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Sample records for active metal sites

  1. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  2. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

    PubMed Central

    Colombo, Matteo; Girard, Eric; Franzetti, Bruno

    2016-01-01

    TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn2+, hyperthermophilic TETs prefers Co2+. Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites. PMID:26853450

  3. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts.

    PubMed

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and (57)Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  4. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    NASA Astrophysics Data System (ADS)

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-10-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity.

  5. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  6. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  7. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  8. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

    PubMed

    Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

    2014-04-01

    The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins. PMID:24635441

  9. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  10. Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases.

    PubMed

    Koutsioulis, Dimitris; Lyskowski, Andrzej; Mäki, Seija; Guthrie, Ellen; Feller, Georges; Bouriotis, Vassilis; Heikinheimo, Pirkko

    2010-01-01

    Alkaline phosphatases (APs) are commercially applied enzymes that catalyze the hydrolysis of phosphate monoesters by a reaction involving three active site metal ions. We have previously identified H135 as the key residue for controlling activity of the psychrophilic TAB5 AP (TAP). In this article, we describe three X-ray crystallographic structures on TAP variants H135E and H135D in complex with a variety of metal ions. The structural analysis is supported by thermodynamic and kinetic data. The AP catalysis essentially requires octahedral coordination in the M3 site, but stability is adjusted with the conformational freedom of the metal ion. Comparison with the mesophilic Escherichia coli, AP shows differences in the charge transfer network in providing the chemically optimal metal combination for catalysis. Our results provide explanation why the TAB5 and E. coli APs respond in an opposite way to mutagenesis in their active sites. They provide a lesson on chemical fine tuning and the importance of the second coordination sphere in defining metal specificity in enzymes. Understanding the framework of AP catalysis is essential in the efforts to design even more powerful tools for modern biotechnology. PMID:19916164

  11. Formation of nanostructured Group IIA metal activated sensors: The transformation of Group IIA metal compound sites

    NASA Astrophysics Data System (ADS)

    Tune, Travis C.; Baker, Caitlin; Hardy, Neil; Lin, Arthur; Widing, Timothy J.; Gole, James L.

    2015-05-01

    Trends in the Group IIA metal oxides and hydroxides of magnesium, calcium, and barium are unique in the periodic table. In this study we find that they display novel trends as decorating nanostructures for extrinsic semiconductor interfaces. The Group IIA metal ions are strong Lewis acids. We form these M2+ ions in aqueous solution and bring these solutions in contact with a porous silicon interface to form interfaces for conductometric measurements. Observed responses are consistent with the formation of MgO whereas the heavier elements display behaviors which suggest the effect of their more basic nature. Mg(OH)2, when formed, represents a weak base whereas the heavier metal hydroxides of Ca, Sr, and Ba are strong bases. However, the hydroxides tend to give up hydrogen and act as Brönsted acids. For the latter elements, the reversible interaction response of nanostructures deposited to the porous silicon (PS) interface is modified, as the formation of more basic sites appears to compete with M2+ Lewis acidity and hydroxide Brönsted acidity. Mg2+ forms an interface whose response to the analytes NH3 and NO is consistent with MgO and well explained by the recently developing Inverse Hard/Soft Acid/Base model. The behavior of the Ca2+ and Ba2+ decorated interfaces as they interact with the hard base NH3 follows a reversal of the model, indicating a decrease in acidic character as the observed conductometric response suggests the interaction with hydroxyl groups. A change from oxide-like to hydroxide-like constituents is supported by XPS studies. The changes in conductometric response is easily monitored in contrast to changes associated with the Group IIA oxides and hydroxides observed in XPS, EDAX, IR, and NMR measurements.

  12. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ligands'' with localized surface orbitals perturbed only by these ligands''. These complexes'' are based on a twelve coordinate species with the ligands'' attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  13. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ``ligands`` with localized surface orbitals perturbed only by these ``ligands``. These ``complexes`` are based on a twelve coordinate species with the ``ligands`` attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  14. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites. PMID:26786892

  15. Similarities in the HIV-1 and ASV Integrease Active Site Upon Metal Binding

    SciTech Connect

    Lins, Roberto D.; Straatsma, TP; Briggs, J. M.

    2000-04-05

    The HIV-1 integrase, which is essential for viral replication, catalyzes the insertion of viral DNA into the host chromosome thereby recruiting host cell machinery into making viral proteins. It represents the third main HIV enzyme target for inhibitor design, the first two being the reverse transcriptase and the protease. We report here a fully hydrated 2 ns molecular dynamics simulation performed using parallel NWChem3.2.1 with the AMBER95 force field. The HIV-1 integrase catalytic domain previously determined by crystallography (1B9D) and modeling including two Mg2+ ions placed into the active site based on an alignment against an ASV integrase structure containing two divalent metals (1VSH), was used as the starting structure. The simulation reveals a high degree of flexibility in the region of residues 140-149 even in the presence of a second divalent metal ion and a dramatic conformational change of the side chain of E152 when the second metal ion is present. This study shows similarities in the behavior of the catalytic residues in the HIV-1 and ASV integrases upon metal binding. The present simulation also provides support to the hypothesis that the second metal ion is likely to be carried into the HIV-1 integrase active site by the substrate, a strand of DNA.

  16. The divalent metal ion in the active site of uteroferrin modulates substrate binding and catalysis

    PubMed Central

    Mitić, Nataša; Hadler, Kieran S.; Gahan, Lawrence R; Hengge, Alvan C.; Schenk, Gerhard

    2010-01-01

    The purple acid phosphatases (PAP) are binuclear metallohydrolases that catalyze the hydrolysis of a broad range of phosphomonoester substrates. The mode of substrate binding during catalysis and the identity of the nucleophile is subject to debate. Here, we used native Fe3+-Fe2+ pig PAP (uteroferrin; Uf) and its Fe3+-Mn2+ derivative to investigate the effect of metal ion substitution on the mechanism of catalysis. Replacement of the Fe2+ by Mn2+ lowers the reactivity of Uf. However, using stopped-flow measurements it could be shown that this replacement facilitates approximately a ten-fold faster reaction between both substrate and inorganic phosphate with the chromophoric Fe3+ site. These data also indicate that in both metal forms of Uf, phenyl phosphate hydrolysis occurs faster than formation of a μ-1,3 phosphate complex. The slower rate of interaction between substrate and the Fe3+ site relative to catalysis suggests that the substrate is hydrolyzed while coordinated only to the divalent metal ion. The likely nucleophile is a water molecule in the second coordination sphere, activated by a hydroxide terminally coordinated to Fe3+. The faster rates of interaction with the Fe3+ site in the Fe3+-Mn2+ derivative than the native Fe3+-Fe2+ form are likely mediated via a hydrogen bond network connecting the first and second coordination spheres, and illustrate how the selection of metal ions may be important in fine-tuning the function of this enzyme. PMID:20433174

  17. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  18. Characterizations of Metal Binding in the Active Sites of Acireductone Dioxygenase Isoforms from Klebsiella ATCC 8724

    SciTech Connect

    Chai,S.; Ju, T.; Dang, M.; Goldsmith, R.; Maroney, M.; Pochapsky, T.

    2008-01-01

    The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella ATCC 8724 present an unusual case in which two enzymes with different structures and distinct activities toward their common substrates (1, 2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene and dioxygen) are derived from the same polypeptide chain. Structural and functional differences between the two isozymes are determined by the type of M2+ metal ion bound in the active site. The Ni2+-bound NiARD catalyzes an off-pathway shunt from the methionine salvage pathway leading to the production of formate, methylthiopropionate, and carbon monoxide, while the Fe2+-bound FeARD' catalyzes the on-pathway formation of methionine precursor 2-keto-4-methylthiobutyrate and formate. Four potential protein-based metal ligands were identified by sequence homology and structural considerations. Based on the results of site-directed mutagenesis experiments, X-ray absorption spectroscopy (XAS), and isothermal calorimetry measurements, it is concluded that the same four residues, His96, His98, Glu102 and His140, provide the protein-based ligands for the metal in both the Ni- and Fe-containing forms of the enzyme, and subtle differences in the local backbone conformations trigger the observed structural and functional differences between the FeARD' and NiARD isozymes. Furthermore, both forms of the enzyme bind their respective metals with pseudo-octahedral geometry, and both may lose a histidine ligand upon binding of substrate under anaerobic conditions. However, mutations at two conserved nonligand acidic residues, Glu95 and Glu100, result in low metal contents for the mutant proteins as isolated, suggesting that some of the conserved charged residues may aid in transfer of metal from in vivo sources or prevent the loss of metal to stronger chelators. The Glu100 mutant reconstitutes readily but has low activity. Mutation of Asp101 results in an active enzyme that incorporates metal in vivo but

  19. Characterization of Metal Binding in the Active Sites of acireductone dioxygenase Isoforms from Klebsiella ATCC 8724

    SciTech Connect

    S Chai; T Ju; M Dang; R Goldsmith; M Maroney; T Pochapsky

    2011-12-31

    The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella ATCC 8724 present an unusual case in which two enzymes with different structures and distinct activities toward their common substrates (1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene and dioxygen) are derived from the same polypeptide chain. Structural and functional differences between the two isozymes are determined by the type of M{sup 2+} metal ion bound in the active site. The Ni{sup 2+}-bound NiARD catalyzes an off-pathway shunt from the methionine salvage pathway leading to the production of formate, methylthiopropionate, and carbon monoxide, while the Fe{sup 2+}-bound FeARD catalyzes the on-pathway formation of methionine precursor 2-keto-4-methylthiobutyrate and formate. Four potential protein-based metal ligands were identified by sequence homology and structural considerations. Based on the results of site-directed mutagenesis experiments, X-ray absorption spectroscopy (XAS), and isothermal calorimetry measurements, it is concluded that the same four residues, His96, His98, Glu102 and His140, provide the protein-based ligands for the metal in both the Ni- and Fe-containing forms of the enzyme, and subtle differences in the local backbone conformations trigger the observed structural and functional differences between the FeARD and NiARD isozymes. Furthermore, both forms of the enzyme bind their respective metals with pseudo-octahedral geometry, and both may lose a histidine ligand upon binding of substrate under anaerobic conditions. However, mutations at two conserved nonligand acidic residues, Glu95 and Glu100, result in low metal contents for the mutant proteins as isolated, suggesting that some of the conserved charged residues may aid in transfer of metal from in vivo sources or prevent the loss of metal to stronger chelators. The Glu100 mutant reconstitutes readily but has low activity. Mutation of Asp101 results in an active enzyme that incorporates

  20. Correlation of active site metal content in human diamine oxidase with trihydroxyphenylalanine quinone cofactor biogenesis .

    PubMed

    McGrath, Aaron P; Caradoc-Davies, Tom; Collyer, Charles A; Guss, J Mitchell

    2010-09-28

    Copper-containing amine oxidases (CAOs) require a protein-derived topaquinone cofactor (TPQ) for activity. TPQ biogenesis is a self-processing reaction requiring the presence of copper and molecular oxygen. Recombinant human diamine oxidase (hDAO) was heterologously expressed in Drosophila S2 cells, and analysis indicates that the purified hDAO contains substoichiometric amounts of copper and TPQ. The crystal structure of a complex of an inhibitor, aminoguanidine, and hDAO at 2.05 Å resolution shows that the aminoguanidine forms a covalent adduct with the TPQ and that the site is ∼75% occupied. Aminoguanidine is a potent inhibitor of hDAO with an IC(50) of 153 ± 9 nM. The structure indicates that the catalytic metal site, normally occupied by copper, is fully occupied. X-ray diffraction data recorded below the copper edge, between the copper and zinc edges, and above the zinc edge have been used to show that the metal site is occupied approximately 75% by copper and 25% by zinc and the formation of the TPQ cofactor is correlated with copper occupancy. PMID:20722416

  1. Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism

    PubMed Central

    Zhao, Haiyan; Lin, Zihan; Lynn, Anna Y.; Varnado, Brittany; Beutler, John A.; Murelli, Ryan P.; Le Grice, Stuart F. J.; Tang, Liang

    2015-01-01

    Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg2+ from Ca2+. Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution. PMID:26450964

  2. Oxygen reduction and evolution at single-metal active sites: Comparison between functionalized graphitic materials and protoporphyrins

    NASA Astrophysics Data System (ADS)

    Calle-Vallejo, F.; Martínez, J. I.; García-Lastra, J. M.; Abad, E.; Koper, M. T. M.

    2013-01-01

    A worldwide spread of clean technologies such as low-temperature fuel cells and electrolyzers depends strictly on their technical reliability and economic affordability. Currently, both conditions are hardly fulfilled mainly due to the same reason: the oxygen electrode, which has large overpotentials and is made of precious materials. A possible solution is the use of non-noble electrocatalysts with single-metal active sites. Here, on the basis of DFT calculations of adsorbed intermediates and a thermodynamic analysis, we compare the oxygen reduction (ORR) and evolution (OER) activities of functionalized graphitic materials and gas-phase porphyrins with late transition metals. We find that both kinds of materials follow approximately the same activity trends, and active sites with transition metals from groups 7 to 9 may be good ORR and OER electrocatalysts. However, spin analyses show more flexibility in the possible oxidation states of the metal atoms in solid electrocatalysts, while in porphyrins they must be + 2. These observations reveal that the catalytic activity of these materials is mainly due to nearest-neighbor interactions. Based on this, we propose that this class of electrocatalysts may be improved by careful selections of the support and the ligand properties close to the active sites and/or the ramifications near them, so that charge is transferred back and forth during adsorption and selective hydrogen bonds are formed.

  3. A porous metal-organic framework containing multiple active Cu(2+) sites for highly efficient cross dehydrogenative coupling reaction.

    PubMed

    Zhu, Shu-Lan; Ou, Sha; Zhao, Min; Shen, Hong; Wu, Chuan-De

    2015-02-01

    A novel 3D porous metal-organic framework was constructed from imidazole carboxylate linkers and copper(ii) nodes, which in situ generates multiple active Cu(II) sites in the nanosized channel walls for highly efficient cross dehydrogenative coupling reaction between 1,2,3,4-tetrahydroisoquinoline derivatives and nitroalkanes that are superior to the simple copper salts. PMID:25515613

  4. Two axles threaded using a single template site: active metal template macrobicyclic [3]rotaxanes.

    PubMed

    Goldup, Stephen M; Leigh, David A; McGonigal, Paul R; Ronaldson, Vicki E; Slawin, Alexandra M Z

    2010-01-13

    Template approaches to rotaxanes normally require at least n - 1 template sites to interlock n components. Here we describe the one-pot synthesis of [3]rotaxanes in which a single metal template site induces formation of axles through each cavity of a bicyclic macrocycle. Central to the approach is that a portion of the bicyclic molecule acts as a ligand for a transition metal ion that mediates covalent bond formation through one or other macrocyclic cavity, depending on the ligand's orientation, making a mechanical bond. The ligand can then rotate so that the transition metal can catalyze the formation of a second axle through the other macrocycle. Using this strategy with the Cu(I)-catalyzed azide-alkyne cycloaddition (the CuAAC reaction) generates a [3]rotaxane with two identical axles in up to 86% yield. [3]Rotaxanes with two different axles threaded through the macrobicyclic rings can also be created using a single template site, either by having copper(I) sequentially form both mechanical bonds (via the CuAAC reaction) using different sets of building blocks for each axle or by using two different reactions catalyzed by two different metal ions: a palladium(II)-mediated alkyne homocoupling to assemble the first thread through one cavity, followed by a copper(I)-mediated CuAAC reaction to form the second axle through the other ring. PMID:19968281

  5. Stable isolated metal atoms as active sites for photocatalytic hydrogen evolution.

    PubMed

    Xing, Jun; Chen, Jian Fu; Li, Yu Hang; Yuan, Wen Tao; Zhou, Ying; Zheng, Li Rong; Wang, Hai Feng; Hu, P; Wang, Yun; Zhao, Hui Jun; Wang, Yong; Yang, Hua Gui

    2014-02-17

    The process of using solar energy to split water to produce hydrogen assisted by an inorganic semiconductor is crucial for solving our energy crisis and environmental problems in the future. However, most semiconductor photocatalysts would not exhibit excellent photocatalytic activity without loading suitable co-catalysts. Generally, the noble metals have been widely applied as co-catalysts, but always agglomerate during the loading process or photocatalytic reaction. Therefore, the utilization efficiency of the noble co-catalysts is still very low on a per metal atom basis if no obvious size effect exists, because heterogeneous catalytic reactions occur on the surface active atoms. Here, for the first time, we have synthesized isolated metal atoms (Pt, Pd, Rh, or Ru) stably by anchoring on TiO2 , a model photocatalystic system, by a facile one-step method. The isolated metal atom based photocatalysts show excellent stability for H2 evolution and can lead to a 6-13-fold increase in photocatalytic activity over the metal clusters loaded on TiO2 by the traditional method. Furthermore, the configurations of isolated atoms as well as the originality of their unusual stability were analyzed by a collaborative work from both experiments and theoretical calculations. PMID:24403011

  6. Linking structure to function: The search for active sites in non-platinum group metal oxygen reduction reaction catalysts

    DOE PAGESBeta

    Holby, Edward F.; Zelenay, Piotr

    2016-05-17

    Atomic-scale structures of oxygen reduction reaction (ORR) active sites in non-platinum group metal (non-PGM) catalysts, made from pyrolysis of carbon, nitrogen, and transition-metal (TM) precursors have been the subject of continuing discussion in the fuel cell electrocatalysis research community. We found that quantum chemical modeling is a path forward for understanding of these materials and how they catalyze the ORR. Here, we demonstrate through literature examples of how such modeling can be used to better understand non-PGM ORR active site relative stability and activity and how such efforts can also aid in the interpretation of experimental signatures produced by thesemore » materials.« less

  7. Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions

    SciTech Connect

    Tomanicek, Stephen J.; Hughes, Ronny C.; Ng, Joseph D.; Coates, Leighton

    2010-10-05

    The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5{prime}-phosphodiester bond at an AP site to generate a free 3{prime}-hydroxyl group and a 5{prime}-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

  8. A Dynamic Zn Site in Helicobacter pylori HypA: A Potential Mechanism for Metal-Specific Protein Activity

    SciTech Connect

    Kennedy,D.; Herbst, R.; Iwig, J.; Chivers, P.; Maroney, M.

    2007-01-01

    HypA is an accessory protein and putative metallochaperone that is critical for supplying nickel to the active site of NiFe hydrogenases. In addition to binding Ni(II), HypA is known to contain a Zn site that has been suggested to play a structural role. X-ray absorption spectroscopy has been used to show that the Zn site changes structure upon binding nickel, from a S{sub 3}(O/N)-donor ligand environment to an S{sub 4}-donor ligand environment. This provides a potential mechanism for discriminating Ni(II) from other divalent metal ions. The Ni(II) site is shown to be a six-coordinate complex composed of O/N-donors including two histidines. As such, it resembles the nickel site in UreE, a nickel metallochaperone involved in nickel incorporation into urease.

  9. ROLE OF C AND P SITES ON THE CHEMICAL ACTIVITY OF METAL CARBIDE AND PHOSPHIDES: FROM CLUSTERS TO SINGLE-CRYSTAL SURFACES

    SciTech Connect

    RODRIGUEZ,J.A.; VINES, F.; LIU, P.; ILLAS, F.

    2007-07-01

    Transition metal carbides and phosphides have shown tremendous potential as highly active catalysts. At a microscopic level, it is not well understood how these new catalysts work. Their high activity is usually attributed to ligand or/and ensemble effects. Here, we review recent studies that examine the chemical activity of metal carbide and phosphides as a function of size, from clusters to extended surfaces, and metal/carbon or metal/phosphorous ratio. These studies reveal that the C and P sites in these compounds cannot be considered as simple spectators. They moderate the reactivity of the metal centers and provide bonding sites for adsorbates.

  10. Mobility of heavy metals from tailings to stream waters in a mining activity contaminated site.

    PubMed

    Concas, A; Ardau, C; Cristini, A; Zuddas, P; Cao, G

    2006-04-01

    In this paper the results of a recent characterization of Rio Piscinas (SW of Sardinia, Italy) hydrological basin are reported. In such area (about 50 km2), previous mining activities caused a serious heavy metal contamination of surface waters, groundwater, soils and biota. Acid mine drainage phenomena were observed in the area. The main sources of contamination are the tailings stored in mine tunnels and abandoned along fluvial banks. A methodological approach was adopted in order to identify relations between tailings and water contamination. Representative samples of tailings and stream sediments samples were collected. XRD analyses were performed for mineralogical characterization, while acid digestion was carried out for determining metal contents. Batch sequential leaching tests were performed in order to assess metal mobility. Also groundwater and stream water were sampled in specific locations and suitably characterized. All information collected allowed the understanding of the effect of tailings on water contamination, thus contributing to the qualitative prediction of pollution evolution on the basis of metal mobility. Finally, a potential remediation strategy of stream water is proposed. PMID:16216301

  11. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    NASA Astrophysics Data System (ADS)

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date.

  12. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    PubMed Central

    Holby, Edward F.; Taylor, Christopher D.

    2015-01-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date. PMID:25788358

  13. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: role of *OH ligands.

    PubMed

    Holby, Edward F; Taylor, Christopher D

    2015-01-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date. PMID:25788358

  14. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    DOE PAGESBeta

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-19

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

  15. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    SciTech Connect

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-19

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date.

  16. Elucidating Oxygen Reduction Active Sites in Pyrolyzed Metal–Nitrogen Coordinated Non-Precious-Metal Electrocatalyst Systems

    PubMed Central

    2015-01-01

    Detailed understanding of the nature of the active centers in non-precious-metal-based electrocatalyst, and their role in oxygen reduction reaction (ORR) mechanistic pathways will have a profound effect on successful commercialization of emission-free energy devices such as fuel cells. Recently, using pyrolyzed model structures of iron porphyrins, we have demonstrated that a covalent integration of the Fe–Nx sites into π-conjugated carbon basal plane modifies electron donating/withdrawing capability of the carbonaceous ligand, consequently improving ORR activity. Here, we employ a combination of in situ X-ray spectroscopy and electrochemical methods to identify the various structural and functional forms of the active centers in non-heme Fe/N/C catalysts. Both methods corroboratively confirm the single site 2e– × 2e– mechanism in alkaline media on the primary Fe2+–N4 centers and the dual-site 2e– × 2e– mechanism in acid media with the significant role of the surface bound coexisting Fe/FexOy nanoparticles (NPs) as the secondary active sites. PMID:24817921

  17. On an Easy Way To Prepare Metal-Nitrogen Doped Carbon with Exclusive Presence of MeN4-type Sites Active for the ORR.

    PubMed

    Kramm, Ulrike I; Herrmann-Geppert, Iris; Behrends, Jan; Lips, Klaus; Fiechter, Sebastian; Bogdanoff, Peter

    2016-01-20

    Today, most metal and nitrogen doped carbon catalysts for ORR reveal a heterogeneous composition. This can be reasoned by a nonoptimized precursor composition and various steps in the preparation process to get the required active material. The significant presence of inorganic metal species interferes with the assignment of descriptors related to the ORR activity and stability. In this work we present a simple and feasible way to reduce the contribution of inorganic metal species in some cases even down to zero. Such catalysts reveal the desired homogeneous composition of MeN4 (Me = metal) sites in the carbon that is accompanied by a significant enhancement in ORR activity. Among the work of other international groups, our iron-based catalyst comprises the highest density of FeN4 sites ever reported without interference of inorganic metal sites. PMID:26651534

  18. Examination of metals from aerospace-related activity in surface water samples from sites surrounding the Kennedy Space Center (KSC), Florida.

    PubMed

    Bowden, John A; Cantu, Theresa M; Scheidt, Douglas M; Lowers, Russell H; Nocito, Brian A; Young, Vaneica Y; Guillette, Louis J

    2014-05-01

    Metal contamination from Space Shuttle launch activity was examined using inductively coupled plasma-atomic emission spectroscopy in a two-tier study sampling surface water collected from several sites at the Kennedy Space Center (KSC) and associated Merritt Island National Wildlife Refuge in east central Florida. The primary study examined both temporal changes in baseline metal concentrations (19 metals) in surface water (1996 to 2009, 11 sites) samples collected at specific long-term monitoring sites and metal deposition directly associated with Space Shuttle launch activity at two Launch Complexes (LC39A and LC39B). A secondary study examined metal concentrations at additional sites and increased the amount of elements measured to 48 elements. Our examination places a heavy focus on those metals commonly associated with launch operations (e.g., Al, Fe, Mn, and Zn), but a brief discussion of other metals (As, Cu, Mo, Ni, and Pb) is also included. While no observable accumulation of metals occurred during the time period of the study, the data obtained postlaunch demonstrated a dramatic increase for Al, Fe, Mn, and Zn. Comparing overall trends between the primary and secondary baseline surface water concentrations, elevated concentrations were generally observed at sampling stations located near the launch complexes and from sites isolated from major water systems. While there could be several natural and anthropogenic sources for metal deposition at KSC, the data in this report indicate that shuttle launch events are a significant source. PMID:24738662

  19. A Chemical Route to Activation of Open Metal Sites in the Copper-Based Metal-Organic Framework Materials HKUST-1 and Cu-MOF-2.

    PubMed

    Kim, Hong Ki; Yun, Won Seok; Kim, Min-Bum; Kim, Jeung Yoon; Bae, Youn-Sang; Lee, JaeDong; Jeong, Nak Cheon

    2015-08-12

    Open coordination sites (OCSs) in metal-organic frameworks (MOFs) often function as key factors in the potential applications of MOFs, such as gas separation, gas sorption, and catalysis. For these applications, the activation process to remove the solvent molecules coordinated at the OCSs is an essential step that must be performed prior to use of the MOFs. To date, the thermal method performed by applying heat and vacuum has been the only method for such activation. In this report, we demonstrate that methylene chloride (MC) itself can perform the activation role: this process can serve as an alternative "chemical route" for the activation that does not require applying heat. To the best of our knowledge, no previous study has demonstrated this function of MC, although MC has been popularly used in the pretreatment step prior to the thermal activation process. On the basis of a Raman study, we propose a plausible mechanism for the chemical activation, in which the function of MC is possibly due to its coordination with the Cu(2+) center and subsequent spontaneous decoordination. Using HKUST-1 film, we further demonstrate that this chemical activation route is highly suitable for activating large-area MOF films. PMID:26197386

  20. Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active Site Metal Ion

    PubMed Central

    Zalatan, Jesse G.; Fenn, Timothy D.; Herschlag, Daniel

    2009-01-01

    Mechanistic models for biochemical systems are frequently proposed from structural data. Site-directed mutagenesis can be used to test the importance of proposed functional sites, but these data do not necessarily indicate how these sites contribute to function. Herein we apply an alternative approach to the catalytic mechanism of alkaline phosphatase (AP), a widely-studied, prototypical bimetallo enzyme. A third metal ion site in AP has been suggested to provide general base catalysis, but comparison with an evolutionarily-related enzyme casts doubt on this model. Removal of this metal site from AP has large differential effects on reactions of cognate and promiscuous substrates, and the results are inconsistent with general base catalysis. Instead, these and additional results suggest that the third metal ion stabilizes the transferred phosphoryl group in the transition state. These results establish a new mechanistic model for this prototypical bimetallo enzyme and demonstrate the power of a comparative approach for probing biochemical function. PMID:18851975

  1. Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: Does a third metal binding site modulate endonuclease activity?

    PubMed Central

    Ho, Ming-Hsun; De Vivo, Marco; Peraro, Matteo Dal; Klein, Michael L.

    2010-01-01

    Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkage on the RNA strand of a DNA/RNA hybrid duplex. Due to its activity in HIV reverse transcription, it represents a promising target for anti-HIV drug design. While crystallographic data have located two ions in the catalytic site, there is ongoing debate concerning just how many metal ions bound at the active site are optimal for catalysis. Indeed, experiments have shown a dependency of the catalytic activity on the Mg2+ concentration. Moreover, in RNase H the glutamate residue E188 has been shown to be essential for full enzymatic activation regardless of the Mg2+ concentration. The catalytic center is known to contain two Mg2+ ions (Nowotny et al.) and E188 is not one of the primary metal ligands. Herein, classical molecular dynamics (MD) simulations are employed to study the metal-ligand coordination in RNase H at different concentration of Mg2+. Importantly, the presence of a third Mg2+ ion, bound to the second-shell ligand E188, is persistent feature of the MD simulations. Free energy calculations have identified two distinct conformations depending on the concentration of Mg2+. At standard concentration, a third Mg2+ is found in the catalytic pocket but it does not perturb the optimal RNase H active conformation. However, at higher concentration, the third Mg2+ ion heavily perturbs the nucleophilic water and thereby influences the catalytic efficiency of RNase H. In addition, the E188A mutant shows no ability to engage additional Mg2+ ions nearby the catalytic pocket. This finding likely explains the decrease in catalytic activity of E188A, and also supports the key role of E188 in localizing the third Mg2+ ion at the active site. Glutamate residues are commonly found surrounding the metal center in the endonuclease family, which suggests that this structural motif may be an important feature to enhance catalytic activity. The present MD

  2. Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding.

    PubMed

    Giannotti, Marina I; Cabeza de Vaca, Israel; Artés, Juan M; Sanz, Fausto; Guallar, Victor; Gorostiza, Pau

    2015-09-10

    The structural basis of the low reorganization energy of cupredoxins has long been debated. These proteins reconcile a conformationally heterogeneous and exposed metal-chelating site with the highly rigid copper center required for efficient electron transfer. Here we combine single-molecule mechanical unfolding experiments with statistical analysis and computer simulations to show that the metal-binding region of apo-azurin is mechanically flexible and that high mechanical stability is imparted by copper binding. The unfolding pathway of the metal site depends on the pulling residue and suggests that partial unfolding of the metal-binding site could be facilitated by the physical interaction with certain regions of the redox protein. PMID:26305718

  3. The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

    SciTech Connect

    Gopal, B.; Madan, Lalima L.; Betz, Stephen F.; Kossiakoff, Anthony A.

    2010-11-10

    Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s), whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.

  4. Stabilization of soils contaminated with explosives and metals from the ammunition demolition activity area and miscellaneous sites at the Umatilla Depot

    SciTech Connect

    Lear, P.R.; Gemarr, D.

    1997-12-31

    The US Army Umatilla Depot (UMD) was established as an ordnance depot in 1941 to store, preserve, and perform minor maintenance on conventional and chemical munitions. From the 1940`s until the present, UMD operated periodically at the 32 miscellaneous sites identified as OU-5. OU-4 consists of twenty sites within the Ammunition Demolition Activity Area. Typical activities conducted at these sites consisted of operations to burn, detonate, and otherwise dispose of ordnance, munitions casings, and other solids wastes. Five sites were selected for remedial action. The remediation contaminants of concern for the sites encompassed both metallic and non-metallic elements and both inorganic and organic compounds. The remedial action selected for the contaminated soil at these sites was stabilization/solidification (S/S). The site remediation activities for the five sites were performed by OHM Remediation Services Corp. (OHM) under the supervision of the US Army Corps of Engineers (USACE) Seattle District. The remedial action included treatability mix design testing, mobilization and field setup, soil excavation and processing, and S/S treatment. Stabilized soil samples were collected as grab samples from the pugmill discharge conveyor at a rate of every 75 tons of soil feed, corresponding to an individual production lot. None of the 437 production lots failed to meet the UCS requirement of 50 psi, however, 31 (7%) of the 437 lots failed for either TCLP-leachable metals or explosives. With one exception, all production lots which failed were due to exceedances of the TCLP-leachable explosives requirements. Of these 30 lots, 22 lots were from the OU-5 metals sites and were not expected to contain significant amounts of explosives. The areas in the landfill corresponding to these lots were excavated and the material reprocessed.

  5. A microporous Cu-MOF with optimized open metal sites and pore spaces for high gas storage and active chemical fixation of CO2.

    PubMed

    Gao, Chao-Ying; Tian, Hong-Rui; Ai, Jing; Li, Lei-Jiao; Dang, Song; Lan, Ya-Qian; Sun, Zhong-Ming

    2016-09-25

    A microporous Cu-MOF with optimized open metal sites and pore space was constructed based on a designed bent ligand; it exhibits high-capacity multiple gas storage under atmospheric pressure and efficient catalytic activity for chemical fixation of CO2 under mild conditions. PMID:27550833

  6. Cobalt activation of Escherichia coli 5'-nucleotidase is due to zinc ion displacement at only one of two metal-ion-binding sites.

    PubMed Central

    McMillen, Lyle; Beacham, Ifor R; Burns, Dennis M

    2003-01-01

    Escherichia coli 5'-nucleotidase activity is stimulated 30- to 50-fold in vitro by the addition of Co(2+). Seven residues from conserved sequence motifs implicated in the catalytic and metal-ion-binding sites of E. coli 5'-nucleotidase (Asp(41), His(43), Asp(84), His(117), Glu(118), His(217) and His(252)) were selected for modification using site-directed mutagenesis of the cloned ushA gene. On the basis of comparative studies between the resultant mutant proteins and the wild-type enzyme, a model is proposed for E. coli 5'-nucleotidase in which a Co(2+) ion may displace the Zn(2+) ion at only one of two metal-ion-binding sites; the other metal-ion-binding site retains the Zn(2+) ion already present. The studies reported herein suggest that displacement occurs at the metal-ion-binding site consisting of residues Asp(84), Asn(116), His(217) and His(252), leading to the observed increase in 5'-nucleotidase activity. PMID:12603203

  7. Redox-active on-surface polymerization of single-site divalent cations from pure metals by a ketone-functionalized phenanthroline

    SciTech Connect

    Skomski, Daniel; Tempas, Christopher D.; Bukowski, Gregory S.; Smith, Kevin A.; Tait, Steven L.

    2015-03-14

    Metallic iron, chromium, or platinum mixing with a ketone-functionalized phenanthroline ligand on a single crystal gold surface demonstrates redox activity to a well-defined oxidation state and assembly into thermally stable, one dimensional, polymeric chains. The diverging ligand geometry incorporates redox-active sub-units and bi-dentate binding sites. The gold surface provides a stable adsorption environment and directs growth of the polymeric chains, but is inert with regard to the redox chemistry. These systems are characterized by scanning tunnelling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy under ultra-high vacuum conditions. The relative propensity of the metals to interact with the ketone group is examined, and it is found that Fe and Cr more readily complex the ligand than Pt. The formation and stabilization of well-defined transition metal single-sites at surfaces may open new routes to achieve higher selectivity in heterogeneous catalysts.

  8. Redox-active on-surface polymerization of single-site divalent cations from pure metals by a ketone-functionalized phenanthroline

    NASA Astrophysics Data System (ADS)

    Skomski, Daniel; Tempas, Christopher D.; Bukowski, Gregory S.; Smith, Kevin A.; Tait, Steven L.

    2015-03-01

    Metallic iron, chromium, or platinum mixing with a ketone-functionalized phenanthroline ligand on a single crystal gold surface demonstrates redox activity to a well-defined oxidation state and assembly into thermally stable, one dimensional, polymeric chains. The diverging ligand geometry incorporates redox-active sub-units and bi-dentate binding sites. The gold surface provides a stable adsorption environment and directs growth of the polymeric chains, but is inert with regard to the redox chemistry. These systems are characterized by scanning tunnelling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy under ultra-high vacuum conditions. The relative propensity of the metals to interact with the ketone group is examined, and it is found that Fe and Cr more readily complex the ligand than Pt. The formation and stabilization of well-defined transition metal single-sites at surfaces may open new routes to achieve higher selectivity in heterogeneous catalysts.

  9. In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination.

    PubMed

    Pedebos, Conrado; Arantes, Pablo Ricardo; Giesel, Guilherme Menegon; Verli, Hugo

    2015-11-01

    The last step of the bacterial N-glycosylation pathway involves PglB, an oligosaccharyltransferase, which is responsible for the en bloc transfer of a fully assembled oligosaccharide chain to a protein possessing the extended motif D/E-X-N-X-S/T. Recently, this molecule had its full structure elucidated, enabling the description of its domains and the proposition of a catalytic mechanism. By employing molecular dynamics simulations, we were able to evaluate structural aspects of PglB, suggesting prevalent motions that may bring insights into the mechanism of the glycosylated peptide detachment. Additionally, we identified transient states at the catalytic site, in which the previously described carboxamide twisting mechanism was observed. Aided by quantum mechanics calculations for each different conformational states of the catalytic site, we determined the presence of an octahedral metal coordination, along with the presence of one water molecule at the catalytic site. PMID:26220543

  10. Mapping the triphosphatase active site of baculovirus mRNA capping enzyme LEF4 and evidence for a two-metal mechanism

    PubMed Central

    Martins, Alexandra; Shuman, Stewart

    2003-01-01

    The 464-amino acid baculovirus LEF4 protein is a bifunctional mRNA capping enzyme with triphosphatase and guanylyltransferase activities. The N-terminal half of LEF4 constitutes an autonomous triphosphatase catalytic domain. The LEF4 triphosphatase belongs to a family of metal-dependent phosphohydrolases, which includes the RNA triphosphatases of fungi, protozoa, Chlorella virus and poxviruses. The family is defined by two glutamate-containing motifs (A and C), which form a metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight stranded β barrel (the so-called ‘triphosphate tunnel’). Here we probed whether baculovirus LEF4 is a member of the tunnel subfamily, via mutational mapping of amino acids required for triphosphatase activity. We identified four new essential side chains in LEF4 via alanine scanning and illuminated structure–activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight five acidic and four basic amino acids that are likely to comprise the LEF4 triphosphatase active site (Glu9, Glu11, Arg51, Arg53, Glu97, Lys126, Arg179, Glu181 and Glu183). These nine essential residues are conserved in LEF4 orthologs from all strains of baculoviruses. We discerned no pattern of clustering of the catalytic residues of the baculovirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). However, there is similarity to the active site of vaccinia RNA triphosphatase. We infer that the baculovirus and poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Synergistic activation of the LEF4 triphosphatase by manganese and magnesium suggests a two-metal mechanism of γ phosphate hydrolysis. PMID:12595553

  11. NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights into RNA–Metal-Ion Interactions

    PubMed Central

    2013-01-01

    Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa’s of two key nucleobases that contribute to the general acid–base mechanism. Recently, we determined the NMR structure of the A730 loop of the VS ribozyme active site (SLVI) that contributes the general acid (A756) in the enzymatic mechanism of the cleavage reaction. Our studies showed that magnesium (Mg2+) ions are essential to stabilize the formation of the S-turn motif within the A730 loop that exposes the A756 nucleobase for catalysis. In this article, we extend these NMR investigations by precisely mapping the Mg2+-ion binding sites using manganese-induced paramagnetic relaxation enhancement and cadmium-induced chemical-shift perturbation of phosphorothioate RNAs. These experiments identify five Mg2+-ion binding sites within SLVI. Four Mg2+ ions in SLVI are associated with known RNA structural motifs, including the G–U wobble pair and the GNRA tetraloop, and our studies reveal novel insights about Mg2+ ion binding to these RNA motifs. Interestingly, one Mg2+ ion is specifically associated with the S-turn motif, confirming its structural role in the folding of the A730 loop. This Mg2+ ion is likely important for formation of the active site and may play an indirect role in catalysis. PMID:24364590

  12. Selective Metal-Site-Guided Arylation of Proteins.

    PubMed

    Willwacher, Jens; Raj, Ritu; Mohammed, Shabaz; Davis, Benjamin G

    2016-07-20

    We describe palladium-mediated S-arylation that exploits natural metal-binding motifs to ensure high site selectivity for a proximal reactive residue. This allows the chemical identification not only of proteins that bind metals but also the environment of the metal-binding site itself through proteomic analysis of arylation sites. The transformation is easy to perform under standard conditions, does not require the isolation of a reactive Ar-Pd complex, is broad in scope, and is applicable in cell lysates as well as to covalent inhibition/modulation of metal-dependent enzymatic activity. PMID:27336299

  13. Preferred Metal Binding Site of Aniline

    NASA Astrophysics Data System (ADS)

    Kumari, Sudesh; Sohnlein, Brad; Yang, Dong-Sheng

    2012-06-01

    Group III metal-aniline complexes, M-aniline (M = Sc, Y, and La), were produced by interactions between laser-vaporized metal atoms and aniline vapor in a pulsed molecular beam source, identified by photoionization time-of-flight mass spectrometry, and studied by pulsed-field ionization zero electron kinetic energy (ZEKE) spectroscopy and density functional theory calculations. Adiabatic ionization energies and several vibrational intervals were measured from the ZEKE spectra. Metal binding sites and electronic states were determined by combining the ZEKE measurements and theoretical calculations. Although aniline has various possible sites for metal coordination, the preferred site was determined to be phenyl ring. The metal binding with the phenyl ring yields syn and anti conformers. In these conformers, the neutral complexes are in doublet ground states and the corresponding singly charged cations in singlet states.

  14. Postsynthetic Metal and Ligand Exchange in MFU-4l: A Screening Approach toward Functional Metal-Organic Frameworks Comprising Single-Site Active Centers.

    PubMed

    Denysenko, Dmytro; Jelic, Jelena; Reuter, Karsten; Volkmer, Dirk

    2015-05-26

    The isomorphous partial substitution of Zn(2+) ions in the secondary building unit (SBU) of MFU-4l leads to frameworks with the general formula [M(x)Zn(5-x)Cl4(BTDD)3], in which x≈2, M = Mn(II), Fe(II), Co(II), Ni(II), or Cu(II), and BTDD = bis(1,2,3-triazolato-[4,5-b],[4',5'-i])dibenzo-[1,4]-dioxin. Subsequent exchange of chloride ligands by nitrite, nitrate, triflate, azide, isocyanate, formate, acetate, or fluoride leads to a variety of MFU-4l derivatives, which have been characterized by using XRPD, EDX, IR, UV/Vis-NIR, TGA, and gas sorption measurements. Several MFU-4l derivatives show high catalytic activity in a liquid-phase oxidation of ethylbenzene to acetophenone with air under mild conditions, among which Co- and Cu derivatives with chloride side-ligands are the most active catalysts. Upon thermal treatment, several side-ligands can be transformed selectively into reactive intermediates without destroying the framework. Thus, at 300 °C, Co(II)-azide units in the SBU of Co-MFU-4l are converted into Co(II)-isocyanate under continuous CO gas flow, involving the formation of a nitrene intermediate. The reaction of Cu(II)-fluoride units with H2 at 240 °C leads to Cu(I) and proceeds through the heterolytic cleavage of the H2 molecule. PMID:25882594

  15. Lanthanide Metal-Organic Frameworks with Six-Coordinated Ln(III) Ions and Free Functional Organic Sites for Adsorptions and Extensive Catalytic Activities

    NASA Astrophysics Data System (ADS)

    Zhu, Yu; Zhu, Min; Xia, Li; Wu, Yunlong; Hua, Hui; Xie, Jimin

    2016-07-01

    Three chelating-amino-functionalized lanthanide metal-organic frameworks, Y-DDQ, Dy-DDQ and Eu-DDQ, were synthesized with a flexible dicarboxylate ligand based on quinoxaline (H2DDQ = N, N‧-dibenzoic acid-2,3-diaminoquinoxaline). The three-dimensional framework is constructed by the H2DDQ linkers connecting the zigzag ladders, showing a net of sra topology. In the structures, one kind of Ln(III) ions metal centers are six-coordinated and thus can potentially behave as open metal sites (OMSs), while the free chelating amino groups can act as free functional organic sites (FOSs). The N2 and Ar adsorption behaviors indicate that these Ln-DDQ exhibits stable microporous frameworks with high surface area after remove of the solvents. Owing to presence of OMSs and FOSs, these MOFs show good ability of CO2, dyes captures and Lewis acid catalyst for cyanosilylation reaction. In view of the existing FOSs in the framework, Pd NPs were immobilized onto the MOFs through graft interactions between free chelating amino groups and metal ions precursor using postsynthetic modification. The well dispersed Pd@Ln-DDQs exhibit efficient and recyclable catalytic reduction of 4-nitrophenol to 4-aminophenol, and they can also act as an excellent catalyst for Suzuki-Miyaura cross-coupling reactions with the exposed Pd NPs.

  16. Lanthanide Metal-Organic Frameworks with Six-Coordinated Ln(III) Ions and Free Functional Organic Sites for Adsorptions and Extensive Catalytic Activities.

    PubMed

    Zhu, Yu; Zhu, Min; Xia, Li; Wu, Yunlong; Hua, Hui; Xie, Jimin

    2016-01-01

    Three chelating-amino-functionalized lanthanide metal-organic frameworks, Y-DDQ, Dy-DDQ and Eu-DDQ, were synthesized with a flexible dicarboxylate ligand based on quinoxaline (H2DDQ = N, N'-dibenzoic acid-2,3-diaminoquinoxaline). The three-dimensional framework is constructed by the H2DDQ linkers connecting the zigzag ladders, showing a net of sra topology. In the structures, one kind of Ln(III) ions metal centers are six-coordinated and thus can potentially behave as open metal sites (OMSs), while the free chelating amino groups can act as free functional organic sites (FOSs). The N2 and Ar adsorption behaviors indicate that these Ln-DDQ exhibits stable microporous frameworks with high surface area after remove of the solvents. Owing to presence of OMSs and FOSs, these MOFs show good ability of CO2, dyes captures and Lewis acid catalyst for cyanosilylation reaction. In view of the existing FOSs in the framework, Pd NPs were immobilized onto the MOFs through graft interactions between free chelating amino groups and metal ions precursor using postsynthetic modification. The well dispersed Pd@Ln-DDQs exhibit efficient and recyclable catalytic reduction of 4-nitrophenol to 4-aminophenol, and they can also act as an excellent catalyst for Suzuki-Miyaura cross-coupling reactions with the exposed Pd NPs. PMID:27431731

  17. Lanthanide Metal-Organic Frameworks with Six-Coordinated Ln(III) Ions and Free Functional Organic Sites for Adsorptions and Extensive Catalytic Activities

    PubMed Central

    Zhu, Yu; Zhu, Min; Xia, Li; Wu, Yunlong; Hua, Hui; Xie, Jimin

    2016-01-01

    Three chelating-amino-functionalized lanthanide metal-organic frameworks, Y-DDQ, Dy-DDQ and Eu-DDQ, were synthesized with a flexible dicarboxylate ligand based on quinoxaline (H2DDQ = N, N′-dibenzoic acid-2,3-diaminoquinoxaline). The three-dimensional framework is constructed by the H2DDQ linkers connecting the zigzag ladders, showing a net of sra topology. In the structures, one kind of Ln(III) ions metal centers are six-coordinated and thus can potentially behave as open metal sites (OMSs), while the free chelating amino groups can act as free functional organic sites (FOSs). The N2 and Ar adsorption behaviors indicate that these Ln-DDQ exhibits stable microporous frameworks with high surface area after remove of the solvents. Owing to presence of OMSs and FOSs, these MOFs show good ability of CO2, dyes captures and Lewis acid catalyst for cyanosilylation reaction. In view of the existing FOSs in the framework, Pd NPs were immobilized onto the MOFs through graft interactions between free chelating amino groups and metal ions precursor using postsynthetic modification. The well dispersed Pd@Ln-DDQs exhibit efficient and recyclable catalytic reduction of 4-nitrophenol to 4-aminophenol, and they can also act as an excellent catalyst for Suzuki-Miyaura cross-coupling reactions with the exposed Pd NPs. PMID:27431731

  18. Active Metal-Insulator-Metal Plasmonic Devices

    NASA Astrophysics Data System (ADS)

    Diest, Kenneth Alexander

    As the field of photonics constantly strives for ever smaller devices, the diffraction limit of light emerges as a fundamental limitation in this pursuit. A growing number of applications for optical "systems on a chip" have inspired new ways of circumventing this issue. One such solution to this problem is active plasmonics. Active plasmonics is an emerging field that enables light compression into nano-structures based on plasmon resonances at a metal-dielectric interface and active modulation of these plasmons with an applied external field. One area of active plasmonics has focused on replacing the dielectric layer in these waveguides with an electro-optic material and designing the resulting structures in such a way that the transmitted light can be modulated. These structures can be utilized to design a wide range of devices including optical logic gates, modulators, and filters. This thesis focuses on replacing the dielectric layer within a metal-insulator-metal plasmonic waveguide with a range of electrically active materials. By applying an electric field between the metal layers, we take advantage of the electro-optic effect in lithium niobate, and modulating the carrier density distribution across the structure in n-type silicon and indium tin oxide. The first part of this thesis looks at fabricating metal-insulator-metal waveguides with ion-implantation induced layer transferred lithium niobate. The process is analyzed from a thermodynamic standpoint and the ion-implantation conditions required for layer transfer are determined. The possible failure mechanisms that can occur during this process are analyzed from a thin-film mechanics standpoint, and a metal-bonding method to improve successful layer transfer is proposed and analyzed. Finally, these devices are shown to naturally filter white light into individual colors based on the interference of the different optical modes within the dielectric layer. Full-field electromagnetic simulations show that

  19. Chemoselective single-site Earth-abundant metal catalysts at metal-organic framework nodes.

    PubMed

    Manna, Kuntal; Ji, Pengfei; Lin, Zekai; Greene, Francis X; Urban, Ania; Thacker, Nathan C; Lin, Wenbin

    2016-01-01

    Earth-abundant metal catalysts are critically needed for sustainable chemical synthesis. Here we report a simple, cheap and effective strategy of producing novel earth-abundant metal catalysts at metal-organic framework (MOF) nodes for broad-scope organic transformations. The straightforward metalation of MOF secondary building units (SBUs) with cobalt and iron salts affords highly active and reusable single-site solid catalysts for a range of organic reactions, including chemoselective borylation, silylation and amination of benzylic C-H bonds, as well as hydrogenation and hydroboration of alkenes and ketones. Our structural, spectroscopic and kinetic studies suggest that chemoselective organic transformations occur on site-isolated, electron-deficient and coordinatively unsaturated metal centres at the SBUs via σ-bond metathesis pathways and as a result of the steric environment around the catalytic site. MOFs thus provide a novel platform for the development of highly active and affordable base metal catalysts for the sustainable synthesis of fine chemicals. PMID:27574182

  20. Triphenylamine-Based Metal-Organic Frameworks as Cathode Materials in Lithium-Ion Batteries with Coexistence of Redox Active Sites, High Working Voltage, and High Rate Stability.

