are parameters common to both systems. The resulting crystallite size (L a) constrained in the carbon/sulfur phase diagram, computed by a Gibbs energy minimization technique, is presented for 1 atm and temperatures between 1500 K and 2500 K (1227 °C and 2227 °C). A very good agreement is obtained between the predicted thermal desulfurization of petroleum cokes and critically assessed experimental data. The removal of sulfur from coke crystallites is predicted to occur mostly between 1600 K and 1850 K (1327 °C and 1577 °C) at 1 atm, depending on the L a value. The precision in the predictive calculations and the transferability of the model parameters are two aspects that tend to support the usefulness and the theoretical basis of the entire approach.

  18. Influence of COD/sulfate ratios on the integrated reactor system for simultaneous removal of carbon, sulfur and nitrogen.

    Science.gov (United States)

    Yuan, Ye; Chen, Chuan; Zhao, Youkang; Wang, Aijie; Sun, Dezhi; Huang, Cong; Liang, Bin; Tan, Wenbo; Xu, Xijun; Zhou, Xu; Lee, Duu-Jung; Ren, Nanqi

    2015-01-01

    An integrated reactor system was developed for the simultaneous removal of carbon, sulfur and nitrogen from sulfate-laden wastewater and for elemental sulfur (S°) reclamation. The system mainly consisted of an expanded granular sludge bed (EGSB) for sulfate reduction and organic carbon removal (SR-CR), an EGSB for denitrifying sulfide removal (DSR), a biological aerated filter for nitrification and a sedimentation tank for sulfur reclamation. This work investigated the influence of chemical oxygen demand (COD)/sulfate ratios on the performance of the system. Influent sulfate and ammonium were fixed to the level of 600 mg SO(4)(2-) L⁻¹ and 120 mg NH(4)(+) L⁻¹, respectively. Lactate was introduced to generate COD/SO(4)(2-) = 0.5:1, 1:1, 1.5:1, 2:1, 3:1, 3.5:1 and 4:1. The experimental results indicated that sulfate could be efficiently reduced in the SR-CR unit when the COD/SO(4)(2-) ratio was between 1:1 and 3:1, and sulfate reduction was inhibited by the growth of methanogenic bacteria when the COD/SO(4)(2-) ratio was between 3.5:1 and 4:1. Meanwhile, the Org-C/S²⁻/NO(3)(-) ratios affected the S(0) reclamation efficiency in the DSR unit. When the influent COD/SO(4)(2-) ratio was between 1:1 and 3:1, appropriate Org-C/S²⁻/NO(3)(-) ratios could be achieved to obtain a maximum S° recovery in the DSR unit. For the microbial community of the SR-CR unit at different COD/SO(4)(2-) ratios, 16S rRNA gene-based high throughput Illumina MiSeq sequencing was used to analyze the diversity and potential function of the dominant species. PMID:25768217

  19. Inhibition of RecA-mediated cleavage in covalent dimers of UmuD.

    OpenAIRE

    Lee, M. H.; Guzzo, A; Walker, G C

    1996-01-01

    Disulfide-cross-linked UmuD2 derivatives were cleaved poorly upon incubation with activated RecA. Reducing the disulfide bonds prior to incubating the derivatives with RecA dramatically increased their extent of cleavage. These observations suggest that the UmuD monomer is a better substrate for the RecA-mediated cleavage reaction than the dimer.

  20. Phosphate diester cleavage promoted by the novel artificial biomimetic agent

    Czech Academy of Sciences Publication Activity Database

    Bím, Daniel; Rulíšek, Lubomír; Hodačová, J.

    Praha: Czech Chemical Society, 2014. s. 51. [Liblice 2014. Advances in Organic, Bioorganic and Pharmaceutical Chemistry /49./. 07.11.2014-09.11.2014, Lázně Bělohrad] Institutional support: RVO:61388963 Keywords : phosphate diesters * bond cleavage Subject RIV: CF - Physical ; Theoretical Chemistry

  1. Invasive cleavage of nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  2. Invasive cleavage of nucleic acids

    Science.gov (United States)

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  3. Studies on pharmacological activation of human serum immunoglobulin G by chemical modification and active subfragments. IV. Induction of anti-inflammatory activity by chemical cleavage of interchain disulfide bonds in human immunoglobulin G and pharmacological activity of alkylated subfragments.

    Science.gov (United States)

    Mimura, T; Tsujikawa, K; Nakajima, H; Okabe, M; Kohama, Y; Iwai, M; Yokoyama, K

    1986-01-01

    Commercially available human serum immunoglobulin G (IgG, native IgG) was separated into two fractions (Fr.I and II) using a diethylaminoethyl cellulose column. Heavy and light chains containing fractions were obtained from these two fractions after carboxamide-methylation. Thus, these fractions were subjected to an anti-inflammatory screening procedure and were shown to have a potent inhibitory activity against rat carrageenin induced paw edema, while no effect was observed in native IgG, Fr.I or II. The reduction and alkylation of the interchain disulfide bonds were essential to induce the anti-inflammatory activity. The anti-inflammatory activity of alkylated heavy and light chains of Fr.I (Fr.I-H and I-L) was also noted in subacute inflammation caused by the felt pellet and croton oil granuloma methods. Moreover, strong membrane stabilizing activities of Fr.I-H and I-L were demonstrated in vitro using rat red blood cell membrane and liver lysosomal membrane. PMID:3712209

  4. Heterolytic cleavage of ammonia N-H bond by bifunctional activation in silica-grafted single site Ta(V) imido amido surface complex. Importance of the outer sphere NH3 assistance

    KAUST Repository

    Gouré, Eric

    2011-01-01

    Ammonia N-H bond is cleaved at room temperature by the silica-supported tantalum imido amido complex [(≡SiO)2Ta(NH)(-NH2)], 2, if excess ammonia is present, but requires 150 °C to achieve the same reaction if only one equivalent NH3 is added to 2. MAS solid-state 15N NMR and in situ IR spectroscopic studies of the reaction of either 15N or 2H labeled ammonia with 2 show that initial coordination of the ammonia is followed by scrambling of either 15N or 2H among ammonia, amido and imido groups. Density functional theory (DFT) calculations with a cluster model [{(μ-O)[(H3SiO) 2SiO]2}Ta(NH)(-NH2)(NH3)], 2 q·NH3, show that the intramolecular H transfer from Ta-NH2 to TaNH is ruled out, but the H transfers from the coordinated ammonia to the amido and imido groups have accessible energy barriers. The energy barrier for the ammonia N-H activation by the Ta-amido group is energetically preferred relative to the Ta-imido group. The importance of excess NH3 for getting full isotope scrambling is rationalized by an outer sphere assistance of ammonia acting as proton transfer agent, which equalizes the energy barriers for H transfer from coordinated ammonia to the amido and imido groups. In contrast, additional coordinated ammonia does not favor significantly the H transfer. These results rationalize the experimental conditions used. © The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2011.

  5. Cleavage behaviors in nuclear vessel steels

    International Nuclear Information System (INIS)

    Cleavage behaviors of nuclear vessel steels in the transition temperature range are reviewed. Viewpoints are presented to assist understanding of cleavage crack speed, cleavage initiation, cleavage arrest, and the sensitivity of fracture toughness to constraint and temperature. The importance of high local stress elevations by high strain rate is emphasized. This report is designated as HSST Report No. 149

  6. Selective cleavage enhanced by acetylating the side chain of lysine.

    Science.gov (United States)

    Fu, Leixiaomeng; Chen, Tingting; Xue, Gaiqing; Zu, Lily; Fang, Weihai

    2013-01-01

    Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision-induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N-terminal of the peptide. After acetylation of the lysine side-chain, b(n)+ ions were the most abundant primary fragment products and the Lys(Ac)-Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side-chain of lysine promoted the selective cleavage of Lys-Xxx amide bond and generated much more information of the peptide backbone sequence. The results re-evaluate the selective cleavage due to the lysine basic side-chain and provide information for studying the post-translational modification of proteins and other bio-molecules containing Lys residues. PMID:23303756

  7. Multielectron redox reactions involving C-C coupling and cleavage in uranium Schiff base complexes

    International Nuclear Information System (INIS)

    The reaction of U(III) with Schiff base ligands and the reduction of U(IV) Schiff base complexes both promote C-C bond formation to afford dinuclear or mononuclear U(IV) amido complexes, which can release up to four electrons to substrates through the oxidative cleavage of the C-C bond. (authors)

  8. Restricted Active Site Docking by Enzyme-bound Substrate Enforces the Ordered Cleavage of Prothrombin by Prothrombinase*

    OpenAIRE

    Hacisalihoglu, Ayse; Panizzi, Peter; Bock, Paul E.; Camire, Rodney M.; Krishnaswamy, Sriram

    2007-01-01

    The preferred pathway for prothrombin activation by prothrombinase involves initial cleavage at Arg320 to produce meizothrombin, which is then cleaved at Arg271 to liberate thrombin. Exosite binding drives substrate affinity and is independent of the bond being cleaved. The pathway for cleavage is determined by large differences in Vmax for cleavage at the two sites within intact prothrombin. By fluorescence binding studies in the absence of catalysis, we have assessed the ability of the indi...

  9. A mild and highly efficient one-pot three-component reaction for carbon-sulfur bond formation catalyzed by potassium tert-butoxide

    Institute of Scientific and Technical Information of China (English)

    Barahman Movassagh; Amir Rakhshani

    2011-01-01

    Potassium tert-butoxide has been found to be a highly efficient catalyst for one-pot, three-component reaction of aryl aldehydes, acetophenones, and thiols via Claisen-Schmidt/Michael addition reactions for the synthesis of thia-Michael adducts in high yields. The reactions are best carried out in tert-butyl alcohol at room temperature.

  10. Thermal and electrochemically assisted Pd-Cl bond cleavage in the d9-d9 Pd2dppm2Cl2 complex by Pd3 dppm3COn+ clusters (n = 2, 1, 0).

    Science.gov (United States)

    Cugnet, Cyril; Mugnier, Yves; Dal Molin, Sophie; Brevet, David; Lucas, Dominique; Harvey, Pierre D

    2007-04-16

    A new aspect of reactivity of the cluster [Pd3(dppm)3(micro3-CO)]n+, ([Pd3]n+, n = 2, 1, 0) with the low-valent metal-metal-bonded Pd2(dppm)2Cl2 dimer (Pd2Cl2) was observed using electrochemical techniques. The direct reaction between [Pd3]2+ and Pd2Cl2 in THF at room temperature leads to the known [Pd3(dppm)3(micro3-CO)(Cl)]+ ([Pd3(Cl)]+) adduct and the monocationic species Pd2(dppm)2Cl+ (very likely as Pd2(dppm)2(Cl)(THF)+, [Pd2Cl]+) as unambiguously demonstrated by UV-vis and 31P NMR spectroscopy. In this case, [Pd3]2+ acts as a strong Lewis acid toward the labile Cl- ion, which weakly dissociates from Pd2Cl2 (i.e., dissociative mechanism). Host-guest interactions between [Pd3]2+ and Pd2Cl2 seem unlikely on the basis of computer modeling because of the strong screening of the Pd-Cl fragment by the Ph-dppm groups in Pd2Cl2. The electrogenerated clusters [Pd3]+ and [Pd3]0 also react with Pd2Cl2 to unexpectedly form the same oxidized adduct, [Pd3(Cl)]+, despite the known very low affinity of [Pd3]+ and [Pd3]0 toward Cl- ions. The reduced biproduct in this case is the highly reactive zerovalent species "Pd2(dppm)2" or "Pd(dppm)" as demonstrated by quenching with CDCl3 (forming the well-known complex Pd(dppm)Cl2) or in presence of dppm (forming the known Pd2(dppm)3 d10-d10 dimer). To bring these halide-electron exchange reactions to completion for [Pd3]+ and [Pd3]0, 0.5 and 1.0 equiv of Pd2Cl2 are necessary, respectively, accounting perfectly for the number of exchanged electrons. The presence of a partial dissociation of Pd2Cl2 into the Cl- ion and the monocation [Pd2Cl]+, which is easier to reduce than Pd2Cl2, is suggested to explain the overall electrochemical results. It is possible to regulate the nature of the species formed from Pd2Cl2 by changing the state of charge of the title cluster. PMID:17371010

  11. Intrinsic transcript cleavage activity of RNA polymerase.

    OpenAIRE

    Orlova, M; Newlands, J; Das, A; Goldfarb, A; Borukhov, S

    1995-01-01

    The GreA and GreB transcript cleavage factors of Escherichia coli suppress elongation arrest and may have a proofreading role in transcription. With the use of E. coli greA-greB- mutant, RNA polymerase is demonstrated to possess substantial intrinsic transcript cleavage activity. Mildly alkaline pH mimics the effect of the Gre proteins by inducing transcript cleavage in ternary complexes and antagonizing elongation arrest through a cleavage-and-restart reaction. Thus, transcript cleavage cons...

  12. Facile scission of isonitrile carbon–nitrogen triple bond using a diborane(4) reagent

    OpenAIRE

    Asakawa, Hiroki; Lee, Ka-Ho; Lin, Zhenyang; Yamashita, Makoto

    2014-01-01

    Transition metal reagents and catalysts are generally effective to cleave all three bonds (one σ and two π) in a triple bond despite its high bonding energy. Recently, chemistry of single-bond cleavage by using main-group element compounds is rapidly being developed in the absence of transition metals. However, the cleavage of a triple bond using non-transition-metal compounds is less explored. Here we report that an unsymmetrical diborane(4) compound could react with carbon monoxide and tert...

  13. Regioselective Cleavage of Thioether Linkages in Microcystin Conjugates.

    Science.gov (United States)

    Zemskov, Ivan; Kropp, Heike M; Wittmann, Valentin

    2016-07-25

    Microcystins are cyanobacterial toxins that can be found in fresh and coastal waters during algal blooms. Microcystin contamination of water can cause severe poisoning of animals and humans. Quantification of these toxins in biological samples is complicated because a major proportion of microcystins is covalently linked to proteins through thioether bonds formed through a Michael-type addition of cysteine residues of proteins to an N-methyldehydroalanine residue in the microcystins. We investigated chemical methods that can be used to cleave such thioether bonds by means of an elimination reaction that leaves the microcystin backbone intact for subsequent analysis. The known reagent O-mesitylenesulfonylhydroxylamine (MSH) led to regioselective thioether cleavage, but a large excess of reagent was needed, thus making purification challenging. An unexpected side reaction observed during the investigation of the base-induced elimination inspired us to develop a new thioether-cleavage methodology based on the addition of propargylamine as a nucleophile that can trap the elimination product. This methodology could be successfully applied to the quantitative cleavage of a microcystin-LF-glutathione conjugate. The alkyne moiety introduced by this procedure offers the possibility for further reactions with azides by using click chemistry, which might be useful for the derivatization or isolation of microcystins. PMID:27346324

  14. Supercritical carbon dioxide and sulfur in the Madison Limestone: A natural analog in southwest Wyoming for geologic carbon-sulfur co-sequestration

    Science.gov (United States)

    Kaszuba, John P.; Navarre-Sitchler, Alexis; Thyne, Geoffrey; Chopping, Curtis; Meuzelaar, Tom

    2011-09-01

    The Madison Limestone on the Moxa Arch, southwest Wyoming, USA contains large volumes (65-95%) of supercritical CO 2 that it has stored naturally for 50 million years. This reservoir also contains supercritical H 2S, aqueous sulfur complexes (SO 42- and HS -), and sulfur-bearing minerals (anhydrite and pyrite). Although SO 2 is not present, these sulfur-bearing phases are known products of SO 2 disproportionation in other water-rock systems. The natural co-occurrence of SO 42-, S 2-, supercritical CO 2 and brine affords the opportunity to evaluate the fate of a carbon-sulfur co-sequestration scenario. Mineralogic data was obtained from drill core and aqueous geochemical data from wells outside and within the current supercritical CO 2-sulfur-brine-rock system. In addition to dolomite, calcite, and accessory sulfur-bearing minerals, the Madison Limestone contains accessory quartz and the aluminum-bearing minerals feldspar, illite, and analcime. Dawsonite (NaAlCO 3(OH) 2), predicted as an important carbon sink in sequestration modeling studies, is not present. After confirming equilibrium conditions for the Madison Limestone system, reaction path models were constructed with initial conditions based on data from outside the reservoir. Addition of supercritical CO 2 to the Madison Limestone was simulated and the results compared to data from inside the reservoir. The model accurately predicts the observed mineralogy and captures the fundamental changes expected in a Madison Limestone-brine system into which CO 2 is added. pH decreases from 5.7 to 4.5 at 90 °C and to 4.0 at 110 °C, as expected from dissolution of supercritical CO 2, creation of carbonic acid, and buffering by the carbonate rock. The calculated redox potential increases by 0.1 V at 90 °C and 0.15 V at 110 °C due to equilibrium among CO 2, anhydrite, and pyrite. Final calculated Eh and pH match conditions for the co-existing sulfur phases present in produced waters and core from within the reservoir

  15. Dinitrogen cleavage and hydrogenation by a trinuclear titanium polyhydride complex.

    Science.gov (United States)

    Shima, Takanori; Hu, Shaowei; Luo, Gen; Kang, Xiaohui; Luo, Yi; Hou, Zhaomin

    2013-06-28

    Both the Haber-Bosch and biological ammonia syntheses are thought to rely on the cooperation of multiple metals in breaking the strong N≡N triple bond and forming an N-H bond. This has spurred investigations of the reactivity of molecular multimetallic hydrides with dinitrogen. We report here the reaction of a trinuclear titanium polyhydride complex with dinitrogen, which induces dinitrogen cleavage and partial hydrogenation at ambient temperature and pressure. By (1)H and (15)N nuclear magnetic resonance, x-ray crystallographic, and computational studies of some key reaction steps and products, we have determined that the dinitrogen (N2) reduction proceeds sequentially through scission of a N2 molecule bonded to three Ti atoms in a μ-η(1):η(2):η(2)-end-on-side-on fashion to give a μ2-N/μ3-N dinitrido species, followed by intramolecular hydrogen migration from Ti to the μ2-N nitrido unit. PMID:23812710

  16. Centralspindlin in Rappaport's cleavage signaling.

    Science.gov (United States)

    Mishima, Masanori

    2016-05-01

    Cleavage furrow in animal cell cytokinesis is formed by cortical constriction driven by contraction of an actomyosin network activated by Rho GTPase. Although the role of the mitotic apparatus in furrow induction has been well established, there remain discussions about the detailed molecular mechanisms of the cleavage signaling. While experiments in large echinoderm embryos highlighted the role of astral microtubules, data in smaller cells indicate the role of central spindle. Centralspindlin is a constitutive heterotetramer of MKLP1 kinesin and the non-motor CYK4 subunit and plays crucial roles in formation of the central spindle and recruitment of the downstream cytokinesis factors including ECT2, the major activator of Rho during cytokinesis, to the site of division. Recent reports have revealed a role of this centralspindlin-ECT2 pathway in furrow induction both by the central spindle and by the astral microtubules. Here, a unified view of the stimulation of cortical contractility by this pathway is discussed. Cytokinesis, the division of the whole cytoplasm, is an essential process for cell proliferation and embryonic development. In animal cells, cytokinesis is executed using a contractile network of actin filaments driven by a myosin-II motor that constricts the cell cortex (cleavage furrow ingression) into a narrow channel between the two daughter cells, which is resolved by scission (abscission) [1-3]. The anaphase-specific organization of the mitotic apparatus (MA, spindle with chromosomes plus asters) positions the cleavage furrow and plays a major role in spatial coupling between mitosis and cytokinesis [4-6]. The nucleus and chromosomes are dispensable for furrow specification [7-10], although they contribute to persistent furrowing and robust completion in some cell types [11,12]. Likewise, centrosomes are not essential for cytokinesis, but they contribute to the general fidelity of cell division [10,13-15]. Here, classical models of cleavage furrow

  17. Kinetics of hairpin ribozyme cleavage in yeast.

    OpenAIRE

    Donahue, C P; Fedor, M J

    1997-01-01

    Hairpin ribozymes catalyze a self-cleavage reaction that provides a simple model for quantitative analyses of intracellular mechanisms of RNA catalysis. Decay rates of chimeric mRNAs containing self-cleaving ribozymes give a direct measure of intracellular cleavage kinetics in yeast. Intracellular ribozyme-mediated cleavage occurs at similar rates and shows similar inhibition by ribozyme mutations as ribozyme-mediated reactions in vitro, but only when ribozymes are located in a favorable mRNA...

  18. Cleavage speed and implantation potential of early-cleavage embryos in IVF or ICSI cycles

    OpenAIRE

    Lee, Meng-Ju; Lee, Robert Kuo-Kuang; Lin, Ming-Huei; Hwu, Yuh-Ming

    2012-01-01

    We examined whether there is a correlation among early embryo cleavage, speed of cleavage, and implantation potential for in-vitro fertilization (IVF) treatment and intracytoplasmic sperm injection (ICSI). This retrospective study examined 112 cycles of IVF and 82 cycles of ICSI in patients less than 40 years of age. Early cleavage was defined as embryonic mitosis occurring 25–27 h after insemination. These day-3 embryos were then grouped according to cleavage speed (rapid, normal, and slow) ...

  19. Pre-mRNA 3’ Cleavage is Reversibly Inhibited In Vitro by Cleavage Factor Dephosphorylation

    OpenAIRE

    Ryan, Kevin

    2007-01-01

    During 3' end formation most pre-mRNAs undergo endonucleolytic cleavage and polyadenylation in the 3' untranslated region. Very little is known concerning the role that post-translational modifications play in the function and regulation of the factors required for 3' cleavage. Using the reconstituted pre-mRNA cleavage reaction, we find that non-specific dephosphorylation of HeLa cell nuclear extract leads to the loss of 3' cleavage activity. A variety of serine/threonine phosphatases inhibit...

  20. Fracto—emissions in Catastrophic Cleavage Process

    Institute of Scientific and Technical Information of China (English)

    HonglaiTAN; WeiYANG

    1996-01-01

    Fracto-emissions accompanying crack propagation are observed in the recent experiments.The energy impulses during and after fracture stimulate the fracto-emissions.Model concerning atomic scale cleavage processes is proposed to formulate a catastrophic fracure theory relevant to these phenomena.A criterion for catastrophic jump of the cleavage potential is applied to representative crystals.

  1. Microstructure and cleavage in lath martensitic steels

    International Nuclear Information System (INIS)

    In this paper we discuss the microstructure of lath martensitic steels and the mechanisms by which it controls cleavage fracture. The specific experimental example is a 9Ni (9 wt% Ni) steel annealed to have a large prior austenite grain size, then examined and tested in the as-quenched condition to produce a relatively coarse lath martensite. The microstructure is shown to approximate the recently identified ‘classic’ lath martensite structure: prior austenite grains are divided into packets, packets are subdivided into blocks, and blocks contain interleaved laths whose variants are the two Kurjumov–Sachs relations that share the same Bain axis of the transformation. When the steel is fractured in brittle cleavage, the laths in the block share {100} cleavage planes and cleave as a unit. However, cleavage cracks deflect or blunt at the boundaries between blocks with different Bain axes. It follows that, as predicted, the block size governs the effective grain size for cleavage. (paper)

  2. The role of the plasma membrane and a non-lysosomal compartment in the disulfide cleavage of endocytosed macromolecules

    International Nuclear Information System (INIS)

    The cleavage of disulfide bonds in endocytosed macromolecules was investigated using new disulfide containing macromolecular conjugates. A conjugate, in which (125I-tyr) was linked to the nondegradable macromolecular carrier poly D-lysine (PDL) through a disulfide spacer (125I-tyr-SS-PDL), was used to monitor disulfide cleavage in adsorptive endocytosis in Chinese hamster ovary cells. Reductive cleavage of this probe released 3-thiopropionyl-125125I-tyramine, measurable as acid soluble radioactivity. In pulse experiments, reductive cleavage of 125I-tyr-SS-PDL differed in its kinetics from the proteolysis of 125I-labeled Poly L-lysine. Proteolytic degradation began after a 15 to 30 min lag, i.e. the time required for transport of poly(lysine) to heavy lysosomes, while reductive cleavage increased linearly between 0 and 15 min. In the first hour of chase, proteolytic and reductive cleavage amounted to 30% and 7% of the total cell bound radioactivity, respectively. The reductive cleavage observed during the first 30 min of chase was inhibited by 80-90% with cell impermeant sulfhydryl reagents [dithiobis-(2-nitrobenzoic acid) and p-chloromercuriphenyl-sulfonate], which indicated that cleavage occurred at the cell surface. In contrast, disulfide cleavage observed after 1 hr chase was not significantly inhibited by these reagents and, therefore, resulted from an intracellular process. Subcellular fractionation demonstrated that lysosomes could be excluded as a site of disulfide cleavage, but that a subcellular fraction characterized by a buoyant density of 1.03g/ml was associated with the cleavage of 125I-tyr-SS-PDL. Of the relevant structures which constitute this subcellular fraction, early endosomes and plasma membrane could be excluded as the reducing structures on the basis of kinetic considerations

  3. Experiments on schistosity and slaty cleavage

    Science.gov (United States)

    Becker, George Ferdinand

    1904-01-01

    Schistosity as a structure is important, and it is a part of the business of geologists to explain its origin. Slaty cleavage has further and greater importance as a possible tectonic feature. Scarcely a great mountain range exists, or has existed, along the course of which belts of slaty rock are not found, the dip of the cleavage usually approaching verticality. Are these slate belts equivalent to minutely distributed step faults of great total throw, or do they indicate compression perpendicular to the cleavage without attendant relative dislocation? Evidently the answer to this question is of first importance in the interpretation of orogenic phenomena.

  4. Cleavage site analysis in picornaviral polyproteins

    DEFF Research Database (Denmark)

    Blom, Nikolaj; Hansen, Jan; Blaas, Dieter;

    1996-01-01

    Picornaviral proteinases are responsible for maturation cleavages of the viral polyprotein, but also catalyze the degradation of cellular targets. Using graphical visualization techniques and neural network algorithms, we have investigated the sequence specificity of the two proteinases 2Apro and 3......Cpro. The cleavage of VP0 (giving rise to VP2 and VP4), which is carried out by a so-far unknown proteinase, was also examined. In combination with a novel surface exposure prediction algorithm, our neural network approach successfully distinguishes known cleavage sites from nocleavage sites and yields...... a more consistent definition of features common to these sites. The method is able to predict experimentally determined cleavage sites in cellular proteins. We present a list of mammalian and other proteins that are predicted to be possible targets for the viral proteinases. Whether these proteins...

  5. Centrosomes: CNN's Broadcast Reaches the Cleavage Furrow

    OpenAIRE

    Sullivan, William

    2009-01-01

    Centrosomin (CNN), a core Drosophila centrosome protein, interacts with the newly identified protein Centrocortin to promote cleavage furrow formation in the early embryo. Significantly, this activity is distinct from CNN's well-established role in centrosome-based microtubule organization.

  6. Distinct mechanisms for DNA cleavage by myoglobin with a designed heme active center.

    Science.gov (United States)

    Zhao, Yuan; Du, Ke-Jie; Gao, Shu-Qin; He, Bo; Wen, Ge-Bo; Tan, Xiangshi; Lin, Ying-Wu

    2016-03-01

    Heme proteins perform diverse biological functions, of which myoglobin (Mb) is a representative protein. In this study, the O2 carrier Mb was shown to cleave double stranded DNA upon aerobic dithiothreitol-induced reduction, which is fine-tuned by an additional distal histidine, His29 or His43, engineered in the heme active center. Spectroscopic (UV-vis and EPR) and inhibition studies suggested that free radicals including singlet oxygen and hydroxyl radical are responsible for efficient DNA cleavage via an oxidative cleavage mechanism. On the other hand, L29E Mb, with a distinct heme active center involving three water molecules in the met form, was found to exhibit an excellent DNA cleavage activity that was not depending on O2. Inhibition and ligation studies demonstrated for the first time that L29E Mb cleaves double stranded DNA into both the nicked circular and linear forms via a hydrolytic cleavage mechanism, which resembles native endonucleases. This study provides valuable insights into the distinct mechanisms for DNA cleavage by heme proteins, and lays down a base for creating artificial DNA endonucleases by rational design of heme proteins. Moreover, this study suggests that the diverse functions of heme proteins can be fine-tuned by rational design of the heme active center with a hydrogen-bonding network. PMID:26775281

  7. Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites.

    Science.gov (United States)

    Minko, Irina G; Jacobs, Aaron C; de Leon, Arnie R; Gruppi, Francesca; Donley, Nathan; Harris, Thomas M; Rizzo, Carmelo J; McCullough, Amanda K; Lloyd, R Stephen

    2016-01-01

    Apurinic/apyrimidinic (AP) sites are constantly formed in cellular DNA due to instability of the glycosidic bond, particularly at purines and various oxidized, alkylated, or otherwise damaged nucleobases. AP sites are also generated by DNA glycosylases that initiate DNA base excision repair. These lesions represent a significant block to DNA replication and are extremely mutagenic. Some DNA glycosylases possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a β- or β,δ-elimination reaction. Various amines can incise AP sites via a similar mechanism, but this non-enzymatic cleavage typically requires high reagent concentrations. Herein, we describe a new class of small molecules that function at low micromolar concentrations as both β- and β,δ-elimination catalysts at AP sites. Structure-activity relationships have established several characteristics that appear to be necessary for the formation of an iminium ion intermediate that self-catalyzes the elimination at the deoxyribose ring. PMID:27363485

  8. Does Cleavage Work at Work? Men, but Not Women, Falsely Believe Cleavage Sells a Weak Product

    Science.gov (United States)

    Glick, Peter; Chrislock, Karyna; Petersik, Korinne; Vijay, Madhuri; Turek, Aleksandra

    2008-01-01

    We examined whether men, but not women, would be distracted by a female sales representative's exposed cleavage, leading to greater perceived efficacy for a weak, but not for a strong product. A community sample of 88 men and 97 women viewed a video of a female pharmaceutical sales representative who (a) had exposed cleavage or dressed modestly…

  9. The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage of β-ionone ring-containing carotenes and non-epoxidated xanthophylls.

    Science.gov (United States)

    Bruno, Mark; Beyer, Peter; Al-Babili, Salim

    2015-04-15

    Down-regulation of the potato carotenoid cleavage dioxygenase 4 (StCCD4) transcript level led to tubers with altered morphology and sprouting activity, which also accumulated higher levels of violaxanthin and lutein leading to elevated carotenoid amounts. This phenotype indicates a role of this enzyme in tuber development, which may be exerted by a cleavage product. In this work, we investigated the enzymatic activity of StCCD4, by expressing the corresponding cDNA in carotenoid accumulating Escherichia coli strains and by performing in vitro assays with heterologously expressed enzyme. StCCD4 catalyzed the cleavage of all-trans-β-carotene at the C9'-C10' double bond, leading to β-ionone and all-trans-β-apo-10'-carotenal, both in vivo and in vitro. The enzyme also cleaved β,β-cryptoxanthin, zeaxanthin and lutein either at the C9'-C10' or the C9-C10 double bond in vitro. In contrast, we did not observe any conversion of violaxanthin and only traces of activity with 9-cis-β-carotene, which led to 9-cis-β-apo-10'-carotenal. Our data indicate that all-trans-β-carotene is the likely substrate of StCCD4 in planta, and that this carotene may be precursor of an unknown compound involved in tuber development. PMID:25703194

  10. The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage of β-ionone ring-containing carotenes and non-epoxidated xanthophylls

    KAUST Repository

    Bruno, Mark

    2015-04-01

    Down-regulation of the potato carotenoid cleavage dioxygenase 4 (StCCD4) transcript level led to tubers with altered morphology and sprouting activity, which also accumulated higher levels of violaxanthin and lutein leading to elevated carotenoid amounts. This phenotype indicates a role of this enzyme in tuber development, which may be exerted by a cleavage product. In this work, we investigated the enzymatic activity of StCCD4, by expressing the corresponding cDNA in carotenoid accumulating Escherichia coli strains and by performing in vitro assays with heterologously expressed enzyme. StCCD4 catalyzed the cleavage of all-. trans-β-carotene at the C9\\'-C10\\' double bond, leading to β-ionone and all-. trans-β-apo-10\\'-carotenal, both in vivo and in vitro. The enzyme also cleaved β,β-cryptoxanthin, zeaxanthin and lutein either at the C9\\'-C10\\' or the C9-C10 double bond in vitro. In contrast, we did not observe any conversion of violaxanthin and only traces of activity with 9-. cis-β-carotene, which led to 9-. cis-β-apo-10\\'-carotenal. Our data indicate that all-. trans-β-carotene is the likely substrate of StCCD4 in planta, and that this carotene may be precursor of an unknown compound involved in tuber development.

  11. THE BIOCHEMICAL CHARACTERIZATION OF FERRET CAROTENE-9', 10'-MONOOXYGENASE CATALYZING CLEAVAGE OF CAROTENOIDS IN VITRO AND IN VIVO

    Science.gov (United States)

    Previous studies have shown that beta -carotene 15,15'-monooxygenase (CMO1) catalyzes the cleavage of beta -carotene at the central carbon 15, 15’-double bond, but cleaves lycopene with much lower activity. However, expressing the mouse carotene-9’,10’-monooxygenase (CMO2) in beta-carotene/lycopene...

  12. Eurosceptism: the Birth of a New Cleavage?

    Directory of Open Access Journals (Sweden)

    Lorenzo Viviani

    2010-05-01

    Full Text Available Euroscepticism is an ambivalent and polysemic concept, consisting of the theme of the European identity, the construction of European Union as new polity, the development of an opposition as expression of new social cleavage, and finally the perspective of an ideological politicization of the european integration by national and supranational political actors. The article attempts to make light on the nature and on the dynamics of development of the euroscepticism through a sequence of analysis that starts from the identity of Europe (what we mean by euroscepticism, then addresses the social dimension of Europe (what we mean by the new european cleavage, and it finally examines the political dimension (the risks and opportunities of politicization by political parties of the european cleavage.

  13. Activation of the C−N Bond in Nitromethane by Palladium α-Diimine Complexes

    OpenAIRE

    Golisz, Suzanne R.; Hazari, Nilay; Labinger, Jay A.; Bercaw, John E.

    2009-01-01

    The reaction of glyoxal-derived α-diimines with palladium acetates in nitromethane leads to cleavage of the C−N bond in nitromethane, to give palladium nitro complexes in which the α-diimine ligand has been methylated.

  14. Cleavage of cytoplasm within the oligonucleate zoosporangia of allomyces macrogynus.

    Science.gov (United States)

    Ji, Yunjeong; Song, Youngsun; Kim, Namhun; Youn, Hyunjoo; Kang, Minkook; Song, Yurim; Cho, Chungwon

    2014-01-01

    Allomyces macrogynus produces zoosporangia that discharge uninucleate zoospores after cleavage of multinucleate cytoplasm. Cleavage of cytoplasm within the oligonucleate zoosporangia of A. macrogynus was visualized by constructing three-dimensional models based on electron micrographs and confocal images. In oligonucleate zoosporangia, three adjacent nuclei can form three cleavage planes with a line of intersection of the planes. The position and boundary of the cleavage planes are thought to be determined by the relative positions of the nuclei. The establishment of three cleavage planes by cleavage membranes occurred sequentially, and the nuclear axis connecting the centers of two nuclei affected the development of cleavage membranes on each cleavage plane. In multinucleate zoosporangia, groups of three neighboring nuclei near the cell cortex may initiate the sequential establishment of cleavage planes and then may interact with the nuclei further from the cortex until the interactions of nuclei are propagated to the central region of the cytoplasm. PMID:24871589

  15. Role of trypsin-like cleavage at arginine 192 in the enzymatic and cytotonic activities of Escherichia coli heat-labile enterotoxin.

    OpenAIRE

    C.C. Grant; Messer, R J; Cieplak, W

    1994-01-01

    Previous studies of cholera toxin and Escherichia coli heat-labile enterotoxin have suggested that proteolytic cleavage plays an important role in the expression of ADP-ribosyltransferase activity and toxicity. Specifically, several studies have implicated a trypsin-like cleavage at arginine 192, which lies within an exposed region subtended by a disulfide bond in the intact A subunit, in toxicity. To investigate the role of this modification in the enzymatic and cytotonic properties of heat-...

  16. Prediction of proprotein convertase cleavage sites

    DEFF Research Database (Denmark)

    Duckert, Peter; Brunak, Søren; Blom, Nikolaj

    2004-01-01

    has created additional focus on proprotein processing. We have developed a method for prediction of cleavage sites for PCs based on artificial neural networks. Two different types of neural networks have been constructed: a furin-specific network based on experimental results derived from the...

  17. Cleavage site analysis in picornaviral polyproteins

    DEFF Research Database (Denmark)

    Blom, Nikolaj; Hansen, Jan; Blaas, Dieter; Brunak, Søren

    1996-01-01

    are indeed cleaved awaits experimental verification. Additionally, we report several errors detected in the protein databases. A computer server for prediction of cleavage sites by picornaviral proteinases is publicly available at the e-mail address NetPicoRNA@cbs.dtu.dk or via WWW at http://www.cbs.dtu.dk/services/NetPicoRNA...

  18. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    Science.gov (United States)

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-12-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave-accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contains four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5% acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein.

  19. Cross talk between the +73/294 interaction and the cleavage site in RNase P RNA mediated cleavage

    OpenAIRE

    Brännvall, Mathias; Kikovska, Ema; Kirsebom, Leif A.

    2004-01-01

    To monitor functionally important metal ions and possible cross talk in RNase P RNA mediated cleavage we studied cleavage of substrates, where the 2′OH at the RNase P cleavage site (at −1) and/or at position +73 had been replaced with a 2′ amino group (or 2′H). Our data showed that the presence of 2′ modifications at these positions affected cleavage site recognition, ground state binding of substrate and/or rate of cleavage. Cleavage of 2′ amino substituted substrates at different pH showed ...

  20. Bond Boom

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The Ministry of Finance recently kick-started a pilot program allowing local governments of Shanghai and Shenzhen,and Zhejiang and Guangdong provinces to issue bonds for the first time.How will the new policy affect fiscal capacities of local governments and the broader economy? What else should the country do to build a healthy bond market? Economists and experts discussed these issues in an interview with the Shanghai Securities Journal.Edited excerpts follow.

  1. Bond Boom

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The Ministry of Finance recently kick-started a pilot program allowing local governments of Shanghai and Shenzhen, and Zhejiang and Guangdong provinces to issue bonds for the first time. How will the new policy affect fiscal capacities of local governments and the broader economy? What else should the country do to build a healthy bond market? Economists and experts discussed these issues in an interview with the ShanghaiSecuritiesJournal. Edited excerpts follow:

  2. Autoproteolytic Cleavage and Activation of Human Acid Ceramidase*

    OpenAIRE

    Shtraizent, Nataly; Eliyahu, Efrat; Park, Jae-Ho; He, Xingxuan; Shalgi, Ruth; Schuchman, Edward H.

    2008-01-01

    Herein we report the mechanism of human acid ceramidase (AC; N-acylsphingosine deacylase) cleavage and activation. A highly purified, recombinant human AC precursor underwent self-cleavage into α and β subunits, similar to other members of the N-terminal nucleophile hydrolase superfamily. This reaction proceeded with first order kinetics, characteristic of self-cleavage. AC self-cleavage occurred most rapidly at acidic pH, but also at neutral pH. Site-directed mutagene...

  3. Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.

    Science.gov (United States)

    Edgell, David R; Stanger, Matthew J; Belfort, Marlene

    2004-11-01

    To maximize spread of their host intron or intein, many homing endonucleases recognize nucleotides that code for important and conserved amino acid residues of the target gene. Here, we examine the cleavage requirements for I-TevI, which binds a stretch of thymidylate synthase (TS) DNA that codes for functionally critical residues in the TS active site. Using an in vitro selection scheme, we identified two base-pairs in the I-TevI cleavage site region as important for cleavage efficiency. These were confirmed by comparison of I-TevI cleavage efficiencies on mutant and on wild-type substrates. We also showed that nicking of the bottom strand by I-TevI is not affected by mutation of residues surrounding the bottom-strand cleavage site, unlike other homing endonucleases. One of these two base-pairs is universally conserved in all TS sequences, and is identical with a previously identified cleavage determinant of I-BmoI, a related GIY-YIG endonuclease that binds a homologous stretch of TS-encoding DNA. The other base-pair is conserved only in a subset of TS genes that includes the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and I-BmoI cleavage site requirements correspond to functionally critical residues involved in an extensive hydrogen bond network within the TS active site. Remarkably, these cleavage requirements correlate with TS phylogeny in bacteria, suggesting that each endonuclease has individually adapted to efficiently cleave distinct TS substrates. PMID:15491609

  4. Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs using PICS with proteome-derived peptide libraries.

    Directory of Open Access Journals (Sweden)

    Olivier Barré

    Full Text Available BACKGROUND: Type II transmembrane serine proteases (TTSPs are a family of cell membrane tethered serine proteases with unclear roles as their cleavage site specificities and substrate degradomes have not been fully elucidated. Indeed just 52 cleavage sites are annotated in MEROPS, the database of proteases, their substrates and inhibitors. METHODOLOGY/PRINCIPAL FINDING: To profile the active site specificities of the TTSPs, we applied Proteomic Identification of protease Cleavage Sites (PICS. Human proteome-derived database searchable peptide libraries were assayed with six human TTSPs (matriptase, matriptase-2, matriptase-3, HAT, DESC and hepsin to simultaneously determine sequence preferences on the N-terminal non-prime (P and C-terminal prime (P' sides of the scissile bond. Prime-side cleavage products were isolated following biotinylation and identified by tandem mass spectrometry. The corresponding non-prime side sequences were derived from human proteome databases using bioinformatics. Sequencing of 2,405 individual cleaved peptides allowed for the development of the family consensus protease cleavage site specificity revealing a strong specificity for arginine in the P1 position and surprisingly a lysine in P1' position. TTSP cleavage between R↓K was confirmed using synthetic peptides. By parsing through known substrates and known structures of TTSP catalytic domains, and by modeling the remainder, structural explanations for this strong specificity were derived. CONCLUSIONS: Degradomics analysis of 2,405 cleavage sites revealed a similar and characteristic TTSP family specificity at the P1 and P1' positions for arginine and lysine in unfolded peptides. The prime side is important for cleavage specificity, thus making these proteases unusual within the tryptic-enzyme class that generally has overriding non-prime side specificity.

  5. Direct measurement of acylenzyme hydrolysis demonstrates rate-limiting deacylation in cleavage of physiological sequences by the processing protease Kex2.