    PubMed

    Peng, Zhe; Yi, Xiaohui; Liu, Zixuan; Shang, Jie; Wang, Deyu

    2016-06-15

    Through rational organization of two redox active building block, a triphenylamine-based metal-organic framework (MOF) material, Cu-TCA (H3TCA = tricarboxytriphenyl amine), was synthesized and applied as a cathode active material for the first time in lithium batteries. Cu-TCA exhibited redox activity both in the metal clusters (Cu(+)/Cu(2+)) and organic ligand radicals (N/N(+)) with separated voltage plateaus and a high working potential vs Li/Li(+) up to 4.3 V, comparing with the current commercial LiCoO2 cathode materials. The electrochemical behaviors of this MOF electrode material at different states of charge were carefully studied by cyclic voltammetry, X-ray photoelectron spectroscopy, and photoluminescence techniques. Long cycling stability of this MOF was achieved with an average Coulombic efficiency of 96.5% for 200 cycles at a 2 C rate. Discussing the electrochemical performances on the basis of capacity contributions from the metal clusters (Cu(+)/Cu(2+)) and organic ligands (N/N(+)) proposes an alternative mechanism of capacity loss for the MOF materials used in lithium batteries. This improved understanding will shed light on the designing principle of MOF-based cathode materials for their practical application in battery sciences. PMID:27225327

  1. Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

    PubMed

    Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

    2016-02-23

    In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL. PMID:26820485

  2. Actively convected liquid metal divertor

    NASA Astrophysics Data System (ADS)

    Shimada, Michiya; Hirooka, Yoshi

    2014-12-01

    The use of actively convected liquid metals with j × B force is proposed to facilitate heat handling by the divertor, a challenging issue associated with magnetic fusion experiments such as ITER. This issue will be aggravated even more for DEMO and power reactors because the divertor heat load will be significantly higher and yet the use of copper would not be allowed as the heat sink material. Instead, reduced activation ferritic/martensitic steel alloys with heat conductivities substantially lower than that of copper, will be used as the structural materials. The present proposal is to fill the lower part of the vacuum vessel with liquid metals with relatively low melting points and low chemical activities including Ga and Sn. The divertor modules, equipped with electrodes and cooling tubes, are immersed in the liquid metal. The electrode, placed in the middle of the liquid metal, can be biased positively or negatively with respect to the module. The j × B force due to the current between the electrode and the module provides a rotating motion for the liquid metal around the electrodes. The rise in liquid temperature at the separatrix hit point can be maintained at acceptable levels from the operation point of view. As the rotation speed increases, the current in the liquid metal is expected to decrease due to the v × B electromotive force. This rotating motion in the poloidal plane will reduce the divertor heat load significantly. Another important benefit of the convected liquid metal divertor is the fast recovery from unmitigated disruptions. Also, the liquid metal divertor concept eliminates the erosion problem.

  3. Studying Activity Series of Metals.

    ERIC Educational Resources Information Center

    Hoon, Tien-Ghun; And Others

    1995-01-01

    Presents teaching strategies that illustrate the linking together of numerous chemical concepts involving the activity of metals (quantitative analysis, corrosion, and electrolysis) through the use of deep-level processing strategies. Concludes that making explicit links in the process of teaching chemistry can lead effectively to meaningful…

  4. Metal ion effects on enolase activity

    SciTech Connect

    Lee, M.E.; Nowak, T.

    1986-05-01

    Most metal binding studies with yeast enolase suggest that two metals per monomer are required for catalytic activity. The functions of metal I and metal II have not been unequivocally defined. In a series of kinetic experiments where the concentration of MgII is kept constant at subsaturating levels (1mM), the addition of MnII or of ZnII gives a hyperbolic decrease in activity. The final velocity of these mixed metal systems is the same velocity obtained with either only MnII or ZnII respectively. The concentration of MnII (40 ..mu..M) or of Zn (2..mu..M) which gives half maximal effect in the presence of (1mM) MgII is approximately the same as the Km' value for MnII (9..mu..M) or ZnII (3..mu..M) respectively. Direct binding of MnII to enolase in the absence and presence of MgII shows that MnII and MgII compete for the same metal site on enolase. In the presence of 2-phosphoglycerate (2-PGA) and MgII, only a single site is occupied by MnII. Results suggest MnII at site I and MgII at site II. PRR and high resolution /sup 1/H and /sup 31/P NMR studies of enzyme-ligand complexes containing MnII and MgII and MnII are consistent with this model. /sub 31/P measurements allow a measure of the equilibrium constant (0.36) for enolase. Saturation transfer measurements yield net rate constants (k/sub f/ = 0.49s/sup -1/; k/sub r/ = 1.3s/sup -1/) for the overall reaction. These values are smaller than k/sub cat/ (38s/sup -1/) measured under analogous conditions. The cation at site I appears to determine catalytic activity.

  5. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  6. Coronal Metallicities of Active Binaries

    NASA Astrophysics Data System (ADS)

    Kashyap, V.; Drake, J. J.; Pease, D. O.; Schmitt, J. H. M. M.

    1998-09-01

    We analyze EUV and X-ray data on a sample of X-ray active binary stars to determine coronal abundances. EUVE spectrometer data are used to obtain line fluxes, which are then used to determine Differential Emission Measures (DEMs). The continuum emission predicted for these DEMs (constrained at high temperatures by measurements in the X-ray regime where available) are then compared with EUVE/DS counts to derive coronal metallicities. These measurements indicate whether the coronae on these stars are metal deficient (the ``MAD Syndrome'') or subject to the FIP-effect (low First Ionization Potential elements have enhanced abundances relative to the photospheres).

  7. Tuning reactivity and site selectivity of simple arenes in C-H activation: ortho-arylation of anisoles via arene-metal π-complexation.

    PubMed

    Ricci, Paolo; Krämer, Katrina; Larrosa, Igor

    2014-12-31

    Current approaches to achieve site selectivity in the C-H activation of arenes involve the use of directing groups or highly electron-poor arenes. In contrast, simple arenes, such as anisole, are characterized by poor reactivity and selectivity. We report that π-complexation to a Cr(CO)3 unit enhances the reactivity of anisoles providing an unprecedented ortho-selective arylation. This mild methodology can be used for the late stage functionalization of bioactive compounds containing the anisole motif, allowing the construction of novel organic scaffolds with few synthetic steps. PMID:25510851

  8. Tuning Reactivity and Site Selectivity of Simple Arenes in C–H Activation: Ortho-Arylation of Anisoles via Arene–Metal π-Complexation

    PubMed Central

    2014-01-01

    Current approaches to achieve site selectivity in the C–H activation of arenes involve the use of directing groups or highly electron-poor arenes. In contrast, simple arenes, such as anisole, are characterized by poor reactivity and selectivity. We report that π-complexation to a Cr(CO)3 unit enhances the reactivity of anisoles providing an unprecedented ortho-selective arylation. This mild methodology can be used for the late stage functionalization of bioactive compounds containing the anisole motif, allowing the construction of novel organic scaffolds with few synthetic steps. PMID:25510851

  9. In Situ Studies of the Active Sites for the Water Gas Shift Reaction over Cu-CeO2 Catalysts: Complex Interaction Between Metallic Copper and Oxygen Vacancies of Ceria

    SciTech Connect

    Wang,X.; Rodriguez, J.; Hanson, J.; Gamarra, D.; Martinez-Arias, A.; Fernandez-Garcia, M.

    2006-01-01

    New information about the active sites for the water gas shift (WGS) reaction over Cu-CeO{sub 2} systems was obtained using in-situ, time-resolved X-ray diffraction (TR-XRD), X-ray absorption spectroscopy (TR-XAS, Cu K and Ce L3 edges), and infrared spectroscopy (DRIFTS). Cu-CeO{sub 2} nanoparticles prepared by a novel reversed microemulsion method (doped Ce1-xCuxO2 sample) and an impregnation method (impregnated CuO{sub x}/CeO{sub 2} sample) were studied. The results from all of the samples indicate that both metallic copper and oxygen vacancies in ceria were involved in the generation of active sites for the WGS reaction. Evidence was found for a synergistic Cu-O vacancy interaction. This interaction enhances the chemical activity of Cu, and the presence of Cu facilitates the formation of O vacancies in ceria under reaction conditions. Water dissociation occurred on the O vacancy sites or the Cu-O vacancy interface. No significant amounts of formate were formed on the catalysts during the WGS reaction. The presence of strongly bound carbonates is an important factor for the deactivation of the catalysts at high temperatures. This work identifies for the first time the active sites for the WGS reaction on Cu-CeO{sub 2} catalysts and illustrates the importance of in situ structural studies for heterogeneous catalytic reactions.

  10. Validating metal binding sites in macromolecule structures using the CheckMyMetal web server

    PubMed Central

    Zheng, Heping; Chordia, Mahendra D.; Cooper, David R.; Chruszcz, Maksymilian; Müller, Peter; Sheldrick, George M.

    2015-01-01

    Metals play vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules where metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal binding environments. The "CheckMyMetal" (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal binding sites in macromolecular structures in respect to 7350 metal binding sites observed in a benchmark dataset of 2304 high resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal binding sites and alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the anticipated results section. CMM was designed for a broad audience—biomedical researchers studying metal-containing proteins and nucleic acids—but is equally well suited for structural biologists to validate new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure modeled with a few hundred amino acids. PMID:24356774

  11. CONTAMINANTS AND REMEDIAL OPTIONS AT SELECTED METAL-CONTAMINATED SITES

    EPA Science Inventory

    This document provides information that facilitates characterization of the site and selection of treatment technologies at metals-contaminated sites that would be capable of meeting site-specific cleanup levels. he document does not facilitate the determination of cleanup levels...

  12. The active site behaviour of electrochemically synthesised gold nanomaterials.

    PubMed

    Plowman, Blake J; O'Mullane, Anthony P; Bhargava, Suresh K

    2011-01-01

    Even though gold is the noblest of metals, a weak chemisorber and is regarded as being quite inert, it demonstrates significant electrocatalytic activity in its nanostructured form. It is demonstrated here that nanostructured and even evaporated thin films of gold are covered with active sites which are responsible for such activity. The identification of these sites is demonstrated with conventional electrochemical techniques such as cyclic voltammetry as well as a large amplitude Fourier transformed alternating current (FT-ac) method under acidic and alkaline conditions. The latter technique is beneficial in determining if an electrode process is either Faradaic or capacitive in nature. The observed behaviour is analogous to that observed for activated gold electrodes whose surfaces have been severely disrupted by cathodic polarisation in the hydrogen evolution region. It is shown that significant electrochemical oxidation responses occur at discrete potential values well below that for the formation of the compact monolayer oxide of bulk gold and are attributed to the facile oxidation of surface active sites. Several electrocatalytic reactions are explored in which the onset potential is determined by the presence of such sites on the surface. Significantly, the facile oxidation of active sites is used to drive the electroless deposition of metals such as platinum, palladium and silver from their aqueous salts on the surface of gold nanostructures. The resultant surface decoration of gold with secondary metal nanoparticles not only indicates regions on the surface which are rich in active sites but also provides a method to form interesting bimetallic surfaces. PMID:22455038

  13. The Use of Molecular and Genomic Techniques Applied to Microbial Diversity, Community Structure, and Activities at DNAPL and Metal Contaminated Sites

    EPA Science Inventory

    A wide variety of in situ subsurface remediation strategies have been developed to mitigate contamination by chlorinated solvent dense non-aqueous phase liquids (DNAPLS) and metals. Geochemical methods include: zerovalent iron emplacement, various electrolytic applications, elec...

  14. Earliest evidence of pollution by heavy metals in archaeological sites

    PubMed Central

    Monge, Guadalupe; Jimenez-Espejo, Francisco J.; García-Alix, Antonio; Martínez-Ruiz, Francisca; Mattielli, Nadine; Finlayson, Clive; Ohkouchi, Naohiko; Sánchez, Miguel Cortés; de Castro, Jose María Bermúdez; Blasco, Ruth; Rosell, Jordi; Carrión, José; Rodríguez-Vidal, Joaquín; Finlayson, Geraldine

    2015-01-01

    Homo species were exposed to a new biogeochemical environment when they began to occupy caves. Here we report the first evidence of palaeopollution through geochemical analyses of heavy metals in four renowned archaeological caves of the Iberian Peninsula spanning the last million years of human evolution. Heavy metal contents reached high values due to natural (guano deposition) and anthropogenic factors (e.g. combustion) in restricted cave environments. The earliest anthropogenic pollution evidence is related to Neanderthal hearths from Gorham's Cave (Gibraltar), being one of the first milestones in the so-called “Anthropocene”. According to its heavy metal concentration, these sediments meet the present-day standards of “contaminated soil”. Together with the former, the Gibraltar Vanguard Cave, shows Zn and Cu pollution ubiquitous across highly anthropic levels pointing to these elements as potential proxies for human activities. Pb concentrations in Magdalenian and Bronze age levels at El Pirulejo site can be similarly interpreted. Despite these high pollution levels, the contaminated soils might not have posed a major threat to Homo populations. Altogether, the data presented here indicate a long-term exposure of Homo to these elements, via fires, fumes and their ashes, which could have played certain role in environmental-pollution tolerance, a hitherto neglected influence. PMID:26388184

  15. Earliest evidence of pollution by heavy metals in archaeological sites

    NASA Astrophysics Data System (ADS)

    Monge, Guadalupe; Jimenez-Espejo, Francisco J.; García-Alix, Antonio; Martínez-Ruiz, Francisca; Mattielli, Nadine; Finlayson, Clive; Ohkouchi, Naohiko; Sánchez, Miguel Cortés; de Castro, Jose María Bermúdez; Blasco, Ruth; Rosell, Jordi; Carrión, José; Rodríguez-Vidal, Joaquín; Finlayson, Geraldine

    2015-09-01

    Homo species were exposed to a new biogeochemical environment when they began to occupy caves. Here we report the first evidence of palaeopollution through geochemical analyses of heavy metals in four renowned archaeological caves of the Iberian Peninsula spanning the last million years of human evolution. Heavy metal contents reached high values due to natural (guano deposition) and anthropogenic factors (e.g. combustion) in restricted cave environments. The earliest anthropogenic pollution evidence is related to Neanderthal hearths from Gorham's Cave (Gibraltar), being one of the first milestones in the so-called “Anthropocene”. According to its heavy metal concentration, these sediments meet the present-day standards of “contaminated soil”. Together with the former, the Gibraltar Vanguard Cave, shows Zn and Cu pollution ubiquitous across highly anthropic levels pointing to these elements as potential proxies for human activities. Pb concentrations in Magdalenian and Bronze age levels at El Pirulejo site can be similarly interpreted. Despite these high pollution levels, the contaminated soils might not have posed a major threat to Homo populations. Altogether, the data presented here indicate a long-term exposure of Homo to these elements, via fires, fumes and their ashes, which could have played certain role in environmental-pollution tolerance, a hitherto neglected influence.

  16. Earliest evidence of pollution by heavy metals in archaeological sites.

    PubMed

    Monge, Guadalupe; Jimenez-Espejo, Francisco J; García-Alix, Antonio; Martínez-Ruiz, Francisca; Mattielli, Nadine; Finlayson, Clive; Ohkouchi, Naohiko; Sánchez, Miguel Cortés; de Castro, Jose María Bermúdez; Blasco, Ruth; Rosell, Jordi; Carrión, José; Rodríguez-Vidal, Joaquín; Finlayson, Geraldine

    2015-01-01

    Homo species were exposed to a new biogeochemical environment when they began to occupy caves. Here we report the first evidence of palaeopollution through geochemical analyses of heavy metals in four renowned archaeological caves of the Iberian Peninsula spanning the last million years of human evolution. Heavy metal contents reached high values due to natural (guano deposition) and anthropogenic factors (e.g. combustion) in restricted cave environments. The earliest anthropogenic pollution evidence is related to Neanderthal hearths from Gorham's Cave (Gibraltar), being one of the first milestones in the so-called "Anthropocene". According to its heavy metal concentration, these sediments meet the present-day standards of "contaminated soil". Together with the former, the Gibraltar Vanguard Cave, shows Zn and Cu pollution ubiquitous across highly anthropic levels pointing to these elements as potential proxies for human activities. Pb concentrations in Magdalenian and Bronze age levels at El Pirulejo site can be similarly interpreted. Despite these high pollution levels, the contaminated soils might not have posed a major threat to Homo populations. Altogether, the data presented here indicate a long-term exposure of Homo to these elements, via fires, fumes and their ashes, which could have played certain role in environmental-pollution tolerance, a hitherto neglected influence. PMID:26388184

  17. Adsorption of two gas molecules at a single metal site in a metal-organic framework.

    PubMed

    Runčevski, Tomče; Kapelewski, Matthew T; Torres-Gavosto, Rodolfo M; Tarver, Jacob D; Brown, Craig M; Long, Jeffrey R

    2016-07-01

    One strategy to markedly increase the gas storage capacity of metal-organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules-specifically hydrogen, methane, or carbon dioxide. PMID:27284590

  18. Metalloprotein-inhibitor binding: Human carbonic anhydrase II as a model for probing metal-ligand interactions in a metalloprotein active site

    PubMed Central

    Martin, David P.; Hann, Zachary S.; Cohen, Seth M.

    2013-01-01

    An ever increasing number of metalloproteins are being discovered that play essential roles in physiological processes. Inhibitors of these proteins have significant potential for the treatment of human disease, but clinical success of these compounds has been limited. Herein, Zn(II)-dependent metalloprotein inhibitors in clinical use are reviewed, and the potential for using novel metal-binding groups (MBGs) in the design of these inhibitors is discussed. By using human carbonic anhydrase II (hCAII) as a model system, the nuances of MBG-metal interactions in the context of a protein environment can be probed. Understanding how metal coordination influences inhibitor binding may help in the design new therapeutics targeting metalloproteins. PMID:23706138

  19. METAL ATTENUATION PROCESSES AT MINING SITES

    EPA Science Inventory

    The purpose of this Issue Paper is to provide scientists and engineers responsible for assessing remediation technologies with background information on MNA processes at mining-impacted sites. The global magnitude of the acid drainage problem is clear evidence that in most cases...

  20. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  1. Effect of the piperazine unit and metal-binding site position on the solubility and anti-proliferative activity of ruthenium(II)- and osmium(II)- arene complexes of isomeric indolo[3,2-c]quinoline-piperazine hybrids.

    PubMed

    Filak, Lukas K; Kalinowski, Danuta S; Bauer, Theresa J; Richardson, Des R; Arion, Vladimir B

    2014-07-01

    In this study, the indoloquinoline backbone and piperazine were combined to prepare indoloquinoline-piperazine hybrids and their ruthenium- and osmium-arene complexes in an effort to generate novel antitumor agents with improved aqueous solubility. In addition, the position of the metal-binding unit was varied, and the effect of these structural alterations on the aqueous solubility and antiproliferative activity of their ruthenium- and osmium-arene complexes was studied. The indoloquinoline-piperazine hybrids L(1-3) were prepared in situ and isolated as six ruthenium and osmium complexes [(η(6)-p-cymene)M(L(1-3))Cl]Cl, where L(1) = 6-(4-methylpiperazin-1-yl)-N-(pyridin-2-yl-methylene)-11H-indolo[3,2-c]quinolin-2-N-amine, M = Ru ([1a]Cl), Os ([1b]Cl), L(2) = 6-(4-methylpiperazin-1-yl)-N-(pyridin-2-yl-methylene)-11H-indolo[3,2-c]quinolin-4-N-amine, M = Ru ([2a]Cl), Os ([2b]Cl), L(3) = 6-(4-methylpiperazin-1-yl)-N-(pyridin-2-yl-methylene)-11H-indolo[3,2-c]quinolin-8-N-amine, M = Ru ([3a]Cl), Os ([3b]Cl). The compounds were characterized by elemental analysis, one- and two-dimensional NMR spectroscopy, ESI mass spectrometry, IR and UV-vis spectroscopy, and single-crystal X-ray diffraction. The antiproliferative activity of the isomeric ruthenium and osmium complexes [1a,b]Cl-[3a,b]Cl was examined in vitro and showed the importance of the position of the metal-binding site for their cytotoxicity. Those complexes containing the metal-binding site located at the position 4 of the indoloquinoline scaffold ([2a]Cl and [2b]Cl) demonstrated the most potent antiproliferative activity. The results provide important insight into the structure-activity relationships of ruthenium- and osmium-arene complexes with indoloquinoline-piperazine hybrid ligands. These studies can be further utilized for the design and development of more potent chemotherapeutic agents. PMID:24927493

  2. Effect of the Piperazine Unit and Metal-Binding Site Position on the Solubility and Anti-Proliferative Activity of Ruthenium(II)- and Osmium(II)- Arene Complexes of Isomeric Indolo[3,2-c]quinoline—Piperazine Hybrids

    PubMed Central

    2014-01-01

    In this study, the indoloquinoline backbone and piperazine were combined to prepare indoloquinoline–piperazine hybrids and their ruthenium- and osmium-arene complexes in an effort to generate novel antitumor agents with improved aqueous solubility. In addition, the position of the metal-binding unit was varied, and the effect of these structural alterations on the aqueous solubility and antiproliferative activity of their ruthenium- and osmium-arene complexes was studied. The indoloquinoline–piperazine hybrids L1–3 were prepared in situ and isolated as six ruthenium and osmium complexes [(η6-p-cymene)M(L1–3)Cl]Cl, where L1 = 6-(4-methylpiperazin-1-yl)-N-(pyridin-2-yl-methylene)-11H-indolo[3,2-c]quinolin-2-N-amine, M = Ru ([1a]Cl), Os ([1b]Cl), L2 = 6-(4-methylpiperazin-1-yl)-N-(pyridin-2-yl-methylene)-11H-indolo[3,2-c]quinolin-4-N-amine, M = Ru ([2a]Cl), Os ([2b]Cl), L3 = 6-(4-methylpiperazin-1-yl)-N-(pyridin-2-yl-methylene)-11H-indolo[3,2-c]quinolin-8-N-amine, M = Ru ([3a]Cl), Os ([3b]Cl). The compounds were characterized by elemental analysis, one- and two-dimensional NMR spectroscopy, ESI mass spectrometry, IR and UV–vis spectroscopy, and single-crystal X-ray diffraction. The antiproliferative activity of the isomeric ruthenium and osmium complexes [1a,b]Cl–[3a,b]Cl was examined in vitro and showed the importance of the position of the metal-binding site for their cytotoxicity. Those complexes containing the metal-binding site located at the position 4 of the indoloquinoline scaffold ([2a]Cl and [2b]Cl) demonstrated the most potent antiproliferative activity. The results provide important insight into the structure–activity relationships of ruthenium- and osmium-arene complexes with indoloquinoline–piperazine hybrid ligands. These studies can be further utilized for the design and development of more potent chemotherapeutic agents. PMID:24927493

  3. Evolution of Metal(Loid) Binding Sites in Transcriptional Regulators

    SciTech Connect

    Ordonez, E.; Thiyagarajan, S.; Cook, J.D.; Stemmler, T.L.; Gil, J.A.; Mateos, L.M.; Rosen, B.P.

    2009-05-22

    Expression of the genes for resistance to heavy metals and metalloids is transcriptionally regulated by the toxic ions themselves. Members of the ArsR/SmtB family of small metalloregulatory proteins respond to transition metals, heavy metals, and metalloids, including As(III), Sb(III), Cd(II), Pb(II), Zn(II), Co(II), and Ni(II). These homodimeric repressors bind to DNA in the absence of inducing metal(loid) ion and dissociate from the DNA when inducer is bound. The regulatory sites are often three- or four-coordinate metal binding sites composed of cysteine thiolates. Surprisingly, in two different As(III)-responsive regulators, the metalloid binding sites were in different locations in the repressor, and the Cd(II) binding sites were in two different locations in two Cd(II)-responsive regulators. We hypothesize that ArsR/SmtB repressors have a common backbone structure, that of a winged helix DNA-binding protein, but have considerable plasticity in the location of inducer binding sites. Here we show that an As(III)-responsive member of the family, CgArsR1 from Corynebacterium glutamicum, binds As(III) to a cysteine triad composed of Cys{sup 15}, Cys{sup 16}, and Cys{sup 55}. This binding site is clearly unrelated to the binding sites of other characterized ArsR/SmtB family members. This is consistent with our hypothesis that metal(loid) binding sites in DNA binding proteins evolve convergently in response to persistent environmental pressures.

  4. Laboratory Study of Polychlorinated Biphenyl (PCB) Contamination and Mitigation in Buildings -- Part 4. Evaluation of the Activated Metal Treatment System (AMTS) for On-site Destruction of PCBs

    EPA Science Inventory

    This is the fourth, also the last, report of the report series entitled “Laboratory Study of Polychlorinated Biphenyl (PCB) Contamination and Mitigation in Buildings.” This report evaluates the performance of an on-site PCB destruction method, known as the AMTS method, developed ...

  5. Laboratory Study of Polychlorinated Biphenyl Contamination and Mitigation in Buildings -- Part 4. Evaluation of the Activated Metal Treatment System (AMTS) for On-site Destruction of PCBs

    EPA Science Inventory

    This is the fourth, also the last, report of the report series entitled “Laboratory Study of Polychlorinated Biphenyl (PCB) Contamination and Mitigation in Buildings.” This report evaluates the performance of an on-site PCB destruction method, known as the AMTS method...

  6. Antimicrobial activity of the metals and metal oxide nanoparticles.

    PubMed

    Dizaj, Solmaz Maleki; Lotfipour, Farzaneh; Barzegar-Jalali, Mohammad; Zarrintan, Mohammad Hossein; Adibkia, Khosro

    2014-11-01

    The ever increasing resistance of pathogens towards antibiotics has caused serious health problems in the recent years. It has been shown that by combining modern technologies such as nanotechnology and material science with intrinsic antimicrobial activity of the metals, novel applications for these substances could be identified. According to the reports, metal and metal oxide nanoparticles represent a group of materials which were investigated in respect to their antimicrobial effects. In the present review, we focused on the recent research works concerning antimicrobial activity of metal and metal oxide nanoparticles together with their mechanism of action. Reviewed literature indicated that the particle size was the essential parameter which determined the antimicrobial effectiveness of the metal nanoparticles. Combination therapy with the metal nanoparticles might be one of the possible strategies to overcome the current bacterial resistance to the antibacterial agents. However, further studies should be performed to minimize the toxicity of metal and metal oxide nanoparticles to apply as proper alternatives for antibiotics and disinfectants especially in biomedical applications. PMID:25280707

  7. Toward "metalloMOFzymes": Metal-Organic Frameworks with Single-Site Metal Catalysts for Small-Molecule Transformations.

    PubMed

    Cohen, Seth M; Zhang, Zhenjie; Boissonnault, Jake A

    2016-08-01

    Metal-organic frameworks (MOFs) are being increasingly studied as scaffolds and supports for catalysis. The solid-state structures of MOFs, combined with their high porosity, suggest that MOFs may possess advantages shared by both heterogeneous and homogeneous catalysts, with few of the shortcomings of either. Herein, efforts to create single-site catalytic metal centers appended to the organic ligand struts of MOFs will be discussed. Reactions important for advanced energy applications, such as H2 production and CO2 reduction, will be highlighted. Examining how these active sites can be introduced, their performance, and their existing limitations should provide direction for design of the next generation of MOF-based catalysts for energy-relevant, small-molecule transformations. Finally, the introduction of second-sphere interactions (e.g., hydrogen bonding via squaramide groups) as a possible route to enhancing the activity of these metal centers is reported. PMID:27231968

  8. Evaluating three trace metal contaminated sites: a field and laboratory investigation.

    PubMed

    Murray, P; Ge, Y; Hendershot, W H

    2000-01-01

    Selecting guidelines to evaluate elevated metals in urban brownfields is hindered by the lack of information for these sites on ecosystem structure and function. A study was performed to compare three trace metal-contaminated sites in the metropolitan Montreal area. The goal was to obtain an idea of the organisms that may be present on urban brownfields and to measure if elevated metals alter the presence and activity of the indigenous biota. Field and laboratory studies were conducted using simple methodologies to determine the extent to which microbial activity affected by trace metal content, to assess diversity of plant and soil invertebrate communities and to measure phytoaccumulation of trace metals. It was found that microbial activity, as measured by substrate-induced respiration (SIR) and nitrification, was not affected by the levels of soil Cd, Cu, Ni, Pb and Zn recorded on the sites. Seven of the 12 invertebrate groups collected were sampled on soils with similar Cd, Cu, Ni, Pb and Zn concentrations. Diversity of plant species increased as a function of the length of time the sites had been inactive. Levels of metals in plant tissue were influenced by soil characteristics and not by total soil Cd, Cu, Ni, Pb and Zn. PMID:15093016

  9. Divalent metal activation of a GH43 β-xylosidase.

    PubMed

    Lee, Charles C; Braker, Jay D; Grigorescu, Arabela A; Wagschal, Kurt; Jordan, Douglas B

    2013-02-01

    Depolymerization of xylan, a major fraction of lignocellulosic biomass, releases xylose which can be converted into transportation fuels and chemical feedstocks. A requisite enzyme for the breakdown of xylan is β-xylosidase. A gene encoding the 324-amino acid β-xylosidase, RS223-BX, was cloned from an anaerobic mixed microbial culture. This glycoside hydrolase belongs to family 43. Unlike other GH43 enzymes, RS223-BX can be strongly activated by exogenously supplied Ca(2+), Co(2+), Fe(2+), Mg(2+), Mn(2+) and Ni(2+) (e.g., 28-fold by Mg(2+)) and it is inhibited by Cu(2+) or Zn(2+). Sedimentation equilibrium centrifugation experiments indicated that the divalent metal cations mediate multimerization of the enzyme from a dimeric to a tetrameric state, which have equal catalytic activity on an active-site basis. Compared to the determined active sites of other GH43 β-xylosidases, the predicted active site of RS223-BX contains two additional amino acids with carboxylated side chains that provide potential sites for divalent metal cations to reside. Thus, the divalent metal cations likely occupy the active site and participate in the catalytic mechanism. RS223-BX accepts as substrate xylobiose, arabinobiose, 4-nitrophenyl-β-D-xylopyranoside, and 4-nitrophenyl-α-L-arabinofuranoside. Additionally, the enzyme has good pH and temperature stabilities and a large K(i) for D-glucose (1.3 M), favorable properties for performance in saccharification reactors. PMID:23273276

  10. GUIDE TO SITE AND SOIL DESCRIPTION FOR HAZARDOUS WASTE SITE CHARACTERIZATION VOLUME 1: METALS

    EPA Science Inventory

    This guide is intended to assist field personnel who must identify, describe, and interpret site and soil characteristics of hazardous waste sites where metals contamination is suspected or known. he approach presented, including the knowledge frames of an expert system, will be ...

  11. High metal reactivity and environmental risks at a site contaminated by glass waste.

    PubMed

    Augustsson, A; Åström, M; Bergbäck, B; Elert, M; Höglund, L O; Kleja, D B

    2016-07-01

    This study addresses the reactivity and risks of metals (Ba, Cd, Co, Cr, Cu, Ni, Pb, Zn, As and Sb) at a Swedish site with large glass waste deposits. Old glassworks sites typically have high total metal concentrations, but as the metals are mainly bound within the glass waste and considered relatively inert, environmental investigations at these kinds of sites are limited. In this study, soil and landfill samples were subjected to a sequential chemical extraction procedure. Data from batch leaching tests and groundwater upstream and downstream of the waste deposits were also interpreted. The sequential extraction revealed that metals in <2 mm soil/waste samples were largely associated with geochemically active fractions, indicating that metals are released from pristine glass and subsequently largely retained in the surrounding soil and/or on secondary mineral coatings on fine glass particles. From the approximately 12,000 m(3) of coarse glass waste at the site, almost 4000 kg of Pb is estimated to have been lost through corrosion, which, however, corresponds to only a small portion of the total amount of Pb in the waste. Metal sorption within the waste deposits or in underlying soil layers is supported by fairly low metal concentrations in groundwater. However, elevated concentrations in downstream groundwater and in leachates of batch leaching tests were observed for several metals, indicating on-going leaching. Taken together, the high metal concentrations in geochemically active forms and the high amounts of as yet uncorroded metal-rich glass, indicate considerable risks to human health and the environment. PMID:27077538

  12. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1990-10-01

    DOE Order 5820.2A requires that low-level waste (LLW) disposal sites active on or after September 1988 and all transuranic (TRU) waste storage sites be monitored periodically to assure that radioactive contamination does not escape from the waste sites and pose a threat to the public or to the environment. This plan describes such a monitoring program for the active LLW disposal sites in SWSA 6 and the TRU waste storage sites in SWSA 5 North. 14 refs., 8 figs.

  13. Low resolution X-ray structure of γ-glutamyltranspeptidase from Bacillus licheniformis: opened active site cleft and a cluster of acid residues potentially involved in the recognition of a metal ion.

    PubMed

    Lin, Long-Liu; Chen, Yi-Yu; Chi, Meng-Chun; Merlino, Antonello

    2014-09-01

    γ-Glutamyltranspeptidases (γ-GTs) cleave the γ-glutamyl amide bond of glutathione and transfer the released γ-glutamyl group to water (hydrolysis) or acceptor amino acids (transpeptidation). These ubiquitous enzymes play a key role in the biosynthesis and degradation of glutathione, and in xenobiotic detoxification. Here we report the 3Å resolution crystal structure of Bacillus licheniformis γ-GT (BlGT) and that of its complex with l-Glu. X-ray structures confirm that BlGT belongs to the N-terminal nucleophilic hydrolase superfamily and reveal that the protein possesses an opened active site cleft similar to that reported for the homologous enzyme from Bacillus subtilis, but different from those observed for human γ-GT and for γ-GTs from other microorganisms. Data suggest that the binding of l-Glu induces a reordering of the C-terminal tail of BlGT large subunit and allow the identification of a cluster of acid residues that are potentially involved in the recognition of a metal ion. The role of these residues on the conformational stability of BlGT has been studied by characterizing the autoprocessing, enzymatic activity, chemical and thermal denaturation of four new Ala single mutants. The results show that replacement of Asp568 with an Ala affects both the autoprocessing and structural stability of the protein. PMID:24780583

  14. Small mammal-heavy metal concentrations from mined and control sites

    USGS Publications Warehouse

    Smith, G.J.; Rongstad, O.J.

    1982-01-01

    Total body concentrations of zinc, copper, cadmium, lead, nickel, mercury and arsenic were determined for Peromyscus maniculatus and Microtus pennsylvanicus from an active zinc-copper mine near Timmins, Ontario, Canada, and a proposed zinc-copper mine near Crandon, Wisconsin, USA. Metal concentrations were evaluated with respect to area, species, sex and age groups. Metal concentrations in Peromyscus from the proposed mine site were not different from those collected in a third area where no mine or deposit exists. This is probably due to the 30 m of glacial material over the proposed mine site deposit. A statistical interaction between area, species, sex and age was observed for zinc and copper concentrations in small mammals we examined. Peromyscus from the mine site had consistently higher metal concentrations than Peromyscus from the control site. Greater total body cadmium and lead concentrations in adult?compared with juvenile?Peromyscus collected at the mine site suggests age-dependent accumulation of these toxic metals. Microtus did not exhibit this age-related response, and responded to other environmental metals more erratically and to a lesser degree. Differences in the response of these two species to environmental metal exposure may be due to differences in food habits. Nickel, mercury and arsenic concentrations in small mammals from the mine site were not different from controls. Heavy metal concentrations are also presented for Sorex cinereus, Blarina brevicauda and Zapus hudsonicus without respect to age and sex cohorts. Peromyscus may be a potentially important species for the monitoring of heavy metal pollution.

  15. Highly active oxygen reduction non-platinum group metal electrocatalyst without direct metal-nitrogen coordination

    NASA Astrophysics Data System (ADS)

    Strickland, Kara; Miner, Elise; Jia, Qingying; Tylus, Urszula; Ramaswamy, Nagappan; Liang, Wentao; Sougrati, Moulay-Tahar; Jaouen, Frédéric; Mukerjee, Sanjeev

    2015-06-01

    Replacement of noble metals in catalysts for cathodic oxygen reduction reaction with transition metals mostly create active sites based on a composite of nitrogen-coordinated transition metal in close concert with non-nitrogen-coordinated carbon-embedded metal atom clusters. Here we report a non-platinum group metal electrocatalyst with an active site devoid of any direct nitrogen coordination to iron that outperforms the benchmark platinum-based catalyst in alkaline media and is comparable to its best contemporaries in acidic media. In situ X-ray absorption spectroscopy in conjunction with ex situ microscopy clearly shows nitrided carbon fibres with embedded iron particles that are not directly involved in the oxygen reduction pathway. Instead, the reaction occurs primarily on the carbon-nitrogen structure in the outer skin of the nitrided carbon fibres. Implications include the potential of creating greater active site density and the potential elimination of any Fenton-type process involving exposed iron ions culminating in peroxide initiated free-radical formation.

  16. Heavy metal contamination of soil and water in the vicinity of an abandoned e-waste recycling site: implications for dissemination of heavy metals.

    PubMed

    Wu, Qihang; Leung, Jonathan Y S; Geng, Xinhua; Chen, Shejun; Huang, Xuexia; Li, Haiyan; Huang, Zhuying; Zhu, Libin; Chen, Jiahao; Lu, Yayin

    2015-02-15

    Illegal e-waste recycling activity has caused heavy metal pollution in many developing countries, including China. In recent years, the Chinese government has strengthened enforcement to impede such activity; however, the heavy metals remaining in the abandoned e-waste recycling site can still pose ecological risk. The present study aimed to investigate the concentrations of heavy metals in soil and water in the vicinity of an abandoned e-waste recycling site in Longtang, South China. Results showed that the surface soil of the former burning and acid-leaching sites was still heavily contaminated with Cd (>0.39 mg kg(-1)) and Cu (>1981 mg kg(-1)), which exceeded their respective guideline levels. The concentration of heavy metals generally decreased with depth in both burning site and paddy field, which is related to the elevated pH and reduced TOM along the depth gradient. The pond water was seriously acidified and contaminated with heavy metals, while the well water was slightly contaminated since heavy metals were mostly retained in the surface soil. The use of pond water for irrigation resulted in considerable heavy metal contamination in the paddy soil. Compared with previous studies, the reduced heavy metal concentrations in the surface soil imply that heavy metals were transported to the other areas, such as pond. Therefore, immediate remediation of the contaminated soil and water is necessary to prevent dissemination of heavy metals and potential ecological disaster. PMID:25460954

  17. Transition metals activate TFEB in overexpressing cells

    PubMed Central

    Peña, Karina A.; Kiselyov, Kirill

    2015-01-01

    Transition metal toxicity is an important factor in the pathogenesis of numerous human disorders, including neurodegenerative diseases. Lysosomes have emerged as important factors in transition metal toxicity because they handle transition metals via endocytosis, autophagy, absorption from the cytoplasm and exocytosis. Transcription factor EB (TFEB) regulates lysosomal biogenesis and the expression of lysosomal proteins in response to lysosomal and/or metabolic stresses. Since transition metals cause lysosomal dysfunction, we proposed that TFEB may be activated to drive gene expression in response to transition metal exposure and that such activation may influence transition metal toxicity. We found that transition metals copper (Cu) and iron (Fe) activate recombinant TFEB and stimulate the expression of TFEB-dependent genes in TFEB-overexpressing cells. In cells that show robust lysosomal exocytosis, TFEB was cytoprotective at moderate levels of Cu exposure, decreasing oxidative stress as reported by the expression of heme oxygenase-1 (HMOX1) gene. However, at high levels of Cu exposure, particularly in cells with low levels of lysosomal exocytosis, activation of overexpressed TFEB was toxic, increasing oxidative stress and mitochondrial damage. Based on these data, we conclude that TFEB-driven gene network is a component of the cellular response to transition metals. These data suggest limitations and disadvantages of TFEB overexpression as a therapeutic approach. PMID:26251447

  18. Functional Identification of Catalytic Metal Ion Binding Sites within RNA

    PubMed Central

    2005-01-01

    The viability of living systems depends inextricably on enzymes that catalyze phosphoryl transfer reactions. For many enzymes in this class, including several ribozymes, divalent metal ions serve as obligate cofactors. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). In the Tetrahymena group I intron, previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified three metal ions (MA, MB, and MC) that make five interactions with the ribozyme substrates in the reaction's transition state. Here, we combine substrate atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to develop a powerful, general strategy for defining the ligands of catalytic metal ions within RNA. In applying this strategy to the Tetrahymena group I intron, we have identified the pro-SP phosphoryl oxygen at nucleotide C262 as a ribozyme ligand for MC. Our findings establish a direct connection between the ribozyme core and the functionally defined model of the chemical transition state, thereby extending the known set of transition-state interactions and providing information critical for the application of the recent group I intron crystallographic structures to the understanding of catalysis. PMID:16092891

  19. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  20. MeRNA: a Database of Metal Ion Binding Sites in RNAStructures

    SciTech Connect

    Stefan, Liliana R.; Zhang, Rui; Levitan, Aaron G.; Hendrix, DonnaF.; Brenner, Steven E.; Holbrook, Stephen R.

    2005-10-05

    Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering.

  1. Exoemissive noise activity of different metallic materials

    NASA Astrophysics Data System (ADS)

    Bichevin, V.; Käämbre, H.; Sammelselg, V.; Kelle, H.; Asari, E.; Saks, O.

    1996-11-01

    A method is proposed for testing the exoemission activity of different metals, used as materials in high sensitivity electrometry (attoammetry). The presented test results allow us to select materials with weaker exoelectron spurious currents.

  2. Adsorption of heavy metals on sonicated activated sludge.

    PubMed

    Commenges-Bernole, N; Marguerie, J

    2009-01-01

    The objective of this work is to assess heavy metals fixation capacity on sonicated activated sludge. Ultrasonic treatment of sludge has lead to its desintegration and changes physico-chemical characteristics such as soluble chemical oxygen demand, proteins or particle size distribution. This study has shown that these modifications have improved significantly the capacity of sludge to fix heavy metals. Indeed, after a sonication of 15 min and storage of three days after irradiation, the equilibrium capacity is increased about 45%. The restructuration of sludge during the storage seems to increase the accessibility to active binding sites. PMID:18599337

  3. Educational Activity Sites for High School Students

    ERIC Educational Resources Information Center

    Troutner, Joanne

    2005-01-01

    Finding quality Internet resources for high school students is a continuing challenge. Several high-quality web sites are presented for educators and students. These sites offer activities to learn how an art conservator looks at paintings, create a newspaper, research and develop an end product, build geometry and physics skills, explore science…

  4. Aquatic snails from mining sites have evolved to detect and avoid heavy metals.

    PubMed

    Lefcort, H; Abbott, D P; Cleary, D A; Howell, E; Keller, N C; Smith, M M

    2004-05-01

    Toxicants in polluted environments are often patchily distributed. Hence, rather than being passive absorbers of pollution, some organisms have evolved the ability to detect and avoid toxicants. We studied the avoidance behavior of Physella columbiana, an aquatic pulmonate snail, in a pond that has been polluted with heavy metals for more than 120 years. Populations of this snail are rare at reference sites and are only robust at heavy-metal-polluted sites. We hypothesized that the snails are able to persist because they have evolved the ability to minimize their exposure to metals by actively avoiding metals in their environment. Using a Y-maze flow tank, we tested the avoidance behavior of snails to heavy-metal-polluted sediments and single-metal solutions of cadmium, zinc, or lead. We also tested the avoidance behaviors of the snails' laboratory-reared offspring raised in nonpolluted conditions. In addition, we tested the avoidance behavior of a small population of snails from a reference pond. Although all the snails we tested were able to detect low concentrations of heavy metals, we found that snails from the polluted site were the most sensitive, that their offspring were somewhat less sensitive, and that snails from the reference site were the least sensitive. This suggests that the ability of polluted-site snails to avoid heavy metals is both genetic and environmental. The concentrations of metals avoided by the snails from the polluted site were below the levels found at hot spots within their natal pond. The snails may be able to persist at this site because they decrease their exposure by moving to less-polluted sections of the pond. One application of our findings is the use of aquatic snails and our Y-maze design as an inexpensive pollution detector. Environmental pollutants such as lead, zinc, and arsenic are a problem throughout the world. People in underdeveloped countries often lack sophisticated pollution detection devices. We have developed a

  5. Why Is There an “Inert” Metal Center in the Active Site of Nitrile Hydratase? Reactivity and Ligand Dissociation from a Five-Coordinate Co(III) Nitrile Hydratase Model

    PubMed Central

    Shearer, Jason; Kung, Irene Y.; Lovell, Scott; Kaminsky, Werner; Kovacs, Julie A.

    2015-01-01

    To determine how a substitutionally inert metal can play a catalytic role in the metalloenzyme nitrile hydratase (NHase), a reactive five-coordinate CoIII thiolate complex ([CoIII(S2Me2N3(Pr,Pr))](PF6) (1)) that resembles the active site of cobalt containing nitrile hydratase (Co NHase) was prepared. This was screened for reactivity, by using low-temperature electronic absorption spectroscopy, toward a number of biologically relevant “substrates”. It was determined 1 will react with azide, thiocyanate, and ammonia, but is unreactive toward nitriles, NO, and butyrate. Substrate-bound 1 has similar spectroscopic and structural properties as [CoIII(ADIT2)](PF6) (2). Complex 2 is a six-coordinate CoIII complex containing cis-thiolates and imine nitrogens, and has properties similar to the cobalt center of Co NHase. Substrate binding to 1 is reversible and temperature-dependent, allowing for the determination of the thermodynamic parameters of azide and thiocyanate binding and the rates of ligand dissociation. Azide and thiocyanate bind trans to a thiolate, and with similar entropies and enthalpies (thiocyanate: ΔH = −7.5 ± 1.1 kcal/mol, ΔS = −17.2 ± 3.2 eu; azide: ΔH = −6.5 ± 1.0 kcal/mol, ΔS = −12.6 ± 2.4 eu). The rates of azide and thiocyanate displacement from the metal center are also comparable to one another (kd = (7.22 ± 0.04) × 10−1 s−1 for thiocyanate and kd = 2.14 ± 0.50) × 10−2 s−1 for azide), and are considerably faster than one would expect for a low-spin d6 six-coordinate CoIII complex. These rates are comparable to those of an analogous Fe(III) complex, demonstrating that Co(III) and Fe(III) react at comparable rates when in this ligand environment. This study therefore indicates that ligand displacement from a low-spin CoIII center in a ligand environment that resembles NHase is not prohibitivly slow so as to disallow catalytic action in nonredox active cobalt metalloenzymes. PMID:11456548

  6. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  7. Twelve Year Study of Underground Corrosion of Activated Metals

    SciTech Connect

    M. Kay Adler Flitton; Timothy S. Yoder

    2012-03-01

    The subsurface radioactive disposal facility located at the U.S. Department of Energy’s Idaho site contains neutron-activated metals from non-fuel nuclear-reactor-core components. A long-term corrosion study is being conducted to obtain site-specific corrosion rates to support efforts to more accurately estimate the transfer of activated elements in an arid vadose zone environment. The study uses non-radioactive metal coupons representing the prominent neutron-activated material buried at the disposal location, namely, two types of stainless steels, welded stainless steel, welded nickel-chromium steel alloy, zirconium alloy, beryllium, and aluminum. Additionally, carbon steel (the material used in cask disposal liners and other disposal containers) and duplex stainless steel (high-integrity containers) are also included in the study. This paper briefly describes the test program and presents the corrosion rate results through twelve years of underground exposure.

  8. Microbial characterization of a radionuclide- and metal-contaminated waste site

    SciTech Connect

    Bolton, H. Jr.; Lumppio, H.L.; Ainsworth, C.C.; Plymale, A.E.

    1993-04-01

    The operation of nuclear processing facilities and defense-related nuclear activities has resulted in contamination of near-surface and deep-subsurface sediments with both radionuclides and metals. The presence of mixed inorganic contaminants may result in undetectable microbial populations or microbial populations that are different from those present in uncontaminated sediments. To determine the impact of mixed radionuclide and metal contaminants on sediment microbial communities, we sampled a processing pond that was used from 1948 to 1975 for the disposal of radioactive and metal-contaminated wastewaters from laboratories and nuclear fuel fabrication facilities on the Hanford Site in Washington State. Because the Hanford Site is located in a semiarid environment with average rainfall of 159 mm/year, the pond dried and a settling basin remained after wastewater input into the pond ceased in 1975. This processing pond basin offered a unique opportunity to obtain near-surface sediments that had been contaminated with both radionuclides and metals for several decades. Our objectives were to determine the viable populations of microorganisms in the sediments and to test several hypotheses about how the addition of both radionuclides and metals influenced the microbial ecology of the sediments. Our first hypothesis was that viable populations of microorganisms would be lower in the more contaminated sediments. Second, we expected that long-term metal exposure would result in enhanced metal resistance. Finally, we hypothesized that microorganisms from the most radioactive sediments should have had enhanced radiation resistance.

  9. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  10. Heavy metals and adsorbents effects on activated sludge microorganisms.

    PubMed

    Ong, S A; Lim, P E; Seng, C E

    2004-01-01

    The sorption of Cu(II) and Cd(II) from synthetic solution by powdered activated carbon (PAC), biomass, rice husk (RH) and activated rice husk (ARH) were investigate under batch conditions. After activated by concentrated nitric acid for 15 hours at 60-65 degrees C, the adsorption capacity for RH was increased. The adsorbents arranged in the increasing order of adsorption capacities to the Langmuir Q degree parameter were biomass > PAC > ARH > RH. The addition of adsorbents in base mix solution had increased the specific oxygen uptake rate (SOUR) activated sludge microorganisms with and without the presence of metals. The increased of SOUR were due to the ability of PAC and RH in reducing the inhibitory effect of metals on microorganisms and provide a reaction site between activated sludge microorganisms and substrates. PMID:15141467

  11. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  12. Public health consequences of heavy metals in dump sites.

    PubMed Central

    Clarkson, T W; Weiss, B; Cox, C

    1983-01-01

    Metals differ from most synthetic organic chemicals in that their clinical manifestations are well known and methods for their measurement in the body are generally well established. Since metals are ubiquitous, special care should be taken to identify the source, whether dump site or not. Isotopic ratios may be used for lead. Time of exposure may be highly variable so estimates will be necessary of integrated "dose-commitment." Transmission to man will follow many pathways. The contamination of children's hands and clothing by dust may be an important route. Because effects are so different, the chemical species (e.g., organic versus inorganic forms) of each metal must be identified. Exposure assessment requires identification of suitable indicator media, usually blood in the case of lead, urine with cadmium and inorganic mercury, and blood or hair with regard to methylmercury. Human head hair may have considerable potential, as it may provide a recapitulation of past exposures. The first health complaints associated with most metals are usually nonspecific. The complex social, political, and legal issues strongly indicate the need for objective tests for health effects. Most important is the identification and measurement of the critical effect, i.e., an effect that alerts the public health authorities that further exposure should cease. For example, in the case of lead, the critical effect is hematologic; with cadmium it is the presence in urine of abnormally high concentration of small molecular weight protein; and with mercury no early objective test has yet been devised. PMID:6825626

  13. Metallic Magnetic Calorimeters for Absolute Activity Measurement

    NASA Astrophysics Data System (ADS)

    Loidl, M.; Leblanc, E.; Rodrigues, M.; Bouchard, J.; Censier, B.; Branger, T.; Lacour, D.

    2008-05-01

    We present a prototype of metallic magnetic calorimeters that we are developing for absolute activity measurements of low energy emitting radionuclides. We give a detailed description of the realization of the prototype, containing an 55Fe source inside the detector absorber. We present the analysis of first data taken with this detector and compare the result of activity measurement with liquid scintillation counting. We also propose some ways for reducing the uncertainty on the activity determination with this new technique.

  14. The Design, Synthesis, and Characterization of Open Sites on Metal Clusters

    NASA Astrophysics Data System (ADS)

    Nigra, Michael Mark

    Coordinatively unsaturated corner and edge atoms have been hypothesized to have the highest activity of sites responsible for many catalytic reactions on a metal surface. Recent studies have validated this hypothesis in varied reaction systems. However, quantification of different types of coordinatively unsaturated sites, and elucidation of their individual catalytic rates has remained a largely unresolved challenge when understanding catalysis on metal surfaces. Yet such structure-function knowledge would be invaluable to the design of more active and selective metal-surface catalysts in the future. I investigated the catalytic contributions of undercoordinated sites such as corner and edge atoms are investigated in a model reaction system using organic ligands bound to the gold nanoparticle surface. The catalyst consisted of 4 nm gold nanoparticles on a metal oxide support, using resazurin to resorufin as a model reaction system. My results demonstrate that in this system, corner atom sites are the most undercoordinated sites, and are over an order of magnitude more active when compared to undercoordinated edge atom sites, while terrace sites remain catalytically inactive for the reduction reaction of resazurin to resorufin. Catalytic activity has been also demonstrated for calixarene-bound gold nanoparticles using the reduction of 4-nitrophenol. With the 4-nitrophenol reduction reaction, a comparative study was undertaken to compare calixarene phosphine and calixarene thiol bound 4 nm gold particles. The results of the study suggested that a leached site was responsible for catalysis and not sites on the original gold nanoparticles. Future experiments with calixarene bound gold clusters could investigate ligand effects in reactions where the active site is not a leached or aggregated gold species, possibly in oxidation reactions, where electron-rich gold is hypothesized to be a good catalyst. The results that emphasize the enhanced catalytic activity of

  15. METALS DISTRIBUTIONS IN ACTIVATED SLUDGE SYSTEMS

    EPA Science Inventory

    This project developed models to predict the distribution of metals in activated sludge system process streams. The data used to develop the models were obtained through extended pilot studies from a previous project. The objectives of the study were to evaluate the effects of wa...

  16. On the origin of high activity of hcp metals for ammonia synthesis.

    PubMed

    Ahmadi, Shideh; Kaghazchi, Payam

    2016-02-10

    Structure and activity of nanoparticles of hexagonal close-packed (hcp) metals are studied using first-principles calculations. Results show that, in contact with a nitrogen environment, high-index {134[combining macron]2} facets are formed on hcp metal nanoparticles. Nitrogen molecules dissociate easily at kink sites on these high-index facets (activation barriers of <0.2 eV). Analysis of the site blocking effect and adsorption energies on {134[combining macron]2} facets explains the order of activity of hcp metals for ammonia synthesis: Re < Os < Ru. Our results indicate that the high activity of hcp metals for ammonia synthesis is due to the N-induced formation of {134[combining macron]2} facets with high activity for the dissociation of nitrogen molecules. However, quite different behavior for adsorption of dissociated N atoms leads to distinctive activity of hcp metals. PMID:26818719

  17. Heavy Metals in the Vegetables Collected from Production Sites

    PubMed Central

    Taghipour, Hassan; Mosaferi, Mohammad

    2013-01-01

    Background: Contamination of vegetable crops (as an important part of people's diet) with heavy metals is a health concern. Therefore, monitoring levels of heavy metals in vegetables can provide useful information for promoting food safety. The present study was carried out in north-west of Iran (Tabriz) on the content of heavy metals in vegetable crops. Methods: Samples of vegetables including kurrat (n=20) (Allium ampeloprasumssp. Persicum), onion (n=20) (Allium cepa) and tomato (n=18) (Lycopersiconesculentum var. esculentum), were collected from production sites in west of Tabriz and analyzed for presence of Cd, Cr, Cu, Ni, Pb and Zn by atomic absorption spectroscopy (AAS) after extraction by aqua regia method (drying, grounding and acid diges­tion). Results: Mean ± SD (mg/kg DW) concentrations of Cd, Cu, Cr, Ni and Zn were 0.32 ± 0.58, 28.86 ± 28.79, 1.75 ± 2.05, 6.37± 5.61 and 58.01 ± 27.45, respec­tively. Cr, Cu and Zn were present in all the samples and the highest concentra­tions were observed in kurrat (leek). Levels of Cd, Cr and Cu were higher than the acceptable limits. There was significant difference in levels of Cr (P<0.05) and Zn (P<0.001) among the studied vegetables. Positive correlation was observed be­tween Cd:Cu (R=0.659, P<0.001) Cr:Ni (R=0.326, P<0.05) and Cr:Zn (R=0.308, P<0.05).   Conclusion: Level of heavy metals in some of the analyzed vegetables, especially kurrat samples, was higher than the standard levels. Considering the possi­ble health outcomes due to the consumption of contaminated vegetables, it is re­quired to take proper actions for avoiding people's chronic exposure. PMID:24688968

  18. Active site specificity of plasmepsin II.

    PubMed Central

    Westling, J.; Cipullo, P.; Hung, S. H.; Saft, H.; Dame, J. B.; Dunn, B. M.

    1999-01-01

    Members of the aspartic proteinase family of enzymes have very similar three-dimensional structures and catalytic mechanisms. Each, however, has unique substrate specificity. These distinctions arise from variations in amino acid residues that line the active site subsites and interact with the side chains of the amino acids of the peptides that bind to the active site. To understand the unique binding preferences of plasmepsin II, an enzyme of the aspartic proteinase class from the malaria parasite, Plasmodium falciparum, chromogenic octapeptides having systematic substitutions at various positions in the sequence were analyzed. This enabled the design of new, improved substrates for this enzyme (Lys-Pro-Ile-Leu-Phe*Nph-Ala/Glu-Leu-Lys, where * indicates the cleavage point). Additionally, the crystal structure of plasmepsin II was analyzed to explain the binding characteristics. Specific amino acids (Met13, Ser77, and Ile287) that were suspected of contributing to active site binding and specificity were chosen for site-directed mutagenesis experiments. The Met13Glu and Ile287Glu single mutants and the Met13Glu/Ile287Glu double mutant gain the ability to cleave substrates containing Lys residues. PMID:10548045

  19. Biochemical Characterization of HydF, a Scaffolding Enzyme, in the Synthesis of the Hydrogenase Active Site Metal Center: Implications Towards the Evolution of Biocatalysts from Mineral-based Components on Early Earth

    NASA Astrophysics Data System (ADS)

    Duffus, B. R.; Shepard, E. M.; McGlynn, S. E.; Bueling, A. L.; Winslow, M. A.; Peters, J. W.; Broderick, J. B.

    2010-04-01

    [FeFe]-hydrogenase active site biosynthesis utilizes radical chemistry on a scaffold protein whose ancestor may have been one of the earliest examples of a protein that couples the chemistry of an Fe-S peptide nest with a nucleotide binding nest.

  20. Release of Radioactive Scrap Metal/Scrap Metal (RSM/SM) at Nevada Test Site (NTS)

    SciTech Connect

    Not Available

    1993-07-01

    Reynolds Electrical and Engineering Company, Inc. (REECo) is the prime contractor to the US Department of Energy (DOE) in providing service and support for NTS operations. Mercury Base Camp is the main control point for the many forward areas at NTS, which covers 1,350 square miles. The forward areas are where above-ground and underground nuclear tests have been performed over the last 41 years. No metal (or other material) is returned to Mercury without first being tested for radioactivity. No radioactive metals are allowed to reenter Mercury from the forward areas, other than testing equipment. RAMATROL is the monitor check point. They check material in various ways, including swipe tests, and have a large assortment of equipment for testing. Scrap metal is also checked to address Resource Conservation and Recovery Act concerns. After addressing these issues, the scrap metals are categorized. Federal Property Management Regulations (FPMR) are followed by REECo. The nonradioactive scrap material is sold through the GSA on a scheduled basis. Radioactive scrap metal are presently held in forward areas where they were used. REECo has gained approval of their Nevada Test Site Defense Waste Acceptance Criteria, Certification, and Transfer Requirements, NVO-325 application, which will allow disposal on site, when RSM is declared a waste. The guideline that REECo uses for release limits is DOE Order 5480.11, Radiation Protection for Occupational Works, Attachment 2, Surface Radioactivity Guides, of this order, give release limits for radioactive materials. However, the removal of radioactive materials from NTS require approval by DOE Nevada Operations Office (DOE/NV) on a case-by-case basis. Requirements to consider before removal are found in DOE Order 5820.2A, Radioactive Waste Management.

  1. Antiretroviral activity of thiosemicarbazone metal complexes.

    PubMed

    Pelosi, Giorgio; Bisceglie, Franco; Bignami, Fabio; Ronzi, Paola; Schiavone, Pasqualina; Re, Maria Carla; Casoli, Claudio; Pilotti, Elisabetta

    2010-12-23

    Thiosemicarbazones display a wide antimicrobial activity by targeting bacteria, fungi, and viruses. Here, we report our studies on the antiviral activity of two thiosemicarbazone metal complexes, [bis(citronellalthiosemicarbazonato)nickel(II)] and [aqua(pyridoxalthiosemicarbazonato)copper(II)] chloride monohydrate, against the retroviruses HIV-1 and HTLV-1/-2. Both compounds exhibit antiviral properties against HIV but not against HTLVs . In particular, the copper complex shows the most potent anti-HIV activity by acting at the post-entry steps of the viral cycle. PMID:21121632

  2. Corrosion Research And Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2001-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  3. Corrosion Research and Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2002-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  4. Metal A and Metal B Sites of Nuclear RNA Polymerases Pol IV and Pol V Are Required for siRNA-Dependent DNA Methylation and Gene Silencing

    PubMed Central

    Haag, Jeremy R.; Pontes, Olga; Pikaard, Craig S.

    2009-01-01

    Plants are unique among eukaryotes in having five multi-subunit nuclear RNA polymerases: the ubiquitous RNA polymerases I, II and III plus two plant-specific activities, nuclear RNA polymerases IV and V (previously known as Polymerases IVa and IVb). Pol IV and Pol V are not required for viability but play non-redundant roles in small interfering RNA (siRNA)-mediated pathways, including a pathway that silences retrotransposons and endogenous repeats via siRNA-directed DNA methylation. RNA polymerase activity has not been demonstrated for Polymerases IV or V in vitro, making it unclear whether they are catalytically active enzymes. Their largest and second-largest subunit sequences have diverged considerably from Pol I, II and III in the vicinity of the catalytic center, yet retain the invariant Metal A and Metal B amino acid motifs that bind magnesium ions essential for RNA polymerization. By using site-directed mutagenesis in conjunction with in vivo functional assays, we show that the Metal A and Metal B motifs of Polymerases IV and V are essential for siRNA production, siRNA-directed DNA methylation, retrotransposon silencing, and the punctate nuclear localization patterns typical of both polymerases. Collectively, these data show that the minimal core sequences of polymerase active sites, the Metal A and B sites, are essential for Pol IV and Pol V biological functions, implying that both are catalytically active. PMID:19119310

  5. Self-Supporting Metal-Organic Layers as Single-Site Solid Catalysts.

    PubMed

    Cao, Lingyun; Lin, Zekai; Peng, Fei; Wang, Weiwei; Huang, Ruiyun; Wang, Cheng; Yan, Jiawei; Liang, Jie; Zhang, Zhiming; Zhang, Teng; Long, Lasheng; Sun, Junliang; Lin, Wenbin

    2016-04-11

    Metal-organic layers (MOLs) represent an emerging class of tunable and functionalizable two-dimensional materials. In this work, the scalable solvothermal synthesis of self-supporting MOLs composed of [Hf6 O4 (OH)4 (HCO2 )6 ] secondary building units (SBUs) and benzene-1,3,5-tribenzoate (BTB) bridging ligands is reported. The MOL structures were directly imaged by TEM and AFM, and doped with 4'-(4-benzoate)-(2,2',2''-terpyridine)-5,5''-dicarboxylate (TPY) before being coordinated with iron centers to afford highly active and reusable single-site solid catalysts for the hydrosilylation of terminal olefins. MOL-based heterogeneous catalysts are free from the diffusional constraints placed on all known porous solid catalysts, including metal-organic frameworks. This work uncovers an entirely new strategy for designing single-site solid catalysts and opens the door to a new class of two-dimensional coordination materials with molecular functionalities. PMID:26954885

  6. SEQUESTERING AGENTS FOR ACTIVE CAPS - REMEDIATION OF METALS AND ORGANICS

    SciTech Connect

    Knox, A; Michael Paller, M; Danny D. Reible, D; Xingmao Ma, X; Ioana G. Petrisor, I

    2007-05-10

    This research evaluated organoclays, zeolites, phosphates, and a biopolymer as sequestering agents for inorganic and organic contaminants. Batch experiments were conducted to identify amendments and mixtures of amendments for metal and organic contaminants removal and retention. Contaminant removal was evaluated by calculating partitioning coefficients. Metal retention was evaluated by desorption studies in which residue from the removal studies was extracted with 1 M MgCl{sub 2} solution. The results indicated that phosphate amendments, some organoclays, and the biopolymer, chitosan, were very effective sequestering agents for metals in fresh and salt water. Organoclays were very effective sorbents for phenanthrene, pyrene, and benzo(a)pyrene. Partitioning coefficients for the organoclays were 3000-3500 ml g{sup -1} for benzo(a)pyrene, 400-450 ml g{sup -1} for pyrene, and 50-70 ml g{sup -1} for phenanthrene. Remediation of sites with a mixture of contaminants is more difficult than sites with a single contaminant because metals and organic contaminants have different fate and transport mechanisms in sediment and water. Mixtures of amendments (e.g., organoclay and rock phosphate) have high potential for remediating both organic and inorganic contaminants under a broad range of environmental conditions, and have promise as components in active caps for sediment remediation.

  7. Use of amendments to restore ecosystem function to metal mining impacted sites; Tools to evaluate efficacy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is a long history of using residuals based soil amendments for restoration of disturbed sites. More recently, this approach has been tested for use on metal contaminated mining sites. For these sites, amendment mixtures are targeted to reduce metal availability in situ as well as restore eco...

  8. Mechanism of Metal Ion Activation of the Diphtheria Toxin Repressor DtxR

    NASA Astrophysics Data System (ADS)

    D'Aquino, J. Alejandro; Ringe, Dagmar

    2006-08-01

    The diphtheria toxin repressor, DtxR, is a metal ion-activated transcriptional regulator that has been linked to the virulence of Corynebacterium diphtheriae. Structure determination has shown that there are two metal ion binding sites per repressor monomer, and site-directed mutagenesis has demonstrated that binding site 2 (primary) is essential for recognition of the target DNA repressor, leaving the role of binding site 1 (ancillary) unclear (1 - 3). Calorimetric techniques have demonstrated that while binding site 1 (ancillary) has high affinity for metal ion with a binding constant of 2 × 10-7, binding site 2 (primary) is a low affinity binding site with a binding constant of 6.3 × 10-4. These two binding sites act independently and their contribution can be easily dissected by traditional mutational analysis. Our results clearly demonstrate that binding site 1 (ancillary) is the first one to be occupied during metal ion activation, playing a critical role in stabilization of the repressor. In addition, structural data obtained for the mutants Ni-DtxR(H79A,C102D), reported here and the previously reported DtxR(H79A) (4) has allowed us to propose a mechanism of metal ion activation for DtxR.

  9. Mechanism of Metal Ion Activation of the Diphtheria Toxin Repressor DtxR

    SciTech Connect

    D'Aquino,J.; Tetenbaum-Novatt, J.; White, A.; Berkovitch, F.; Ringe, D.

    2005-01-01

    The diphtheria toxin repressor (DtxR) is a metal ion-activated transcriptional regulator that has been linked to the virulence of Corynebacterium diphtheriae. Structure determination has shown that there are two metal ion binding sites per repressor monomer, and site-directed mutagenesis has demonstrated that binding site 2 (primary) is essential for recognition of the target DNA repressor, leaving the role of binding site 1 (ancillary) unclear. Calorimetric techniques have demonstrated that although binding site 1 (ancillary) has high affinity for metal ion with a binding constant of 2 x 10{sup -7}, binding site 2 (primary) is a low-affinity binding site with a binding constant of 6.3 x 10{sup -4}. These two binding sites act in an independent fashion, and their contribution can be easily dissected by traditional mutational analysis. Our results clearly demonstrate that binding site 1 (ancillary) is the first one to be occupied during metal ion activation, playing a critical role in stabilization of the repressor. In addition, structural data obtained for the mutants Ni-DtxR(H79A, C102D), reported here, and the previously reported DtxR(H79A) have allowed us to propose a mechanism of metal activation for DtxR.

  10. Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme.

    PubMed Central

    Hansen, M R; Simorre, J P; Hanson, P; Mokler, V; Bellon, L; Beigelman, L; Pardi, A

    1999-01-01

    A novel metal-binding site has been identified in the hammerhead ribozyme by 31P NMR. The metal-binding site is associated with the A13 phosphate in the catalytic core of the hammerhead ribozyme and is distinct from any previously identified metal-binding sites. 31P NMR spectroscopy was used to measure the metal-binding affinity for this site and leads to an apparent dissociation constant of 250-570 microM at 25 degrees C for binding of a single Mg2+ ion. The NMR data also show evidence of a structural change at this site upon metal binding and these results are compared with previous data on metal-induced structural changes in the core of the hammerhead ribozyme. These NMR data were combined with the X-ray structure of the hammerhead ribozyme (Pley HW, Flaherty KM, McKay DB. 1994. Nature 372:68-74) to model RNA ligands involved in binding the metal at this A13 site. In this model, the A13 metal-binding site is structurally similar to the previously identified A(g) metal-binding site and illustrates the symmetrical nature of the tandem G x A base pairs in domain 2 of the hammerhead ribozyme. These results demonstrate that 31P NMR represents an important method for both identification and characterization of metal-binding sites in nucleic acids. PMID:10445883

  11. A sensitive rapid on-site immunoassay for heavy metal contamination

    SciTech Connect

    Blake, R.; Blake, D.; Flowers, G.

    1996-05-02

    This project concerns the development of immunoassays for heavy metals that will permit the rapid on-site analysis of specific heavy metals, including lead and chromium in water and soil samples. 2 refs.

  12. X-ray Crystal Structure of Divalent Metal-Activated β-xylosidase, RS223BX.

    PubMed

    Jordan, Douglas B; Braker, Jay D; Wagschal, Kurt; Lee, Charles C; Chan, Victor J; Dubrovska, Ievgeniia; Anderson, Spencer; Wawrzak, Zdzislaw

    2015-10-01

    We report the X-ray crystal structure of a glycoside hydrolase family 43 β-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca(2+) cation is located at the back of the active-site pocket. The Ca(2+) is held in the active site by the carboxylate of D85, an "extra" acid residue in comparison to other GH43 active sites. The Ca(2+) is in close contact with a histidine imidazole, which in turn is in contact with the catalytic base (D15) thus providing a mechanism for stabilizing the carboxylate anion of the base and achieve metal activation. The active-site pocket is mirrored by an "inactive-site" pocket of unknown function that resides on the opposite side of the monomer. PMID:26201482

  13. Noble metal ionic sites for catalytic hydrogen combustion: spectroscopic insights.

    PubMed

    Deshpande, Parag A; Madras, Giridhar

    2011-01-14

    A catalytic hydrogen combustion reaction was carried out over noble metal catalysts substituted in ZrO(2) and TiO(2) in ionic form. The catalysts were synthesized by the solution combustion technique. The compounds showed high activity and CO tolerance for the reaction. The activity of Pd and Pt ion substituted TiO(2) was comparable and was higher than Pd and Pt ion substituted ZrO(2). The mechanisms of the reaction over the two supports were proposed by making use of the X-ray photoelectron spectroscopy and FT infrared spectroscopic observations. The reaction over ZrO(2) supported catalysts was proposed to take place by the utilization of the surface hydroxyl groups while the reaction over TiO(2) supported catalysts was hypothesized to be a hybrid mechanism utilizing surface hydroxyl groups and the lattice oxygen. PMID:21060910

  14. Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

    PubMed

    Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

    2008-11-21

    Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS. PMID:18820259

  15. Fabrication of 3D metal/polymer microstructures by site-selective metal coating

    NASA Astrophysics Data System (ADS)

    Takeyasu, N.; Tanaka, T.; Kawata, S.

    2008-02-01

    Three-dimensional silver/polymer conjugated microstructures were fabricated by site-selective metal deposition on photopolymer structures in the sub-micrometer scale. Photopolymerizable resins with and without an amide group were independently prepared, and a three-dimensional polymer structure was fabricated with those resins by means of the two-photon-induced photopolymerization technique to confine the photopolymerization to a sub-micrometer volume. Silver was selectively deposited on the surface of the amide-containing polymer parts by electroless plating. This method can provide 3D arbitrary silver/polymer composite microstructures with sub-micrometer resolution.

  16. Catalytic glucose isomerization by porous coordination polymers with open metal sites.

    PubMed

    Akiyama, George; Matsuda, Ryotaro; Sato, Hiroshi; Kitagawa, Susumu

    2014-10-01

    Highly efficient catalytic isomerization reactions from glucose to fructose in aqueous media using porous coordination polymers (PCPs) or metal-organic frameworks (MOFs) is reported for the first time. The catalytic activity of PCPs functionalized with -NH2, -(CH3)2, -NO2, and -SO3H groups on the pore surface is systematically tested. The catalytic activity can be tuned by the acidity of open metal sites (OMSs) by modifying the organic linkers with the functional groups. As a result, it is demonstrated that MIL-101 functionalized with -SO3H not only shows high conversion of glucose but also selectively produces fructose. Further, catalytic one-pot conversion of amylose to fructose is achieved, thanks to the high stability of the framework in an acidic solution. These results show that MOF/PCP compounds having OMSs are promising materials for various useful heterogeneous catalytic reactions, in particular in the biomass field. PMID:25080129

  17. Metal binding sites of the estradiol receptor from calf uterus and their possible role in the regulation of receptor function

    SciTech Connect

    Medici, N.; Minucci, S.; Nigro, V.; Abbondanza, C.; Armetta, I.; Molinari, A.M.; Puca, G.A. )

    1989-01-10

    The existence of putative metal binding sites on the estradiol receptor (ER) molecule from calf uterus was evaluated by immobilizing various divalent metals to iminodiacetate-Sepharose. ER from both crude and highly purified preparations binds to metal-containing adsorbents complexed with Zn(II), Ni(II), Co(II), and Cu(II), but not to those complexed with Fe(II) and Cd(II). Analysis of affinity-labeled ER by ({sup 3}H)tamoxifen aziridine after elution from a column of Zn(II)-charged iminodiacetate-Sepharose showed that ER fragments obtained by extensive trypsinization were also bound. Zn(II) and the same other metals able to bind ER, when immobilized on resins, inhibit the binding of estradiol to the receptor at micromolar concentration. This inhibition is noncompetitive and can be reversed by EDTA. The inhibition of the hormone binding was still present after trypsin treatment of the cytosol, and it was abolished by preincubation with the hormone. Micromolar concentrations of these metals were able to block those chemical-physical changes occurring during the process of ER transformation in vitro. The presence of metal binding sites that modulate the ER activity in the hormone binding domain of ER is speculated. Since progesterone receptor showed the same pattern of binding and elution from metal-containing adsorbents, the presence of metal binding regulatory sites could be a property of all steroid receptors.

  18. Characterizing the Environmental Availability of Trace Metals in Savannah River Site Soils

    SciTech Connect

    Serkiz, S.M.

    1999-03-18

    An eight step sequential extraction technique was used to characterize the environmental availability of trace metals from background and waste site soil samples collected from the US Department of Energy's Savannah River Site (SRS).

  19. Interaction of metallic clusters with biologically active curcumin molecules

    NASA Astrophysics Data System (ADS)

    Gupta, Sanjeev K.; He, Haiying; Liu, Chunhui; Dutta, Ranu; Pandey, Ravindra

    2015-09-01

    We have investigated the interaction of subnano metallic Gd and Au clusters with curcumin, an important biomolecule having pharmacological activity. Gd clusters show different site preference to curcumin and much stronger interaction strength, in support of the successful synthesis of highly stable curcumin-coated Gd nanoparticles as reported recently. It can be attributed to significant charge transfer from the Gd cluster to curcumin together with a relatively strong hybridization of the Gd df-orbitals with curcumin p-orbitals. These results suggest that Gd nanoparticles can effectively be used as delivery carriers for curcumin at the cellular level for therapy and medical imaging applications.

  20. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  1. Heavy Metals Environmental Study of A Brownfield Site and of Soils of Napoli Metropolitan Area

    NASA Astrophysics Data System (ADS)

    de Vivo, B.; Cicchella, D.; Lima, A.; Albanese, S.; Somma, R.

    Heavy metal concentrations and Pb isotopic composition were determined in the soils, slags, scums and land fill materials from a shut down industrial (brownfield) site and in the soils of Napoli metropolitan area. The brownfield site, the second largest steel- works in Italy, is now under remediation by a Government project. It is located at the outskirts of Napoli in the Bagnoli-Fuorigrotta plain (BFP), which is part of the Campi Flegrei (CF) volcanic caldera, where many spas and geothermal springs occur. The pyroclastics of Campi Flegrei represent as well the rocks on which is sitting the City of Napoli. Purpose of this work is to distinguish the natural (geogenic) component (to which contributed as well hydrothermal activity in the BFP) from anthropogenic contamination due both to the industrial activity and urban pollution. For this purpose, have been sampled in situ sediments (soils), slags, scums and land fill materials from 20 drill cores, selected from a network of 197 drill carried out on a 100x100 m grid, on the entire brownfield site, and top soils (grid of 500x500 and 1000x1000 m) in the metropolitan and sub-urban area. In general, in the brownfield site, heavy metal en- richments strongly suggest mixing between a natural (geogenic) and an anthropogenic component. Pb isotopic data, are suggestive of three potential end members, and con- firm the existence of a strong natural component in addition to contamination from anthropogenic activities. The natural contribution of hydrothermal fluids to soil pollu- tion, in addition to the non bio-availability of metal pollutants from industrial materi- als, demonstrated, - through leachate experiments - indicate that heavy metals reme- diation of soils in this area would be of little use. Viceversa in the metropolitan area of Napoli it is mostly indicated a strong Pb, Pd and Pt contamination due to motor vehicles circulation. Pd and Pt pollution is certainly due to emission of abraded frag- ments of catalytic

  2. Metal-Metal Interactions in Heterobimetallic Complexes with Dinucleating Redox-Active Ligands.

    PubMed

    Broere, Daniël L J; Modder, Dieuwertje K; Blokker, Eva; Siegler, Maxime A; van der Vlugt, Jarl Ivar

    2016-02-12

    The tuning of metal-metal interactions in multinuclear assemblies is a challenge. Selective P coordination of a redox-active PNO ligand to Au(I) followed by homoleptic metalation of the NO pocket with Ni(II) affords a unique trinuclear Au-Ni-Au complex. This species features two antiferromagnetically coupled ligand-centered radicals and a double intramolecular d(8)-d(10) interaction, as supported by spectroscopic, single-crystal X-ray diffraction, and computational data. A corresponding cationic dinuclear Au-Ni analogue with a stronger d(8)-d(10) interaction is also reported. Although both heterobimetallic structures display rich electrochemistry, only the trinuclear Au-Ni-Au complex facilitates electrocatalytic C-X bond activation of alkyl halides in its doubly reduced state. Hence, the presence of a redox-active ligand framework, an available coordination site at gold, and the nature of the nickel-gold interaction appear to be essential for this reactivity. PMID:26762546

  3. Tailorable chiroptical activity of metallic nanospiral arrays

    NASA Astrophysics Data System (ADS)

    Deng, Junhong; Fu, Junxue; Ng, Jack; Huang, Zhifeng

    2016-02-01

    The engineering of the chiroptical activity of the emerging chiral metamaterial, metallic nanospirals, is in its infancy. We utilize glancing angle deposition (GLAD) to facilely sculpture the helical structure of silver nanospirals (AgNSs), so that the scope of chiroptical engineering factors is broadened to include the spiral growth of homochiral AgNSs, the combination of left- and right-handed helical chirality to create heterochiral AgNSs, and the coil-axis alignment of the heterochiral AgNSs. It leads to flexible control over the chiroptical activity of AgNS arrays with respect to the sign, resonance wavelength and amplitude of circular dichroism (CD) in the UV and visible regime. The UV chiroptical mode has a distinct response from the visible mode. Finite element simulation together with LC circuit theory illustrates that the UV irradiation is mainly adsorbed in the metal and the visible is preferentially scattered by the AgNSs, accounting for the wavelength-related chiroptical distinction. This work contributes to broadening the horizons in understanding and engineering chiroptical responses, primarily desired for developing a wide range of potential chiroplasmonic applications.The engineering of the chiroptical activity of the emerging chiral metamaterial, metallic nanospirals, is in its infancy. We utilize glancing angle deposition (GLAD) to facilely sculpture the helical structure of silver nanospirals (AgNSs), so that the scope of chiroptical engineering factors is broadened to include the spiral growth of homochiral AgNSs, the combination of left- and right-handed helical chirality to create heterochiral AgNSs, and the coil-axis alignment of the heterochiral AgNSs. It leads to flexible control over the chiroptical activity of AgNS arrays with respect to the sign, resonance wavelength and amplitude of circular dichroism (CD) in the UV and visible regime. The UV chiroptical mode has a distinct response from the visible mode. Finite element simulation

  4. A single-site model for divalent transition and heavy metal adsorption over a range of metal concentrations.

    PubMed

    Criscenti, Louise J; Sverjensky, Dimitri A

    2002-09-15

    Metal adsorption data over a range of surface coverages typically are characterized by curvilinear metal adsorption isotherms. These isotherms generally have a slope of 1 at low surface coverage and a shallower slope at higher surface coverages. The curvature of metal adsorption isotherms with increasing surface coverage is frequently interpreted in terms of sequential adsorption onto different types of surface sites, multinuclear surface complexation, or nonideality of metal adsorption. We demonstrate that the curvature of metal adsorption isotherms can also be attributed to changes in surface charge and potential that depend on the predominant type of metal surface complex. A single-site extended triple-layer model is used to reinterpret previously studied metal adsorption isotherms and pH edges for a wide variety of metals (Cd2+, Co2+, Cu2+, Pb2+, and Zn2+) and solids (goethite, hydrous ferric oxide, corundum, and magnetite) in different electrolyte solutions (NaNO3 and NaClO4). Only metal adsorption on ferrihydrite at very low surface coverages is not consistent with the single-site triple-layer model. This discrepancy might be explained if ferrihydrite is in fact not a single phase but a mixture of two or more phases. Metal surface coverages ranging from 10(-4) to 10.2 mmol/m2 on the other minerals can be accounted for with a single-site extended triple-layer model if appropriate metal adsorption reactions are chosen. In addition, several examples suggest that, within the context of the model, surface complexation schemes can be established that describe metal adsorption over both a wide range of surface coverage and a wide range of ionic strength. PMID:16290865

  5. Sintering-Resistant Single-Site Nickel Catalyst Supported by Metal-Organic Framework.

    PubMed

    Li, Zhanyong; Schweitzer, Neil M; League, Aaron B; Bernales, Varinia; Peters, Aaron W; Getsoian, Andrew Bean; Wang, Timothy C; Miller, Jeffrey T; Vjunov, Aleksei; Fulton, John L; Lercher, Johannes A; Cramer, Christopher J; Gagliardi, Laura; Hupp, Joseph T; Farha, Omar K

    2016-02-17

    Developing supported single-site catalysts is an important goal in heterogeneous catalysis since the well-defined active sites afford opportunities for detailed mechanistic studies, thereby facilitating the design of improved catalysts. We present herein a method for installing Ni ions uniformly and precisely on the node of a Zr-based metal-organic framework (MOF), NU-1000, in high density and large quantity (denoted as Ni-AIM) using atomic layer deposition (ALD) in a MOF (AIM). Ni-AIM is demonstrated to be an efficient gas-phase hydrogenation catalyst upon activation. The structure of the active sites in Ni-AIM is proposed, revealing its single-site nature. More importantly, due to the organic linker used to construct the MOF support, the Ni ions stay isolated throughout the hydrogenation catalysis, in accord with its long-term stability. A quantum chemical characterization of the catalyst and the catalytic process complements the experimental results. With validation of computational modeling protocols, we further targeted ethylene oligomerization catalysis by Ni-AIM guided by theoretical prediction. Given the generality of the AIM methodology, this emerging class of materials should prove ripe for the discovery of new catalysts for the transformation of volatile substrates. PMID:26836273

  6. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-01-01

    One strategy to markedly increase the gas storage capacity of metal-organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules--specifically hydrogen, methane, or carbon dioxide.

  7. Tailorable chiroptical activity of metallic nanospiral arrays.

    PubMed

    Deng, Junhong; Fu, Junxue; Ng, Jack; Huang, Zhifeng

    2016-02-18

    The engineering of the chiroptical activity of the emerging chiral metamaterial, metallic nanospirals, is in its infancy. We utilize glancing angle deposition (GLAD) to facilely sculpture the helical structure of silver nanospirals (AgNSs), so that the scope of chiroptical engineering factors is broadened to include the spiral growth of homochiral AgNSs, the combination of left- and right-handed helical chirality to create heterochiral AgNSs, and the coil-axis alignment of the heterochiral AgNSs. It leads to flexible control over the chiroptical activity of AgNS arrays with respect to the sign, resonance wavelength and amplitude of circular dichroism (CD) in the UV and visible regime. The UV chiroptical mode has a distinct response from the visible mode. Finite element simulation together with LC circuit theory illustrates that the UV irradiation is mainly adsorbed in the metal and the visible is preferentially scattered by the AgNSs, accounting for the wavelength-related chiroptical distinction. This work contributes to broadening the horizons in understanding and engineering chiroptical responses, primarily desired for developing a wide range of potential chiroplasmonic applications. PMID:26530309

  8. Assessment of selected metals in the ambient air PM10 in urban sites of Bangkok (Thailand).

    PubMed

    Pongpiachan, Siwatt; Iijima, Akihiro

    2016-02-01

    Estimating the atmospheric concentrations of PM10-bounded selected metals in urban air is crucial for evaluating adverse health impacts. In the current study, a combination of measurements and multivariate statistical tools was used to investigate the influence of anthropogenic activities on variations in the contents of 18 metals (i.e., Al, Sc, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Cd, Sb, Ba, La, Ce and Pb) in ambient air. The concentrations of PM10-bounded metals were measured simultaneously at eight air quality observatory sites during a half-year period at heavily trafficked roads and in urban residential zones in Bangkok, Thailand. Although the daily average concentrations of Al, V, Cr, Mn and Fe were almost equivalent to those of other urban cities around the world, the contents of the majority of the selected metals were much lower than the existing ambient air quality guidelines and standard limit values. The sequence of average values of selected metals followed the order of Al > Fe > Zn > Cu > Pb > Mn > Ba > V > Sb > Ni > As > Cr > Cd > Se > Ce > La > Co > Sc. The probability distribution function (PDF) plots showed sharp symmetrical bell-shaped curves in V and Cr, indicating that crustal emissions are the predominant sources of these two elements in PM10. The comparatively low coefficients of divergence (COD) that were found in the majority of samples highlight that site-specific effects are of minor importance. A principal component analysis (PCA) revealed that 37.74, 13.51 and 11.32 % of the total variances represent crustal emissions, vehicular exhausts and the wear and tear of brakes and tires, respectively. PMID:26631022

  9. Underground Corrosion of Activated Metals, 6-Year Exposure Analysis

    SciTech Connect

    M. K. Adler Flitton; T. S. Yoder

    2006-03-01

    The subsurface radioactive disposal site located at the Idaho National Laboratory contains neutronactivated metals from non-fuel nuclear-reactor-core components. A long-term underground corrosion test is being conducted to obtain site-specific corrosion rates to support efforts to more accurately estimate the transfer of activated elements in the surrounding arid vadose zone environment. The test uses nonradioactive metal coupons representing the prominent neutron-activated materials buried at the disposal location, namely, Type 304L stainless steel (UNS S30403), Type 316L stainless steel (S31603), nickel-chromium alloy (UNS NO7718), beryllium, aluminum 6061-T6 (A96061), and a zirconium alloy (UNS R60804). In addition, carbon steel (the material presently used in the cask disposal liners and other disposal containers) and a duplex stainless steel (UNS S32550) are also included in the test. This paper briefly describes the ongoing test and presents the results of corrosion analysis from coupons exposed underground for 1, 3, and 6 years.

  10. Removal and recovery of toxic metal ions from aqueous waste sites using polymer pendant ligands

    SciTech Connect

    Fish, D.

    1996-10-01

    The purpose of this project is to investigate the use of polymer pendant ligand technology to remove and recover toxic metal ions from DOE aqueous waste sites. Polymer pendant lgiands are organic ligands, anchored to crosslinked, modified divinylbenzene-polystyrene beads, that can selectively complex metal ions. The metal ion removal step usually occurs through a complexation or ion exchange phenomena, thus recovery of the metal ions and reuse of the beads is readily accomplished.

  11. A DNAzyme requiring two different metal ions at two distinct sites.

    PubMed

    Zhou, Wenhu; Zhang, Yupei; Huang, Po-Jung Jimmy; Ding, Jinsong; Liu, Juewen

    2016-01-01

    Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na(+) and a trivalent lanthanide (e.g. Ce(3+)), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na(+)-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb(3+) luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na(+)-binding. The Na(+) dissociation constants of Ce13d measured from the cleavage activity assay, Tb(3+) luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce(3+) might be replaced by G23 in NaA43. Ce(3+) functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce(3+) (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes. PMID:26657636

  12. A DNAzyme requiring two different metal ions at two distinct sites

    PubMed Central

    Zhou, Wenhu; Zhang, Yupei; Huang, Po-Jung Jimmy; Ding, Jinsong; Liu, Juewen

    2016-01-01

    Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G23 in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce3+ (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes. PMID:26657636

  13. Forest floor leachate fluxes under six different tree species on a metal contaminated site.

    PubMed

    Van Nevel, Lotte; Mertens, Jan; De Schrijver, An; Baeten, Lander; De Neve, Stefaan; Tack, Filip M G; Meers, Erik; Verheyen, Kris

    2013-03-01

    Trees play an important role in the biogeochemical cycling of metals, although the influence of different tree species on the mobilization of metals is not yet clear. This study examined effects of six tree species on fluxes of Cd, Zn, DOC, H(+) and base cations in forest floor leachates on a metal polluted site in Belgium. Forest floor leachates were sampled with zero-tension lysimeters in a 12-year-old post-agricultural forest on a sandy soil. The tree species included were silver birch (Betula pendula), oak (Quercus robur and Q. petraea), black locust (Robinia pseudoacacia), aspen (Populus tremula), Scots pine (Pinus sylvestris) and Douglas fir (Pseudotsuga menziesii). We show that total Cd fluxes in forest floor leachate under aspen were slightly higher than those in the other species' leachates, yet the relative differences between the species were considerably smaller when looking at dissolved Cd fluxes. The latter was probably caused by extremely low H(+) amounts leaching from aspen's forest floor. No tree species effect was found for Zn leachate fluxes. We expected higher metal leachate fluxes under aspen as its leaf litter was significantly contaminated with Cd and Zn. We propose that the low amounts of Cd and Zn leaching under aspen's forest floor were possibly caused by high activity of soil biota, for example burrowing earthworms. Furthermore, our results reveal that Scots pine and oak were characterized by high H(+) and DOC fluxes as well as low base cation fluxes in their forest floor leachates, implying that those species might enhance metal mobilization in the soil profile and thus bear a potential risk for belowground metal dispersion. PMID:23376521

  14. Metal Cofactors in the Structure and Activity of the Fowlpox Resolvase

    PubMed Central

    Culyba, Matthew J.; Hwang, Young; Hu, Jimmy Yan; Minkah, Nana; Ocwieja, Karen E.; Bushman, Frederic D.

    2010-01-01

    Poxvirus DNA replication generates linear concatemers containing many copies of the viral genome with inverted repeat sequences at the junctions between monomers. The inverted repeats refold to generate Holliday junctions, which are cleaved by the virus-encoded resolvase enzyme to form unit-length genomes. Here we report studies of the influence of metal cofactors on the activity and structure of the resolvase of fowlpox virus (FPV), which provides a tractable model for in vitro studies. Small molecule inhibitors of related enzymes bind simultaneously to metal cofactors and nearby surface amino-acid residues, so understanding enzyme-cofactor interactions is important for the design of antiviral agents. Analysis of inferred active site residues (D7, E60, K102, D132, D135) by mutagenesis and metal rescue experiments specified residues that contribute to binding metal ions, and that multiple binding sites are probably involved. Differential electrophoretic analysis was used to map the conformation of the DNA junction when bound by resolvase. For the wild-type complex in the presence of EDTA or Ca2+, migration was consistent with the DNA arms arranged in near tetrahedral geometry. However, the D7N active site mutant resolvase held the arms in a more planar arrangement in EDTA, Ca2+ or Mg2+ conditions, implicating metal-dependent contacts at the active site in the larger architecture of the complex. These data show how divalent metals dictate the conformation of FPV resolvase/ DNA complexes and subsequent DNA cleavage. PMID:20380839

  15. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  16. The Copper Active Site of CBM33 Polysaccharide Oxygenases

    PubMed Central

    2013-01-01

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme’s three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  17. Investigation of metal binding and activation of Escherichia coli glyoxalase I: kinetic, thermodynamic and mutagenesis studies.

    PubMed Central

    Clugston, Susan L; Yajima, Rieko; Honek, John F

    2004-01-01

    GlxI (glyoxalase I) isomerizes the hemithioacetal formed between glutathione and methylglyoxal. Unlike other GlxI enzymes, Escherichia coli GlxI exhibits no activity with Zn(2+) but maximal activation with Ni(2+). To elucidate further the metal site in E. coli GlxI, several approaches were undertaken. Kinetic studies indicate that the catalytic metal ion affects the k (cat) without significantly affecting the K (m) for the substrate. Inductively coupled plasma analysis and isothermal titration calorimetry confirmed one metal ion bound to the enzyme, including Zn(2+), which produces an inactive enzyme. Isothermal titration calorimetry was utilized to determine the relative binding affinity of GlxI for various bivalent metals. Each metal ion examined bound very tightly to GlxI with an association constant ( K (a))>10(7) M(-1), with the exception of Mn(2+) ( K (a) of the order of 10(6) M(-1)). One of the ligands to the catalytic metal, His(5), was altered to glutamine, a side chain found in the Zn(2+)-active Homo sapiens GlxI. The affinity of the mutant protein for all bivalent metals was drastically decreased. However, low levels of activity were now observed for Zn(2+)-bound GlxI. Although this residue has a marked effect on metal binding and activation, it is not the sole factor determining the differential metal activation between the human and E. coli GlxI enzymes. PMID:14556652

  18. Spatial distribution of heavy metal contamination in soils near a primitive e-waste recycling site.

    PubMed

    Quan, Sheng-Xiang; Yan, Bo; Yang, Fan; Li, Ning; Xiao, Xian-Ming; Fu, Jia-Mo

    2015-01-01

    The total concentrations of 12 heavy metals in surface soils (SS, 0-20 cm), middle soils (MS, 30-50 cm) and deep soils (DS, 60-80 cm) from an acid-leaching area, a deserted paddy field and a deserted area of Guiyu were measured. The results showed that the acid-leaching area was heavily contaminated with heavy metals, especially in SS. The mean concentrations of Ni, Cu, Zn, Cd, Sn, Sb and Pb in SS from the acid-leaching area were 278.4, 684.1, 572.8, 1.36, 3,472, 1,706 and 222.8 mg/kg, respectively. Heavy metal pollution in the deserted paddy field was mainly concentrated in SS and MS. The average values of Sb in SS and MS from the deserted paddy field were 16.3 and 20.2 mg/kg, respectively. However, heavy metal contamination of the deserted area was principally found in the DS. Extremely high concentrations of heavy metals were also observed at some special research sites, further confirming that the level of heavy metal pollution was very serious. The geoaccumulation index (Igeo) values revealed that the acid-leaching area was severely polluted with heavy metals in the order of Sb > Sn > Cu > Cd > Ni > Zn > Pb, while deserted paddy field was contaminated predominately by metals in the order of Sb > Sn > Cu. It was obvious that the concentrations of some uncommon contaminants, such as Sb and Sn, were higher than principal contaminants, such as Ni, Cu, Zn and Pb, suggesting that particular attention should be directed to Sn and Sb contamination in the future research of heavy metals in soils from e-waste-processing areas. Correlation analysis suggested that Li and Be in soils from the acid-leaching area and its surrounding environment might have originated from other industrial activities and from batteries, whereas Ni, Cu, Zn, Cd, Pb, Sn and Sb contamination was most likely caused by uncontrolled electronic waste (e-waste) processing. These results indicate the significant need for optimisation of e-waste-dismantling technologies and remediation of polluted soil

  19. X-ray crystal structure of divalent metal-activated ß-xyloisdase, RS223BX

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report the first X-ray structure of a glycoside hydrolase family 43 ß-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca2+ cation is located at the back of the active site pocket. The Ca2+ coordinates to H274 to sta...

  20. Remediation of heavy metal contaminated sites in the Venice lagoon and conterminous areas (Northern Italy)

    NASA Astrophysics Data System (ADS)

    Bini, Claudio; Wahsha, Mohammad; Fontana, Silvia; Maleci, Laura

    2013-04-01

    The lagoon of Venice and the conterminous land are affected by heavy contamination of anthropogenic origin, and for this reason the whole area has been classified as site of national interest, and must be restored. Heavy metals (As, Cd, Cr, Cu, Hg, Mn, Pb, Sb, Se, Zn) and organic compounds (IPA, PCB, Dioxine) have been identified as the main contaminants at various sites, owing to agriculture and industrial wastes discharged on soils and convoyed to the lagoon. Five case studies of soil remediation are here reported. S. Giuliano is a former palustrine area reclaimed since the 60's with various human transported materials (HTM). In this area, hot spots overpassing the reference limits for residential and green areas have been recorded for Cd, Cu, Pb, Zn and IPA. Campalto is a site bordering the Venice lagoon and subjected to oscillating water level, that enhances metal mobility; diffuse contamination by heavy metals, particularly Pb, has been recorded at this site, utilized since 30 years for military and sport (skate) activities. Marghera is dramatically famous for its numerous factories and for oil refineries that affected the lagoon sediments since the 50's. Sediments proved heavily contaminated by As (up to 137 mgkg-1), Cd (57 mgkg-1), Hg (30mgkg-1), Ni, Pb (700 mgkg-1), Zn (5818 mgkg-1). Murano is a small island where many glass factories (the most famous all over the world) are running since XIII century. Glass is stained with several metals and, moreover, some substances are used to regulate fusion temperature, purity, etc., and therefore the surrounding environment is heavily contaminated by these substances. Mean concentrations of As (429 mgkg-1), Cd (1452 mgkg-1), Pb (749 mgkg-1), Zn (1624 mgkg-1), Se (341 mgkg-1), Sb (74 mgkg-1) widely overpass the reference values for both residential and industrial areas in national guidelines. Molo Serbatoi is a former oil container currently under restoration in the port of Venice. Soil contamination by As, Hg, Zn and

  1. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  2. PCB and heavy metal contamination and effects in European starlings (Sturnus vulgaris) at a superfund site

    SciTech Connect

    Arenal, C.A.; Halbrook, R.S.