    Science.gov (United States)

    Rockwell, N C; Fuller, R S

    2001-03-27

    Saccharomyces cerevisiae Kex2 protease is the prototype for the family of eukaryotic proprotein convertases that includes furin, PC1/3, and PC2. These enzymes belong to the subtilase superfamily of serine proteases and are distinguished from degradative subtilisins by structural features and by their much more stringent substrate specificity. Pre-steady-state studies have shown that both Kex2 and furin exhibit an initial burst of 7-amino-4-methylcoumarin release in cleavage of peptidyl methylcoumarinamide substrates that are based on physiological cleavage sites. Thus, in cleavage of such substrates, formation of the acylenzyme intermediate is fast relative to some later step (deacylation or N-terminal product release). This behavior is significant, because Kex2 also exhibits burst kinetics in cleavage of peptide bonds. k(cat) for cleavage of a tetrapeptidyl methylcoumarinamide substrate based on the physiological yeast substrate pro-alpha-factor exhibits a weak solvent isotope effect, but neither this isotope effect nor temperature dependence studies with this substrate conclusively identify the rate-limiting step for Kex2 cleavage of this substrate. We therefore developed an assay to measure deacylation directly by pulse-chase incorporation of H(2)(18)O in a rapid-quenched-flow mixer followed by mass spectrometric quantitation. The results given by this assay rule out rate-limiting product release for cleavage of this substrate by Kex2. These experiments demonstrate that cleavage of the acylenzyme ester bond, as opposed to either the initial attack on the amide bond or product release, is rate-limiting for the action of Kex2 at physiological sequences. This work demonstrates a fundamental difference in the catalytic strategy of proprotein processing enzymes and degradative subtilisins. PMID:11297433

  6. Calcium waves along the cleavage furrows in cleavage-stage Xenopus embryos and its inhibition by heparin

    OpenAIRE

    1996-01-01

    Calcium signaling is known to be associated with cytokinesis; however, the detailed spatio-temporal pattern of calcium dynamics has remained unclear. We have studied changes of intracellular free calcium in cleavage-stage Xenopus embryos using fluorescent calcium indicator dyes, mainly Calcium Green-1. Cleavage formation was followed by calcium transients that localized to cleavage furrows and propagated along the furrows as calcium waves. The calcium transients at the cleavage furrows were o...

  7. On the Relative Merits of Non-Orthogonal and Orthogonal Valence Bond Methods Illustrated on the Hydrogen Molecule

    Science.gov (United States)

    Angeli, Celestino; Cimiraglia, Renzo; Malrieu, Jean-Paul

    2008-01-01

    Valence bond (VB) is one of the cornerstone theories of quantum chemistry. Even if in practical applications the molecular orbital (MO) approach has obtained more attention, some basic chemical concepts (such as the nature of the chemical bond and the failure of the single determinant-based MO methods in describing the bond cleavage) are normally…

  8. Distinguishing Bonds.

    Science.gov (United States)

    Rahm, Martin; Hoffmann, Roald

    2016-03-23

    The energy change per electron in a chemical or physical transformation, ΔE/n, may be expressed as Δχ̅ + Δ(VNN + ω)/n, where Δχ̅ is the average electron binding energy, a generalized electronegativity, ΔVNN is the change in nuclear repulsions, and Δω is the change in multielectron interactions in the process considered. The last term can be obtained by the difference from experimental or theoretical estimates of the first terms. Previously obtained consequences of this energy partitioning are extended here to a different analysis of bonding in a great variety of diatomics, including more or less polar ones. Arguments are presented for associating the average change in electron binding energy with covalence, and the change in multielectron interactions with electron transfer, either to, out, or within a molecule. A new descriptor Q, essentially the scaled difference between the Δχ̅ and Δ(VNN + ω)/n terms, when plotted versus the bond energy, separates nicely a wide variety of bonding types, covalent, covalent but more correlated, polar and increasingly ionic, metallogenic, electrostatic, charge-shift bonds, and dispersion interactions. Also, Q itself shows a set of interesting relations with the correlation energy of a bond. PMID:26910496

  9. Cleavage crystallography of liquid metal embrittled aluminum alloys

    Science.gov (United States)

    Reynolds, A. P.; Stoner, G. E.

    1991-01-01

    The crystallography of liquid metal-induced transgranular cleavage in six aluminum alloys having a variety of microstructures has been determined via Laue X-ray back reflection. The cleavage crystallography was independent of alloy microstructure, and the cleavage plane was 100-plane oriented in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surface indicated that there was not a unique direction of crack propagation. In addition, the existence of 100-plane cleavage on alloy 2024 fracture surfaces was inferred by comparison of secondary cleavage crack intersection geometry on the 2024 surfaces with the geometry of secondary cleavage crack intersections on the test alloys.

  10. Effect of mutations in the human immunoglobulin A1 (IgA1) hinge on its susceptibility to cleavage by diverse bacterial IgA1 proteases.

    Science.gov (United States)

    Senior, Bernard W; Woof, Jenny M

    2005-03-01

    Components of the human immunoglobulin A1 (IgA1) hinge governing sensitivity to cleavage by bacterial IgA1 proteases were investigated. Recombinant antibodies with distinct hinge mutations were constructed from a hybrid comprised of human IgA2 bearing half of the human IgA1 hinge region. This hybrid antibody and all the mutant antibodies derived from it were resistant to cleavage by the IgA1 proteases from Streptococcus oralis and Streptococcus mitis biovar 1 strains but were cleaved to various degrees by those of Streptococcus pneumoniae, some Streptococcus sanguis strains, and the type 1 and 2 IgA1 proteases of Haemophilus influenzae, Neisseria meningitidis, and Neisseria gonorrhoeae. Remarkably, those proteases that cleave a Pro-Ser peptide bond in the wild-type IgA1 hinge were able to cleave mutant antibodies lacking a Pro-Ser peptide bond in the hinge, and those that cleave a Pro-Thr peptide bond in the wild-type IgA1 hinge were able to cleave mutant antibodies devoid of a Pro-Thr peptide bond in the hinge. Thus, the enzymes can cleave alternatives to their preferred postproline peptide bond when such a bond is unavailable. Peptide sequence analysis of a representative antibody digestion product confirmed this conclusion. The presence of a cleavable peptide bond near the CH2 end of the hinge appeared to result in greater cleavage than if the scissile bond was at the CH1 end of the hinge. Proline-to-serine substitution at residue 230 in a hinge containing potentially cleavable Pro-Ser and Pro-Thr peptide bonds increased the resistance of the antibody to cleavage by many IgA1 proteases. PMID:15731049

  11. Quantum-mechanical derivation of angular and torsional forces in well-bonded systems

    International Nuclear Information System (INIS)

    A quantum-mechanically based method of deriving real-space interatomic potential functions for covalently bonded systems, without broken bonds, is developed. The method focuses on the one-electron energy, which is modeled via a tight-binding Hamiltonian. The potentials are derived via a general formalism based on perturbation theory, using a starting state in which the electrons reside in bond orbitals. The perturbing terms correspond to overlap and Hamiltonian couplings between the bond orbitals and with other occupied and unoccupied states. The interactions are given in terms of simple trigonometric functions, and the parameters of the quantum-mechanical Hamiltonian. A major contribution to the angular forces comes from the overlap between occupied bonding orbitals. Examples are given for model Hamiltonians relevant to phosphorus, carbon, sulfur, and the ethane molecule. The functional forms of the derived potentials are generally similar in form to those assumed in simulations. However, the actual appearance of the potentials is sometimes quite different from that obtained by an empirical fitting to molecular properties. In addition, it is found that the open-quote open-quote improper close-quote close-quote torsion terms that are often included in polymer simulations can be replaced by angular terms that are much more physically transparent. copyright 1996 The American Physical Society

  12. Regulated Cleavage of Prothrombin by Prothrombinase: REPOSITIONING A CLEAVAGE SITE REVEALS THE UNIQUE KINETIC BEHAVIOR OF THE ACTION OF PROTHROMBINASE ON ITS COMPOUND SUBSTRATE*♦

    OpenAIRE

    Bradford, Harlan N.; Micucci, Joseph A.; Krishnaswamy, Sriram

    2009-01-01

    Prothrombinase converts prothrombin to thrombin via cleavage at Arg320 followed by cleavage at Arg271. Exosite-dependent binding of prothrombin to prothrombinase facilitates active site docking by Arg320 and initial cleavage at this site. Precise positioning of the Arg320 site for cleavage is implied by essentially normal cleavage at Arg320 in recombinant prothrombin variants...

  13. Diffusion bonding

    Science.gov (United States)

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

  14. A potent inhibitor of endothelial cell proliferation is generated by proteolytic cleavage of the chemokine platelet factor 4.

    OpenAIRE

    Gupta, S K; Hassel, T; Singh, J. P.

    1995-01-01

    Platelet factor 4 (PF-4) is an archetype of the "chemokine" family of low molecular weight proteins that play an important role in injury responses and inflammation. From activated human leukocyte culture supernatants, we have isolated a form of PF-4 that acts as a potent inhibitor of endothelial cell proliferation. The PF-4 derivative is generated by peptide bond cleavage between Thr-16 and Ser-17, a site located downstream from the highly conserved and structurally important CXC motif. The ...

  15. Reductive Cleavage of Demeton-S-Methyl by Corynebacterium glutamicum in Cometabolism on More Readily Metabolizable Substrates

    OpenAIRE

    Girbal, Laurence; Hilaire, Didier; Leduc, Sébastien; Delery, Laure; Rols, Jean-Luc; Lindley, Nicholas D.

    2000-01-01

    Corynebacterium glutamicum is able to biotransform demeton-S-methyl, an organophosphorus compound, during cometabolism with more readily metabolizable substrates. Among the cosubstrates used, fructose is the growth substrate that is most favorable for demeton-S-methyl biotransformation. The reaction mechanism of demeton-S-methyl biotransformation involves reductive cleavage of an S-C bond, which leads to accumulation of dimethyl thiophosphate in the culture medium.

  16. A Historical Trend of Ethnic Cleavages in Contemporary Iran

    Directory of Open Access Journals (Sweden)

    Hussein Mohammadzadeh

    2013-10-01

    Full Text Available The goal of this study is evaluation social and historical content of social cleavage in contemporary Iran. Analytical framework rooted in Rokan theory. Rokan believed that social cleavage appearance post of revolutions. Method of study was historical comparatives.The method of this research is comparative historical in which we used of historical documents and data. In this field, I have compared data of indexes of socio-economic of ethnic states.Assessment of data and documents show that social cleavages and particularly ethnic cleavages rise after Reza shah revolution. He established centralized and dictated government and divided society of Iran and institutionalization the inequality in social structure. Sense of deprivation about inequality and suited circumstance activated ethnic cleavage in Iran. Decrease of inequality and justice could decrease of social deprivation and deactivated social cleavages.

  17. SVM-based prediction of caspase substrate cleavage sites

    OpenAIRE

    Wee, Lawrence JK; Tan, Tin Wee; Ranganathan, Shoba

    2006-01-01

    Background Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. Recently, different computational methods have been developed to predict the cleavage sites of caspase substrates with varying degrees of success. As the support vector...

  18. Modeling and Inferring Cleavage Patterns in Proliferating Epithelia

    OpenAIRE

    Patel, Ankit B.; Gibson, William T.; Gibson, Matthew C; Radhika Nagpal

    2009-01-01

    The regulation of cleavage plane orientation is one of the key mechanisms driving epithelial morphogenesis. Still, many aspects of the relationship between local cleavage patterns and tissue-level properties remain poorly understood. Here we develop a topological model that simulates the dynamics of a 2D proliferating epithelium from generation to generation, enabling the exploration of a wide variety of biologically plausible cleavage patterns. We investigate a spectrum of models that incorp...

  19. Two Spin-State Reactivity in the Activation and Cleavage of CO2 by [ReO2](.).

    Science.gov (United States)

    Canale, Valentino; Robinson, Robert; Zavras, Athanasios; Khairallah, George N; d'Alessandro, Nicola; Yates, Brian F; O'Hair, Richard A J

    2016-05-19

    The rhenium dioxide anion [ReO2](-) reacts with carbon dioxide in a linear ion trap mass spectrometer to produce [ReO3](-) corresponding to activation and cleavage of a C-O bond. Isotope labeling experiments using [Re(18)O2](-) reveal that (18)O/(16)O scrambling does not occur prior to cleavage of the C-O bond. Density functional theory calculations were performed to examine the mechanism for this oxygen atom abstraction reaction. Because the spins of the ground states are different for the reactant and product ions ((3)[ReO2](-) versus (1)[ReO3](-)), both reaction surfaces were examined in detail and multiple [O2Re-CO2](-) intermediates and transition structures were located and minimum energy crossing points were calculated. The computational results show that the intermediate [O2Re(η(2)-C,O-CO2)](-) species most likely initiates C-O bond activation and cleavage. The stronger binding affinity of CO2 within this species and the greater instabilities of other [O2Re-CO2)](-) intermediates are significant enough that oxygen atom exchange is avoided. PMID:27193088

  20. Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin

    Energy Technology Data Exchange (ETDEWEB)

    Salameh,M.; Soares, A.; Hockla, A.; Radisky, E.

    2008-01-01

    Human mesotrypsin is an isoform of trypsin that displays unusual resistance to polypeptide trypsin inhibitors and has been observed to cleave several such inhibitors as substrates. Whereas substitution of arginine for the highly conserved glycine 193 in the trypsin active site has been implicated as a critical factor in the inhibitor resistance of mesotrypsin, how this substitution leads to accelerated inhibitor cleavage is not clear. Bovine pancreatic trypsin inhibitor (BPTI) forms an extremely stable and cleavage-resistant complex with trypsin, and thus provides a rigorous challenge of mesotrypsin catalytic activity toward polypeptide inhibitors. Here, we report kinetic constants for mesotrypsin and the highly homologous (but inhibitor sensitive) human cationic trypsin, describing inhibition by, and cleavage of BPTI, as well as crystal structures of the mesotrypsin-BPTI and human cationic trypsin-BPTI complexes. We find that mesotrypsin cleaves BPTI with a rate constant accelerated 350-fold over that of human cationic trypsin and 150,000-fold over that of bovine trypsin. From the crystal structures, we see that small conformational adjustments limited to several side chains enable mesotrypsin-BPTI complex formation, surmounting the predicted steric clash introduced by Arg-193. Our results show that the mesotrypsin-BPTI interface favors catalysis through (a) electrostatic repulsion between the closely spaced mesotrypsin Arg-193 and BPTI Arg-17, and (b) elimination of two hydrogen bonds between the enzyme and the amine leaving group portion of BPTI. Our model predicts that these deleterious interactions accelerate leaving group dissociation and deacylation.

  1. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

    Science.gov (United States)

    Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Keller, Ulrich Auf dem; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M

    2016-01-01

    leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond. PMID:26407638

  2. Pi Bond Orders and Bond Lengths

    Science.gov (United States)

    Herndon, William C.; Parkanyi, Cyril

    1976-01-01

    Discusses three methods of correlating bond orders and bond lengths in unsaturated hydrocarbons: the Pauling theory, the Huckel molecular orbital technique, and self-consistent-field techniques. (MLH)

  3. Analysis of the cleavage site of the human immunodeficiency virus type 1 glycoprotein: requirement of precursor cleavage for glycoprotein incorporation.

    OpenAIRE

    Dubay, J W; Dubay, S R; Shin, H. J.; Hunter, E

    1995-01-01

    Endoproteolytic cleavage of the glycoprotein precursor to the mature SU and TM proteins is an essential step in the maturation of retroviral glycoproteins. Cleavage of the precursor polyprotein occurs at a conserved, basic tetrapeptide sequence and is carried out by a cellular protease. The glycoprotein of the human immunodeficiency virus type 1 contains two potential cleavage sequences immediately preceding the N terminus of the TM protein. To determine the functional significance of these t...

  4. Cleavage of nicotinamide adenine dinucleotide by the ribosome-inactivating protein from Momordica charantia.

    Science.gov (United States)

    Vinkovic, M; Dunn, G; Wood, G E; Husain, J; Wood, S P; Gill, R

    2015-09-01

    The interaction of momordin, a type 1 ribosome-inactivating protein from Momordica charantia, with NADP(+) and NADPH has been investigated by X-ray diffraction analysis of complexes generated by co-crystallization and crystal soaking. It is known that the proteins of this family readily cleave the adenine-ribose bond of adenosine and related nucleotides in the crystal, leaving the product, adenine, bound to the enzyme active site. Surprisingly, the nicotinamide-ribose bond of oxidized NADP(+) is cleaved, leaving nicotinamide bound in the active site in the same position but in a slightly different orientation to that of the five-membered ring of adenine. No binding or cleavage of NADPH was observed at pH 7.4 in these experiments. These observations are in accord with current views of the enzyme mechanism and may contribute to ongoing searches for effective inhibitors. PMID:26323301

  5. Presence of Meiotic Spindles Indicates Early Cleavage of Embryos

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective To assess whether the detection of the meiotic spindle could anticipate the appearance of early cleavage.Methods Oocytes were obtained from stimulated ovaries of consenting patients undergoing oocytes retrieval for ICSI.Spindles were imaged with the Polscope.After ICSI,oocytes with or without spindles were cultured for examination of early cleavage and embryo development.A total of 328 oocytes from 50 cycles were examined with the Polscope and inseminated by ICSI.Results Spindles were imaged in 81.7% of oocytes.After ICSI,more oocytes with spindles (78.4%) fertilized normally than oocytes without spindles (53.3%)(P<0.001).At 25-27 h post ICSI.more fertilized oocytes developed from oocytes with spindles (81.9%) were detected early cleavage than those from oocytes without spindles(28.1%)(P<0.001).Significantly more embryos with early cleavage (82.2%) developed to high quality embryos at d 3 compared with the embryos without early cleavage(48.3%)(P=0.001).The value of rs related to the relationship between spindles and early cleavage was 0.420(P<0.0001).Conclusion The existing of the early cleavage may have a predictive value on the opportunity of high quality embryos and the existing of the spindle may have a predictive value in the appearance of early cleavage.

  6. Deletion Mapping of the Encephalomyocarditis Virus Primary Cleavage Site

    OpenAIRE

    Hahn, Harry; Palmenberg, Ann C.

    2001-01-01

    The cotranslational, primary self-cleavage reaction of cardiovirus polyprotein relies on a highly conserved, short segment of amino acids at the 2A-2B protein boundary. The amino terminus of the required element for encephalomyocarditis virus has now been mapped to include Tyr126 of the 2A protein, the 18th amino acid before the cleavage site.

  7. A photoinduced cleavage of DNA useful for determining T residues.

    OpenAIRE

    Simoncsits, A; Török, I

    1982-01-01

    Irradiation of 5'-[32P]-phosphate labeled DNA fragments with ultraviolet light in the presence of primary amines followed by piperidine treatment resulted in base-specific cleavage of the DNA chain at T residues, accompanied by a less intensive G reaction. This simple, T greater than G cleavage offers an alternative method for determining T residues in chemical DNA sequencing.

  8. Alkali metal control over N-N cleavage in iron complexes.

    Science.gov (United States)

    Grubel, Katarzyna; Brennessel, William W; Mercado, Brandon Q; Holland, Patrick L

    2014-12-01

    Though N2 cleavage on K-promoted Fe surfaces is important in the large-scale Haber-Bosch process, there is still ambiguity about the number of Fe atoms involved during the N-N cleaving step and the interactions responsible for the promoting ability of K. This work explores a molecular Fe system for N2 reduction, particularly focusing on the differences in the results obtained using different alkali metals as reductants (Na, K, Rb, Cs). The products of these reactions feature new types of Fe-N2 and Fe-nitride cores. Surprisingly, adding more equivalents of reductant to the system gives a product in which the N-N bond is not cleaved, indicating that the reducing power is not the most important factor that determines the extent of N2 activation. On the other hand, the results suggest that the size of the alkali metal cation can control the number of Fe atoms that can approach N2, which in turn controls the ability to achieve N2 cleavage. The accumulated results indicate that cleaving the triple N-N bond to nitrides is facilitated by simultaneous approach of least three low-valent Fe atoms to a single molecule of N2. PMID:25412468

  9. The Oxygenase CAO-1 of Neurospora crassa Is a Resveratrol Cleavage Enzyme

    KAUST Repository

    Diaz-Sanchez, V.

    2013-07-26

    The genome of the ascomycete Neurospora crassa encodes CAO-1 and CAO-2, two members of the carotenoid cleavage oxygenase family that target double bonds in different substrates. Previous studies demonstrated the role of CAO-2 in cleaving the C40 carotene torulene, a key step in the synthesis of the C35 apocarotenoid pigment neurosporaxanthin. In this work, we investigated the activity of CAO-1, assuming that it may provide retinal, the chromophore of the NOP-1 rhodopsin, by cleaving β-carotene. For this purpose, we tested CAO-1 activity with carotenoid substrates that were, however, not converted. In contrast and consistent with its sequence similarity to family members that act on stilbenes, CAO-1 cleaved the interphenyl Cα-Cβ double bond of resveratrol and its derivative piceatannol. CAO-1 did not convert five other similar stilbenes, indicating a requirement for a minimal number of unmodified hydroxyl groups in the stilbene background. Confirming its biological function in converting stilbenes, adding resveratrol led to a pronounced increase in cao-1 mRNA levels, while light, a key regulator of carotenoid metabolism, did not alter them. Targeted Δcao-1 mutants were not impaired by the presence of resveratrol, a phytoalexin active against different fungi, which did not significantly affect the growth and development of wild-type Neurospora. However, under partial sorbose toxicity, the Δcao-1 colonies exhibited faster radial growth than control strains in the presence of resveratrol, suggesting a moderate toxic effect of resveratrol cleavage products.

  10. Semiconductor Surface Structure Determination via Low Energy Positron Diffraction: Cleavage Faces of Cadmium-Selenide

    Science.gov (United States)

    Horsky, Thomas Neil

    Low energy positron diffraction (LEPD) is used to determine the surface structure of the wurtzite CdSe(1010) and CdSe(1120) cleavage faces. Low energy electron diffraction (LEED) is also performed, utilizing a beam optical system which produces both a e^+ and e ^- beam with the same phase-space characteristics, i.e. 1 mm-deg. Both e^+ and e^- measurements were collected from the same sample surface of each cleavage face, removing systematic errors from the comparison. Dynamical calculations were performed for both the LEPD and LEED using the R-factor methodology of Duke et al. For the (1010) surface, the calculations and analyses were performed at Brandeis via link to the John Von Neumann Supercomputer Center at Princeton, NJ. For the (1120) surface, the LEPD calculations and analysis was performed by Battelle Pacific Northwest Laboratories, while the LEED calculations were performed by Princeton University. Resulting surface structures for CdSe(1010) are in accord with the proposed reconstruction model of Wang and Duke, indicating a bond-length-conserving rotation of the surface dimer. The best-fit values of the bond-rotation angle omega are 15^circ +/- 5^circ as determined by LEPD and omega = 21.5^ circ +/- 4^ circ as determined by LEED. These values are in agreement with the predicted value of omega = 17^circ. For CdSe(1120), the best-fit LEPD results indicate an omega of 27^circ +/- 7^circ while preliminary LEED results indicate an omega of 35^circ +/- 5^circ. Both values for this previously undetermined surface are also in agreement with the theoretically predicted value of omega = 32^circ . These results serve to confirm a universal model of reconstruction which describes the surface structures of both the zincblende and wurtzite compound semiconductor cleavage faces.

  11. A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments

    KAUST Repository

    Rodrigo, María J.

    2013-09-04

    Citrus is the first tree crop in terms of fruit production. The colour of Citrus fruit is one of the main quality attributes, caused by the accumulation of carotenoids and their derivative C30 apocarotenoids, mainly ?-citraurin (3-hydroxy-?-apo-8?-carotenal), which provide an attractive orange-reddish tint to the peel of oranges and mandarins. Though carotenoid biosynthesis and its regulation have been extensively studied in Citrus fruits, little is known about the formation of C30 apocarotenoids. The aim of this study was to the identify carotenoid cleavage enzyme(s) [CCD(s)] involved in the peel-specific C30 apocarotenoids. In silico data mining revealed a new family of five CCD4-type genes in Citrus. One gene of this family, CCD4b1, was expressed in reproductive and vegetative tissues of different Citrus species in a pattern correlating with the accumulation of C30 apocarotenoids. Moreover, developmental processes and treatments which alter Citrus fruit peel pigmentation led to changes of ?-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in ?-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and ?-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7?,8? double bond in zeaxanthin and ?-cryptoxanthin, confrming its role in C30 apocarotenoid biosynthesis. Thus, a novel plant carotenoid cleavage activity targeting the 7?,8? double bond of cyclic C40 carotenoids has been identified. These results suggest that the presented enzyme is responsible for the biosynthesis of C30 apocarotenoids in Citrus which are key pigments in fruit coloration. The Author 2013.

  12. Cleavage factor Im (CFIm) as a regulator of alternative polyadenylation.

    Science.gov (United States)

    Hardy, Jessica G; Norbury, Chris J

    2016-08-15

    Most mammalian protein coding genes are subject to alternative cleavage and polyadenylation (APA), which can generate distinct mRNA 3'UTRs with differing regulatory potential. Although this process has been intensely studied in recent years, it remains unclear how and to what extent cleavage site selection is regulated under different physiological conditions. The cleavage factor Im (CFIm) complex is a core component of the mammalian cleavage machinery, and the observation that its depletion causes transcriptome-wide changes in cleavage site use makes it a key candidate regulator of APA. This review aims to summarize current knowledge of the CFIm complex, and explores the evidence surrounding its potential contribution to regulation of APA. PMID:27528751

  13. Distinct oxidative cleavage and modification of bovine [Cu- Zn]-SOD by an ascorbic acid/Cu(II) system: Identification of novel copper binding site on SOD molecule.

    Science.gov (United States)

    Uehara, Hiroshi; Luo, Shen; Aryal, Baikuntha; Levine, Rodney L; Rao, V Ashutosh

    2016-05-01

    We investigated the combined effect of ascorbate and copper [Asc/Cu(II)] on the integrity of bovine [Cu-Zn]-superoxide dismutase (bSOD1) as a model system to study the metal catalyzed oxidation (MCO) and fragmentation of proteins. We found Asc/Cu(II) mediates specific cleavage of bSOD1 and generates 12.5 and 3.2kDa fragments in addition to oxidation/carbonylation of the protein. The effect of other tested transition metals, a metal chelator, and hydrogen peroxide on the cleavage and oxidation indicated that binding of copper to a previously unknown site on SOD1 is responsible for the Asc/Cu(II) specific cleavage and oxidation. We utilized tandem mass spectrometry to identify the specific cleavage sites of Asc/Cu(II)-treated bSOD1. Analyses of tryptic- and AspN-peptides have demonstrated the cleavage to occur at Gly31 with peptide bond breakage with Thr30 and Ser32 through diamide and α-amidation pathways, respectively. The three-dimensional structure of bSOD1 reveals the imidazole ring of His19 localized within 5Å from the α-carbon of Gly31 providing a structural basis that copper ion, most likely coordinated by His19, catalyzes the specific cleavage reaction. PMID:26872685

  14. Amino acid sequence requirements in the human IgA1 hinge for cleavage by streptococcal IgA1 proteases

    DEFF Research Database (Denmark)

    Senior, BW; Batten, MR; Kilian, Mogens;

    2002-01-01

    All the IgA1 proteases of the different pathogenic species of Streptococcus cleave the hinge of the alpha chain of human IgA1 only at one proline-threonine peptide bond. In order to study the importance of these amino acids for cleavage, several hinge mutant recombinant IgA1 antibodies were...... constructed. The mutations were found to be without major effect upon the structure or functional abilities of the antibodies. However, they had a major effect upon their sensitivity to cleavage by some of the IgA1 proteases....

  15. Amino acid sequence requirements in the human IgA1 hinge for cleavage by streptococcal IgA1 proteases.

    Science.gov (United States)

    Senior, B W; Batten, M R; Kilian, M; Woof, J M

    2002-08-01

    All the IgA1 proteases of the different pathogenic species of Streptococcus cleave the hinge of the alpha chain of human IgA1 only at one proline-threonine peptide bond. In order to study the importance of these amino acids for cleavage, several hinge mutant recombinant IgA1 antibodies were constructed. The mutations were found to be without major effect upon the structure or functional abilities of the antibodies. However, they had a major effect upon their sensitivity to cleavage by some of the IgA1 proteases. PMID:12196126

  16. Use of Cleavage as an Aid in the Optical Determination of Minerals.

    Science.gov (United States)

    Ehlers, Ernest G.

    1980-01-01

    Described is the use of cleavage as an aid to microscopic determination of unknown minerals by immersion methods. Cleavages are examined in relation to fragment shapes, types of extinction, and cleavage-optical relationships. (Author/DS)

  17. Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation.

    Science.gov (United States)

    Rawlings, Neil D

    2016-03-01

    One peptidase can usually be distinguished from another biochemically by its action on proteins, peptides and synthetic substrates. Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages. The total number of peptidases for which at least one cleavage is known is 1700 out of a total of 2457 different peptidases. This paper describes how the cleavages are obtained from the scientific literature, how they are annotated and how cleavages in peptides and proteins are cross-referenced to entries in the UniProt protein sequence database. The specificity profiles of 556 peptidases are shown for which ten or more substrate cleavages are known. However, it has been proposed that at least 40 cleavages in disparate proteins are required for specificity analysis to be meaningful, and only 163 peptidases (6.6%) fulfil this criterion. Also described are the various displays shown on the website to aid with the understanding of peptidase specificity, which are derived from the substrate cleavage collection. These displays include a logo, distribution matrix, and tables to summarize which amino acids or groups of amino acids are acceptable (or not acceptable) in each substrate binding pocket. For each protein substrate, there is a display to show how it is processed and degraded. Also described are tools on the website to help with the assessment of the physiological relevance of cleavages in a substrate. These tools rely on the hypothesis that a cleavage site that is conserved in orthologues is likely to be physiologically relevant, and alignments of substrate protein sequences are made utilizing the UniRef50 database, in which in each entry sequences are 50% or more identical. Conservation in this case means substitutions are permitted only if the amino acid is known to occupy the same substrate binding pocket from at least one other substrate cleaved by the same peptidase. PMID

  18. Silver(I) NHC mediated C-C bond activation of alkyl nitriles and catalytic efficiency in oxazoline synthesis.

    Science.gov (United States)

    Heath, Rachael; Müller-Bunz, Helge; Albrecht, Martin

    2015-05-21

    Preparation of silver triazolylidene (trz) species from triazolium salts and Ag2O in refluxing MeCN leads to a selective C-C bond cleavage and the formation of complexes of general formula [(trz)Ag(CN)] from Calkyl-CN bond activation. Moreover, these silver carbene complexes are precursors of highly active catalysts for oxazoline formation via aldol condensation. PMID:25913007

  19. Specific Cleavage of the Nucleoprotein of Fish Rhabdovirus.

    Science.gov (United States)

    Zhou, G-Z; Yi, Y-J; Chen, Z-Y; Zhang, Q-Y

    2015-11-01

    Siniperca chuatsi rhabdovirus (SCRV) is one of myriad rhabdoviruses recorded in fish. Preliminary data show that inhibition of the SCRV nucleoprotein (N) could significantly reduce the progeny virus titers in infected Epithelioma papulosum cyprinid (EPC) cells. Here, the authors propose that cleavage of the viral 47-kDa N protein is caspase-mediated based on caspase inhibition experiments, transient expression in EPC transfection, and analysis of cleavage sites. Cleavage of the SCRV N protein in culture was prevented by a pan-caspase inhibitor, z-VAD-FMK (z-Val-Ala-DL-Asp-fluoromethyl ketone). Subsequently, N was transiently expressed in EPC cells, the results of which indicated that the specific cleavage of N also occurred in the cells transfected with N-GFP plasmid. Several truncated fragments of the N gene were constructed and transiently transfected into EPC cells. Immunoblotting results indicated that D324 and D374 are the cleavage sites of N by caspases. The authors also found that z-VAD-FMK could inhibit the cytopathic effect in SCRV-infected EPC cells but not affect the production of infectious progeny, suggesting that the caspase-mediated cleavage of N protein is not required for in vitro SCRV replication. To the authors' knowledge, this is the first report on the cleavage of rhabdovirus proteins. PMID:25689989

  20. Bundled slaty cleavage in laminated argillite, north-central minnesota

    Science.gov (United States)

    Southwick, D.L.

    1987-01-01

    Exceptional bundled slaty cleavage (defined herein) has been found in drill cores of laminated, folded, weakly metamorphosed argillite at several localities in the early Proterozoic Animikie basin of north-central Minnesota. The cleavage domains are more closely spaced within the cleavage bundles than outside them, the mean tectosilicate grain size of siltstone layers, measured normal to cleavage, is less in the cleavage bundles than outside them, and the cleavage bundles are enriched in opaque phases and phyllosilicates relative to extra-bundle segments. These facts suggest that pressure solution was a major factor in bundle development. If it is assumed that opaque phases have been conserved during pressure solution, the modal differences in composition between intra-bundle and extra-bundle segments of beds provide a means for estimating bulk material shortening normal to cleavage. Argillite samples from the central part of the Animikie basin have been shortened a minimum of about 22%, as estimated by this method. These estimates are similar to the shortening values derived from other strain markers in other rock types interbedded with the argillite, and are also consistent with the regional pattern of deformation. ?? 1987.

  1. Measurement of temperature rise during Si cleavage

    International Nuclear Information System (INIS)

    A transient temperature change has been measured during the cleavage of Si(100) wafers both in air and in vacuum (5xl06 torr). A fine thermocouple(TC) (E type) formed by wires of diameter 25 μm was placed in a groove cut on the (100) surface where the crack was to occur. A tiny drop of thermal transfer compound was applied to enhance the thermal conduction between TC and sample surface. The thermocouple signal was recorded by a digital storage adaptor after an amplification of 10,000 by a special low noise amplifier. The width of the pulse appeared to be narrower in vacuum than in air. The difference is ascribed to effects of adsorption. Great care was taken to avoid spurious effects. The technique was tested by experiments on perspex and glass, where the results show reasonable agreement with those from previous work. Theoretical analysis of the measurements shows that the freshly cleaved surface can temporarily attain high temperatures, which is very significant for formation of surface structures

  2. A cleavage toughness master curve model

    International Nuclear Information System (INIS)

    Development of fusion power will require a fracture toughness database, derived largely from small specimen tests, closely integrated with methods to assess first wall and blanket structural integrities. A master curve-shift (MC-ΔT) method has been proposed as an engineering expedient to treat the effects of structural geometry, irradiation, loading rates and safety margins. However, a number of issues related to the MC-ΔT method remain to be resolved, including the universality of MC shapes. A new micromechanical model of fracture toughness in the cleavage transition regime is proposed that combines analytical representations of finite element analysis simulations of crack-tip stress fields with a local critical stress-critical stressed area (σ*-A*) fracture criterion. This model, has been successful in predicting geometry effects, as well as high loading rate and irradiation hardening-induced Charpy shifts. By incorporating a modest temperature dependence in σ*(T), an inconsistency between model predictions and an observed universal-type MC shape is resolved

  3. Localized Calcium Signals along the Cleavage Furrow of the Xenopus Egg Are Not Involved in Cytokinesis

    OpenAIRE

    Noguchi, Tatsuhiko; Mabuchi, Issei

    2002-01-01

    It has been proposed that a localized calcium (Ca) signal at the growing end of the cleavage furrow triggers cleavage furrow formation in large eggs. We have examined the possible role of a Ca signal in cleavage furrow formation in the Xenopus laevis egg during the first cleavage. We were able to detect two kinds of Ca waves along the cleavage furrow. However, the Ca waves appeared after cleavage furrow formation in late stages of the first cleavage. In addition, cleavage was not affected by ...

  4. Detection of nucleic acid sequences by invader-directed cleavage

    Energy Technology Data Exchange (ETDEWEB)

    Brow, Mary Ann D. (Madison, WI); Hall, Jeff Steven Grotelueschen (Madison, WI); Lyamichev, Victor (Madison, WI); Olive, David Michael (Madison, WI); Prudent, James Robert (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  5. Detection of nucleic acid sequences by invader-directed cleavage

    Science.gov (United States)

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  6. Prediction of proteasome cleavage motifs by neural networks

    DEFF Research Database (Denmark)

    Kesimir, C.; Nussbaum, A.K.; Schild, H.;

    2002-01-01

    We present a predictive method that can simulate an essential step in the antigen presentation in higher vertebrates, namely the step involving the proteasomal degradation of polypeptides into fragments which have the potential to bind to MHC Class I molecules. Proteasomal cleavage prediction...... the prediction of MHC Class I ligand boundaries more accurate: 65% of the cleavage sites and 85% of the non-cleavage sites are correctly determined. Moreover, we show that the neural networks trained on the constitutive proteasome data learns a specificity that differs from that of the networks...

  7. Detection of nucleic acids by multiple sequential invasive cleavages 02

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  8. Detection of nucleic acids by multiple sequential invasive cleavages

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  9. Implementation of a combinatorial cleavage and deprotection scheme

    DEFF Research Database (Denmark)

    Nielsen, John; Rasmussen, Palle H.

    1996-01-01

    Phthalhydrazide libraries are synthesized in solution from substituted hydrazines and phthalimides in several different library formats including single compounds, indexed sub-libraries and a full library. When carried out during solid-phase synthesis, this combinatorial cleavage and deprotection...

  10. Scanning tunneling microscopy of the cleavage surface of bismuth crystals

    International Nuclear Information System (INIS)

    The results of in situ studies of the surface structure of the cleavages of bismuth crystals by the method of scanning tunneling microscopy are presented. It is established that cleavage 'opens' the (111) surface with atomically smooth terraces of diatomic steps whose heights are equal to 0.4 nm or a multiple of this value. If the cleavage is made at room temperature, the boundaries of the terraces are usually curved and diffuse owing to the thermal motion with the activation energy of ∼700 K. The cleavage at liquid nitrogen or helium temperatures provides the formation of straight boundaries along the atomic rows on the surface. Twin interlayers of the quantized width of ∼7 nm are revealed. This width value indicates that the atomic planes on both sides of such interlayers intergrow with the interlayer planes inclined to them at a small angle

  11. Detection of nucleic acids by multiple sequential invasive cleavages

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

    2012-10-16

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  12. Mechanisms for ribotoxin-induced ribosomal RNA cleavage

    Energy Technology Data Exchange (ETDEWEB)

    He, Kaiyu [Department of Microbiology and Molecular Genetics (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Zhou, Hui-Ren [Food Science and Human Nutrition (United States); Pestka, James J., E-mail: pestka@msu.edu [Department of Microbiology and Molecular Genetics (United States); Food Science and Human Nutrition (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States)

    2012-11-15

    The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (≥ 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (≥ 10 ng/ml) and ribosome-inactivating protein ricin (≥ 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activated kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-μ and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ► Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ► Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ► Ribotoxins induce rRNA cleavage via

  13. Mechanisms for ribotoxin-induced ribosomal RNA cleavage

    International Nuclear Information System (INIS)

    The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (≥ 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (≥ 10 ng/ml) and ribosome-inactivating protein ricin (≥ 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activated kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-μ and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ► Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ► Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ► Ribotoxins induce rRNA cleavage via

  14. Cross Shear Roll Bonding

    DEFF Research Database (Denmark)

    Bay, Niels; Bjerregaard, Henrik; Petersen, Søren. B;

    1994-01-01

    The present paper describes an investigation of roll bonding an AlZn alloy to mild steel. Application of cross shear roll bonding, where the two equal sized rolls run with different peripheral speed, is shown to give better bond strength than conventional roll bonding. Improvements of up to 20......-23% in bond strength are found and full bond strength is obtained at a reduction of 50% whereas 65% is required in case of conventional roll bonding. Pseudo cross shear roll bonding, where the cross shear effect is obtained by running two equal sized rolls with different speed, gives the same results....

  15. A Historical Trend of Ethnic Cleavages in Contemporary Iran

    OpenAIRE

    Hussein Mohammadzadeh

    2013-01-01

    The goal of this study is evaluation social and historical content of social cleavage in contemporary Iran. Analytical framework rooted in Rokan theory. Rokan believed that social cleavage appearance post of revolutions. Method of study was historical comparatives.The method of this research is comparative historical in which we used of historical documents and data. In this field, I have compared data of indexes of socio-economic of ethnic states.Assessment of data and documents show that so...

  16. Mutational analysis of the encephalomyocarditis virus primary cleavage.

    OpenAIRE

    Hahn, H.; Palmenberg, A C

    1996-01-01

    Sixteen substitution mutations of the conserved DvExNPGP sequence, implicated in cardiovirus and aphthovirus primary polyprotein cleavage, were created in encephalomyocarditis virus cDNA, expressed, and characterized for processing activity. Nearly all the mutations severely decreased the efficiency of the primary cleavage reaction during cell-free synthesis of viral precursors, indicating a stringent requirement for the natural sequence in this processing event. When representative mutations...

  17. Cleavage of a viral polyprotein by a cellular proteolytic activity.

    OpenAIRE

    Tian, Y. C.; Shih, D S

    1986-01-01

    The 200,000-dalton polyprotein encoded by the bottom component RNA of cowpea mosaic virus was synthesized in rabbit reticulocyte lysates, and this in vitro-synthesized protein was isolated from the lysate reaction mixture by sucrose density gradient centrifugation. Incubation of the isolated polyprotein with buffer caused no change in the protein, but incubation with reticulocyte lysates or with fractionated lysate proteins resulted in cleavage of the protein into the expected cleavage produc...

  18. Evidence for intramolecular self-cleavage of picornaviral replicase precursors.

    OpenAIRE

    Palmenberg, A C; Rueckert, R R

    1982-01-01

    It has previously been shown that when encephalomyocarditis viral RNA is translated in cell-free extracts of rabbit reticulocytes, it synthesizes a virus-coded protease, p22, which is derived by cleavage of a precursor protein, C. Protein C is shown here to be cleaved by two different mechanisms, which were distinguished by their sensitivity to dilution. One mechanism was sensitive to dilution; the other was not. The biphasic cleavage behavior was unchanged by diluting incubation mixtures wit...

  19. Catalysis and co-catalysis of bond cleavages in coal and coal analogs

    Energy Technology Data Exchange (ETDEWEB)

    Miller, B.

    1992-01-01

    The catalytic efficiency of 2-pyridone and 4-pyridone (tautomers of 2-hydroxy and 4-hydroxypyridine) for transfer hydrogenolysis of dinaphthyl ether in tetralin at 450 C was investigated. The effectiveness of 2-pyridone dropped when the reaction time was increased, suggesting that the catalyst is destroyed. Reaction of a compound with bromine in CCl[sub 4] yielded a rearrangement product with a minor amount of the cyclization product; in acetonitrile, only the rearrangement product is obtained.

  20. Chemistry of zerumbone. 2. Regulation of ring bond cleavage and unique antibacterial activities of zerumbone derivatives.