    1997-02-01

    From 1946-1967 industrial activities at the Crab Orchard National Wildlife Refuge (CONWR) included the construction of landfills and dumps for disposal of hazardous waste. Heavy metals such as cadmium, chromium, mercury, and lead and polychlorinated biphenyls (PCBs) are a special concern because of transport to biotic communities. During routine monitoring, Hite and King found elevated concentrations of mercury in fish from Crab Orchard Lake, and Kohler et al. reported PCB concentrations greater than FDA safety limits (2 ppm) in 38% of the fish collected in the eastern portion of Crab Orchard Lake. Additionally, livers from hunter harvested white-tailed deer killed on CONWR contained significantly greater concentrations of nickel and lead compared to deer collected off CONWR. In 1984, the Environmental Protection Agency (EPA) added 7 sites within CONWR to the National Priorities List under the Comprehensive Environmental Recovery, Compensation and Liabilities Act. These site contained varying concentrations of PCBs (Aroclor 1254) and heavy metals that were assessed as posing risk to wildlife. Because few studies have been completed on the effects of PCB and heavy metal concentrations on avian species among sites on the refuge, and preliminary studies by McKee indicated possible avian reproductive impairment due to contaminant exposure, additional study to evaluate adverse effects in avian species was initiated. Using the European starling (Sturnus vulgaris) as an avian model, this project provided biological and contaminant baseline data for evaluating avian exposure and effects, and provides a benchmark for determining the effectiveness of proposed remedial actions on CONWR. 18 refs., 5 figs., 2 tabs.

  3. The Identity of the Nucleophile Substitution may Influence Metal Interactions with the Cleavage Site of the Minimal Hammerhead Ribozyme

    PubMed Central

    Osborne, Edith M.; Ward, W. Luke; Ruehle, Max Z.; DeRose, Victoria J.

    2010-01-01

    Potential metal interactions with the cleavage site of a minimal hammerhead ribozyme (mHHRz) were probed using 31P NMR-detected Cd2+ titration studies of HHRz constructs containing a phosphorothioate (PS) modification at the cleavage site. The mHHRz nucleophile position was replaced by either a 2′-F or a 2′-NH2 in order to block cleavage activity during the study. The 2′-F/PS cleavage site mHHRz construct, in which the 2′-F should closely imitate the atom size and electronegativity of a 2′OH, demonstrates low levels of metal ion association (<1 ppm 31P chemical shift changes). This observation indicates that having an atom size and electrostatic properties that are similar to the 2′-OH are not the governing factors in allowing metal interactions with the scissile phosphate of the mHHRz. With a 2′-NH2 substitution, a large upfield change in 31P NMR chemical shift of the phosphorothioate peak (Δ~3 ppm with 6 equivalents added Cd2+) indicates observable Cd2+ interactions with the substituted site. Since a 2′-NH2, but not a 2′-F, can serve as a metal ligand, these data suggest that a metal ion interaction with the HHRz cleavage site may include both the scissile phosphate and the 2′ nucleophile. Control samples in which the 2′-NH2/PS unit is placed either next to the mHHRz cleavage site (at U16.1), in a duplex, or in a amUPSU dinucleotide, show much weaker interactions with Cd2+. Results with these control samples indicate that simply the presence of a 2′-NH2/PS unit does not create a strong metal binding site, reinforcing the possibility that the 2′-NH2-moderated Cd-PS interaction is specific to the mHHRz cleavage site. Upfield chemical shifts of both 31P and H2′ 1H resonances in amUPSU are observed with addition of Cd2+, consistent with the predicted metal coordination to both 2′-NH2 and phosphorothioate ligands. These data suggest that metal ion association with the HHRz cleavage site may include an interaction with the 2

  4. Metal binding sites of the estradiol receptor from calf uterus and their possible role in the regulation of receptor function.

    PubMed

    Medici, N; Minucci, S; Nigro, V; Abbondanza, C; Armetta, I; Molinari, A M; Puca, G A

    1989-01-10

    The existence of putative metal binding sites on the estradiol receptor (ER) molecule from calf uterus was evaluated by immobilizing various divalent metals to iminodiacetate-Sepharose. ER from both crude and highly purified preparations binds to metal-containing adsorbents complexed with Zn(II), Ni(II), Co(II), and Cu(II), but not to those complexed with Fe(II) and Cd(II). Elution of ER was obtained by chelating agents or by imidazole, thus indicating that histidine residues on the ER molecule are involved in the interaction with the metal. Analysis of affinity-labeled ER by [3H]tamoxifen aziridine after elution from a column of Zn(II)-charged iminodiacetate-Sepharose showed that ER fragments obtained by extensive trypsinization were also bound. Zn(II) and the same other metals able to bind ER, when immobilized on resins, inhibit the binding of estradiol to the receptor at micromolar concentrations. This inhibition is noncompetitive and can be reversed by EDTA. The inhibition of the hormone binding was still present after trypsin treatment of the cytosol, and it was abolished by preincubation with the hormone. Micromolar concentrations of these metals were able to block those chemical-physical changes occurring during the process of ER transformation in vitro. Furthermore, if added to pretransformed ER-hormone complex, they strongly inhibited the binding of the complex to isolated nuclei. The presence of metal binding sites that modulate the ER activity in the hormone binding domain of ER is therefore speculated. Since progesterone receptor showed the same pattern of binding and elution from metal-containing adsorbents, the presence of metal binding regulatory sites could be a property of all steroid receptors. PMID:2706244

  5. Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

    PubMed Central

    Lee, Tai-Sung; Giambaşu, George M.; Sosa, Carlos P.; Martick, Monika; Scott, William G.; York, Darrin M.

    2009-01-01

    The relationship between formation of active in-line attack conformations and monovalent (Na+) and divalent (Mg2+) metal ion binding in the hammerhead ribozyme has been explored with molecular dynamics simulations. To stabilize repulsions between negatively charged groups, different requirements of threshold occupancy of metal ions were observed in the reactant and activated precursor states both in the presence or absence of a Mg2+ in the active site. Specific bridging coordination patterns of the ions are correlated with the formation of active in-line attack conformations and can be accommodated in both cases. Furthermore, simulation results suggest that the hammerhead ribozyme folds to form an electronegative recruiting pocket that attracts high local concentrations of positive charge. The present simulations help to reconcile experiments that probe the metal ion sensitivity of hammerhead ribozyme catalysis and support the supposition that Mg2+, in addition to stabilizing active conformations, plays a specific chemical role in catalysis. PMID:19265710

  6. Target-classification approach applied to active UXO sites

    NASA Astrophysics Data System (ADS)

    Shubitidze, F.; Fernández, J. P.; Shamatava, Irma; Barrowes, B. E.; O'Neill, K.

    2013-06-01

    This study is designed to illustrate the discrimination performance at two UXO active sites (Oklahoma's Fort Sill and the Massachusetts Military Reservation) of a set of advanced electromagnetic induction (EMI) inversion/discrimination models which include the orthonormalized volume magnetic source (ONVMS), joint diagonalization (JD), and differential evolution (DE) approaches and whose power and flexibility greatly exceed those of the simple dipole model. The Fort Sill site is highly contaminated by a mix of the following types of munitions: 37-mm target practice tracers, 60-mm illumination mortars, 75-mm and 4.5'' projectiles, 3.5'', 2.36'', and LAAW rockets, antitank mine fuzes with and without hex nuts, practice MK2 and M67 grenades, 2.5'' ballistic windshields, M2A1-mines with/without bases, M19-14 time fuzes, and 40-mm practice grenades with/without cartridges. The site at the MMR site contains targets of yet different sizes. In this work we apply our models to EMI data collected using the MetalMapper (MM) and 2 × 2 TEMTADS sensors. The data for each anomaly are inverted to extract estimates of the extrinsic and intrinsic parameters associated with each buried target. (The latter include the total volume magnetic source or NVMS, which relates to size, shape, and material properties; the former includes location, depth, and orientation). The estimated intrinsic parameters are then used for classification performed via library matching and the use of statistical classification algorithms; this process yielded prioritized dig-lists that were submitted to the Institute for Defense Analyses (IDA) for independent scoring. The models' classification performance is illustrated and assessed based on these independent evaluations.

  7. Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites

    NASA Astrophysics Data System (ADS)

    Valasatava, Yana; Andreini, Claudia; Rosato, Antonio

    2015-03-01

    Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new computational protocol to systematically compare and classify metal-binding sites on the basis of their structural similarity. These sites are extracted from the MetalPDB database of minimal functional sites (MFSs) in metal-binding biological macromolecules. Structural similarity is measured by the scoring function of the available MetalS2 program. Hierarchical clustering was used to organize MFSs into clusters, for each of which a representative MFS was identified. The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. As examples, the application of the proposed computational protocol to all heme-binding proteins and zinc-binding proteins of known structure highlighted the existence of structural subtypes, validated known evolutionary links and shed new light on the occurrence of similar sites in systems at different evolutionary distances. The present approach thus makes available an innovative viewpoint on metalloproteins, where the functionally crucial metal sites effectively lead the discovery of structural and functional relationships in a largely protein-independent manner.

  8. Role of Metal Ions on the Activity of Mycobacterium tuberculosis Pyrazinamidase

    PubMed Central

    Sheen, Patricia; Ferrer, Patricia; Gilman, Robert H.; Christiansen, Gina; Moreno-Román, Paola; Gutiérrez, Andrés H.; Sotelo, Jun; Evangelista, Wilfredo; Fuentes, Patricia; Rueda, Daniel; Flores, Myra; Olivera, Paula; Solis, José; Pesaresi, Alessandro; Lamba, Doriano; Zimic, Mirko

    2012-01-01

    Pyrazinamidase of Mycobacterium tuberculosis catalyzes the conversion of pyrazinamide to the active molecule pyrazinoic acid. Reduction of pyrazinamidase activity results in a level of pyrazinamide resistance. Previous studies have suggested that pyrazinamidase has a metal-binding site and that a divalent metal cofactor is required for activity. To determine the effect of divalent metals on the pyrazinamidase, the recombinant wild-type pyrazinamidase corresponding to the H37Rv pyrazinamide-susceptible reference strain was expressed in Escherichia coli with and without a carboxy terminal. His-tagged pyrazinamidase was inactivated by metal depletion and reactivated by titration with divalent metals. Although Co2+, Mn2+, and Zn2+ restored pyrazinamidase activity, only Co2+ enhanced the enzymatic activity to levels higher than the wild-type pyrazinamidase. Cu2+, Fe2+, Fe3+, and Mg2+ did not restore the activity under the conditions tested. Various recombinant mutated pyrazinamidases with appropriate folding but different enzymatic activities showed a differential pattern of recovered activity. X-ray fluorescence and atomic absorbance spectroscopy showed that recombinant wild-type pyrazinamidase expressed in E. coli most likely contained Zn. In conclusion, this study suggests that M. tuberculosis pyrazinamidase is a metalloenzyme that is able to coordinate several ions, but in vivo, it is more likely to coordinate Zn2+. However, in vitro, the metal-depleted enzyme could be reactivated by several divalent metals with higher efficiency than Zn. PMID:22764307

  9. Merging open metal sites and Lewis basic sites in a NbO-type metal-organic framework for improved C2H2/CH4 and CO2/CH4 separation.

    PubMed

    Song, Chengling; Hu, Jiayi; Ling, Yajing; Feng, Yunlong; Chen, De-Li; He, Yabing

    2015-09-01

    A new three-dimensional NbO-type porous metal-organic framework ZJNU-47 was synthesized via a solvothermal reaction of Cu(NO3)2·3H2O and a Lewis basic nitrogen donor site-rich tetracarboxylate, namely, 5,5'-(pyridazine-3,6-diyl)-diisophthalate, and the structure was characterized by single-crystal X-ray diffraction to be isostructural with NOTT-101. With the synergistic effect of open metal sites, Lewis basic sites and a suitable pore space, the MOF material ZJNU-47a after activation can take up a large amount of C2H2 and CO2. The gravimetric C2H2 uptake of 214 cm(3) (STP) g(-1) at room temperature and 1 atm is the highest among all reported MOFs to date, and the gravimetric CO2 uptake of 108 cm(3) (STP) g(-1) is also among the highest reported for MOFs. Compared to the isostructural MOF NOTT-101a, ZJNU-47a exhibits a significant increase in C2H2 and CO2 uptake and thus improved C2H2/CH4 and CO2/CH4 separations. Significantly, comprehensive DFT studies of C2H2 and CO2 adsorption have revealed that the open nitrogen donor sites are comparable and even superior to open metal sites regarding the adsorption sites. This work demonstrated that the simultaneous introduction of Lewis basic nitrogen donor sites and Lewis acidic metal sites into the framework is a promising approach to improve the gas sorption toward CO2 and C2H2 and thus to produce materials possessing enhanced C2H2/CH4 and CO2/CH4 separation performance. PMID:26223674

  10. Reference site selection report for the advanced liquid metal reactor at the Idaho National Engineering Laboratory

    SciTech Connect

    Sivill, R.L.

    1990-03-01

    This Reference Site Selection Report was prepared by EG G, Idaho Inc., for General Electric (GE) to provide information for use by the Department of Energy (DOE) in selecting a Safety Test Site for an Advanced Liquid Metal Reactor. Similar Evaluation studies are planned to be conducted at other potential DOE sites. The Power Reactor Innovative Small Module (PRISM) Concept was developed for ALMR by GE. A ALMR Safety Test is planned to be performed on a DOE site to demonstrate features and meet Nuclear Regulatory Commission Requirements. This study considered possible locations at the Idaho National Engineering Laboratory that met the ALMR Prototype Site Selection Methodology and Criteria. Four sites were identified, after further evaluation one site was eliminated. Each of the remaining three sites satisfied the criteria and was graded. The results were relatively close. Thus concluding that the Idaho National Engineering Laboratory is a suitable location for an Advanced Liquid Metal Reactor Safety Test. 23 refs., 13 figs., 9 tabs.

  11. XAS on Rh and Ir metal sites in post synthetically functionalized UiO-67 Zirconium MOFs

    NASA Astrophysics Data System (ADS)

    Braglia, L.; Borfecchia, E.; Lomachenko, K. A.; Øien, S.; Lillerud, K. P.; Lamberti, C.

    2016-05-01

    We synthesized UiO-67 metal-organic-frameworks (MOFs) functionalized with different transition metals (Rh, Ir). Using EXAFS we verified that the synthesis has been successful. Furthermore, we observed the change of local environment while varying of metal site. XAS spectroscopy is the most informative technique to characterize these kind of materials and to study the local environment around the metal site.

  12. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  13. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  14. Waste site reclamation with recovery of radionuclides and metals

    DOEpatents

    Francis, Arokiasamy J.; Dodge, Cleveland J.

    1994-01-01

    A method for decontaminating radionuclides and other toxic metal-contaminate The U.S. government has certain rights in this invention pursuant to Contract Number DE-AC02-76CH00016 between the U.S. Department of Energy and Associated Universities, Inc.

  15. Waste site reclamation with recovery of radionuclides and metals

    DOEpatents

    Francis, A.J.; Dodge, C.J.

    1994-03-08

    A method for decontaminating radionuclides and other toxic metal-contaminate The U.S. government has certain rights in this invention pursuant to Contract Number DE-AC02-76CH00016 between the U.S. Department of Energy and Associated Universities, Inc.

  16. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-01-01

    One strategy to markedly increase the gas storage capacity of metal–organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules—specifically hydrogen, methane, or carbon dioxide.

  17. Metal Toxicity Affects Fungal and Bacterial Activities in Soil Differently

    PubMed Central

    Rajapaksha, R. M. C. P.; Tobor-Kapłon, M. A; Bååth, E.

    2004-01-01

    Although the toxic effect of heavy metals on soil microorganism activity is well known, little is known about the effects on different organism groups. The influence of heavy metal addition on total, bacterial, and fungal activities was therefore studied for up to 60 days in a laboratory experiment using forest soil contaminated with different concentrations of Zn or Cu. The effects of the metals differed between the different activity measurements. During the first week after metal addition, the total activity (respiration rate) decreased by 30% at the highest level of contamination and then remained stable during the 60 days of incubation. The bacterial activity (thymidine incorporation rate) decreased during the first days with the level of metal contamination, resulting in a 90% decrease at the highest level of contamination. Bacterial activity then slowly recovered to values similar to those of the control soil. The recovery was faster when soil pH, which had decreased due to metal addition, was restored to control values by liming. Fungal activity (acetate-in-ergosterol incorporation rate) initially increased with the level of metal contamination, being up to 3 and 7 times higher than that in the control samples during the first week at the highest levels of Zn and Cu addition, respectively. The positive effect of metal addition on fungal activity then decreased, but fungal activity was still higher in contaminated than in control soil after 35 days. This is the first direct evidence that fungal and bacterial activities in soil are differently affected by heavy metals. The different responses of bacteria and fungi to heavy metals were reflected in an increase in the relative fungal/bacterial ratio (estimated using phospholipid fatty acid analysis) with increased metal load. PMID:15128558

  18. Metal toxicity affects fungal and bacterial activities in soil differently.

    PubMed

    Rajapaksha, R M C P; Tobor-Kapłon, M A; Bååth, E

    2004-05-01

    Although the toxic effect of heavy metals on soil microorganism activity is well known, little is known about the effects on different organism groups. The influence of heavy metal addition on total, bacterial, and fungal activities was therefore studied for up to 60 days in a laboratory experiment using forest soil contaminated with different concentrations of Zn or Cu. The effects of the metals differed between the different activity measurements. During the first week after metal addition, the total activity (respiration rate) decreased by 30% at the highest level of contamination and then remained stable during the 60 days of incubation. The bacterial activity (thymidine incorporation rate) decreased during the first days with the level of metal contamination, resulting in a 90% decrease at the highest level of contamination. Bacterial activity then slowly recovered to values similar to those of the control soil. The recovery was faster when soil pH, which had decreased due to metal addition, was restored to control values by liming. Fungal activity (acetate-in-ergosterol incorporation rate) initially increased with the level of metal contamination, being up to 3 and 7 times higher than that in the control samples during the first week at the highest levels of Zn and Cu addition, respectively. The positive effect of metal addition on fungal activity then decreased, but fungal activity was still higher in contaminated than in control soil after 35 days. This is the first direct evidence that fungal and bacterial activities in soil are differently affected by heavy metals. The different responses of bacteria and fungi to heavy metals were reflected in an increase in the relative fungal/bacterial ratio (estimated using phospholipid fatty acid analysis) with increased metal load. PMID:15128558

  19. A Relaxed Active Site After Exon Ligation by the Group I Intron

    SciTech Connect

    Lipchock,S.; Strobel, S.

    2008-01-01

    During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.

  20. Synthesis of supported bimetallic nanoparticles with controlled size and composition distributions for active site elucidation

    SciTech Connect

    Hakim, Sikander H.; Sener, Canan; Alba Rubio, Ana C.; Gostanian, Thomas M.; O'neill, Brandon J; Ribeiro, Fabio H.; Miller, Jeffrey T.; Dumesic, James A

    2015-08-01

    Elucidation of active sites in supported bimetallic catalysts is complicated by the high level of dispersity in the nanoparticle size and composition that is inherent in conventional methods of catalyst preparation. We present a synthesis strategy that leads to highly dispersed, bimetallic nanoparticles with uniform particle size and composition by means of controlled surface reactions. We demonstrate the synthesis of three systems, RhMo, PtMo, and RhRe, consisting of a highly reducible metal with an oxophilic promoter. These catalysts are characterized by FTIR, CO chemisorption, STEM/EDS, TPR, and XAS analysis. The catalytic properties of these bimetallic nanoparticles were probed for the selective CO hydrogenolysis of (hydroxymethyl)tetrahydropyran to produce 1,6 hexanediol. Based on the characterization results and reactivity trends, the active sites in the hydrogenolysis reaction are identified to be small ensembles of the more noble metal (Rh, Pt) adjacent to highly reduced moieties of the more oxophilic metal (Mo, Re).

  1. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    PubMed

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO. PMID:15901543

  2. Size-dependent catalytic activity of supported metal clusters

    NASA Astrophysics Data System (ADS)

    Xu, Z.; Xiao, F.-S.; Purnell, S. K.; Alexeev, O.; Kawi, S.; Deutsch, S. E.; Gates, B. C.

    1994-11-01

    BECAUSE catalysis by metals is a surface phenomenon, many technological catalysts contain small (typically nanometre-sized) supported metal particles with a large fraction of the atoms exposed1. Many reactions, such as hydrocarbon hydrogenations, are structure-insensitive, proceeding at approximately the same rate on metal particles of various sizes provided that they are larger than about 1 nm and show bulk-like metallic behaviour1. But it is not known whether the catalytic properties of metal particles become size-dependent as the particles become so small that they are no longer metallic in character. Here we investigate the catalytic behaviour of precisely defined clusters of just four and six iridium atoms on solid supports. We find that the Ir4 and Ir6 clusters differ in catalytic activity both from each other and from metallic Ir particles. This raises the possibility of tailoring the catalytic behaviour of metal clusters by controlling the cluster size.

  3. Pharmacological activity of metal binding agents that alter copper bioavailability

    PubMed Central

    Helsel, Marian E.

    2015-01-01

    Iron, copper and zinc are required nutrients for many organisms but also potent toxins if misappropriated. An overload of any of these metals can be cytotoxic and ultimately lead to organ failure, whereas deficiencies can result in anemia, weakened immune system function, and other medical conditions. Cellular metal imbalances have been implicated in neurodegenerative diseases, cancer and infection. It is therefore critical for living organisms to maintain careful control of both the total levels and subcellular distributions of these metals to maintain healthy function. This perspective explores several strategies envisioned to alter the bioavailability of metal ions by using synthetic metal-binding agents targeted for diseases where misappropriated metal ions are suspected of exacerbating cellular damage. Specifically, we discuss chemical properties that influence the pharmacological outcome of a subset of metal-binding agents known as ionophores, and review several examples that have shown multiple pharmacological activities in metal-related diseases, with a specific focus on copper. PMID:25797044

  4. Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations.

    PubMed

    Ratheal, Ian M; Virgin, Gail K; Yu, Haibo; Roux, Benoît; Gatto, Craig; Artigas, Pablo

    2010-10-26

    The Na/K pump is a P-type ATPase that exchanges three intracellular Na(+) ions for two extracellular K(+) ions through the plasmalemma of nearly all animal cells. The mechanisms involved in cation selection by the pump's ion-binding sites (site I and site II bind either Na(+) or K(+); site III binds only Na(+)) are poorly understood. We studied cation selectivity by outward-facing sites (high K(+) affinity) of Na/K pumps expressed in Xenopus oocytes, under voltage clamp. Guanidinium(+), methylguanidinium(+), and aminoguanidinium(+) produced two phenomena possibly reflecting actions at site III: (i) voltage-dependent inhibition (VDI) of outwardly directed pump current at saturating K(+), and (ii) induction of pump-mediated, guanidinium-derivative-carried inward current at negative potentials without Na(+) and K(+). In contrast, formamidinium(+) and acetamidinium(+) induced K(+)-like outward currents. Measurement of ouabain-sensitive ATPase activity and radiolabeled cation uptake confirmed that these cations are external K(+) congeners. Molecular dynamics simulations indicate that bound organic cations induce minor distortion of the binding sites. Among tested metals, only Li(+) induced Na(+)-like VDI, whereas all metals tested except Na(+) induced K(+)-like outward currents. Pump-mediated K(+)-like organic cation transport challenges the concept of rigid structural models in which ion specificity at site I and site II arises from a precise and unique arrangement of coordinating ligands. Furthermore, actions by guanidinium(+) derivatives suggest that Na(+) binds to site III in a hydrated form and that the inward current observed without external Na(+) and K(+) represents cation transport when normal occlusion at sites I and II is impaired. These results provide insights on external ion selectivity at the three binding sites. PMID:20937860

  5. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  6. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  7. Metal-Organic Framework Nodes Support Single-Site Magnesium-Alkyl Catalysts for Hydroboration and Hydroamination Reactions.

    PubMed

    Manna, Kuntal; Ji, Pengfei; Greene, Francis X; Lin, Wenbin

    2016-06-22

    Here we present the first example of a single-site main group catalyst stabilized by a metal-organic framework (MOF) for organic transformations. The straightforward metalation of the secondary building units of a Zr-MOF with Me2Mg affords a highly active and reusable solid catalyst for hydroboration of carbonyls and imines and for hydroamination of aminopentenes. Impressively, the Mg-functionalized MOF displayed very high turnover numbers of up to 8.4 × 10(4) for ketone hydroboration and could be reused more than 10 times. MOFs can thus be used to develop novel main group solid catalysts for sustainable chemical synthesis. PMID:27282364

  8. Metal binding 'finger' structures in the glucocorticoid receptor defined by site-directed mutagenesis.

    PubMed Central

    Severne, Y; Wieland, S; Schaffner, W; Rusconi, S

    1988-01-01

    The glucocorticoid receptor and the other members of the steroid receptor super-family share a highly conserved, cysteine-rich region which coincides with the DNA binding/transactivating domain. It has been postulated that this region is folded into two 'zinc finger' structures, similar to those originally reported for the transcription factor TFIIIA. The first potential finger domain contains four conserved cysteines and one conserved histidine, while the second contains five conserved cysteines. Using site-directed mutagenesis, we have analysed the consequences of altering the proposed finger-like structures. Our results show that most of the mutations affecting the conserved cysteines result in a total loss of glucocorticoid receptor function. In one important exception, however, a conserved cysteine (Cys500) is dispensable for glucocorticoid receptor activity and therefore cannot be involved in complexing a metal ion to form a finger structure. Moreover, the replacement of either Cys476 or Cys482 by His residues maintains partial in vivo activity of the glucocorticoid receptor, while their exchange for an alanine or serine residue, respectively, eliminates receptor function. These results support, at a genetic level, the involvement of cysteines of the glucocorticoid receptor DNA binding domain in metal ion complexation and define the candidate residues involved in such coordination. Images PMID:3191912

  9. Phytoremediation and long-term site management of soil contaminated with pentachlorophenol (PCP) and heavy metals.

    PubMed

    Mills, Tessa; Arnold, Barbara; Sivakumaran, Siva; Northcott, Grant; Vogeler, Iris; Robinson, Brett; Norling, Cara; Leonil, Doris

    2006-05-01

    Pentachlorophenol (PCP) is a persistent organic pollutant (POP) previously used as a timber treatment chemical to prevent sap stain and wood rot. Commonly used in wood treatment industries for the last 50 years, there are now many sites worldwide that are contaminated with PCP. Although persistent, PCP is a mobile contaminant and therefore has a propensity to leach and contaminate surrounding environments. Both willow (Salix sp., 'Tangoio') and poplar (Populus sp. 'Kawa') growing in an open-ended plastic greenhouse were found to tolerate soil PCP concentrations of 250 mg kg(-1) or less and both species stimulated a significant increase in soil microbial activity when compared to unplanted controls. Both poplar and willow could not survive PCP concentrations above 250 mg kg(-1) in soil. Pentachlorophenol degradation occurred in both planted and unplanted pots, but a higher rate of degradation was observed in the planted pots. Soil contaminated by wood-treatment activities often contains co-contaminants such as B, Cr, Cu and As, that are also used as timber preservatives. An additional column leaching experiment, done along side the potted trial, found that PCP, B, Cr, Cu and As were all present in the column leachate. This indicates that although Cu, Cr and As are generally considered immobile in the soil, they were mobilised under our column conditions. If a contaminated site were to be hydraulically 'sealed' using plants, a reticulation irrigation system should be installed to capture any contaminant leachate resulting from heavy rains. This captured leachate can either be independently treated, or reapplied to the site. Our data demonstrate a reduction in soil hydraulic conductivity with repeated application of leachate containing PCP and metal compounds but the soil did not become anaerobic. This would need to be considered in site remediation design. PMID:16202508

  10. Mutants of metal binding site M1 in APP E2 show metal specific differences in binding of heparin but not of sorLA.

    PubMed

    Dienemann, Christian; Coburger, Ina; Mehmedbasic, Arnela; Andersen, Olav M; Than, Manuel E

    2015-04-21

    The amyloid precursor protein (APP) and its neurotoxic cleavage product Aβ are key players in the development of Alzheimer's disease (AD) and appear to be essential for neuronal development and cell homeostasis. Proteolytic processing of APP and its physiological function depend on its interaction with heparin and are influenced by the binding of metal ions and sorLA. We created various mutations of metal binding site M1 residing within the extracellular E2 domain of APP. Using isothermal titration calorimetry and circular dichroism spectroscopy, we analyzed the binding of Cu(2+) and Zn(2+) to APP E2 and identified two mutations that are most suited for functional studies to dissect ion specific effects of metal binding. The H313A mutation abrogates only copper-based effects, whereas the H382A mutation weakens any metal binding at M1 of APP E2. Subsequently, we tested the effect of Cu(2+) and Zn(2+) on the binding of heparin and sorLA to APP E2 using a chromatographic technique and surface plasmon resonance. We show that Zn(2+) and to a larger degree also Cu(2+) enhance the binding of heparin to APP E2, consistent with an extracellular regulation of the function of APP by both metal ions. In contrast, neither ion seemed to affect the interaction between APP E2 and sorLA. This supports an intracellular interaction between the latter two partners that would not sense extracellular variations of metal ions upon synaptic activity. PMID:25835329

  11. Heavy metal concentrations in marine fishes collected from fish culture sites in Hong Kong.

    PubMed

    Wong, C K; Wong, P P; Chu, L M

    2001-01-01

    The levels of six heavy metals (Cd, Cr, Cu, Ni, Pb, and Zn) in different tissues of three species of cultured marine fishes (Epinephelus areolatus, Lutjanus russelli, and Sparus sarba) collected from three fish culture sites in Hong Kong were evaluated. Metal pollution problems in the fish culture sites were serious, as reflected by the high metal concentrations recorded in sea water, sediments, and the biomonitor Perna viridis. In general, tissues of all three species contained high concentrations of Zn and Cu, but much lower concentrations of Ni, Pb, Cd, and Cr. Similar pattern of heavy metal concentrations was observed in sea water, sediment, and P. viridis. Metal concentrations in various tissues varied greatly among species and among fish culture sites. Different tissues showed different capacity for accumulating heavy metals. Gonad of all three species contained high concentrations of Zn. On the other hand, liver seemed to be the primary organ for Cu accumulation. Overall, metal concentrations in the tissues of culture marine fishes were much lower than those in P. viridis. Despite high metal levels in sea water and sediments, concentrations of Cd, Cr, and Pb in edible tissues, including muscle and skin, did not exceed permissible levels recommended by the Hong Kong Government for human consumption. PMID:11116341

  12. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  13. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    PubMed Central

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B; Sagi, Irit; Havenith, Martina

    2012-01-01

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site. PMID:21926991

  14. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    SciTech Connect

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B.; Sagi, Irit; Havenith, Martina

    2011-09-18

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.

  15. A study on the flexibility of enzyme active sites

    PubMed Central

    2011-01-01

    Background A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted. Results Most of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites. Conclusions This proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites. PMID:21342563

  16. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.

  17. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions.

  18. Site-directed mutagenesis and metal ion studies with E. coli L-threonine dehydrogenase (TDH)

    SciTech Connect

    Yenwen Chen; Epperly, B.R.; Dekker, E.E. )

    1991-03-11

    TDH, which catalyzes L-threonine + NAD{sup +}{yields}2-amino-3-ketobutyrate + NADH + H{sup +}, initiates the primary route for threonine utilization in eukaryotes and prokaryotes. E. coli TDH is a homotetramer of mass {congruent} 50 kD. Chemical inactivation/peptide sequencing studies showed that Cys-38 and 1 Arg residue/subunit are required for catalytic activity. The primary structure of E. coli TDH has been deduced by DNA sequencing of the tdh gene; homology comparisons with other dehydrogenases place it with the zinc-containing long-chain alcohol/polyol dehydrogenase family. Neutron activation and atomic absorption analyses of pure E. coli TDH as isolated now show it contains 1 Zn{sup 2+}/enzyme subunit. Timed removal of Zn{sup 2+} with 1,10-phenanthroline gives a good correlation between remaining activity and zinc content; inactive enzyme has no Zn{sup 2+}. The native metal ion can be exchanged with either {sup 65}Zn{sup 2+}, Co{sup 2+}, or Cd{sup 2+} with no change in sp. act. Exchange studies with {sup 65}Zn{sup 2+} frequently yields 1.9 to 1.0 Zn{sup 2+}/TDH subunit with no increase in sp. act. above 1 Zn{sup 2+}/subunit, suggesting a possible second Zn{sup 2+}-binding site. Cys-38 was projected to be one possible zinc ligand. Cys-38 was changed to Ser by site-directed mutagenesis. The pure mutant protein as isolated contains 1 Zn{sup 2+}/subunit but shows no TDH activity; very low activity is seen in the presence of high (Zn{sup 2+}).

  19. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  20. The use of tetragnathid spiders as bioindicators of metal exposure at a coal ash spill site.

    PubMed

    Otter, Ryan R; Hayden, Mary; Mathews, Teresa; Fortner, Allison; Bailey, Frank C

    2013-09-01

    On 22 December 2008, a dike containing coal fly ash from the Tennessee Valley Authority Kingston Fossil Fuel Plant (TN, USA) failed, resulting in the largest coal ash spill in US history. The present study was designed to determine sediment metal concentrations at multiple site locations and to determine whether site-specific bioaccumulation of metals existed in tetragnathid spiders. Selenium and nickel were the only 2 metals to exceed the US Environmental Protection Agency sediment screening levels. Selenium concentrations in spiders were significantly higher at ash-affected sites than in those from reference sites. The ratio of methylmercury to total mercury in spiders was found to be similar to that in other organisms (65-75%), which highlights the potential use of tetragnathid spiders as an indicator species for tracing contaminant transfer between the aquatic and terrestrial ecosystems. PMID:23686551

  1. [Biological activity of selenorganic compounds at heavy metal salts intoxication].

    PubMed

    Rusetskaya, N Y; Borodulin, V B

    2015-01-01

    Possible mechanisms of the antitoxic action of organoselenium compounds in heavy metal poisoning have been considered. Heavy metal toxicity associated with intensification of free radical oxidation, suppression of the antioxidant system, damage to macromolecules, mitochondria and the genetic material can cause apoptotic cell death or the development of carcinogenesis. Organic selenium compounds are effective antioxidants during heavy metal poisoning; they exhibit higher bioavailability in mammals than inorganic ones and they are able to activate antioxidant defense, bind heavy metal ions and reactive oxygen species formed during metal-induced oxidative stress. One of promising organoselenium compounds is diacetophenonyl selenide (DAPS-25), which is characterized by antioxidant and antitoxic activity, under conditions including heavy metal intoxication. PMID:26350735

  2. Catalytic activity of noble metals for metal-assisted chemical etching of silicon

    NASA Astrophysics Data System (ADS)

    Yae, Shinji; Morii, Yuma; Fukumuro, Naoki; Matsuda, Hitoshi

    2012-06-01

    Metal-assisted chemical etching of silicon is an electroless method that can produce porous silicon by immersing metal-modified silicon in a hydrofluoric acid solution without electrical bias. We have been studying the metal-assisted hydrofluoric acid etching of silicon using dissolved oxygen as an oxidizing agent. Three major factors control the etching reaction and the porous silicon structure: photoillumination during etching, oxidizing agents, and metal particles. In this study, the influence of noble metal particles, silver, gold, platinum, and rhodium, on this etching is investigated under dark conditions: the absence of photogenerated charges in the silicon. The silicon dissolution is localized under the particles, and nanopores are formed whose diameters resemble the size of the metal nanoparticles. The etching rate of the silicon and the catalytic activity of the metals for the cathodic reduction of oxygen in the hydrofluoric acid solution increase in the order of silver, gold, platinum, and rhodium.

  3. Catalytic activity of noble metals for metal-assisted chemical etching of silicon

    PubMed Central

    2012-01-01

    Metal-assisted chemical etching of silicon is an electroless method that can produce porous silicon by immersing metal-modified silicon in a hydrofluoric acid solution without electrical bias. We have been studying the metal-assisted hydrofluoric acid etching of silicon using dissolved oxygen as an oxidizing agent. Three major factors control the etching reaction and the porous silicon structure: photoillumination during etching, oxidizing agents, and metal particles. In this study, the influence of noble metal particles, silver, gold, platinum, and rhodium, on this etching is investigated under dark conditions: the absence of photogenerated charges in the silicon. The silicon dissolution is localized under the particles, and nanopores are formed whose diameters resemble the size of the metal nanoparticles. The etching rate of the silicon and the catalytic activity of the metals for the cathodic reduction of oxygen in the hydrofluoric acid solution increase in the order of silver, gold, platinum, and rhodium. PMID:22738277

  4. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  5. Plant growth promotion, metabolite production and metal tolerance of dark septate endophytes isolated from metal-polluted poplar phytomanagement sites.

    PubMed

    Berthelot, Charlotte; Leyval, Corinne; Foulon, Julie; Chalot, Michel; Blaudez, Damien

    2016-10-01

    Numerous studies address the distribution and the diversity of dark septate endophytes (DSEs) in the literature, but little is known about their ecological role and their effect on host plants, especially in metal-polluted soils. Seven DSE strains belonging to Cadophora, Leptodontidium, Phialophora and Phialocephala were isolated from roots of poplar trees from metal-polluted sites. All strains developed on a wide range of carbohydrates, including cell-wall-related compounds. The strains evenly colonized birch, eucalyptus and ryegrass roots in re-synthesis experiments. Root and shoot growth promotion was observed and was both plant and strain dependent. Two Phialophora and Leptodontidium strains particularly improved plant growth. However, there was no correlation between the level of root colonization by DSEs and the intensity of growth promotion. All strains produced auxin and six also stimulated plant growth through the release of volatile organic compounds (VOCs). SPME-GC/MS analyses revealed four major VOCs emitted by Cadophora and Leptodontidium The strains exhibited growth at high concentrations of several metals. The ability of metal-resistant DSE strains to produce both soluble and volatile compounds for plant growth promotion indicates interesting microbial resources with high potential to support sustainable production of bioenergy crops within the context of the phytomanagement of metal-contaminated sites. PMID:27364359

  6. Highly active oxygen reduction non-platinum group metal electrocatalyst without direct metal–nitrogen coordination

    PubMed Central

    Strickland, Kara; Miner, Elise; Jia, Qingying; Tylus, Urszula; Ramaswamy, Nagappan; Liang, Wentao; Sougrati, Moulay-Tahar; Jaouen, Frédéric; Mukerjee, Sanjeev

    2015-01-01

    Replacement of noble metals in catalysts for cathodic oxygen reduction reaction with transition metals mostly create active sites based on a composite of nitrogen-coordinated transition metal in close concert with non-nitrogen-coordinated carbon-embedded metal atom clusters. Here we report a non-platinum group metal electrocatalyst with an active site devoid of any direct nitrogen coordination to iron that outperforms the benchmark platinum-based catalyst in alkaline media and is comparable to its best contemporaries in acidic media. In situ X-ray absorption spectroscopy in conjunction with ex situ microscopy clearly shows nitrided carbon fibres with embedded iron particles that are not directly involved in the oxygen reduction pathway. Instead, the reaction occurs primarily on the carbon–nitrogen structure in the outer skin of the nitrided carbon fibres. Implications include the potential of creating greater active site density and the potential elimination of any Fenton-type process involving exposed iron ions culminating in peroxide initiated free-radical formation. PMID:26059552

  7. The Distribution and Health Risk Assessment of Metals in Soils in the Vicinity of Industrial Sites in Dongguan, China.

    PubMed

    Liu, Chao; Lu, Liwen; Huang, Ting; Huang, Yalin; Ding, Lei; Zhao, Weituo

    2016-01-01

    Exponential industrialization and rapid urbanization have resulted in contamination of soil by metals from anthropogenic sources in Dongguan, China. The aims of this research were to determine the concentration and distribution of various metals (arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn)) in soils and identify their potential health risks for local residents. A total of 106 soil samples were collected from the vicinity of industrial sites in Dongguan. Two types of samples were collected from each site: topsoil (0-20 cm, TS) and shallow soil (20-50 cm, SS). Results showed that the soils were contaminated by metals and pollution was mainly focused on TS. The geoaccumulation index (Igeo) and pollution indexes (PI) implied that there was a slight increase in the concentrations of Cd, Cu, Hg, Ni, and Pb, but the metal pollution caused by industrial activities was less severe, and elements of As and Cr exhibited non-pollution level. The risk assessment results suggested that there was a potential health risk associated with As and Cr exposure for residents because the carcinogenic risks of As and Cr via corresponding exposure pathways exceeded the safety limit of 10(-6) (the acceptable level of carcinogenic risk for humans). Furthermore, oral ingestion and inhalation of soil particles are the main exposure pathways for As and Cr to enter the human body. This study may provide basic information of metal pollution control and human health protection in the vicinity of industrial regions. PMID:27548198

  8. The Distribution and Health Risk Assessment of Metals in Soils in the Vicinity of Industrial Sites in Dongguan, China

    PubMed Central

    Liu, Chao; Lu, Liwen; Huang, Ting; Huang, Yalin; Ding, Lei; Zhao, Weituo

    2016-01-01

    Exponential industrialization and rapid urbanization have resulted in contamination of soil by metals from anthropogenic sources in Dongguan, China. The aims of this research were to determine the concentration and distribution of various metals (arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn)) in soils and identify their potential health risks for local residents. A total of 106 soil samples were collected from the vicinity of industrial sites in Dongguan. Two types of samples were collected from each site: topsoil (0–20 cm, TS) and shallow soil (20–50 cm, SS). Results showed that the soils were contaminated by metals and pollution was mainly focused on TS. The geoaccumulation index (Igeo) and pollution indexes (PI) implied that there was a slight increase in the concentrations of Cd, Cu, Hg, Ni, and Pb, but the metal pollution caused by industrial activities was less severe, and elements of As and Cr exhibited non-pollution level. The risk assessment results suggested that there was a potential health risk associated with As and Cr exposure for residents because the carcinogenic risks of As and Cr via corresponding exposure pathways exceeded the safety limit of 10−6 (the acceptable level of carcinogenic risk for humans). Furthermore, oral ingestion and inhalation of soil particles are the main exposure pathways for As and Cr to enter the human body. This study may provide basic information of metal pollution control and human health protection in the vicinity of industrial regions. PMID:27548198

  9. Effect of metal ion on the structure and function of LiPDF: The study of the fine structure around the metal site using XANES

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Chu, Wangsheng; Yang, Feifei; Yu, Meijuan; Zhao, Haifeng; Gong, Weimin; Dong, Yuhui; Xie, Yaning; Wu, Ziyu

    2010-07-01

    We used X-ray absorption near edge structure (XANES) spectroscopy to investigate the metal-dependent enzymatic activity of the peptide deformylase from Leptospira interrogans ( LiPDF). Ab initio full multiple scattering calculations performed by MXAN are applied to obtain the local structure of the cobalt-containing LiPDF (Co- LiPDF) and zinc-containing LiPDF (Zn- LiPDF) around the metal sites in pH9.0 buffer solution. The result shows the cobalt-wat1 (the bond water molecule) distance of Co- LiPDF is 1.89 Å, much shorter than that of Zn- LiPDF, 2.50 Å. That is an essential factor for its low catalytic activity.

  10. Metal-carbon nanocomposites based on activated IR pyrolized polyacrylonitrile

    NASA Astrophysics Data System (ADS)

    Efimov, Mikhail N.; Zhilyaeva, Natalya A.; Vasilyev, Andrey A.; Muratov, Dmitriy G.; Zemtsov, Lev M.; Karpacheva, Galina P.

    2016-05-01

    In this paper we report about new approach to preparation of metal-carbon nanocomposites based on activated carbon. Polyacrylonitrile is suggested as a precursor for Co, Pd and Ru nanoparticles carbon support which is prepared under IR pyrolysis conditions of a precursor. The first part of the paper is devoted to study activated carbon structural characteristics dependence on activation conditions. In the second part the effect of type of metal introduced in precursor on metal-carbon nanocomposite structural characteristics is shown. Prepared AC and nanocomposite samples are characterized by BET, TEM, SEM and X-ray diffraction.

  11. Speciation dynamics of metals in dispersion of nanoparticles with discrete distribution of charged binding sites.

    PubMed

    Polyakov, Pavel D; Duval, Jérôme F L

    2014-02-01

    We report a comprehensive theory to evaluate the kinetics of complex formation between metal ions and charged spherical nanoparticles. The latter consist of an ion-impermeable core surrounded by a soft shell layer characterized by a discrete axisymmetric 2D distribution of charged sites that bind metal ions. The theory explicitly integrates the conductive diffusion of metal ions from bulk solution toward the respective locations of the reactive sites within the particle shell volume. The kinetic constant k for outer-sphere nanoparticle-metal association is obtained from the sum of the contributions stemming from all reactive sites, each evaluated from the corresponding incoming flux of metal ions derived from steady-state Poisson-Nernst-Planck equations. Illustrations are provided to capture the basic intertwined impacts of particle size, overall particle charge, spatial heterogeneity in site distribution, type of particle (hard, core-shell or porous) and concentration of the background electrolyte on k. As a limit, k converges with predictions from previously reported analytical expressions derived for porous particles with low and high charge density, cases that correspond to coulombic and mean-field (smeared-out) electrostatic treatments, respectively. The conditions underlying the applicability of these latter approaches are rigorously identified in terms of (i) the extent of overlap between electric double layers around charged neighbouring sites, and (ii) the magnitude of the intraparticulate metal concentration gradient. For the first time, the proposed theory integrates the differentiated impact of the local potential around the charged binding sites amidst the overall particle field, together with that of the so-far discarded intraparticulate flux of metal ions. PMID:24336523

  12. Protein carbonyls and antioxidant defenses in corkwing wrasse (Symphodus melops) from a heavy metal polluted and a PAH polluted site.

    PubMed

    Almroth, Bethanie Carney; Sturve, Joachim; Stephensen, Eiríkur; Holth, Tor Fredrik; Förlin, Lars

    2008-08-01

    The use of fish in environmental monitoring has become increasingly important in recent years as anthropogenic substances, many of which function as prooxidants, are accumulating in aquatic environments. We have measured a battery of antioxidant defenses as a measure of oxidative status, as well as protein carbonylation as a measure of oxidative damage, in corkwing wrasse (Symphodus melops) captured near a disused copper mine, where water and sediment are contaminated with heavy metals, and an aluminum smelter, a site contaminated with PAHs. Results were compared to two different reference sites. Fish at the heavy metal site had lower glucose-6-phosphate dehydrogenase activity and elevated protein carbonyls (1.8 times) compared to fish from the reference site. At the PAH site, EROD was increased 2-fold, while total glutathione and methemoglobin reductase concentration, were decreased. No differences were seen in protein carbonyl levels at the PAH site. Measures of both antioxidant defenses and oxidative damage should be used when assessing effects of xenobiotics on oxidative stress in fish species. PMID:18490050

  13. Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from DFT Studies

    SciTech Connect

    Das, Ujjal; Zhang, Guanghui; Hu, Bo; Hock, Adam S.; Redfern, Paul C.; Miller, Jeffrey T.; Curtiss, Larry A.

    2015-12-01

    Amorphous silica (SiO2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure and activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. The molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.

  14. Trace Metal Content of Sediments Close to Mine Sites in the Andean Region

    PubMed Central

    Yacoub, Cristina; Pérez-Foguet, Agustí; Miralles, Nuria

    2012-01-01

    This study is a preliminary examination of heavy metal pollution in sediments close to two mine sites in the upper part of the Jequetepeque River Basin, Peru. Sediment concentrations of Al, As, Cd, Cu, Cr, Fe, Hg, Ni, Pb, Sb, Sn, and Zn were analyzed. A comparative study of the trace metal content of sediments shows that the highest concentrations are found at the closest points to the mine sites in both cases. The sediment quality analysis was performed using the threshold effect level of the Canadian guidelines (TEL). The sediment samples analyzed show that potential ecological risk is caused frequently at both sites by As, Cd, Cu, Hg, Pb, and Zn. The long-term influence of sediment metals in the environment is also assessed by sequential extraction scheme analysis (SES). The availability of metals in sediments is assessed, and it is considered a significant threat to the environment for As, Cd, and Sb close to one mine site and Cr and Hg close to the other mine site. Statistical analysis of sediment samples provides a characterization of both subbasins, showing low concentrations of a specific set of metals and identifies the main characteristics of the different pollution sources. A tentative relationship between pollution sources and possible ecological risk is established. PMID:22606058

  15. Unusual adsorption site behavior in PCN-14 metal-organic framework predicted from Monte Carlo simulation.

    PubMed

    Lucena, Sebastião M P; Mileo, Paulo G M; Silvino, Pedro F G; Cavalcante, Célio L

    2011-12-01

    The adsorption equilibrium of methane in PCN-14 was simulated by the Monte Carlo technique in the grand canonical ensemble. A new force field was proposed for the methane/PCN-14 system, and the temperature dependence of the molecular siting was investigated. A detailed study of the statistics of the center of mass and potential energy showed a surprising site behavior with no energy barriers between weak and strong sites, allowing open metal sites to guide methane molecules to other neighboring sites. Moreover, this study showed that a model assuming weakly adsorbing open metal clusters in PCN-14, densely populated only at low temperatures (below 150 K), can explain published experimental data. These results also explain previously observed discrepancies between neutron diffraction experiments and Monte Carlo simulations. PMID:22044392

  16. Active-site mobility revealed by the crystal structure of arylmalonate decarboxylase from Bordetella bronchiseptica.

    PubMed

    Kuettner, E Bartholomeus; Keim, Antje; Kircher, Markus; Rosmus, Susann; Sträter, Norbert

    2008-03-21

    Arylmalonate decarboxylase (AMDase) from Bordetella bronchiseptica catalyzes the enantioselective decarboxylation of arylmethylmalonates without the need for an organic cofactor or metal ion. The decarboxylation reaction is of interest for the synthesis of fine chemicals. As basis for an analysis of the catalytic mechanism of AMDase and for a rational enzyme design, we determined the X-ray structure of the enzyme up to 1.9 A resolution. Like the distantly related aspartate or glutamate racemases, AMDase has an aspartate transcarbamoylase fold consisting of two alpha/beta domains related by a pseudo dyad. However, the domain orientation of AMDase differs by about 30 degrees from that of the glutamate racemases, and also significant differences in active-site structures are observed. In the crystals, four independent subunits showing different conformations of active-site loops are present. This finding is likely to reflect the active-site mobility necessary for catalytic activity. PMID:18258259

  17. Ternary metal complexes of guaifenesin drug: Synthesis, spectroscopic characterization and in vitro anticancer activity of the metal complexes.

    PubMed

    Mahmoud, W H; Mahmoud, N F; Mohamed, G G; El-Sonbati, A Z; El-Bindary, A A

    2015-01-01

    The coordination behavior of a series of transition metal ions named Cr(III), Fe(III), Mn(II), Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) with a mono negative tridentate guaifenesin ligand (GFS) (OOO donation sites) and 1,10-phenanthroline (Phen) is reported. The metal complexes are characterized based on elemental analyses, IR, (1)H NMR, solid reflectance, magnetic moment, molar conductance, UV-vis spectral studies, mass spectroscopy, ESR, XRD and thermal analysis (TG and DTG). The ternary metal complexes were found to have the formulae of [M(GFS)(Phen)Cl]Cl·nH2O (M=Cr(III) (n=1) and Fe(III) (n=0)), [M(GFS)(Phen)Cl]·nH2O (M=Mn(II) (n=0), Zn(II) (n=0) and Cu(II) (n=3)) and [M(GFS)(Phen)(H2O)]Cl·nH2O (M=Co(II) (n=0), Ni(II) (n=0) and Cd(II) (n=4)). All the chelates are found to have octahedral geometrical structures. The ligand and its ternary chelates are subjected to thermal analyses (TG and DTG). The GFS ligand, in comparison to its ternary metal complexes also was screened for their antibacterial activity on gram positive bacteria (Bacillus subtilis and Staphylococcus aureus), gram negative bacteria (Escherichia coli and Neisseria gonorrhoeae) and for in vitro antifungal activity against (Candida albicans). The activity data show that the metal complexes have antibacterial and antifungal activity more than the parent GFS ligand. The complexes were also screened for its in vitro anticancer activity against the Breast cell line (MFC7) and the results obtained show that they exhibit a considerable anticancer activity. PMID:26067934

  18. Four-electron deoxygenative reductive coupling of carbon monoxide at a single metal site

    NASA Astrophysics Data System (ADS)

    Buss, Joshua A.; Agapie, Theodor

    2016-01-01

    Carbon dioxide is the ultimate source of the fossil fuels that are both central to modern life and problematic: their use increases atmospheric levels of greenhouse gases, and their availability is geopolitically constrained. Using carbon dioxide as a feedstock to produce synthetic fuels might, in principle, alleviate these concerns. Although many homogeneous and heterogeneous catalysts convert carbon dioxide to carbon monoxide, further deoxygenative coupling of carbon monoxide to generate useful multicarbon products is challenging. Molybdenum and vanadium nitrogenases are capable of converting carbon monoxide into hydrocarbons under mild conditions, using discrete electron and proton sources. Electrocatalytic reduction of carbon monoxide on copper catalysts also uses a combination of electrons and protons, while the industrial Fischer-Tropsch process uses dihydrogen as a combined source of electrons and electrophiles for carbon monoxide coupling at high temperatures and pressures. However, these enzymatic and heterogeneous systems are difficult to probe mechanistically. Molecular catalysts have been studied extensively to investigate the elementary steps by which carbon monoxide is deoxygenated and coupled, but a single metal site that can efficiently induce the required scission of carbon-oxygen bonds and generate carbon-carbon bonds has not yet been documented. Here we describe a molybdenum compound, supported by a terphenyl-diphosphine ligand, that activates and cleaves the strong carbon-oxygen bond of carbon monoxide, enacts carbon-carbon coupling, and spontaneously dissociates the resulting fragment. This complex four-electron transformation is enabled by the terphenyl-diphosphine ligand, which acts as an electron reservoir and exhibits the coordinative flexibility needed to stabilize the different intermediates involved in the overall reaction sequence. We anticipate that these design elements might help in the development of efficient catalysts for

  19. Four-electron deoxygenative reductive coupling of carbon monoxide at a single metal site.

    PubMed

    Buss, Joshua A; Agapie, Theodor

    2016-01-01

    Carbon dioxide is the ultimate source of the fossil fuels that are both central to modern life and problematic: their use increases atmospheric levels of greenhouse gases, and their availability is geopolitically constrained. Using carbon dioxide as a feedstock to produce synthetic fuels might, in principle, alleviate these concerns. Although many homogeneous and heterogeneous catalysts convert carbon dioxide to carbon monoxide, further deoxygenative coupling of carbon monoxide to generate useful multicarbon products is challenging. Molybdenum and vanadium nitrogenases are capable of converting carbon monoxide into hydrocarbons under mild conditions, using discrete electron and proton sources. Electrocatalytic reduction of carbon monoxide on copper catalysts also uses a combination of electrons and protons, while the industrial Fischer-Tropsch process uses dihydrogen as a combined source of electrons and electrophiles for carbon monoxide coupling at high temperatures and pressures. However, these enzymatic and heterogeneous systems are difficult to probe mechanistically. Molecular catalysts have been studied extensively to investigate the elementary steps by which carbon monoxide is deoxygenated and coupled, but a single metal site that can efficiently induce the required scission of carbon-oxygen bonds and generate carbon-carbon bonds has not yet been documented. Here we describe a molybdenum compound, supported by a terphenyl-diphosphine ligand, that activates and cleaves the strong carbon-oxygen bond of carbon monoxide, enacts carbon-carbon coupling, and spontaneously dissociates the resulting fragment. This complex four-electron transformation is enabled by the terphenyl-diphosphine ligand, which acts as an electron reservoir and exhibits the coordinative flexibility needed to stabilize the different intermediates involved in the overall reaction sequence. We anticipate that these design elements might help in the development of efficient catalysts for

  20. The Origin of the Catalytic Activity of a Metal Hydride in CO2 Reduction.

    PubMed

    Kato, Shunsuke; Matam, Santhosh Kumar; Kerger, Philipp; Bernard, Laetitia; Battaglia, Corsin; Vogel, Dirk; Rohwerder, Michael; Züttel, Andreas

    2016-05-10

    Atomic hydrogen on the surface of a metal with high hydrogen solubility is of particular interest for the hydrogenation of carbon dioxide. In a mixture of hydrogen and carbon dioxide, methane was markedly formed on the metal hydride ZrCoHx in the course of the hydrogen desorption and not on the pristine intermetallic. The surface analysis was performed by means of time-of-flight secondary ion mass spectroscopy and near-ambient pressure X-ray photoelectron spectroscopy, for the in situ analysis. The aim was to elucidate the origin of the catalytic activity of the metal hydride. Since at the initial stage the dissociation of impinging hydrogen molecules is hindered by a high activation barrier of the oxidised surface, the atomic hydrogen flux from the metal hydride is crucial for the reduction of carbon dioxide and surface oxides at interfacial sites. PMID:27061237

  1. The effect of the metal-on-metal hip controversy on Internet search activity.

    PubMed

    Phelan, Nigel; Kelly, John C; Moore, David P; Kenny, Patrick

    2014-10-01

    The recall of the articular surface replacement (ASR) hip prosthesis in 2010 represents one of the most controversial areas in orthopaedic surgery in recent years. The aim of this study was to compare the impact of the metal-on-metal hip controversy on Internet search activity in four different regions and determine whether the number of related news reports affected Internet search activity. The Google Trends, Keywords and News applications were used to record the number of news articles and Internet search activity for the terms "hip recall", "metal-on-metal hip" and "ASR hip" from October 2009 to October 2012 in the USA, the UK, Australia and Ireland. There was a large increase in search activity following the official recall in August 2010 in all countries. There was significantly greater search activity after the recall in Ireland compared with the UK for the search term "hip recall" (P = 0.004). For the term "metal-on-metal hip", the UK had significantly more search activity (P = 0.0009). There was a positive correlation between the number of news stories in UK and Ireland with Internet search activity but not in the USA or Australia. Differences between countries affected by the same recall highlight the complex effects of the media on public awareness. The data demonstrates a window of opportunity prior to the official recall for the development of an awareness campaign to provide patients with accurate information. PMID:24390041

  2. Isolation and divalent-metal activation of a β-xylosidase, RUM630-BX.

    PubMed

    Jordan, Douglas B; Braker, Jay D; Wagschal, Kurt; Stoller, J Rose; Lee, Charles C

    2016-01-01

    The gene encoding RUM630-BX, a β-xylosidase/arabinofuranosidase, was identified from activity-based screening of a cow rumen metagenomic library. The recombinant enzyme is activated as much as 14-fold (kcat) by divalent metals Mg(2+), Mn(2+) and Co(2+) but not by Ca(2+), Ni(2+), and Zn(2+). Activation of RUM630-BX by Mg(2+) (t0.5 144 s) is slowed two-fold by prior incubation with substrate, consistent with the X-ray structure of closely related xylosidase RS223-BX that shows the divalent-metal activator is at the back of the active-site pocket so that bound substrate could block its entrance. The enzyme is considerably more active on natural substrates than artificial substrates, with activity (kcat/Km) of 299 s(-1) mM(-1) on xylotetraose being the highest reported. PMID:26672463

  3. Active Sites Environmental Monitoring Program FY 1996 annual report

    SciTech Connect

    Morrissey, C.M.; Marshall, D.S.; Cunningham, G.R.

    1997-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1995 through September 1996. The Radioactive Solid Waste Operations Group (RSWOG) of the Waste Management and Remedial Action Division (WMRAD) and the Environmental Sciences Division (ESD) at Oak Ridge National Laboratory (ORNL) established ASEMP in 1989. The purpose of the program is to provide early detection and performance monitoring at active low-level waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 North as required by Chapters 2 and 3 of US Department of Energy Order 5820.2A.

  4. Active sites environmental monitoring Program - Program Plan: Revision 2

    SciTech Connect

    Morrissey, C.M.; Hicks, D.S.; Ashwood, T.L.; Cunningham, G.R.

    1994-05-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of active low-level-waste (LLW) and transuranic (TRU) waste facilities at Oak Ridge National Laboratory (ORNL). Several changes have recently occurred in regard to the sites that are currently used for waste storage and disposal. These changes require a second set of revisions to the ASEMP program plan. This document incorporates those revisions. This program plan presents the organization and procedures for monitoring the active sites. The program plan also provides internal reporting levels to guide the evaluation of monitoring results.

  5. Pollution distribution of heavy metals in surface soil at an informal electronic-waste recycling site.

    PubMed

    Fujimori, Takashi; Takigami, Hidetaka

    2014-02-01

    We studied distribution of heavy metals [lead (Pb), copper (Cu) and zinc (Zn)] in surface soil at an electronic-waste (e-waste) recycling workshop near Metro Manila in the Philippines to evaluate the pollution size (spot size, small area or the entire workshop), as well as to assess heavy metal transport into the surrounding soil environment. On-site length-of-stride-scale (~70 cm) measurements were performed at each surface soil point using field-portable X-ray fluorescence (FP-XRF). The surface soil at the e-waste recycling workshop was polluted with Cu, Zn and Pb, which were distributed discretely in surface soil. The site was divided into five areas based on the distance from an entrance gate (y-axis) of the e-waste recycling workshop. The three heavy metals showed similar concentration gradients in the y-axis direction. Zn, Pb and Cu concentrations were estimated to decrease to half of their maximum concentrations at ~3, 7 and 7 m from the pollution spot, respectively, inside the informal e-waste recycling workshop. Distance from an entrance may play an important role in heavy metal transport at the soil surface. Using on-site FP-XRF, we evaluated the metal ratio to characterise pollution features of the solid surface. Variability analysis of heavy metals revealed vanishing surficial autocorrelation over metre ranges. Also, the possibility of concentration prediction at unmeasured points using geostatistical kriging was evaluated, and heavy metals had a relative "small" pollution scales and remained inside the original workshop compared with toxic organohalogen compounds. Thus, exposure to heavy metals may directly influence the health of e-waste workers at the original site rather than the surrounding habitat and environmental media. PMID:23645478

  6. Activation of the C-H bond by metal complexes

    NASA Astrophysics Data System (ADS)

    Shilov, Aleksandr E.; Shul'pin, Georgiy B.

    1990-09-01

    Reactions involving the cleavage of C-H bonds by metal complexes in saturated and aromatic hydrocarbons and also in other compounds are examined. Some of these processes occur with formation of a carbon-metal bond, whilst in others the interaction of the complexes with the hydrocarbon takes place without direct contact between the metal atom and the C-H bonds. Metal compounds are widely used as initiators of the liquid-phase oxidation of hydrocarbons at relatively low temperatures. There is a prospect of creating new technologies for the chemical processing of petroleum and gas hydrocarbons, whereby they can be converted into valuable products, for example, into alcohols, ketones, and carboxylic acids, on the basis of processes involving metal complexes. The study of the metal complex activation of the C-H bond also makes it possible to understand and model the metalloenzyme-catalysed hydrocarbon oxidation reactions in the living cell. The bibliography includes 340 references.

  7. The second metal-binding site of 70 kDa heat-shock protein is essential for ADP binding, ATP hydrolysis and ATP synthesis.

    PubMed Central

    Wu, Xueji; Yano, Mihiro; Washida, Hiroyo; Kido, Hiroshi

    2004-01-01

    The chaperone activity of Hsp70 (70 kDa heat-shock protein) in protein folding and its conformational switch, including oligomeric and monomeric interconversion, are regulated by the hydrolysis of ATP and the ATP-ADP exchange cycle. The crystal structure of human ATPase domain shows two metal-binding sites, the first for ATP binding and a second, in close proximity to the first, whose function remains unknown [Sriram, Osipiuk, Freeman, Morimoto and Joachimiak (1997) Structure 5, 403-414]. In this study, we have characterized the second metal-binding motif by site-directed mutagenesis and the kinetics of ATP and ADP binding, and found that the second metal-binding site, comprising a loop co-ordinated by His-227, Glu-231 and Asp-232, participates both in ATP hydrolysis and ATP-synthetic activities, in co-operation with the first metal-binding site. The first metal-binding site, a catalytic centre, is essential for ATP binding and the second site for ADP binding in the reactions of ATP hydrolysis and ATP synthesis. PMID:14664695

  8. Active sites of ligand-protected Au25 nanoparticle catalysts for CO2 electroreduction to CO

    NASA Astrophysics Data System (ADS)

    Alfonso, Dominic R.; Kauffman, Douglas; Matranga, Christopher

    2016-05-01

    Recent experimental studies have reported the electrochemical reduction of carbon dioxide (CO2) into CO at atomically precise negatively charged Au25- nanoclusters. The studies showed CO2 conversion at remarkably low overpotentials, but the exact mechanisms and nature of the active sites remain unclear. We used first-principles density functional theory and continuum solvation models to examine the role of the cluster during electrochemical CO2 reduction and analyze the free energies of proposed intermediate species. Contrary to previous assumptions, our results show that the fully ligand protected cluster is not an active CO2 reduction catalyst because formation of the crucial carboxyl intermediate required very high electrochemical potentials. Instead, our calculations suggest that the reduction process likely occurs on a dethiolated gold site, and adsorbed carboxyl intermediate formation was significantly stabilized at dethiolated gold sites. These findings point to the crucial role of exposed metal sites during electrochemical CO2 reduction at gold nanocluster catalysts.

  9. Active sites of ligand-protected Au25 nanoparticle catalysts for CO2 electroreduction to CO.

    PubMed

    Alfonso, Dominic R; Kauffman, Douglas; Matranga, Christopher

    2016-05-14

    Recent experimental studies have reported the electrochemical reduction of carbon dioxide (CO2) into CO at atomically precise negatively charged Au25 (-) nanoclusters. The studies showed CO2 conversion at remarkably low overpotentials, but the exact mechanisms and nature of the active sites remain unclear. We used first-principles density functional theory and continuum solvation models to examine the role of the cluster during electrochemical CO2 reduction and analyze the free energies of proposed intermediate species. Contrary to previous assumptions, our results show that the fully ligand protected cluster is not an active CO2 reduction catalyst because formation of the crucial carboxyl intermediate required very high electrochemical potentials. Instead, our calculations suggest that the reduction process likely occurs on a dethiolated gold site, and adsorbed carboxyl intermediate formation was significantly stabilized at dethiolated gold sites. These findings point to the crucial role of exposed metal sites during electrochemical CO2 reduction at gold nanocluster catalysts. PMID:27179498

  10. Processing capabilties for the elimination of contaminated metal scrapyards at DOE/ORO-managed sites. [Metal smelting facility

    SciTech Connect

    Mack, J.E.; Williams, L.C.

    1982-01-01

    Capabilities exist for reducing all the contaminated nickel, aluminum, and copper scrap to ingot form by smelting. Processing these metals at existing facilities could be completed in about 5 or 6 years. However, these metals represent only about 20% of the total metal inventories currently on hand at the DOE/ORO-managed sites. No provisions have been made for the ferrous scrap. Most of the ferrous scrap is unclassified and does not require secured storage. Also, the potential resale value of the ferrous scrap at about $100 per ton is very low in comparison. Consequently, this scrap has been allowed to accumulate. With several modifications and equipment additions, the induction melter at PGDP could begin processing ferrous scrap after its commitment to nickel and aluminum. The PGDP smelter is a retrofit installation, and annual throughput capabilities are limited. Processing of the existing ferrous scrap inventories would not be completed until the FY 1995-2000 time frame. An alternative proposal has been the installation of induction melters at the other two enrichment facilities. Conceptual design of a generic metal smelting facility is under way. The design study includes capital and operating costs for scrap preparation through ingot storage at an annual throughput of 10,000 tons per year. Facility design includes an induction melter with the capability of melting both ferrous and nonferrous metals. After three years of operation with scrapyard feed, the smelter would have excess capacity to support on-site decontamination and decomissioning projects or upgrading programs. The metal smelting facility has been proposed for FY 1984 line item funding with start-up operations in FY 1986.

  11. Content and fractionation of heavy metals in soils of two contaminated sites in Taiwan

    SciTech Connect

    Shu, G.Y.; Liu, J.C. )

    1994-05-01

    The rice paddies near Taoyuan County, Taiwan, were contaminated with trace metals by the effluent from two plasticizer plants in the seventies. A study was conducted to: (i) determine the total metal contents, (ii) compare the extraction strength of different solutions, and (iii) investigate the metal speciation. Total soil metals at site 1 range from : Lead = 201 to 1995 mg Kg[sup [minus]1]; cadmium = 18 to 205 mg Kg[sup [minus]1]; and zinc = 131 to 282 mg Kg[sup [minus]1]. Total soil metals at site 2 ranged from: Lead = 80 to 148 mg Kg[sup [minus]1]; cadmium = 8 to 82 mg Kg[sup [minus]1]; and zinc = 55 to 65 mg Kg[sup [minus]1]. Five different extractants (4 N HNO[sub 3], aqua regia, 0.1 N HCl, 0.002 M EDTA, and 0.002 M NTA) were utilized and compared. Sequential extraction was conducted to assess the metal speciation in soil systems. Lead was found to be predominantly organic-bound or oxide-bound. The exchangeable fraction was the dominant form of cadmium in both sites. Zinc was mostly oxide-bound. The potential impacts on groundwater quality by cadmium were assessed. 21 refs., 5 figs., 5 tabs.

  12. Assessment of heavy metal contamination in soil due to leachate migration from an open dumping site

    NASA Astrophysics Data System (ADS)

    Kanmani, S.; Gandhimathi, R.

    2013-03-01

    The concentration of heavy metals was studied in the soil samples collected around the municipal solid waste (MSW) open dumpsite, Ariyamangalam, Tiruchirappalli, Tamilnadu to understand the heavy metal contamination due to leachate migration from an open dumping site. The dump site receives approximately 400-470 tonnes of municipal solid waste. Solid waste characterization was carried out for the fresh and old municipal solid waste to know the basic composition of solid waste which is dumped in the dumping site. The heavy metal concentration in the municipal solid waste fine fraction and soil samples were analyzed. The heavy metal concentration in the collected soil sample was found in the following order: Mn > Pb > Cu > Cd. The presence of heavy metals in soil sample indicates that there is appreciable contamination of the soil by leachate migration from an open dumping site. However, these pollutants species will continuously migrated and attenuated through the soil strata and after certain period of time they might contaminate the groundwater system if there is no action to be taken to prevent this phenomenon.

  13. Elevated temperature creep properties for selected active metal braze alloys

    SciTech Connect

    Stephens, J.J.

    1997-02-01

    Active metal braze alloys reduce the number of processes required for the joining of metal to ceramic components by eliminating the need for metallization and/or Ni plating of the ceramic surfaces. Titanium (Ti), V, and Zr are examples of active element additions which have been used successfully in such braze alloys. Since the braze alloy is expected to accommodate thermal expansion mismatch strains between the metal and ceramic materials, a knowledge of its elevated temperature mechanical properties is important. In particular, the issue of whether or not the creep strength of an active metal braze alloy is increased or decreased relative to its non-activated counterpart is important when designing new brazing processes and alloy systems. This paper presents a survey of high temperature mechanical properties for two pairs of conventional braze alloys and their active metal counterparts: (a) the conventional 72Ag-28Cu (Cusil) alloy, and the active braze alloy 62.2Ag- 36.2Cu-1.6Ti (Cusil ABA), and (b) the 82Au-18Ni (Nioro) alloy and the active braze alloy Mu-15.5M-0.75Mo-1.75V (Nioro ABA). For the case of the Cusil/Cusil ABA pair, the active metal addition contributes to solid solution strengthening of the braze alloy, resulting in a higher creep strength as compared to the non-active alloy. In the case of the Nioro/Nioro ABA pair, the Mo and V additions cause the active braze alloy to have a two-phase microstructure, which results in a reduced creep strength than the conventional braze alloy. The Garofalo sinh equation has been used to quantitatively describe the stress and temperature dependence of the deformation behavior. It will be observed that the effective stress exponent in the Garofalo sinh equation is a function of the instantaneous value of the stress argument.

  14. Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis.

    PubMed

    Kliegman, Joseph I; Griner, Sarah L; Helmann, John D; Brennan, Richard G; Glasfeld, Arthur

    2006-03-21

    The manganese transport regulator (MntR) of Bacillus subtilis is activated by Mn(2+) to repress transcription of genes encoding transporters involved in the uptake of manganese. MntR is also strongly activated by cadmium, both in vivo and in vitro, but it is poorly activated by other metal cations, including calcium and zinc. The previously published MntR.Mn(2+) structure revealed a binuclear complex of manganese ions with a metal-metal separation of 3.3 A (herein designated the AB conformer). Analysis of four additional crystal forms of MntR.Mn(2+) reveals that the AB conformer is only observed in monoclinic crystals at 100 K, suggesting that this conformation may be stabilized by crystal packing forces. In contrast, monoclinic crystals analyzed at room temperature (at either pH 6.5 or pH 8.5), and a second hexagonal crystal form (analyzed at 100 K), all reveal the shift of one manganese ion by 2.5 A, thereby leading to a newly identified conformation (the AC conformer) with an internuclear distance of 4.4 A. Significantly, the cadmium and calcium complexes of MntR also contain binuclear complexes with a 4.4 A internuclear separation. In contrast, the zinc complex of MntR contains only one metal ion per subunit, in the A site. Isothermal titration calorimetry confirms the stoichiometry of Mn(2+), Cd(2+), and Zn(2+) binding to MntR. We propose that the specificity of MntR activation is tied to productive binding of metal ions at two sites; the A site appears to act as a selectivity filter, determining whether the B or C site will be occupied and thereby fully activate MntR. PMID:16533030

  15. Efficiency of metal activators of accelerated sulfur vulcanization

    SciTech Connect

    Duchacek, V.; Kuta, A.; Pribyl, P. )

    1993-01-20

    The effects of copper, mercury, nickel, zinc, cadmium, indium, magnesium, and calcium stearates on the course of N-cyclohexyl-2-benzthiazylsulphenamide-accelerated sulfur vulcanization of natural rubber have been investigated on the basis of curemeter measurements at 145 C. The differences in the efficiencies of these metal activators of accelerated sulfur vulcanization have been discussed from the points of view of the electron configurations of the metals and their affinities to sulfur. The authors attempted to determine why zinc oxide is generally accepted as the best metal vulcanization activator.

  16. Distribution of trace metals at Hopewell Furnace National Historic Site, Berks and Chester Counties, Pennsylvania

    USGS Publications Warehouse

    Sloto, Ronald A.; Reif, Andrew G.

    2011-01-01

    Hopewell Furnace, located approximately 50 miles northwest of Philadelphia, was a cold-blast, charcoal iron furnace that operated for 113 years (1771 to 1883). The purpose of this study by the U.S. Geological Survey, in cooperation with the National Park Service, was to determine the distribution of trace metals released to the environment from an historical iron smelter at Hopewell Furnace National Historic Site (NHS). Hopewell Furnace used iron ore from local mines that contained abundant magnetite and accessory sulfide minerals enriched in arsenic, cobalt, copper, and other metals. Ore, slag, cast iron furnace products, soil, groundwater, stream base flow, streambed sediment, and benthic macroinvertebrates were sampled for this study. Soil samples analyzed in the laboratory had concentrations of trace metals low enough to meet Pennsylvania Department of Environmental Protection standards for non-residential use. Groundwater samples from the supply well met U.S. Environmental Protection Agency drinking-water regulations. Concentrations of metals in surface-water base flow at the five stream sampling sites were below continuous concentration criteria for protection of aquatic organisms. Concentrations of metals in sediment at the five stream sites were below probable effects level guidelines for protection of aquatic organisms except for copper at site HF-3. Arsenic, copper, lead, zinc, and possibly cobalt were incorporated into the cast iron produced by Hopewell Furnace. Manganese was concentrated in slag along with iron, nickel, and zinc. The soil near the furnace has elevated concentrations of chromium, copper, iron, lead, and zinc compared to background soil concentrations. Concentrations of toxic elements were not present at concentrations of concern in water, soil, or stream sediments, despite being elevated in ore, slag, and cast iron furnace products. The base-flow surface-water samples indicated good overall quality. The five sampled sites generally had

  17. Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

    PubMed

    Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

    2016-06-17

    Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes. PMID:26990764

  18. Arsenic and metals in soils in the vicinity of the Imperial Oil Company Superfund Site, Marlboro Township, Monmouth County, New Jersey. Water-resources investigations

    SciTech Connect

    Barringer, J.L.; Szabo, Z.; Barringer, T.H.

    1998-09-01

    Concentrations of arsenic exceed the New Jersey State Cleanup Criterion of 20 parts per million in sandy and clay-rich soils of two residential areas in the vicinity of the Imperial Oil Company Superfund site in Marlboro Township, Monmouth County, New Jersey. In order to determine the source of the arsenic and metals in soils in the two residential areas, soil samples were collected from (1) long-term forested areas, to determine background geologic and regional atmospheric inputs of arsenic and metals; (2) former and current orchards, to assess the range of concentrations of arsenic and metals that could be contributed by past use of pesticides; (3) the Imperial Oil Company Superfund site, to characterize the chemical composition of contamination from activities at the site; (4) a wooded area adjacent to the Superfund site, to determine whether arsenic and metals from the Superfund site were evident; and (5) the two residential areas, to compare soil chemistry in these areas with the chemistry of soils from forests, orchards, and the Superfund site. The soil samples were divided by soil horizon and were analyzed for 23 metals and metalloids, total organic carbon, and total sulfur. Additionally, air-flow models were used to determine whether roasting of arsenic at the Imperial Oil Company Superfund site was a possible source of arsenic in the soils.

  19. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    SciTech Connect

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  20. Encapsulating Metal Clusters and Acid Sites within Small Voids: Synthetic Strategies and Catalytic Consequences

    NASA Astrophysics Data System (ADS)

    Goel, Sarika

    The selective encapsulation of metal clusters within zeolites can be used to prepare clusters that are uniform in diameter and to protect them against sintering and contact with feed impurities, while concurrently allowing active sites to select reactants based on their molecular size, thus conferring enzyme-like specificity to chemical catalysis. The apertures in small and medium-pore zeolites preclude the use of post-synthetic protocols to encapsulate the relevant metal precursors because cationic or anionic precursors with their charge-balancing double layer and gaseous complexes cannot diffuse through their windows or channels. We have developed general strategies to encapsulate metal clusters within small-pore zeolites by using metal precursors stabilized by ammonia or organic amine ligands, which stabilize metal precursors against their premature precipitation at the high temperature and pH conditions required for the hydrothermal synthesis of the target zeolite structures and favor interactions between metal precursors and incipient aluminosilicate nuclei during the self-assembly of microporous frameworks. When synthesis temperatures were higher than 400 K, available ligands were unable to prevent the premature precipitation of the metal precursors. In such cases, encapsulation was achieved instead via interzeolite transformations after successfully encapsulating metal precursors or clusters via post-synthesis exchange or ligand protection into parent zeolites and subsequently converting them into the target structures while retaining the encapsulated clusters or precursors. Such strategies led to the successful selective encapsulation of a wide range of metal clusters (Pt, Pd, Ru, Rh, Ir, Re, and Ag) within small-pore (SOD (sodalite), LTA (Linde type A (zeolite A)), GIS (gismondine), and ANA (analcime)) and medium-pore (MFI (ZSM-5)) zeolites. These protocols provide novel and diverse mechanism-based strategies for the design of catalysts with protected

  1. Fuzzy hierarchical cross-clustering of data from abandoned mine site contaminated with heavy metals

    NASA Astrophysics Data System (ADS)

    Pourjabbar, A.; Sârbu, C.; Kostarelos, K.; Einax, J. W.; Büchel, G.

    2014-11-01

    The characteristics of pore water and slate samples are critically analyzed using fuzzy hierarchical cross-clustering statistical techniques. The main aim of this study was to investigate the source of contamination near an abandoned uranium mine in Germany. The mining activities were abandoned in 1990 the site was closed, and the surrounding area was remediated. However, heavy metal contamination is still detectable in water, soil and plants today. Hence, investigating the source of the current contamination is an important task. In order to achieve the goal, results from chemical analysis of both pore water samples and leachates from slate samples were initially analyzed using hard (classical) hierarchical clustering algorithms that did not provide meaningful results. By using two fuzzy clustering algorithms, Fuzzy Divisive Hierarchical Clustering (FDHC) and Fuzzy Hierarchical Cross-Clustering (FHCC), a relationship between the leachate from Ordovician-Silurian slate samples (10 samples collected from the test site and the surrounding area) and pore water samples (53 samples collected from 3 locations within the test site at 3 depths over the course of 4 years) was identified. The leachate data formed a cluster which was statistically similar to the cluster formed by the pore water samples collected from two of three locations. In addition, the fuzzy cross-clustering approach allowed for the identification of the characteristics (qualitative and quantitative) responsible for the observed similarities between all the samples. We conclude that the fuzzy algorithms were a better tool for the analysis and interpretation of geological/hydrogeological data where the data sets have an inherent vagueness/uncertainty.

  2. Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

    PubMed Central

    2015-01-01

    Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

  3. Active Insolubilized Antibiotics Based on Cellulose-Metal Chelates1

    PubMed Central

    Kennedy, J. F.; Barker, S. A.; Zamir, A.

    1974-01-01

    Cellulose was converted into a more reactive form by chelation with the transition metals titaniumIII, ironIII, tinIV, vanadiumIII, and zirconiumIV. The remaining unsubstituted ligands of the transition metal ions were found to be amenable to replacement by electron-donating groups of antibiotic molecules. Ampicillin, gentamicin, kanamycin, neomycin, paromomycin, polymyxin B, and streptomycin were used as antibacterial antibiotics, and amphotericin B and natamycin were used as antifungal antibiotics. Antibacterial activity of the products was tested against two gram-positive and two gram-negative bacteria, and antifungal activity was tested against four fungi. That the antibacterial antibiotics had complexed with the cellulose-metal chelates was demonstrated in that the product cellulose-metal-antibiotic chelates exhibited antibiotic activities whereas the metal chelates of cellulose themselves were inactive. Of 140 tests conducted, cellulose-metal-antibiotic chelates were active in 102 cases. Since the antibiotic derivatives were water insoluble and in fact retain some of the antibacterial activities of the parent compounds, the chelation method provides a facile way of rendering cellulose surfaces, etc., resistant to microbial attack over and above that degree of protection afforded by noncovalent adsorption of the antibiotic to cellulose itself. The underlying principles of the chelation reactions involved are discussed in detail. PMID:4451349

  4. Heavy metal migration in soils and rocks at historical smelting sites.

    PubMed

    Maskall, J; Whitehead, K; Thornton, I

    1995-09-01

    The vertical migration of metals through soils and rocks was investigated at five historical lead smelting sites ranging in age between 220 and 1900 years. Core samples were taken through metal-contaminated soils and the underlying strata. Concentration profiles of lead and zinc are presented from which values for the distances and rates of migration have been derived. Slag-rich soil horizons contain highly elevated metal concentrations and some contamination of underlying strata has occurred at all sites. However, the amounts of lead and zinc that have migrated from soils and been retained at greater depths are comparatively low. This low metal mobility in contaminated soils is partly attributed to the elevation of soil pH by the presence of calcium and carbonate originating from slag wastes and perhaps gangue minerals. Distances and rates of vertical migration were higher at those sites with soils underlain by sandstone than at those with soils underlain by clay. For sites with the same parent material, metal mobility appears to be increased at lower soil pH. The mean migration rates for lead and zinc reach maxima of 0.75 and 0.46 cm yr(-1) respectively in sandstone at Bole A where the elements have moved mean distances of 4.3 and 2.6 m respectively. There is some evidence that metal transport in the sandstone underlying Bole A and Cupola B occurs preferentially along rock fractures. The migration of lead and zinc is attenuated by subsurface clays leading to relatively low mean migration rates which range from 0.03 to 0.31 cm yr(-1) with many values typical of migration solely by diffusion. However, enhanced metal migration in clays at Cupola A suggest a preferential transport mechanism possibly in cracks or biopores. PMID:24194183

  5. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    SciTech Connect

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-03-20

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme.

  6. Innovative use of activated carbon for the removal of heavy metals from ground water sources

    SciTech Connect

    Lewis, T. III

    1996-12-31

    This report discusses the evaluation of the ENVIRO-CLEAN PROCESS, a technology developed by Lewis Environmental Services, Inc. for the recovery of metals such as chromium, mercury, copper, cadmium, lead, and zinc from surface and groundwater streams. This new heavy metal removal process (patent-pending) utilizes granular activated carbon with a proprietary conditioning pretreatment to enhance heavy metal adsorption combined with electrolytic metal recovery to produce a saleable metallic product. The process generates no sludge or hazardous waste and the effluent meets EPA limits. A 50 gpm system was installed for recovering hexavalent chromium from a ground water stream at a site located in Fresno, California. The effluent from the activated carbon system was reinjected into the ground water table with the hexavalent chromium concentration < 10 ppb. The system simultaneously removed trichloroethylene (TCE) to concentrations levels < 05 ppb. The activated carbon is regenerated off-site and the chromium electrolytically recovered. The full scale system has treated over 5 million gallons of ground water since installation. 5 refs., 1 fig., 3 tabs.

  7. Biologically active compounds of semi-metals.

    PubMed

    Rezanka, Tomás; Sigler, Karel

    2008-02-01

    Semi-metals (boron, silicon, arsenic and selenium) form organo-metal compounds, some of which are found in nature and affect the physiology of living organisms. They include, e.g., the boron-containing antibiotics aplasmomycin, borophycin, boromycin, and tartrolon or the silicon compounds present in "silicate" bacteria, relatives of the genus Bacillus, which release silicon from aluminosilicates through the secretion of organic acids. Arsenic is incorporated into arsenosugars and arsenobetaines by marine algae and invertebrates, and fungi and bacteria can produce volatile methylated arsenic compounds. Some prokaryotes can use arsenate as a terminal electron acceptor while others can utilize arsenite as an electron donor to generate energy. Selenium is incorporated into selenocysteine that is found in some proteins. Biomethylation of selenide produces methylselenide and dimethylselenide. Selenium analogues of amino acids, antitumor, antibacterial, antifungal, antiviral, anti-infective drugs are often used as analogues of important pharmacological sulfur compounds. Other metalloids, i.e. the rare and toxic tellurium and the radioactive short-lived astatine, have no biological significance. PMID:17991498

  8. Heavy metal levels in Nucella lapillus (gastropoda: prosobranchia) from sites with normal and penis-bearing females from New England

    SciTech Connect

    Miller, E.R. III; Pondick, J.S.

    1984-11-01

    Pseudohermaphroditism, as manifested by reproductively normal females possessing non-functioning penises, has been reported for more than thirty species of dioecious neogastropods. This anomaly was shown to be unrelated to age or parasitism, but the geographic distribution of this phenomenon indicated that it was environmentally induced rather than genetically controlled. In a survey of N. lapillus populations along the New England Coast, Pondick found abnormal females at sites directly under the influence of industrial discharges, sewage effluent, or vessel-related activities. Histological sections revealed the presence of a penial duct. The purpose of this study was to determine if there were differences in metal levels in the snail populations studied by Pondick, with particular attention to metals associated with boating activity.

  9. Quantification by PIXE of metallic sites in proteins separated by electrophoresis

    NASA Astrophysics Data System (ADS)

    Strivay, D.; Schoefs, B.; Weber, G.

    1998-03-01

    Electrophoresis on polyacrylamide gel (PAGE) is widely used in life sciences to determine the molecular weight of proteins in solution by separating them into different bands. By coupling electrophoresis and Particle Induced X-ray Emission (PIXE), the nature and the quantity of metals contained in proteins can be investigated. After the electrophoresis, the gel is dried and each track is scanned with a 2.5 MeV proton beam which induces X-ray emission. Analysis of these spectra allows the determination of the metals contained in an electrophoretic band. The metal content in each band is obtained by comparing the characteristic X-ray peak area with those obtained with polyacrylamide gels doped with the same metal. Finally, the relative concentration of each protein is determined by densitometry in order to compute the protein/metal ratio. An example of metallic site determination is presented. This procedure seems to be a very useful multielementary method for the determination of the metal amounts inside proteins after their separation by electrophoresis. Furthermore it allows to check if metals remain bound to proteins.

  10. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  11. Tuning Metal-Organic Frameworks with Open-Metal Sites and Its Origin for Enhancing CO2 Affinity by Metal Substitution.

    PubMed

    Park, Joonho; Kim, Heejin; Han, Sang Soo; Jung, Yousung

    2012-04-01

    Reducing anthropogenic carbon emission is a problem that requires immediate attention. Metal-organic frameworks (MOFs) have emerged as a promising new materials platform for carbon capture, of which Mg-MOF-74 offers chemospecific affinity toward CO2 because of the open Mg sites. Here we tune the binding affinity of CO2 for M-MOF-74 by metal substitution (M = Mg, Ca, and the first transition metal elements) and show that Ti- and V-MOF-74 can have an enhanced affinity compared to Mg-MOF-74 by 6-9 kJ/mol. Electronic structure calculations suggest that the origin of the major affinity trend is the local electric field effect of the open metal site that stabilizes CO2, but forward donation from the lone-pair electrons of CO2 to the empty d-levels of transition metals as in a weak coordination bond makes Ti and V have an even higher binding strength than Mg, Ca, and Sc. PMID:26286404

  12. Assessment of heavy metal pollution in soils and crops of industrial sites, Isfahan, Iran.

    PubMed

    Moradi, Anahita; Honarjoo, Naser; Fallahzade, Jaber; Najafi, Payam

    2013-01-15

    This study was planned to investigate the concentrations of heavy metal in soils and crops and estimate the potential health risks of metals to humans via consumption of crops grown at industrial sites (Zarrinshahr and Mobarakeh) and control site (Natanz) in Isfahan province, central Iran. The soils and food crops (wheat and rice grains and onion bulbs) were digested by acid digestion method and then were analyzed for Mn, Cu and Zn by atomic absorption spectrophotometer. The results showed that the concentration of Zn in the soils of Mobarakeh was higher than the soils of Zarrinshahr and Natanz. The concentrations of Mn in the soils of Natanz and Mobarakeh were higher than the soils of Zarrinshahr. The concentration of Zn in the wheat was significantly higher than that rice and onion crops. The concentrations of Zn and Cu were higher in wheat crop in Mobarakeh compared with other cases. Results of this study revealed that the concentrations of Zn, Cu and Mn in the soils of studied sites were below than the maximum allowable levels. The average concentration of Zn, Cu and Mn metals in rice, wheat and onion crops were below than the maximum allowable levels of WHO guideline. The estimated daily intakes of heavy metals from the crops of three sites were lower than the tolerable daily intake recommended by FAO/WHO. Consequently, these crops cannot be an important source of Zn, Cu and Mn for risk to human health. PMID:24199494

  13. Preliminary study of the metal binding site of an anti-DTPA-indium antibody by equilibrium binding immunoassays and immobilized metal ion affinity chromatography.

    PubMed

    Boden, V; Colin, C; Barbet, J; Le Doussal, J M; Vijayalakshmi, M

    1995-01-01

    Creating metal coordination sites by modifying an existing enzyme or by eliciting antibodies against metal chelate haptens is of great interest in biotechnology to create enzyme catalysts with novel specificities. Here, we investigate the metal binding potential of a monoclonal antibody raised against a DTPA-In(III) hapten (mAb 734). We study its relative binding efficiency to metals of biological relevance by equilibrium binding immunoassays and immobilized metal ion affinity chromatography, two approaches which can give complementary information regarding composition and/or structure of the metal binding site(s). Fe(III), Fe(II), Cu(II), Mg(II), Ca(II), and Zn(II) binding was compared to In(III). All of them were shown to displace indium, but their affinity for mAb 734 decreased by 100-fold compared to indium. Competitive metal binding immunoassays between Zn(II) and In(III) revealed an unusual behavior by Zn(II) which remains to be explained. Moreover, IMAC allowed us to predict the metal binding amino acids involved in the antibody paratope. The antibody metal binding site was shown to contain at least two histidine residues in a cluster, and the presence of aspartic and glutamic acid as well as cysteine residues could not be excluded. Thus, simple competition studies allows us to obtain some partial information on the metal binding structural features of this anti-metal chelate antibody and to guide our screening of its catalytic potential. PMID:7578356

  14. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor

    PubMed Central

    Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

    2015-01-01

    Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32–1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis. DOI: http://dx.doi.org/10.7554/eLife.11620.001 PMID:26673079

  15. Theoretical Insights into the Tuning of Metal Binding Sites of Paddlewheels in rht-Metal-Organic Frameworks.

    PubMed

    Pham, Tony; Forrest, Katherine A; Gao, Wen-Yang; Ma, Shengqian; Space, Brian

    2015-10-26

    Theoretical investigations of CO2 sorption are performed in four members of the highly tunable rht-metal-organic framework (MOF) platform. rht-MOFs contain two Cu(2+) ions that comprise the metal paddlewheels and both are in chemically distinct environments. Indeed, one type of Cu(2+) ion faces toward the center of the linker whereas the other type faces away from the center of the linker. Electronic structure calculations on the series of rht-MOFs demonstrate that one of the Cu(2+) ions has a consistently higher charge magnitude relative to the other. As a consequence, the Cu(2+) ion with the higher partial positive charge acts as the favored sorbate binding site at initial loading as revealed by grand canonical Monte Carlo (GCMC) simulations that include many-body polarization. It was found that the charge distribution about the copper paddlewheels is dependent on the type of functional groups present on the linker. This study demonstrates how the binding site about the metal paddlewheels in the rht-MOF platform can be controlled by changing the functionality on the organic ligand. PMID:26489059

  16. Effect of Transport and Aging Processes on Metal Speciation in Iron Oxyhydroxide Aggregates, Tar Creek Superfund Site, Oklahoma

    NASA Astrophysics Data System (ADS)

    Estes, E. R.; Schaider, L. A.; Shine, J. P.; Brabander, D. J.

    2010-12-01

    Following the cessation of mining activity in the late 20th century, Tar Creek Superfund Site was left highly contaminated by Pb, Zn, and Cd. Tar Creek, which flows through the site and into the Neosho River, has been studied extensively because of its potential to transport metals from the mining site to downstream communities. Previous research identified aggregated iron oxyhydroxide material, which forms when mine seepage mixes with Tar Creek surface water, as a major transport vector of metals. Frequent flooding in Tar Creek deposits aggregates on downstream floodplains, where wetting and drying processes alter the speciation of iron and other metals. This study seeks to better quantify those changes and to determine how transport and aging affects the human and ecological health risk. Sequential extractions of aggregate samples collected from the creek demonstrate that Fe is present in both amorphous (10-35% of Fe extracted) and more crystalline (8-23% of Fe extracted) phases. Substantial portions of heavy metals sorb to amorphous iron oxyhydroxide phases (accounting for 10-30% of Pb and Zn extracted) but are not associated with more crystalline iron oxide phases (representing only 1% or less of the Pb and Zn extracted). Samples have a high organic matter content (18-25% mass loss on ignition), but only Fe was significantly extracted by the oxidizing step targeting organic matter (1-2% of Pb and Zn extracted, but 10-26% of Fe extracted). The majority of metals were extracted by the soluble or residual steps. If metals and organic matter inhibit transformation of amorphous iron oxyhydroxide material to nano and crystalline iron oxides, then a steady-state volume of amorphous iron oxyhydroxide material with a high total sorption capacity may exist within Tar Creek, enhancing the metal flux accommodated by this transport mechanism. Once transported downstream and deposited on floodplains, however, it is hypothesized that repeated changes in soil matrix

  17. Characterization of activation energy for flow in metallic glasses

    SciTech Connect

    Wang, J. Q.; Wang, W. H.; Liu, Y. H.; Bai, H. Y.

    2011-01-15

    The molar volume (V{sub m}) scaled flow activation energy ({Delta}E), namely as the activation energy density {rho}{sub E}={Delta}E/V{sub m}, is proposed to describe the flow of metallic glasses. Based on the energy landscape, both the shear and bulk moduli are critical parameters accounting for the {rho}{sub E} of both homogeneous and inhomogeneous flows in metallic glasses. The expression of {rho}{sub E} is determined experimentally to be a simple expression of {rho}{sub E}=(10/11)G+(1/11)K. The energy density perspective depicts a realistic picture for the flow in metallic glasses and is suggestive for understanding the glass transition and deformation in metallic glasses.

  18. Accumulation of heavy metals and antioxidant responses in Pinus sylvestris L. needles in polluted and non-polluted sites.

    PubMed

    Kandziora-Ciupa, Marta; Ciepał, Ryszard; Nadgórska-Socha, Aleksandra; Barczyk, Gabriela

    2016-07-01

    The purpose of this study was to determine the concentrations of heavy metals (cadmium, iron, manganese, lead and zinc) in current-year, 1-year old and 2-year old needles of Pinus sylvestris L. Trees were from three heavily polluted (immediate vicinity of zinc smelter, iron smelter and power plant) and three relatively clean sites (nature reserve, ecologically clean site and unprotected natural forest community) in southern Poland. Analysis also concerned the antioxidant response and contents of protein, proline, total glutathione, non-protein thiols and activity of guaiacol peroxidase (GPX) in the needles. Generally, in pine needles from the polluted sites, the concentrations of the metals were higher and increased with the age of needles, and in most cases, antioxidant responses also were elevated. The highest levels of Cd, Pb and Zn were found in 2-year old pine needles collected near the polluted zinc smelter (respectively: 6.15, 256.49, 393.5 mg kg(-1)), Fe in 2-year old pine needles in the vicinity of the iron smelter (206.82 mg kg(-1)) and Mn in 2-year old needles at the ecologically clean site (180.32 mg kg(-1)). Positive correlations were found between Fe, Mn and Pb and the content of proteins and NPTs, between Cd and non-protein -SH groups, and between Zn and proline levels. The activity of GPX increased under the influence of Mn, while glutathione levels tended to decrease as Mn levels rose. The data obtained show that the levels of protein and non-protein -SH groups may be useful in biological monitoring, and that these ecophysiological parameters seem to be good evidence of elevated oxidative stress caused by heavy metals. PMID:27033856

  19. Dashboard applications to monitor experiment activities at sites

    NASA Astrophysics Data System (ADS)

    Andreeva, Julia; Belforte, Stefano; Boehm, Max; Casajus, Adrian; Flix, Josep; Gaidioz, Benjamin; Grigoras, Costin; Kokoszkiewicz, Lukasz; Lanciotti, Elisa; Rocha, Ricardo; Saiz, Pablo; Santinelli, Roberto; Sidorova, Irina; Sciabà, Andrea; Tsaregorodtsev, Andrei

    2010-04-01

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  20. Site-selective electroless nickel plating on patterned thin films of macromolecular metal complexes.

    PubMed

    Kimura, Mutsumi; Yamagiwa, Hiroki; Asakawa, Daisuke; Noguchi, Makoto; Kurashina, Tadashi; Fukawa, Tadashi; Shirai, Hirofusa

    2010-12-01

    We demonstrate a simple route to depositing nickel layer patterns using photocross-linked polymer thin films containing palladium catalysts, which can be used as adhesive interlayers for fabrication of nickel patterns on glass and plastic substrates. Electroless nickel patterns can be obtained in three steps: (i) the pattern formation of partially quaterized poly(vinyl pyridine) by UV irradiation, (ii) the formation of macromolecular metal complex with palladium, and (iii) the nickel metallization using electroless plating bath. Metallization is site-selective and allows for a high resolution. And the resulting nickel layered structure shows good adhesion with glass and plastic substrates. The direct patterning of metallic layers onto insulating substrates indicates a great potential for fabricating micro/nano devices. PMID:21069972

  1. Determination of noble metals in Savannah River Site high-level radioactive sludge

    SciTech Connect

    Coleman, C.J.; Kinard, W.F.; Bibler, N.E.; Bickford, D.F.; Ramsey, W.G.