    Science.gov (United States)

    Kitayama, T; Yamamoto, K; Utsumi, R; Takatani, M; Hill, R K; Kawai, Y; Sawada, S; Okamoto, T

    2001-10-01

    Further investigation of the chemistry of the eleven-membered cyclic sesquiterpene, zerumbone, the major component of the wild ginger, Zingiber zerumbet Smith, has revealed a new selective epoxidation process, a further example of a novel Favorskii-initiated double ring contraction, and a regiospecific fragmentation of zerumbone dibromide derivatives. Several zerumbone derivatives were found to be selective inhibitors of the growth of gram-positive bacteria. PMID:11758909

  1. Mild N-O Bond Cleavage Reactions of a Pyramidalized Nitrosyl Ligand Bridging a Dimolybdenum Center.

    Science.gov (United States)

    Alvarez, M Angeles; García, M Esther; García-Vivó, Daniel; Ruiz, Miguel A; Toyos, Adrián

    2015-11-16

    Complex [Mo2Cp2(μ-PCy2)(μ-NO)(NO)2] (1) was prepared by reacting [Mo2Cp2(μ-H)(μ-PCy2)(CO)4] with 2 equiv of [NO]BF4 and then treating the resulting product [Mo2Cp2(μ-PCy2)(CO)2(NO)2](BF4) with NaNO2 at 323 K, and it was shown to display a bridging nitrosyl ligand with significant pyramidalization at the N atom, a circumstance related to an unusual behavior concerning degradation of the bridging nitrosyl. Indeed, complex 1 reacts with HBF4·OEt2 to give the nitroxyl-bridged derivative [Mo2Cp2(μ-PCy2)(μ-κ(1):η(2)-HNO)(NO)2](BF4), is reduced by Zn(Hg) in the presence of trace H2O to give the amido complex [Mo2Cp2(μ-PCy2)(μ-NH2)(NO)2], and reacts with excess P(OPh)3 to give the phosphoraniminato-bridged derivative [Mo2Cp2(μ-PCy2){μ-NP(OPh)3}(NO)2]. PMID:26529181

  2. On the radical scavenging activity of isoflavones: thermodynamics of O–H bond cleavage

    Czech Academy of Sciences Publication Activity Database

    Lengyel, Jozef; Rimarčík, J.; Vagánek, A.; Klein, E.

    2013-01-01

    Roč. 15, č. 26 (2013), s. 10895-10903. ISSN 1463-9076 R&D Projects: GA ČR GA203/09/0422 Institutional support: RVO:61388955 Keywords : LOSS ELECTRON-TRANSFER * DISSOCIATION ENTHALPIES * ANTIOXIDANT PROPERTIES Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.198, year: 2013

  3. Dramatically Enhanced Cleavage of the C–C Bond Using an Electrocatalytically Coupled Reaction

    Czech Academy of Sciences Publication Activity Database

    He, Q. P.; Shyam, B.; Macounová, Kateřina; Krtil, Petr; Ramaker, D.; Mukerjee, S.

    2012-01-01

    Roč. 134, č. 20 (2012), s. 8655-8661. ISSN 0002-7863 Institutional support: RVO:61388955 Keywords : RAY-ABSORPTION SPECTROSCOPY * IN-SITU XANES * ETHANOL ELECTROOXIDATION Subject RIV: CG - Electrochemistry Impact factor: 10.677, year: 2012

  4. Oxidation of sterols: Energetics of C–H and O–H bond cleavage

    Czech Academy of Sciences Publication Activity Database

    Lengyel, Jozef; Rimarčík, J.; Vagánek, A.; Fedor, J.; Lukeš, V.; Klein, E.

    2012-01-01

    Roč. 133, č. 4 (2012), s. 1435-1440. ISSN 0308-8146 R&D Projects: GA ČR GAP208/11/0161 Institutional research plan: CEZ:AV0Z40400503 Keywords : phytosterol * oxidation * antioxidant Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.334, year: 2012

  5. Intercapsomeric Disulfide Bonds in Papillomavirus Assembly and Disassembly

    OpenAIRE

    Li, Maolin; Beard, Peter; Estes, Patricia A.; Lyon, Mary K.; Garcea, Robert L.

    1998-01-01

    In order to analyze bonding contacts that stabilize the virion or promote capsid assembly, bovine papillomavirus (BPV) virions were subjected to buffer conditions known to disrupt polyomavirus virions. At physiologic ionic strength, incubation with dithiothreitol (DTT), EGTA, or DTT plus EGTA did not disrupt BPV virions as determined by electron microscopy. However, incubation of virions with DTT rendered the BPV L1 protein susceptible to trypsin cleavage at its carboxy terminus and rendered ...

  6. Internal guide RNA interactions interfere with Cas9-mediated cleavage

    Science.gov (United States)

    Thyme, Summer B.; Akhmetova, Laila; Montague, Tessa G.; Valen, Eivind; Schier, Alexander F.

    2016-01-01

    The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9–gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic factors such as CTCF inhibit mutagenesis. Comparing near-identical gRNA sequences with different in vitro activities reveals that internal gRNA interactions reduce cleavage. Even though gRNAs containing these structures do not yield cleavage-competent complexes, they can compete with active gRNAs for binding to Cas9. These results reveal that both genomic context and internal gRNA interactions can interfere with Cas9-mediated cleavage and illuminate previously uncharacterized features of Cas9–gRNA complex formation. PMID:27282953

  7. Wire bonding in microelectronics

    CERN Document Server

    Harman, George G

    2010-01-01

    Wire Bonding in Microelectronics, Third Edition, has been thoroughly revised to help you meet the challenges of today's small-scale and fine-pitch microelectronics. This authoritative guide covers every aspect of designing, manufacturing, and evaluating wire bonds engineered with cutting-edge techniques. In addition to gaining a full grasp of bonding technology, you'll learn how to create reliable bonds at exceedingly high yields, test wire bonds, solve common bonding problems, implement molecular cleaning methods, and much more. Coverage includes: Ultrasonic bonding systems and technologies, including high-frequency systems Bonding wire metallurgy and characteristics, including copper wire Wire bond testing Gold-aluminum intermetallic compounds and other interface reactions Gold and nickel-based bond pad plating materials and problems Cleaning to improve bondability and reliability Mechanical problems in wire bonding High-yield, fine-pitch, specialized-looping, soft-substrate, and extreme-temperature wire bo...

  8. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-06-15

    We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ∼15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ∼1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

  9. Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-01-01

    We use quantum mechanics/molecular mechanics (QM/MM) simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ~15 kcal mol−1, encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ~1–100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The non-monotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA cleavage reaction. PMID:21539371

  10. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

    KAUST Repository

    Frusciante, Sarah

    2014-08-05

    Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7′,8′ double bonds adjacent to a 3-OH-β-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-β-apo-8′-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-β-apo-8′-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the β-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope.

  11. CD44 Binding to Hyaluronic Acid Is Redox Regulated by a Labile Disulfide Bond in the Hyaluronic Acid Binding Site

    OpenAIRE

    Kellett-Clarke, Helena; Stegmann, Monika; Barclay, A. Neil; Metcalfe, Clive

    2015-01-01

    CD44 is the primary leukocyte cell surface receptor for hyaluronic acid (HA), a component of the extracellular matrix. Enzymatic post translational cleavage of labile disulfide bonds is a mechanism by which proteins are structurally regulated by imparting an allosteric change and altering activity. We have identified one such disulfide bond in CD44 formed by Cys77 and Cys97 that stabilises the HA binding groove. This bond is labile on the surface of leukocytes treated with chemical and enzyma...

  12. Palladium-Catalyzed Deaminative Phenanthridinone Synthesis from Aniline via C-H Bond Activation.

    Science.gov (United States)

    Yedage, Subhash L; Bhanage, Bhalchandra M

    2016-05-20

    This work reports palladium-catalyzed phenanthridinone synthesis using the coupling of aniline and amide by formation of C-C and C-N bonds in a one-pot fashion via dual C-H bond activation. It involves simultaneous cleavage of four bonds and the formation of two new bonds. The present protocol is ligand-free, takes place under mild reaction conditions, and is environmentally benign as nitrogen gas and water are the only side products. This transformation demonstrates a broad range of aniline and amide substrates with different functional groups and has been scaled up to gram level. PMID:27088815

  13. Location of spermine and other polyamines on DNA as revealed by photoaffinity cleavage with polyaminobenzenediazonium salts

    International Nuclear Information System (INIS)

    Although polyamines interact strongly with nucleic acids, X-ray and NMR studies have not revealed much structural information about spermine-DNA complexes. Therefore, it was of interest to look at the binding of polyamines to 32P-labeled DNA restriction fragments by sequencing gel electrophoresis of the photoaffinity cleavage products induced by polyaminobenzenediazonium salts. The shift of cleavage patterns observed on opposite strands as well as competition experiments with distamycin shows polyamines to be located in the minor groove of B-DNA and to depend on the nucleic acid polymorphism, jumping to the major groove in the A-form. The sequence selectivities of various polycations (spermine, putrescine, and cobalt(III) hexaammine) are similar and slightly favor A,T-rich regions. Taken together, these results show that polycations which are not point charges are guided by the electronegative potential along the nucleic acid and suggest fast crawling of the polyamine within the minor groove, due to individual NH2+ jumping between multiple equidistant and isoenergetic bidentate hydrogen-bonding sites. Such a picture could be the clue to the unexpected NMR and to the frequently silent X-ray behavior of polyamines when bound to DNA

  14. Optimization schemes for selective molecular cleavage with tailored ultrashort laser pulses

    International Nuclear Information System (INIS)

    Graphical abstract: Isosurface plot of the electronic density, and positions of the nuclei, during the irradiation of a formaldiminium ion with an optimized laser pulse, leading to the selective cleavage of a proton. Display Omitted Highlights: ► We use QOCT in combination with mixed quantum-classical molecular models. ► TDDFT models the electrons coupled to the nuclei through Ehrenfest equations. ► Both gradient-free and gradient-based algorithms are explored for the optimization. ► We explore different options for the definition of the target functional. - Abstract: We present some approaches to the computation of ultra-fast laser pulses capable of selectively breaking molecular bonds. The calculations are based on a mixed quantum-classical description: The electrons are treated quantum mechanically (making use of time-dependent density-functional theory), whereas the nuclei are treated classically. The temporal shape of the pulses is tailored to maximize a control target functional which is designed to produce the desired molecular cleavage. The precise definition of this functional is a crucial ingredient: we explore expressions based on the forces, on the momenta and on the velocities of the nuclei. The algorithm used to find the optimum pulse is also relevant; we test both direct gradient-free algorithms, as well as schemes based on formal optimal control theory. The tests are performed both on one dimensional models of atomic chains, and on first-principles descriptions of molecules.

  15. On Bond Portfolio Management

    OpenAIRE

    Vladislav Kargin

    2002-01-01

    This paper describes a new method of bond portfolio optimization based on stochastic string models of correlation structure in bond returns. The paper shows how to approximate correlation function of bond returns, compute the optimal portfolio allocation using Wiener-Hopf factorization, and check whether a collection of bonds presents arbitrage opportunities.

  16. Molecular Basis of Catalytic Chamber-assisted Unfolding and Cleavage of Human Insulin by Human Insulin-degrading Enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Manolopoulou, Marika; Guo, Qing; Malito, Enrico; Schilling, Alexander B.; Tang, Wei-Jen; (UC); (UIC)

    2009-06-02

    Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together. Using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to obtain high mass accuracy, and electron capture dissociation (ECD) to selectively break the disulfide bonds in gas phase fragmentation, we determined the cleavage sites and composition of human insulin fragments generated by human IDE. Our time-dependent analysis of IDE-digested insulin fragments reveals that IDE is highly processive in its initial cleavage at the middle of both the insulin A and B chains. This ensures that IDE effectively splits insulin into inactive N- and C-terminal halves without breaking the disulfide bonds. To understand the molecular basis of the recognition and unfolding of insulin by IDE, we determined a 2.6-A resolution insulin-bound IDE structure. Our structure reveals that IDE forms an enclosed catalytic chamber that completely engulfs and intimately interacts with a partially unfolded insulin molecule. This structure also highlights how the unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity ( approximately 100 nm) for insulin. In addition, this structure shows how IDE utilizes the interaction of its exosite with the N terminus of the insulin A chain as well as other properties of the catalytic chamber to guide the unfolding of insulin and allowing for the processive cleavages.

  17. Multicenter bonds, bond valence and bond charge apportion

    International Nuclear Information System (INIS)

    In the same way that the valence of an atom issues from the definition of bond index, we shoe here that the three-center bond index lends itself to the definition of a bond valence. Within the charge of a bond, we show that its self-charge (i.e., the amount of electron kept by the atoms involved in the bond) is parted in a such a way that the more electronegative atom tends to allot more electronic charge than the other atom. We give examples of these quantities and discuss the results for different kinds of chemical systems. We also show some results for four-center indices and report six-center indices for hexagonal rings. (author). 54 refs., 4 figs., 8 tabs

  18. Size effects and strain localization in atomic-scale cleavage modeling.

    Science.gov (United States)

    Elsner, B A M; Müller, S

    2015-09-01

    In this work, we study the adhesion and decohesion of Cu(1 0 0) surfaces using density functional theory (DFT) calculations. An upper stress to surface decohesion is obtained via the universal binding energy relation (UBER), but the model is limited to rigid separation of bulk-terminated surfaces. When structural relaxations are included, an unphysical size effect arises if decohesion is considered to occur as soon as the strain energy equals the energy of the newly formed surfaces. We employ the nudged elastic band (NEB) method to show that this size effect is opposed by a size-dependency of the energy barriers involved in the transition. Further, we find that the transition occurs via a localization of bond strain in the vicinity of the cleavage plane, which resembles the strain localization at the tip of a sharp crack that is predicted by linear elastic fracture mechanics. PMID:26219654

  19. Size effects and strain localization in atomic-scale cleavage modeling

    International Nuclear Information System (INIS)

    In this work, we study the adhesion and decohesion of Cu(1 0 0) surfaces using density functional theory (DFT) calculations. An upper stress to surface decohesion is obtained via the universal binding energy relation (UBER), but the model is limited to rigid separation of bulk-terminated surfaces. When structural relaxations are included, an unphysical size effect arises if decohesion is considered to occur as soon as the strain energy equals the energy of the newly formed surfaces. We employ the nudged elastic band (NEB) method to show that this size effect is opposed by a size-dependency of the energy barriers involved in the transition. Further, we find that the transition occurs via a localization of bond strain in the vicinity of the cleavage plane, which resembles the strain localization at the tip of a sharp crack that is predicted by linear elastic fracture mechanics. (paper)

  20. Optimization Schemes for Selective Molecular Cleavage with Tailored Ultrashort Laser Pulses

    CERN Document Server

    Krieger, Kevin; Gross, E K U

    2011-01-01

    We present some approaches to the computation of ultra-fast laser pulses capable of selectively breaking molecular bonds. The calculations are based on a mixed quantum-classical description: The electrons are treated quantum mechanically (making use of time-dependent density-functional theory), whereas the nuclei are treated classically. The temporal shape of the pulses is tailored to maximise a control target functional which is designed to produce the desired molecular cleavage. The precise definition of this functional is a crucial ingredient: we explore expressions based on the forces, on the momenta and on the velocities of the nuclei. The algorithm used to find the optimum pulse is also relevant; we test both direct gradient-free algorithms, as well as schemes based on formal optimal control theory. The tests are performed both on one dimensional models of atomic chains, and on first-principles descriptions of molecules.

  1. Small molecule activators of pre-mRNA 3′ cleavage

    OpenAIRE

    Ryan, Kevin; Khleborodova, Asya; Pan, Jingyi; Ryan, Xiaozhou P.

    2009-01-01

    3′ Cleavage and polyadenylation are obligatory steps in the biogenesis of most mammalian pre-mRNAs. In vitro reconstitution of the 3′ cleavage reaction from human cleavage factors requires high concentrations of creatine phosphate (CP), though how CP activates cleavage is not known. Previously, we proposed that CP might work by competitively inhibiting a cleavage-suppressing serine/threonine (S/T) phosphatase. Here we show that fluoride/EDTA, a general S/T phosphatase inhibitor, activates in ...

  2. Local approach to strength mis-match effect on cleavage fracture of notched material

    International Nuclear Information System (INIS)

    This paper discusses the strength mis-match effect on cleavage fracture of notched materials based on the local approach. The aim of the study is to verify the independence of the critical Weibull stress at fracture on the strength mis-match condition. Diffusion bonded joints were made with two materials S and H different in strength level. Two types of 3-point bend specimen were extracted. One had a notch in the lower strength material S near the bonded interface, and another in the higher strength material H. Homogeneous specimens were also made for each material. The critical CTOD value at cleavage fracture for the overmatched specimen with a notch in the material S was smaller than that of the homogeneous specimen of the material S. By contrast, the undermatched specimen with a notch in the material H showed apparently larger critical CTOD value than the homogeneous specimen of the material H. The strength mis-match effect on the CTOD results was explained in terms of the constraint effect on the near-tip stress field. Namely, the near-tip stress is elevated by strength overmatching and relaxed by strength undermatching. The Weibull stresses for the homogeneous and mis-matched specimens were evaluated in the light of the near-tip stress fields. The critical Weibull stress at fracture did not depend on the strength mis-match condition near the notch. By using the critical Weibull stress obtained for the homogeneous specimen, the strength mis-match effect on the CTOD results can be predicted. Close agreement was observed between the critical CTOD value predicted and that obtained by the experiment. (orig.)

  3. Mechanism of intramembrane cleavage of alcadeins by γ-secretase.

    Directory of Open Access Journals (Sweden)

    Yi Piao

    Full Text Available BACKGROUND: Alcadein proteins (Alcs; Alcα, Alcβand Alcγ are predominantly expressed in neurons, as is Alzheimer's β-amyloid (Aβ precursor protein (APP. Both Alcs and APP are cleaved by primary α- or β-secretase to generate membrane-associated C-terminal fragments (CTFs. Alc CTFs are further cleaved by γ-secretase to secrete p3-Alc peptide along with the release of intracellular domain fragment (Alc ICD from the membrane. In the case of APP, APP CTFβ is initially cleaved at the ε-site to release the intracellular domain fragment (AICD and consequently the γ-site is determined, by which Aβ generates. The initial ε-site is thought to define the final γ-site position, which determines whether Aβ40/43 or Aβ42 is generated. However, initial intracellular ε-cleavage sites of Alc CTF to generate Alc ICD and the molecular mechanism that final γ-site position is determined remains unclear in Alcs. METHODOLOGY: Using HEK293 cells expressing Alcs plus presenilin 1 (PS1, a catalytic unit of γ-secretase and the membrane fractions of these cells, the generation of p3-Alc possessing C-terminal γ-cleavage site and Alc ICD possessing N-terminal ε-cleavage site were analysed with MALDI-TOF/MS. We determined the initial ε-site position of all Alcα, Alcβ and Alcγ, and analyzed the relationship between the initially determined ε-site position and the final γ-cleavage position. CONCLUSIONS: The initial ε-site position does not always determine the final γ-cleavage position in Alcs, which differed from APP. No additional γ-cleavage sites are generated from artificial/non-physiological positions of ε-cleavage for Alcs, while the artificial ε-cleavage positions can influence in selection of physiological γ-site positions. Because alteration of γ-secretase activity is thought to be a pathogenesis of sporadic Alzheimer's disease, Alcs are useful and sensitive substrate to detect the altered cleavage of substrates by γ-secretase, which may

  4. Pripper: prediction of caspase cleavage sites from whole proteomes

    Directory of Open Access Journals (Sweden)

    Salmi Jussi

    2010-06-01

    Full Text Available Abstract Background Caspases are a family of proteases that have central functions in programmed cell death (apoptosis and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed well in predicting caspase cleavage sites, and when combining different classifiers the accuracy increased further. A new tool, Pripper, was developed to utilize the classifiers and predict the caspase cut sites from an arbitrary number of input sequences. A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. Both known caspase cleavage products as well as novel cleavage products were identified using the database demonstrating the usefulness of the tool. Pripper is not restricted to predicting only caspase cut sites, but it gives the possibility to scan protein sequences for any given motif(s and predict cut sites once a suitable cut site prediction model for any other protease has been developed. Pripper is freely available and can be downloaded from http://users.utu.fi/mijopi/Pripper. Conclusions We have developed Pripper, a tool for

  5. Cell-surface acceleration of urokinase-catalyzed receptor cleavage

    DEFF Research Database (Denmark)

    Høyer-Hansen, G; Ploug, M; Behrendt, N;

    1997-01-01

    or indirectly mediated by uPA itself. In a soluble system, uPA can cleave purified uPAR, but the low efficiency of this reaction has raised doubts as to whether uPA is directly responsible for uPAR cleavage on the cells. We now report that uPA-catalyzed cleavage of uPAR on the cell surface is...... strongly favored relative to the reaction in solution. The time course of uPA-catalyzed cleavage of cell-bound uPAR was studied using U937 cells stimulated with phorbol 12-myristate 13-acetate. Only 30 min was required for 10 nM uPA to cleave 50% of the cell-bound uPAR. This uPA-catalyzed cleavage reaction...... was inhibited by a prior incubation of the cells with uPA inactivated by diisopropyl fluorophosphate, demonstrating a requirement for specific receptor binding of the active uPA to obtain the high-efficiency cleavage of cell-bound uPAR. Furthermore, amino-terminal sequence analysis revealed that u...

  6. C-Terminally modified peptides via cleavage of the HMBA linker by O-, N- or S-nucleophiles

    DEFF Research Database (Denmark)

    Hansen, Jonas; Diness, Frederik; Meldal, Morten Peter

    2016-01-01

    A large variety of C-terminally modified peptides was obtained by nucleophilic cleavage of the ester bond in solid phase linked peptide esters of 4-hydroxymethyl benzamide (HMBA). The developed methods provided peptides, C-terminally functionalized as esters, amides and thioesters, with high puri...

  7. Short RNA guides cleavage by eukaryotic RNase III.

    Directory of Open Access Journals (Sweden)

    Bruno Lamontagne

    Full Text Available In eukaryotes, short RNAs guide a variety of enzymatic activities that range from RNA editing to translation repression. It is hypothesized that pre-existing proteins evolved to bind and use guide RNA during evolution. However, the capacity of modern proteins to adopt new RNA guides has never been demonstrated. Here we show that Rnt1p, the yeast orthologue of the bacterial dsRNA-specific RNase III, can bind short RNA transcripts and use them as guides for sequence-specific cleavage. Target cleavage occurred at a constant distance from the Rnt1p binding site, leaving the guide RNA intact for subsequent cleavage. Our results indicate that RNase III may trigger sequence-specific RNA degradation independent of the RNAi machinery, and they open the road for a new generation of precise RNA silencing tools that do not trigger a dsRNA-mediated immune response.

  8. Analytical model for intergrain expansion and cleavage: random grain boundaries

    International Nuclear Information System (INIS)

    A description of rigid-body grain boundary relaxation and cleavage in tungsten is performed using a pair-wise Morse interatomic potential in real and reciprocal spaces. Cleavage energies and grain boundary dilatation of random grain boundaries were formulated and computed using atomic layer interaction energies. These values were determined using a model for a relaxed random grain boundary that consists of rigid grains on either side of the boundary plane that are allowed to float to reach the equilibrium position. Expressions are given that describe in real space the energy of interatomic interaction on random grain boundaries with twist orientation. It was shown that grain-boundary expansion and cleavage energies of the most widespread random grain boundaries are mainly determined by grain boundary atomic density

  9. A new cultural cleavage in post-modern society

    Directory of Open Access Journals (Sweden)

    Jan-Erik Lane

    2007-09-01

    Full Text Available The attitudes towards gender and homosexuality tend to be linked at the micro level (individuals, which explains the political saliency of this newly emerging cleavage. At the macro level (country, the main finding is that the value orientations towards gender and homosexuality are strongly embedded in the basic cultural or civilisation differences among countries. As developing countries modernise and enter post-modernity, they will also experience the gender cleavage, especially when they adhere to an individualistic culture. Cultural cleavages in the post-modern society, whether in rich or developing countries, can only be properly researched by the survey method. It opens up a large area for both micro and macro analyses in the social sciences.

  10. Three-dimensional interpretation of cleavage fracture tests of cladded specimens with local approach to cleavage fracture

    International Nuclear Information System (INIS)

    Electricite de France has conducted during these last years an experimental and numerical research programme in order to evaluate fracture mechanics analyses used in nuclear reactor pressure vessels integrity assessment, regarding the risk of brittle fracture. Two cladded specimens made of ferritic steel A508 Cl3 with stainless steel cladding, and containing shallow subclad flaws, have been tested in four point bending at very low temperature to obtain cleavage failure. The crack instability was obtained in base metal by cleavage fracture, without crack arrest. The tests have been interpreted by local approach to cleavage fracture (Beremin model) using three-dimensional finite element computations. After the elastic-plastic computation of stress intensity factor KJ along the crack front, the probability of cleavage failure of each specimen is evaluated using m, σu Beremin model parameters identified on the same material. The failure of two specimens is conservatively predicted by both analyses. The elastic-plastic stress intensity factor KJ in base metal is always greater than base metal fracture toughness K1c. The calculated probabilities of cleavage failure are in agreement with experimental results. The sensitivity of Beremin model to numerical aspects is finally exposed. (orig.)

  11. Hydrogen bonded supramolecular structures

    CERN Document Server

    Li, Zhanting

    2015-01-01

    This book covers the advances in the studies of hydrogen-bonding-driven supramolecular systems  made over the past decade. It is divided into four parts, with the first introducing the basics of hydrogen bonding and important hydrogen bonding patterns in solution as well as in the solid state. The second part covers molecular recognition and supramolecular structures driven by hydrogen bonding. The third part introduces the formation of hollow and giant macrocycles directed by hydrogen bonding, while the last part summarizes hydrogen bonded supramolecular polymers. This book is designed to b

  12. Synthesis, antioxidant and DNA cleavage activities of novel indole derivatives.

    Science.gov (United States)

    Biradar, J S; Sasidhar, B S; Parveen, R

    2010-09-01

    A new series of novel indole derivatives containing barbitone moiety (5a-i) are synthesized by simple and efficient condensation of chalcones (3a-i) with barbituric acid (4). The synthesized compounds are screened for their antioxidant (free radical scavenging, total antioxidant capacity and ferric reducing antioxidant power) and DNA cleavage activities were evaluated. Among the synthesized compounds (5a), (5d) and (5g) exhibited excellent antioxidant activity and all the tested compounds in the series have exhibited promising DNA cleavage activities. The structures of the synthesized compounds are assigned on the basis of elemental analysis, IR, (1)H NMR, (13)C NMR and mass spectral data. PMID:20594623

  13. Sensitive and fast mutation detection by solid phase chemical cleavage

    DEFF Research Database (Denmark)

    Hansen, Lise Lotte; Justesen, Just; Kruse, Torben A

    1996-01-01

    We have developed a solid phase chemical cleavage method (SpCCM) for screening large DNA fragments for mutations. All reactions can be carried out in microtiterwells from the first amplification of the patient (or test) DNA through the search for mutations. The reaction time is significantly...... reduced compared to the conventional chemical cleavage method (CCM), and even by using a uniformly labelled probe, the exact position and nature of the mutation can be revealed. The SpCCM is suitable for automatization using a workstation to carry out the reactions and a fluorescent detection-based DNA...

  14. Bonding silicones with epoxies

    Energy Technology Data Exchange (ETDEWEB)

    Tira, J.S.

    1980-01-01

    It is shown that silicones, both room temperature vulcanizing (RTV) and millable rubber (press cured) can be successfully bonded to other materials using plasma treatment and epoxy adhesives. The plasma treatment using dry air atmosphere increases the surface energy of the silicone and thus provides a lower water contact angle. This phenomenon allows the epoxy adhesive to wet the silicone surface and ultimately bond. Bond strengths are sufficiently high to result in failures in the silicone materials rather than the adhesive bond.

  15. Australia's Bond Home Bias

    OpenAIRE

    Mishra, Anil V; Umaru B. Conteh

    2014-01-01

    This paper constructs the float adjusted measure of home bias and explores the determinants of bond home bias by employing the International Monetary Fund's high quality dataset (2001 to 2009) on cross-border bond investment. The paper finds that Australian investors' prefer investing in countries with higher economic development and more developed bond markets. Exchange rate volatility appears to be an impediment for cross-border bond investment. Investors prefer investing in countries with ...

  16. Malaysia : Bond Market Development

    OpenAIRE

    International Monetary Fund; World Bank

    2013-01-01

    This paper pertains to the bond market development in Malaysia, and provides an overview of the market scenario in the country. Malaysia has been successful in developing the capital markets, particularly bond markets, in the recent past. Now, it faces the challenge of how to improve broader access and efficiency of the bond market. A high degree of investor concentration, dominated by gov...

  17. Chemical bond fundamental aspects of chemical bonding

    CERN Document Server

    Frenking, Gernot

    2014-01-01

    This is the perfect complement to ""Chemical Bonding - Across the Periodic Table"" by the same editors, who are two of the top scientists working on this topic, each with extensive experience and important connections within the community. The resulting book is a unique overview of the different approaches used for describing a chemical bond, including molecular-orbital based, valence-bond based, ELF, AIM and density-functional based methods. It takes into account the many developments that have taken place in the field over the past few decades due to the rapid advances in quantum chemica

  18. Fe-Catalyzed Oxidative Cleavage of Unsaturated Fatty Acids

    NARCIS (Netherlands)

    Spannring, P.

    2013-01-01

    The oxidative cleavage of unsaturated fatty acids into aldehydes or carboxylic acids gives access to valuable products. The products can be used as chemical building blocks, as emulsifiers or in the paint or polymer industry. Ozonolysis is applied industrially to cleave the fatty acid oleic acid int

  19. Perceiving Social Cleavages and Inequalities: The Case of Israeli Adolescents.

    Science.gov (United States)

    Dar, Yechezkel; Erhard, Rachel; Resh, Nura

    1998-01-01

    An analysis of perceptions of social cleavage and inequality among approximately 9000 Israeli eighth and ninth graders showed students accurately comprehended a multifaceted society with major social divisions. A social map with inequality was revealed in which ethnicity played the least prominent role. Personal and social traits influenced…

  20. The pattern of DNA cleavage intensity around indels.

    Science.gov (United States)

    Chen, Wei; Zhang, Liqing

    2015-01-01

    Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensities in the 200 base pair regions surrounding these indels. Our results show that DNA cleavage intensities close to the start and end points of indels are significantly lower than other regions, for both small human germline and somatic indels and also for mouse small indels. Compared to small indels, the patterns of DNA cleavage intensity around large indels are more complex, and there are two low intensity regions near each end of the indels that are approximately 13 bp apart from each other. Detailed analyses of a subset of indels show that there is slight difference in cleavage intensity distribution between insertion indels and deletion indels that could be contributed by their respective enrichment of different repetitive elements. These results will provide new insight into indel generation mechanisms. PMID:25660536

  1. Cleavage sites within the poliovirus capsid protein precursors

    International Nuclear Information System (INIS)

    Partial amino-terminal sequence analysis was performed on radiolabeled poliovirus capsid proteins VP1, VP2, and VP3. A computer-assisted comparison of the amino acid sequences obtained with that predicted by the nucleotide sequence of the poliovirus genome allows assignment of the amino terminus of each capsid protein to a unique position within the virus polyprotein. Sequence analysis of trypsin-digested VP4, which has a blocked amino terminus, demonstrates that VP4 is encoded at or very near to the amino terminus of the polyprotein. The gene order of the capsid proteins is VP4-VP2-VP3-VP1. Cleavage of VP0 to VP4 and VP2 is shown to occur between asparagine and serine, whereas the cleavages that separate VP2/VP3 and VP3/VP1 occur between glutamine and glycine residues. This finding supports the hypothesis that the cleavage of VP0, which occurs during virion morphogenesis, is distinct from the cleavages that separate functional regions of the polyprotein

  2. Modeling Radial Holoblastic Cleavage: A Laboratory Activity for Developmental Biology.

    Science.gov (United States)

    Ellis, Linda K.

    2000-01-01

    Introduces a laboratory activity designed for an undergraduate developmental biology course. Uses Play-Doh (plastic modeling clay) to build a multicellular embryo in order to provide a 3-D demonstration of cleavage. Includes notes for the instructor and student directions. (YDS)

  3. Sequence specific inhibition of DNA restriction enzyme cleavage by PNA

    DEFF Research Database (Denmark)

    Nielsen, P.E.; Egholm, M.; Berg, R.H.;

    1993-01-01

    Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets proximally flanked by two restriction enzyme sites were challenged with the complementary PNA or PNAs having one or two mismatches, and the effect on the restriction enzyme cleavage of the flanking sites was...

  4. Crack tip blunting and cleavage under dynamic conditions

    Science.gov (United States)

    Rajan, V. P.; Curtin, W. A.

    2016-05-01

    In structural materials with both brittle and ductile phases, cracks often initiate within the brittle phase and propagate dynamically towards the ductile phase. The macroscale, quasistatic toughness of the material thus depends on the outcome of this microscale, dynamic process. Indeed, dynamics has been hypothesized to suppress dislocation emission, which may explain the occurrence of brittle transgranular fracture in mild steels at low temperatures (Lin et al., 1987). Here, crack tip blunting and cleavage under dynamic conditions are explored using continuum mechanics and molecular dynamics simulations. The focus is on two questions: (1) whether dynamics can affect the energy barriers for dislocation emission and cleavage, and (2) what happens in the dynamic "overloaded" situation, in which both processes are energetically possible. In either case, dynamics may shift the balance between brittle cleavage and ductile blunting, thereby affecting the intrinsic ductility of the material. To explore these effects in simulation, a novel interatomic potential is used for which the intrinsic ductility is tunable, and a novel simulation technique is employed, termed as a "dynamic cleavage test", in which cracks can be run dynamically at a prescribed energy release rate into a material. Both theory and simulation reveal, however, that the intrinsic ductility of a material is unaffected by dynamics. The energy barrier to dislocation emission appears to be identical in quasi-static and dynamic conditions, and, in the overloaded situation, ductile crack tip behavior ultimately prevails since a single emission event can blunt and arrest the crack, preventing further cleavage. Thus, dynamics cannot embrittle a ductile material, and the origin of brittle failure in certain alloys (e.g., mild steels) appears unrelated to dynamic effects at the crack tip.

  5. C-H bond activation by f-block complexes.

    Science.gov (United States)

    Arnold, Polly L; McMullon, Max W; Rieb, Julia; Kühn, Fritz E

    2015-01-01

    Most homogeneous catalysis relies on the design of metal complexes to trap and convert substrates or small molecules to value-added products. Organometallic lanthanide compounds first gave a tantalizing glimpse of their potential for catalytic C-H bond transformations with the selective cleavage of one C-H bond in methane by bis(permethylcyclopentadienyl)lanthanide methyl [(η(5) -C5 Me5 )2 Ln(CH3 )] complexes some 25 years ago. Since then, numerous metal complexes from across the periodic table have been shown to selectively activate hydrocarbon C-H bonds, but the challenges of closing catalytic cycles still remain; many f-block complexes show great potential in this important area of chemistry. PMID:25384554

  6. School Desegregation and Racial Cleavage, 1954-1970: A Review of the Literature

    Science.gov (United States)

    Carithers, Martha W.

    1970-01-01

    Reviews the empirical studies dealing with school desegregation and racial cleavage which have appeared since the 1954 Supreme Court decision. Focuses on patterns and consequences of interracial association, and attitude change relevant to racial cleavage. (DM)

  7. The effect of structure in a long target RNA on ribozyme cleavage efficiency.

    OpenAIRE

    Campbell, T B; McDonald, C K; Hagen, M.

    1997-01-01

    Inhibition of gene expression by catalytic RNA (ribozymes) requires that ribozymes efficiently cleave specific sites within large target RNAs. However, the cleavage of long target RNAs by ribozymes is much less efficient than cleavage of short oligonucleotide substrates because of higher order structure in the long target RNA. To further study the effects of long target RNA structure on ribozyme cleavage efficiency, we determined the accessibility of seven hammerhead ribozyme cleavage sites i...

  8. Mutational analysis of a type II topoisomerase cleavage site: distinct requirements for enzyme and inhibitors.

    OpenAIRE

    Freudenreich, C H; Kreuzer, K. N.

    1993-01-01

    We have analyzed the DNA sequence requirements for cleavage of a 30 bp oligonucleotide that contains a strong bacteriophage T4 type II topoisomerase site. A novel method was used to generate substrates with each of the four nucleotides at 10 positions surrounding the cleavage site, and mutant substrates were also prepared for the four internal positions of the staggered cleavage site. The substrates were tested for cleavage in the presence of several inhibitors that induce enzyme-mediated cle...

  9. Cleavage patterns and the topology of the metazoan tree of life

    OpenAIRE

    Valentine, James W.

    1997-01-01

    Several major alliances of metazoan phyla have been identified by small subunit rRNA sequence comparisons. It is possible to arrange the phyla to produce a parsimonious distribution of cleavage types, requiring only one change from a radial ancestral condition to spiral cleavage and one other to “idiosyncratic” cleavage; this arrangement is consistent with most of the recent molecular phylogenies. The cleavage shifts are correlated with changes in many of the features that once were used to d...

  10. Weak bond screening system

    Science.gov (United States)

    Chuang, S. Y.; Chang, F. H.; Bell, J. R.

    Consideration is given to the development of a weak bond screening system which is based on the utilization of a high power ultrasonic (HPU) technique. The instrumentation of the prototype bond strength screening system is described, and the adhesively bonded specimens used in the system developmental effort are detailed. Test results obtained from these specimens are presented in terms of bond strength and level of high power ultrasound irradiation. The following observations were made: (1) for Al/Al specimens, 2.6 sec of HPU irradiation will screen weak bond conditions due to improper preparation of bonding surfaces; (2) for composite/composite specimens, 2.0 sec of HPU irradiation will disrupt weak bonds due to under-cured conditions; (3) for Al honeycomb core with composite skin structure, 3.5 sec of HPU irradiation will disrupt weak bonds due to bad adhesive or oils contamination of bonding surfaces; and (4) for Nomex honeycomb with Al skin structure, 1.3 sec of HPU irradiation will disrupt weak bonds due to bad adhesive.

  11. Bond Markets in Africa

    OpenAIRE

    Yibin Mu; Peter Phelps; Janet Gale Stotsky

    2013-01-01

    African bond markets have been steadily growing in recent years, but nonetheless remain undeveloped. African countries would benefit from greater access to financing and deeper financial markets. This paper compiles a unique set of data on corporate bond markets in Africa. It then applies an econometric model to analyze the key determinants of African government securities market and corporate bond market capitalization. Government securities market capitalization is directly related to bette...

  12. Build America Bonds

    OpenAIRE

    Andrew Ang; Vineer Bhansali; Yuhang Xing

    2010-01-01

    Build America Bonds (BABs) are a new form of municipal financing introduced in 2009. Investors in BAB municipal bonds receive interest payments that are taxable, but issuers receive a subsidy from the U.S. Treasury. The BAB program has succeeded in lowering the cost of funding for state and local governments with BAB issuers obtaining finance 54 basis points lower, on average, compared to issuing regular municipal bonds. For institutional investors, BAB issue yields are 116 basis points highe...

  13. Sequence specificity of DNA cleavage by Micrococcus luteus γ endonuclease

    International Nuclear Information System (INIS)

    DNA fragments of defined sequence have been used to determine the sites of cleavage by γ-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus γ endonuclease and analyzed on irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to γ radiation

  14. The Bond Market's q

    OpenAIRE

    Thomas Philippon

    2006-01-01

    I propose an implementation of the q-theory of investment using bond prices instead of equity prices. Credit risk makes corporate bond prices sensitive to future asset values, and q can be inferred from bond prices. The bond market's q performs much better than the usual measure in standard investment equations. With aggregate data, the fit is three times better, cash flows are driven out and the implied adjustment costs are reduced by more than an order of magnitude. The new measure also imp...

  15. Copper wire bonding

    CERN Document Server

    Chauhan, Preeti S; Zhong, ZhaoWei; Pecht, Michael G

    2014-01-01

    This critical volume provides an in-depth presentation of copper wire bonding technologies, processes and equipment, along with the economic benefits and risks.  Due to the increasing cost of materials used to make electronic components, the electronics industry has been rapidly moving from high cost gold to significantly lower cost copper as a wire bonding material.  However, copper wire bonding has several process and reliability concerns due to its material properties.  Copper Wire Bonding book lays out the challenges involved in replacing gold with copper as a wire bond material, and includes the bonding process changes—bond force, electric flame off, current and ultrasonic energy optimization, and bonding tools and equipment changes for first and second bond formation.  In addition, the bond–pad metallurgies and the use of bare and palladium-coated copper wires on aluminum are presented, and gold, nickel and palladium surface finishes are discussed.  The book also discusses best practices and re...

  16. Hydrogen bonding and anaesthesia

    Science.gov (United States)

    Sándorfy, C.

    2004-12-01

    General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics. Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.

  17. Mutagenesis of the yellow fever virus NS2B/3 cleavage site: determinants of cleavage site specificity and effects on polyprotein processing and viral replication.

    OpenAIRE

    Chambers, T J; Nestorowicz, A.; Rice, C.M.

    1995-01-01

    The determinants of cleavage site specificity of the yellow fever virus (YF) NS3 proteinase for its 2B/3 cleavage site have been studied by using site-directed mutagenesis. Mutations at residues within the GARR decreases S sequence were tested for effects on cis cleavage of an NS2B-3(181) polyprotein during cell-free translation. At the P1 position, only the conservative substitution R-->K exhibited significant levels of cleavage. Conservative and nonconservative substitutions were tolerated ...

  18. Small Molecule-Mediated Cleavage of RNA in Living Cells

    OpenAIRE

    Guan, Lirui; Disney, Matthew D.

    2012-01-01

    Antisense oligonucleotides and small interfering RNAs (siRNAs) control gene expression by triggering the degradation of a mRNA via recruitment of RNase H or the RNA-induced silencing complex (RISC), respectively.[1] These approaches are hampered, however, by the poor cellular permeability of oligonucleotides. A small molecule approach to cleave RNA targets could obviate uptake issues. Several compounds can induce RNA cleavage in vitro,[2] however, to the best of our knowledge no small molecul...

  19. Effects of Cysteamine on Sheep Embryo Cleavage Rates

    OpenAIRE

    ENGİNLER, Sinem Ö; ÖZDAŞ, Özen B.; SANDAL, Asiye İ.; ARICI, Ramazan; GÜNDÜZ, Mehmet C.; BARAN, Alper; TEK, Çağatay; KILIÇARSLAN, Mehmet R.; Ak, Kemal

    2015-01-01

    Oxidative stress during in vitro culture leads to defects in development of gametes and embryos. Several antioxidants such as cysteamine, L-ascorbic acid, beta mercaptoethanol, cysteine, glutathione, proteins, vitamins have been used to supplement culture media to counter the oxidative stress. This study was conducted to detect the effect of adding cysteamine to the maturation medium to subsequent cleavage rates of sheep embryos. Totally 604 ovaries were obtained by ten replica and 2060 oocyt...