    1990-01-01

    High-level radioactive sludge at the Savannah River Site (SRS) will be processed at the Defense Waste Processing Facility (DWPF) into durable borosilicate glass wasteforms. The sludges are analyzed for elemental content before processing to ensure compatibility with the glass-making processes. Noble metal fission products in sludge, can under certain conditions, cause problems in the glass melter. Therefore, reliable noble metal determinations are important. The scheme used to measure noble metals in SRS sludges consists of dissolving sludge with hot aqua regia followed by determinations with inductively coupled plasma-atomic emission spectroscopy (ICP-AES) and ICP-Mass Spectroscopy (ICP-MS) techniques. ICP-MS is the preferred method for measuring trace levels of noble metals in SRS radioactive waste because of superior sensitivity. Analytical results are presented for the two major types of SRS sludge.

  2. Determination of noble metals in Savannah River Site high-level radioactive sludge

    SciTech Connect

    Coleman, C.J.; Kinard, W.F.; Bibler, N.E.; Bickford, D.F.; Ramsey, W.G.

    1990-12-31

    High-level radioactive sludge at the Savannah River Site (SRS) will be processed at the Defense Waste Processing Facility (DWPF) into durable borosilicate glass wasteforms. The sludges are analyzed for elemental content before processing to ensure compatibility with the glass-making processes. Noble metal fission products in sludge, can under certain conditions, cause problems in the glass melter. Therefore, reliable noble metal determinations are important. The scheme used to measure noble metals in SRS sludges consists of dissolving sludge with hot aqua regia followed by determinations with inductively coupled plasma-atomic emission spectroscopy (ICP-AES) and ICP-Mass Spectroscopy (ICP-MS) techniques. ICP-MS is the preferred method for measuring trace levels of noble metals in SRS radioactive waste because of superior sensitivity. Analytical results are presented for the two major types of SRS sludge.

  3. Mathematical modeling of heavy metals contamination from MSW landfill site in Khon Kaen, Thailand.

    PubMed

    Tantemsapya, N; Naksakul, Y; Wirojanagud, W

    2011-01-01

    Kham Bon landfill site is one of many municipality waste disposal sites in Thailand which are in an unsanitary condition. The site has been receiving municipality wastes without separating hazardous waste since 1968. Heavy metals including, Pb, Cr and Cd are found in soil and groundwater around the site, posing a health risk to people living nearby. In this research, contamination transport modelling of Pb, Cr and Cd was simulated using MODFLOW for two periods, at the present (2010) and 20 years prediction (2030). Model results showed that heavy metals, especially Pb and Cr migrated toward the north-eastern and south-eastern direction. The 20 years prediction showed that, heavy metals tend to move from the top soil to the deeper aquifer. The migration would not exceed 500 m radius from the landfill centre in the next 20 years, which is considered to be a slow process. From the simulation model, it is recommended that a mitigation measure should be performed to reduce the risk from landfill contamination. Hazardous waste should be separated for proper management. Groundwater contamination in the aquifer should be closely monitored. Consumption of groundwater in a 500 m radius must be avoided. In addition, rehabilitation of the landfill site should be undertaken to prevent further mobilization of pollutants. PMID:22020476

  4. Site-Specific Scaling Relations for Hydrocarbon Adsorption on Hexagonal Transition Metal Surfaces

    SciTech Connect

    Montemore, Matthew M.; Medlin, James W.

    2013-10-03

    Screening a large number of surfaces for their catalytic performance remains a challenge, leading to the need for simple models to predict adsorption properties. To facilitate rapid prediction of hydrocarbon adsorption energies, scaling relations that allow for calculation of the adsorption energy of any intermediate attached to any symmetric site on any hexagonal metal surface through a carbon atom were developed. For input, these relations require only simple electronic properties of the surface and of the gas-phase reactant molecules. Determining adsorption energies consists of up to four steps: (i) calculating the adsorption energy of methyl in the top site using density functional theory or by simple relations based on the electronic structure of the surface; (ii) using modified versions of classical scaling relations to scale between methyl in the top site and C₁ species with more metal-surface bonds (i.e., C, CH, CH₂) in sites that complete adsorbate tetravalency; (iii) using gas-phase bond energies to predict adsorption energies of longer hydrocarbons (i.e., CR, CR₂, CR₃); and (iv) expressing energetic changes upon translation of hydrocarbons to various sites in terms of the number of agostic interactions and the change in the number of carbon-metal bonds. Combining all of these relations allows accurate scaling over a wide range of adsorbates and surfaces, resulting in efficient screening of catalytic surfaces and a clear elucidation of adsorption trends. The relations are used to explain trends in methane reforming, hydrocarbon chain growth, and propane dehydrogenation.

  5. Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study

    PubMed Central

    Li, Xiong; Li, Hang; Yang, Gang

    2015-01-01

    Defect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb2+ ions predominate for all models (regular and defective), while inner-sphere Na+ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption, and (quasi) inner-sphere Pb2+ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals. PMID:26403873

  6. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2domains reveal that the (HhH)2domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  7. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  8. Antischistosomal Activity of Oxindolimine-Metal Complexes

    PubMed Central

    Dario, Bruno S.; Couto, Ricardo A. A.; Pinto, Pedro L. S.; da Costa Ferreira, Ana M.

    2015-01-01

    In recent years, a class of oxindole-copper and -zinc complex derivatives have been reported as compounds with efficient proapoptotic activity toward different tumor cells (e.g., neuroblastomas, melanomas, monocytes). Here we assessed the efficacy of synthesized oxindole-copper(II), -zinc(II), and -vanadyl (VO2+) complexes against adult Schistosoma mansoni worms. The copper(II) complexes (50% inhibitory concentrations of 30 to 45 μM) demonstrated greater antischistosomal properties than the analogous zinc and vanadyl complexes regarding lethality, reduction of motor activity, and oviposition. PMID:26239976

  9. Antischistosomal Activity of Oxindolimine-Metal Complexes.

    PubMed

    de Moraes, Josué; Dario, Bruno S; Couto, Ricardo A A; Pinto, Pedro L S; da Costa Ferreira, Ana M

    2015-10-01

    In recent years, a class of oxindole-copper and -zinc complex derivatives have been reported as compounds with efficient proapoptotic activity toward different tumor cells (e.g., neuroblastomas, melanomas, monocytes). Here we assessed the efficacy of synthesized oxindole-copper(II), -zinc(II), and -vanadyl (VO(2+)) complexes against adult Schistosoma mansoni worms. The copper(II) complexes (50% inhibitory concentrations of 30 to 45 μM) demonstrated greater antischistosomal properties than the analogous zinc and vanadyl complexes regarding lethality, reduction of motor activity, and oviposition. PMID:26239976

  10. ZrO2 -Based Alternatives to Conventional Propane Dehydrogenation Catalysts: Active Sites, Design, and Performance.

    PubMed

    Otroshchenko, Tatyana; Sokolov, Sergey; Stoyanova, Mariana; Kondratenko, Vita A; Rodemerck, Uwe; Linke, David; Kondratenko, Evgenii V

    2015-12-21

    Non-oxidative dehydrogenation of propane to propene is an established large-scale process that, however, faces challenges, particularly in catalyst development; these are the toxicity of chromium compounds, high cost of platinum, and catalyst durability. Herein, we describe the design of unconventional catalysts based on bulk materials with a certain defect structure, for example, ZrO2 promoted with other metal oxides. Comprehensive characterization supports the hypothesis that coordinatively unsaturated Zr cations are the active sites for propane dehydrogenation. Their concentration can be adjusted by varying the kind of ZrO2 promoter and/or supporting tiny amounts of hydrogenation-active metal. Accordingly designed Cu(0.05 wt %)/ZrO2 -La2 O3 showed industrially relevant activity and durability over ca. 240 h on stream in a series of 60 dehydrogenation and oxidative regeneration cycles between 550 and 625 °C. PMID:26566072

  11. Crystal Structure of Phosphatidylglycerophosphatase (PGPase), a Putative Membrane-Bound Lipid Phosphatase, Reveals a Novel Binuclear Metal Binding Site and Two Proton Wires

    SciTech Connect

    Kumaran,D.; Bonnano, J.; Burley, S.; Swaminathan, S.

    2006-01-01

    Phosphatidylglycerophosphatase (PGPase), an enzyme involved in lipid metabolism, catalyzes formation of phosphatidylglycerol from phosphatidylglycerophosphate. Phosphatidylglycerol is a multifunctional phospholipid, found in the biological membranes of many organisms. Here, we report the crystal structure of Listeria monocytogenes PGPase at 1.8 Angstroms resolution. PGPase, an all-helical molecule, forms a homotetramer. Each protomer contains an independent active site with two metal ions, Ca{sup 2+} and Mg{sup 2+}, forming a hetero-binuclear center located in a hydrophilic cavity near the surface of the molecule. The binuclear center, conserved ligands, metal-bound water molecules, and an Asp-His dyad form the active site. The catalytic mechanism of this enzyme is likely to proceed via binuclear metal activated nucleophilic water. The binuclear metal-binding active-site environment of this structure should provide insights into substrate binding and metal-dependent catalysis. A long channel with inter-linked linear water chains, termed 'proton wires', is observed at the tetramer interface. Comparison of similar water chain structures in photosynthetic reaction centers (RCs), Cytochrome f, gramicidin, and bacteriorhodopsin, suggests that PGPase may conduct protons via proton wires.

  12. New mode for divalent metal activation of glycoside hydrolases: X-ray structure of ß-xyloisdase-Ca2+

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report the first X-ray structure of a glycoside hydrolase family 43 ß-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca2+ cation is located at the back of the active site pocket. The Ca2+ coordinates to H274 to sta...

  13. SITE demonstration of the Dynaphore/Forager Sponge technology to remove dissolved metals from contaminated groundwater

    SciTech Connect

    Esposito, C.R.; Vaccaro, G.

    1995-10-01

    A Superfund Innovative Technology Evaluation (SITE) demonstration was conducted of the Dynaphore/Forager Sponge technology during the week of April 3, 1994 at the N.L. Industries Superfund Site in Pedricktown, New Jersey. The Forager Sponge is an open-celled cellulose sponge incorporating an amine-containing chelating polymer that selectively absorbs dissolved heavy metals in both cationic and anionic states. This technology is a volume reduction technology in which heavy metal contaminants from an aqueous medium are concentrated into a smaller volume for facilitated disposal. The developer states that the technology can be used to remove heavy metals from a wide variety of aqueous media, such as groundwater, surface waters and process waters. The sponge matrix can be directly disposed, or regenerated with chemical solutions. For this demonstration the sponge was set up as a mobile pump-and-treat system which treated groundwater contaminated with heavy metals. The demonstration focused on the system`s ability to remove lead, cadmium, chromium and copper from the contaminated groundwater over a continuous 72-hour test. The removal of heavy metals proceeded in the presence of significantly higher concentrations of innocuous cations such as calcium, magnesium, sodium, potassium and aluminum.

  14. PROGENITOR DIAGNOSTICS FOR STRIPPED CORE-COLLAPSE SUPERNOVAE: MEASURED METALLICITIES AT EXPLOSION SITES

    SciTech Connect

    Modjaz, M.; Bloom, J. S.; Filippenko, A. V.; Perley, D.; Silverman, J. M.; Kewley, L.

    2011-04-10

    Metallicity is expected to influence not only the lives of massive stars but also the outcome of their deaths as supernovae (SNe) and gamma-ray bursts (GRBs). However, there are surprisingly few direct measurements of the local metallicities of different flavors of core-collapse SNe (CCSNe). Here, we present the largest existing set of host-galaxy spectra with H II region emission lines at the sites of 35 stripped-envelope CCSNe. We derive local oxygen abundances in a robust manner in order to constrain the SN Ib/c progenitor population. We obtain spectra at the SN sites, include SNe from targeted and untargeted surveys, and perform the abundance determinations using three different oxygen-abundance calibrations. The sites of SNe Ic (the demise of the most heavily stripped stars, having lost both H and He layers) are systematically more metal rich than those of SNe Ib (arising from stars that retained their He layer) in all calibrations. A Kolmogorov-Smirnov test yields the very low probability of 1% that SN Ib and SN Ic environment abundances, which are different on average by {approx}0.2 dex (in the Pettini and Pagel scale), are drawn from the same parent population. Broad-lined SNe Ic (without GRBs) occur at metallicities between those of SNe Ib and SNe Ic. Lastly, we find that the host-galaxy central oxygen abundance is not a good indicator of the local SN metallicity; hence, large-scale SN surveys need to obtain local abundance measurements in order to quantify the impact of metallicity on stellar death.

  15. Tolerance to Cadmium of Agave lechuguilla (Agavaceae) Seeds and Seedlings from Sites Contaminated with Heavy Metals

    PubMed Central

    Méndez-Hurtado, Alejandra; Rangel-Méndez, René; Flores, Joel

    2013-01-01

    We investigated if seeds of Agave lechuguilla from contaminated sites with heavy metals were more tolerant to Cd ions than seeds from noncontaminated sites. Seeds from a highly contaminated site (Villa de la Paz) and from a noncontaminated site (Villa de Zaragoza) were evaluated. We tested the effect of Cd concentrations on several ecophysiological, morphological, genetical, and anatomical responses. Seed viability, seed germination, seedling biomass, and radicle length were higher for the non-polluted site than for the contaminated one. The leaves of seedlings from the contaminated place had more cadmium and showed peaks attributed to chemical functional groups such as amines, amides, carboxyl, and alkenes that tended to disappear due to increasing the concentration of cadmium than those from Villa de Zaragoza. Malformed cells in the parenchyma surrounding the vascular bundles were found in seedlings grown with Cd from both sites. The leaves from the contaminated place showed a higher metallothioneins expression in seedlings from the control group than that of seedlings at different Cd concentrations. Most of our results fitted into the hypothesis that plants from metal-contaminated places do not tolerate more pollution, because of the accumulative effect that cadmium might have on them. PMID:24453802

  16. Molecular Imprint of Enzyme Active Site by Camel Nanobodies

    PubMed Central

    Li, Jiang-Wei; Xia, Lijie; Su, Youhong; Liu, Hongchun; Xia, Xueqing; Lu, Qinxia; Yang, Chunjin; Reheman, Kalbinur

    2012-01-01

    Screening of inhibitory Ab1 antibodies is a critical step for producing catalytic antibodies in the anti-idiotypic approach. However, the incompatible surface of the active site of the enzyme and the antigen-binding site of heterotetrameric conventional antibodies become the limiting step. Because camelid-derived nanobodies possess the potential to preferentially bind to the active site of enzymes due to their small size and long CDR3, we have developed a novel approach to produce antibodies with alliinase activities by exploiting the molecular mimicry of camel nanobodies. By screening the camelid-derived variable region of the heavy chain cDNA phage display library with alliinase, we obtained an inhibitory nanobody VHHA4 that recognizes the active site. Further screening with VHHA4 from the same variable domain of the heavy chain of a heavy-chain antibody library led to a higher incidence of anti-idiotypic Ab2 abzymes with alliinase activities. One of the abzymes, VHHC10, showed the highest activity that can be inhibited by Ab1 VHHA4 and alliinase competitive inhibitor penicillamine and significantly suppressed the B16 tumor cell growth in the presence of alliin in vitro. The results highlight the feasibility of producing abzymes via anti-idiotypic nanobody approach. PMID:22374998

  17. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  18. An active-site peptide from pepsin C

    PubMed Central

    Kay, J.; Ryle, A. P.

    1971-01-01

    Porcine pepsin C is inactivated rapidly and irreversibly by diazoacetyl-dl-norleucine methyl ester in the presence of cupric ions at pH values above 4.5. The inactivation is specific in that complete inactivation accompanies the incorporation of 1mol of inhibitor residue/mol of enzyme and evidence has been obtained to suggest that the reaction occurs with an active site residue. The site of reaction is the β-carboxyl group of an aspartic acid residue in the sequence Ile-Val-Asp-Thr. This sequence is identical with the active-site sequence in pepsin and the significance of this in terms of the different activities of the two enzymes is discussed. PMID:4942834

  19. Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli.

    PubMed Central

    Kazakov, S; Altman, S

    1991-01-01

    The location of phosphate residues involved in specific centers for binding of metal ions in M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, was determined by analysis of induction of cleavage of RNA by metal ions. At pH 9.5, Mg2+ catalyzes cleavage of M1 RNA at five principal sites. Under certain conditions, Mn2+ and Ca2+ can each replace Mg2+ as the cofactor in the processing of precursor tRNAs by M1 RNA and P RNA, the RNA subunit of RNase P from Bacillus subtilis. These cations, as well as various metal ion inhibitors of the catalytic activity of M1 RNA, also promote cleavage of M1 RNA in a specific manner. Certain conditions that affect the catalytic activity of M1 RNA also alter the rate of metal ion-induced cleavage at the various sites. From these results and a comparison of cleavage of M1 RNA with that of a deletion mutant of M1 RNA and of P RNA, we have identified two different centers for binding of metal ions in M1 RNA that are important for the processing of the precursor to tRNA(Tyr) from E. coli. There is also a center for the binding of metal ions in the substrate, close to the site of cleavage by M1 RNA. Images PMID:1718000

  20. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  1. Magnetic Measurements and Heavy Metal Concentrations at Formosa Mine Superfund Site, Douglas County, OR

    NASA Astrophysics Data System (ADS)

    Upton, T. L.

    2015-12-01

    Advances in the field of environmental magnetism have led to exciting new applications for this field. Magnetic minerals are ubiquitous in the environment and tend to have an affinity for heavy metals. It has been demonstrated that magnetic properties are often significantly related to concentrations of heavy metals and/or pollution loading index (PLI). As a result, magnetic techniques have been used as proxy for determining hot spots of several types of pollution produced from a diversity of anthropogenic sources. Magnetic measurements are non-destructive and relatively inexpensive compared to geochemical analyses. The utility of environmental magnetic methods varies widely depending on biological, chemical and physical processes that create and transform soils and sediments. Applications in the direction of mapping heavy metals have been studied and shown to be quite useful in countries such as China and India but to date, little research has been done in the US. As such, there is need to expand the scope of research to a wider range of soil types and land uses, especially within the US. This study investigates the application of environmental magnetic techniques to mapping of heavy metal concentrations and PLI at the Formosa Mine Superfund Site, an abandoned mine about 25 miles southwest of Roseburg, OR. Using hotspot analysis, correlation and cluster analyses, interactions between metals and magnetic parameters are examined in relation to environmental factors such as proximity to seeps and adits. Preliminary results suggest significant correlation of magnetic susceptibility with certain heavy metals, signifying that magnetic methods may be useful in mapping heavy metal hotspots at this site.

  2. Enhancing H[subscript 2] Uptake by 'Close-Packing' Alignment of Open Copper Sites in Metal-Organic Frameworks

    SciTech Connect

    Wang, Xi-Sen; Ma, Shengqian; Forster, Paul M.; Yuan, Daqiang; Eckert, Juergen; López, Joseph J.; Murphy, Brandon J.; Parise, John B.; Zhou, Hong-Cai

    2010-10-15

    Inspired by close-packing of spheres, to strengthen the framework-H{sub 2} interaction in MOFs (metal-organic frameworks), a strategy is devised to increase the number of nearest neighboring open metal sites ofe ach H{sub 2}-hosting cage, and to align the open metal sites toward the H{sub 2} molecules. Two MOF polymorphs were made, one exhibiting a record high hydrogen uptake of 3.0 wt% at 1 bar and 77 k.

  3. Oxidation Protection in Metal-Binding Peptide Motif and Its Application to Antibody for Site-Selective Conjugation

    PubMed Central

    Chung, Hye-Shin; Lee, Sunbae; Park, Soon Jae

    2016-01-01

    Here, we demonstrate that a metal ion binding motif could serve as an efficient and robust tool for site-specific conjugation strategy. Cysteine-containing metal binding motifs were constructed as single repeat or tandem repeat peptides and their metal binding characteristics were investigated. The tandem repeats of the Cysteine-Glycine-Histidine (CGH) metal ion binding motif exhibited concerted binding to Co(II) ions, suggesting that conformational transition of peptide was triggered by the sequential metal ion binding. Evaluation of the free thiol content after reduction by reducing reagent showed that metal-ion binding elicited strong retardation of cysteine oxidation in the order of Zn(II)>Ni(II)>Co(II). The CGH metal ion binding motif was then introduced to the C-terminus of antibody heavy chain and the metal ion-dependent characteristics of oxidation kinetics were investigated. As in the case of peptides, CGH-motif-introduced antibody exhibited strong dependence on metal ion binding to protect against oxidation. Zn(II)-saturated antibody with tandem repeat of CGH motif retains the cysteine reactivity as long as 22 hour even with saturating O2 condition. Metal-ion dependent fluorophore labeling clearly indicated that metal binding motifs could be employed as an efficient tool for site-specific conjugation. Whereas Trastuzumab without a metal ion binding site exhibited site-nonspecific dye conjugation, Zn(II) ion binding to antibody with a tandem repeat of CGH motif showed that fluorophores were site-specifically conjugated to the heavy chain of antibody. We believe that this strong metal ion dependence on oxidation protection and the resulting site-selective conjugation could be exploited further to develop a highly site-specific conjugation strategy for proteins that contain multiple intrinsic cysteine residues, including monoclonal antibodies. PMID:27420328

  4. Microalloying of transition metal silicides by mechanical activation and field-activated reaction

    DOEpatents

    Munir, Zuhair A.; Woolman, Joseph N.; Petrovic, John J.

    2003-09-02

    Alloys of transition metal suicides that contain one or more alloying elements are fabricated by a two-stage process involving mechanical activation as the first stage and densification and field-activated reaction as the second stage. Mechanical activation, preferably performed by high-energy planetary milling, results in the incorporation of atoms of the alloying element(s) into the crystal lattice of the transition metal, while the densification and field-activated reaction, preferably performed by spark plasma sintering, result in the formation of the alloyed transition metal silicide. Among the many advantages of the process are its ability to accommodate materials that are incompatible in other alloying methods.

  5. Lossless propagation in metal-semiconductor-metal plasmonic waveguides using quantum dot active medium.

    PubMed

    Sheikhi, K; Granpayeh, N; Ahmadi, V; Pahlavan, S

    2015-04-01

    In this paper, we analyze and simulate the lossless propagation of lightwaves in the active metal-semiconductor-metal plasmonic waveguides (MSMPWs) at the wavelength range of 1540-1560 nm using a quantum dot (QD) active medium. The Maxwell's equations are solved in the waveguide, and the required gains for achieving lossless propagation are derived. On the other hand, the rate equations in quantum dot active regions are solved by using the Runge-Kutta method, and the achievable optical gain is derived. The analyses results show that the required optical gain for lossless propagation in MSMPWs is achievable using the QD active medium. Also, by adjusting the active medium parameters, the MSMPWs loss can be eliminated in a specific bandwidth, and the propagation length increases obviously. PMID:25967191

  6. Process for carbonaceous material conversion and recovery of alkali metal catalyst constituents held by ion exchange sites in conversion residue

    DOEpatents

    Sharp, David W.

    1980-01-01

    In a coal gasification operation or similar conversion process carried out in the presence of an alkali metal-containing catalyst wherein solid particles containing alkali metal residues are produced, alkali metal constituents are recovered for the particles by contacting or washing them with an aqueous solution containing calcium or magnesium ions in an alkali metal recovery zone at a low temperature, preferably below about 249.degree. F. During the washing or leaching process, the calcium or magnesium ions displace alkali metal ions held by ion exchange sites in the particles thereby liberating the ions and producing an aqueous effluent containing alkali metal constituents. The aqueous effluent from the alkali metal recovery zone is then recycled to the conversion process where the alkali metal constituents serve as at least a portion of the alkali metal constituents which comprise the alkali metal-containing catalyst.

  7. The structures of the CutA1 proteins from Thermus thermophilus and Pyrococcus horikoshii: characterization of metal-binding sites and metal-induced assembly

    PubMed Central

    Bagautdinov, Bagautdin

    2014-01-01

    CutA1 (copper tolerance A1) is a widespread cytoplasmic protein found in archaea, bacteria, plants and animals, including humans. In Escherichia coli it is implicated in divalent metal tolerance, while the mammalian CutA1 homologue has been proposed to mediate brain enzyme acetylcholinesterase activity and copper homeostasis. The X-ray structures of CutA1 from the thermophilic bacterium Thermus thermophilus (TtCutA1) with and without bound Na+ at 1.7 and 1.9 Å resolution, respectively, and from the hyperthermophilic archaeon Pyrococcus horikoshii (PhCutA1) in complex with Na+ at 1.8 Å resolution have been determined. Both are short and rigid proteins of about 12 kDa that form intertwined compact trimers in the crystal and solution. The main difference in the structures is a wide-type β-bulge on top of the TtCutA1 trimer. It affords a mechanism for lodging a single-residue insertion in the middle of β2 while preserving the interprotomer main-chain hydrogen-bonding network. The liganded forms of the proteins provide new structural information about the metal-binding sites and CutA1 assembly. The Na+–TtCutA1 structure unveils a dodecameric assembly with metal ions in the trimer–trimer interfaces and the lateral clefts of the trimer. For Na+–PhCutA1, the metal ion associated with six waters in an octahedral geometry. The structures suggest that CutA1 may contribute to regulating intracellular metal homeostasis through various binding modes. PMID:24699729

  8. The structures of the CutA1 proteins from Thermus thermophilus and Pyrococcus horikoshii: characterization of metal-binding sites and metal-induced assembly.

    PubMed

    Bagautdinov, Bagautdin

    2014-04-01

    CutA1 (copper tolerance A1) is a widespread cytoplasmic protein found in archaea, bacteria, plants and animals, including humans. In Escherichia coli it is implicated in divalent metal tolerance, while the mammalian CutA1 homologue has been proposed to mediate brain enzyme acetylcholinesterase activity and copper homeostasis. The X-ray structures of CutA1 from the thermophilic bacterium Thermus thermophilus (TtCutA1) with and without bound Na(+) at 1.7 and 1.9 Å resolution, respectively, and from the hyperthermophilic archaeon Pyrococcus horikoshii (PhCutA1) in complex with Na(+) at 1.8 Å resolution have been determined. Both are short and rigid proteins of about 12 kDa that form intertwined compact trimers in the crystal and solution. The main difference in the structures is a wide-type β-bulge on top of the TtCutA1 trimer. It affords a mechanism for lodging a single-residue insertion in the middle of β2 while preserving the interprotomer main-chain hydrogen-bonding network. The liganded forms of the proteins provide new structural information about the metal-binding sites and CutA1 assembly. The Na(+)-TtCutA1 structure unveils a dodecameric assembly with metal ions in the trimer-trimer interfaces and the lateral clefts of the trimer. For Na(+)-PhCutA1, the metal ion associated with six waters in an octahedral geometry. The structures suggest that CutA1 may contribute to regulating intracellular metal homeostasis through various binding modes. PMID:24699729

  9. Coordination Environment of a Site-Bound Metal Ion in the Hammerhead Ribozyme Determined by 15N and 2H ESEEM Spectroscopy

    PubMed Central

    Vogt, Matthew; Lahiri, Simanti; Hoogstraten, Charles G.; Britt, R. David; DeRose, Victoria J.

    2010-01-01

    Although site-bound Mg2+ ions have been proposed to influence RNA structure and function, establishing the molecular properties of such sites has been challenging due largely to the unique electrostatic properties of the RNA biopolymer. We have previously determined that, in solution, the hammerhead ribozyme (a self-cleaving RNA) has a high-affinity metal ion binding site characterized by a Kd,app < 10 µM for Mn2+ in 1 M NaCl and speculated that this site has functional importance in the ribozyme cleavage reaction. Here we determine both the precise location and the hydration level of Mn2+ in this site using ESEEM (electron spin–echo envelope modulation) spectroscopy. Definitive assignment of the high-affinity site to the activity-sensitive A9/G10.1 region is achieved by site-specific labeling of G10.1 with 15N guanine. The coordinated metal ion retains four water ligands as measured by 2H ESEEM spectroscopy. The results presented here show that a functionally important, specific metal binding site is uniquely populated in the hammerhead ribozyme even in a background of high ionic strength. Although it has a relatively high thermodynamic affinity, this ion remains partially hydrated and is chelated to the RNA by just two ligands. PMID:17177426

  10. Rat intestinal trehalase. Studies of the active site.

    PubMed

    Chen, C C; Guo, W J; Isselbacher, K J

    1987-11-01

    Rat intestinal trehalase was solubilized, purified and reconstituted into proteoliposomes. With octyl glucoside as the solubilizing detergent, the purified protein appeared as a single band on SDS/polyacrylamide-gel electrophoresis with an apparent molecular mass of 67 kDa. Kinetic studies indicated that the active site of this enzyme can be functionally divided into two adjacent regions, namely a binding site (with pKa 4.8) and a catalytic site (with pKa 7.2). Other findings suggested that the catalytic site contains a functional thiol group, which is sensitive to inhibition by N-ethylmaleimide, Hg2+ and iodoacetate. Substrate protection and iodoacetate labelling of the thiol group demonstrated that only a protein of 67 kDa was labelled. Furthermore, sucrose and phlorizin protected the thiol group, but Tris-like inhibitors did not. Structure-inhibition analysis of Tris-like inhibitors, the pH effect of Tris inhibition and Tris protection of 1-(3-dimethylaminopropyl)-3-ethylcarbodi-imide inactivation permitted characterization and location of a separate site containing a carboxy group for Tris binding, which may also be the binding region. On the basis of these findings, a possible structure for the active site of trehalase is proposed. PMID:3426558

  11. Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases

    PubMed Central

    Thomas, Keisha; Cameron, Scott A.; Almo, Steven C.; Burgos, Emmanuel S.; Gulab, Shivali A.; Schramm, Vern L.

    2015-01-01

    5′-Methylthioadenosine/S-adenosyl-L-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5′-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. We mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation of altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. The overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences. PMID:25806409

  12. DNA binding induces active site conformational change in the human TREX2 3'-exonuclease.

    PubMed

    de Silva, Udesh; Perrino, Fred W; Hollis, Thomas

    2009-04-01

    The TREX enzymes process DNA as the major 3'-->5' exonuclease activity in mammalian cells. TREX2 and TREX1 are members of the DnaQ family of exonucleases and utilize a two metal ion catalytic mechanism of hydrolysis. The structure of the dimeric TREX2 enzyme in complex with single-stranded DNA has revealed binding properties that are distinct from the TREX1 protein. The TREX2 protein undergoes a conformational change in the active site upon DNA binding including ordering of active site residues and a shift of an active site helix. Surprisingly, even when a single monomer binds DNA, both monomers in the dimer undergo the structural rearrangement. From this we have proposed a model for DNA binding and 3' hydrolysis for the TREX2 dimer. The structure also shows how TREX proteins potentially interact with double-stranded DNA and suggest features that might be involved in strand denaturation to provide a single-stranded substrate for the active site. PMID:19321497

  13. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  14. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  15. Heavy metal bioaccumulation in vegetation and small mammals inhabiting a coal ash disposal site

    SciTech Connect

    Baron, L.A.; Garten, C.T.; Ashwood, T.L.

    1994-12-31

    Coal ash is exempted from treatment as a hazardous waste under RCRA Subtitle C. The US Environmental Protection Agency justifies this exemption contending that coal ash does not possess any of the four RCRA hazardous properties (ignitability, corrosivity, reactivity, or toxicity). However, metals in coal ash may accumulate to toxic levels in biota on ash disposal sites. From 1955 to 1989, the Department of Energy`s Oak Ridge Y-12 Plant sluiced coal ash to a 36-ha earthen retention basin (Filled Coal Ash Pond; FCAP); the basin drains to a small local stream. The FCAP is now revegetated, and a productive terrestrial ecosystem now exists on the site. Vegetation and small mammals were collected from the FCAP and a nearby reference site in September 1992, and June--September 1993. Vegetation and small mammals were analyzed for As, Cd, Cr, Pb, Se, Tl and Hg. Mean concentrations of Se and As for FCAP vs. reference site samples were significantly higher in deciduous tree foliage (18.9 {+-} 19.1 /{mu}g Se/g and 1.6 {+-} 0.69 /{mu}g As/g) and small mammals (2.4 {+-} 1.4 {mu}g Se/g and 0.16 {+-} 0.1 {mu}g As/g) inhabiting the FCAP. Thus, biota living on or near the ash disposal site have bioaccumulated Se and As. Concentrations of these metals in vegetation and small mammals are sufficient to cause toxic effects in their consumers.

  16. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes

    PubMed Central

    Herschlag, Daniel

    2016-01-01

    Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes. PMID:27501145

  17. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

  18. Flexible macrocycles as versatile supports for catalytically active metal clusters.

    PubMed

    Ryan, Jason D; Gagnon, Kevin J; Teat, Simon J; McIntosh, Ruaraidh D

    2016-07-12

    Here we present three structurally diverse clusters stabilised by the same macrocyclic polyphenol; t-butylcalix[8]arene. This work demonstrates the range of conformations the flexible ligand is capable of adopting, highlighting its versatility in metal coordination. In addition, a Ti complex displays activity for the ring-opening polymerisation of lactide. PMID:26892948

  19. Site Selective Doping of Ultrathin Metal Dichalcogenides by Laser-Assisted Reaction.

    PubMed

    Kim, Eunpa; Ko, Changhyun; Kim, Kyunghoon; Chen, Yabin; Suh, Joonki; Ryu, Sang-Gil; Wu, Kedi; Meng, Xiuqing; Suslu, Aslihan; Tongay, Sefaattin; Wu, Junqiao; Grigoropoulos, Costas P

    2016-01-13

    Laser-assisted phosphorus doping is demonstrated on ultrathin transition-metal dichalcogenides (TMDCs) including n-type MoS2 and p-type WSe2 . Temporal and spatial control of the doping is achieved by varying the laser irradiation power and time, demonstrating wide tunability and high site selectivity with high stability. The laser-assisted doping method may enable a new avenue for functionalizing TMDCs for customized nanodevice applications. PMID:26567761

  20. Anticancer Activity of Metal Complexes: Involvement of Redox Processes

    PubMed Central

    Jungwirth, Ute; Kowol, Christian R.; Keppler, Bernhard K.; Hartinger, Christian G.; Berger, Walter; Heffeter, Petra

    2012-01-01

    Cells require tight regulation of the intracellular redox balance and consequently of reactive oxygen species for proper redox signaling and maintenance of metal (e.g., of iron and copper) homeostasis. In several diseases, including cancer, this balance is disturbed. Therefore, anticancer drugs targeting the redox systems, for example, glutathione and thioredoxin, have entered focus of interest. Anticancer metal complexes (platinum, gold, arsenic, ruthenium, rhodium, copper, vanadium, cobalt, manganese, gadolinium, and molybdenum) have been shown to strongly interact with or even disturb cellular redox homeostasis. In this context, especially the hypothesis of “activation by reduction” as well as the “hard and soft acids and bases” theory with respect to coordination of metal ions to cellular ligands represent important concepts to understand the molecular modes of action of anticancer metal drugs. The aim of this review is to highlight specific interactions of metal-based anticancer drugs with the cellular redox homeostasis and to explain this behavior by considering chemical properties of the respective anticancer metal complexes currently either in (pre)clinical development or in daily clinical routine in oncology. PMID:21275772

  1. Metals other than uranium affected microbial community composition in a historical uranium-mining site.

    PubMed

    Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

    2015-12-01

    To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination. PMID:26122566

  2. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  3. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  4. Mining the potential interrelationships between human health and ecological risk assessments of metal-contaminated sites

    SciTech Connect

    Appling, J.W.

    1994-12-31

    Conservative approaches to human health or ecological risk assessment often result in evaluations that indicate a risk at metal concentrations near or below background levels. This presents a complex dilemma to regulators, responsible parties, and the public: How can risk be more realistically estimated so that the public is not unnecessarily alarmed into thinking normal exposures pose abnormal risk, and site remediation can be responsible yet cost-effective? One answer is using-ecological and human health studies together to improve the quality of both types of assessments. Mammalian herbivores and roving children are good spatial and temporal integrators of exposure; biomarkers or Monte Carlo-based models of exposure to herbivores can support realistic estimates of exposure to children. Reduced bioavailability of metals in soils at mining sites is well recognized for many metals and is amenable to study in ecological species; such studies reduce the overestimate of risk to humans through direct contact or exposure via the food chain. Recent and current human health studies of lead and arsenic bioavailability also support ecological assessments. Mixtures of metals pose special challenges because of the potential for antagonistic, additive, or synergistic effects with respect to bioavailability, absorption, distribution, excretion, toxic effects and nutritional or physiological essentiality. Combining results from pharmacokinetic, mechanistic, and environmental studies of mixtures enhances the predictive abilities of risk assessments.

  5. Heavy Metal Contamination of Soils around a Hospital Waste Incinerator Bottom Ash Dumps Site.

    PubMed

    Adama, M; Esena, R; Fosu-Mensah, B; Yirenya-Tawiah, D

    2016-01-01

    Waste incineration is the main waste management strategy used in treating hospital waste in many developing countries. However, the release of dioxins, POPs, and heavy metals in fly and bottom ash poses environmental and public health concerns. To determine heavy metal (Hg, Pb, Cd, Cr, and Ag) in levels in incinerator bottom ash and soils 100 m around the incinerator bottom ash dump site, ash samples and surrounding soil samples were collected at 20 m, 40 m, 60 m, 80 m, 100 m, and 1,200 m from incinerator. These were analyzed using the absorption spectrophotometer method. The geoaccumulation (I geo) and pollution load indices (PLI) were used to assess the level of heavy metal contamination of surrounding soils. The study revealed high concentrations in mg/kg for, Zn (16417.69), Pb (143.80), Cr (99.30), and Cd (7.54) in bottom ash and these were above allowable limits for disposal in landfill. The study also found soils within 60 m radius of the incinerator to be polluted with the metals. It is recommended that health care waste managers be educated on the implication of improper management of incinerator bottom ash and regulators monitor hospital waste incinerator sites. PMID:27034685

  6. Heavy Metal Contamination of Soils around a Hospital Waste Incinerator Bottom Ash Dumps Site

    PubMed Central

    Adama, M.; Esena, R.; Fosu-Mensah, B.; Yirenya-Tawiah, D.

    2016-01-01

    Waste incineration is the main waste management strategy used in treating hospital waste in many developing countries. However, the release of dioxins, POPs, and heavy metals in fly and bottom ash poses environmental and public health concerns. To determine heavy metal (Hg, Pb, Cd, Cr, and Ag) in levels in incinerator bottom ash and soils 100 m around the incinerator bottom ash dump site, ash samples and surrounding soil samples were collected at 20 m, 40 m, 60 m, 80 m, 100 m, and 1,200 m from incinerator. These were analyzed using the absorption spectrophotometer method. The geoaccumulation (Igeo) and pollution load indices (PLI) were used to assess the level of heavy metal contamination of surrounding soils. The study revealed high concentrations in mg/kg for, Zn (16417.69), Pb (143.80), Cr (99.30), and Cd (7.54) in bottom ash and these were above allowable limits for disposal in landfill. The study also found soils within 60 m radius of the incinerator to be polluted with the metals. It is recommended that health care waste managers be educated on the implication of improper management of incinerator bottom ash and regulators monitor hospital waste incinerator sites. PMID:27034685

  7. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  8. Communication between the Zinc and Nickel Sites in Dimeric HypA: Metal Recognition and pH Sensing

    SciTech Connect

    Herbst, R.; Perovic, I; Martin-Diaconescu, V; O’Brien, K; Chivers, P; Sondej Pochapsky, S; Pochapsky, T; Maroney, M

    2010-01-01

    Helicobacter pylori, a pathogen that colonizes the human stomach, requires the nickel-containing metalloenzymes urease and NiFe-hydrogenase to survive this low pH environment. The maturation of both enzymes depends on the metallochaperone, HypA. HypA contains two metal sites, an intrinsic zinc site and a low-affinity nickel binding site. X-ray absorption spectroscopy (XAS) shows that the structure of the intrinsic zinc site of HypA is dynamic and able to sense both nickel loading and pH changes. At pH 6.3, an internal pH that occurs during acid shock, the zinc site undergoes unprecedented ligand substitutions to convert from a Zn(Cys){sub 4} site to a Zn(His){sub 2}(Cys){sub 2} site. NMR spectroscopy shows that binding of Ni(II) to HypA results in paramagnetic broadening of resonances near the N-terminus. NOEs between the {beta}-CH{sub 2} protons of Zn cysteinyl ligands are consistent with a strand-swapped HypA dimer. Addition of nickel causes resonances from the zinc binding motif and other regions to double, indicating more than one conformation can exist in solution. Although the structure of the high-spin, 5-6 coordinate Ni(II) site is relatively unaffected by pH, the nickel binding stoichiometry is decreased from one per monomer to one per dimer at pH = 6.3. Mutation of any cysteine residue in the zinc binding motif results in a zinc site structure similar to that found for holo-WT-HypA at low pH and is unperturbed by the addition of nickel. Mutation of the histidines that flank the CXXC motifs results in a zinc site structure that is similar to holo-WT-HypA at neutral pH (Zn(Cys){sub 4}) and is no longer responsive to nickel binding or pH changes. Using an in vitro urease activity assay, it is shown that the recombinant protein is sufficient for recovery of urease activity in cell lysate from a HypA deletion mutant, and that mutations in the zinc-binding motif result in a decrease in recovered urease activity. The results are interpreted in terms of a model

  9. The active site of low-temperature methane hydroxylation in iron-containing zeolites.

    PubMed

    Snyder, Benjamin E R; Vanelderen, Pieter; Bols, Max L; Hallaert, Simon D; Böttger, Lars H; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2016-08-18

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(ii), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species-α-Fe(ii) and α-O-are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive 'spectator' iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(ii) to be a mononuclear, high-spin, square planar Fe(ii) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(iv)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function-producing what is known in the context of metalloenzymes as an 'entatic' state-might be a useful way to tune the activity of heterogeneous catalysts. PMID:27535535

  10. Active sites environmental monitoring program. Annual report FY 1992

    SciTech Connect

    Morrissey, C.M.; Ashwood, T.L.; Hicks, D.S.

    1994-04-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) at ORNL from October 1991 through September 1992. Solid Waste Operations and the Environmental Sciences Division established ASEMP in 1989 to provide early detection and performance monitoring at active low-level waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by Chapter 2 and 3 of US Department of Energy Order 5820.2A. The Interim Waste Management Facility (IWMF) began operation in December 1991. Monitoring results from the tumulus and IWMF disposal pads continue to indicate that no LLW is leaching from the storage vaults. Storm water falling on the IWMF active pad was collected and transported to the Process Waste Treatment Plant while operators awaited approval of the National Pollutant Discharge Elimination System (NPDES) permit. Several of the recent samples collected from the active IWMF pad had pH levels above the NPDES limit of 9.0 because of alkali leached from the concrete. The increase in gross beta activity has been slight; only 1 of the 21 samples collected contained activity above the 5.0 Bq/L action level. Automated sample-collection and flow-measurement equipment has been installed at IWMF and is being tested. The flume designed to electronically measure flow from the IWMF pads and underpads is too large to be of practical value for measuring most flows at this site. Modification of this system will be necessary. A CO{sub 2} bubbler system designed to reduce the pH of water from the pads is being tested at IWMF.

  11. UTSA-74: A MOF-74 Isomer with Two Accessible Binding Sites per Metal Center for Highly Selective Gas Separation.

    PubMed

    Luo, Feng; Yan, Changsheng; Dang, Lilong; Krishna, Rajamani; Zhou, Wei; Wu, Hui; Dong, Xinglong; Han, Yu; Hu, Tong-Liang; O'Keeffe, Michael; Wang, Lingling; Luo, Mingbiao; Lin, Rui-Biao; Chen, Banglin

    2016-05-01

    A new metal-organic framework Zn2(H2O)(dobdc)·0.5(H2O) (UTSA-74, H4dobdc = 2,5-dioxido-1,4-benzenedicarboxylic acid), Zn-MOF-74/CPO-27-Zn isomer, has been synthesized and structurally characterized. It has a novel four coordinated fgl topology with one-dimensional channels of about 8.0 Å. Unlike metal sites in the well-established MOF-74 with a rod-packing structure in which each of them is in a five coordinate square pyramidal coordination geometry, there are two different Zn(2+) sites within the binuclear secondary building units in UTSA-74 in which one of them (Zn1) is in a tetrahedral while another (Zn2) in an octahedral coordination geometry. After activation, the two axial water molecules on Zn2 sites can be removed, generating UTSA-74a with two accessible gas binding sites per Zn2 ion. Accordingly, UTSA-74a takes up a moderately high and comparable amount of acetylene (145 cm(3)/cm(3)) to Zn-MOF-74. Interestingly, the accessible Zn(2+) sites in UTSA-74a are bridged by carbon dioxide molecules instead of being terminally bound in Zn-MOF-74, so UTSA-74a adsorbs a much smaller amount of carbon dioxide (90 cm(3)/cm(3)) than Zn-MOF-74 (146 cm(3)/cm(3)) at room temperature and 1 bar, leading to a superior MOF material for highly selective C2H2/CO2 separation. X-ray crystal structures, gas sorption isotherms, molecular modeling, and simulated and experimental breakthroughs comprehensively support this result. PMID:27113684

  12. Health risk assessments of heavy metal exposure via consumption of marine mussels collected from anthropogenic sites.

    PubMed

    Yap, Chee Kong; Cheng, Wan Hee; Karami, Ali; Ismail, Ahmad

    2016-05-15

    A total of 40 marine mussel Perna viridis populations collected (2002-2009) from 20 geographical sites located in two busy shipping lanes namely the Straits of Malacca (10 sites; 16 populations) and the Straits of Johore (8 sites; 21 populations) and three populations (2 sites) on the east coast of Peninsular Malaysia, was determined for Cd, Cu, Fe, Ni, Pb and Zn concentrations. In comparison with the maximum permissible limits (MPLs) set by existing food safety guidelines, all metal concentrations found in all the mussel populations were lower than the prescribed MPLs. In terms of the provisional tolerable weekly intake prescribed by the Joint FAO/WHO Expert Committee on Food Additives (JECFA) and oral reference doses (ORDs) by the USEPA, all the studied metals (except for Pb) were unlikely to become the limiting factors or unlikely to pose a risk for the consumption of the mussel populations. The estimated daily intake (EDI) for average level mussel (ALM) and high level mussel (HLM) consumers of mussels was found to be lower than the ORD guidelines for Cd, Cu, Fe, Ni and Zn. Furthermore, the target hazard quotient (THQ) was found to be less than 1 for ALM consumers but higher than 1 for HLM consumers in some sites. Therefore, there were no potential human health risks to the ALM consumers of the mussels. However, for Pb THQ values, the Pb levels in some mussel populations could create a health risk problem. Present results indicate that the consumption amounts of mussels should be limited for minimizing potential health risks of heavy metals to the HLM consumers. PMID:26925739

  13. Oxidative stress in the mollusk Echinolittorina peruviana (Gasteropoda: Littorinidae, Lamarck, 1822) and trace metals in coastal sectors with mining activity.

    PubMed

    Jara, C; Gaete, H; Lobos, G; Hidalgo, M E

    2014-08-01

    The aim of the study was to evaluate the effect of coastal waters of sites with mining activity in Echinolittorina peruviana, through oxidative stress biomarkers and heavy metals determination both in water and in tissue. Organisms were collected in the intertidal zone in areas with and without mining activity. Metal concentrations in the water and tissues, and also, the following biomarkers of oxidative stress: antioxidant enzyme activity, superoxide dismutase and catalase, non-enzymatic oxidative capacity (TRAP), oxidative damage to proteins (carbonyls) and TBARS, were measured The concentrations of accumulated metals had the following order Fe > Cu > Cd > Zn > Cr > Mo > As; the highest concentrations of metals in water and tissues were found in Caleta Palito and Chañaral. Results suggest that the coastal waters with mining activity and greatest concentrations of copper and iron induced the greater antioxidant response and oxidative damage to lipids in E. peruviana. PMID:24829115

  14. Trace metal bioavailability in sediments from a reference site, Ribeira Bay, Brazil.

    PubMed

    Chiappetta, Janine M M; Machado, Wilson; Santos, Joana M; Lessa, Josane A

    2016-05-15

    Surface sediments were collected near potential contamination sources impacting Ribeira Bay (Brazil), a system considered as a 'reference site' for trace metals. Physicochemical properties (pH and Eh), grain size and concentrations of total organic carbon (TOC), total phosphorus (TP), acid-volatile sulfides (AVS) and simultaneously-extracted metals (Fe, Mn, Cd, Cu, Ni, Pb and Zn) were analyzed. Although relatively low metal concentrations were found, correlations of Zn and Ni with high TP levels suggested an association with sewage inputs, while other metals presented associations with specific geochemical carriers (TOC, Fe and Mn compounds). AVS levels exceeding those of the sums of Cd, Cu, Ni, Pb and Zn (ΣSEM) by at least one order of magnitude and TOC-normalized differences between ΣSEM and AVS ((ΣSEM-AVS)/fOC) near to or below than -200μmolgOC(-1) indicated that there were sufficient AVS and TOC levels to control trace metal bioavailability in sediment pore water. PMID:26992748

  15. Adsorption of Carbon Dioxide on Unsaturated Metal Sites in M2 (dobpdc) Frameworks with Exceptional Structural Stability and Relation between Lewis Acidity and Adsorption Enthalpy.