  20. Interrelation between local and global characteristics of cleavage fracture

    Czech Academy of Sciences Publication Activity Database

    Grishchenko, W.; Kotrechko, S.; Mamedov, S.; Zatsarna, O.; Dlouhý, Ivo

    Zurich : Trans Tech Publications, 2014 - (Šandera, P.), s. 221-224 ISBN 978-3-03785-934-6. ISSN 1013-9826. - (Key Engineering Materials. 592-593). [MSMF 7 - International Conference on Materials Structure and Micromechanics of Fracture /7./. Brno (CZ), 01.07.2013-03.07.2013] Institutional support: RVO:68081723 Keywords : local stress * fracture * cleavage * embrittlement * strength Subject RIV: JL - Materials Fatigue, Friction Mechanics

  1. Fe-Catalyzed Oxidative Cleavage of Unsaturated Fatty Acids

    OpenAIRE

    Spannring, P.

    2013-01-01

    The oxidative cleavage of unsaturated fatty acids into aldehydes or carboxylic acids gives access to valuable products. The products can be used as chemical building blocks, as emulsifiers or in the paint or polymer industry. Ozonolysis is applied industrially to cleave the fatty acid oleic acid into the aldehydes nonanal and 9-oxo-nonanoic acid or into pelargonic and azelaic acid. Considerable hazards, including explosion risks, are associated with the use of ozone, and alternative processes...

  2. Developing a programmed restriction endonuclease for highly specific DNA cleavage

    OpenAIRE

    Eisenschmidt, Kristin; Lanio, Thomas; Simoncsits, András; Jeltsch, Albert; Pingoud, Vera; Wende, Wolfgang; Pingoud, Alfred

    2005-01-01

    Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4–8 bp are not sufficiently specific for this purpose. In principle, the specificity of REases can be extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or triple-helix forming oligonucleotid...

  3. The pattern of DNA cleavage intensity around indels

    OpenAIRE

    Wei Chen; Liqing Zhang

    2015-01-01

    Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensiti...

  4. Mycothiol synthesis by an anomerization reaction through endocyclic cleavage

    Science.gov (United States)

    2016-01-01

    Summary Mycothiol is found in Gram-positive bacteria, where it helps in maintaining a reducing intracellular environment and it plays an important role in protecting the cell from toxic chemicals. The inhibition of the mycothiol biosynthesis is considered as a treatment for tuberculosis. Mycothiol contains an α-aminoglycoside, which is difficult to prepare stereoselectively by a conventional glycosylation reaction. In this study, mycothiol was synthesized by an anomerization reaction from an easily prepared β-aminoglycoside through endocyclic cleavage. PMID:26977192

  5. Centrocortin Cooperates with Centrosomin to Organize Drosophila Embryonic Cleavage Furrows

    OpenAIRE

    Kao, Ling-Rong; Timothy L Megraw

    2009-01-01

    In the Drosophila early embryo the centrosome coordinates assembly of cleavage furrows [1–3]. Currently, the molecular pathway that links the centrosome and the cortical microfilaments is unknown. In centrosomin (cnn) mutants, where the centriole forms but the centrosome pericentriolar material (PCM) fails to assemble [4, 5], actin microfilaments are not organized into furrows at the syncytial cortex [6]. While CNN is required for centrosome assembly and function [4, 6, 7], little is known of...

  6. Embryo apoptosis identification: Oocyte grade or cleavage stage?

    OpenAIRE

    Bakri, Noraina Mohd; Ibrahim, Siti Fatimah; Osman, Nurul Atikah; Hasan, Nurhaslina; Jaffar, Farah Hanan Fathihah; Rahman, Zulaiha Abdul; Osman, Khairul

    2015-01-01

    Apoptosis is a programed cell death that is vital for tissue homeostasis. However, embryo apoptosis had been known to be related to embryo fragmentation which should be avoided in in vitro fertilization (IVF). The purpose of this study was to evaluate the relationship of embryo apoptosis with the grade of immature oocytes and cleavage stage of in vitro produced (IVP) cattle embryos. This study consisted of 345 oocytes collected through ovary slicing. Immature oocytes were graded as A, B and C...

  7. DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles.

    Science.gov (United States)

    Wu, Na; Willner, Itamar

    2016-04-13

    Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging. PMID:26931508

  8. Cleavage mechanoluminescence in elemental and III-V semiconductors

    CERN Document Server

    Chandra, B P; Gour, A S; Chandra, V K; Gupta, R K

    2003-01-01

    The present paper reports the theory of mechanoluminescence (ML) produced during cleavage of elemental and III-V semiconductors. It seems that the formation of crack-induced localized states is responsible for the ML excitation produced during the cleavage of elemental and III-V semiconductors. According to this mechanism, as the atoms are drawn away from each other in an advancing crack tip, the decreasing wave function overlap across the crack may result in localized states which is associated with increasing electron energy. If the energy of these localized states approach that of the conduction band, transition to the conduction band via tunnelling would be possible, creating minority carriers, and consequently the electron-hole recombination may give rise to mechanoluminescence. When an elemental or III-V semiconductor is cleaved, initially the ML intensity increases with time, attains a peak value I sub m at the time t sub m corresponding to completion of the cleavage of the semiconductor, and then it d...

  9. Mechanism of metabolic cleavage of a furan ring

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, T.; Sugihara, J.; Harigaya, S.

    1987-11-01

    We studied the mechanism of metabolic cleavage of a furan ring, using a new hypolipidemic agent, ethyl 2-(4-chlorophenyl)-5-(2-furyl)oxazole-4-acetate (TA-1801), as a model compound. A TA-1801 analogue labeled with deuterium at the 5-position of its furan ring was administered orally to rats. The analysis of urinary metabolites by GC/MS revealed that the deuterium of the furan was retained in the ring-opened metabolite (M3). Metabolic cleavage of furan has been generally considered to proceed by hydroxylation of the 5-position followed by tautomerism and hydrolysis of the resulting 5-hydroxyfuran derivative. However, if the cleavage proceeded by this pathway, the deuterium of the 5-position would be eliminated during hydroxylation. Therefore, we propose that the ring was cleaved directly to form an unsaturated aldehyde, considering the mechanism of oxidation by cytochrome P-450. Although this intermediate was not detected in the biological specimens, a synthetic unsaturated aldehyde was transformed to the actual urinary metabolites M2 and M3 (major ring-opened metabolites) in the isolated rat liver.

  10. Mechanism of metabolic cleavage of a furan ring

    International Nuclear Information System (INIS)

    We studied the mechanism of metabolic cleavage of a furan ring, using a new hypolipidemic agent, ethyl 2-(4-chlorophenyl)-5-(2-furyl)oxazole-4-acetate (TA-1801), as a model compound. A TA-1801 analogue labeled with deuterium at the 5-position of its furan ring was administered orally to rats. The analysis of urinary metabolites by GC/MS revealed that the deuterium of the furan was retained in the ring-opened metabolite (M3). Metabolic cleavage of furan has been generally considered to proceed by hydroxylation of the 5-position followed by tautomerism and hydrolysis of the resulting 5-hydroxyfuran derivative. However, if the cleavage proceeded by this pathway, the deuterium of the 5-position would be eliminated during hydroxylation. Therefore, we propose that the ring was cleaved directly to form an unsaturated aldehyde, considering the mechanism of oxidation by cytochrome P-450. Although this intermediate was not detected in the biological specimens, a synthetic unsaturated aldehyde was transformed to the actual urinary metabolites M2 and M3 (major ring-opened metabolites) in the isolated rat liver

  11. Cleavage mechanoluminescence in elemental and III-V semiconductors

    International Nuclear Information System (INIS)

    The present paper reports the theory of mechanoluminescence (ML) produced during cleavage of elemental and III-V semiconductors. It seems that the formation of crack-induced localized states is responsible for the ML excitation produced during the cleavage of elemental and III-V semiconductors. According to this mechanism, as the atoms are drawn away from each other in an advancing crack tip, the decreasing wave function overlap across the crack may result in localized states which is associated with increasing electron energy. If the energy of these localized states approach that of the conduction band, transition to the conduction band via tunnelling would be possible, creating minority carriers, and consequently the electron-hole recombination may give rise to mechanoluminescence. When an elemental or III-V semiconductor is cleaved, initially the ML intensity increases with time, attains a peak value Im at the time tm corresponding to completion of the cleavage of the semiconductor, and then it decreases following power law decay. Expressions are derived for the ML intensity Im corresponding to the peak of the ML intensity versus time curve and for the total ML intensity IT. It is shown that both Im and IT should increase directly with the area of the newly created surfaces of the crystals. From the measurements of the ML intensity, the velocity of crack propagation in material can be determined by using the relation v=H/tm

  12. Demethylation and cleavage of dimethylsulfoniopropionate in marine intertidal sediments

    Science.gov (United States)

    Visscher, P.T.; Kiene, R.P.; Taylor, B.F.

    1994-01-01

    Demethylation and cleavage of dimethylsulfoniopropionate (DMSP) was measured in three different types of,intertidal marine sediments: a cyanobacterial mat, a diatom-covered tidal flat and a carbonate sediment. Consumption rates of added DMSP were highest in cyanobacterial mat slurries (59 ?? mol DMSP l-1 slurry h-1) and lower in slurries from a diatom mat and a carbonate tidal sediment (24 and 9 ??mol DMSP l-1 h-1, respectively). Dimethyl sulfide (DMS) and 3-mercaptopropionate (MPA) were produced simultaneously during DMSP consumption, indicating that cleavage and demethylation occurred at the same time. Viable counts of DMSP-utilizing bacteria revealed a population of 2 x 107 cells cm-3 sediment (90% of these cleaved DMSP to DMS, 10% demethylated DMSP to MPA) in the cyanobacterial mat, 7 x 105 cells cm-3 in the diatom mat (23% cleavers, 77% demethylators), and 9 x 104 cells cm-3 (20% cleavers and 80% demethylators) in the carbonate sediment. In slurries of the diatom mat, the rate of MPA production from added 3-methiolpropionate (MMPA) was 50% of the rate of MPA formation from DMSP. The presence of a large population of demethylating bacteria and the production of MPA from DMSP suggest that the demethylation pathway, in addition to cleavage, contributes significantly to DMSP consumption in coastal sediments.

  13. Numerical modeling of ductile tearing effects on cleavage fracture toughness

    International Nuclear Information System (INIS)

    Experimental studies demonstrate a significant effect of specimen size, a/W ratio and prior ductile tearing on cleavage fracture toughness values (Jc) measured in the ductile-to-brittle transition region of ferritic materials. In the lower-transition region, cleavage fracture often occurs under conditions of large-scale yielding but without prior ductile crack extension. The increased toughness develops when plastic zones formed at the crack tip interact with nearby specimen surfaces which relaxes crack-tip constraint (stress triaxiality). In the mid-to-upper transition region, small amounts of ductile crack extension (often c-values. Previous work by the authors described a micromechanics fracture model to correct measured Jc-values for the mechanistic effects of large-scale yielding. This new work extends the model to also include the influence of ductile crack extension prior to cleavage. The paper explores development of the new model, provides necessary graphs and procedures for its application and demonstrates the effects of the model on fracture data sets for two pressure vessel steels (A533B and A515)

  14. Hyperphosphorylation and cleavage at D421 enhance tau secretion.

    Directory of Open Access Journals (Sweden)

    Vanessa Plouffe

    Full Text Available It is well established that tau pathology propagates in a predictable manner in Alzheimer's disease (AD. Moreover, tau accumulates in the cerebrospinal fluid (CSF of AD's patients. The mechanisms underlying the propagation of tau pathology and its accumulation in the CSF remain to be elucidated. Recent studies have reported that human tau was secreted by neurons and non-neuronal cells when it was overexpressed indicating that tau secretion could contribute to the spreading of tau pathology in the brain and could lead to its accumulation in the CSF. In the present study, we showed that the overexpression of human tau resulted in its secretion by Hela cells. The main form of tau secreted by these cells was cleaved at the C-terminal. Surprisingly, secreted tau was dephosphorylated at several sites in comparison to intracellular tau which presented a strong immunoreactivity to all phospho-dependent antibodies tested. Our data also revealed that phosphorylation and cleavage of tau favored its secretion by Hela cells. Indeed, the mimicking of phosphorylation at 12 sites known to be phosphorylated in AD enhanced tau secretion. A mutant form of tau truncated at D421, the preferential cleavage site of caspase-3, was also significantly more secreted than wild-type tau. Taken together, our results indicate that hyperphosphorylation and cleavage of tau by favoring its secretion could contribute to the propagation of tau pathology in the brain and its accumulation in the CSF.

  15. Sequence specificity of DNA cleavage by Micrococcus luteus gamma endonuclease

    International Nuclear Information System (INIS)

    Gamma irradiation induces the formation of lesions in DNA that are cleaved by an endonuclease activity in Micrococcus luteus extract. DNA fragments of defined sequence an DNA sequencing techniques were used to determine the sites of cleavage by this activity. /sup 32/P end-labelled DNA restriction fragments were gamma irradiated under N/sub 2/ and in the presence of KI (conditions which maximize the enzyme sensitive site to strand break ratio), treated with M. luteus extract, and analyzed by electrophoresis on denaturing polyacrylamide gels. Irradiated DNA was preferentially cleaved by the extract at sites of cytosine and thymine. Little or no cleavage was observed at purines. Scission of 3' end-labelled DNA at altered pyrimidines resulted in fragments that had electrophoretic mobilities similar to those of DNA fragments that were phosphorylated at the 5' terminus. The presence of a 5' phosphate was confirmed by a change in electrophoretic mobility after phosphatase treatment of the fragments. The sites of endonucleolytic cleavage by M. luteus extract were compared to those of the purified Escherichia coli endonuclease III, which has been shown to be active against x-irradiated DNA. Preliminary results from velocity sedimentation studies indicate that these two enzyme preparations differ in specificity

  16. Energy-dependent reversal of secondary isotope effects on simple cleavage reactions: tertiary amine radical cations with deuterium at remote positions

    International Nuclear Information System (INIS)

    Deuterium substitution at remote sites gives rise to inverse secondary kinetic isotope effects on the α-cleavage of a number of tertiary amines in the ion source, but to normal isotope effects on reactions occurring in the field-free regions. The change from normal to inverse secondary isotope effects when the internal energy of the reacting ions increases is consistent with transition-state models that involve slight lowering of vibrational frequencies also for bonds well removed from the site of cleavage. The isotope effect on the reactions of ions of high internal energy is caused by the influence that even small changes of isotope-dependent frequencies have on the state sums (a statistical weight effect favouring loss of the labelled radical), whereas the behaviour of low-energy ions is determined by the zero-point energy changes which favour loss of the unlabelled fragment. (author)

  17. Comparison of Gold Bonding with Mercury Bonding

    NARCIS (Netherlands)

    Kraka, Elfi; Filatov, Michael; Cremer, Dieter

    2009-01-01

    Nine AuX molecules (X = H, O, S, Se, Te, F, Cl, Br, I), their isoelectronic HgX(+) analogues, and the corresponding neutral HgX diatomics have been investigated using NESC (Normalized Elimination of the Small Component) and B3LYP theory to determine relativistic effects for bond dissociation energie

  18. Coupled valence bond theory

    NARCIS (Netherlands)

    Havenith, R.W.A.

    2005-01-01

    In this Letter, the formulation and implementation of a parallel response property code for non-orthogonal, valence bond wave-functions are described. Test calculations on benzene and cyclobutadiene show that the polarisability and magnetisability tensors obtained using valence bond theory are compa

  19. Bonded labour in Pakistan

    OpenAIRE

    Ercelawn, Aly; Nauman, Muhammad

    2001-01-01

    Examines the continuing prevalence of debt bondage in the 1990s despite the introduction of national legislation banning the practice. Makes recommendations to the Government and the international community for actions to be taken to eliminate bonded labour and provide rehabilitation for freed workers. Includes texts of Land Reforms Regulations, 1972, the Sindh Tenancy Act, 1950 and the Bonded Labour System (Abolition) Act, 1992.

  20. The samurai bond market

    OpenAIRE

    Frank Packer; Elizabeth Reynolds

    1997-01-01

    Issuance in the samurai bond market has more than tripled over the past several years. Some observers have attributed this growth to a systematic underestimation of credit risk in the market. A detailed review of credit quality, ratings differences, and initial issue pricing in the samurai bond market, however, turns up little evidence to support this concern.

  1. Money and Nominal Bonds

    OpenAIRE

    Marchesiani, Alessandro; Senesi, Pietro

    2007-01-01

    This paper studies an economy with trading frictions, ex post heterogeneity and nominal bonds in a model à la Lagos and Wright (2005). It is shown that a strictly positive interest rate is a sufficient condition for the allocation with nominal bonds to be welfare improving. This result comes from the protection against the inflation tax.

  2. Hydrogen bonding in polyanilines

    Energy Technology Data Exchange (ETDEWEB)

    Bahceci, S. (Department of Chemistry, Middle East Technical University, Ankara 06531 (Turkey)); Toppare, L. (Department of Chemistry, Middle East Technical University, Ankara 06531 (Turkey)); Yurtsever, E. (Department of Chemistry, Middle East Technical University, Ankara 06531 (Turkey))

    1994-11-29

    Hydrogen bonding between poly(bisphenol A carbonate) (PC) and polyaniline (PAn) is analyzed using semi-empirical quantum methodology. Fully optimized AM1 molecular orbital calculations are reported for various aniline structures (monomer, dimer and trimer), the monomer of the PC and the hydrogen-bonded model of PAn-PC oligomer. ((orig.))

  3. The influences of hinge length and composition on the susceptibility of human IgA to cleavage by diverse bacterial IgA1 proteases.

    Science.gov (United States)

    Senior, Bernard W; Woof, Jenny M

    2005-06-15

    The influences of IgA hinge length and composition on its susceptibility to cleavage by bacterial IgA1 proteases were examined using a panel of IgA hinge mutants. The IgA1 proteases of Streptococcus pneumoniae, Streptococcus sanguis strains SK4 and SK49, Neisseria meningitidis, Neisseria gonorrhoeae, and Haemophilus influenzae cleaved IgA2-IgA1 half hinge, an Ab featuring half of the IgA1 hinge incorporated into the equivalent site in IgA1 protease-resistant IgA2, whereas those of Streptococcus mitis, Streptococcus oralis, and S. sanguis strain SK1 did not. Hinge length reduction by removal of two of the four C-terminal proline residues rendered IgA2-IgA1 half hinge resistant to all streptococcal IgA1 metalloproteinases but it remained sensitive to cleavage by the serine-type IgA1 proteases of Neisseria and Haemophilus spp. The four C-terminal proline residues could be substituted by alanine residues or transferred to the N-terminal extremity of the hinge without affect on the susceptibility of the Ab to cleavage by serine-type IgA1 proteases. However, their removal rendered the Ab resistant to cleavage by all the IgA1 proteases. We conclude that the serine-type IgA1 proteases of Neisseria and Haemophilus require the Fab and Fc regions to be separated by at least ten (or in the case of N. gonorrhoeae type I protease, nine) amino acids between Val(222) and Cys(241) (IgA1 numbering) for efficient access and cleavage. By contrast, the streptococcal IgA1 metalloproteinases require 12 or more appropriate amino acids between the Fab and Fc to maintain a minimum critical distance between the scissile bond and the start of the Fc. PMID:15944283

  4. Shape Bonding method

    Science.gov (United States)

    Pontius, James T. (Inventor)

    2010-01-01

    The present invention is directed to a method of bonding at least two surfaces together. The methods step of the present invention include applying a strip of adhesive to a first surface along a predefined outer boundary of a bond area and thereby defining a remaining open area there within. A second surface, or gusset plate, is affixed onto the adhesive before the adhesive cures. The strip of adhesive is allowed to cure and then a second amount of adhesive is applied to cover the remaining open area and substantially fill a void between said first and second surfaces about said bond area. A stencil may be used to precisely apply the strip of adhesive. When the strip cures, it acts as a dam to prevent overflow of the subsequent application of adhesive to undesired areas. The method results in a precise bond area free of undesired shapes and of a preferred profile which eliminate the drawbacks of the prior art bonds.

  5. Water's Hydrogen Bond Strength

    CERN Document Server

    Chaplin, Martin

    2007-01-01

    Water is necessary both for the evolution of life and its continuance. It possesses particular properties that cannot be found in other materials and that are required for life-giving processes. These properties are brought about by the hydrogen bonded environment particularly evident in liquid water. Each liquid water molecule is involved in about four hydrogen bonds with strengths considerably less than covalent bonds but considerably greater than the natural thermal energy. These hydrogen bonds are roughly tetrahedrally arranged such that when strongly formed the local clustering expands, decreasing the density. Such low density structuring naturally occurs at low and supercooled temperatures and gives rise to many physical and chemical properties that evidence the particular uniqueness of liquid water. If aqueous hydrogen bonds were actually somewhat stronger then water would behave similar to a glass, whereas if they were weaker then water would be a gas and only exist as a liquid at sub-zero temperature...

  6. Corporate Bonds in Denmark

    DEFF Research Database (Denmark)

    Tell, Michael

    2015-01-01

    Corporate financing is the choice between capital generated by the corporation and capital from external investors. However, since the financial crisis shook the markets in 2007–2008, financing opportunities through the classical means of financing have decreased. As a result, corporations have...... to think in alternative ways such as issuing corporate bonds. A market for corporate bonds exists in countries such as Norway, Germany, France, the United Kingdom and the United States, while Denmark is still behind in this trend. Some large Danish corporations have instead used foreign corporate bonds...

  7. Transversely Compressed Bonded Joints

    DEFF Research Database (Denmark)

    Hansen, Christian Skodborg; Schmidt, Jacob Wittrup; Stang, Henrik

    2012-01-01

    The load capacity of bonded joints can be increased if transverse pressure is applied at the interface. The transverse pressure is assumed to introduce a Coulomb-friction contribution to the cohesive law for the interface. Response and load capacity for a bonded single-lap joint was derived using...... non-linear fracture mechanics. The results indicated a good correlation between theory and tests. Furthermore, the model is suggested as theoretical base for determining load capacity of bonded anchorages with transverse pressure, in externally reinforced concrete structures....

  8. The Halogen Bond

    Science.gov (United States)

    2016-01-01

    The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design. PMID:26812185

  9. Micelle-Vesicle Transition by Cleavage of Disulfide Spacer Chain for Gemini Surfactant in Didodecyldimethylammonium Chloride Aqueous Solutions.

    Science.gov (United States)

    Mizuhashi, Toshinari; Asakawa, Tsuyoshi; Ohta, Akio

    2015-01-01

    We examined the "micelle-vesicle transition" through the mixing effect of single-tailed thiol surfactants produced by the cleavage of gemini surfactants, [C12H25N(CH3)2CH2CH2SSCH2CH2N(CH3)2C12H25] 2Cl (C12SSC12), which have a disulfide bond in the spacer chain. Phase diagrams of C12H25N(CH3)2CH2CH2SHCl-didodecyldimethylammonium chloride (C12SH-DDAC) and C12SSC12-DDAC were determined by conductivity and pyrene fluorescence probe methods. The aggregate diameters were evaluated by dynamic light scattering (DLS). The critical vesicle concentration (CVC) was confirmed by the abrupt increase in the intensity of light scattering with excitation at 335 nm. Vesicle formation was confined to the DDAC-rich region of the C12SSC12-DDAC system, while the vesicle formation region for the C12SH-DDAC system spread out with the addition of dithiothreitol (DTT) to C12SSC12-DDAC. This implies that single-tailed surfactants can induce a more favorable environment for molecular packing of the vesicular surface. The micelle-vesicle transition occurs with disulfide spacer chain cleavage of gemini surfactants at a particular specific concentration range. PMID:26250426

  10. The Structural Basis of [beta]-Peptide-Specific Cleavage by the Serine Protease Cyanophycinase

    Energy Technology Data Exchange (ETDEWEB)

    Law, Adrienne M.; Lai, Sandy W.S.; Tavares, John; Kimber, Matthew S.; (Guelph)

    2010-10-01

    Cyanophycin, or poly-L-Asp-multi-L-Arg, is a non-ribosomally synthesized peptidic polymer that is used for nitrogen storage by cyanobacteria and other select eubacteria. Upon synthesis, it self-associates to form insoluble granules, the degradation of which is uniquely catalyzed by a carboxy-terminal-specific protease, cyanophycinase. We have determined the structure of cyanophycinase from the freshwater cyanobacterium Synechocystis sp. PCC6803 at 1.5-{angstrom} resolution, showing that the structure is dimeric, with individual protomers resembling aspartyl dipeptidase. Kinetic characterization of the enzyme demonstrates that the enzyme displays Michaelis-Menten kinetics with a k{sub cat} of 16.5 s{sup -1} and a k{sub cat}/K{sub M} of 7.5 x 10{sup -6} M{sup -1} s{sup -1}. Site-directed mutagenesis experiments confirm that cyanophycinase is a serine protease and that Gln101, Asp172, Gln173, Arg178, Arg180 and Arg183, which form a conserved pocket adjacent to the catalytic Ser132, are functionally critical residues. Modeling indicates that cyanophycinase binds the {beta}-Asp-Arg dipeptide residue immediately N-terminal to the scissile bond in an extended conformation in this pocket, primarily recognizing this penultimate {beta}-Asp-Arg residue of the polymeric chain. Because binding and catalysis depend on substrate features unique to {beta}-linked aspartyl peptides, cyanophycinase is able to act within the cytosol without non-specific cleavage events disrupting essential cellular processes.

  11. Copper-dependent cleavage of DNA of bleomycin

    International Nuclear Information System (INIS)

    DNA strand scission by bleomycin in the presence of Cu and Fe was further characterized. It was found that DNA degradation occurred readily upon admixture of Cu(I) or Cu(II) + dithiothreitol + bleomycin, but only where the order of addition precluded initial formation of Cu(II)-bleomycin or where sufficient time was permitted for reduction of formed Cu(II)-bleomycin to Cu(I)-bleomycin. DNA strand scission mediated by Cu + dithiothreitol + bleomycin was inhibited by the copper-selective agent bathocuproine when the experiment was carried out under conditions consistent with Cu chelation by bathocuproine on the time scale of the experiment. Remarkably, it was found that the extent of DNA degradation obtained with bleomycin in the presence of Fe and Cu was greater than that obtained with either metal ion alone. A comparison of the sequence selectivity of bleomycin in the presence of Cu and Fe using32P-end-labeled DNA duplexes as substrates revealed significant differences in sites of DNA cleavage and in the extent of cleavage at sites shared in common. For deglycobleomycin and decarbamoylbleomycin, whose metal ligation is believed to differ from that of bleomycin itself, it was found that the relative extents of DNA cleavage in the presence of Cu were not in the same order as those obtained in the presence of Fe. The results of these experiments are entirely consistent with the work of Sugiura who first demonstrate the generation of reactive oxygen species upon admixture of O2 and Cu(I)-bleomycin

  12. Synthesis and enzymatic cleavage of dual-ligand quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Sewell, Sarah L. [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Giorgio, Todd D., E-mail: todd.d.giorgio@vanderbilt.edu [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN (United States)

    2009-05-05

    Site directed therapy promises to minimize treatment-limiting systemic effects associated with cytotoxic agents that have no specificity for pathologic tissues. One general strategy is to target cell surface receptors uniquely presented on particular tissues. Highly specific in vivo targeting of an emerging neoplasm through a single molecular recognition mechanism has not generally been successful. Nonspecific binding and specific binding to non-target cells compromise the therapeutic index of small molecule, ubiquitous cancer targeting ligands. In this work, we have designed and fabricated a nanoparticle (NP) construct that could potentially overcome the current limitations of targeted in vivo delivery. Quantum dots (QDs) were functionalized with a poly(ethylene glycol) (PEG) modified to enable specific cleavage by matrix metalloprotease-7 (MMP-7). The QDs were further functionalized with folic acid, a ligand for a cell surface receptor that is overexpressed in many tumors, but also expressed in some normal tissues. The nanomolecular construct is designed so that the PEG initially conceals the folate ligand and construct binding to cells is inhibited. MMP-7 activated peptide cleavage and subsequent unmasking of the folate ligand occurs only near tumor tissue, resulting in a proximity activated (PA) targeting system. QDs functionalized with both the MMP-7 cleavable substrate and folic acid were successfully synthesized and characterized. The proteolytic capability of the dual ligand QD construct was quantitatively assessed by fluorometric analysis and compared to a QD construct functionalized with only the PA ligand. The dual ligand PA nanoparticles studied here exhibit significant susceptibility to cleavage by MMP-7 at physiologically relevant conditions. The capacity to autonomously convert a biopassivated nanostructure to a tissue-specific targeted delivery agent in vivo represents a paradigm change for site-directed therapies.

  13. Synthesis and enzymatic cleavage of dual-ligand quantum dots

    International Nuclear Information System (INIS)

    Site directed therapy promises to minimize treatment-limiting systemic effects associated with cytotoxic agents that have no specificity for pathologic tissues. One general strategy is to target cell surface receptors uniquely presented on particular tissues. Highly specific in vivo targeting of an emerging neoplasm through a single molecular recognition mechanism has not generally been successful. Nonspecific binding and specific binding to non-target cells compromise the therapeutic index of small molecule, ubiquitous cancer targeting ligands. In this work, we have designed and fabricated a nanoparticle (NP) construct that could potentially overcome the current limitations of targeted in vivo delivery. Quantum dots (QDs) were functionalized with a poly(ethylene glycol) (PEG) modified to enable specific cleavage by matrix metalloprotease-7 (MMP-7). The QDs were further functionalized with folic acid, a ligand for a cell surface receptor that is overexpressed in many tumors, but also expressed in some normal tissues. The nanomolecular construct is designed so that the PEG initially conceals the folate ligand and construct binding to cells is inhibited. MMP-7 activated peptide cleavage and subsequent unmasking of the folate ligand occurs only near tumor tissue, resulting in a proximity activated (PA) targeting system. QDs functionalized with both the MMP-7 cleavable substrate and folic acid were successfully synthesized and characterized. The proteolytic capability of the dual ligand QD construct was quantitatively assessed by fluorometric analysis and compared to a QD construct functionalized with only the PA ligand. The dual ligand PA nanoparticles studied here exhibit significant susceptibility to cleavage by MMP-7 at physiologically relevant conditions. The capacity to autonomously convert a biopassivated nanostructure to a tissue-specific targeted delivery agent in vivo represents a paradigm change for site-directed therapies.

  14. Embryo apoptosis identification: Oocyte grade or cleavage stage?

    Science.gov (United States)

    Bakri, Noraina Mohd; Ibrahim, Siti Fatimah; Osman, Nurul Atikah; Hasan, Nurhaslina; Jaffar, Farah Hanan Fathihah; Rahman, Zulaiha Abdul; Osman, Khairul

    2016-01-01

    Apoptosis is a programed cell death that is vital for tissue homeostasis. However, embryo apoptosis had been known to be related to embryo fragmentation which should be avoided in in vitro fertilization (IVF). The purpose of this study was to evaluate the relationship of embryo apoptosis with the grade of immature oocytes and cleavage stage of in vitro produced (IVP) cattle embryos. This study consisted of 345 oocytes collected through ovary slicing. Immature oocytes were graded as A, B and C. This grading was based on cumulus cell thickness and compactness. All oocytes then underwent an in vitro maturation (IVM) procedure. An IVF was done 24 h after IVM culture. Prior to staining, stage of cleaved embryos was determined and classified as either 2, 4, 8 or >8-cell embryo stage. Apoptosis status of cleaved IVP embryos was determined by using annexin V-FITC staining technique at 48 and 72 h post insemination (hpi). Apoptosis status for each embryo was classified as either early or late. The result showed that there was no significant difference (p > 0.05) of apoptosis status among grade A, B and C embryos. All grades of oocytes showed embryo apoptosis where 1.5% late apoptosis for grade A, 4.5% and 10.4% of early and late apoptosis for grade B and grade C. Early apoptosis was not seen in grade A embryo. We also noted no significant difference (p > 0.05) of apoptosis status between 2, 4, 8 and >8-cell embryo stage. Early apoptosis was also not seen in >8-cell stage. Even though there were no differences in apoptosis expression between the three classes, the cleavage rate of grade A oocytes was significantly higher (p quality and the cleavage stage of the embryo produced. PMID:26858565

  15. Molecular Basis of Catalytic Chamber-assisted Unfolding and Cleavage of Human Insulin by Human Insulin-degrading Enzyme*S⃞

    Science.gov (United States)

    Manolopoulou, Marika; Guo, Qing; Malito, Enrico; Schilling, Alexander B.; Tang, Wei-Jen

    2009-01-01

    Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together. Using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to obtain high mass accuracy, and electron capture dissociation (ECD) to selectively break the disulfide bonds in gas phase fragmentation, we determined the cleavage sites and composition of human insulin fragments generated by human IDE. Our time-dependent analysis of IDE-digested insulin fragments reveals that IDE is highly processive in its initial cleavage at the middle of both the insulin A and B chains. This ensures that IDE effectively splits insulin into inactive N- and C-terminal halves without breaking the disulfide bonds. To understand the molecular basis of the recognition and unfolding of insulin by IDE, we determined a 2.6-Å resolution insulin-bound IDE structure. Our structure reveals that IDE forms an enclosed catalytic chamber that completely engulfs and intimately interacts with a partially unfolded insulin molecule. This structure also highlights how the unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity (∼100 nm) for insulin. In addition, this structure shows how IDE utilizes the interaction of its exosite with the N terminus of the insulin A chain as well as other properties of the catalytic chamber to guide the unfolding of insulin and allowing for the processive cleavages. PMID:19321446

  16. Programmable RNA recognition and cleavage by CRISPR/Cas9

    OpenAIRE

    O’Connell, Mitchell R.; Oakes, Benjamin L.; Sternberg, Samuel H.; East-Seletsky, Alexandra; Kaplan, Matias; Doudna, Jennifer A.

    2014-01-01

    The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA:DNA complementarity to identify target sites for sequence-specific doublestranded DNA (dsDNA) cleavage 1-5 . In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, the protospacer adjacent motif (PAM), next to and on the strand opposite the 20-nucleotide target site in dsDNA 4-7 . Cas9 has proven to be a versatile tool for g...

  17. Features of Controlled Laser Thermal Cleavage of Crystalline Silicon

    International Nuclear Information System (INIS)

    Controlled laser thermal cleavage of crystalline silicon has been numerically simulated. A 3D analysis of the thermoelastic fields formed in a single-crystal silicon wafer as a result of successive laser heating and exposure to a coolant was performed for three different versions of anisotropy. The simulation was performed for laser irradiation with different wavelengths: 1.06 and 0.808 μm. The calculation results have been experimentally verified using a YAG laser. The results can be used in the electronics industry to optimize the precise separation of silicon wafers into crystals.

  18. Bond dissociation & electronegativity equalization

    OpenAIRE

    Verstraelen, Toon; Ayers, Paul W.; Van Speybroeck, Veronique; Waroquier, Michel

    2012-01-01

    It is well known that the Electrongativity Equalization Mtehod (EEM) fails to describe the charge distribution upon bond dissocation. In this presentation, the bond dissocation is studied with the Atom-Condensed Kohn-Sham DFT approximated to second order (ACKS2). After reviewing the basic equations, a two-fragment system is studied in the dissociation limit. The limiting behavior of the Coulomb interaction (1/r) and the Kohn-Sham matrix elements (exponentially decaying) are plugged into the e...

  19. Anodic bonded graphene

    OpenAIRE

    Balan, Adrian; Kumar, Rakesh; Boukhicha, Mohamed; Beyssac, Olivier; Bouillard, Jean-Claude; Taverna, Dario; Sacks, William; Marangolo, Massimiliano; Lacaze, Emmanuelle; Escoffier, Walter; Poumirol, Jean-Marie; Shukla, Abhay

    2010-01-01

    Abstract We show how to prepare graphene samples on a glass substrate with the anodic bonding method. In this method, a graphite precursor in flake form is bonded to a glass substrate with the help of an electrostatic field and then cleaved off to leave few layer graphene on the substrate. Now that several methods are available for producing graphene, the relevance of our method is in its simplicity and practicality for producing graphene samples of about 100 ?m lateral dimensions. This me...

  20. Handbook of wafer bonding

    CERN Document Server

    Ramm, Peter; Taklo, Maaike M V

    2011-01-01

    Written by an author and editor team from microsystems companies and industry-near research organizations, this handbook and reference presents dependable, first-hand information on bonding technologies.In the first part, researchers from companies and institutions around the world discuss the most reliable and reproducible technologies for the production of bonded wafers. The second part is devoted to current and emerging applications, including microresonators, biosensors and precise measuring devices.

  1. N-N Bond Forming Reductive Elimination via a Mixed-Valent Nickel(II)-Nickel(III) Intermediate.

    Science.gov (United States)

    Diccianni, Justin B; Hu, Chunhua; Diao, Tianning

    2016-06-20

    Natural products containing N-N bonds exhibit important biological activity. Current methods for constructing N-N bonds have limited scope. An advanced understanding of the fundamental N-N bond formation/cleavage processes occurring at the transition-metal center would facilitate the development of catalytic reactions. Herein we present an N-N bond-forming reductive elimination, which proceeds via a mixed-valent Ni(II) -Ni(III) intermediate with a Ni-Ni bond order of zero. The discrete Ni(II) -Ni(III) oxidation states contrast with the cationic dimeric Ni analogue, in which both Ni centers are equivalent with an oxidation state of 2.5. The electronic structures of these mixed-valent complexes have implications for the fundamental understanding of metal-metal bonding interactions. PMID:27144682

  2. K3[Fe(CN)6].3H2O supported on silica gel: An efficient and selective reagent for the cleavage of oximes to their corresponding carbonyl compounds in aqueous medium

    Indian Academy of Sciences (India)

    Abbas Amini Manesh; Behzad Shirmardi Shaghasemi

    2015-03-01

    K3[Fe(CN)6].3H2O supported on silica gel, a new oxidant, for efficient, simple and selective cleavage of ketoximes and aldoximes to their corresponding carbonyl compounds in aqueous medium is described. Further oxidation of aldehydes to carboxylic acid and formation of by-products were not observed. − unsaturated oxime was deoximated smoothly without oxidation of the double bond.

  3. Cleavage of silicon by laser-based shock waves: Interpretation by nanoscopic length scales

    International Nuclear Information System (INIS)

    Cleavage along the weakest Si{1 1 1} cleavage plane is measured by impulsive fracture using surface acoustic waves (SAWs) with steep shock fronts, generated by pulsed laser irradiation and recorded with a laser probe–beam-deflection setup. The theoretical cleavage strength, obtained by ab initio calculations for perfect single-crystal silicon lattices is compared with the strength resulting from an improved Polanyi–Orowan cleavage model. The critical strength of a real silicon crystal, measured by using calibrated elastic surface pulses with shocks, was employed to extract the corresponding critical length scale characterizing the cleavage process on the basis of the modified cleavage model. The extracted length scale of 7 nm can be connected with the size of the microstructural defect initiating failure. Usually stress generating surface defects are responsible for the nucleation of brittle fracture, especially in nanoscale systems with large surface areas.

  4. Microscopic investigation of cleavage initiation in modified A508B pressure vessel steel

    International Nuclear Information System (INIS)

    A microscopic study on ductile-brittle crack growth in a modified version of the A508B pressure vessel steel has been performed. Small SEN(B)-specimens tested at different temperatures in and above the transition region have been thoroughly examined with a scanning electron microscope. Focus was directed towards: amount of ductile crack growth prior to cleavage, distance from the crack front to cleavage initiation sites, and type of defect that caused the cleavage initiation. The results show, among other things, that cleavage facets are present in specimens tested at all temperatures, even on the upper shelf where no global failure by cleavage was observed. These preliminary results give an indication that the ability of the matrix material to arrest and sustain small cleavage cracks can be crucial in explaining why ferritic steels show a transition behaviour. (orig.)

  5. Study of mechanism of cleavage fracture at low temperature

    Science.gov (United States)

    Chen, J. H.; Wang, G. Z.

    1992-02-01

    In this investigation, a series of crack opening displacement (COD) tests were carried out at several low temperatures for C-Mn weld steel. Some of the specimens were loaded until fracture, and the mechanical properties and microscopic parameters on fracture surfaces were measured. Other specimens were unloaded before fracture at different applied loads. The distributions of the elongated cavities and the cleavage microcracks ahead of fatigue crack tips were observed in detail. Based on the experimental results, the combined criterion of a critical strain ɛ p ≥ ɛc) for initiating a crack nucleus, a critical stress triaxiality (σ m/σ ≥ tc) for preventing it from blunting, and a critical normal stress (σ yy/σf) for the cleavage extension was proposed again, and the critical values of ɛp and σm/-σ for the C-Mn weld steel were measured. The reason why the minimum COD value could not be zero is explained. The mechanism of generation of the lower limit COD value on the lower shelf of the toughness transition curve is proposed.

  6. Drosha regulates gene expression independently of RNA cleavage function

    DEFF Research Database (Denmark)

    Gromak, Natalia; Dienstbier, Martin; Macias, Sara;

    2013-01-01

    Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically binds promoter-proximal regions of many human genes in a transcription......-terminal protein-interaction domain, which associates with the RNA-binding protein CBP80 and RNA Polymerase II. Consequently, we uncover a previously unsuspected RNA cleavage-independent function of Drosha in the regulation of human gene expression.......Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically binds promoter-proximal regions of many human genes in a transcription......-dependent manner. This binding is not associated with miRNA production or RNA cleavage. Drosha knockdown in HeLa cells downregulated nascent gene transcription, resulting in a reduction of polyadenylated mRNA produced from these gene regions. Furthermore, we show that this function of Drosha is dependent on its N...

  7. Bond Length and Bond Order in One of the Shortest Cr-Cr Bonds

    OpenAIRE

    La Macchia, Giovanni; Aquilante, Francesco; Veryazov, Valera; Roos, Bjorn O.; Gagliardi, Laura

    2008-01-01

    Multiconfigurational quantum chemical calculations on the R-diimines dichromium compound confirm that the Cr-Cr bond, 1.80 A, is among the shortest Cr (I)-Cr (I) bonds. However, the bond between the two Cr atoms is only a quadruple bond rather than a quintuple bond. The reason why the bond is so short has to be attributed to the strain in the NCCN ligand moieties.

  8. Synthesis of Novel High Energy Polyaniline Derivative Containing S-S Bond in Six-membered Cycle

    Institute of Scientific and Technical Information of China (English)

    ZHOU Lei; DENG Shi-Ren; LI Zao-Ying

    2003-01-01

    @@ A novel conducting polymer as new class of high energy storage material, [1,2] which has one six-membered cycle containing S-S bond in the moiety of aniline was synthesized. The polymer had enhanced redox progress due to an intramolecular electrocatalytic effect of polyaniline on S-S bond. The polymer has some advantages because of its high theoretical specific energy and fast kinetics when used in lithium batteries. The most promised advantage of it is that the intramolecular cleavage and recombination of the S-S bond improve the cyclicability greatly.

  9. Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer.

    OpenAIRE

    Vitiello, D; Pecchia, D B; Burke, J M

    2000-01-01

    Small catalytic RNAs like the hairpin ribozyme are proving to be useful intracellular tools; however, most attempts to demonstrate trans-cleavage of RNA by ribozymes in cells have been frustrated by rapid cellular degradation of the cleavage products. Here, we describe a fluorescence resonance energy transfer (FRET) assay that directly monitors cleavage of target RNA in tissue-culture cells. An oligoribonucleotide substrate was modified to inhibit cellular ribonuclease degradation without int...

  10. A pathway sensor for genome-wide screens of intracellular proteolytic cleavage

    OpenAIRE

    Ketteler, Robin; Sun, Zairen; Kovacs, Karl F; He, Wei-Wu; Seed, Brian

    2008-01-01

    Protein cleavage is a central event in many regulated biological processes. We describe a system for detecting intracellular proteolysis based on non-conventional secretion of Gaussia luciferase (GLUC). GLUC exits the cell without benefit of a secretory leader peptide, but can be anchored in the cell by fusion to \\(\\beta\\)-actin. By including protease cleavage sites between GLUC and \\(\\beta\\)-actin, proteolytic cleavage can be detected. Using this assay, we have identified regulators of autop...

  11. A real-time assay for monitoring nucleic acid cleavage by quadruplex formation

    OpenAIRE

    Kankia, Besik I.

    2006-01-01

    Direct and straightforward methods to follow nucleic acid cleavage are needed. A spectrophotometric quadruplex formation assay (QFA) was developed, which allows real-time monitoring of site-specific cleavage of nucleic acids. QFA was applied to study both protein and nucleic acid restriction enzymes, and was demonstrated to accurately determine Michaelis–Menten parameters for the cleavage reaction catalyzed by EcoRI. QFA can be used to study the mechanisms of protein–nucleic acid recognition....

  12. RNase II is important for A-site mRNA cleavage during ribosome pausing

    OpenAIRE

    Garza-Sánchez, Fernando; Shoji, Shinichiro; Fredrick, Kurt; Hayes, Christopher S.

    2009-01-01

    In Escherichia coli, translational arrest can elicit cleavage of codons within the ribosomal A site. This A-site mRNA cleavage is independent of RelE, and has been proposed to be an endonucleolytic activity of the ribosome. Here, we show that the 3′→5′ exonuclease RNase II plays an important role in RelE-independent A-site cleavage. Instead of A-site cleavage, translational pausing in ΔRNase II cells produces transcripts that are truncated +12 and +28 nucleotides downstream of the A-site codo...

  13. Hairpin DNA Sequences Bound Strongly by Bleomycin Exhibit Enhanced Double-Strand Cleavage

    OpenAIRE

    Roy, Basab; Hecht, Sidney M.

    2014-01-01

    Clinically used bleomycin A5 has been employed in a study of double-strand cleavage of a library of 10 hairpin DNAs originally selected on the basis of their strong binding to bleomycin. Each of the DNAs underwent double-strand cleavage at more than one site, and all of the cleavage sites were within, or in close proximity to, an eight-base-pair region of the duplex that had been randomized to create the original library. A total of 31 double-strand cleavage sites were identified on the 10 DN...

  14. Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage

    OpenAIRE

    Li, Xiaochun; Wang, Boyuan; Feng, Lihui; Kang, Hui; Qi, Yang; Wang, Jiawei; Shi, Yigong

    2009-01-01

    Regulated intramembrane proteolysis (RIP) by the Site-2 protease (S2P) results in the release of a transmembrane signaling protein. Curiously, however, S2P cleavage must be preceded by the action of the Site-1 protease (S1P). To decipher the underlying mechanism, we reconstituted sequential, in vitro cleavages of the Escherichia coli transmembrane protein RseA by DegS (S1P) and RseP (S2P). After DegS cleavage, the newly exposed carboxyl-terminal residue Val-148 of RseA plays an essential role...

  15. Specific pre-cleavage and post-cleavage complexes involved in the formation of SV40 late mRNA 3' termini in vitro.

    OpenAIRE

    Zarkower, D; Wickens, M

    1987-01-01

    Complexes form between processing factors present in a crude nuclear extract from HeLa cells and a simian virus 40 (SV40) late pre-mRNA which spans the polyadenylation [poly(A)] site. A specific 'pre-cleavage complex' forms on the pre-mRNA before cleavage. Formation of this complex requires the highly conserved sequence AAUAAA: it is prevented by mutations in AAUAAA, and by annealing DNA oligonucleotides to that sequence. After cleavage, the 5' half-molecule is found in a distinct 'post-cleav...

  16. Romanian government bond market

    Directory of Open Access Journals (Sweden)

    Cornelia POP

    2012-12-01

    Full Text Available The present paper aims to present the level of development reached by Romanian government bond market segment, as part of the country financial market. The analysis will be descriptive (the data series available for Romania are short, based on the secondary data offered by the official bodies involved in the process of issuing and trading the Romanian government bonds (Romanian Ministry of Public Finance, Romanian National Bank and Bucharest Stock Exchange, and also on secondary data provided by the Federation of European Stock Exchanges.To enhance the market credibility as a benchmark, a various combination of measures is necessary; among these measures are mentioned: the extension of the yield curve; the issuance calendars in order to improve transparency; increasing the disclosure of information on public debt issuance and statistics; holding regular meetings with dealers, institutional investors and rating agencies; introducing a system of primary dealers; establishing a repurchase (repo market in the government bond market. These measures will be discussed based on the evolution presented inside the paper.The paper conclude with the fact that, until now, the Romanian government bond market did not provide a benchmark for the domestic financial market and that further efforts are needed in order to increase the government bond market transparency and liquidity.

  17. Embryo apoptosis identification: Oocyte grade or cleavage stage?

    Science.gov (United States)

    Bakri, Noraina Mohd; Ibrahim, Siti Fatimah; Osman, Nurul Atikah; Hasan, Nurhaslina; Jaffar, Farah Hanan Fathihah; Rahman, Zulaiha Abdul; Osman, Khairul

    2015-01-01

    Apoptosis is a programed cell death that is vital for tissue homeostasis. However, embryo apoptosis had been known to be related to embryo fragmentation which should be avoided in in vitro fertilization (IVF). The purpose of this study was to evaluate the relationship of embryo apoptosis with the grade of immature oocytes and cleavage stage of in vitro produced (IVP) cattle embryos. This study consisted of 345 oocytes collected through ovary slicing. Immature oocytes were graded as A, B and C. This grading was based on cumulus cell thickness and compactness. All oocytes then underwent an in vitro maturation (IVM) procedure. An IVF was done 24 h after IVM culture. Prior to staining, stage of cleaved embryos was determined and classified as either 2, 4, 8 or >8-cell embryo stage. Apoptosis status of cleaved IVP embryos was determined by using annexin V-FITC staining technique at 48 and 72 h post insemination (hpi). Apoptosis status for each embryo was classified as either early or late. The result showed that there was no significant difference (p > 0.05) of apoptosis status among grade A, B and C embryos. All grades of oocytes showed embryo apoptosis where 1.5% late apoptosis for grade A, 4.5% and 10.4% of early and late apoptosis for grade B and grade C. Early apoptosis was not seen in grade A embryo. We also noted no significant difference (p > 0.05) of apoptosis status between 2, 4, 8 and >8-cell embryo stage. Early apoptosis was also not seen in >8-cell stage. Even though there were no differences in apoptosis expression between the three classes, the cleavage rate of grade A oocytes was significantly higher (p < 0.01) than grade B and grade C. In conclusion, the apoptosis expression in the embryo can occur regardless of the oocyte quality and the cleavage stage of the embryo produced. PMID:26858565

  18. TEXT tf coil bonding system

    International Nuclear Information System (INIS)

    An extensive bond test program was conducted prior to manufacturing and bonding the toroidal field (TF) coils for the Texas Experimental Tokamak (TEXT). The bonding materials consisted of fiberglass cloth with pre-impregnated, 'B' staged Hexcel F-159 resin. Approximately 100 double lap bond samples were constructed to test quality, strength, and repeatability of the bonds. The variables investigated included surface machining methods, surface preparations, bond sample size (planform area), bonding pressure, bonding temperature, and the number of laminations bonded simultaneously. Double lap shear tests conducted at room temperature resulted in ultimate shear strengths for all variables in the range of 3000 to 7000 psi with an average value of 5650 psi. Fatigue tests were also conducted to demonstrate bond integrity over the anticipated cycle lifetime of the TEXT machine (10/sup 6/ cycles) under simulated worst case conditions. 2 refs

  19. Insulation bonding test system

    Science.gov (United States)

    Beggs, J. M.; Johnston, G. D.; Coleman, A. D.; Portwood, J. N.; Saunders, J. M.; Redmon, J. W.; Porter, A. C. (Inventor)

    1984-01-01

    A method and a system for testing the bonding of foam insulation attached to metal is described. The system involves the use of an impacter which has a calibrated load cell mounted on a plunger and a hammer head mounted on the end of the plunger. When the impacter strikes the insulation at a point to be tested, the load cell measures the force of the impact and the precise time interval during which the hammer head is in contact with the insulation. This information is transmitted as an electrical signal to a load cell amplifier where the signal is conditioned and then transmitted to a fast Fourier transform (FFT) analyzer. The FFT analyzer produces energy spectral density curves which are displayed on a video screen. The termination frequency of the energy spectral density curve may be compared with a predetermined empirical scale to determine whether a igh quality bond, good bond, or debond is present at the point of impact.

  20. The Illiquidity of Corporate Bonds

    OpenAIRE

    Bao, Jack; Pan, Jun; Wang, Jiang

    2011-01-01

    This paper examines the illiquidity of corporate bonds and its asset-pricing implications. Using transactions data from 2003 to 2009, we show that the illiquidity in corporate bonds is substantial, significantly greater than what can be explained by bid–ask spreads. We establish a strong link between bond illiquidity and bond prices. In aggregate, changes in market-level illiquidity explain a substantial part of the time variation in yield spreads of high-rated (AAA through A) bonds, overshad...

  1. Partial vapor-phase hydrolysis of peptide bonds: A method for mass spectrometric determination of O-glycosylated sites in glycopeptides

    DEFF Research Database (Denmark)

    Mirgorodskaya, E; Hassan, H; Wandall, H H;

    1999-01-01

    resulting mass spectra allowed unambiguous determination of the glycosylation sites. Examples are shown with mannosyl- and mucin-type glycopeptides. Performing the hydrolysis in vapor eliminates the risk for contamination of the sample with impurities from the reagents, thus allowing analysis of the......In this study we present a method for determination of O-glycosylation sites in glycopeptides, based on partial vapor-phase acid hydrolysis in combination with mass spectrometric analysis. Pentafluoropropionic acid and hydrochloric acid were used for the hydrolysis of glycosylated peptides. The...... reaction conditions were optimized for efficient polypeptide backbone cleavages with minimal cleavage of glycosidic bonds. The glycosylated residues were identified by mass spectrometric analysis of the hydrolytic cleavage products. Although glycosidic bonds are partially cleaved under acid hydrolysis, the...

  2. Anodic bonded graphene

    Energy Technology Data Exchange (ETDEWEB)

    Balan, Adrian; Kumar, Rakesh; Boukhicha, Mohamed; Beyssac, Olivier; Bouillard, Jean-Claude; Taverna, Dario; Sacks, William; Shukla, Abhay [Universite Pierre et Marie Curie-Paris 6, CNRS-UMR7590, Institut de Mineralogie et de Physique des Milieux Condenses, 140 rue de Lourmel, Paris, F-75015 France (France); Marangolo, Massimiliano; Lacaze, Emanuelle; Gohler, Roger [Universite Pierre et Marie Curie-Paris 6, CNRS-UMR7588, Institut des Nanosciences de Paris, 140 rue de Lourmel, Paris, F-75015 France (France); Escoffier, Walter; Poumirol, Jean-Marie, E-mail: abhay.shukla@upmc.f [Laboratoire National des Champs Magnetiques Intenses, INSA UPS CNRS, UPR 3228, Universite de Toulouse, 143 avenue de Rangueil, 31400 Toulouse (France)

    2010-09-22

    We show how to prepare graphene samples on a glass substrate with the anodic bonding method. In this method, a graphite precursor in flake form is bonded to a glass substrate with the help of an electrostatic field and then cleaved off to leave few layer graphene on the substrate. Now that several methods are available for producing graphene, the relevance of our method is in its simplicity and practicality for producing graphene samples of about 100 {mu}m lateral dimensions. This method is also extensible to other layered materials. We discuss some detailed aspects of the fabrication and results from Raman spectroscopy, local probe microscopy and transport measurements on these samples.

  3. The Trouble With Bonds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ In early June,global financial markets gyrated downwards in the wake of central banks'tough language on inflation.At one point bond prices reflected expectations of four rate hikes by the US Federal Reserve (Fed) in the next 12 months.As a result,the dollar firmed,oil prices stabilized,and yield curves flattened around the world.If all these inflation-fighting measures are real,the situation bodes well for bonds.But,I think otherwise.

  4. Modelling of ductile and cleavage fracture by local approach

    International Nuclear Information System (INIS)

    This report describes the modelling of ductile and cleavage fracture processes by local approach. It is now well known that the conventional fracture mechanics method based on single parameter criteria is not adequate to model the fracture processes. It is because of the existence of effect of size and geometry of flaw, loading type and rate on the fracture resistance behaviour of any structure. Hence, it is questionable to use same fracture resistance curves as determined from standard tests in the analysis of real life components because of existence of all the above effects. So, there is need to have a method in which the parameters used for the analysis will be true material properties, i.e. independent of geometry and size. One of the solutions to the above problem is the use of local approaches. These approaches have been extensively studied and applied to different materials (including SA33 Gr.6) in this report. Each method has been studied and reported in a separate section. This report has been divided into five sections. Section-I gives a brief review of the fundamentals of fracture process. Section-II deals with modelling of ductile fracture by locally uncoupled type of models. In this section, the critical cavity growth parameters of the different models have been determined for the primary heat transport (PHT) piping material of Indian pressurised heavy water reactor (PHWR). A comparative study has been done among different models. The dependency of the critical parameters on stress triaxiality factor has also been studied. It is observed that Rice and Tracey's model is the most suitable one. But, its parameters are not fully independent of triaxiality factor. For this purpose, a modification to Rice and Tracery's model is suggested in Section-III. Section-IV deals with modelling of ductile fracture process by locally coupled type of models. Section-V deals with the modelling of cleavage fracture process by Beremins model, which is based on Weibulls

  5. Delay of HeLa cell cleavage into interphase using dihydrocytochalasin B: retention of a postmitotic spindle and telophase disc correlates with synchronous cleavage recovery

    OpenAIRE

    1995-01-01

    The molecular signals that determine the position and timing of the cleavage furrow during mammalian cell cytokinesis are presently unknown. We have studied in detail the effect of dihydrocytochalasin B (DCB), a drug that interferes with actin assembly, on specific late mitotic events in synchronous HeLa cells. When cleavage furrow formation is blocked at 10 microM DCB, cells return to interphase by the criteria of reformation of nuclei with lamin borders, degradation of the cyclin B componen...

  6. SARS coronavirus nsp1 protein induces template-dependent endonucleolytic cleavage of mRNAs: viral mRNAs are resistant to nsp1-induced RNA cleavage.

    Directory of Open Access Journals (Sweden)

    Cheng Huang

    2011-12-01

    Full Text Available SARS coronavirus (SCoV nonstructural protein (nsp 1, a potent inhibitor of host gene expression, possesses a unique mode of action: it binds to 40S ribosomes to inactivate their translation functions and induces host mRNA degradation. Our previous study demonstrated that nsp1 induces RNA modification near the 5'-end of a reporter mRNA having a short 5' untranslated region and RNA cleavage in the encephalomyocarditis virus internal ribosome entry site (IRES region of a dicistronic RNA template, but not in those IRES elements from hepatitis C or cricket paralysis viruses. By using primarily cell-free, in vitro translation systems, the present study revealed that the nsp1 induced endonucleolytic RNA cleavage mainly near the 5' untranslated region of capped mRNA templates. Experiments using dicistronic mRNAs carrying different IRESes showed that nsp1 induced endonucleolytic RNA cleavage within the ribosome loading region of type I and type II picornavirus IRES elements, but not that of classical swine fever virus IRES, which is characterized as a hepatitis C virus-like IRES. The nsp1-induced RNA cleavage of template mRNAs exhibited no apparent preference for a specific nucleotide sequence at the RNA cleavage sites. Remarkably, SCoV mRNAs, which have a 5' cap structure and 3' poly A tail like those of typical host mRNAs, were not susceptible to nsp1-mediated RNA cleavage and importantly, the presence of the 5'-end leader sequence protected the SCoV mRNAs from nsp1-induced endonucleolytic RNA cleavage. The escape of viral mRNAs from nsp1-induced RNA cleavage may be an important strategy by which the virus circumvents the action of nsp1 leading to the efficient accumulation of viral mRNAs and viral proteins during infection.

  7. Amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by streptococcal IgA1 proteases.

    Science.gov (United States)

    Batten, Margaret R; Senior, Bernard W; Kilian, Mogens; Woof, Jenny M

    2003-03-01

    The amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by IgA1 proteases of different species of Streptococcus were investigated. Recombinant IgA1 antibodies were generated with point mutations at proline 227 and threonine 228, the residues lying on either side of the peptide bond at which all streptococcal IgA1 proteases cleave wild-type human IgA1. The amino acid substitutions produced no major effect upon the structure of the mutant IgA1 antibodies or their functional ability to bind to Fcalpha receptors. However, the substitutions had a substantial effect upon sensitivity to cleavage with some streptococcal IgA1 proteases, with, in some cases, a single point mutation rendering the antibody resistant to a particular IgA1 protease. This effect was least marked with the IgA1 protease from Streptococcus pneumoniae, which showed no absolute requirement for either proline or threonine at residues 227 to 228. By contrast, the IgA1 proteases of Streptococcus oralis, Streptococcus sanguis, and Streptococcus mitis had an absolute requirement for proline at 227 but not for threonine at 228, which could be replaced by valine. There was evidence in S. mitis that proteases from different strains may have different amino acid requirements for cleavage. Remarkably, some streptococcal proteases appeared able to cleave the hinge at a distant alternative site if substitution prevented efficient cleavage of the original site. Hence, this study has identified key residues required for the recognition of the IgA1 hinge as a substrate by streptococcal IgA1 proteases, and it marks a preliminary step towards development of specific enzyme inhibitors. PMID:12595464

  8. Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-[alpha], and Amylin by Human Insulin-Degrading Enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Qing; Manolopoulou, Marika; Bian, Yao; Schilling, Alexander B.; Tang, Wei-Jen (UC); (UIC)

    2010-02-11

    Insulin-degrading enzyme (IDE) is involved in the clearance of many bioactive peptide substrates, including insulin and amyloid-{beta}, peptides vital to the development of diabetes and Alzheimer's disease, respectively. IDE can also rapidly degrade hormones that are held together by intramolecular disulfide bond(s) without their reduction. Furthermore, IDE exhibits a remarkable ability to preferentially degrade structurally similar peptides such as the selective degradation of insulin-like growth factor (IGF)-II and transforming growth factor-{alpha} (TGF-{alpha}) over IGF-I and epidermal growth factor, respectively. Here, we used high-accuracy mass spectrometry to identify the cleavage sites of human IGF-II, TGF-{alpha}, amylin, reduced amylin, and amyloid-{beta} by human IDE. We also determined the structures of human IDE-IGF-II and IDE-TGF-{alpha} at 2.3 {angstrom} and IDE-amylin at 2.9 {angstrom}. We found that IDE cleaves its substrates at multiple sites in a biased stochastic manner. Furthermore, the presence of a disulfide bond in amylin allows IDE to cut at an additional site in the middle of the peptide (amino acids 18-19). Our amylin-bound IDE structure offers insight into how the structural constraint from a disulfide bond in amylin can alter IDE cleavage sites. Together with NMR structures of amylin and the IGF and epidermal growth factor families, our work also reveals the structural basis of how the high dipole moment of substrates complements the charge distribution of the IDE catalytic chamber for the substrate selectivity. In addition, we show how the ability of substrates to properly anchor their N-terminus to the exosite of IDE and undergo a conformational switch upon binding to the catalytic chamber of IDE can also contribute to the selective degradation of structurally related growth factors.

  9. Molecular basis for the recognition and cleavages of IGF-II, TGF-α, and amylin by human insulin degrading enzyme

    Science.gov (United States)

    Guo, Qing; Manolopoulou, Marika; Bian, Yao; Schilling, Alexander B.; Tang, Wei-Jen

    2009-01-01

    Insulin-degrading enzyme (IDE) is involved in the clearance of many bioactive peptide substrates, including insulin and amyloid-β (Aβ), peptides vital to the development of diabetes and Alzheimer's disease, respectively. IDE can also rapidly degrade hormones that are held together by intra-molecular disulfide bond(s) without their reduction. Furthermore, IDE exhibits a remarkable ability to preferentially degrade structurally similar peptides such as the selective degradation of insulin-growth factor-II (IGF-II) and transforming growth factor-α (TGF-α) over IGF-I and epidermal growth factor (EGF), respectively. Here, we used high accuracy mass spectrometry to identify the cleavage sites of human IGF-II, TGF-α, amylin, reduced amylin, and Aβ by human IDE. We also determined the structures of human IDE-IGF-II and IDE-TGF-α at 2.3 Å and IDE-amylin at 2.9 Å. We found that IDE cleaves its substrates at multiple sites in a biased stochastic manner. Furthermore, the presence of a disulfide bond in amylin allows IDE to cut at an additional site in the middle of the peptide (aa 18-19). Our amylin-bound IDE structure offers insight into how the structural constraint from a disulfide bond in amylin can alter IDE cleavage sites. Together with NMR structures of amylin and the IGF and EGF families, our work also reveals the structural basis of how the high dipole moment of substrates complements the charge distribution of the IDE catalytic chamber for the substrate selectivity. In addition, we show how the ability of substrates to properly anchor their N-terminus to the exosite of IDE and undergo a conformational switch upon binding to the catalytic chamber of IDE can also contribute to the selective degradation of structurally related growth factors. PMID:19896952

  10. Cleavage-based voting behavior in cross-national perspective : Evidence from six postwar democracies

    NARCIS (Netherlands)

    Brooks, Clem; Nieuwbeerta, Paul; Manza, Jeff

    2006-01-01

    We investigate trends and cross-national variation in the impact of class, religious, and gender cleavages on voting behavior in six advanced capitalist democracies in the postwar period. Earlier research on cleavage voting has been criticized for utilizing outdated ‘‘two-class’’ models of class str

  11. Cleavage-based voting behavior in cross-national perspective: evidence from six postwar democracies

    NARCIS (Netherlands)

    Brooks, Clem; Nieuwbeerta, Paul; Manza, Jeff

    2006-01-01

    We investigate trends and cross-national variation in the impact of class, religious, and gender cleavages on voting behavior in six advanced capitalist democracies in the postwar period. Earlier research on cleavage voting has been criticized for utilizing outdated “two-class” models of class struc

  12. Coronavirus 3CL(pro) proteinase cleavage sites: Possible relevance to SARS virus pathology

    DEFF Research Database (Denmark)

    Kiemer, Lars; Lund, Ole; Brunak, Søren;

    2004-01-01

    in proteins such as the cystic fibrosis transmembrane conductance regulator ( CFTR), transcription factors CREB-RP and OCT-I, and components of the ubiquitin pathway. Conclusions: Our prediction method NetCorona predicts coronavirus cleavage sites with high specificity and several potential cleavage...

  13. Unexpected tolerance of alpha-cleavage of the prion protein to sequence variations.

    Directory of Open Access Journals (Sweden)

    José B Oliveira-Martins

    Full Text Available The cellular form of the prion protein, PrP(C, undergoes extensive proteolysis at the alpha site (109K [see text]H110. Expression of non-cleavable PrP(C mutants in transgenic mice correlates with neurotoxicity, suggesting that alpha-cleavage is important for PrP(C physiology. To gain insights into the mechanisms of alpha-cleavage, we generated a library of PrP(C mutants with mutations in the region neighbouring the alpha-cleavage site. The prevalence of C1, the carboxy adduct of alpha-cleavage, was determined for each mutant. In cell lines of disparate origin, C1 prevalence was unaffected by variations in charge and hydrophobicity of the region neighbouring the alpha-cleavage site, and by substitutions of the residues in the palindrome that flanks this site. Instead, alpha-cleavage was size-dependently impaired by deletions within the domain 106-119. Almost no cleavage was observed upon full deletion of this domain. These results suggest that alpha-cleavage is executed by an alpha-PrPase whose activity, despite surprisingly limited sequence specificity, is dependent on the size of the central region of PrP(C.

  14. Flax Fiber - Interfacial Bonding

    Science.gov (United States)

    Measured flax fiber physical and chemical properties potentially impact bonding and thus stress transfer between the matrix and fiber within composites. These first attempts at correlating flax fiber quality and biofiber composites contain the initial steps towards identifying key flax fiber charac...

  15. Bonds Between Atoms.

    Science.gov (United States)

    Holden, Alan

    The field of inquiry into how atoms are bonded together to form molecules and solids crosses the borderlines between physics and chemistry encompassing methods characteristic of both sciences. At one extreme, the inquiry is pursued with care and rigor into the simplest cases; at the other extreme, suggestions derived from the more careful inquiry…

  16. Thread bonds in molecules

    CERN Document Server

    Ivlev, B

    2015-01-01

    Unusual chemical bonds are proposed. Each bond is almost covalent but is characterized by the thread of a small radius $\\sim 0.6\\times 10^{-11}$cm, between two nuclei in a molecule. The main electron density is concentrated outside the thread as in a covalent bond. The thread is formed by the electron wave function which has a tendency to be singular on it. The singularity along the thread is cut off by electron "vibrations" due to the interaction with zero point electromagnetic oscillations. The electron energy has its typical value of (1-10)eV. Due to the small tread radius the uncertainty of the electron momentum inside the thread is large resulting in a large electron kinetic energy $\\sim 1 MeV$. This energy is compensated by formation of a potential well due to the reduction of the energy of electromagnetic zero point oscillations. This is similar to formation of a negative van der Waals potential. Thread bonds are stable and cannot be created or destructed in chemical or optical processes.

  17. Role of Austenite in Brittle Fracture of Bond Region of Super Duplex Stainless Steel

    Science.gov (United States)

    Kitagawa, Yoshihiko; Ikeuchi, Kenji; Kuroda, Toshio

    Weld simulation of heat-affected zone (HAZ) was performed to investigate the mechanism by which austenite affects the toughness of super duplex stainless steel. Thermal cycles of various peak temperatures in the range from 1373 K to 1673 K corresponding to the HAZ were applied to SAF2507 super duplex stainless steel specimens. Charpy impact test was carried out using the specimens after the weld simulation, and the fracture surfaces were observed by SEM using three-dimensionally reconstruction technique. Austenite content decreased with increasing the peak temperature when the peak temperature exceeded 1473 K and the impact value decreased with increasing the peak temperature and decreasing the austenite content. The thermal cycle of the peak temperature of 1673 K corresponding to weld bond region caused decreasing of austenite content which was 22% lower than that of the base metal. The ductile-brittle transition temperature was measured. As a result the temperature increased rapidly in the weld bond region, the peak temperature of which exceeded 1623 K by the grain growth of ferrite matrix occurring subsequently to the completely dissolution of austenite. The morphology of the fracture surfaces after impact testing at 77 K showed cleavage fracture of ferrite. The {100} orientations of cleavage fracture facets were measured using three-dimensional images of the fracture surfaces and the results were visualized as the orientation color maps. The results showed that there were cleavage fractures consisting of a few facets parallel to each other. It was considered that a few facets existed in one ferrite grain. It was concluded that Widmanstätten austenite divided the large fracture into smaller cleavage facets in a ferrite grain and then suppressed the degradation of bond toughness of duplex stainless steel.

  18. Ultrasensitive monitoring of ribozyme cleavage product using molecular-beacon-ligation system

    Institute of Scientific and Technical Information of China (English)

    MENG XiangXian; TANG ZhiWen; WANG KeMin; TAN WeiHong; YANG XiaoHai; LI Jun; GUO QiuPing

    2007-01-01

    This paper reports a new approach to detect ribozyme cleavage product based on the molecular- beacon-ligation system. The molecular beacon, designed in such a way that one-half of its loop is complementary to ribozyme cleavage product, is used to monitor ligation process of RNA/DNA complex in a homogeneous solution and to convert directly cleavage product information into fluorescence signal. The method need not label ribozyme and ribozyme substrate, which is fast, simple and ultrasensitive for detection of cleavage product. Detection limit of the assay is 0.05 nmol/L. The cleavage product of hammerhead ribozyme against hepatitis C virus RNA (HCV-RNA) was detected perfectly based on this assay. Owing to its ultrasensitivity, excellent specificity, convenience and fidelity, this method might hold out great promise in ribozyme reaction and ribozyme gene therapy.

  19. Review and perspective on approaches of evaluating cleavage fracture toughness of pressure vessel steels

    International Nuclear Information System (INIS)

    Although efforts have been made to establish cleavage fracture model in the past 30 years or so, uncertainties remain in predicting the cleavage fracture toughness behavior of reactor pressure vessel steels in the transition region. Confusions may be raised in cases such as that there are still outliers while ASME fracture toughness curve indexed to the reference temperature is generally considered as very conservative. The advantage and potentials of using Finite Element method to predict the cleavage fracture behavior of irradiated materials are obvious. However, its effectiveness depends on the rightness of the physical model and criteria established. In this paper, approaches of describing cleavage fracture toughness of pressure vessel steels in the transition region are discussed and compared. The need for focusing on the physical fundamental and criteria of cleavage fracture is addressed. (authors)

  20. Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions.

    Directory of Open Access Journals (Sweden)

    Davide Mercadante

    Full Text Available Pectin methylesterases (PMEs hydrolyze the methylester groups that are found on the homogalacturonan (HG chains of pectic polysaccharides in the plant cell wall. Plant and bacterial PMEs are especially interesting as the resulting de-methylesterified (carboxylated sugar residues are found to be arranged contiguously, indicating a so-called processive nature of these enzymes. Here we report the results of continuum electrostatics calculations performed along the molecular dynamics trajectory of a PME-HG-decasaccharide complex. In particular it was observed that, when the methylester groups of the decasaccharide were arranged in order to mimic the just-formed carboxylate product of de-methylesterification, a net unidirectional sliding of the model decasaccharide was subsequently observed along the enzyme's binding groove. The changes that occurred in the electrostatic binding energy and protein dynamics during this translocation provide insights into the mechanism by which the enzyme rectifies Brownian motions to achieve processivity. The free energy that drives these molecular motors is thus demonstrated to be incorporated endogenously in the methylesterified groups of the HG chains and is not supplied exogenously.

  1. Heterogeneous Catalysis of C–O Bond Cleavage for Cellulose Deconstruction: A Potential Pathway for Ethanol Production

    OpenAIRE

    Crews, Kristy; Reeves, Crystal; Thomas, Porsha; Abugri, Daniel; Russell, Albert; Michael L. Curry

    2014-01-01

    Due to difficulty deconstructing the linkages between lignin, hemicellulose and cellulose during the conversion of cellulose to sugar, the commercial production of cellulosic ethanol is limited. This can be overcome by using a high surface-area metal catalyst. In this study, high surface-area metal NPs were synthesized using 20 mM of chloroplatinic acid and cobalt chloride prepared in THF with 0.1 mM of generation four poly(amido)amine (PAMAM) terminated dendrimer (G4-NH2) prepared in methano...

  2. Fe-promoted cross coupling of homobenzylic methyl ethers with Grignard reagents via sp3 C-O bond cleavage.

    Science.gov (United States)

    Luo, Shuang; Yu, Da-Gang; Zhu, Ru-Yi; Wang, Xin; Wang, Lei; Shi, Zhang-Jie

    2013-09-14

    The first iron-catalyzed formal cross coupling of homobenzylic methyl ethers with alkyl Grignard reagents is realized. The reaction is proposed to proceed through a sequence of dehydroalkoxylation to form the vinyl-intermediate, followed by Fe-catalyzed selective carbometalation to form a benzylic Grignard reagent. PMID:23884449

  3. Atomistic Details of the Associative Phosphodiester Cleavage in Human Ribonuclease H

    International Nuclear Information System (INIS)

    During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O30 oxygen to generate the product state. During the reaction mechanism two Mg2+ ions support the formation of a stable associated in-line SN2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol*1 is in excellent agreement with experimental findings (20.5 kcal mol*1). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.

  4. Atomistic Details of the Associative Phosphodiester Cleavage in Human Ribonuclease H

    Energy Technology Data Exchange (ETDEWEB)

    Elsasser, Brigitta M.; Fels, Gregor

    2010-07-30

    During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O30 oxygen to generate the product state. During the reaction mechanism two Mg2+ ions support the formation of a stable associated in-line SN2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol*1 is in excellent agreement with experimental findings (20.5 kcal mol*1). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.

  5. Oxidative cleavage of a phenolic diarylpropane lignin model dimer by manganese peroxidase from Phanerochaete chrysosporium

    International Nuclear Information System (INIS)

    In the presence of MnII and H2O2, homogeneous manganese peroxidase oxidized 1-(3,5-dimethoxy-4-hydroxyphenyl)-2-(4-methoxyphenyl)-1,3-dihydroxypropane (I) to yield 1-(3,5-dimethoxy-4-hydroxyphenyl)-2-(4-methoxyphenyl)-1-oxo-3-hydroxypropane (II), 2,6-dimethoxy-1,4-benzoquinone (III), 2,6-dimethoxy-1,4-dihydroxybenzene (IV), 1-(4-methoxyphenyl)-1-oxo-2-hydroxyethane (V), 1-(4-methoxyphenyl)-1,2-dihydroxyethane (VI), syringaldehyde (VIII), and 2-(4-methoxyphenyl)-3-hydroxypropanal (IX). Chemically prepared manganese(III) malonate catalyzed the same reactions. Oxidation of I in H218O under argon resulted in >80% incorporation of 18O into the phenylglycol VI, the hydroquinone IV, and the quinone III. Oxidation of I in H218O under aerobic conditions resulted in 40% incorporation of 18O into VI but no 18O incorporation into V. Finally, oxidation of I under 18O2 resulted in 89% and 28% incorporation of 18O into V and VI, respectively. These results are explained by mechanisms involving the one-electron oxidation of the substrate I by enzyme-generated MnIII to produce a phenoxy radical intermediate I'. Subsequent Cα-Cβ bond cleavage of the radical intermediate yields syringaldehyde (VIII) and a C6-C2 benzylic radical. Syringaldehyde is oxidized by MnIII in several steps to a cyclohexadiene cation intermediate I double-prime, which is attacked by water to yield the benzoquinone III. The C6-C2 radical is scavenged by O2 to form a peroxy radical that decomposes to V and VI. In these reactions, MnIII generated by manganese peroxidase catalyzes both formation of the substrate phenoxy radical and oxidation of carbon-centered radical intermediates, to yield reactive cations

  6. Convertible bond valuation focusing on Chinese convertible bond market

    OpenAIRE

    Yang, Ke

    2010-01-01

    This paper mainly discusses the methods of valuation of convertible bonds in Chinese market. Different from common convertible bonds in European market, considering the complicate features of Chinese convertible bond, this paper represents specific pricing approaches for pricing convertible bonds with different provisions along with the increment of complexity of these provisions. More specifically, this paper represents the decomposing method and binomial tree method for pricing both of Non-...

  7. Structural and functional basis for RNA cleavage by Ire1

    Directory of Open Access Journals (Sweden)

    Stroud Robert M

    2011-07-01

    Full Text Available Abstract Background The unfolded protein response (UPR controls the protein folding capacity of the endoplasmic reticulum (ER. Central to this signaling pathway is the ER-resident bifunctional transmembrane kinase/endoribonuclease Ire1. The endoribonuclease (RNase domain of Ire1 initiates a non-conventional mRNA splicing reaction, leading to the production of a transcription factor that controls UPR target genes. The mRNA splicing reaction is an obligatory step of Ire1 signaling, yet its mechanism has remained poorly understood due to the absence of substrate-bound crystal structures of Ire1, the lack of structural similarity between Ire1 and other RNases, and a scarcity of quantitative enzymological data. Here, we experimentally define the active site of Ire1 RNase and quantitatively evaluate the contribution of the key active site residues to catalysis. Results This analysis and two new crystal structures suggest that Ire1 RNase uses histidine H1061 and tyrosine Y1043 as the general acid-general base pair contributing ≥ 7.6 kcal/mol and 1.4 kcal/mol to transition state stabilization, respectively, and asparagine N1057 and arginine R1056 for coordination of the scissile phosphate. Investigation of the stem-loop recognition revealed that additionally to the stem-loops derived from the classic Ire1 substrates HAC1 and Xbp1 mRNA, Ire1 can site-specifically and rapidly cleave anticodon stem-loop (ASL of unmodified tRNAPhe, extending known substrate specificity of Ire1 RNase. Conclusions Our data define the catalytic center of Ire1 RNase and suggest a mechanism of RNA cleavage: each RNase monomer apparently contains a separate catalytic apparatus for RNA cleavage, whereas two RNase subunits contribute to RNA stem-loop docking. Conservation of the key residues among Ire1 homologues suggests that the mechanism elucidated here for yeast Ire1 applies to Ire1 in metazoan cells, and to the only known Ire1 homologue RNase L.

  8. Synthesis, spectral, crystal structure, thermal behavior, antimicrobial and DNA cleavage potential of two octahedral cadmium complexes: A supramolecular structure

    Science.gov (United States)

    Montazerozohori, M.; Musavi, S. A.; Masoudiasl, A.; Naghiha, A.; Dusek, M.; Kucerakova, M.

    2015-02-01

    Two new cadmium(II) complexes with the formula of CdL2(NCS)2 and CdL2(N3)2 (in which L is 2,2-dimethyl-N,N‧-bis-(3-phenyl-allylidene)-propane-1,3-diamine) have been synthesized and characterized by elemental analysis, molar conductivity measurements, FT/IR, UV-Visible, 1H and 13C NMR spectra and X-ray studies. The crystal structure analysis of CdL2(NCS)2 indicated that it crystallizes in orthorhombic system with space group of Pbca. Two Schiff base ligands are bonded to cadmium(II) ion as N2-donor chelate. Coordination geometry around the cadmium ion was found to be partially distorted octahedron. The Cd-Nimine bond distances are found in the range of 2.363(2)-2.427(2) Å while the Cd-Nisothiocyanate bond distances are 2.287(2) Å and 2.310(2) Å. The existence of C-H⋯π and C-H⋯S interactions in the CdL2(NCS)2 crystal leads to a supramolecular structure in its network. Then cadmium complexes were screened in vitro for their antibacterial and antifungal activities against two Gram-negative and two Gram-positive bacteria and also against Candida albicans as a fungus. Moreover, the compounds were subjected for DNA-cleavage potential by gel electrophoresis method. Finally thermo-gravimetric analysis of the complexes was applied for thermal behavior studies and then some thermo-kinetics activation parameters were evaluated.

  9. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    OpenAIRE

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-01-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MA...

  10. Not all social cleavages are the same: On the relationship between religious diversity and party system fragmentation

    OpenAIRE

    Raymond, Christopher D.

    2016-01-01

    Most studies examining the relationship between social cleavages and party system fragmentation maintain that higher levels of social diversity lead to greater party system fragmentation. However, most aggregate-level studies focus on one type of social cleavage:ethnic diversity. In order to develop a better understanding of how different cleavages impact electoral competition, this paper considers another type of social cleavage: religious diversity.Contrary to previous literature, higher le...

  11. Party agency and the religious-secular cleavage in post-Communist countries: The case of Romania

    OpenAIRE

    Raymond, Christopher

    2014-01-01

    Research focusing on several post-communist countries has found evidence of social cleavage effects on political behaviour similar to those found in Western Europe. In some post-communist countries, however, social cleavage effects appear far weaker (if at all). To understand why this is the case, I perform a case study of Romania, focusing on the religious–secular cleavage. Drawing upon research that emphasises the role of parties in forming cleavages, I argue that the reason for the absence...

  12. Fusion function of the Semliki Forest virus spike is activated by proteolytic cleavage of the envelope glycoprotein precursor p62.

    OpenAIRE

    Lobigs, M; Garoff, H

    1990-01-01

    The precursor protein p62 of the prototype alphavirus Semliki Forest virus (SFV) undergoes during transport to the cell surface a proteolytic cleavage to form the mature envelope glycoprotein E2. To investigate the biological significance of this cleavage event, single amino acid substitutions were introduced at the cleavages site through mutagenesis of cDNA corresponding to the structural region of the SFV genome. The phenotypes of the cleavage site mutants were studied in BHK cells by using...

  13. Modulation of enteroviral proteinase cleavage of poly(A)-binding protein (PABP) by conformation and PABP-associated factors

    OpenAIRE

    Rivera, Carlos I.; Lloyd, Richard E.

    2008-01-01

    Poliovirus (PV) causes a drastic inhibition of cellular cap-dependant protein synthesis due to the cleavage of translation factors eukaryotic initiation factor 4G (eIF4G) and poly (A) binding protein (PABP). Only about half of cellular PABP is cleaved by viral 2A and 3C proteinases during infection. We have investigated PABP cleavage determinants that regulate this partial cleavage. PABP cleavage kinetics analyses indicate that PABP exists in multiple conformations, some of which are resistan...

  14. Domestic Bond Market Development

    OpenAIRE

    Jonathan A. Batten; Szilagyi, Peter G.

    2007-01-01

    A two-tiered approach to financial market development aimed at both bank and bond market reform would also be complementary to longer term economic development, provided services could be delivered through efficient financial and legal institutions (Chakraborty and Ray 2006) and there was strong protection for investors and sound fiscal and monetary policy management by government (Burger and Warnock 2006b). Historically, local issuers tend to issue in the major currencies (U.S. dollars, yen,...