    PubMed

    Yoo, Ga Young; Lee, Woo Ram; Jo, Hyuna; Park, Joonho; Song, Jeong Hwa; Lim, Kwang Soo; Moon, Dohyun; Jung, Hyun; Lim, Juhyung; Han, Sang Soo; Jung, Yousung; Hong, Chang Seop

    2016-05-23

    A series of metal-organic frameworks (MOFs) M2 (dobpdc) (M=Mn, Co, Ni, Zn; H4 dobpdc=4,4'-dihydroxy-1,1'-biphenyl-3,3'-dicarboxylic acid), with a highly dense arrangement of open metal sites along hexagonal channels were prepared by microwave-assisted or simple solvothermal reactions. The activated materials were structurally expanded when guest molecules including CO2 were introduced into the pores. The Lewis acidity of the open metal sites varied in the order MnZn, as confirmed by C=O stretching bands in the IR spectra, which are related to the CO2 adsorption enthalpy. DFT calculations revealed that the high CO2 binding affinity of transition-metal-based M2 (dobpdc) is primarily attributable to the favorable charge transfer from CO2 (oxygen lone pair acting as a Lewis base) to the open metal sites (Lewis acid), while electrostatic effects, the underlying factor responsible for the particular order of binding strength observed across different transition metals, also play a role. The framework stability against water coincides with the order of Lewis acidity. In this series of MOFs, the structural stability of Ni2 (dobpdc) is exceptional; it endured in water vapor, liquid water, and in refluxing water for one month, and the solid remained intact on exposure to solutions of pH 2-13. The DFT calculations also support the experimental finding that Ni2 (dobpdc) has higher chemical stability than the other frameworks. PMID:27105924

  16. FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal binding site prediction at the proteome level

    PubMed Central

    Brylinski, Michal; Skolnick, Jeffrey

    2010-01-01

    The rapid accumulation of gene sequences, many of which are hypothetical proteins with unknown function, has stimulated the development of accurate computational tools for protein function prediction with evolution/structure-based approaches showing considerable promise. In this paper, we present FINDSITE-metal, a new threading-based method designed specifically to detect metal binding sites in modeled protein structures. Comprehensive benchmarks using different quality protein structures show that weakly homologous protein models provide sufficient structural information for quite accurate annotation by FINDSITE-metal. Combining structure/evolutionary information with machine learning results in highly accurate metal binding annotations; for protein models constructed by TASSER, whose average Cα RMSD from the native structure is 8.9 Å, 59.5% (71.9%) of the best of top five predicted metal locations are within 4 Å (8 Å) from a bound metal in the crystal structure. For most of the targets, multiple metal binding sites are detected with the best predicted binding site at rank 1 and within the top 2 ranks in 65.6% and 83.1% of the cases, respectively. Furthermore, for iron, copper, zinc, calcium and magnesium ions, the binding metal can be predicted with high, typically 70-90%, accuracy. FINDSITE-metal also provides a set of confidence indexes that help assess the reliability of predictions. Finally, we describe the proteome-wide application of FINDSITE-metal that quantifies the metal binding complement of the human proteome. FINDSITE-metal is freely available to the academic community at http://cssb.biology.gatech.edu/findsite-metal/. PMID:21287609

  17. Diagnostics of metal inert gas and metal active gas welding processes

    NASA Astrophysics Data System (ADS)

    Uhrlandt, D.

    2016-08-01

    The paper gives a review on studies on metal inert gas (MIG) and metal active gas (MAG) welding processes with the focus on diagnostics of the arc, the material transfer, and the temporal process behaviour in welding experiments. Recent findings with respect to an improved understanding of the main mechanisms in the welding arc and the welding process are summarized. This is linked to actual developments in welding arc and welding process modelling where measurements are indispensable for validation. Challenges of forthcoming studies are illustrated by means of methods under development for welding process control as well as remaining open questions with respect to arc-surface interaction and arc power balance.

  18. Probing the promiscuous active site of myo-inositol dehydrogenase using synthetic substrates, homology modeling, and active site modification.

    PubMed

    Daniellou, Richard; Zheng, Hongyan; Langill, David M; Sanders, David A R; Palmer, David R J

    2007-06-26

    The active site of myo-inositol dehydrogenase (IDH, EC 1.1.1.18) from Bacillus subtilis recognizes a variety of mono- and disaccharides, as well as 1l-4-O-substituted inositol derivatives. It catalyzes the NAD+-dependent oxidation of the axial alcohol of these substrates with comparable kinetic constants. We have found that 4-O-p-toluenesulfonyl-myo-inositol does not act as a substrate for IDH, in contrast to structurally similar compounds such as those bearing substituted benzyl substituents in the same position. X-ray crystallographic analysis of 4-O-p-toluenesulfonyl-myo-inositol and 4-O-(2-naphthyl)methyl-myo-inositol, which is a substrate for IDH, shows a distinct difference in the preferred conformation of the aryl substituent. Conformational analysis of known substrates of IDH suggests that this conformational difference may account for the difference in reactivity of 4-O-p-toluenesulfonyl-myo-inositol in the presence of IDH. A sequence alignment of IDH with the homologous glucose-fructose oxidoreductase allowed the construction of an homology model of inositol dehydrogenase, to which NADH and 4-O-benzyl-scyllo-inosose were docked and the active site energy minimized. The active site model is consistent with all experimental results and suggests that a conserved tyrosine-glycine-tyrosine motif forms the hydrophobic pocket adjoining the site of inositol recognition. Y233F and Y235F retain activity, while Y233R and Y235R do not. A histidine-aspartate pair, H176 and D172, are proposed to act as a dyad in which H176 is the active site acid/base. The enzyme is inactivated by diethyl pyrocarbonate, and the mutants H176A and D172N show a marked loss of activity. Kinetic isotope effect experiments with D172N indicate that chemistry is rate-determining for this mutant. PMID:17539607

  19. A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity

    PubMed Central

    Gwyn, Lori M.; Peak, Mandy M.; De, Pallabi; Rahman, Negar S.; Rodgers, Karla K.

    2009-01-01

    The recombination activating protein, RAG1, a key component of the V(D)J recombinase, binds multiple Zn2+ ions in its catalytically-required core region. However, the role of zinc in the DNA cleavage activity of RAG1 is not well-resolved. To address this issue, we determined the stoichiometry of Zn2+ ions bound to the catalytically active core region of RAG1 under various conditions. Using metal quantitation methods, we determined that core RAG1 can bind up to four Zn2+ ions. Stripping the full complement of bound Zn2+ ions to produce apo-protein abrogated DNA cleavage activity. Moreover, even partial removal of zinc-binding equivalents resulted in a significant diminishment of DNA cleavage activity, as compared to holo-Zn2+ core RAG1. Mutants of the intact core RAG1 and the isolated core RAG1 domains were studied to identify the location of zinc-binding sites. Significantly, the C-terminal domain in core RAG1 binds at least two Zn2+ ions, with one zinc-binding site containing C902 and C907 as ligands (termed the CC zinc site) and H937 and H942 coordinating a Zn2+ ion in a separate site (HH zinc site). The latter zinc-binding site is essential for DNA cleavage activity, given that the H937A and H942A mutants were defective in both in vitro DNA cleavage assays and cellular recombination assays. Furthermore, as mutation of the active site residue E962 reduces Zn2+ coordination, we propose that the HH zinc site is located in close proximity to the DDE active site. Overall, these results demonstrate that Zn2+ serves an important auxiliary role for RAG1 DNA cleavage activity. Furthermore, we propose that one of the zinc-binding sites is linked to the active site of core RAG1 directly or indirectly by E962. PMID:19500590

  20. Activation of the binuclear metal center through formation of phosphotriesterase-inhibitor complexes.

    PubMed

    Samples, Cynthia R; Raushel, Frank M; DeRose, Victoria J

    2007-03-20

    Phosphotriesterase (PTE) from Pseudomonas diminuta is a binuclear metalloenzyme that catalyzes the hydrolysis of organophosphate nerve agents at rates approaching the diffusion-controlled limit. The proposed catalytic mechanism postulates the interaction of the substrate with the metal center and subsequent nucleophilic attack by the bridging hydroxide. X-band EPR spectroscopy was utilized to monitor the active site of Mn/Mn-substituted PTE upon addition of two inhibitors, diisopropyl methyl phosphonate and triethyl phosphate, and the product of hydrolysis, diethyl phosphate. The effects of inhibitor and product binding on the magnetic properties of the metal center and the hydroxyl bridge were evaluated by measuring changes in the features of the EPR spectra. The EPR spectra support the proposal that the binding of substrate analogues to the binuclear metal center diminishes the population of hydroxide-bridged species. These results, in conjunction with previously published kinetic and crystallographic data, suggest that substrate binding via the phosphoryl oxygen at the beta-metal weakens the coordination of the hydroxide bridge to the beta-metal. The weakened coordination to the beta-metal ion increases the nucleophilic character of the hydroxide and is coupled to the increase in the electrophilic character of the substrate. PMID:17315951

  1. Transition Metal Ions in Zeolites: Coordination and activation of O2

    PubMed Central

    Smeets, Pieter J.; Woertink, Julia S.; Sels, Bert F.; Solomon, Edward I.; Schoonheydt, Robert A.

    2010-01-01

    Zeolites containing transition metal ions (TMI) often show promising activity as heterogeneous catalysts in pollution abatement and selective oxidation reactions. In this paper, two aspects of research on the TMI Cu, Co and Fe in zeolites are discussed: (i) coordination to the lattice and (ii) activated oxygen species. At low loading, TMI preferably occupy exchange sites in six-membered oxygen rings (6MR) where the TMI preferentially coordinate with the oxygen atoms of Al tetrahedra. High TMI loadings result in a variety of TMI species formed at the zeolite surface. Removal of the extra-lattice oxygens during high temperature pretreatments can result in auto-reduction. Oxidation of reduced TMI sites often results in the formation of highly reactive oxygen species. In Cu-ZSM-5, calcination with O2 results in the formation of a species, which was found to be a crucial intermediate in both the direct decomposition of NO and N2O and the selective oxidation of methane into methanol. An activated oxygen species, called α-oxygen, is formed in Fe-ZSM5 and reported to be the active site in the partial oxidation of methane and benzene into methanol and phenol, respectively. However, this reactive α-oxygen can only be formed with N2O, not with O2. O2 activated Co intermediates in Faujasite (FAU) zeolites can selectively oxidize α-pinene and epoxidize styrene. In Co-FAU, CoIII superoxo and peroxo complexes are suggested to be the active cores, whereas in Cu and Fe-ZSM-5 various monomeric and dimeric sites have been proposed, but no consensus has been obtained. Very recently, the active site in Cu-ZSM-5 was identified as a bent [Cu-O-Cu]2+ core (Proc. Natl. Acad. Sci. USA 2009, 106, 18908-18913). Overall, O2 activation depends on the interplay of structural factors such as type of zeolite, size of the channels and cages and chemical factors such as Si/Al ratio and the nature, charge and distribution of the charge balancing cations. The presence of several different TMI sites

  2. Structural Basis for the Inhibition of RNase H Activity of HIV-1 Reverse Transcriptase by RNase H Active Site-Directed Inhibitors

    SciTech Connect

    Su, Hua-Poo; Yan, Youwei; Prasad, G. Sridhar; Smith, Robert F.; Daniels, Christopher L.; Abeywickrema, Pravien D.; Reid, John C.; Loughran, H. Marie; Kornienko, Maria; Sharma, Sujata; Grobler, Jay A.; Xu, Bei; Sardana, Vinod; Allison, Timothy J.; Williams, Peter D.; Darke, Paul L.; Hazuda, Daria J.; Munshi, Sanjeev

    2010-09-02

    HIV/AIDS continues to be a menace to public health. Several drugs currently on the market have successfully improved the ability to manage the viral burden in infected patients. However, new drugs are needed to combat the rapid emergence of mutated forms of the virus that are resistant to existing therapies. Currently, approved drugs target three of the four major enzyme activities encoded by the virus that are critical to the HIV life cycle. Although a number of inhibitors of HIV RNase H activity have been reported, few inhibit by directly engaging the RNase H active site. Here, we describe structures of naphthyridinone-containing inhibitors bound to the RNase H active site. This class of compounds binds to the active site via two metal ions that are coordinated by catalytic site residues, D443, E478, D498, and D549. The directionality of the naphthyridinone pharmacophore is restricted by the ordering of D549 and H539 in the RNase H domain. In addition, one of the naphthyridinone-based compounds was found to bind at a second site close to the polymerase active site and non-nucleoside/nucleotide inhibitor sites in a metal-independent manner. Further characterization, using fluorescence-based thermal denaturation and a crystal structure of the isolated RNase H domain reveals that this compound can also bind the RNase H site and retains the metal-dependent binding mode of this class of molecules. These structures provide a means for structurally guided design of novel RNase H inhibitors.

  3. Anticancer activity of Arkeshwara Rasa - A herbo-metallic preparation

    PubMed Central

    Nafiujjaman, Md; Nurunnabi, Md; Saha, Samir Kumar; Jahan, Rownak; Lee, Yong-kyu; Rahmatullah, Mohammed

    2015-01-01

    Introduction: Though metal based drugs have been prescribed in Ayurveda for centuries to treat various diseases, such as rheumatoid arthritis and cancer, toxicity of these drugs containing heavy metal is a great drawback for practical application. So, proper scientific validation of herbo-metallic drugs like Arkeshwara Rasa (AR) have become one of the focused research arena of new drugs against cancers. Aim: To investigate the in vitro anticancer effects of AR. Materials and Methods: Anticancer activity of AR was investigated on two human cancer cell lines, which represent two different tissues (pancreas and skin). Lactate dehydrogenase (LDH) assay for enzyme activity and trypan blue assay for cell morphology were performed for further confirmation. Results: AR showed potent activity against pancreatic cancer cells (MIA-PaCa-2). LDH activity confirmed that AR was active against pancreatic cancer cells. Finally, it was observed that AR exhibited significant effects on cancer cells due to synergistic effects of different compounds of AR. Conclusion: The study strongly suggests that AR has the potential to be an anticancer drug against pancreatic cancer. PMID:27313425

  4. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.

    PubMed

    Gajadeera, Chathurada S; Zhang, Xinyi; Wei, Yinan; Tsodikov, Oleg V

    2015-02-01

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme. PMID:25576794

  5. Effect of heavy metals on soil enzyme activity at different field conditions in Middle Spis mining area (Slovakia).

    PubMed

    Angelovičová, Lenka; Lodenius, Martin; Tulisalo, Esa; Fazekašová, Danica

    2014-12-01

    Heavy metals concentrations were measured in the former mining area located in Hornad river valley (Slovakia). Soil samples were taken in 2012 from 20 sites at two field types (grasslands, heaps of waste material) and two different areas. Total content of heavy metals (Cu, Pb, Zn, Hg), urease (URE), acid phosphatase (ACP), alkaline phosphatase (ALP), soil reaction (pH) were changing depending on the field/area type. The tailing pond and processing plants have been found as the biggest sources of pollution. URE, ACP and ALP activities significantly decreased while the heavy metal contents increased. Significant differences were found among area types in the heavy metal contents and activity of URE. No statistical differences in the content of heavy metals but significant statistical differences for soil pH were found for field types (grassland and heaps). Significant negative correlation was found for URE-Pb, URE-Zn and also between soil reaction and ACP and ALP. PMID:25293393

  6. The Active Site of Oligogalacturonate Lyase Provides Unique Insights into Cytoplasmic Oligogalacturonate β-Elimination*

    PubMed Central

    Abbott, D. Wade; Gilbert, Harry J.; Boraston, Alisdair B.

    2010-01-01

    Oligogalacturonate lyases (OGLs; now also classified as pectate lyase family 22) are cytoplasmic enzymes found in pectinolytic members of Enterobacteriaceae, such as the enteropathogen Yersinia enterocolitica. OGLs utilize a β-elimination mechanism to preferentially catalyze the conversion of saturated and unsaturated digalacturonate into monogalacturonate and the 4,5-unsaturated monogalacturonate-like molecule, 5-keto-4-deoxyuronate. To provide mechanistic insights into the specificity of this enzyme activity, we have characterized the OGL from Y. enterocolitica, YeOGL, on oligogalacturonides and determined its three-dimensional x-ray structure to 1.65 Å. The model contains a Mn2+ atom in the active site, which is coordinated by three histidines, one glutamine, and an acetate ion. The acetate mimics the binding of the uronate group of galactourono-configured substrates. These findings, in combination with enzyme kinetics and metal supplementation assays, provide a framework for modeling the active site architecture of OGL. This enzyme appears to contain a histidine for the abstraction of the α-proton in the −1 subsite, a residue that is highly conserved throughout the OGL family and represents a unique catalytic base among pectic active lyases. In addition, we present a hypothesis for an emerging relationship observed between the cellular distribution of pectate lyase folding and the distinct metal coordination chemistries of pectate lyases. PMID:20851883

  7. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

  8. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils.

  9. Mycorrhizal fungi modulate phytochemical production and antioxidant activity of Cichorium intybus L. (Asteraceae) under metal toxicity.

    PubMed

    Rozpądek, P; Wężowicz, K; Stojakowska, A; Malarz, J; Surówka, E; Sobczyk, Ł; Anielska, T; Ważny, R; Miszalski, Z; Turnau, K

    2014-10-01

    Cichorium intybus (common chicory), a perennial plant, common in anthropogenic sites, has been the object of a multitude of studies in recent years due to its high content of antioxidants utilized in pharmacy and food industry. Here, the role of arbuscular mycorrhizal fungi (AMF) in the biosynthesis of plant secondary metabolites and the activity of enzymatic antioxidants under toxic metal stress was studied. Plants inoculated with Rhizophagus irregularis and non-inoculated were grown on non-polluted and toxic metal enriched substrata. The results presented here indicate that AMF improves chicory fitness. Fresh and dry weight was found to be severely affected by the fungi and heavy metals. The concentration of hydroxycinnamates was increased in the shoots of mycorrhizal plants cultivated on non-polluted substrata, but no differences were found in plants cultivated on metal enriched substrata. The activity of SOD and H2O2 removing enzymes CAT and POX was elevated in the shoots of mycorrhizal plants regardless of the cultivation environment. Photochemical efficiency of inoculated chicory was significantly improved. Our results indicate that R. irregularis inoculation had a beneficial role in sustaining the plants ability to cope with the deleterious effects of metal toxicity. PMID:25048909

  10. Activated metallic gold as an agent for direct methoxycarbonylation.

    PubMed

    Xu, Bingjun; Madix, Robert J; Friend, Cynthia M

    2011-12-21

    We have discovered that metallic gold is a highly effective vehicle for the low-temperature vapor-phase carbonylation of methanol by insertion of CO into the O-H bond to form methoxycarbonyl. This reaction contrasts sharply to the carbonylation pathway well known for homogeneously catalyzed carbonylation reactions, such as the synthesis of acetic acid. The methoxycarbonyl intermediate can be further employed in a variety of methoxycarbonylation reactions, without the use or production of toxic chemicals. More generally we observe facile, selective methoxycarbonylation of alkyl and aryl alcohols and secondary amines on metallic gold well below room temperature. A specific example is the synthesis of dimethyl carbonate, which has extensive use in organic synthesis. This work establishes a unique framework for using oxygen-activated metallic gold as a catalyst for energy-efficient, environmentally benign production of key synthetic chemical agents. PMID:22035206

  11. On-site screened Coulomb interactions for localized electrons in transition metal oxides and defect systems

    NASA Astrophysics Data System (ADS)

    Shih, Bi-Ching; Zhang, Peihong; Department of Physics Team

    2011-03-01

    Electronic and structural properties of strongly correlated material systems are largely determined by the strength of the on-site Coulomb interaction. Theoretical models devised to capture the physics of strongly correlated materials usually involve screened Coulomb interactions as adjustable parameters. We present first-principles results for the screened on-site Coulomb and exchange energy for transition metal oxides. The dielectric screening is calculated within the random phase approximation and the localized electrons are represented by maximally localized Wannier functions. We further extend our study to calculate on-site Coulomb interactions for localized defect states in semiconductors. We acknowledge the computational support provided by the Center for Computational Research at the University at Buffalo, SUNY. This work is supported by the National Science Foundation under Grant No. DMR-0946404 and by the Department of Energy under Grant No. DE-SC0002623.

  12. Bimetallic Metal-Organic Frameworks: Probing the Lewis Acid Site for CO2 Conversion.

    PubMed

    Zou, Ruyi; Li, Pei-Zhou; Zeng, Yong-Fei; Liu, Jia; Zhao, Ruo; Duan, Hui; Luo, Zhong; Wang, Jin-Gui; Zou, Ruqiang; Zhao, Yanli

    2016-05-01

    A highly porous metal-organic framework (MOF) incorporating two kinds of second building units (SBUs), i.e., dimeric paddlewheel (Zn2 (COO)4 ) and tetrameric (Zn4 (O)(CO2 )6 ), is successfully assembled by the reaction of a tricarboxylate ligand with Zn(II) ion. Subsequently, single-crystal-to-single-crystal metal cation exchange using the constructed MOF is investigated, and the results show that Cu(II) and Co(II) ions can selectively be introduced into the MOF without compromising the crystallinity of the pristine framework. This metal cation-exchangeable MOF provides a useful platform for studying the metal effect on both gas adsorption and catalytic activity of the resulted MOFs. While the gas adsorption experiments reveal that Cu(II) and Co(II) exchanged samples exhibit comparable CO2 adsorption capability to the pristine Zn(II) -based MOF under the same conditions, catalytic investigations for the cycloaddition reaction of CO2 with epoxides into related carbonates demonstrate that Zn(II) -based MOF affords the highest catalytic activity as compared with Cu(II) and Co(II) exchanged ones. Molecular dynamic simulations are carried out to further confirm the catalytic performance of these constructed MOFs on chemical fixation of CO2 to carbonates. This research sheds light on how metal exchange can influence intrinsic properties of MOFs. PMID:26900671

  13. Heavy metals in bivalve mussels and their habitats from different sites along the Chilean Coast

    SciTech Connect

    De Gregori, I.; Pinochet, H.; Delgado, D. ); Gras, N.; Munoz, L. )

    1994-02-01

    It is well known that heavy metals have a great ecological significance due to their toxicity and accumulative behaviour playing a prominent role in marine ecosystems. They occur in all compartments in the marine environment with a tendency to accumulate in organism from different trophic levels of the marine webs. Along this pathway, toxic trace metals become a potential hazard for man and mammals. Coastal and estuarine zones are more vulnerable to anthropogenic pollution with toxic metals and it must be kept in mind that these zones have high seafood production. Chile is in a favourable position to develop fishing activities since it has approximately 4.500 km. of coastline bordering the South Pacific Ocean. The seawater is rich in nutrients and new aquaculture projects have been developed during the last year. However, these seafoods, like other marine organisms, are susceptible to being contaminated by trace metals, produced especially by the mining and industrial processing of ores and metals (i.e., Cu, Mo). This activity is well known as an important source of heavy metals, due to the enormous quantities of waste products, some of which were formerly released directly to the marine environment. Actually there are many aspects demanding better and more detailed knowledge on the occurrence, inventory, of the Chilean marine ecosystem. For these reasons we are developing a programme for monitoring some heavy metals in marine samples. The development of analytical quality control procedures and the analysis of toxic trace elements in fresh and canned mussels were recently published. In this paper, we present the results obtained for the Cadmium, Copper and Zinc contents in water, sediment and mollusc samples collected from different geographical areas located along the coast of Chile. 11 refs., 1 fig., 1 tab.

  14. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  15. Nest predation increases with parental activity: separating nest site and parental activity effects.

    PubMed Central

    Martin, T E; Scott, J; Menge, C

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection. PMID:11413645

  16. Mobilization and attenuation of metals downstream from a base-metal mining site in the Matra Mountains, northeastern Hungary

    USGS Publications Warehouse

    Odor, L.; Wanty, R.B.; Horvath, I.; Fugedi, U.

    1999-01-01

    Regional geochemical baseline values have been established for Hungary by the use of low-density stream-sediment surveys of flood-plain deposits of large drainage basins and of the fine fraction of stream sediments. The baseline values and anomaly thresholds thus produced helped to evaluate the importance of high toxic element concentrations found in soils in a valley downstream of a polymetallic vein-type base-metal mine. Erosion of the mine dumps and flotation dump, losses of metals during filtering, storage and transportation, human neglects, and operational breakdowns, have all contributed to the contamination of a small catchment basin in a procession of releases of solid waste. The sulfide-rich waste material weathers to a yellow color; this layer of 'yellow sand' blankets a narrow strip of the floodplain of Toka Creek in the valley near the town of Gyongyosoroszi. Contamination was spread out in the valley by floods. Metals present in the yellow sand include Pb, As, Cd, Cu, Zn, and Sb. Exposure of the local population to these metals may occur through inhalation of airborne particulates or by ingestion of these metals that are taken up by crops grown in the valley. To evaluate the areal extent and depth of the contamination, active stream sediment, flood-plain deposits, lake or reservoir sediments, soils, and surface water were sampled along the erosion pathways downstream of the mine and dumps. The flood-plain profile was sampled in detail to see the vertical distribution of elements and to relate the metal concentrations to the sedimentation and contamination histories of the flood plain. Downward migration of mobile Zn and Cd from the contaminated upper layers under supergene conditions is observed, while vertical migration of Pb, As, Hg and Sb appears to be insignificant. Soil profiles of 137Cs which originated from above-ground atomic bomb tests and the Chernobyl accident, provide good evidence that the upper 30-40 cm of the flood-plain sections, which

  17. Identification of Ice Nucleation Active Sites on Silicate Dust Particles

    NASA Astrophysics Data System (ADS)

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-04-01

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts [1-3]. Nevertheless, among those structures K-feldspar showed by far the highest ice nucleation activity. In this study, the reasons for its activity and the difference in the activity of the different feldspars were investigated in closer details. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. We give a potential explanation of the increased ice nucleation activity of K-feldspar. The ice nucleating sites are very much dependent on the alkali ion present by altering the water structure and the feldspar surface. The higher activity of K-feldspar can be attributed to the presence of potassium ions on the surface and surface bilayer. The alkali-ions have different hydration shells and thus an influence on the ice nucleation activity of feldspar. Chaotropic behavior of Calcium and Sodium ions are lowering the ice nucleation potential of the other feldspars, while kosmotropic Potassium has a neutral or even positive effect. Furthermore we investigated the influence of milling onto the ice nucleation of quartz particles. The ice nucleation activity can be increased by mechanical milling, by introducing more molecular, nucleation active defects to the particle surface. This effect is larger than expected by plane surface increase. [1] Atkinson et al. The Importance of Feldspar for Ice Nucleation by Mineral Dust in Mixed-Phase Clouds. Nature 2013, 498, 355-358. [2] Yakobi-Hancock et al.. Feldspar Minerals as Efficient Deposition Ice Nuclei. Atmos. Chem. Phys. 2013, 13, 11175-11185. [3] Zolles et al. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles. J. Phys. Chem. A 2015 accepted.

  18. Anaerobic bioleaching of metals from waste activated sludge.

    PubMed

    Meulepas, Roel J W; Gonzalez-Gil, Graciela; Teshager, Fitfety Melese; Witharana, Ayoma; Saikaly, Pascal E; Lens, Piet N L

    2015-05-01

    Heavy metal contamination of anaerobically digested waste activated sludge hampers its reuse as fertilizer or soil conditioner. Conventional methods to leach metals require aeration or the addition of leaching agents. This paper investigates whether metals can be leached from waste activated sludge during the first, acidifying stage of two-stage anaerobic digestion without the supply of leaching agents. These leaching experiments were done with waste activated sludge from the Hoek van Holland municipal wastewater treatment plant (The Netherlands), which contained 342 μg g(-1) of copper, 487 μg g(-1) of lead, 793 μg g(-1) of zinc, 27 μg g(-1) of nickel and 2.3 μg g(-1) of cadmium. During the anaerobic acidification of 3 gdry weight L(-1) waste activated sludge, 80-85% of the copper, 66-69% of the lead, 87% of the zinc, 94-99% of the nickel and 73-83% of the cadmium were leached. The first stage of two-stage anaerobic digestion can thus be optimized as an anaerobic bioleaching process and produce a treated sludge (i.e., digestate) that meets the land-use standards in The Netherlands for copper, zinc, nickel and cadmium, but not for lead. PMID:25659306

  19. Active Immobilized Antibiotics Based on Metal Hydroxides1

    PubMed Central

    Kennedy, John F.; Humphreys, John D.

    1976-01-01

    The water-insoluble hydroxides of zirconium (IV), titanium (IV), titanium (III), iron (II), vanadium (III), and tin (II) have been used to prepare insoluble derivatives of a cyclic peptide antibiotic by a facile chelation process. Testing of the antibacterial activities of the products against two gram-positive and two gram-negative bacteria showed that in the majority of cases the water-insoluble antibiotics remained active against those bacteria susceptible to the parent antibiotic. The power of the assay system has been extended by the novel use of colored organisms to aid determinations where the growth of normal organisms could not be distinguished from the appearance of the supporting material. Insoluble derivatives of neomycin, polymyxin B, streptomycin, ampicillin, penicillin G, and chloramphenicol were prepared by chelation with zirconium hydroxide, and these derivatives similarly reflected the antibacterial activities of the parent compounds. Several of the metal hydroxides themselves possess antibacterial activity due to complex formation with the bacteria. However, the use of selected metal hydroxides can afford a simple, inexpensive, and inert matrix for antibiotic immobilization, resulting in an antibacterial product that may possess slow-release properties. The mechanisms by which the metal hydroxide-antibiotic association-dissociation may occur are discussed. PMID:949174

  20. Ligational behavior of Schiff bases towards transition metal ion and metalation effect on their antibacterial activity

    NASA Astrophysics Data System (ADS)

    Devi, Jai; Batra, Nisha; Malhotra, Rajesh

    2012-11-01

    New Schiff bases pyrazine-2-carboxylicacid (phenyl-pyridin-2-yl-methylene)-hydrazide (Hpch-bp) HL1 and pyrazine-2-carboxylicacid (pyridin-2-ylmethylene)-hydrazide (Hpch-pc) HL2 derived from condensation of pyrazine carboxylic hydrazide (Hpch) with 2-benzoyl pyridine (bp) or pyridine 2-carbaldehyde (pc) and their transition metal complexes of type ML(1-2)2 have been synthesized, where M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). Characterization of ligands and their metal complexes was carried out by elemental analysis, conductimetric studies, magnetic susceptibility, spectroscopic techniques (IR, UV-VIS, NMR, ESR, Mass) and thermogravimetric analysis. The physico-chemical studies revealed octahedral geometry or distorted octahedral geometry around metal ion. These azomethine Schiff base ligands acted as tridentate ? coordinating through carbonyl, azomethine and pyridine nitrogen present in the ligand. The thermodynamic and thermal properties of the complexes have been investigated and it was observed on the basis of these studies that thermal stability of complexes follows the order Mn < Zn < Cu < Co < Ni. The ligands and their complexes were tested for in vitro antibacterial activity at different concentrations against bacteria viz. Gram positive Bacillus subtilis, Micrococcus luteus and Gram negative Pseudomonas aeruginosa, Pseudomonas mendocina. A marked enhancement in biocidal activity of the ligands under similar experimental conditions was observed as a consequence of coordination with metal ions. The trend of growth inhibition in the complexes was found to be in the order: Cu > Mn > Ni > Co > Zn.

  1. Arginine 116 stabilizes the entrance to the metal ion-binding site of the MntC protein

    PubMed Central

    Kanteev, Margarita; Adir, Noam

    2013-01-01

    The cyanobacterium Synechocystis sp. PCC 6803 imports Mn2+ ions via MntCAB, an ABC transport system that is expressed at submicromolar Mn2+ concentrations. The structures of the wild type (WT) and a site-directed mutant of the MntC solute-binding protein have been determined at 2.7 and 3.5 Å resolution, respectively. The WT structure is significantly improved over the previously determined structure (PDB entry 1xvl), showing improved Mn2+ binding site parameters, disulfide bonds in all three monomers and ions bound to the protein surface, revealing the role of Zn2+ ions in the crystallization liquor. The structure of MntC reveals that the active site is surrounded by neutral-to-­positive electrostatic potential and is dominated by a network of polar interactions centred around Arg116. The mutation of this residue to alanine was shown to destabilize loops in the entrance to the metal-ion binding site and suggests a possible role in MntC function. PMID:23519795

  2. Active Sites Environmental Monitoring Program. FY 1993: Annual report

    SciTech Connect

    Morrissey, C.M.; Ashwood, T.L.; Hicks, D.S.; Marsh, J.D.

    1994-08-01

    This report continues a series of annual and semiannual reports that present the results of the Active Sites Environmental Monitoring Program (ASEMP) monitoring activities. The report details monitoring data for fiscal year (FY) 1993 and is divided into three major areas: SWSA 6 [including tumulus pads, Interim Waste Management Facility (IWMF), and other sites], the low-level Liquid-Waste Solidification Project (LWSP), and TRU-waste storage facilities in SWSA 5 N. The detailed monitoring methodology is described in the second revision of the ASEMP program plan. This report also presents a summary of the methodology used to gather data for each major area along with the results obtained during FY 1993.

  3. Binding of Mn-deoxyribonucleoside Triphosphates to the Active Site of the DNA Polymerase of Bacteriophage T7

    SciTech Connect

    B Akabayov; C Richardson

    2011-12-31

    Divalent metal ions are crucial as cofactors for a variety of intracellular enzymatic activities. Mg{sup 2+}, as an example, mediates binding of deoxyribonucleoside 5'-triphosphates followed by their hydrolysis in the active site of DNA polymerase. It is difficult to study the binding of Mg{sup 2+} to an active site because Mg{sup 2+} is spectroscopically silent and Mg{sup 2+} binds with low affinity to the active site of an enzyme. Therefore, we substituted Mg{sup 2+} with Mn{sup 2+}:Mn{sup 2+} that is not only visible spectroscopically but also provides full activity of the DNA polymerase of bacteriophage T7. In order to demonstrate that the majority of Mn{sup 2+} is bound to the enzyme, we have applied site-directed titration analysis of T7 DNA polymerase using X-ray near edge spectroscopy. Here we show how X-ray near edge spectroscopy can be used to distinguish between signal originating from Mn{sup 2+} that is free in solution and Mn{sup 2+} bound to the active site of T7 DNA polymerase. This method can be applied to other enzymes that use divalent metal ions as a cofactor.

  4. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  5. Analyzing relationships between surface perturbations and local chemical reactivity of metal sites: Alkali promotion of O2 dissociation on Ag(111)

    NASA Astrophysics Data System (ADS)

    Xin, Hongliang; Linic, Suljo

    2016-06-01

    Many commercial heterogeneous catalysts are complex structures that contain metal active sites promoted by multiple additives. Developing fundamental understanding about the impact of these perturbations on the local surface reactivity is crucial for catalyst development and optimization. In this contribution, we develop a general framework for identifying underlying mechanisms that control the changes in the surface reactivity of a metal site (more specifically the adsorbate-surface interactions) upon a perturbation in the local environment. This framework allows us to interpret fairly complex interactions on metal surfaces in terms of specific, physically transparent contributions that can be evaluated independently of each other. We use Cs-promoted dissociation of O2 as an example to illustrate our approach. We concluded that the Cs adsorbate affects the outcome of the chemical reaction through a strong alkali-induced electric field interacting with the static dipole moment of the O2/Ag(111) system.

  6. Analyzing relationships between surface perturbations and local chemical reactivity of metal sites: Alkali promotion of O2 dissociation on Ag(111).

    PubMed

    Xin, Hongliang; Linic, Suljo

    2016-06-21

    Many commercial heterogeneous catalysts are complex structures that contain metal active sites promoted by multiple additives. Developing fundamental understanding about the impact of these perturbations on the local surface reactivity is crucial for catalyst development and optimization. In this contribution, we develop a general framework for identifying underlying mechanisms that control the changes in the surface reactivity of a metal site (more specifically the adsorbate-surface interactions) upon a perturbation in the local environment. This framework allows us to interpret fairly complex interactions on metal surfaces in terms of specific, physically transparent contributions that can be evaluated independently of each other. We use Cs-promoted dissociation of O2 as an example to illustrate our approach. We concluded that the Cs adsorbate affects the outcome of the chemical reaction through a strong alkali-induced electric field interacting with the static dipole moment of the O2/Ag(111) system. PMID:27334187

  7. Metallic conduction induced by direct anion site doping in layered SnSe2

    NASA Astrophysics Data System (ADS)

    Kim, Sang Il; Hwang, Sungwoo; Kim, Se Yun; Lee, Woo-Jin; Jung, Doh Won; Moon, Kyoung-Seok; Park, Hee Jung; Cho, Young-Jin; Cho, Yong-Hee; Kim, Jung-Hwa; Yun, Dong-Jin; Lee, Kyu Hyoung; Han, In-Taek; Lee, Kimoon; Sohn, Yoonchul

    2016-01-01

    The emergence of metallic conduction in layered dichalcogenide semiconductor materials by chemical doping is one of key issues for two-dimensional (2D) materials engineering. At present, doping methods for layered dichalcogenide materials have been limited to an ion intercalation between layer units or electrostatic carrier doping by electrical bias owing to the absence of appropriate substitutional dopant for increasing the carrier concentration. Here, we report the occurrence of metallic conduction in the layered dichalcogenide of SnSe2 by the direct Se-site doping with Cl as a shallow electron donor. The total carrier concentration up to ~1020 cm-3 is achieved by Cl substitutional doping, resulting in the improved conductivity value of ~170 S·cm-1 from ~1.7 S·cm-1 for non-doped SnSe2. When the carrier concentration exceeds ~1019 cm-3, the conduction mechanism is changed from hopping to degenerate conduction, exhibiting metal-insulator transition behavior. Detailed band structure calculation reveals that the hybridized s-p orbital from Sn 5s and Se 4p states is responsible for the degenerate metallic conduction in electron-doped SnSe2.

  8. Metallic conduction induced by direct anion site doping in layered SnSe2.

    PubMed

    Kim, Sang Il; Hwang, Sungwoo; Kim, Se Yun; Lee, Woo-Jin; Jung, Doh Won; Moon, Kyoung-Seok; Park, Hee Jung; Cho, Young-Jin; Cho, Yong-Hee; Kim, Jung-Hwa; Yun, Dong-Jin; Lee, Kyu Hyoung; Han, In-taek; Lee, Kimoon; Sohn, Yoonchul

    2016-01-01

    The emergence of metallic conduction in layered dichalcogenide semiconductor materials by chemical doping is one of key issues for two-dimensional (2D) materials engineering. At present, doping methods for layered dichalcogenide materials have been limited to an ion intercalation between layer units or electrostatic carrier doping by electrical bias owing to the absence of appropriate substitutional dopant for increasing the carrier concentration. Here, we report the occurrence of metallic conduction in the layered dichalcogenide of SnSe2 by the direct Se-site doping with Cl as a shallow electron donor. The total carrier concentration up to ~10(20) cm(-3) is achieved by Cl substitutional doping, resulting in the improved conductivity value of ~170 S · cm(-1) from ~1.7 S · cm(-1) for non-doped SnSe2. When the carrier concentration exceeds ~10(19) cm(-3), the conduction mechanism is changed from hopping to degenerate conduction, exhibiting metal-insulator transition behavior. Detailed band structure calculation reveals that the hybridized s-p orbital from Sn 5s and Se 4p states is responsible for the degenerate metallic conduction in electron-doped SnSe2. PMID:26792630

  9. Metallic conduction induced by direct anion site doping in layered SnSe2

    PubMed Central

    Kim, Sang Il; Hwang, Sungwoo; Kim, Se Yun; Lee, Woo-Jin; Jung, Doh Won; Moon, Kyoung-Seok; Park, Hee Jung; Cho, Young-Jin; Cho, Yong-Hee; Kim, Jung-Hwa; Yun, Dong-Jin; Lee, Kyu Hyoung; Han, In-taek; Lee, Kimoon; Sohn, Yoonchul

    2016-01-01

    The emergence of metallic conduction in layered dichalcogenide semiconductor materials by chemical doping is one of key issues for two-dimensional (2D) materials engineering. At present, doping methods for layered dichalcogenide materials have been limited to an ion intercalation between layer units or electrostatic carrier doping by electrical bias owing to the absence of appropriate substitutional dopant for increasing the carrier concentration. Here, we report the occurrence of metallic conduction in the layered dichalcogenide of SnSe2 by the direct Se-site doping with Cl as a shallow electron donor. The total carrier concentration up to ~1020 cm−3 is achieved by Cl substitutional doping, resulting in the improved conductivity value of ~170 S·cm−1 from ~1.7 S·cm−1 for non-doped SnSe2. When the carrier concentration exceeds ~1019 cm−3, the conduction mechanism is changed from hopping to degenerate conduction, exhibiting metal-insulator transition behavior. Detailed band structure calculation reveals that the hybridized s-p orbital from Sn 5s and Se 4p states is responsible for the degenerate metallic conduction in electron-doped SnSe2. PMID:26792630

  10. Phytoaccumulation of Heavy Metals in Natural Vegetation at the Municipal Wastewater Site in Abbottabad, Pakistan.

    PubMed

    Irshad, Muhammad; Ruqia, Bibi; Hussain, Zahid

    2015-01-01

    Heavy metal accumulation in crops and soils from wastewater irrigation poses a significant threat to the human health. A study was carried out to investigate the removal potential of heavy metals (HM) by native plant species, namely Cannabis sativa L., Chenopodium album L., Datura stramonium L., Sonchus asper L., Amaranthus viridus L., Oenothera rosea (LHer), Xanthium stramonium L., Polygonum macalosa L., Nasturtium officinale L. and Conyza canadensis L. growing at the municipal wastewater site in Abbottabad city, Pakistan. The HM concentrations varied among plants depending on the species. Metal concentrations across species varied in the order iron (Fe) > zinc (Zn) > chromium (Cr) > nickel (Ni) > cadmium (Cd). Majority of the species accumulated more HM in roots than shoots. Among species, the concentrations (both in roots and shoots) were in the order C. sativa > C. album > X. stramonium > C. canadensis > A. viridus > N. officinale > P. macalosa > D. stramonium > S. asper > O. rosea. No species was identified as a hyperaccumulator. All species exhibited a translocation factor (TF) less than 1. Species like C. sativa, C. album and X. stramonium gave higher (> 1) biological concentration factor (BCF) and biological accumulation coefficient (BAC) especially for Fe, Cr and Cd than other species. Higher accumulation of heavy metals in these plant species signifies the general application of these species for phytostabilization and phytoextraction of HM from polluted soils. PMID:26366840

  11. Spectroscopic analysis of soil metal contamination around a derelict mine site in the Blue Mountains, Australia

    NASA Astrophysics Data System (ADS)

    Shamsoddini, A.; Raval, S.; Taplin, R.

    2014-09-01

    Abandoned mine sites pose the potential threat of the heavy metal pollution spread through streams and via runoff leading to contamination of soil and water in their surrounding areas. Regular monitoring of these areas is critical to minimise impacts on water resources, flora and fauna. Conventional ground based monitoring is expensive and sometimes impractical; spectroscopic methods have been emerged as a reliable alternative for this purpose. In this study, the capabilities of the spectroscopy method were examined for modelling soil contamination from around the abandoned silver-zinc mine located at Yerranderie, NSW Australia. The diagnostic characteristics of the original reflectance data were compared with models derived from first and second derivatives of the reflectance data. The results indicate that the models derived from the first derivative of the reflectance data estimate heavy metals significantly more accurately than model derived from the original reflectance. It was also found in this study that there is no need to use second derivative for modelling heavy metal soil contamination. Finally, the results indicate that estimates were of greater accuracy for arsenic and lead compared to other heavy metals, while the estimation for silver was found to be the most erroneous.

  12. Potential sites of CFTR activation by tyrosine kinases.

    PubMed

    Billet, Arnaud; Jia, Yanlin; Jensen, Timothy J; Hou, Yue-Xian; Chang, Xiu-Bao; Riordan, John R; Hanrahan, John W

    2016-05-01

    The CFTR chloride channel is tightly regulated by phosphorylation at multiple serine residues. Recently it has been proposed that its activity is also regulated by tyrosine kinases, however the tyrosine phosphorylation sites remain to be identified. In this study we examined 2 candidate tyrosine residues near the boundary between the first nucleotide binding domain and the R domain, a region which is important for channel function but devoid of PKA consensus sequences. Mutating tyrosines at positions 625 and 627 dramatically reduced responses to Src or Pyk2 without altering the activation by PKA, suggesting they may contribute to CFTR regulation. PMID:26645934

  13. Brownian aggregation rate of colloid particles with several active sites

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

  14. The impact of metal pollution on soil faunal and microbial activity in two grassland ecosystems.

    PubMed

    Boshoff, Magdalena; De Jonge, Maarten; Dardenne, Freddy; Blust, Ronny; Bervoets, Lieven

    2014-10-01

    In this study the influence of metal pollution on soil functional activity was evaluated by means of Bait lamina and BIOLOG(®) EcoPlates™ assays. The in situ bait lamina assay investigates the feeding activity of macrofauna, mesofauna and microarthropods while the BIOLOG(®) EcoPlate™ assay measures the metabolic fingerprint of a selectively extracted microbial community. Both assays proved sensitive enough to reveal changes in the soil community between the plots nearest to and further away from a metal pollution source. Feeding activity (FA) at the less polluted plots reached percentages of 90% while plots nearer to the source of pollution reached percentages as low as 10%. After 2 and 6 days of incubation average well color development (AWCD) and functional richness (R') were significantly lower at the plots closest to the source of pollution. While the Shannon Wiener diversity index (H') decreased significantly at sites nearer to the source of pollution after 2 days but not after 6 days of incubation. Arsenic, Cu and Pb correlated significantly and negatively with feeding activity and functional indices while the role of changing environmental factors such as moisture percentage could not be ruled out completely. Compared to the Bait lamina method that is used in situ and which is therefore more affected by site specific variation, the BIOLOG assay, which excludes confounding factors such as low moisture percentage, may be a more reliable assay to measure soil functional activity. PMID:25173048

  15. Health assessment for Metal Working Shop Site, Lake Ann, Michigan, Region 5. CERCLIS No. MID980992952. Preliminary report

    SciTech Connect

    Not Available

    1988-09-30

    The Metal Working Shop Site is listed on the National Priorities List. The site consists of an operating metal-working facility in a sparsely populated rural area in Benzie, Michigan. Identified contaminants of potential concern on the site include chromium, tetrachloroethylene (PCE), trichloroethane, and toluene in water and trichloroethylene (TCE), trichloroethane, xylenes, ethylbenzene, and toluene in soil. The site is considered to be of potential public health concern because of the risk to human health caused by the possibility of exposure to hazardous substances via contaminated well water and soil. Confirmation of sampling results that show contamination in well water and soil is needed.

  16. Functional copper at the acetyl-CoA synthase active site

    PubMed Central

    Seravalli, Javier; Gu, Weiwei; Tam, Annie; Strauss, Erick; Begley, Tadhg P.; Cramer, Stephen P.; Ragsdale, Stephen W.

    2003-01-01

    The bifunctional CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) plays a central role in the Wood–Ljungdahl pathway of autotrophic CO2 fixation. A recent structure of the Moorella thermoacetica enzyme revealed that the ACS active site contains a [4Fe-4S] cluster bridged to a binuclear Cu-Ni site. Here, biochemical and x-ray absorption spectroscopic (XAS) evidence is presented that the copper ion at the M. thermoacetica ACS active site is essential. Depletion of copper correlates with reduction in ACS activity and in intensity of the “NiFeC” EPR signal without affecting either the activity or the EPR spectroscopic properties associated with CODH. In contrast, Zn content is negatively correlated with ACS activity without any apparent relationship to CODH activity. Cu is also found in the methanogenic CODH/ACS from Methanosarcina thermophila. XAS studies are consistent with a distorted Cu(I)–S3 site in the fully active enzyme in solution. Cu extended x-ray absorption fine structure analysis indicates an average Cu–S bond length of 2.25 Å and a metal neighbor at 2.65 Å, consistent with the Cu–Ni distance observed in the crystal structure. XAS experiments in the presence of seleno-CoA reveal a Cu–S3Se environment with a 2.4-Å Se–Cu bond, strongly implicating a Cu–SCoA intermediate in the mechanism of acetyl-CoA synthesis. These results indicate an essential and functional role for copper in the CODH/ACS from acetogenic and methanogenic organisms. PMID:12589021

  17. Metal(loid)s in sediment, lobster and mussel tissues near historical gold mine sites.

    PubMed

    Walker, Tony R; Grant, Jon

    2015-12-15

    Previous studies near historical gold mining districts in Nova Scotia have identified significant enrichment of metal(loid)s in coastal marine sediments. Most of this inventory is buried below biologically active zones, although in some areas arsenic has bioaccumulated in marine biota resulting in localised bivalve shellfish closures. Isaacs Harbour is poised for future industrial development, but before potential impacts are predicted, current marine baseline conditions must be determined. To address this gap, this study established a baseline using surface sediments and biota (mussel and lobster tissues), to provide a broader picture of metal(loid)s in the marine environment. Results confirmed previous studies showing that most sediment metal(loid) concentrations still exceeded Canadian Marine Sediment Quality Guidelines, and also provided evidence of Canadian Food Inspection Agency fish tissue exceedances of arsenic in lobster and lead in mussel tissues indicating that some bioaccumulation of legacy contaminants in marine biota continues to the present day. PMID:26475024

  18. Heavy metal contents of epiphytic acrocarpous mosses within inhabited sites in southwest Nigeria

    SciTech Connect

    Onianwa, P.C.; Ajayi, S.O.

    1987-01-01

    The levels of the metals Pb, Zn, Cu, Cd, Ni, Mn, and Fe accumulated in acrocarpous mosses within inhabited parts of villages and towns in the southwest region of Nigeria were determined, and then used for a classification of the area into relative pollution zones. Ibadan City was found to be the most polluted in the study area. Other zones of low and medium polluted villages and towns were identified. The zonations based on metal levels in these mosses were to some extent similar to that already obtained in a separate study of the same area with epiphytic forest mosses. The enrichment factors show that the gradients between zones of different pollution levels were higher in mosses within the inhabited sites.

  19. Vertical Transport of Heavy Metals in the Soil at a Field Test Site

    NASA Astrophysics Data System (ADS)

    Oswald, S.; Wenger, K.; Wettstein, B.; Fruth, D.