  15. Disulfide bonds of acetylcholinesterase

    International Nuclear Information System (INIS)

    The positions of the inter- and intrasubunit disulfide bridges were established for the 11S form of acetylcholinesterase (AChE) isolated from Torpedo californica. A major form of AChE localized within the basal lamina of the synapse is a dimensionally asymmetric molecule which contains either two (13S) or three (17S) sets of catalytic subunits linked to collagenous and non-collagenous structural subunits. Limited proteolysis yields a tetramer of catalytic subunits which sediments at 11S. Each catalytic subunit contains 8 cysteine residues. Initially, these Cys residues were identified following trypsin digestion of the reduced protein alkylated with [14C]-iodoacetate. Peptides were resolved by gel filtration followed by reverse phase HPLC. To determine the disulfide bonding profile, native non-reduced 11S AChE was treated with a fluorescent, sulfhydryl-specific reagent, monobromobimane, prior to proteolytic digestion. One fluorescent Cys peptide was identified indicating that a single sulfhydryl residue was present in its reduced form. Three pairs of disulfide bonded peptides were identified, sequenced, and localized in the polypeptide chain. The Cys residue that is located in the C-terminal tryptic peptide was disulfide bonded to an identical peptide and thus forms the intersubunit crosslink. Finally, the cysteine positions have been compared with the sequence of the homologous protein, thyroglobulin. Both likely share a common pattern of folding

  16. Integration of European Bond Markets

    OpenAIRE

    Christiansen, Charlotte

    2012-01-01

    I investigate the time variation in the integration of EU government bond markets. The integration is measured by the explanatory power of European factor portfolios for the individual bond markets for each year. The integration of the government bond markets is stronger for EMU than non-EMU members and stronger for old than new EU members. The integration is weaker for the sovereign debt crisis countries than for other countries. The integration of the EU bond markets is decreasing over time...

  17. Doseringsutrustningen SafeBond Electronic

    OpenAIRE

    Bodegren, Patrik

    2003-01-01

    This thesis for the Master of Science degree was performed at Oppunda Electronics AB. The assignment was to further develop an existing prototype of a dispensing equipment. The dispensing equipment doses a kind of glue, bonding which dentist use to mend teeth. The dispensing equipment is adjusted to dose 12 micro litres of bonding. With the dispensing equipment SafeBond Electronic the user can reduce the bonding consumption with approximately 50 percent. Furthermore will the handling of the b...

  18. Irreversible and reversible topoisomerase II DNA cleavage stimulated by clerocidin: sequence specificity and structural drug determinants.

    Science.gov (United States)

    Binaschi, M; Zagotto, G; Palumbo, M; Zunino, F; Farinosi, R; Capranico, G

    1997-05-01

    In contrast to other topoisomerase II poisons, the microbial terpenoid clerocidin was shown to stimulate irreversible topoisomerase II-mediated DNA cleavage. To establish the structural determinants for drug activity, in this study we have investigated intensity patterns and sequence specificity of clerocidin-stimulated DNA cleavage using 5'-end 32P-labeled DNA fragments. At a majority of the sites, clerocidin-stimulated cleavage did not revert upon NaCl addition; nevertheless, at some sites, cleavage completely reverted. Statistical analyses showed that drug-preferred bases were different in the two cases: guanine and cytosine were highly preferred at position -1 at irreversible and reversible sites, respectively. These results demonstrated that cleavage irreversibility was site selective and required a guanine at the 3' end of the cut. Further experiments revealed that some irreversible sites showed an abnormal electrophoretic mobility in sequencing gels with respect to cleaved bands generated by 4-(9-acridinylamino)methanesulfon-m-anisidide, suggesting a chemical alteration of the DNA strand. Interestingly, the ability to stimulate irreversible cleavage progressively decreased over time when clerocidin was stored in ethanol. Under these conditions, nuclear magnetic resonance measurements demonstrated that the drug underwent structural modifications that involved the C-12-C-15 side chain. Thus, the results indicate that a specific moiety of clerocidin may react with the DNA (guanine at -1) in the ternary complex, resulting in cleavage irreversibility and in altered DNA mobility in sequencing gels. PMID:9135013

  19. Role of early cleavage in predicting success of intra cytoplasmic sperm injection in assisted reproductive technologies

    Directory of Open Access Journals (Sweden)

    Manjula Gopalakrishnan, Sanjeeva Reddy Nellapalli, Muthiah sinvaniah surulimuthu

    2014-07-01

    Full Text Available Aim and Objective: The present study is aimed to carry out the impact of early cleavage over late cleavage in assessing the pregnancy outcome using of Intra Cytoplasmic Sperm Injection (ICSI in assisted reproductive technologies. Materials and Methods A total of 154 patients enrolled for Intra Cytoplasmic Sperm Injection (ICSI fulfilling the selection criteria were recruited for the study at a tertiary care assisted reproductive centre. ICSI was performed 3–5 h after oocyte aspiration with the prepared sperm. All embryos were checked for early cleavage at 27 hours post intra cytoplasmic sperm injection. They were divided into two groups. Group I- Embryos which cleaved before 27 hours after Intra Cytoplasmic Sperm Injection (ICSI. Group II- Embryos which cleaved after 27 hours. The pregnancy rates were compared between the two groups. Results: All the 154 patients were analysed. There was no difference in the mean age, duration of ovarian stimulation, number of oocytes retrieved, fertilization, cleavage rates and embryo quality between the two groups. Early cleavage was observed in 98 patients (63.64 %. Late cleavage was observed in 56 patients (36.36%. The clinical pregnancy was confirmed in 59 patients (60.20% in Group I and 20 patients (35.71% in Group II which was statistically significant P <0.001. Conclusion: Early cleavage is a strong predictor of embryo quality and can predict ICSI outcome.

  20. Cleavage Site Localization Differentially Controls Interleukin-6 Receptor Proteolysis by ADAM10 and ADAM17.

    Science.gov (United States)

    Riethmueller, Steffen; Ehlers, Johanna C; Lokau, Juliane; Düsterhöft, Stefan; Knittler, Katharina; Dombrowsky, Gregor; Grötzinger, Joachim; Rabe, Björn; Rose-John, Stefan; Garbers, Christoph

    2016-01-01

    Limited proteolysis of the Interleukin-6 Receptor (IL-6R) leads to the release of the IL-6R ectodomain. Binding of the cytokine IL-6 to the soluble IL-6R (sIL-6R) results in an agonistic IL-6/sIL-6R complex, which activates cells via gp130 irrespective of whether the cells express the IL-6R itself. This signaling pathway has been termed trans-signaling and is thought to mainly account for the pro-inflammatory properties of IL-6. A Disintegrin And Metalloprotease 10 (ADAM10) and ADAM17 are the major proteases that cleave the IL-6R. We have previously shown that deletion of a ten amino acid long stretch within the stalk region including the cleavage site prevents ADAM17-mediated cleavage, whereas the receptor retained its full biological activity. In the present study, we show that deletion of a triple serine (3S) motif (Ser-359 to Ser-361) adjacent to the cleavage site is sufficient to prevent IL-6R cleavage by ADAM17, but not ADAM10. We find that the impaired shedding is caused by the reduced distance between the cleavage site and the plasma membrane. Positioning of the cleavage site in greater distance towards the plasma membrane abrogates ADAM17-mediated shedding and reveals a novel cleavage site of ADAM10. Our findings underline functional differences in IL-6R proteolysis by ADAM10 and ADAM17. PMID:27151651

  1. Sox11 Reduces Caspase-6 Cleavage and Activity.

    Directory of Open Access Journals (Sweden)

    Elaine Waldron-Roby

    Full Text Available The apoptotic cascade is an orchestrated event, whose final stages are mediated by effector caspases. Regulatory binding proteins have been identified for caspases such as caspase-3, -7, -8, and -9. Many of these proteins belong to the inhibitor of apoptosis (IAP family. By contrast, caspase-6 is not believed to be influenced by IAPs, and little is known about its regulation. We therefore performed a yeast-two-hybrid screen using a constitutively inactive form of caspase-6 for bait in order to identify novel regulators of caspase-6 activity. Sox11 was identified as a potential caspase-6 interacting protein. Sox11 was capable of dramatically reducing caspase-6 activity, as well as preventing caspase-6 self- cleavage. Several regions, including amino acids 117-214 and 362-395 within sox11 as well as a nuclear localization signal (NLS all contributed to the reduction in caspase-6 activity. Furthermore, sox11 was also capable of decreasing other effector caspase activity but not initiator caspases -8 and -9. The ability of sox11 to reduce effector caspase activity was also reflected in its capacity to reduce cell death following toxic insult. Interestingly, other sox proteins also had the ability to reduce caspase-6 activity but to a lesser extent than sox11.

  2. Calpain-mediated cleavage of DARPP-32 in Alzheimer's disease.

    Science.gov (United States)

    Cho, Kwangmin; Cho, Mi-Hyang; Seo, Jung-Han; Peak, Jongjin; Kong, Kyoung-Hye; Yoon, Seung-Yong; Kim, Dong-Hou

    2015-10-01

    Toxicity induced by aberrant protein aggregates in Alzheimer's disease (AD) causes synaptic disconnection and concomitant progressive neurodegeneration that eventually impair cognitive function. cAMP-response element-binding protein (CREB) is a transcription factor involved in the molecular switch that converts short-term to long-term memory. Although disturbances in CREB function have been suggested to cause memory deficits in both AD and AD animal models, the mechanism of CREB dysfunction is still unclear. Here, we show that the dopamine- and cAMP-regulated phosphoprotein 32 kDa (DARPP-32), a key inhibitor of protein phosphate-1 (PP-1) that regulates CREB phosphorylation, is cleaved by activated calpain in both AD brains and neuronal cells treated with amyloid-β or okadaic acid, a protein phosphatase-2A inhibitor that induces tau hyperphosphorylation and neuronal death. We found that DARPP-32 is mainly cleaved at Thr(153) by calpain and that this cleavage of DARPP-32 reduces CREB phosphorylation via loss of its inhibitory function on PP1. Our results suggest a novel mechanism of DARPP-32-CREB signalling dysregulation in AD. PMID:26178297

  3. Large volume loss during cleavage formation, Hamburg sequence, Pennsylvania

    Science.gov (United States)

    Beutner, Edward C.; Charles, Emmanuel G.

    1985-11-01

    Green reduction spots in red slate of the Hamburg sequence exposed near Shartlesville, Pennsylvania, have axial ratios of 1.42:1.0:0.28 on the limbs of near-isoclinal folds and 1.0:0.79:0.41 in fold hinge zones. Conodont cusps and denticles within the reduction spots have been brittlely pulled apart and give independent measures of extension in various directions. Comparison of conodont extensions with reduction spot shapes on limbs and hinges indicates that sedimentary compaction of 44% preceded the tectonic strain associated with cleavage formation. This strain, having identical maximum extensions but greater shortening in fold hinges as compared to limbs, was characterized by 41% extension in X, no change in Y, 50% to 59% shortening in Z, and 29% to 42% tectonic volume loss. The general lack of directed overgrowths on grains reflects the large volume loss and contrasts with other slates, where deformation was an almost constant volume process and extension in X compensated for shortening in Z. *Present address: Department of Geology, Miami University, Oxford, Ohio 45056

  4. Hamiltonian formulation of bond graphs

    NARCIS (Netherlands)

    Golo, Goran; Schaft, van der Arjan; Breedveld, Peter C.; Maschke, Bernhard M.; Johansson, R.; Rantzer, A.

    2003-01-01

    This paper deals with the mathematical formulation of bond graphs. It is proven that the power continuous part of bond graphs, the junction structure, can be associated with a Dirac structure and that the equations describing a bond graph model correspond to a port Hamiltonian system. The conditions

  5. Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX.

    Directory of Open Access Journals (Sweden)

    Marta Maria Gaglia

    2015-12-01

    Full Text Available Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV. Previous studies indicated that cleavage of messenger RNAs (mRNA by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity.

  6. Characterization of the (0001) cleavage surface of antimony single crystals using scanning probe microscopy: Atomic structure, vacancies, cleavage steps, and twinned interlayers

    Science.gov (United States)

    Stegemann, Bert; Ritter, Claudia; Kaiser, Bernhard; Rademann, Klaus

    2004-04-01

    Atomically resolved scanning tunneling microscopy images of the unreconstructed hexagonal structure of surface atoms on Sb(0001) are presented. Lateral and vertical lattice parameters have been determined. The interatomic spacing of 4.31 Å (±0.05 Å) on the Sb(0001) surface corresponds to the known bulk data. Cleavage has been found to occur always between adjacent double layers, yielding at least diatomic cleavage steps of 3.75 Å (±0.10 Å) height. Different kinds of defect structures on the cleavage plane have been imaged with atomic resolution. Point defects, caused by a single or by three missing surface atoms, have been uncovered. Stable imaging of cleavage steps, which were found to be straight along the atomic rows, has been achieved. Twinned interlayers formed upon cleavage of Sb even at room temperature have been revealed by atomic force microscopy. The mean twinning angle of 2.42° (±0.20°) is quantitatively in accord with the value of 2.45° predicted by the model of twinning in Sb crystals. The observed features are discussed with respect to other layered materials and with regard to their relevance for the use of Sb(0001) as a support of nanostructures.

  7. Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer.

    Science.gov (United States)

    Vitiello, D; Pecchia, D B; Burke, J M

    2000-04-01

    Small catalytic RNAs like the hairpin ribozyme are proving to be useful intracellular tools; however, most attempts to demonstrate trans-cleavage of RNA by ribozymes in cells have been frustrated by rapid cellular degradation of the cleavage products. Here, we describe a fluorescence resonance energy transfer (FRET) assay that directly monitors cleavage of target RNA in tissue-culture cells. An oligoribonucleotide substrate was modified to inhibit cellular ribonuclease degradation without interfering with ribozyme cleavage, and donor (fluorescein) and acceptor (tetramethylrhodamine) fluorophores were introduced at positions flanking the cleavage site. In simple buffers, the intact substrate produces a strong FRET signal that is lost upon cleavage, resulting in a red-to-green shift in dominant fluorescence emission. Hairpin ribozyme and fluorescent substrate were microinjected into murine fibroblasts under conditions in which substrate cleavage can occur only inside the cell. A strong FRET signal was observed by fluorescence microscopy when substrate was injected, but rapid decay of the FRET signal occurred when an active, cognate ribozyme was introduced with the substrate. No acceleration in cleavage rates was observed in control experiments utilizing a noncleavable substrate, inactive ribozyme, or an active ribozyme with altered substrate specificity. Subsequently, the fluorescent substrates were injected into clonal cell lines that expressed cognate or noncognate ribozymes. A decrease in FRET signal was observed only when substrate was microinjected into cells expressing its cognate ribozyme. These results demonstrate trans-cleavage of RNA within mammalian cells, and provide an experimental basis for quantitative analysis of ribozyme activity and specificity within the cell. PMID:10786853

  8. Synthesis of a Novel Organic Molecule for DNA Cleavage%新型有机小分子DNA切割试剂的合成

    Institute of Scientific and Technical Information of China (English)

    安东; 赵晓辉; 周密; 叶志文

    2014-01-01

    The artificial nucleic acid cleaving agents have attracted extensive attention due to their potential applications in molecular biological technology and drug development. Metal-free cleaving reagents have been considered safer for their hydrolytic pathway of cleaving the P-O bond of phosphodiester in nucleic acids and have shown clinical potential. It is known that guanidinium is the arginine residue and the key functionality at the active site in staphylococcal nuclease( SNase) for DNA hydrolysis. Some small organic molecules as guani-dinium derivatives have been used to cleave phosphodiester for DNA hydrolysis. We report here, according to active groups synergetic catalysis principle, the design and synthsis of a novel phosphodiester receptor 1-( N-guanidinoethyl)-4-( N-hydroxyethyl)-piperazidine hydrochloride ( 4 ) and the preliminary studies of its DNA cleavage activity. In the compound, the guanidinium group serves to recognize, bind, and electrophili-cally activate the anionic phosphodiester through hydrogen bonding and electrostatic interaction. The hydroxyl group works as a nucleophilic group in the transphosphorylation reaction, which is expected to be highly effi-cient because of the proximity effect. A “couple hardness with softness” piperazidine is designed to connect these two groups. Compound 4 was synthesized via a three-step reaction( nucleophilic substitution, hydrazinol-ysis and guanylation) . Its structure was confirmed by 1 H NMR, 13 C NMR and LC-MS. The influence of pH on the cleaving of pUC 19 DNA was studied by sugar gel electrophoresis. The mechanism of cleaving DNA by the compound was proved through the free radicals quenches experiments. The way of DNA cleavage was dis-cussed through density functional theory and theoretical investigation by Gaussian. The results indicate that with pH value of 7.2 is the optimal pH for DNA cleavage in the presence of compound 4 , the phosphodiester bond of DNA would be cleaved by compound 4 via a

  9. The short transcript of Leishmania RNA virus is generated by RNA cleavage.

    OpenAIRE

    MacBeth, K J; Patterson, J. L.

    1995-01-01

    Leishmania RNA virus 1 produces a short viral RNA transcript corresponding to the 5' end of positive-sense single-stranded RNAs both in virally infected cells and in in vitro polymerase assays. We hypothesized that this short transcript was generated via cleavage of full-length positive-sense single-stranded RNA. A putative cleavage site was mapped by primer extension analysis to nucleotide 320 of the viral genome. To address the hypothesis that the short transcript is generated via cleavage ...

  10. Methylase-limited partial NotI cleavage for physical mapping of genomic DNA.

    OpenAIRE

    Hanish, J; McClelland, M

    1990-01-01

    Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking methylase M. BspRI (5'...GGmCC...3') for competition digests with NotI. The resulting methylase-limited partial DNA cleavage is shown to be superior to standard techniques on bacterial genomic...

  11. Enhanced cleavage of type II collagen by collagenases in osteoarthritic articular cartilage.

    OpenAIRE

    Billinghurst, R.C.; Dahlberg, L; Ionescu, M.; Reiner, A; Bourne, R; Rorabeck, C; Mitchell, P; Hambor, J; Diekmann, O.; Tschesche, H; Chen, J; Van Wart, H; Poole, A. R.

    1997-01-01

    We demonstrate the direct involvement of increased collagenase activity in the cleavage of type II collagen in osteoarthritic human femoral condylar cartilage by developing and using antibodies reactive to carboxy-terminal (COL2-3/4C(short)) and amino-terminal (COL2-1/4N1) neoepitopes generated by cleavage of native human type II collagen by collagenase matrix metalloproteinase (MMP)-1 (collagenase-1), MMP-8 (collagenase-2), and MMP-13 (collagenase-3). A secondary cleavage followed the initia...

  12. Processing of pestivirus polyprotein: cleavage site between autoprotease and nucleocapsid protein of classical swine fever virus.

    OpenAIRE

    Stark, R; Meyers, G; Rümenapf, T.; Thiel, H J

    1993-01-01

    The polyprotein of classical swine fever virus starts with the nonstructural protein p23, which is followed by the nucleocapsid protein p14. Proteolytic cleavage between p23 and p14 was demonstrated in a cell-free transcription-translation system. Successive truncation of the cDNA used for the transcription indicated that the proteolytic activity responsible for the cleavage between p23 and p14 resides within p23. In order to determine the cleavage site between these two proteins, the respect...

  13. Preferential DNA Cleavage under Anaerobic Conditions by a DNA Binding Ruthenium Dimer

    OpenAIRE

    Janaratne, Thamara K.; Ongeri, Fiona; Yadav, Abishek; MacDonnell, Frederick M.

    2007-01-01

    In the absence of O2, the cationic complex, [(phen)2Ru(tatpp)Ru(phen)2]4+ (P4+), undergoes in situ reduction by glutathione (GSH) to form a species that induces DNA cleavage. Exposure to air strongly attenuates the cleavage activity, even in the presence of a large excess of reducing agent (e.g., 40 equiv GSH per P4+) suggesting the complex may be useful in targeting cells with a low oxygen microenvironment (hypoxia) for destruction via DNA cleavage. The active species is identified as the do...

  14. Mechanisms of RNAi: mRNA cleavage fragments may indicate stalled RISC

    OpenAIRE

    Holen, Torgeir

    2005-01-01

    The molecular mechanism of RNA interference (RNAi) is under intense investigation. We previously demonstrated the existence of inactive siRNAs and also of mRNA cleavage in vivo in human cells. Here it is shown that some siRNAs with low activity leave mRNA cleavage fragments while an siRNA with higher activity does not. The pattern is consistent with both short-term (4-24 hours) and long-term (1-4 days) time-series. Analysis of the putative 3′ mRNA cleavage product showed high GC content immed...

  15. Guest-host interactions in the cleavage of phenylphenyl acetates by -cyclodextrin in alkaline medium

    Indian Academy of Sciences (India)

    V Raj; T Chandrakala; K Rajasekaran

    2008-05-01

    Kinetics of cleavage of phenylphenyl acetates (PPA) and several para-substituted PPAs in basic aqueous sodium carbonate-bicarbonate buffer containing -cyclodextrin (CD) have been studied. The reaction exhibits saturation type kinetics and CD accelerates the rate of cleavage by the formation of 1G : 1H inclusion complex. The kinetic results indicate that aryloxy moiety of PPA is included in the hydrophobic cavity of CD. The overall rate constants for the cleavage of the [CD-ester] complex correlate with the Hammett -constants and Hansch hydrophobicity parameters . At higher concentrations of CD, there is an additional catalysis due to the formation of weak 1G : 2H complex.

  16. Isotopic Effects on Covalent Bond Confined in a Penetrable Sphere.

    Science.gov (United States)

    Sarsa, Antonio; Alcaraz-Pelegrina, José M; Le Sech, Claude

    2015-11-12

    A model of confinement of the covalent bond by a finite potential beyond the Born-Oppenheimer approximation is presented. A two-electron molecule is located at the center of a penetrable spherical cavity. The Schrödinger equation has been solved by using the diffusion Monte Carlo method. Total energies, internuclear distances, and vibrational frequencies of the confined molecular system have been obtained. Even for confining potentials of a few electronvolts, a noticeable increase in the bond energy and the nuclear vibrational frequency is observed, and the internuclear distance is lowered. The gap between the zero point energy of different molecular isotopes increases with confinement. The confinement of the electron pair might play a role in chemical reactivity, providing an alternative explanation for the tunnel effect, when large values of primary kinetic isotopic effect are observed. The Swain-Schaad relation is still verified when confinement changes the zero point energy. A semiquantitative illustration is proposed using the data relative to an hydrogen transfer involving a C-H cleavage catalyzed by the bovine serum amine oxidase. Changes on the confining conditions, corresponding to a confinement/deconfinement process, result in a significant decrease in the activation energy of the chemical transformation. It is proposed that confinement/deconfinement of the electron-pair bonding by external electrostatic forces inside the active pocket of an enzyme could be one of the basic mechanisms of the enzyme catalysis. PMID:26484576

  17. Reversed DNA strand cleavage specificity in initiation of Cre-LoxP recombination induced by the His289Ala active-site substitution.

    Science.gov (United States)

    Gelato, Kathy A; Martin, Shelley S; Baldwin, Enoch P

    2005-11-25

    During the first steps of site-specific recombination, Cre protein cleaves and religates a specific homologous pair of LoxP strands to form a Holliday junction (HJ) intermediate. The HJ is resolved into recombination products through exchange of the second homologous strand pair. CreH289A, containing a His to Ala substitution in the conserved R-H-R catalytic motif, has a 150-fold reduced recombination rate and accumulates HJs. However, to produce these HJs, CreH289A exchanges the opposite set of strands compared to wild-type Cre (CreWT). To investigate how CreH289A and CreWT impose strand exchange order, we characterized their reactivities and strand cleavage preferences toward LoxP duplex and HJ substrates containing 8bp spacer substitutions. Remarkably, CreH289A had different and often opposite strand exchange preferences compared to CreWT with nearly all substrates. CreH289N was much less perturbed, implying that overall recombination rate and strand exchange depend more on His289 hydrogen bonding capability than on its acid/base properties. LoxP substitutions immediately 5' (S1 nucleotide) or 3' (S1' nucleotide) of the scissile phosphate had large effects on substrate utilization and strand exchange order. S1' substitutions, designed to alter base-unstacking events concomitant with Cre-induced LoxP bending, caused HJ accumulation and dramatically inverted the cleavage preferences. That pre-formed HJs were resolved via either strand in vitro suggests that inhibition of the "conformational switch" isomerization required to trigger the second strand exchange accounts for the observed HJ accumulation. Rather than reflecting CreWT behavior, CreH289A accumulates HJs of opposite polarity through a combination of its unique cleavage specificity and an HJ isomerization defect. The overall implication is that cleavage specificity is mediated by sequence-dependent DNA deformations that influence the scissile phosphate positioning and reactivity. A role of His289 may be to

  18. Reversed DNA Strand Cleavage Specificity in Initiation of Cre–LoxP Recombination Induced by the His289Ala Active-site Substitution

    Science.gov (United States)

    Gelato, Kathy A.; Martin, Shelley S.; Baldwin, Enoch P.

    2010-01-01

    During the first steps of site-specific recombination, Cre protein cleaves and religates a specific homologous pair of LoxP strands to form a Holliday junction (HJ) intermediate. The HJ is resolved into recombination products through exchange of the second homologous strand pair. CreH289A, containing a His to Ala substitution in the conserved R-H-R catalytic motif, has a 150-fold reduced recombination rate and accumulates HJs. However, to produce these HJs, CreH289A exchanges the opposite set of strands compared to wild-type Cre (CreWT). To investigate how CreH289A and CreWT impose strand exchange order, we characterized their reactivities and strand cleavage preferences toward LoxP duplex and HJ substrates containing 8 bp spacer substitutions. Remarkably, CreH289A had different and often opposite strand exchange preferences compared to CreWT with nearly all substrates. CreH289N was much less perturbed, implying that overall recombination rate and strand exchange depend more on His289 hydrogen bonding capability than on its acid/base properties. LoxP substitutions immediately 5′(S1 nucleotide) or 3′(S1′nucleotide) of the scissile phosphate had large effects on substrate utilization and strand exchange order. S1′substitutions, designed to alter base-unstacking events concomitant with Cre-induced LoxP bending, caused HJ accumulation and dramatically inverted the cleavage preferences. That pre-formed HJs were resolved via either strand in vitro suggests that inhibition of the “conformational switch” isomerization required to trigger the second strand exchange accounts for the observed HJ accumulation. Rather than reflecting CreWT behavior, CreH289A accumulates HJs of opposite polarity through a combination of its unique cleavage specificity and an HJ isomerization defect. The overall implication is that cleavage specificity is mediated by sequence-dependent DNA deformations that influence the scissile phosphate positioning and reactivity. A role of His289

  19. ASEAN+3 Bond Market Guides

    OpenAIRE

    Asian Development Bank (ADB)

    2012-01-01

    The ASEAN+3 Bond Market Guide contains the comprehensive reports of the ASEAN+3 Bond Market Forum Sub-Forum 1 (SF1) and Sub-Forum 2 (SF2). The SF1 report (Volume 1) analyzes the harmonization and standardization of the existing bond markets in the ASEAN+3. It also contains the individual market guides of 11 economies under the ASEAN+3 Bond Market Forum (ABMF). The SF2 report (Volume 2) provides an overview of the ASEAN+3 bond markets and their infrastructures, as well as issues confronted by ...

  20. Optimal Investment in Structured Bonds

    DEFF Research Database (Denmark)

    Jessen, Pernille; Jørgensen, Peter Løchte

    The paper examines the role of structured bonds in the optimal portfolio of a small retail investor. We consider the typical structured bond essentially repacking an exotic option and a zero coupon bond, i.e. an investment with portfolio insurance. The optimal portfolio is found when the investment...... opportunities consist of a risky reference fund, a risk-free asset and a structured bond. Key model elements are the trading strategy and utility function of the investor. Our numerical results indicate structured bonds do have basis for consideration in the optimal portfolio. The product holdings are...

  1. Isomerization of Olefins Triggered by Rhodium-Catalyzed C–H Bond Activation: Control of Endocyclic β-Hydrogen Elimination**

    OpenAIRE

    Yip, Stephanie Y Y; Aïssa, Christophe

    2015-01-01

    Five-membered metallacycles are typically reluctant to undergo endocyclic β-hydrogen elimination. The rhodium-catalyzed isomerization of 4-pentenals into 3-pentenals occurs through this elementary step and cleavage of two C–H bonds, as supported by deuterium-labeling studies. The reaction proceeds without decarbonylation, leads to trans olefins exclusively, and tolerates other olefins normally prone to isomerization. Endocyclic β-hydrogen elimination can also be controlled in an enantiodiverg...

  2. Kinetics and regulation of site-specific endonucleolytic cleavage of human IGF-II mRNAs

    OpenAIRE

    van Dijk, Erwin L.; Sussenbach, John S.; Holthuizen, P. Elly

    2001-01-01

    Human insulin-like growth factor II (IGF-II) mRNA can be cleaved at a specific site in its 4 kb long 3′-UTR. This yields a stable 3′ cleavage product of 1.8 kb consisting of a 3′-UTR and a poly(A) tail and an unstable 5′ cleavage product containing the IGF-II coding region. After cleavage, the 5′ cleavage product is targeted to rapid degradation and consequently is no longer involved in IGF-II protein synthesis. Cleavage is therefore thought to provide an addit...

  3. The intramembrane cleavage site of the amyloid precursor protein depends on the length of its transmembrane domain

    OpenAIRE

    Lichtenthaler, Stefan F.; Beher, Dirk; Heike S Grimm; Wang, Rong; Shearman, Mark S.; Masters, Colin L.; Beyreuther, Konrad

    2002-01-01

    Proteolytic processing of the amyloid precursor protein by β-secretase generates C99, which subsequently is cleaved by γ-secretase, yielding the amyloid β peptide (Aβ). This γ-cleavage occurs within the transmembrane domain (TMD) of C99 and is similar to the intramembrane cleavage of Notch. However, Notch and C99 differ in their site of intramembrane cleavage. The main γ-cleavage of C99 occurs in the middle of the TMD, whereas the cleavage of Notch occurs close to the C-terminal end of the TM...

  4. An investigation into the role of ATP in the mammalian pre-mRNA 3' cleavage reaction.

    Science.gov (United States)

    Khleborodova, Asya; Pan, Xiaozhou; Nagre, Nagaraja N; Ryan, Kevin

    2016-06-01

    RNA Polymerase II transcribes beyond what later becomes the 3' end of a mature messenger RNA (mRNA). The formation of most mRNA 3' ends results from pre-mRNA cleavage followed by polyadenylation. In vitro studies have shown that low concentrations of ATP stimulate the 3' cleavage reaction while high concentrations inhibit it, but the origin of these ATP effects is unknown. ATP might enable a cleavage factor kinase or activate a cleavage factor directly. To distinguish between these possibilities, we tested several ATP structural analogs in a pre-mRNA 3' cleavage reaction reconstituted from DEAE-fractionated cleavage factors. We found that adenosine 5'-(β,γ-methylene)triphosphate (AMP-PCP) is an effective in vitro 3' cleavage inhibitor with an IC50 of ∼300 μM, but that most other ATP analogs, including adenosine 5'-(β,γ-imido)triphosphate, which cannot serve as a protein kinase substrate, promoted 3' cleavage but less efficiently than ATP. In combination with previous literature data, our results do not support ATP stimulation of 3' cleavage through cleavage factor phosphorylation in vitro. Instead, the more likely mechanism is that ATP stimulates cleavage factor activity through direct cleavage factor binding. The mammalian 3' cleavage factors known to bind ATP include the cleavage factor II (CF IIm) Clp1 subunit, the CF Im25 subunit and poly(A) polymerase alpha (PAP). The yeast homolog of the CF IIm complex also binds ATP through yClp1. To investigate the mammalian complex, we used a cell-line expressing FLAG-tagged Clp1 to co-immunoprecipitate Pcf11 as a function of ATP concentration. FLAG-Clp1 co-precipitated Pcf11 with or without ATP and the complex was not affected by AMP-PCP. Diadenosine tetraphosphate (Ap4A), an ATP analog that binds the Nudix domain of the CF Im25 subunit with higher affinity than ATP, neither stimulated 3' cleavage in place of ATP nor antagonized ATP-stimulated 3' cleavage. The ATP-binding site of PAP was disrupted by site

  5. Application of Ni(II-assisted peptide bond hydrolysis to non-enzymatic affinity tag removal.

    Directory of Open Access Journals (Sweden)

    Edyta Kopera

    Full Text Available In this study, we demonstrate a non-enzymatic method for hydrolytic peptide bond cleavage, applied to the removal of an affinity tag from a recombinant fusion protein, SPI2-SRHWAP-His(6. This method is based on a highly specific Ni(II reaction with (S/TXHZ peptide sequences. It can be applied for the protein attached to an affinity column or to the unbound protein in solution. We studied the effect of pH, temperature and Ni(II concentration on the efficacy of cleavage and developed an analytical protocol, which provides active protein with a 90% yield and ∼100% purity. The method works well in the presence of non-ionic detergents, DTT and GuHCl, therefore providing a viable alternative for currently used techniques.

  6. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors

    OpenAIRE

    de Vries, H.; Rüegsegger, U.; Hübner, W; Friedlein, A.; van Langen, H; Keller, W.

    2000-01-01

    Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Five of the factors have been purified and most of their components cloned, but cleavage factor II(m) (CF II(m)) remained uncharacterized. We have purified CF II(m) from HeLa cell nuclear extract by several chromatographic steps. During purification, CF II(m) activity separated into two components, one essential (CF IIA(m)) and one stimulatory (CF II...

  7. Dynamic propagation and cleavage crack arrest in bainitic steel

    International Nuclear Information System (INIS)

    In complement of the studies of harmfulness of defects, generally realized in term of initiation, the concept of crack arrest could be used as complementary analyses to the studies of safety. The stop occurs when the stress intensity factor becomes lower than crack arrest toughness (KIa) calculated in elasto-statics (KI ≤ KIa). The aim of this thesis is to understand and predict the stop of a crack propagating at high speed in a 18MND5 steel used in the pressure water reactor (PWR). The test chosen to study crack arrest is the disc thermal shock test. The observations under the scanning electron microscope of the fracture surface showed that the crack arrest always occurs in cleavage mode and that the critical microstructural entity with respect to the propagation and crack arrest corresponds to at least the size of the prior austenitic grain. The numerical analyses in elasto-statics confirm the conservatism of the codified curve of the RCC-M with respect to the values of KIa. The dynamic numerical analyses show that the deceleration of the crack measured at the end of the propagation is related to the global dynamic of the structure (vibrations). The transferability to components of crack arrest toughness obtained from tests analysed in static is thus not assured. The disc thermal shock tests were also modelled by considering a criterion of propagation and arrest of the type 'RKR' characterized by a critical stress sc which depends on the temperature. The results obtained account well for the crack jump measured in experiments as well as the shape of the crack arrest front. (author)

  8. Dinitrogen binding and cleavage by multinuclear iron complexes.

    Science.gov (United States)

    McWilliams, Sean F; Holland, Patrick L

    2015-07-21

    The iron-molybdenum cofactor of nitrogenase has unprecedented coordination chemistry, including a high-spin iron cluster called the iron-molybdenum cofactor (FeMoco). Thus, understanding the mechanism of nitrogenase challenges coordination chemists to understand the fundamental N2 chemistry of high-spin iron sites. This Account summarizes a series of studies in which we have synthesized a number of new compounds with multiple iron atoms, characterized them using crystallography and spectroscopy, and studied their reactions in detail. These studies show that formally iron(I) and iron(0) complexes with three- and four-coordinate metal atoms have the ability to weaken and break the triple bond of N2. These reactions occur at or below room temperature, indicating that they are kinetically facile. This in turn implies that iron sites in the FeMoco are chemically reasonable locations for N2 binding and reduction. The careful evaluation of these compounds and their reaction pathways has taught important lessons about what characteristics make iron more effective for N2 activation. Cooperation of two iron atoms can lengthen and weaken the N-N bond, while three working together enables iron atoms to completely cleave the N-N bond to nitrides. Alkali metals (typically introduced into the reaction as part of the reducing agent) are thermodynamically useful because the alkali metal cations stabilize highly reduced complexes, pull electron density into the N2 unit, and make reduced nitride products more stable. Alkali metals can also play a kinetic role, because cation-π interactions with the supporting ligands can hold iron atoms near enough to one another to facilitate the cooperation of multiple iron atoms. Many of these principles may also be relevant to the iron-catalyzed Haber-Bosch process, at which collections of iron atoms (often promoted by the addition of alkali metals) break the N-N bond of N2. The results of these studies teach more general lessons as well. They

  9. Urokinase-catalysed cleavage of the urokinase receptor requires an intact glycolipid anchor

    DEFF Research Database (Denmark)

    Høyer-Hansen, G; Pessara, U; Holm, A;

    2001-01-01

    reaction, even though the actual cleavage occurs between the first and second domains. Purified full-length GPI-anchored uPAR (GPI-uPAR) proved much more susceptible to uPA-mediated cleavage than recombinant truncated soluble uPAR (suPAR), which lacks the glycolipid anchor. This was not a general...... difference in proteolytic susceptibility since GPI-uPAR and suPAR were cleaved with equal efficiency by plasmin. Since the amino acid sequences of GPI-uPAR and suPAR are identical except for the C-terminal truncation, the different cleavage patterns suggest that the two uPAR variants differ in the......PAR, purified from plasma, was found to have a similar resistance to uPA cleavage as phospholipase C-treated GPI-uPAR and recombinant suPAR....

  10. Silicon carbide wafer bonding by modified surface activated bonding method

    Science.gov (United States)

    Suga, Tadatomo; Mu, Fengwen; Fujino, Masahisa; Takahashi, Yoshikazu; Nakazawa, Haruo; Iguchi, Kenichi

    2015-03-01

    4H-SiC wafer bonding has been achieved by the modified surface activated bonding (SAB) method without any chemical-clean treatment and high temperature annealing. Strong bonding between the SiC wafers with tensile strength greater than 32 MPa was demonstrated at room temperature under 5 kN force for 300 s. Almost the entire wafer has been bonded very well except a small peripheral region and few voids. The interface structure was analyzed to verify the bonding mechanism. It was found an amorphous layer existed as an intermediate layer at the interface. After annealing at 1273 K in vacuum for 1 h, the bonding tensile strength was still higher than 32 MPa. The interface changes after annealing were also studied. The results show that the thickness of the amorphous layer was reduced to half after annealing.

  11. The short transcript of Leishmania RNA virus is generated by RNA cleavage.

    Science.gov (United States)

    MacBeth, K J; Patterson, J L

    1995-01-01

    Leishmania RNA virus 1 produces a short viral RNA transcript corresponding to the 5' end of positive-sense single-stranded RNAs both in virally infected cells and in in vitro polymerase assays. We hypothesized that this short transcript was generated via cleavage of full-length positive-sense single-stranded RNA. A putative cleavage site was mapped by primer extension analysis to nucleotide 320 of the viral genome. To address the hypothesis that the short transcript is generated via cleavage at this site, two substrate RNAs that possessed viral sequence encompassing the putative cleavage site were created. When incubated with sucrose-purified viral particles, these substrate RNAs were site-specifically cleaved. The cleavage site of the in vitro-processed RNAs also mapped to viral nucleotide 320. The short-transcript-generating activity could be specifically abolished by proteinase K treatment of sucrose-purified viral particles and high concentrations of EGTA [ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid], suggesting that the activity requires a proteinaceous factor and possibly intact viral particles. The cleavage activity is directly associated with short-transcript-generating activity, since only viral particle preparations which were capable of generating the short transcript in polymerase assays were also active in the cleavage assay. Furthermore, the short-transcript-generating activity is independent of the viral polymerase's transcriptase and replicase activities. We present a working model whereby cleavage of Leishmaniavirus RNA transcripts functions in the maintenance of a low-level persistent infection. PMID:7745692

  12. Proteolytic Cleavage of the Red Blood Cell Glycocalyx in a Genetic Form of Hypertension

    OpenAIRE

    Pot, Cécile; Chen, Angela Y.; Ha, Jessica N.; Schmid-Schönbein, Geert W

    2011-01-01

    Recent evidence suggests that the spontaneously hypertensive rat (SHR) has an elevated level of proteases, including matrix metalloproteinases (MMPs), involved in cell membrane receptor cleavage. We hypothesize that SHR red blood cells (RBCs) may be subject to an enhanced glycocalyx cleavage compared to the RBCs of the normotensive Wistar-Kyoto (WKY) rats. By direct observation of RBC rouleaux, we found no significant difference in RBC aggregation for unseparated SHR and WKY RBCs. However, li...

  13. Cleavage Fracture in a Ferritic Steel Weld: Characterization of Second Phase Particles

    OpenAIRE

    S. Schilling, N. Chapeau, A.P. Jivkov, E. Keim, S.R. Ortner, M.G. Burke

    2013-01-01

    Cleavage fracture can initiate by the cracking of second phase particles in metals. Understanding the size distribution, morphologies and compositions of initiating particles for a particular material is key to successful micromechanical modelling of cleavage. The second phase particles responsible for the fracture initiation in P141 CAC-S7, a reactor pressure vessel (RPV) weld metal from the EU-funded PERFORM 60 Multiscale Modelling Programme, have been identified and characterised in order ...

  14. Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor

    Science.gov (United States)

    Jepsen, Morten Leth; Harmsen, Charlotte; Godbole, Adwait Anand; Nagaraja, Valakunja; Knudsen, Birgitta R.; Ho, Yi-Ping

    2015-12-01

    We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes. Electronic supplementary information (ESI) available: Characterization of the QD-based DNA Nanosensor. See DOI: 10.1039/c5nr06326d

  15. Engineering a ribozyme cleavage-induced split fluorescent aptamer complementation assay

    OpenAIRE

    Ausländer, Simon; Fuchs, David; Hürlemann, Samuel; Ausländer, David; Fussenegger, Martin

    2016-01-01

    Hammerhead ribozymes are self-cleaving RNA molecules capable of regulating gene expression in living cells. Their cleavage performance is strongly influenced by intra-molecular loop–loop interactions, a feature not readily accessible through modern prediction algorithms. Ribozyme engineering and efficient implementation of ribozyme-based genetic switches requires detailed knowledge of individual self-cleavage performances. By rational design, we devised fluorescent aptamer-ribozyme RNA archit...

  16. Spatial organization of topoisomerase I-mediated DNA cleavage induced by camptothecin–oligonucleotide conjugates

    OpenAIRE

    Arimondo, Paola B.; Angenault, Stéphane; Halby, Ludovic; Boutorine, Alexandre; Schmidt, Frédéric; Monneret, Claude; Garestier, Thérèse; Sun, Jian-Sheng; Bailly, Christian; Hélène, Claude

    2003-01-01

    Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analysis of the DNA cleavage efficiency as a function of the positioning of the camptothecin derivative, either on the 3′ or the 5′ side of the triplex, and the location of the cleava...

  17. Nanorelief of the natural cleavage surface of triglycine sulphate crystals with substitutional and interstitial impurities

    International Nuclear Information System (INIS)

    Ferroelectric triglycine sulphate crystals (TGS) with substitutional (LADTGS+ADP, DTGS) and interstitial (Cr) impurities have been studied by atomic-force microscopy, X-ray diffraction, and X-ray fluorescence. The nanorelief parameters of the mirror cleavage TGS(010) surface have been measured with a high accuracy. A correlation between the crystal defect density in the bulk and the cleavage surface nanorelief is revealed at the submicrometer level.

  18. A hingeless Fc fusion system for site-specific cleavage by IdeS.

    Science.gov (United States)

    Novarra, Shabazz; Grinberg, Luba; Rickert, Keith W; Barnes, Arnita; Wilson, Susan; Baca, Manuel

    2016-01-01

    Fusion of proteins to the Fc region of IgG is widely used to express cellular receptors and other extracellular proteins, but cleavage of the fusion partner is sometimes required for downstream applications. Immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) is a protease with exquisite specificity for human IgG, and it can also cleave Fc-fusion proteins at a single site in the N-terminal region of the CH2 domain. However, the site of IdeS cleavage results in the disulfide-linked hinge region partitioning with the released protein, complicating downstream usage of the cleaved product. To tailor the Fc fragment for release of partner proteins by IdeS treatment, we investigated the effect of deleting regions of IgG-derived sequence that are upstream of the cleavage site. Elimination of the IgG-derived hinge sequence along with several residues of the CH2 domain had negligible effects on expression and purity of the fusion protein, while retaining efficient processing by IdeS. An optimal Fc fragment comprising residues 235-447 of the human IgG1 heavy chain sufficed for efficient production of fusion proteins and minimized the amount of residual Ig-derived sequence on the cleavage product following IdeS treatment. Pairing of this truncated Fc fragment with IdeS cleavage enables highly specific cleavage of Fc-fusion proteins, thus eliminating the need to engineer extraneous cleavage sequences. This system should be helpful for producing Fc-fusion proteins requiring downstream cleavage, particularly those that are sensitive to internal miscleavage if treated with alternative proteases. PMID:27210548

  19. Evidence that Transcript Cleavage Is Essential for RNA Polymerase II Transcription and Cell Viability

    OpenAIRE

    Sigurdsson, Stefan; Dirac-Svejstrup, A. Barbara; Svejstrup, Jesper Q.

    2010-01-01

    Summary During transcript elongation in vitro, backtracking of RNA polymerase II (RNAPII) is a frequent occurrence that can lead to transcriptional arrest. The polymerase active site can cleave the transcript during such backtracking, allowing transcription to resume. Transcript cleavage is either stimulated by elongation factor TFIIS or occurs much more slowly in its absence. However, whether backtracking actually occurs in vivo, and whether transcript cleavage is important to escape it, has...

  20. Protein cleavage strategies for an improved analysis of the membrane proteome

    OpenAIRE

    Poetsch Ansgar; Fischer Frank

    2006-01-01

    Abstract Background Membrane proteins still remain elusive in proteomic studies. This is in part due to the distribution of the amino acids lysine and arginine, which are less frequent in integral membrane proteins and almost absent in transmembrane helices. As these amino acids are cleavage targets for the commonly used protease trypsin, alternative cleavage conditions, which should improve membrane protein analysis, were tested by in silico digestion for the three organisms Saccharomyces ce...

  1. Specific cleavage of human type III and IV collagens by Pseudomonas aeruginosa elastase.

    OpenAIRE

    Heck, L W; Morihara, K; McRae, W B; Miller, E J

    1986-01-01

    Purified Pseudomonas aeruginosa elastase cleaved human type III and IV collagens with the formation of specific cleavage products. Furthermore, type I collagen appeared to be slowly cleaved by both P. aeruginosa elastase and alkaline protease. These cleavage fragments from type III and IV collagens were separated from the intact collagen chains by SDS polyacrylamide gradient gel electrophoresis run under reducing conditions, and they were detected by their characteristic Coomassie blue staini...

  2. Association of polyadenylation cleavage factor I with U1 snRNP

    OpenAIRE

    Awasthi, Sita; Alwine, James C.

    2003-01-01

    Splicing and polyadenylation factors interact for the control of polyadenylation and the coupling of splicing and polyadenylation. We document an interaction between the U1 snRNP and mammalian polyadenylation cleavage factor I (CF Im), one of several polyadenylation factors needed for the cleavage of the pre-mRNA at the polyadenylation site. Sucrose density gradient centrifugation demonstrated that CF Im separated into two fractions, a light fraction which contained the known CF Im subunits (...

  3. Credit default swaps, bond spreads and the bond market

    OpenAIRE

    Zhu, Meicheng

    2014-01-01

    With the rapid development of the credit default swap (CDS) market, the issue of how the introduction of CDSs affects the corporate bond market has been of particular interest to researchers and policy makers. This has been investigated in the literature from two perspectives. One is to examine the relationship between the CDS and the bond markets in price discovery, and the other is concerned with researching the CDS trading effects on bond spreads. Referring to the former approach, most rel...

  4. The role of the methyltransferase domain of bifunctional restriction enzyme RM.BpuSI in cleavage activity.

    Directory of Open Access Journals (Sweden)

    Arthur Sarrade-Loucheur

    Full Text Available Restriction enzyme (REase RM.BpuSI can be described as a Type IIS/C/G REase for its cleavage site outside of the recognition sequence (Type IIS, bifunctional polypeptide possessing both methyltransferase (MTase and endonuclease activities (Type IIC and endonuclease activity stimulated by S-adenosyl-L-methionine (SAM (Type IIG. The stimulatory effect of SAM on cleavage activity presents a major paradox: a co-factor of the MTase activity that renders the substrate unsusceptible to cleavage enhances the cleavage activity. Here we show that the RM.BpuSI MTase activity modifies both cleavage substrate and product only when they are unmethylated. The MTase activity is, however, much lower than that of M1.BpuSI and is thought not to be the major MTase for host DNA protection. SAM and sinefungin (SIN increase the Vmax of the RM.BpuSI cleavage activity with a proportional change in Km, suggesting the presence of an energetically more favorable pathway is taken. We further showed that RM.BpuSI undergoes substantial conformational changes in the presence of Ca(2+, SIN, cleavage substrate and/or product. Distinct conformers are inferred as the pre-cleavage/cleavage state (in the presence of Ca(2+, substrate or both and MTase state (in the presence of SIN and substrate, SIN and product or product alone. Interestingly, RM.BpuSI adopts a unique conformation when only SIN is present. This SIN-bound state is inferred as a branch point for cleavage and MTase activity and an intermediate to an energetically favorable pathway for cleavage, probably through increasing the binding affinity of the substrate to the enzyme under cleavage conditions. Mutation of a SAM-binding residue resulted in altered conformational changes in the presence of substrate or Ca(2+ and eliminated cleavage activity. The present study underscores the role of the MTase domain as facilitator of efficient cleavage activity for RM.BpuSI.

  5. Expression and in vitro cleavage activity of anti-caspase-7 hammerhead ribozymes

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Qing Xie; Xia-Qiu Zhou; Shan Jiang; You-Xin Jin

    2004-01-01

    AIM: To prepare hammerhead ribozymes against mouse caspase-7 and identify their cleavage activityin vitro, in order to select a ribozyme with specific cleavage activity against mouse caspase-7 as a potential gene therapy for apoptosis-related diseases.METHODS: Anti-caspase-7 ribozymes targeting sites 333and 394 (named Rz333 and Rz394) were designed by computer software, and their DNA sequences encoding ribozymes were synthesized. Caspase-7 DNA sequence was acquired by RT-PCR. Ribozymes and caspase-7 DNA obtained byin vitro transcription were cloned into pBSKneo U6' and pGEM-T vectors, respectively. The cleavage activity of ribozymes against mouse caspase-7 was identified by cleavage experimentsin vitro.RESULTS: Rz333 and Rz394 were designed and their DNA sequences were synthesized respectively. The expression vector of caspase-7 and plasmids containing Rz333 and Rz394 were reconstructed successfully. Ribozymes and caspase-7 mRNA were expressed byin vitro transcription.In vitro cleavage experiment showed that 243-nt and 744-nt segments were produced after caspase-7 mRNA was mixed with Rz333 in equivalent, and the cleavage efficiency was 67.98%. No cleaved segment was observed when caspase-7 mRNA was mixed with Rz394.CONCLUSION: Rz333 can site-specific cleave mouse caspase-7 mRNA, and it shows a potential for gene therapy of apoptosis-related diseases by down-regulating gene expression of caspase-7.

  6. Altered cleavage patterns in human tripronuclear embryos and their association to fertilization method

    DEFF Research Database (Denmark)

    Joergensen, Mette Warming; Agerholm, Inge; Hindkjaer, Johnny;

    2014-01-01

    stage (p < 0.001), and arrested development from the compaction stage and onwards (p < 0.001). For the IVF embryos, the 2nd and 3rd cleavage cycles were completed within the expected time frame. However, timing of the cell divisions within the cleavage cycles differed between the two groups. In contrast......, the completion of the 1st, 2nd, and 3rd cleavage cycle was delayed, but with a similar division pattern for 3PN ICSI compared with the 2PN ICSI embryos. 3PN, more often than 2PN ICSI embryos, displayed early cleavage into 3 cells (p = 0.03) and arrested development from the compaction stage and......PURPOSE: To analyze the cleavage patterns in dipronuclear (2PN) and tripronuclear (3PN) embryos in relation to fertilization method. METHOD: Time-lapse analysis. RESULTS: Compared to 2PN, more 3PN IVF embryos displayed early cleavage into 3 cells (p < 0.001), displayed longer duration of the 3-cell...

  7. Solder extrusion pressure bonding process and bonded products produced thereby

    Science.gov (United States)

    Beavis, Leonard C.; Karnowsky, Maurice M.; Yost, Frederick G.

    1992-01-01

    Production of soldered joints which are highly reliable and capable of surviving 10,000 thermal cycles between about -40.degree. C. and 110.degree. C. Process involves interposing a thin layer of a metal solder composition between the metal surfaces of members to be bonded and applying heat and up to about 1000 psi compression pressure to the superposed members, in the presence of a reducing atmosphere, to extrude the major amount of the solder composition, contaminants including fluxing gases and air, from between the members being bonded, to form a very thin, strong intermetallic bonding layer having a thermal expansion tolerant with that of the bonded members.

  8. Avoiding silicon/glass bonding damage with fusion bonding method

    Institute of Scientific and Technical Information of China (English)

    Daohong Yang(杨道虹); Chen Xu(徐晨); Guangdi Shen(沈光地)

    2004-01-01

    A novel fusion bonding method between silicon and glass with Nd:YAG laser is described.This method overcomes the movable mechanical parts damage caused by the electrostatics force in micro-electronic machine-system(MEMS)device during the anodic bonding. The diameter of laser spot is 300 μm,the power of laser is 100 W,the laser velocity for bonding is 0.05 m/s,the average bonding tension is 6.3 MPa.It could distinctly reduce and eliminate the defects and damage,especially in movable sensitive mechanical parts of MEMS device.

  9. 19 CFR 113.12 - Bond application.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Bond application. 113.12 Section 113.12 Customs... CUSTOMS BONDS Bond Application and Approval of Bond § 113.12 Bond application. (a) Single entry bond application. In order to insure that the revenue is adequately protected the port director may require...

  10. LAMMPS Framework for Directional Dynamic Bonding

    DEFF Research Database (Denmark)

    2012-01-01

    We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to li...

  11. Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme.

    Science.gov (United States)

    Arbelo-Lopez, Hector D; Simakov, Nikolay A; Smith, Jeremy C; Lopez-Garriga, Juan; Wymore, Troy

    2016-08-01

    Many heme-containing proteins with a histidine in the distal E7 (HisE7) position can form sulfheme in the presence of hydrogen sulfide (H2S) and a reactive oxygen species such as hydrogen peroxide. For reasons unknown, sulfheme derivatives are formed specifically on solvent-excluded heme pyrrole B. Sulfhemes severely decrease the oxygen-binding affinity in hemoglobin (Hb) and myoglobin (Mb). Here, use of hybrid quantum mechanical/molecular mechanical methods has permitted characterization of the entire process of sulfheme formation in the HisE7 mutant of hemoglobin I (HbI) from Lucina pectinata. This process includes a mechanism for H2S to enter the solvent-excluded active site through a hydrophobic channel to ultimately form a hydrogen bond with H2O2 bound to Fe(III). Proton transfer from H2O2 to His64 to form compound (Cpd) 0, followed by hydrogen transfer from H2S to the Fe(III)-H2O2 complex, results in homolytic cleavage of the O-O and S-H bonds to form a reactive thiyl radical (HS(•)), ferryl heme Cpd II, and a water molecule. Subsequently, the addition of HS(•) to Cpd II, followed by three proton transfer reactions, results in the formation of a three-membered ring ferric sulfheme that avoids migration of the radical to the protein matrix, in contrast to that in other peroxidative reactions. The transformation of this three-membered episulfide ring structure to the five-membered thiochlorin ring structure occurs through a significant potential energy barrier, although both structures are nearly isoenergetic. Both three- and five-membered ring structures reveal longer NB-Fe(III) bonds compared with other pyrrole nitrogen-Fe(III) bonds, which would lead to decreased oxygen binding. Overall, these results are in agreement with a wide range of experimental data and provide fertile ground for further investigations of sulfheme formation in other heme proteins and additional effects of H2S on cell signaling and reactivity. PMID:27357070

  12. Integration of European Bond Markets

    DEFF Research Database (Denmark)

    Christiansen, Charlotte

    2014-01-01

    I investigate the time variation in the integration of EU government bond markets. The integration is measured by the explanatory power of European factor portfolios for the individual bond markets for each year. The integration of the government bond markets is stronger for EMU than non-EMU memb......I investigate the time variation in the integration of EU government bond markets. The integration is measured by the explanatory power of European factor portfolios for the individual bond markets for each year. The integration of the government bond markets is stronger for EMU than non......-EMU members and stronger for old than new EU members. For EMU countries, the integration is weaker the lower the credit rating is. During the recent crisis periods, the integration is weaker, particularly for EMU countries....

  13. Additional disulfide bonds in insulin

    DEFF Research Database (Denmark)

    Vinther, Tine N; Pettersson, Ingrid; Huus, Kasper;

    2015-01-01

    -chain is flexible and can adapt multiple conformations. We examined how well disulfide bond predictions algorithms could identify disulfide bonds in this region of insulin. In order to identify stable insulin analogues with additional disulfide bonds, which could be expressed, the Cβ cut-off distance had...... higher yields in comparison to analogues with additional disulfide bonds that were more difficult to predict. In contrast, addition of the fourth disulfide bond rendered all analogues resistant to fibrillation under stress conditions and all stable analogues bound to the insulin receptor with picomolar...... predicts four additional four disulfide insulin analogues which could be expressed. Although the location of the additional disulfide bonds is only slightly shifted, this shift impacts both stability and activity of the resulting insulin analogues....

  14. Combining a PagP fusion protein system with nickel ion-catalyzed cleavage to produce intrinsically disordered proteins in E. coli.

    Science.gov (United States)

    Zahran, Somaya; Pan, Jonathan S; Liu, Philip B; Hwang, Peter M

    2015-12-01

    Many proteins contain intrinsically disordered regions that are highly solvent-exposed and susceptible to post-translational modifications. Studying these protein segments is critical to understanding their physiologic regulation, but proteolytic degradation can make them difficult to express and purify. We have designed a new protein expression vector that fuses the target protein to the N-terminus of the integral membrane protein, PagP. The two proteins are connected by a short linker containing the sequence SRHW, previously shown to be optimal for nickel ion-catalyzed cleavage. The methodology is demonstrated for an intrinsically disordered segment of cardiac troponin I. cTnI[135-209]-SRHW-PagP-His6 fusion protein was overexpressed in Escherichia coli, accumulating in insoluble inclusion bodies. The protein was solubilized, purified using nickel affinity chromatography, and then cleaved with 0.5mM NiSO4 at pH 9.0 and 45 °C, all in 6M guanidine-HCl. Nickel ion-catalyzed peptide bond hydrolysis is an effective chemical cleavage technique under denaturing conditions that preclude the use of proteases. Moreover, nickel-catalyzed cleavage is more specific than the most commonly used agent, cyanogen bromide, which cleaves C-terminal to methionine residues. We were able to produce 15 mg of purified cTnI[135-209] from 1L of M9 minimal media using this protocol. The methodology is more generally applicable to the production of intrinsically disordered protein segments. PMID:26297994

  15. Role of trypsin-like cleavage at arginine 192 in the enzymatic and cytotonic activities of Escherichia coli heat-labile enterotoxin.

    Science.gov (United States)

    Grant, C C; Messer, R J; Cieplak, W

    1994-01-01

    Previous studies of cholera toxin and Escherichia coli heat-labile enterotoxin have suggested that proteolytic cleavage plays an important role in the expression of ADP-ribosyltransferase activity and toxicity. Specifically, several studies have implicated a trypsin-like cleavage at arginine 192, which lies within an exposed region subtended by a disulfide bond in the intact A subunit, in toxicity. To investigate the role of this modification in the enzymatic and cytotonic properties of heat-labile enterotoxin, the response of purified, recombinant A subunit to tryptic activation and the effect of substituting arginine 192 with glycine on the activities of the holotoxin were examined. The recombinant A subunit of heat-labile enterotoxin exhibited significant levels of ADP-ribosyltransferase activity that were only nominally increased (approximately twofold) by prior limited trypsinolysis. The enzymatic activity also did not appear to be affected by auto-ADP-ribosylation that occurs during the high-level synthesis of the recombinant A subunit in E. coli. A mutant form of the holotoxin containing the arginine 192-to-glycine substitution exhibited levels of cytotonic activity for CHO cells that were similar to that of the untreated, wild-type holotoxin but exhibited a marked delay in the ability to increase intracellular levels of cyclic AMP in Caco-2 cells. The results indicate that trypsin-like cleavage of the A subunit of E. coli heat-labile enterotoxin at arginine 192 is not requisite to the expression of enzymatic activity by the A subunit and further reveal that this modification, although it enhances the biological and enzymatic activities of the toxin, is not absolutely required for the enterotoxin to elicit cytotonic effects. Images PMID:7927684

  16. Social economy partnerships and the public/private cleavages

    Directory of Open Access Journals (Sweden)

    Joxerramon Bengoetxea

    2012-06-01

    Full Text Available Public/Private Partnerships can be seen as one particular topos where the divide between the public domain, all levels of the Public Administration and the private initiative and private property is turned into a joint venture rather than a confrontation or a cleavage. Some of the possible combinations of public and private and where public/private partnerships might fit are displayed analytically. The importance of political theory or ideology in conceiving the relationships between ‘public’ and ‘private’, and the conceptions of a market economy as opposed to a social market economy cannot be exaggerated enough, but equally important are the legal or regulatory framework and the underlying dominant legal culture and legal principles, and of course the economic and financial situation. Public/private partnerships thrive in some conditions, but seem to wane in others, and the current predicament is not favourable, taking into account that only the regulatory framework is supportive of these ventures. Los partenariados público-privados se pueden entender como un espacio particular, en el que el sector público, todos los niveles de la administración pública, y la iniciativa privada y la propiedad privada, abordan una empresa conjunta, en lugar mantener posturas contrapuestas. Se muestran algunas de las posibles combinaciones del sector público y privado, en las que tendrían cabida los partenariados público/privados. Es patente la importancia de la teoría o la ideología política para entender las relaciones entre lo público y lo privado, y las concepciones de una economía de mercado frente a una economía social, pero tampoco se puede negar la importancia del marco legal o reglamentario y la cultura jurídica dominante subyacente, y los principios jurídicos, sin olvidar la situación económica y financiera. Los partenariados público-privados prosperan en algunas condiciones, pero no lo hacen siempre, y la situación econ

  17. Supersymmetric Valence Bond Solid States

    OpenAIRE

    Arovas, Daniel P.; Hasebe, Kazuki; Qi, Xiao-Liang; Zhang, Shou-Cheng

    2009-01-01

    In this work we investigate the supersymmetric version of the valence bond solid (SVBS) state. In one dimension, the SVBS states continuously interpolate between the valence bond states for integer and half-integer spin chains, and they generally describe superconducting valence bond liquid states. Spin and superconducting correlation functions can be computed exactly for these states, and their correlation lengths are equal at the supersymmetric point. In higher dimensions, the wave function...

  18. Mezzanine finance and corporate bonds

    OpenAIRE

    Libena TETREVOVA

    2009-01-01

    The article deals with the problems of mezzanine finance in relation to corporate bonds. Firstly, attention is paid to definition of mezzanine finance. The term mezzanine finance is used as a term for hybrid forms of financing that combine elements of debt and equity financing. Mezzanine finance represents an alternative form of financing corporate activities. Secondly, possible forms of mezzanine finance are characterized. We can say that special types of corporate bonds (convertible bonds a...

  19. Hydrogen Bonds Involving Metal Centers

    OpenAIRE

    Pavlović, G.; N. Raos

    2006-01-01

    Hydrogen bonds involving metal center as a hydrogen donor or hydrogen acceptor are only a specific type of metal-hydrogen interactions; it is therefore not easy to differentiate hydrogen bond from other metal-hydrogen interactions, especially agostic ones. The first part of the review is therefore devoted to the results of structural chemistry and molecular spectroscopy (NMR, IR), as a tool for differentiating hydrogen bondings from other hydrogen interactions. The classical examples of Pt···...

  20. Si-H bond activation on Cu: Reaction of silane on Cu(111)

    Energy Technology Data Exchange (ETDEWEB)

    Wiegand, B.C.; Lohokare, S.P.; Nuzzo, R.G. (Univ. of Illinois, Urbana, IL (United States))

    1993-11-04

    The activation and decomposition of silane on Cu(111) have been studied using Fourier transform infrared (FTIR), Auger electron (AES), and temperature-programmed reaction (TPRS) spectroscopies, as well as low-energy electron diffraction (LEED). Silane dissociatively chemisorbs on Cu(111) at 90 K. Cleavage of the Si-H bond yields two structurally distinct adsorbed silyl fragments. Infrared spectroscopy identifies the predominant intermediates formed under these conditions as being adsorbed SiH[sub 2] and SiH species. The relative and absolute concentrations of these intermediates depend sensitively on the surface coverage of both Si and H, which themselves depend upon the silane exposure. SiH[sub 2] is stable over a wide range of coverage up to 180 K, where it then undergoes Si-H bond cleavage to form surface bound SiH. At higher temperatures, bond scission in the Si-H moiety results in the formation of adsorbed silicon atoms and the desorption of dihydrogen in a peak centered at [approximately]330 K. Auger electron spectra show that the amount of silicon deposited on the Cu(111) surface in this way is approximately one-third of the amount deposited on a stable Cu[sub 3]Si surface. This latter surface is readily formed by carrying out the silane exposure at temperatures above 300 K. 39 refs., 15 figs., 1 tab.

  1. Global geochemical cycles of carbon, sulfur and oxygen

    Science.gov (United States)

    Walker, J. C.

    1986-01-01

    Time resolved data on the carbon isotopic composition of carbonate minerals and the sulfur isotopic composition or sulfate minerals show a strong negative correlation during the Cretaceous. Carbonate minerals are isotopically heavy during this period while sulfate minerals are isotopically light. The implication is that carbon is being transferred from the oxidized, carbonate reservoir to the reservoir of isotopically light reduced organic carbon in sedimentary rocks while sulfur is being transferred from the reservoir of isotopically light sedimentary sulfide to the oxidized, sulfate reservoir. These apparently oppositely directed changes in the oxidation state of average sedimentary carbon and sulfur are surprising because of a well-established and easy to understand correlation between the concentrations of reduced organic carbon and sulfide minerals in sedimentary rocks. Rocks rich in reduced carbon are also rich in reduced sulfur. The isotopic and concentration data can be reconciled by a model which invokes a significant flux of hydrothermal sulfide to the deep sea, at least during the Cretaceous.

  2. Photoinduced hydrogen-bonding dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

    Hydrogen bonding dynamics has received extensive research attention in recent years due to the significant advances in femtolaser spectroscopy experiments and quantum chemistry calculations. Usually, photoexcitation would cause changes in the hydrogen bonding formed through the interaction between hydrogen donor and acceptor molecules on their ground electronic states, and such transient strengthening or weakening of hydrogen bonding could be crucial for the photophysical transformations and the subsequent photochemical reactions that occurred on a time scale from tens of femtosecond to a few nanoseconds. In this article, we review the combined experimental and theoretical studies focusing on the ultrafast electronic and vibrational hydrogen bonding dynamics. Through these studies, new mechanisms and proposals and common rules have been put forward to advance our understanding of the hydrogen bondings dynamics in a variety of important photoinduced phenomena like photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer processes, chemosensor fluorescence sensing, rearrangements of the hydrogen-bond network including forming and breaking hydrogen bond in water. Graphical Abstract We review the recent advances on exploring the photoinduced hydrogen bonding dynamics in solutions through a joint approach of laser spectroscopy and theoretical calculation. The reviewed studies have put forward a new mechanism, new proposal, and new rule for a variety of photoinduced phenomena such as photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer, chemosensor fluorescence sensing, and rearrangements of the hydrogen-bond network in water. PMID:27491849

  3. Wafer bonding applications and technology

    CERN Document Server

    Gösele, Ulrich

    2004-01-01

    During the past decade direct wafer bonding has developed into a mature materials integration technology. This book presents state-of-the-art reviews of the most important applications of wafer bonding written by experts from industry and academia. The topics include bonding-based fabrication methods of silicon-on-insulator, photonic crystals, VCSELs, SiGe-based FETs, MEMS together with hybrid integration and laser lift-off. The non-specialist will learn about the basics of wafer bonding and its various application areas, while the researcher in the field will find up-to-date information about this fast-moving area, including relevant patent information.

  4. A simplified indirect bonding technique

    Directory of Open Access Journals (Sweden)

    Radha Katiyar

    2014-01-01

    Full Text Available With the advent of lingual orthodontics, indirect bonding technique has become an integral part of practice. It involves placement of brackets initially on the models and then their transfer to teeth with the help of transfer trays. Problems encountered with current indirect bonding techniques used are (1 the possibility of adhesive flash remaining around the base of the brackets which requires removal (2 longer time required for the adhesive to gain enough bond strength for secure tray removal. The new simplified indirect bonding technique presented here overcomes both these problems.

  5. Identification of BACE1 cleavage sites in human voltage-gated sodium channel beta 2 subunit

    Directory of Open Access Journals (Sweden)

    Kovacs Dora M

    2010-12-01

    Full Text Available Abstract Background The voltage-gated sodium channel β2 subunit (Navβ2 is a physiological substrate of BACE1 (β-site APP cleaving enzyme and γ-secretase, two proteolytic enzymes central to Alzheimer's disease pathogenesis. Previously, we have found that the processing of Navβ2 by BACE1 and γ-secretase regulates sodium channel metabolism in neuronal cells. In the current study we identified the BACE1 cleavage sites in human Navβ2. Results We found a major (147-148 L↓M, where ↓ indicates the cleavage site and a minor (144145 L↓Q BACE1 cleavage site in the extracellular domain of human Navβ2 using a cell-free BACE1 cleavage assay followed by mass spectrometry. Next, we introduced two different double mutations into the identified major BACE1 cleavage site in human Navβ2: 147LM/VI and 147LM/AA. Both mutations dramatically decreased the cleavage of human Navβ2 by endogenous BACE1 in cell-free BACE1 cleavage assays. Neither of the two mutations affected subcellular localization of Navβ2 as confirmed by confocal fluorescence microscopy and subcellular fractionation of cholesterol-rich domains. Finally, wildtype and mutated Navβ2 were expressed along BACE1 in B104 rat neuroblastoma cells. In spite of α-secretase still actively cleaving the mutant proteins, Navβ2 cleavage products decreased by ~50% in cells expressing Navβ2 (147LM/VI and ~75% in cells expressing Navβ2 (147LM/AA as compared to cells expressing wildtype Navβ2. Conclusion We identified a major (147-148 L↓M and a minor (144-145 L↓Q BACE1 cleavage site in human Navβ2. Our in vitro and cell-based results clearly show that the 147-148 L↓M is the major BACE1 cleavage site in human Navβ2. These findings expand our understanding of the role of BACE1 in voltage-gated sodium channel metabolism.

  6. Thermodynamic model of hydrogen-induced silicon surface layer cleavage

    International Nuclear Information System (INIS)

    A thermodynamic model of hydrogen-induced silicon surface layer splitting with the help of a bonded silicon wafer is proposed in this article. Wafer splitting is the result of lateral growth of hydrogen blisters in the entire hydrogen-implanted region during annealing. The blister growth rate depends on the effective activation energies of both hydrogen complex dissociation and hydrogen diffusion. The hydrogen blister radius was studied as a function of annealing time, annealing temperature, and implantation dose. The critical radius was obtained according to the Griffith energy condition. The time required for wafer splitting at the cut temperature was calculated in accordance with the growth of hydrogen blisters. [copyright] 2001 American Institute of Physics

  7. Photosensitized cleavage of dynein heavy chains. Cleavage at the V1 site by irradiation at 365 nm in the presence of ATP and vanadate

    Energy Technology Data Exchange (ETDEWEB)

    Gibbons, I.R.; Lee-Eiford, A.; Mocz, G.; Phillipson, C.A.; Tang, W.J.; Gibbons, B.H.

    1987-02-25

    Irradiation of soluble dynein 1 from sea urchin sperm flagella at 365 nm in the presence of MgATP and 0.05-50 microM vanadate (Vi) cleaves the alpha and beta heavy chains (Mr 428,000) at their V1 sites to give peptides of Mr 228,000 and 200,000, without the nonspecific side effects produced by irradiation at 254 nm as described earlier. The decrease in intact heavy chain material is biphasic; in 10 microM Vi, approximately 80% occurs with a half-time of 7 min and the remainder with a half-time of about 90 min, and the yield of cleavage peptides is better than 90%. Loss of dynein ATPase activity appears to be a direct result of the cleavage process and is not significantly affected by the presence of up to 0.1 M cysteamine (CA, 60-23-1) or 2-aminoethyl carbamimidothioic acid dihydrobromide (CA, 56-10-0) as free radical trapping agents. The concentration of Vi required for 50% maximal initial cleavage rate is 4.5 microM, while that for 50% ATPase inhibition is 0.8 microM, both in a 0.6 M NaCl medium. In the presence of 20 microM Vi, CTP and UTP support cleavage at about half the rate of ATP, whereas GTP and ITP support cleavage only if the Vi concentration is raised to about 200 microM. Substitution of any of the transition metal cations Cr2+, Mn2+, Fe2+, or Co2+ for the usual Mg2+ suppresses the photocleavage, presumably by quenching the excited chromophore prior to scission of the heavy chain. The photocleaved dynein 1 binds to dynein-depleted flagella similarly to intact dynein 1, but upon reactivation of the flagella with 1 mM ATP their motility is partially inhibited, rather than being augmented as with intact dynein.

  8. Reactive Bonding Film for Bonding Carbon Foam Through Metal Extrusion

    CERN Document Server

    Chertok, Maxwell; Irving, Michael; Neher, Christian; Tripathi, Mani; Wang, Ruby; Zheng, Gayle

    2016-01-01

    Future tracking detectors, such as those under development for the High Luminosity LHC, will require mechanical structures employing novel materials to reduce mass while providing excellent strength, thermal conductivity, and radiation tolerance. Adhesion methods for such materials are under study at present. This paper demonstrates the use of reactive bonding film as an adhesion method for bonding carbon foam.

  9. Digital Control of Bonding Force for Gold Wire Bonding Machine

    Directory of Open Access Journals (Sweden)

    Xiaochu Wang

    2013-01-01

    Full Text Available In order to digitally control the bonding force of a wire bonder precisely, this paper uses a DC solenoid as a force source, and by controlling the solenoid’s current, which causes the electromagnetic force, we can control the bonding force that capillary applies. The bonding force control system in this paper is composed of PC (Personal Computer and hypogyny MCU (Micro Controller Unit, which communicate using a RS485 interface. The digital value of a given bonding force is given by the PC to the MCU. By comparing the sampling current of the solenoid, and through PID regulation, D/A converter of the digital potentiometer and the solenoid driver circuit, the half-closed loop control system of bonding force is accomplished. Tuning of the PID parameters is accomplished with fuzzy adaptive control theory and simulated by Matlab simulink. The control system is tested by comparing the desired bonding force and the force actually applied and examming the relationship between bonding quality and bonding force.

  10. Amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by streptococcal IgA1 proteases

    DEFF Research Database (Denmark)

    Batten, MR; Senior, BW; Kilian, Mogens;

    2003-01-01

    effect upon sensitivity to cleavage with some streptococcal IgA1 proteases, with, in some cases, a single point mutation rendering the antibody resistant to a particular IgA1 protease. This effect was least marked with the IgA1 protease from Streptococcus pneumoniae, which showed no absolute requirement......The amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by IgA1 proteases of different species of Streptococcus were investigated. Recombinant IgA1 antibodies were generated with point mutations at proline 227 and threonine 228, the residues lying on either...... side of the peptide bond at which all streptococcal IgA1 proteases cleave wild-type human IgA1. The amino acid substitutions produced no major effect upon the structure of the mutant IgA1 antibodies or their functional ability to bind to Fcalpha receptors. However, the substitutions had a substantial...

  11. Synthesis, DNA-binding, cytotoxicity, photo cleavage, antimicrobial and docking studies of Ru(II) polypyridyl complexes.

    Science.gov (United States)

    Srishailam, A; Kumar, Yata Praveen; Gabra, Nazar M D; Reddy, P Venkat; Deepika, N; Veerababu, Nageti; Satyanarayana, S

    2013-09-01

    Three Ruthenium(II) polypyridine complexes, [Ru(phen)2(mipc)](2+)(1), [Ru(bpy)2(mipc)](2+) (2) and [Ru(dmb)2(mipc)](2+)(3) [mipc = 2-(6-methyl-3-(1H-imidazo[4, 5-f][1,10]-phenanthroline-2-yl)-4H-chromene-4-one, phen = 1,10-phenanthroline,bpy = 2, 2'bipyridine,dmb = 4, 4'-dimethyl-2, 2'-bipyridine] have been synthesized and characterized by elemental analysis, IR, UV-Vis, (1)H& (13)C NMR and mass spectra. The DNA-binding properties of the Ruthenium(II) complexes were investigated by spectrophotometric methods, viscosity measurements and light switch studies. These three complexes have been focused on photo activated cleavage studies with pBR-322 and antimicrobial studies. Experimental results indicate that the three complexes intercalate into DNA base pairs and follows the order of 1 > 2 > 3 respectively. Molecular docking studies also support the DNA interactions with complexes through hydrogen bonding and vander Waal's interactions. Cytotoxicity studies with Hela cell lines has been revealing about anti tumor activity of these complexes. PMID:23553642

  12. Heterolytic Cleavage of H2 by Bifunctional Manganese(I) Complexes: Impact of Ligand Dynamics, Electrophilicity, and Base Positioning

    Energy Technology Data Exchange (ETDEWEB)

    Hulley, Elliott B.; Helm, Monte L.; Bullock, R. Morris

    2014-12-01

    We report the synthesis, characterization, and reactivity with H2 of a series of MnI complexes of the type [(P-P)Mn(L2)CO]+ (L2 = dppm, bppm, or (CO)2; P-P = PPhNMePPh or PPh2 NBn2 ) that bear pendant amine ligands designed to function as proton relays. The pendant amine was found to function as a hemilabile ligand; its binding strength is strongly affected by the ancillary ligand environment around Mn. Tuning the electrophilicity of the Mn center leads to systems capable of reversible heterolytic cleavage of the H-H bond. The strength of pendant amine binding can be balanced to protect the Mn center while still leading to facile reactivity with H2. Neutral amine-bearing MnIH species were found to react with one-electron oxidants and, after proton and electron transfer reactions, regenerate MnI cationic species. The reactivity presented herein indicate that the Mn complexes we have developed are a promising platform for Mn-based H2 oxidation electrocatalyst development. The research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for DOE.

  13. Desulfurization and structural transformation of thiophene on the Pt(111) surface

    International Nuclear Information System (INIS)

    The temperature dependence of near-edge x-ray absorption fine-structure spectra above the C K edge and S L/sub 2,3/ edge for thiophene (C4H4S) on Pt(111) reveals changes in the chemisorption geometry and the cleavage of the carbon-sulfur bond. Our results suggest the formation of a metallocycle intermediate after desulfurization with the S atom replaced by a Pt surface atom. The near-edge x-ray absorption fine-structure results are corroborated by thermal desorption, x-ray photoemission, and electron-energy-loss data

  14. Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology

    Directory of Open Access Journals (Sweden)

    Blom Nikolaj

    2004-06-01

    Full Text Available Abstract Background Despite the passing of more than a year since the first outbreak of Severe Acute Respiratory Syndrome (SARS, efficient counter-measures are still few and many believe that reappearance of SARS, or a similar disease caused by a coronavirus, is not unlikely. For other virus families like the picornaviruses it is known that pathology is related to proteolytic cleavage of host proteins by viral proteinases. Furthermore, several studies indicate that virus proliferation can be arrested using specific proteinase inhibitors supporting the belief that proteinases are indeed important during infection. Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods. Results We retrieved sequence data on seven fully sequenced coronaviruses and identified the main 3CL proteinase cleavage sites in polyproteins using alignments. A neural network was trained to recognise the cleavage sites in the genomes obtaining a sensitivity of 87.0% and a specificity of 99.0%. Several proteins known to be cleaved by other viruses were submitted to prediction as well as proteins suspected relevant in coronavirus pathology. Cleavage sites were predicted in proteins such as the cystic fibrosis transmembrane conductance regulator (CFTR, transcription factors CREB-RP and OCT-1, and components of the ubiquitin pathway. Conclusions Our prediction method NetCorona predicts coronavirus cleavage sites with high specificity and several potential cleavage candidates were identified which might be important to elucidate coronavirus pathology. Furthermore, the method might assist in design of proteinase inhibitors for treatment of SARS and possible future diseases caused by coronaviruses. It is made available for public use at our website: http://www.cbs.dtu.dk/services/NetCorona/.

  15. A Data Mining Approach for the Prediction of Hepatitis C Virus protease Cleavage Sites

    Directory of Open Access Journals (Sweden)

    Ahmed mohamed samir ali gamal eldin

    2011-12-01

    Full Text Available Summary: Several papers have been published about the prediction of hepatitis C virus (HCV polyprotein cleavage sites, using symbolic and non-symbolic machine learning techniques. The published papers achieved different Levels of prediction accuracy. the achieved results depends on the used technique and the availability of adequate and accurate HCV polyprotein sequences with known cleavage sites. We tried here to achieve more accurate prediction results, and more Informative knowledge about the HCV protein cleavage sites using Decision tree algorithm. There are several factors that can affect the overall prediction accuracy. One of the most important factors is the availably of acceptable and accurate HCV polyproteins sequences with known cleavage sites. We collected latest accurate data sets to build the prediction model. Also we collected another dataset for the model testing. Motivation: Hepatitis C virus is a global health problem affecting a significant portion of the world’s population. The World Health Organization estimated that in1999; 170 million hepatitis C virus (HCV carriers were present worldwide, with 3 to 4 million new cases per year. Several approaches have been performed to analyze HCV life cycle to find out the important factors of the viral replication process. HCV polyprotein processing by the viral protease has a vital role in the virus replication. The prediction of HCV protease cleavage sites can help the biologists in the design of suitable viral inhibitors. Results: The ease to use and to understand of the decision tree enabled us to create simple prediction model. We used here the latest accurate viral datasets. Decision tree achieved here acceptable prediction accuracy results. Also it generated informative knowledge about the cleavage process itself. These results can help the researchers in the development of effective viral inhibitors. Using decision tree to predict HCV protein cleavage sites achieved high

  16. A new strategy for the on-column exopeptidase cleavage of poly-histidine tagged proteins.

    Science.gov (United States)

    Kuo, Wen-Hui K; Chase, Howard A

    2011-10-15

    This paper describes a new strategy, which aims to make on-column poly-histidine tag removal more useful in the production of recombinant proteins by improving the yield and efficiency of on-column exopeptidase cleavage. This involves improvement of the on-column cleavage condition by using imidazole concentrations in the range of 100-500 mM in the cleavage buffer. At 300 mM imidazole, maximum on-column cleavage yield (in excess of 99%) was achieved in 3h of incubation. However, as a result of the increased imidazole concentration, this new strategy of on-column cleavage results in some residual uncleaved poly-histidine tagged proteins (~0.1%) and the production of cleaved dipeptides, both of which need to be further removed in a subsequent step. A method involving the recirculation of recovered proteins and peptides through the immobilized metal affinity chromatography (IMAC) column (same-column recirculation) was found to be superior to subtractive IMAC for the purpose of contaminant clearance. Recovery of the detagged target proteins was achieved using 10 column volumes of recovery buffer, which had the effect of diluting the imidazole concentration to a suitably low level for contaminant removal by same-column recirculation. This strategy was also applicable at a higher adsorbent loading of 10 mg protein/mL adsorbent with an optimal ratio of 200 mU of DAPase per mg of adsorbed tagged maltose binding protein (MBP), giving a cleavage yield of 99.1% in 3 h. Finally, on-column cleavage conditions including the effect of protease concentration and incubation time on the new strategy have been investigated and comparisons are made for different tag removal strategies. PMID:21925974

  17. TD-DFT Insight into Photodissociation of Co-C Bond in Coenzyme B12

    OpenAIRE

    PawelMichalKozlowski; PiotrLodowski

    2014-01-01

    Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic featu...

  18. Multiple Bonds Between Metal Atoms

    CERN Document Server

    Cotton, F Albert; Walton, Richard A

    2006-01-01

    Provides a discussion of preparations, reactions, bonding, and physical properties for two of the d-block transition metals in groups 5-10. This title includes catalytic and chemotherapeutic applications, and discusses metal-metal bonds of orders 0.5 to 4 discussed in than 4000 compounds, with citations to approximately 2500 references.

  19. Bondings for tubular solar collectors

    International Nuclear Information System (INIS)

    We studied the following four models of constructing solar collectors: tubes bonded above the absorber plate, tubes bonded under the absorber plate tubes in-line with the absorber plate and bondless tubes in-line with the absorber plate. 2 refs, 6 figs

  20. Computational Chemistry of Adhesive Bonds

    Science.gov (United States)

    Phillips, Donald H.

    1999-01-01

    This investigation is intended to determine the electrical mechanical, and chemical properties of adhesive bonds at the molecular level. The initial determinations will be followed by investigations of the effects of environmental effects on the chemistry and properties of the bond layer.

  1. Quantum Confinement in Hydrogen Bond

    CERN Document Server

    Santos, Carlos da Silva dos; Ricotta, Regina Maria

    2015-01-01

    In this work, the quantum confinement effect is proposed as the cause of the displacement of the vibrational spectrum of molecular groups that involve hydrogen bonds. In this approach the hydrogen bond imposes a space barrier to hydrogen and constrains its oscillatory motion. We studied the vibrational transitions through the Morse potential, for the NH and OH molecular groups inside macromolecules in situation of confinement (when hydrogen bonding is formed) and non-confinement (when there is no hydrogen bonding). The energies were obtained through the variational method with the trial wave functions obtained from Supersymmetric Quantum Mechanics (SQM) formalism. The results indicate that it is possible to distinguish the emission peaks related to the existence of the hydrogen bonds. These analytical results were satisfactorily compared with experimental results obtained from infrared spectroscopy.

  2. Roll bonding of strained aluminium

    DEFF Research Database (Denmark)

    Staun, Jakob M.

    2003-01-01

    This report investigates roll bonding of pre-strained (å ~ 4) aluminium sheets to produce high strain material from high purity aluminium (99.996%) and commercial pure aluminium (99.6%). The degree of bonding is investigated by optical microscopy and ultrasonic scanning. Under the right...... circumstances both materials show good bonding, but the high purity material is excluded because of recrystallisation and the resulting loss of mechanical properties. The effect of cross stacking and roll bonding pre-strained sheets of the commercial purity material is investigated and some dependence of the...... cross rolled volume fraction is found. To further asses this effect, and the anisotropy, it is necessary to acquire knowledge about both texture and microstructure, e.g. by TEM. Roll bonding of pre-strained aluminium is found to be a possible alternative to ARB in the quest for ultra-fine grained...

  3. Dentin-bonding agents

    Directory of Open Access Journals (Sweden)

    João Carlos Gomes

    2008-01-01

    Full Text Available New dental restorative materials have been developed to meet not only the functional demands, but esthetics as well, and in the last few years an enormous range of new materials has appeared for use in dentistry. Among them, several adhesive systems, and different operative techniques for each group materials. Therefore, is indispensable for the professional to know about the properties, characteristics, and association of these materials with the dental structures, in order to select and use them correctly. Should conventional self-etching adhesive systems be used? This question encouraged this literature review to be conducted, with the aim of comparing the conventional adhesive systems with the self-etching systems and to look for scientific data that would help professionals to choose which adhesive system to use. When compared to conventional systems, it was noted that the self-etching systems show less sensitivity to technique, especially as regards errors the operator could commit. The self-etching systems, particularly the 2-step type, have shown equivalent values of bond strength, marginal microleakage and performance, therefore, will be an option for direct composite resin restorations in posterior teeth.

  4. Characteristics of the fast electron emission produced during the cleavage of crystals

    Indian Academy of Sciences (India)

    B P Chandra; N L Patel; S S Rahangdale; R P Patel; V K Patle

    2003-01-01

    The present paper reports the fast electron emission produced during the cleavage of alkali halide crystals and models the dynamics of the process. The mechano-emission arises as a result of the ionization of surface traps at the expense of the energy which is released in the annihilation of the defects which are formed during cleavage. The slow electrons which appear upon the ionization of surface traps are subsequently accelerated in the field of negatively charged segment of the freshly cleaved surface. Considering the basic mechanism of fast electron emission, expressions are derived which are able to explain satisfactorily the temporal, thermal, charge, surface, coloration, water adsorption and other characteristics of the fast electron emission produced during the cleavage of crystals. The decay time of the charges on the newly created surfaces, and the velocity of cracks can be determined from the measurements of fast electron emission produced during the cleavage of crystals. It is shown that two types of diffusing centres are responsible for the charge relaxation and thereby for the emission of fast electrons produced during the cleavage of alkali halide crystals.

  5. Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates.

    Directory of Open Access Journals (Sweden)

    Sonu Kumar

    Full Text Available Caspases are enzymes belonging to a conserved family of cysteine-dependent aspartic-specific proteases that are involved in vital cellular processes and play a prominent role in apoptosis and inflammation. Determining all relevant protein substrates of caspases remains a challenging task. Over 1500 caspase substrates have been discovered in the human proteome according to published data and new substrates are discovered on a daily basis. To aid the discovery process we developed a caspase cleavage prediction method using the recently published curated MerCASBA database of experimentally determined caspase substrates and a Random Forest classification method. On both internal and external test sets, the ranking of predicted cleavage positions is superior to all previously developed prediction methods. The in silico predicted caspase cleavage positions in human proteins are available from a relational database: CaspDB. Our database provides information about potential cleavage sites in a verified set of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation. It also provides information about the positions of disease-annotated single nucleotide polymorphisms, and posttranslational modifications that may modulate the caspase cleaving efficiency.

  6. Focal adhesions control cleavage furrow shape and spindle tilt during mitosis

    Science.gov (United States)

    Taneja, Nilay; Fenix, Aidan M.; Rathbun, Lindsay; Millis, Bryan A.; Tyska, Matthew J.; Hehnly, Heidi; Burnette, Dylan T.

    2016-01-01

    The geometry of the cleavage furrow during mitosis is often asymmetric in vivo and plays a critical role in stem cell differentiation and the relative positioning of daughter cells during development. Early observations of adhesive cell lines revealed asymmetry in the shape of the cleavage furrow, where the bottom (i.e., substrate attached side) of the cleavage furrow ingressed less than the top (i.e., unattached side). This data suggested substrate attachment could be regulating furrow ingression. Here we report a population of mitotic focal adhesions (FAs) controls the symmetry of the cleavage furrow. In single HeLa cells, stronger adhesion to the substrate directed less ingression from the bottom of the cell through a pathway including paxillin, focal adhesion kinase (FAK) and vinculin. Cell-cell contacts also direct ingression of the cleavage furrow in coordination with FAs in epithelial cells—MDCK—within monolayers and polarized cysts. In addition, mitotic FAs established 3D orientation of the mitotic spindle and the relative positioning of mother and daughter centrosomes. Therefore, our data reveals mitotic FAs as a key link between mitotic cell shape and spindle orientation, and may have important implications in our understanding stem cell homeostasis and tumorigenesis. PMID:27432211

  7. Protein cleavage strategies for an improved analysis of the membrane proteome

    Directory of Open Access Journals (Sweden)

    Poetsch Ansgar

    2006-03-01

    Full Text Available Abstract Background Membrane proteins still remain elusive in proteomic studies. This is in part due to the distribution of the amino acids lysine and arginine, which are less frequent in integral membrane proteins and almost absent in transmembrane helices. As these amino acids are cleavage targets for the commonly used protease trypsin, alternative cleavage conditions, which should improve membrane protein analysis, were tested by in silico digestion for the three organisms Saccharomyces cerevisiae, Halobacterium sp. NRC-1, and Corynebacterium glutamicum as hallmarks for eukaryotes, archea and eubacteria. Results For the membrane proteomes from all three analyzed organisms, we identified cleavage conditions that achieve better sequence and proteome coverage than trypsin. Greater improvement was obtained for bacteria than for yeast, which was attributed to differences in protein size and GRAVY. It was demonstrated for bacteriorhodopsin that the in silico predictions agree well with the experimental observations. Conclusion For all three examined organisms, it was found that a combination of chymotrypsin and staphylococcal peptidase I gave significantly better results than trypsin. As some of the improved cleavage conditions are not more elaborate than trypsin digestion and have been proven useful in practice, we suppose that the cleavage at both hydrophilic and hydrophobic amino acids should facilitate in general the analysis of membrane proteins for all organisms.

  8. Two-step cleavage of hairpin RNA with 5' overhangs by human DICER

    Directory of Open Access Journals (Sweden)

    Suzuki Harukazu

    2011-02-01

    Full Text Available Abstract Background DICER is an RNase III family endoribonuclease that processes precursor microRNAs (pre-miRNAs and long double-stranded RNAs, generating microRNA (miRNA duplexes and short interfering RNA duplexes with 20~23 nucleotides (nts in length. The typical form of pre-miRNA processed by the Drosha protein is a hairpin RNA with 2-nt 3' overhangs. On the other hand, production of mature miRNA from an endogenous hairpin RNA with 5' overhangs has also been reported, although the mechanism for this process is unknown. Results In this study, we show that human recombinant DICER protein (rDICER processes a hairpin RNA with 5' overhangs in vitro and generates an intermediate duplex with a 29 nt-5' strand and a 23 nt-3' strand, which was eventually cleaved into a canonical miRNA duplex via a two-step cleavage. The previously identified endogenous pre-miRNA with 5' overhangs, pre-mmu-mir-1982 RNA, is also determined to be a substrate of rDICER through the same two-step cleavage. Conclusions The two-step cleavage of a hairpin RNA with 5' overhangs shows that DICER releases double-stranded RNAs after the first cleavage and binds them again in the inverse direction for a second cleavage. These findings have implications for how DICER may be able to interact with or process differing precursor structures.

  9. Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates.

    Science.gov (United States)

    Kumar, Sonu; van Raam, Bram J; Salvesen, Guy S; Cieplak, Piotr

    2014-01-01

    Caspases are enzymes belonging to a conserved family of cysteine-dependent aspartic-specific proteases that are involved in vital cellular processes and play a prominent role in apoptosis and inflammation. Determining all relevant protein substrates of caspases remains a challenging task. Over 1500 caspase substrates have been discovered in the human proteome according to published data and new substrates are discovered on a daily basis. To aid the discovery process we developed a caspase cleavage prediction method using the recently published curated MerCASBA database of experimentally determined caspase substrates and a Random Forest classification method. On both internal and external test sets, the ranking of predicted cleavage positions is superior to all previously developed prediction methods. The in silico predicted caspase cleavage positions in human proteins are available from a relational database: CaspDB. Our database provides information about potential cleavage sites in a verified set of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation. It also provides information about the positions of disease-annotated single nucleotide polymorphisms, and posttranslational modifications that may modulate the caspase cleaving efficiency. PMID:25330111

  10. The role of spaced cleavage on the porosity and permeability within a reservoir unit

    Energy Technology Data Exchange (ETDEWEB)

    Thorn, P.A.; Lageson, D.R. [Montana State Univ., Bozeman, MT (United States)

    1996-06-01

    Tectonic deformation plays a significant role in both the enhancement and degradation of the porosity and permeability within a reservoir unit. Enhancing mechanisms generally include fracturing and brecciation, whereas reducing mechanisms include cataclasis and pressure solution. Spaced cleavage is common within argillaceous limestone in foreland fold and thrust belts, including the Sawtooth Range, Montana. The presence of spaced cleavage will have a significant impact on both the permeability and porosity within a reservoir. Spaced cleavage is formed by pressure solution, where calcite is dissolved as a tectonic stress is applied. As the calcite is being removed, relatively insoluble minerals, predominately clay and quartz, are concentrated along the dissolution sites and form thin domains. The minerals within these domains are compacted and aligned perpendicular to the direction of maximum stress. Due to the nature of the aligned minerals, fluid flow will be restricted across these domains, creating severe reservoir anisotropy within the unit. Once the calcite has been dissolved, it must re-precipitate out. This will generally occur in the pores and open fractures present in the cleaved unit, significantly reducing the porosity present in the reservoir rock. However, if the cleavage has been folded during a later deformational event, these domains, which represent weaknesses in the rock, could open up around the crests of folds and provide a pathway for increased fluid migration parallel to the cleavage trend.

  11. Non-Enzymatic DNA Cleavage Reaction Induced by 5-Ethynyluracil in Methylamine Aqueous Solution and Application to DNA Concatenation

    OpenAIRE

    Ikeda, Shuji; Tainaka, Kazuki; Matsumoto, Katsuhiko; Shinohara, Yuta; Koji L Ode; Susaki, Etsuo A; Ueda, Hiroki R

    2014-01-01

    DNA can be concatenated by hybridization of DNA fragments with protruding single-stranded termini. DNA cleavage occurring at a nucleotide containing a DNA base analogue is a useful method to obtain DNA with designed protruding termini. Here, we report a novel non-enzymatic DNA cleavage reaction for DNA concatenation. We found that DNA is cleaved at a nucleotide containing 5-ethynyluracil in a methylamine aqueous solution to generate 5′-phosphorylated DNA fragment as a cleavage product. We dem...

  12. Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly.

    OpenAIRE

    Ryner, L C; Takagaki, Y; Manley, J L

    1989-01-01

    To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upst...

  13. The Role of the Methyltransferase Domain of Bifunctional Restriction Enzyme RM.BpuSI in Cleavage Activity

    OpenAIRE

    Arthur Sarrade-Loucheur; Shuang-yong Xu; Siu-Hong Chan

    2013-01-01

    Restriction enzyme (REase) RM.BpuSI can be described as a Type IIS/C/G REase for its cleavage site outside of the recognition sequence (Type IIS), bifunctional polypeptide possessing both methyltransferase (MTase) and endonuclease activities (Type IIC) and endonuclease activity stimulated by S-adenosyl-L-methionine (SAM) (Type IIG). The stimulatory effect of SAM on cleavage activity presents a major paradox: a co-factor of the MTase activity that renders the substrate unsusceptible to cleavag...

  14. In vitro cleavage of the simian virus 40 early polyadenylation site adjacent to a required downstream TG sequence.

    OpenAIRE

    Sperry, A O; Berget, S M

    1986-01-01

    Exogenous RNA containing the simian virus 40 early polyadenylation site was efficiently and accurately polyadenylated in in vitro nuclear extracts. Correct cleavage required ATP. In the absence of ATP, nonpoly(A)+ products accumulated which were 18 to 20 nucleotides longer than the RNA generated by correct cleavage; the longer RNA terminated adjacent to the downstream TG element required for polyadenylation. In the presence of ATP analogs, alternate cleavage was not observed; instead, correct...

  15. In Situ Raman Monitoring of Silver(I)-Aided Laser-Driven Cleavage Reaction of Cyclobutane.

    Science.gov (United States)

    Chen, Dengtai; Han, Xijiang; Du, Yunchen; Wang, Hsing-Lin; Xu, Ping

    2016-01-01

    The cyclobutane cleavage reaction is an important process and has received continuous interest. Herein, we demonstrate the visible laser-driven cleavage reaction of cyclobutane in crystal form by using in situ Raman spectroscopy. Silver(I) coordination-induced strain and thermal effects from the laser irradiation are the two main driving forces for the cleavage of cyclobutane crystals. This work may open up a new avenue for studying cyclobutane cleavage reactions, as compared to the conventional routes using ex situ techniques. PMID:26510491

  16. Identification of RNA sequences and structures involved in site-specific cleavage of IGF-II mRNAs.

    OpenAIRE

    van Dijk, E L; Sussenbach, J S; Holthuizen, P E

    1998-01-01

    Insulin-like growth factor-II (IGF-II) mRNAs are subject to site-specific endonucleolytic cleavage in the 3' untranslated region (UTR), rendering an unstable 5' cleavage product containing the coding region and a very stable 3' cleavage product of 1.8 kb consisting of the 3'-UTR sequence and the poly(A) tail. Previously, it was established that two widely separated elements in the 3'-UTR (elements I and II), that can form a duplex structure, are necessary and sufficient for cleavage. To furth...

  17. Physical Nature of Hydrogen Bond

    CERN Document Server

    Zhyganiuk, I V

    2015-01-01

    The physical nature and the correct definition of hydrogen bond (H-bond) are considered.\\,\\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.\\,\\,The conventional model of H-bonds as sharply directed and saturated bridges between water molecules is incompatible with the behavior of the specific volume, evaporation heat, and self-diffusion and kinematic shear viscosity coefficients of water. On the other hand, it is shown that the variation of the dipole moment of a water molecule and the frequency shift of valence vibrations of a hydroxyl group can be totally explained in the framework of the electrostatic model of H-bond.\\,\\,At the same time, the temperature dependences of the heat capacity of water in the liquid and vapor states clearly testify to the existence of weak H-bonds.\\,\\,The analysis of a water dimer shows that the contribution of weak H-bonds to its ground state energy is approximately 4--5 times lower in comparison with the energy of electr...

  18. Bonding and decomposition of thiophene, sulfhydryl, thiomethoxy and phenyl thiolate on Mo surfaces

    Science.gov (United States)

    Rodriguez, JoséA.

    1992-11-01

    The bonding of thiophene (C 4H 4S), sulfhydryl (HS), thiomethoxy (CH 3S) and phenyl thiolate (C 6H 5S) to molybdenum surfaces has been examined employing MO-SCF calculations (INDO/1) and metal clusters of limited size (Mo n, n=13-19 atoms). The calculations indicate that the preferred binding sites for the RS species on Mo(100) are the four-fold hollows. The bonding mechanism of thiophene involves a large charge transfer from the S-lone pairs of the molecule (6a 1 and 2b 1 orbitals) into the surface, and electron transfer from the substrate into the C-S antibonding 3b 1 orbital of the adsorbate. Adsorption of thiophene on a hollow site leads to a large weakening in the strength of the C-S and C-H bonds, producing a precursor for the dissociation of the molecule. HS, CH 3S and C 6H 5S behave as electron acceptors when bonded to Mo. For these species, the chemisorption bond is dominated by the interaction between the LUMO of the adsorbate and the Mo(4d,5s) bands. The results of a thermochemical analysis indicate that reactions which involve the cleavage of H-S and C-S bonds of alkanethiols on Mo (RSH g → S a + RH g) are very exothermic (- ΔH = 40-50 kcal/mol). The thermodynamics suggests that C-S bond breaking should be the most difficult step in the desulfurization process. The hydrogenolysis of the C-S bond (RS a + H a → S a + RH g) is ˜ 12 kcal/mol more exothermic for CH 3S than for C 6H 5S.

  19. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes

    Energy Technology Data Exchange (ETDEWEB)

    Lyamichev, V.; Mast, A.L.; Hall, J.G. [Third Wave Technologies, Madison, WI (United States)] [and others

    1999-03-01

    Flap endonucleases (FENs) isolated from archaea are shown to recognize and cleave a structure formed when two overlapping oligonucleotides hybridize to a target DNA strand. The downstream oligonucleotide probe is cleaved, and the precise site of cleavage is dependent on the amount of overlap with the upstream oligonucleotide. The authors have demonstrated that use of thermostable archaeal FENs allows the reaction to be performed at temperatures that promote probe turnover without the need for temperature cycling. The resulting amplification of the cleavage signal enables the detection of specific DNA targets at sub-attomole levels within complex mixtures. Moreover, the authors provide evidence that this cleavage is sufficiently specific to enable discrimination of single-base differences and can differentiate homozygotes from heterozygotes in single-copy genes in genomic DNA.

  20. Cleavage-induced termination in U2 snRNA gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Nabavi, Sadeq [Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (Canada); Nazar, Ross N., E-mail: rnnazar@uoguelph.ca [Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (Canada)

    2010-03-12

    The maturation of many small nuclear RNAs is dependent on RNase III-like endonuclease mediated cleavage, which generates a loading site for the exosome complex that trims the precursor at its 3' end. Using a temperature sensitive Pac1 nuclease, here we show that the endonuclease cleavage is equally important in terminating the transcription of the U2 snRNA in Schizosaccharomyces pombe. Using a temperature sensitive Dhp1p 5' {yields} 3' exonuclease, we demonstrate that it also is an essential component of the termination pathway. Taken together the results support a 'reversed torpedoes' model for the termination and maturation of the U2 snRNA; the Pac1 endonuclease cleavage provides entry sites for the 3' and 5' exonuclease activities, leading to RNA maturation in one direction and transcript termination in the other.

  1. TMPRSS2 Independency for Haemagglutinin Cleavage In Vivo Differentiates Influenza B Virus from Influenza A Virus

    Science.gov (United States)

    Sakai, Kouji; Ami, Yasushi; Nakajima, Noriko; Nakajima, Katsuhiro; Kitazawa, Minori; Anraku, Masaki; Takayama, Ikuyo; Sangsriratanakul, Natthanan; Komura, Miyuki; Sato, Yuko; Asanuma, Hideki; Takashita, Emi; Komase, Katsuhiro; Takehara, Kazuaki; Tashiro, Masato; Hasegawa, Hideki; Odagiri, Takato; Takeda, Makoto

    2016-01-01

    Influenza A and B viruses show clear differences in their host specificity and pandemic potential. Recent studies have revealed that the host protease TMPRSS2 plays an essential role for proteolytic activation of H1, H3, and H7 subtype strains of influenza A virus (IAV) in vivo. IAV possessing a monobasic cleavage site in the haemagglutinin (HA) protein replicates poorly in TMPRSS2 knockout mice owing to insufficient HA cleavage. In the present study, human isolates of influenza B virus (IBV) strains and a mouse-adapted IBV strain were analysed. The data showed that IBV successfully underwent HA cleavage in TMPRSS2 knockout mice, and that the mouse-adapted strain was fully pathogenic to these mice. The present data demonstrate a clear difference between IAV and IBV in their molecular mechanisms for spreading in vivo. PMID:27389476

  2. Metabolic cleavage of cell-penetrating peptides in contact with epithelial models

    DEFF Research Database (Denmark)

    Tréhin, Rachel; Nielsen, Hanne Mørck; Jahnke, Heinz-Georg;

    2004-01-01

    We assessed the metabolic degradation kinetics and cleavage patterns of some selected CPP (cell-penetrating peptides) after incubation with confluent epithelial models. Synthesis of N-terminal CF [5(6)-carboxyfluorescein]-labelled CPP, namely hCT (human calcitonin)-derived sequences, Tat(47-57) and...... penetratin(43-58), was through Fmoc (fluoren-9-ylmethoxycarbonyl) chemistry. Metabolic degradation kinetics of the tested CPP in contact with three cell-cultured epithelial models, MDCK (Madin-Darby canine kidney), Calu-3 and TR146, was evaluated by reversed-phase HPLC. Identification of the resulting...... models and the CPP. The Calu-3 model exhibited the highest proteolytic activity. The patterns of metabolic cleavage of hCT(9-32) were similar in all three models. Initial cleavage of this peptide occurred at the N-terminal domain, possibly by endopeptidase activity yielding both the N- and the C...

  3. Prenatal organophosphates exposure alternates the cleavage plane orientation of apical neural progenitor in developing neocortex.

    Directory of Open Access Journals (Sweden)

    Xiao-Ping Chen

    Full Text Available Prenatal organophosphate exposure elicits long-term brain cytoarchitecture and cognitive function impairments, but the mechanism underlying the onset and development of neural progenitors remain largely unclear. Using precise positioned brain slices, we observed an alternated cleavage plane bias that emerged in the mitotic neural progenitors of embryonal neocortex with diazinion (DZN and chlorpyrifos (CPF pretreatment. In comparison with the control, DZN and CPF treatment induced decrease of vertical orientation, increase of oblique orientation, and increase of horizontal orientation. That is, the cleavage plane orientation bias had been rotated from vertical to horizontal after DZN and CPF treatment. Meanwhile, general morphology and mitotic index of the progenitors were unchanged. Acephate (ACP, another common organophosphate, had no significant effects on the cleavage plane orientation, cell morphology and mitotic index. These results represent direct evidence for the toxicity mechanism in onset multiplication of neural progenitors.

  4. Cleavage-induced termination in U2 snRNA gene expression

    International Nuclear Information System (INIS)

    The maturation of many small nuclear RNAs is dependent on RNase III-like endonuclease mediated cleavage, which generates a loading site for the exosome complex that trims the precursor at its 3' end. Using a temperature sensitive Pac1 nuclease, here we show that the endonuclease cleavage is equally important in terminating the transcription of the U2 snRNA in Schizosaccharomyces pombe. Using a temperature sensitive Dhp1p 5' → 3' exonuclease, we demonstrate that it also is an essential component of the termination pathway. Taken together the results support a 'reversed torpedoes' model for the termination and maturation of the U2 snRNA; the Pac1 endonuclease cleavage provides entry sites for the 3' and 5' exonuclease activities, leading to RNA maturation in one direction and transcript termination in the other.

  5. Cleavage of fibrinogen by proteinases elicits allergic responses through Toll-like receptor 4.

    Science.gov (United States)

    Millien, Valentine Ongeri; Lu, Wen; Shaw, Joanne; Yuan, Xiaoyi; Mak, Garbo; Roberts, Luz; Song, Li-Zhen; Knight, J Morgan; Creighton, Chad J; Luong, Amber; Kheradmand, Farrah; Corry, David B

    2013-08-16

    Proteinases and the innate immune receptor Toll-like receptor 4 (TLR4) are essential for expression of allergic inflammation and diseases such as asthma. A mechanism that links these inflammatory mediators is essential for explaining the fundamental basis of allergic disease but has been elusive. Here, we demonstrate that TLR4 is activated by airway proteinase activity to initiate both allergic airway disease and antifungal immunity. These outcomes were induced by proteinase cleavage of the clotting protein fibrinogen, yielding fibrinogen cleavage products that acted as TLR4 ligands on airway epithelial cells and macrophages. Thus, allergic airway inflammation represents an antifungal defensive strategy that is driven by fibrinogen cleavage and TLR4 activation. These findings clarify the molecular basis of allergic disease and suggest new therapeutic strategies. PMID:23950537

  6. TMPRSS2 Independency for Haemagglutinin Cleavage In Vivo Differentiates Influenza B Virus from Influenza A Virus.

    Science.gov (United States)

    Sakai, Kouji; Ami, Yasushi; Nakajima, Noriko; Nakajima, Katsuhiro; Kitazawa, Minori; Anraku, Masaki; Takayama, Ikuyo; Sangsriratanakul, Natthanan; Komura, Miyuki; Sato, Yuko; Asanuma, Hideki; Takashita, Emi; Komase, Katsuhiro; Takehara, Kazuaki; Tashiro, Masato; Hasegawa, Hideki; Odagiri, Takato; Takeda, Makoto

    2016-01-01

    Influenza A and B viruses show clear differences in their host specificity and pandemic potential. Recent studies have revealed that the host protease TMPRSS2 plays an essential role for proteolytic activation of H1, H3, and H7 subtype strains of influenza A virus (IAV) in vivo. IAV possessing a monobasic cleavage site in the haemagglutinin (HA) protein replicates poorly in TMPRSS2 knockout mice owing to insufficient HA cleavage. In the present study, human isolates of influenza B virus (IBV) strains and a mouse-adapted IBV strain were analysed. The data showed that IBV successfully underwent HA cleavage in TMPRSS2 knockout mice, and that the mouse-adapted strain was fully pathogenic to these mice. The present data demonstrate a clear difference between IAV and IBV in their molecular mechanisms for spreading in vivo. PMID:27389476

  7. Alkene Cleavage Catalysed by Heme and Nonheme Enzymes: Reaction Mechanisms and Biocatalytic Applications

    Directory of Open Access Journals (Sweden)

    Francesco G. Mutti

    2012-01-01

    Full Text Available The oxidative cleavage of alkenes is classically performed by chemical methods, although they display several drawbacks. Ozonolysis requires harsh conditions (−78°C, for a safe process and reducing reagents in a molar amount, whereas the use of poisonous heavy metals such as Cr, Os, or Ru as catalysts is additionally plagued by low yield and selectivity. Conversely, heme and nonheme enzymes can catalyse the oxidative alkene cleavage at ambient temperature and atmospheric pressure in an aqueous buffer, showing excellent chemo- and regioselectivities in certain cases. This paper focuses on the alkene cleavage catalysed by iron cofactor-dependent enzymes encompassing the reaction mechanisms (in case where it is known and the application of these enzymes in biocatalysis.

  8. Tensile Bond Strength of Latex-Modified Bonded Concrete Overlays

    Science.gov (United States)

    Dubois, Cameron; Ramseyer, Chris

    2010-10-01

    The tensile bond strength of bonded concrete overlays was tested using the in-situ pull-off method described in ASTM C 1583 with the goal of determining whether adding latex to the mix design increases bond strength. One slab of ductile concrete (f'c > 12,000 psi) was cast with one half tined, i.e. roughened, and one half steel-troweled, i.e. smooth. The slab surface was sectioned off and overlay mixtures containing different latex contents cast in each section. Partial cores were drilled perpendicular to the surface through the overlay into the substrate. A tensile loading device applied a direct tensile load to each specimen and the load was increased until failure occurred. The tensile bond strength was then calculated for comparison between the specimens.

  9. Initiation of cleavage in a low alloy steel: effect of a ductile damage localized around inclusions

    International Nuclear Information System (INIS)

    The fracture mechanism in a low alloy steel, used in the pressurised water reactor vessel, has been studied in the ductile to brittle transition temperature range. We used the local approach of fracture in conjunction with both fractographic observations and numerical simulations. Previous studies suggested the onset of cleavage to be favoured by the presence of nearby manganese sulphide (MnS) clusters: the ductile damaged zone localised inside a cluster increases the stress around it, and so contribute to the triggering of cleavage due to nearby classical sites, like carbides. The experimental study of size dependence and anisotropy on the global fracture behaviour, together with fractographic observations, give here the proof of the influence of MnS clusters on the onset of cleavage in this steel. Fracture behaviour of pre-cracked specimens tested in the transition regime has then been simulated, by three dimensional finite element method computations. Ductile tearing process preceding the cleavage onset at those temperatures regime was well reproduced by the Rousselier's model. Failure probabilities, related to given stress states, has been given by post-processor calculations, using a probabilistic model based on the specific cleavage fracture process. Fracture toughness scatter of the steel, tested in the transition regime, is then well reproduced by those calculations. However, the critical cleavage stress of an elementary volume, that scales for the fracture process, is still assumed to be temperature dependant. Numerical simulations of the local fracture process suggest that this temperature effect can partly be explained by the temperature dependant decrease of the stress amplification due to the MnS clusters. (author)

  10. An investigation of crack-tip stress field criteria of predicting cleavage-crack initiation

    International Nuclear Information System (INIS)

    Cleavage-crack initiation in large-scale wide-plate (WP) specimens could not be accurately predicted from small, compact (CT) specimens by using a linear-elastic fracture-mechanics, KIc, methodology. In the wide-plate tests conducted by the Heavy-Section Steel Technology Program at Oak Ridge National Laboratory, crack initiation has consistently occurred at stress-intensity (KI) values ranging from two to four times those predicted by the CT specimens. Studies were initiated to develop crack-tip stress field criteria incorporating effects of geometry, size, and constraint that will lead to improved predictions of cleavage initiation in WP specimens from CT specimens. The work centers around nonlinear two-and three-dimensional finite-element analyses of the crack-tip stress fields in these geometries. Analyses were conducted on CT and WP specimens for which cleavage initiation fracture had been measured in laboratory tests. The local crack-tip field generated for these specimens were then used in the evaluation of fracture correlation parameters to augment the KI parameter for predicting cleavage initiation. Parameters of hydrostatic constraint and of maximum principal stress, measured volumetrically, are included in these evaluations. The results suggest that the cleavage initiation process can be correlated with the local crack-tip fields via a maximum principal stress criterion based on achieving a critical area within a critical stress contour. This criterion has been successfully applied to correlate cleavage initiation in 2T-CT and WP specimen geometries. 23 refs., 16 figs., 5 tabs

  11. ADAM17-mediated CD44 cleavage promotes orasphere formation or stemness and tumorigenesis in HNSCC

    International Nuclear Information System (INIS)

    CD44, an extracellular matrix (ECM) receptor, has been described as a cancer stem cell marker in multiple cancers, including head and neck squamous cell carcinoma (HNSCC). HNSCC orasphere formation or stemness was characterized by cleavage of CD44, and thus we hypothesized that this proteolytic processing may be critical to stemness and tumorigenesis. We tested this hypothesis by examining the mechanisms that regulate this process in vitro and in vivo, and by exploring its clinical relevance in human specimens. Sphere assays have been used to evaluate stemness in vitro. Spheres comprised of HNSCC cells or oraspheres and an oral cancer mouse model were used to examine the significance of CD44 cleavage using stable suppression and inhibition approaches. These mechanisms were also examined in HNSCC specimens. Oraspheres exhibited increased levels of CD44 cleavage compared to their adherent counterparts. Given that disintegrin and metalloproteinase domain-containing protein 17 (ADAM17) is a major matrix metalloproteinase known to cleave CD44, we chemically inhibited and stably suppressed ADAM17 expression in HNSCC cells and found that these treatments blocked CD44 cleavage and abrogated orasphere formation. Furthermore, stable suppression of ADAM17 in HNSCC cells also diminished tumorigenesis in an oral cancer mouse model. Consistently, stable suppression of CD44 in HNSCC cells abrogated orasphere formation and inhibited tumorigenesis in vivo. The clinical relevance of these findings was confirmed in matched primary and metastatic human HNSCC specimens, which exhibited increased levels of ADAM17 expression and concomitant CD44 cleavage compared to controls. CD44 cleavage by ADAM17 is critical to orasphere formation or stemness and HNSCC tumorigenesis

  12. Initial activation of EpCAM cleavage via cell-to-cell contact

    International Nuclear Information System (INIS)

    Epithelial cell adhesion molecule EpCAM is a transmembrane glycoprotein, which is frequently over-expressed in simple epithelia, progenitors, embryonic and tissue stem cells, carcinoma and cancer-initiating cells. Besides functioning as a homophilic adhesion protein, EpCAM is an oncogenic receptor that requires regulated intramembrane proteolysis for activation of its signal transduction capacity. Upon cleavage, the extracellular domain EpEX is released as a soluble ligand while the intracellular domain EpICD translocates into the cytoplasm and eventually into the nucleus in combination with four-and-a-half LIM domains protein 2 (FHL2) and β-catenin, and drives cell proliferation. EpCAM cleavage, induction of the target genes, and transmission of proliferation signals were investigated under varying density conditions using confocal laser scanning microscopy, immunoblotting, cell counting, and conditional cell systems. EpCAM cleavage, induction of the target genes, and transmission of proliferation signals were dependent on adequate cell-to-cell contact. If cell-to-cell contact was prohibited EpCAM did not provide growth advantages. If cells were allowed to undergo contact to each other, EpCAM transmitted proliferation signals based on signal transduction-related cleavage processes. Accordingly, the pre-cleaved version EpICD was not dependent on cell-to-cell contact in order to induce c-myc and cell proliferation, but necessitated nuclear translocation. For the case of contact-inhibited cells, although cleavage of EpCAM occurred, nuclear translocation of EpICD was reduced, as were EpCAM effects. Activation of EpCAM's cleavage and oncogenic capacity is dependent on cellular interaction (juxtacrine) to provide for initial signals of regulated intramembrane proteolysis, which then support signalling via soluble EpEX (paracrine)

  13. Cleavage strain in the Variscan fold belt, County Cork, Ireland, estimated from stretched arsenopyrite rosettes

    Science.gov (United States)

    Ford, M.; Ferguson, C.C.

    1985-01-01

    In south-west Ireland, hydrothermally formed arsenopyrite crystals in a Devonian mudstone have responded to Variscan deformation by brittle extension fracture and fragment separation. The interfragment gaps and terminal extension zones of each crystal are infilled with fibrous quartz. Stretches within the cleavage plane have been calculated by the various methods available, most of which can be modified to incorporate terminal extension zones. The Strain Reversal Method is the most accurate currently available but still gives a minimum estimate of the overall strain. The more direct Hossain method, which gives only slightly lower estimates with this data, is more practical for field use. A strain ellipse can be estimated from each crystal rosette composed of three laths (assuming the original interlimb angles were all 60??) and, because actual rather than relative stretches are estimated, this provides a lower bound to the area increase in the plane of cleavage. Based on the average of our calculated strain ellipses this area increase is at least 114% and implies an average shortening across the cleavage of at least 53%. However, several lines of evidence suggest that the cleavage deformation was more intense and more oblate than that calculated, and we argue that a 300% area increase in the cleavage plane and 75% shortening across the cleavage are more realistic estimates of the true strain. Furthermore, the along-strike elongation indicated is at least 80%, which may be regionally significant. Estimates of orogenic contraction derived from balanced section construction should therefore take into account the possibility of a substantial strike elongation, and tectonic models that can accommodate such elongations need to be developed. ?? 1985.

  14. Cleavage efficient 2A peptides for high level monoclonal antibody expression in CHO cells.

    Science.gov (United States)

    Chng, Jake; Wang, Tianhua; Nian, Rui; Lau, Ally; Hoi, Kong Meng; Ho, Steven C L; Gagnon, Peter; Bi, Xuezhi; Yang, Yuansheng

    2015-01-01

    Linking the heavy chain (HC) and light chain (LC) genes required for monoclonal antibodies (mAb) production on a single cassette using 2A peptides allows control of LC and HC ratio and reduces non-expressing cells. Four 2A peptides derived from the foot-and-mouth disease virus (F2A), equine rhinitis A virus (E2A), porcine teschovirus-1 (P2A) and Thosea asigna virus (T2A), respectively, were compared for expression of 3 biosimilar IgG1 mAbs in Chinese hamster ovary (CHO) cell lines. HC and LC were linked by different 2A peptides both in the absence and presence of GSG linkers. Insertion of a furin recognition site upstream of 2A allowed removal of 2A residues that would otherwise be attached to the HC. Different 2A peptides exhibited different cleavage efficiencies that correlated to the mAb expression level. The relative cleavage efficiency of each 2A peptide remains similar for expression of different IgG1 mAbs in different CHO cells. While complete cleavage was not observed for any of the 2A peptides, GSG linkers did enhance the cleavage efficiency and thus the mAb expression level. T2A with the GSG linker (GT2A) exhibited the highest cleavage efficiency and mAb expression level. Stably amplified CHO DG44 pools generated using GT2A had titers 357, 416 and 600 mg/L for the 3 mAbs in shake flask batch cultures. Incomplete cleavage likely resulted in incorrectly processed mAb species and aggregates, which were removed with a chromatin-directed clarification method and protein A purification. The vector and methods presented provide an easy process beneficial for both mAb development and manufacturing. PMID:25621616

  15. The chemisorptive bond basic concepts

    CERN Document Server

    Clark, Alfred

    1974-01-01

    The Chemisorptive Bond: Basic Concepts describes the basic concepts of the chemisorptive bond on solid surfaces from the simple analogies with ordinary chemical bonds to the quantum-mechanical approaches.This book is composed of 10 chapters and begins with discussions of simple formulas for correlating measurable quantities in chemisorptions and catalysis. The succeeding chapters deal with theories based on quantum-mechanical principles that describe the mutual interactions of atoms of the solid and foreign atoms on the surface. The remaining chapters consider the possible arrangements

  16. Direct Bonded Pontic (Laporan Kasus

    Directory of Open Access Journals (Sweden)

    Suhandi Sidjaja

    2015-10-01

    Full Text Available Advanced science and technology in dentistry enable dental practitioners to modified she bonding techniques in tooth replacement. A pontic made of composite resin bonded to etched enamel of the adjacent teeth can be used in the replacement of one missing anterior tooth with a virgin or sowed adpicent tooth. The advantages of this technique include a one visit treatment, cow cost, good esthetics, less side effects and easy repair or rebounding. Clinical evaluation showed a high success rate therefore with a proper diagnosis and a perfect skill of the direct bonded technique this treatment can be used as an alternative restoration.

  17. Low-temperature side-chain cleavage and decarboxylation of polythiophene esters by acid catalysis

    DEFF Research Database (Denmark)

    Søndergaard, Roar; Norrman, Kion; Krebs, Frederik C

    2012-01-01

    substituents have been examined by TGA‐MS using different sulphonic acids. A substantial lowering of the cleavage temperature is observed, and the ester cleavage can even be performed in situ on roll‐to‐roll‐coated films on polyethylene terephthalate (PET). © 2011 Wiley Periodicals, Inc. J Polym Sci Part A......Solubility switching of polymers is very useful in thin layer processing of conjugated polymers, as it allows for multilayer processing and increases the stability of the polymer. Acid catalyzed thermocleavage of ester groups from thiophene polymers carrying primary, secondary, and tertiary......: Polym Chem, 2012...

  18. Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome

    Directory of Open Access Journals (Sweden)

    Lafuente Esther M

    2010-09-01

    Full Text Available Abstract Background Proteasomes play a central role in the major histocompatibility class I (MHCI antigen processing pathway. They conduct the proteolytic degradation of proteins in the cytosol, generating the C-terminus of CD8 T cell epitopes and MHCI-peptide ligands (P1 residue of cleavage site. There are two types of proteasomes, the constitutive form, expressed in most cell types, and the immunoproteasome, which is constitutively expressed in mature dendritic cells. Protective CD8 T cell epitopes are likely generated by the immunoproteasome and the constitutive proteasome, and here we have modeled and analyzed the cleavage by these two proteases. Results We have modeled the immunoproteasome and proteasome cleavage sites upon two non-overlapping sets of peptides consisting of 553 CD8 T cell epitopes, naturally processed and restricted by human MHCI molecules, and 382 peptides eluted from human MHCI molecules, respectively, using N-grams. Cleavage models were generated considering different epitope and MHCI-eluted fragment lengths and the same number of C-terminal flanking residues. Models were evaluated in 5-fold cross-validation. Judging by the Mathew's Correlation Coefficient (MCC, optimal cleavage models for the proteasome (MCC = 0.43 ± 0.07 and the immunoproteasome (MCC = 0.36 ± 0.06 were obtained from 12-residue peptide fragments. Using an independent dataset consisting of 137 HIV1-specific CD8 T cell epitopes, the immunoproteasome and proteasome cleavage models achieved MCC values of 0.30 and 0.18, respectively, comparatively better than those achieved by related methods. Using ROC analyses, we have also shown that, combined with MHCI-peptide binding predictions, cleavage predictions by the immunoproteasome and proteasome models significantly increase the discovery rate of CD8 T cell epitopes restricted by different MHCI molecules, including A*0201, A*0301, A*2402, B*0702, B*2705. Conclusions We have developed models that are specific

  19. Exon size affects competition between splicing and cleavage-polyadenylation in the immunoglobulin mu gene.

    OpenAIRE

    Peterson, M L; Bryman, M B; Peiter, M; Cowan, C

    1994-01-01

    The alternative RNA processing of microseconds and microns mRNAs from a single primary transcript depends on competition between a cleavage-polyadenylation reaction to produce microseconds mRNA and a splicing reaction to produce microns mRNA. The ratio of microseconds to microns mRNA is regulated during B-cell maturation; relatively more spliced microns mRNA is made in B cells than in plasma cells. The balance between the efficiencies of splicing and cleavage-polyadenylation is critical to th...

  20. Influence of the austenitizing temperature in the cleavage facet size of Niocor 2

    International Nuclear Information System (INIS)

    Convetional Charpy specimens of Niocor 2 steel cooled in air from various austenitizing temperatures were fractured at -1960 C so as to insure failure by cleavage. The cleavage facet size distribution was determined and then correlated with the grain size and other aspects of the microstructure. The results that the average facet size can be increased through a coarsening of the microstructure. For the case where the γ→α transformation products are predominantely acicular, the facet size is shown to depend on substructural aspects primarily the lath packet size. (Author)