    2003-04-01

    The transport of zinc and copper in soil during a long-term phytoremediation test site was assessed by sampling, analysis and numerical modelling. Initially heavy metal contamination had been applied at different concentration levels using three replicates, and soil properties and vertical heavy metal concentration distribution were measured after 4 years. The results of this study show the change in the vertical distribution of zinc and copper after the following period of ten years. The vertical transport was interpreted considering recharge, evapotranspiration, sorption, plant uptake and outflux. Numerical modelling with Hydrus-1D was applied especially for the zinc movement. It illustrated the vertical movement downwards and the relative importance of the processes involved and the impact of the planned remediation strategy.

  20. Metal patterning on silicon surface by site-selective electroless deposition through colloidal crystal templating.

    PubMed

    Asoh, Hidetaka; Sakamoto, Seiji; Ono, Sachiko

    2007-12-15

    Site-selective Cu deposition on a Si substrate was achieved by a combination of colloidal crystal templating, hydrophobic treatment, and electroless plating. Uniformly sized nano/microstructures were produced on the substrate using a monolayer coating of colloidal spheres instead of a conventional resist. The Cu patterns obtained were of two different types: networklike honeycomb and isolated-island patterns with a minimum period of 200 nm. Each ordered pattern with the desired intervals was composed of clusters of Cu nanoparticles with a size range of 50-100 nm. By the present method, it is possible to control the periodicity of metal arrays by changing the diameter of the colloidal spheres used as an initial mask and to adjust the shape of the metal patterns by changing the mask structure for electroless plating. PMID:17915242

  1. Metal-mediated modulation of streptococcal cysteine protease activity and its biological implications.

    PubMed

    Chella Krishnan, Karthickeyan; Mukundan, Santhosh; Landero Figueroa, Julio A; Caruso, Joseph A; Kotb, Malak

    2014-07-01

    Streptococcal cysteine protease (SpeB), the major secreted protease produced by group A streptococcus (GAS), cleaves both host and bacterial proteins and contributes importantly to the pathogenesis of invasive GAS infections. Modulation of SpeB expression and/or its activity during invasive GAS infections has been shown to affect bacterial virulence and infection severity. Expression of SpeB is regulated by the GAS CovR-CovS two-component regulatory system, and we demonstrated that bacteria with mutations in the CovR-CovS two-component regulatory system are selected for during localized GAS infections and that these bacteria lack SpeB expression and exhibit a hypervirulent phenotype. Additionally, in a separate study, we showed that expression of SpeB can also be modulated by human transferrin- and/or lactoferrin-mediated iron chelation. Accordingly, the goal of this study was to investigate the possible roles of iron and other metals in modulating SpeB expression and/or activity in a manner that would potentiate bacterial virulence. Here, we report that the divalent metals zinc and copper inhibit SpeB activity at the posttranslational level. Utilizing online metal-binding site prediction servers, we identified two putative metal-binding sites in SpeB, one of which involves the catalytic-dyad residues (47)Cys and (195)His. Based on our findings, we propose that zinc and/or copper availability in the bacterial microenvironment can modulate the proteolytic activity of SpeB in a manner that preserves the integrity of several other virulence factors essential for bacterial survival and dissemination within the host and thereby may exacerbate the severity of invasive GAS infections. PMID:24799625

  2. Metal-Mediated Modulation of Streptococcal Cysteine Protease Activity and Its Biological Implications

    PubMed Central

    Chella Krishnan, Karthickeyan; Mukundan, Santhosh; Landero Figueroa, Julio A.; Caruso, Joseph A.

    2014-01-01

    Streptococcal cysteine protease (SpeB), the major secreted protease produced by group A streptococcus (GAS), cleaves both host and bacterial proteins and contributes importantly to the pathogenesis of invasive GAS infections. Modulation of SpeB expression and/or its activity during invasive GAS infections has been shown to affect bacterial virulence and infection severity. Expression of SpeB is regulated by the GAS CovR-CovS two-component regulatory system, and we demonstrated that bacteria with mutations in the CovR-CovS two-component regulatory system are selected for during localized GAS infections and that these bacteria lack SpeB expression and exhibit a hypervirulent phenotype. Additionally, in a separate study, we showed that expression of SpeB can also be modulated by human transferrin- and/or lactoferrin-mediated iron chelation. Accordingly, the goal of this study was to investigate the possible roles of iron and other metals in modulating SpeB expression and/or activity in a manner that would potentiate bacterial virulence. Here, we report that the divalent metals zinc and copper inhibit SpeB activity at the posttranslational level. Utilizing online metal-binding site prediction servers, we identified two putative metal-binding sites in SpeB, one of which involves the catalytic-dyad residues 47Cys and 195His. Based on our findings, we propose that zinc and/or copper availability in the bacterial microenvironment can modulate the proteolytic activity of SpeB in a manner that preserves the integrity of several other virulence factors essential for bacterial survival and dissemination within the host and thereby may exacerbate the severity of invasive GAS infections. PMID:24799625

  3. Novel bis-(−)-nor-meptazinol derivatives act as dual binding site AChE inhibitors with metal-complexing property

    SciTech Connect

    Zheng, Wei; Li, Juan; Qiu, Zhuibai; Xia, Zheng; Li, Wei; Yu, Lining; Chen, Hailin; Chen, Jianxing; Chen, Yan; Hu, Zhuqin; Zhou, Wei; Shao, Biyun; Cui, Yongyao; Xie, Qiong; Chen, Hongzhuan

    2012-10-01

    The strategy of dual binding site acetylcholinesterase (AChE) inhibition along with metal chelation may represent a promising direction for multi-targeted interventions in the pathophysiological processes of Alzheimer's disease (AD). In the present study, two derivatives (ZLA and ZLB) of a potent dual binding site AChE inhibitor bis-(−)-nor-meptazinol (bis-MEP) were designed and synthesized by introducing metal chelating pharmacophores into the middle chain of bis-MEP. They could inhibit human AChE activity with IC{sub 50} values of 9.63 μM (for ZLA) and 8.64 μM (for ZLB), and prevent AChE-induced amyloid-β (Aβ) aggregation with IC{sub 50} values of 49.1 μM (for ZLA) and 55.3 μM (for ZLB). In parallel, molecular docking analysis showed that they are capable of interacting with both the catalytic and peripheral anionic sites of AChE. Furthermore, they exhibited abilities to complex metal ions such as Cu(II) and Zn(II), and inhibit Aβ aggregation triggered by these metals. Collectively, these results suggest that ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency, and may be potential leads of value for further study on disease-modifying treatment of AD. -- Highlights: ► Two novel bis-(−)-nor-meptazinol derivatives are designed and synthesized. ► ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency. ► They are potential leads for disease-modifying treatment of Alzheimer's disease.

  4. Effects of metal ions and disulfide bonds on the activity of phosphodiesterase from Trimeresurus stejnegeri venom.

    PubMed

    Peng, Lili; Xu, Xiaolong; Guo, Mingchun; Yan, Xincheng; Wang, Shasha; Gao, Shang; Zhu, Shanshan

    2013-06-01

    Obviously different from the other known phosphodiesterases, the phosphodiesterase from Trimeresurus stejnegeri venom (TS-PDE) consists of two different chains linked with disulfide bonds and contains both endogenous Cu(2+) and Zn(2+). Cu(2+) and Zn(2+) are important for its phosphodiesterase activity. In this study, the effects of metal ions and small-molecule reductants on its structure and activity have been investigated by polyacrylamide gel electrophoresis, high performance liquid chromatography, fluorescence and electron paramagnetic resonance spectroscopy. The results show that TS-PDE has one class of Zn(2+) binding site and two classes of Cu(2+) binding site, including the high affinity activator sites and the low affinity sites. Cu(2+) ions function as a switch for its phosphodiesterase activity. The catalytic activity of TS-PDE does not have an absolute requirement for Cu(2+) and Zn(2+). Mg(2+), Mn(2+), Ni(2+), Co(2+) and Ca(2+) are all effective for its phosphodiesterase activity. TS-PDE has seven disulfide bonds and ten free cysteine residues. l-Ascorbate inhibits the phosphodiesterase activity of TS-PDE through reduction of the Cu(2+), while dithiothreitol, glutathione and tris(2-carboxyethyl)phosphine inhibit the phosphodiesterase activity of TS-PDE by reducing both the Cu(2+) and disulfide bonds. The catalytic activity of TS-PDE relies on its disulfide bonds and bimetallic cluster. In addition, biologically-relevant reductants, glutathione and l-ascorbate, have been found to be endogenous inhibitors to the phosphodiesterase activity of TS-PDE. PMID:23775423

  5. Individual and cumulative effects of agriculture, forestry and metal mining activities on the metal and phosphorus content of fluvial fine-grained sediment; Quesnel River Basin, British Columbia, Canada.

    PubMed

    Smith, Tyler B; Owens, Philip N

    2014-10-15

    The impact of agriculture, forestry and metal mining on the quality of fine-grained sediment (<63 μm) was investigated in the Quesnel River Basin (QRB) (~11,500 km(2)) in British Columbia, Canada. Samples of fine-grained sediment were collected monthly during the snow-free season in 2008 using time-integrated samplers at replicate sites representative of agriculture, forestry and mining activities in the basin (i.e. "impacted" sites). Samples were also collected from replicate reference sites and also from the main stem of the Quesnel River at the downstream confluence with the Fraser River. Generally, metal(loid) and phosphorus (P) concentrations for "impacted" sites were greater than for reference sites. Furthermore, concentrations of copper (forestry and mining sites), manganese (agriculture and forestry sites) and selenium (agriculture, forestry and mining sites) exceeded upper sediment quality guideline (SQG) thresholds. These results suggest that agriculture, forestry and metal mining activities are having an influence on the concentrations of sediment-associated metal(loid)s and P in the Quesnel basin. Metal(loid) and P concentrations of sediment collected from the downstream site were not significantly greater than values for the reference sites, and were typically lower than the values for the impacted sites. This suggests that the cumulative effects of agriculture, forestry and mining activities in the QRB are presently not having a measureable effect at the river basin-scale. The lack of a cumulative effect at the basin-scale is thought to reflect: (i) the relatively recent occurrence of land use disturbances in this basin; (ii) the dominance of sediment contributions from natural forest and agriculture; and (iii) the potential for storage of contaminants on floodplains and other storage elements between the locations of disturbance activities and the downstream sampling site, which may be attenuating the disturbance signal. PMID:25105754

  6. 75 FR 76037 - General Motors Corporation Grand Rapids Metal Center Metal Fabricating Division Including On-Site...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-07

    ... published in the Federal Register on April 23, 2010 (75 FR 21356). At the request of the State agency, the... Employment and Training Administration General Motors Corporation Grand Rapids Metal Center Metal Fabricating..., applicable to workers of General Motors Corporation, Grand Rapids Metal Center, Metal Fabricating...

  7. Progress report on decommissioning activities at the Fernald Environmental Management Project (FEMP) site

    SciTech Connect

    1998-07-01

    The Fernald Environmental Management Project (FEMP), is located about 18 miles northwest of Cincinnati, Ohio. Between 1953 and 1989, the facility, then called the Feed Material Production Center or FMPC, produced uranium metal products used in the eventual production of weapons grade material for use by other US Department of Energy (DOE) sites. In 1989, FMPC`s production was suspended by the federal government in order to focus resources on environmental restoration versus defense production. In 1992, Fluor Daniel Fernald assumed responsibility for managing all cleanup activities at the FEMP under contract to the DOE. In 1990, as part of the remediation effort, the site was divided into five operable units based on physical proximity of contaminated areas, similar amounts of types of contamination, or the potential for a similar technology to be used in cleanup activities. This report continues the outline of the decontamination and decommissioning (D and D) activities at the FEMP site Operable Unit 3 (OU3) and provides an update on the status of the decommissioning activities. OU3, the Facilities Closure and Demolition Project, involves the remediation of more than 200 uranium processing facilities. The mission of the project is to remove nuclear materials stored in these buildings, then perform the clean out of the buildings and equipment, and decontaminate and dismantle the facilities.

  8. From single crystal surfaces to single atoms: investigating active sites in electrocatalysis.

    PubMed

    O'Mullane, Anthony P

    2014-04-21

    Electrocatalytic processes will undoubtedly be at the heart of energising future transportation and technology with the added importance of being able to create the necessary fuels required to do so in an environmentally friendly and cost effective manner. For this to be successful two almost mutually exclusive surface properties need to be reconciled, namely producing highly active/reactive surface sites that exhibit long term stability. This article reviews the various approaches which have been undertaken to study the elusive nature of these active sites on metal surfaces which are considered as adatoms or clusters of adatoms with low coordination number. This includes the pioneering studies at extended well defined stepped single crystal surfaces using cyclic voltammetry up to the highly sophisticated in situ electrochemical imaging techniques used to study chemically synthesised nanomaterials. By combining the information attained from single crystal surfaces, individual nanoparticles of defined size and shape, density functional theory calculations and new concepts such as mesoporous multimetallic thin films and single atom electrocatalysts new insights into the design and fabrication of materials with highly active but stable active sites can be achieved. The area of electrocatalysis is therefore not only a fascinating and exciting field in terms of realistic technological and economical benefits but also from the fundamental understanding that can be acquired by studying such an array of interesting materials. PMID:24599277

  9. Site-dependent catalytic activity of graphene oxides towards oxidative dehydrogenation of propane.

    PubMed

    Tang, Shaobin; Cao, Zexing

    2012-12-28

    Graphene oxides (GOs) may offer extraordinary potential in the design of novel catalytic systems due to the presence of various oxygen functional groups and their unique electronic and structural properties. Using first-principles calculations, we explore the plausible mechanisms for the oxidative dehydrogenation (ODH) of propane to propene by GOs and the diffusion of the surface oxygen-containing groups under an external electric field. The present results show that GOs with modified oxygen-containing groups may afford high catalytic activity for the ODH of propane to propene. The presence of hydroxyl groups around the active sites provided by epoxides can remarkably enhance the C-H bond activation of propane and the activity enhancement exhibits strong site dependence. The sites of oxygen functional groups on the GO surface can be easily tuned by the diffusion of these groups under an external electric field, which increases the reactivity of GOs towards ODH of propane. The chemically modified GOs are thus quite promising in the design of metal-free catalysis. PMID:22801590

  10. Enzymatic activity in the rhizosphere of Spartina maritima: potential contribution for phytoremediation of metals.

    PubMed

    Reboreda, Rosa; Caçador, Isabel

    2008-02-01

    Extracellular enzymatic activity (EEA) of five enzymes (peroxidase, phenol oxidase, beta-glucosidase, beta-N-acetylglucosaminidase and acid phosphatase) was analysed in sediments colonised by Spartina maritima in two salt marshes (Rosário and Pancas) of the Tagus estuary (Portugal) with different characteristics such as sediment parameters and metal contaminant levels. Our aim was a better understanding of the influence of the halophyte on microbial activity in the rhizosphere under different site conditions, and its potential consequences for metal cycling and phytoremediation in salt marshes. Acid phosphatase and beta-N-acetylglucosaminidase presented significantly higher EEA in Rosário than in Pancas, whereas the opposite occurred for peroxidase. This was mainly attributed to differences in organic matter between the two sites. A positive correlation between root biomass and EEA of hydrolases (beta-glucosidase, beta-N-acetylglucosaminidase and acid phosphatase) was found, indicating a possible influence of the halophyte in sediment microbial function. This would potentially affect metal cycling in the rhizosphere through microbial reactions. PMID:17935772

  11. Calorimetric studies of the interactions of metalloenzyme active site mimetics with zinc-binding inhibitors.

    PubMed

    Robinson, Sophia G; Burns, Philip T; Miceli, Amanda M; Grice, Kyle A; Karver, Caitlin E; Jin, Lihua

    2016-07-19

    The binding of drugs to metalloenzymes is an intricate process that involves several interactions, including binding of the drug to the enzyme active site metal, as well as multiple interactions between the drug and the enzyme residues. In order to determine the free energy contribution of Zn(2+) binding by known metalloenzyme inhibitors without the other interactions, valid active site zinc structural mimetics must be formed and binding studies need to be performed in biologically relevant conditions. The potential of each of five ligands to form a structural mimetic with Zn(2+) was investigated in buffer using Isothermal Titration Calorimetry (ITC). All five ligands formed strong 1 : 1 (ligand : Zn(2+)) binary complexes. The complexes were used in further ITC experiments to study their interaction with 8-hydroxyquinoline (8-HQ) and/or acetohydroxamic acid (AHA), two bidentate anionic zinc-chelating enzyme inhibitors. It was found that tetradentate ligands were not suitable for creating zinc structural mimetics for inhibitor binding in solution due to insufficient coordination sites remaining on Zn(2+). A stable binary complex, [Zn(BPA)](2+), which was formed by a tridentate ligand, bis(2-pyridylmethyl)amine (BPA), was found to bind one AHA in buffer or a methanol : buffer mixture (60 : 40 by volume) at pH 7.25 or one 8-HQ in the methanol : buffer mixture at pH 6.80, making it an effective structural mimetic for the active site of zinc metalloenzymes. These results are consistent with the observation that metalloenzyme active site zinc ions have three residues coordinated to them, leaving one or two sites open for inhibitors to bind. Our findings indicate that Zn(BPA)X2 can be used as an active site structural mimetic for zinc metalloenzymes for estimating the free energy contribution of zinc binding to the overall inhibitor active site interactions. Such use will help aid in the rational design of inhibitors to a variety of zinc metalloenzymes

  12. Influence of Humic Acid Complexation with Metal Ions on Extracellular Electron Transfer Activity.

    PubMed

    Zhou, Shungui; Chen, Shanshan; Yuan, Yong; Lu, Qin

    2015-01-01

    Humic acids (HAs) can act as electron shuttles and mediate biogeochemical cycles, thereby influencing the transformation of nutrients and environmental pollutants. HAs commonly complex with metals in the environment, but few studies have focused on how these metals affect the roles of HAs in extracellular electron transfer (EET). In this study, HA-metal (HA-M) complexes (HA-Fe, HA-Cu, and HA-Al) were prepared and characterized. The electron shuttle capacities of HA-M complexes were experimentally evaluated through microbial Fe(III) reduction, biocurrent generation, and microbial azoreduction. The results show that the electron shuttle capacities of HAs were enhanced after complexation with Fe but were weakened when using Cu or Al. Density functional theory calculations were performed to explore the structural geometry of the HA-M complexes and revealed the best binding sites of the HAs to metals and the varied charge transfer rate constants (k). The EET activity of the HA-M complexes were in the order HA-Fe > HA-Cu > HA-Al. These findings have important implications for biogeochemical redox processes given the ubiquitous nature of both HAs and various metals in the environment. PMID:26593782

  13. Influence of Humic Acid Complexation with Metal Ions on Extracellular Electron Transfer Activity

    PubMed Central

    Zhou, Shungui; Chen, Shanshan; Yuan, Yong; Lu, Qin

    2015-01-01

    Humic acids (HAs) can act as electron shuttles and mediate biogeochemical cycles, thereby influencing the transformation of nutrients and environmental pollutants. HAs commonly complex with metals in the environment, but few studies have focused on how these metals affect the roles of HAs in extracellular electron transfer (EET). In this study, HA-metal (HA-M) complexes (HA-Fe, HA-Cu, and HA-Al) were prepared and characterized. The electron shuttle capacities of HA-M complexes were experimentally evaluated through microbial Fe(III) reduction, biocurrent generation, and microbial azoreduction. The results show that the electron shuttle capacities of HAs were enhanced after complexation with Fe but were weakened when using Cu or Al. Density functional theory calculations were performed to explore the structural geometry of the HA-M complexes and revealed the best binding sites of the HAs to metals and the varied charge transfer rate constants (k). The EET activity of the HA-M complexes were in the order HA-Fe > HA-Cu > HA-Al. These findings have important implications for biogeochemical redox processes given the ubiquitous nature of both HAs and various metals in the environment. PMID:26593782

  14. Influence of Humic Acid Complexation with Metal Ions on Extracellular Electron Transfer Activity

    NASA Astrophysics Data System (ADS)

    Zhou, Shungui; Chen, Shanshan; Yuan, Yong; Lu, Qin

    2015-11-01

    Humic acids (HAs) can act as electron shuttles and mediate biogeochemical cycles, thereby influencing the transformation of nutrients and environmental pollutants. HAs commonly complex with metals in the environment, but few studies have focused on how these metals affect the roles of HAs in extracellular electron transfer (EET). In this study, HA-metal (HA-M) complexes (HA-Fe, HA-Cu, and HA-Al) were prepared and characterized. The electron shuttle capacities of HA-M complexes were experimentally evaluated through microbial Fe(III) reduction, biocurrent generation, and microbial azoreduction. The results show that the electron shuttle capacities of HAs were enhanced after complexation with Fe but were weakened when using Cu or Al. Density functional theory calculations were performed to explore the structural geometry of the HA-M complexes and revealed the best binding sites of the HAs to metals and the varied charge transfer rate constants (k). The EET activity of the HA-M complexes were in the order HA-Fe > HA-Cu > HA-Al. These findings have important implications for biogeochemical redox processes given the ubiquitous nature of both HAs and various metals in the environment.

  15. Electrical active defects in HfO2 based metal/oxide/metal devices

    NASA Astrophysics Data System (ADS)

    El Kamel, F.

    2016-01-01

    Dielectric as well as thermally stimulated current measurements were performed on metal/HfO2/Pt capacitors in order to study the electrical active defects in hafnia thin films. Two thermally activated relaxation processes have been carried out from both measurements. At low temperatures, the relaxation process can be ascribed to the shallow traps level localized at 0.65 eV and generally evidenced by the second ionization of oxygen vacancies. At high temperatures, the relaxation process arises from the diffusion of positively charged oxygen vacancies by overcoming an energetic barrier of about 1 eV.

  16. Activation of Autophagy by Metals in Chlamydomonas reinhardtii

    PubMed Central

    Pérez-Martín, Marta; Blaby-Haas, Crysten E.; Pérez-Pérez, María Esther; Andrés-Garrido, Ascensión; Blaby, Ian K.; Merchant, Sabeeha S.

    2015-01-01

    Autophagy is an intracellular self-degradation pathway by which eukaryotic cells recycle their own material in response to specific stress conditions. Exposure to high concentrations of metals causes cell damage, although the effect of metal stress on autophagy has not been explored in photosynthetic organisms. In this study, we investigated the effect of metal excess on autophagy in the model unicellular green alga Chlamydomonas reinhardtii. We show in cells treated with nickel an upregulation of ATG8 that is independent of CRR1, a global regulator of copper signaling in Chlamydomonas. A similar effect on ATG8 was observed with copper and cobalt but not with cadmium or mercury ions. Transcriptome sequencing data revealed an increase in the abundance of the protein degradation machinery, including that responsible for autophagy, and a substantial overlap of that increased abundance with the hydrogen peroxide response in cells treated with nickel ions. Thus, our results indicate that metal stress triggers autophagy in Chlamydomonas and suggest that excess nickel may cause oxidative damage, which in turn activates degradative pathways, including autophagy, to clear impaired components and recover cellular homeostasis. PMID:26163317

  17. Activation of Autophagy by Metals in Chlamydomonas reinhardtii.

    PubMed

    Pérez-Martín, Marta; Blaby-Haas, Crysten E; Pérez-Pérez, María Esther; Andrés-Garrido, Ascensión; Blaby, Ian K; Merchant, Sabeeha S; Crespo, José L

    2015-09-01

    Autophagy is an intracellular self-degradation pathway by which eukaryotic cells recycle their own material in response to specific stress conditions. Exposure to high concentrations of metals causes cell damage, although the effect of metal stress on autophagy has not been explored in photosynthetic organisms. In this study, we investigated the effect of metal excess on autophagy in the model unicellular green alga Chlamydomonas reinhardtii. We show in cells treated with nickel an upregulation of ATG8 that is independent of CRR1, a global regulator of copper signaling in Chlamydomonas. A similar effect on ATG8 was observed with copper and cobalt but not with cadmium or mercury ions. Transcriptome sequencing data revealed an increase in the abundance of the protein degradation machinery, including that responsible for autophagy, and a substantial overlap of that increased abundance with the hydrogen peroxide response in cells treated with nickel ions. Thus, our results indicate that metal stress triggers autophagy in Chlamydomonas and suggest that excess nickel may cause oxidative damage, which in turn activates degradative pathways, including autophagy, to clear impaired components and recover cellular homeostasis. PMID:26163317

  18. Collaborative Triple Framework Interpenetration and Immobilization of Open Metal Sites within a Microporous Mixed Metal-Organic Framework for Highly Selective Gas Adsorption

    SciTech Connect

    Zhang, Zhangjing; Xiang, Sheng-Chang; Hong, Kunlun; Das, Madhab; Arman, Hadi; Garcia, Maya; Mondal, Jalal; Chen, Banglin

    2012-01-01

    A three-dimensional triply interpenetrated mixed metal-organic framework, Zn{sub 2}(BBA){sub 2}(CuPyen) {center_dot} G{sub x} (M'MOF-20; BBA = biphenyl-4,4'-dicarboxylate; G = guest solvent molecules), of primitive cubic net was obtained through the solvothermal reaction of Zn(NO{sub 3}){sub 2}, biphenyl-4,4'-dicarboxylic acid, and the salen precursor Cu(PyenH{sub 2})(NO{sub 3}){sub 2} by a metallo-ligand approach. The triple framework interpenetration has stabilized the framework in which the activated M'MOF-20a displays type-I N{sub 2} gas sorption behavior with a Langmuir surface area of 62 m{sup 2} g{sup -1}. The narrow pores of about 3.9 {angstrom} and the open metal sites on the pore surfaces within M'MOF-20a collaboratively induce its highly selective C{sub 2}H{sub 2}/CH{sub 4} and CO{sub 2}/CH{sub 4} gas separation at ambient temperature.

  19. Do heavy metals existing in abandoned mining sites represent a real health risk? A study case in the SE Spain.

    NASA Astrophysics Data System (ADS)

    Martinez-Sanchez, Maria Jose; Perez-Sirvent, Carmen; García-Lorenzo, Mari Luz; Martínez-López, Salvadora; Perez-Espinosa, Victor; Hernández-Cordoba, Manuel; Bech, Jaime

    2013-04-01

    Mining activities have been carried out for centuries in Sierra Minera (SE Spain) giving rise to a large number of sites distributed throughout the zone in which residues are accumulated. This communication reports studies as regards metal mobilization and analysis of the health risk that could be posed by inhalation, dermic contact or occasional ingestion of this type of sediments. Lead was used as the metal for the studies due to its particular abundance in the zone. A large number of samples were taken and general analytical determinations (pH, particle size, organic matter, equivalent calcium carbonate content and mineralogical composition) were carried out in order its characterization. An in vitro method for obtaining formation on Pb bioaccessibility in these mine waste materials was also carried out. Our results prove that mineral associations, different alteration states and sorption/desorption processes play an important role in the bioavailability of lead. In addition, it is noteworthy that the metal fraction dissolved by the proposed in vitro methodology is lower than 100%, both in the stomach and intestinal phases. Finally an assessment of the risk posed by lead is achieved. To this respect it should be noted that the IRIS database provide cancer slope factor and reference dose, as a way to assess the risk caused by arsenic, cadmium and copper but no for lead, probably due to the wide variety of real situations, and the discrepancy of the sources. The way here suggested is a novelty in this sense, and the results could be extrapolated to other similar zones and be incorporated to the general protocol of risk assessment applied to contaminated sites.

  20. A Metal-Based Inhibitor of NEDD8-Activating Enzyme

    PubMed Central

    Chan, Daniel Shiu-Hin; Leung, Chung-Hang; Wang, Hui-Min; Ma, Dik-Lung

    2012-01-01

    A cyclometallated rhodium(III) complex [Rh(ppy)2(dppz)]+ (1) (where ppy = 2-phenylpyridine and dppz = dipyrido[3,2-a:2′,3′-c]phenazine dipyridophenazine) has been prepared and identified as an inhibitor of NEDD8-activating enzyme (NAE). The complex inhibited NAE activity in cell-free and cell-based assays, and suppressed the CRL-regulated substrate degradation and NF-κB activation in human cancer cells with potency comparable to known NAE inhibitor MLN4924. Molecular modeling analysis suggested that the overall binding mode of 1 within the binding pocket of the APPBP1/UBA3 heterodimer resembled that for MLN4924. Complex 1 is the first metal complex reported to suppress the NEDDylation pathway via inhibition of the NEDD8-activating enzyme. PMID:23185368

  1. Spatial variability of metal bioaccumulation in estuarine killifish (Fundulus heteroclitus) at the Callahan mine superfund site, Brooksville, ME.

    PubMed

    Broadley, Hannah J; Buckman, Kate L; Bugge, Deenie M; Chen, Celia Y

    2013-11-01

    The former Callahan Mine Site in Brooksville, ME, is an open-pit, hardrock mine site in an intertidal system, thus providing a unique opportunity to evaluate how metal-enriched sediments and overlying water impact estuarine food webs. Copper, zinc, cadmium, and lead concentrations in sediment, whole water, and Atlantic killifish (Fundulus heteroclitus) were evaluated at sites in Goose Pond (GP; Callahan Mine Site) and at reference sites. The metal concentrations of sediment, water, and fish were spatially distinct and significantly greater at the mine site than in the reference estuary. Sediment concentrations were particularly elevated and were above probable effects levels for all four metals adjacent to the tailings pile. Even in this well-mixed system, water metal concentrations were significantly elevated adjacent to the tailings pile, and concentrations of Cu and Zn were above ambient water-quality criteria for chronic marine exposure. Neither organic matter in the sediment nor salinity or pH of the water explained the metal concentrations. Adjacent to the tailings pile, killifish metal body burdens were elevated and were significantly related to both sediment and aqueous concentrations. In conclusion, (1) the contaminated sediment and seepage from the tailings impoundment and waste rock pile no. 3 create a continual flux of metals into the water column, (2) the metals are bioavailable and bioconcentrating as evident in the killifish tissue concentrations, and (3) Callahan Mine is directly affecting metal bioaccumulation in fauna residing in the GP estuary and, potentially, in Penobscot Bay by the way of “trophic nekton relay.” PMID:24022459

  2. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    PubMed Central

    Wang, Yang-Gang; Mei, Donghai; Glezakou, Vassiliki-Alexandra; Li, Jun; Rousseau, Roger

    2015-01-01

    Catalysis by gold supported on reducible oxides has been extensively studied, yet issues such as the nature of the catalytic site and the role of the reducible support remain fiercely debated topics. Here we present ab initio molecular dynamics simulations of an unprecedented dynamic single-atom catalytic mechanism for the oxidation of carbon monoxide by ceria-supported gold clusters. The reported dynamic single-atom catalytic mechanism results from the ability of the gold cation to strongly couple with the redox properties of the ceria in a synergistic manner, thereby lowering the energy of redox reactions. The gold cation can break away from the gold nanoparticle to catalyse carbon monoxide oxidation, adjacent to the metal/oxide interface and subsequently reintegrate back into the nanoparticle after the reaction is completed. Our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in catalysis. PMID:25735407

  3. Metal-particle-induced, highly localized site-specific etching of Si and formation of single-crystalline Si nanowires in aqueous fluoride solution.

    PubMed

    Peng, Kuiqing; Fang, Hui; Hu, Juejun; Wu, Yin; Zhu, Jing; Yan, Yunjie; Lee, ShuitTong

    2006-10-16

    A straightforward metal-particle-induced, highly localized site-specific corrosion-like mechanism was proposed for the formation of aligned silicon-nanowire arrays on silicon in aqueous HF/AgNO3 solution on the basis of convincing experimental results. The etching process features weak dependence on the doping of the silicon wafers and, thus, provides an efficient method to prepare silicon nanowires with desirable doping characteristics. The novel electrochemical properties between silicon and active noble metals should be useful for preparing novel silicon nanostructures and also new optoelectronic devices. PMID:16871502

  4. Porphyrins as Templates for Site-Selective Atomic Layer Deposition: Vapor Metalation and in Situ Monitoring of Island Growth.

    PubMed

    Avila, Jason R; Emery, Jonathan D; Pellin, Michael J; Martinson, Alex B F; Farha, Omar K; Hupp, Joseph T

    2016-08-10

    Examinations of enzymatic catalysts suggest one key to efficient catalytic activity is discrete size metallo clusters. Mimicking enzymatic cluster systems is synthetically challenging because conventional solution methods are prone to aggregation or require capping of the cluster, thereby limiting its catalytic activity. We introduce site-selective atomic layer deposition (ALD) on porphyrins as an alternative approach to grow isolated metal oxide islands that are spatially separated. Surface-bound tetra-acid free base porphyrins (H2TCPP) may be metalated with Mn using conventional ALD precursor exposure to induce homogeneous hydroxide synthetic handles which acts as a nucleation point for subsequent ALD MnO island growth. Analytical fitting of in situ QCM mass uptake reveals island growth to be hemispherical with a convergence radius of 1.74 nm. This growth mode is confirmed with synchrotron grazing-incidence small-angle X-ray scattering (GISAXS) measurements. Finally, we extend this approach to other ALD chemistries to demonstrate the generality of this route to discrete metallo island materials. PMID:27454741

  5. Current activities handbook: formerly utilized sites remedial action program

    SciTech Connect

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  6. Metals and metalloids in hair samples of children living near the abandoned mine sites of Sulcis-Inglesiente (Sardinia, Italy).

    PubMed

    Varrica, D; Tamburo, E; Milia, N; Vallascas, E; Cortimiglia, V; De Giudici, G; Dongarrà, G; Sanna, E; Monna, F; Losno, R

    2014-10-01

    The Sulcis-Iglesiente district (SW Sardinia, Italy) is one of the oldest and most important polymetallic mining areas in Italy. Large outcrops of sulfide and oxide ores, as well as the products of the long-lasting mining activity, are present throughout the district releasing significant quantities of metals and metalloids into the surrounding environment. Here are reported concentrations of 21 elements determined in scalp hair samples from children (aged 11-13 years) living in different geochemical environments of southwestern Sardinia: Iglesias, hosting several abandoned mines, and the island of Sant׳Antioco, not affected by significant base metal mineralization events. Trace element determinations were performed by ICP-MS. Statistically significant differences (p<0.01) in elemental concentration levels between the two study sites were found. Hair of children from Iglesias exhibited higher concentration values for Ag, Ba, Cd, Cr, Ni, Pb, Rb, Sb, U, V, and Zn. Rubidium, V and U resulted more abundant at Sant׳Antioco. Hair samples from Iglesias showed gender-related differences for a larger number of elements (Ag, Ba, Cd, Co, Cu, Ni, Sr, U and Zn) than at Sant׳Antioco, where only U was significantly different. The above elemental concentrations in females were always higher than in male donors. Robust Principal Component Analysis operated on log-transformed elemental concentrations showed components indicative of a) sulfides ore minerals (PC1) reflecting the influence of the diffuse mineralization covering the entire study area, b) the presence of some bioavailable As sources (PC2) as As-rich pyrite and Fe-containing sphalerite and c) other sources of metals overlapping the diffuse mineralizations, as carbonate rocks and coal deposits (PC3). The results provided evidence of a potential risk of adverse effects on the health of the exposed population, with children living at Iglesias being greatly exposed to several metals and metalloids originated in mining

  7. High and Reversible Ammonia Uptake in Mesoporous Azolate Metal-Organic Frameworks with Open Mn, Co, and Ni Sites.

    PubMed

    Rieth, Adam J; Tulchinsky, Yuri; Dincă, Mircea

    2016-08-01

    A series of new mesoporous metal-organic frameworks (MOFs) made from extended bisbenzenetriazolate linkers exhibit coordinatively unsaturated metal sites that are responsible for high and reversible uptake of ammonia. Isostructural Mn, Co, and Ni materials adsorb 15.47, 12.00, and 12.02 mmol of NH3/g, respectively, at STP. Importantly, these near-record capacities are reversible for at least three cycles. These results demonstrate that azolate MOFs are sufficiently thermally and chemically stable to find uses in recyclable sorption, storage, and potentially separation of chemically challenging and/or corrosive gases, especially when designed to exhibit a high density of open metal sites. PMID:27420652

  8. Efficiency of stepwise magnetic-chemical site assessment for fly ash derived heavy metal pollution

    NASA Astrophysics Data System (ADS)

    Cao, Liwan; Appel, Erwin; Rösler, Wolfgang; Magiera, Tadeusz

    2015-11-01

    Previous works revealed a close relationship between magnetic susceptibility (MS) and heavy metal (HM) contents originating from industrial sources. However, despite general statements on the usefulness of magnetic mapping, the benefit of this procedure for geochemistry was not quantified yet. We present a study on fly ash pollution in soil around a coal-burning power plant complex and simulate a stepwise approach of magnetic pre-screening and subsequent targeted sampling for chemical analysis. The aim of this study is not to discuss correlations between MS and HM, but to show that a combined stepwise magnetic-chemical approach is the most efficient way for outlining HM contamination. In order to provide quantitative evidence, we explored map similarities of spatial HM distributions based on magnetochemical data and chemical data only. We determined 3-D triangular planes defined by categorized HM values at the sampling coordinates and calculated the average dihedral angle of the normal vectors as a similarity result. The study shows that the `Targeted' HM map (selection of 30 sites based magnetic pre-screening) has a higher similarity with the `True' Pollution HM map (85 sites) than HM maps resulting from site selections (30 sites) without using magnetic pre-screening information.

  9. Environmental impact assessment of radionuclide and metal contamination at the former U site at Kadji Sai, Kyrgyzstan.

    PubMed

    Lind, O C; Stegnar, P; Tolongutov, B; Rosseland, B O; Strømman, G; Uralbekov, B; Usubalieva, A; Solomatina, A; Gwynn, J P; Lespukh, E; Salbu, B

    2013-09-01

    During 1949-1967, a U mine, a coal-fired thermal power plant and a processing plant for the extraction of U from the produced ash were operated at the Kadji Sai U mining site in Tonsk district, Issyk-Kul County, Kyrgyzstan. The Kadji Sai U legacy site represents a source of contamination of the local environment by naturally occurring radionuclides and associated trace elements. To assess the environmental impact of radionuclides and trace metals at the site, field expeditions were performed in 2007 and 2008 by the Joint collaboration between Norway, Kazakhstan, Kyrgyzstan, Tajikistan (JNKKT) project and the NATO SfP RESCA project. In addition to in situ gamma and Rn dose rate measurements, sampling included at site fractionation of water and sampling of water, fish, sediment, soils and vegetation. The concentrations of radionuclides and trace metals in water from Issyk-Kul Lake were in general low, but surprisingly high for As. Uptake of U and As was also observed in fish from the lake with maximum bioconcentration factors for liver of 1.6 and 75, respectively. The concentrations of U in water within the Kadji Sai area varied from 0.01 to 0.05 mg/L, except for downstream from the mining area where U reached a factor of 10 higher, 0.2 mg/L. Uranium concentrations in the drinking water of Kadji Sai village were about the level recommended by the WHO for drinking water. The (234)U/(238)U activity ratio reflected equilibrium conditions in the mining pond, but far from equilibrium outside this area (reaching 2.3 for an artesian well). Uranium, As and Ni were mainly present as low molecular mass (LMM, less than 10 kDa) species in all samples, indicating that these elemental species are mobile and potentially bioavailable. The soils from the mining sites were enriched in U, As and trace metals. Hot spots with elevated radioactivity levels were easily detected in Kadji Sai and radioactive particles were observed. The presence of particles carrying significant amount of

  10. Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

    2014-01-01

    While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. PMID:25058658

  11. Metal ion sorption and desorption on zeolitized tuffs from the Nevada Test Site

    SciTech Connect

    Um, Wooyong; Papelis, Charalambos

    2004-01-15

    Because of the hundreds of nuclear weapon tests conducted on the Nevada Test Site (NTS) during the Cold War, the migration of radionuclides and contaminants is a potential concern. The mobility of these compounds and our ability to remediate contaminated sites are controlled by sorption and desorption processes, which depend frequently on the nature of the contaminant, the mineralogy of the site, and the geochemical conditions. The sorption and desorption behavior of strontium (Sr) and lead (Pb), two metal cations with different chemistries, commonly found on nuclear test sites were studied. Strontium showed pH-independent and ionic-strength-dependent sorption, consistent with ion exchange processes at permanent charge sorption sites. The sorption uptake of Sr increased with decreasing ionic strength of background solution. Strontium desorption from the adsorbents was enhanced by increased background electrolyte concentration and was a function of background electrolyte composition . The fractional uptake of Pb was higher, compared to Sr, and was only pH dependent at the highest ionic strength used (1.0 M). This pH-dependent sorption behavior, consistent with formation of surface complexes at amphoteric surface hydroxyl sites or formation of surface precipitates, could explain the decreased Pb desorption, compared to Sr, especially at increased background electrolyte concentrations. Under conditions typical for the groundwater at the NTS (I = 0.003 M, pH = 8.0), both Pb and Sr are expected to bind strongly on tuffs with composition similar to the zeolitized tuffs used in this study. Any increase in the dissolved ion concentration of the groundwater, however, may result in, at least partial, release of Sr and enhanced Sr mobility.

  12. An active metallic nanomatryushka with two similar super-resonances

    SciTech Connect

    Wu, D. J.; Cheng, Y.; Wu, X. W.; Liu, X. J.

    2014-07-07

    The optical properties of a simple metallic nanomatryushka (nanosphere-in-a-nanoshell) with gain have been investigated theoretically. The spaser (surface plasmon amplification by stimulated emission of radiation) phenomena can be observed at two critical wavelengths in the active metallic nanomatryushkas. With increasing the gain coefficient of the middle layer, a similar super surface plasmon (SP) resonance is first found at the ω₋⁺|₁ mode of the active nanoparticles and then breaks down. With further increasing the gain coefficient, another similar super-resonance occurs at the ω₋⁻|₁ mode. The near-field enhancements in the active nanomatryushkas also have been greatly amplified at the critical wavelengths for ω₋⁺|₊ and ω₋⁻|₁ modes. It is further found that the amplifications of SPs in the active Ag–SiO₂–Au nanoshell are strongest in four kinds of nanoshells and hence the largest near fields. The giant near-field enhancement can greatly enhance the Raman excitation and emission.

  13. Heavy metal binding to heparin disaccharides. I. Iduronic acid is the main binding site.

    PubMed

    Whitfield, D M; Choay, J; Sarkar, B

    1992-06-01

    As model compounds for Ni(II)-binding heparin-like compounds isolated from human kidneys (Templeton, D.M. & Sarkar, B. (1985) Biochem. J. 230 35-42.), we investigated two disaccharides--4-O-(2-O-sulfo-alpha-L-idopyranosyluronic acid)-2,5-anhydro- D-mannitol, disodium salt (1a), and 4-O-(2-O-sulfo-alpha-L-idopyranosyluronic acid)-6-O- sulfo-2,5-anhydro-D-mannitol, trisodium salt (1b)--that were isolated from heparin after nitrous acid hydrolysis and reduction. The monosulfate (1a) was active whereas the disulfate (1b) was inactive in a high-performance liquid chromatography (HPLC) binding assay with the tracer ions 63Ni(II) 54Mn(II), 65Zn(II), and 109Cd(II). This result is in accord with the isolation of two 67Cu(II) and 63Ni(II) binding fractions from a complete pool of nitrous-acid-derived heparin disaccharides using sulfate gradients and a MonoQ anion exchange column on an FPLC system. One was identified as compound (1a) and the other as a tetrasulfated trisaccharide by high resolution FAB-MS, NMR and HPLC-PAD. Similarly, two synthetic disaccharides-methyl, 2-O-sulfo-4-O-(alpha-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-alpha-D-glucosamine, trisodium salt [IdopA2S(alpha 1,4)GlcNS alpha Me, 2a], and 2-O-sulfo-4-O-(alpha-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-6-O-sulfo- alpha-D-glucosamine, tetrasodium salt [IdopA2S (alpha 1,4)GlcNS6S alpha Me, 2b]--were shown to bind tracer amounts of 63Ni and 67Cu using chromatographic assays. Subsequently, 1H NMR titrations of 1a, 1b, 2a, and 2b with Zn (OAc)2 were analyzed to yield 1:1 Zn(II)-binding constants of 472 +/- 59, 698 +/- 120, 8,758 +/- 2,237 and 20,100 +/- 5,598 M-1, respectively. The values for 2a and 2b suggest chelation. It is suggested that the idopyranosiduronic acid residue is the major metal binding site. NMR evidence for this hypothesis comes from marked 1H and 13C chemical shift changes to the iduronic acid resonances after addition of diamagnetic Zn(II) ions. PMID:1643264

  14. Insights into Substrate Specificity and Metal Activation of Mammalian Tetrahedral Aspartyl Aminopeptidase*

    PubMed Central

    Chen, Yuanyuan; Farquhar, Erik R.; Chance, Mark R.; Palczewski, Krzysztof; Kiser, Philip D.

    2012-01-01

    Aminopeptidases are key enzymes involved in the regulation of signaling peptide activity. Here, we present a detailed biochemical and structural analysis of an evolutionary highly conserved aspartyl aminopeptidase called DNPEP. We show that this peptidase can cleave multiple physiologically relevant substrates, including angiotensins, and thus may play a key role in regulating neuron function. Using a combination of x-ray crystallography, x-ray absorption spectroscopy, and single particle electron microscopy analysis, we provide the first detailed structural analysis of DNPEP. We show that this enzyme possesses a binuclear zinc-active site in which one of the zinc ions is readily exchangeable with other divalent cations such as manganese, which strongly stimulates the enzymatic activity of the protein. The plasticity of this metal-binding site suggests a mechanism for regulation of DNPEP activity. We also demonstrate that DNPEP assembles into a functionally relevant tetrahedral complex that restricts access of peptide substrates to the active site. These structural data allow rationalization of the enzyme's preference for short peptide substrates with N-terminal acidic residues. This study provides a structural basis for understanding the physiology and bioinorganic chemistry of DNPEP and other M18 family aminopeptidases. PMID:22356908

  15. Insights into Substrate Specificity and Metal Activation of Mammalian Tetrahedral Aspartyl Aminopeptidase

    SciTech Connect

    Chen, Yuanyuan; Farquhar, Erik R.; Chance, Mark R.; Palczewski, Krzysztof; Kiser, Philip D.

    2012-07-11

    Aminopeptidases are key enzymes involved in the regulation of signaling peptide activity. Here, we present a detailed biochemical and structural analysis of an evolutionary highly conserved aspartyl aminopeptidase called DNPEP. We show that this peptidase can cleave multiple physiologically relevant substrates, including angiotensins, and thus may play a key role in regulating neuron function. Using a combination of x-ray crystallography, x-ray absorption spectroscopy, and single particle electron microscopy analysis, we provide the first detailed structural analysis of DNPEP. We show that this enzyme possesses a binuclear zinc-active site in which one of the zinc ions is readily exchangeable with other divalent cations such as manganese, which strongly stimulates the enzymatic activity of the protein. The plasticity of this metal-binding site suggests a mechanism for regulation of DNPEP activity. We also demonstrate that DNPEP assembles into a functionally relevant tetrahedral complex that restricts access of peptide substrates to the active site. These structural data allow rationalization of the enzyme's preference for short peptide substrates with N-terminal acidic residues. This study provides a structural basis for understanding the physiology and bioinorganic chemistry of DNPEP and other M18 family aminopeptidases.

  16. Sub-cellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas

    PubMed Central

    Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D; Kropat, Janette; Dodani, Sheel C; Chan, Jefferson; Barupala, Dulmini; Domaille, Dylan W; Shirasaki, Dyna I; Loo, Joseph A; Weber, Peter K; Pett-Ridge, Jennifer; Stemmler, Timothy L; Chang, Christopher J; Merchant, Sabeeha S

    2014-01-01

    We identified a Cu accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulated Cu, dependent on the nutritional Cu sensor CRR1, but was functionally Cu-deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. NanoSIMS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy (XAS) was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu+ became bio-available for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mis-metallation during Zn deficiency and enabling efficient cuproprotein (re)-metallation upon Zn resupply. PMID:25344811

  17. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    NASA Astrophysics Data System (ADS)

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-01

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5‧-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  18. Crystal Structures of Pseudomonas aeruginosa GIM-1: Active-Site Plasticity in Metallo-β-Lactamases

    PubMed Central

    Borra, Pardha Saradhi; Samuelsen, Ørjan; Spencer, James; Walsh, Timothy R.; Lorentzen, Marit Sjo

    2013-01-01

    Metallo-β-lactamases (MBLs) have rapidly disseminated worldwide among clinically important Gram-negative bacteria and have challenged the therapeutic use of β-lactam antibiotics, particularly carbapenems. The blaGIM-1 gene, encoding one such enzyme, was first discovered in a Pseudomonas aeruginosa isolate from 2002 and has more recently been reported in Enterobacteriaceae. Here, we present crystal structures of GIM-1 in the apo-zinc (metal-free), mono-zinc (where Cys221 was found to be oxidized), and di-zinc forms, providing nine independently refined views of the enzyme. GIM-1 is distinguished from related MBLs in possessing a narrower active-site groove defined by aromatic side chains (Trp228 and Tyr233) at positions normally occupied by hydrophilic residues in other MBLs. Our structures reveal considerable flexibility in two loops (loop 1, residues 60 to 66; loop 2, residues 223 to 242) adjacent to the active site, with open and closed conformations defined by alternative hydrogen-bonding patterns involving Trp228. We suggest that this capacity for rearrangement permits GIM-1 to hydrolyze a wide range of β-lactams in spite of possessing a more constrained active site. Our results highlight the structural diversity within the MBL enzyme family. PMID:23208706

  19. VARIABLE ACTIVE SITE LOOP CONFORMATIONS ACCOMMODATE THE BINDING OF MACROCYCLIC LARGAZOLE ANALOGUES TO HDAC8

    PubMed Central

    Decroos, Christophe; Clausen, Dane J.; Haines, Brandon E.; Wiest, Olaf; Williams, Robert M.; Christianson, David W.

    2015-01-01

    The macrocyclic depsipeptide Largazole is a potent inhibitor of metal-dependent histone deacetylases (HDACs), some of which are drug targets for cancer chemotherapy. Indeed, Largazole partially resembles Romidepsin (FK228), a macrocyclic depsipeptide already approved for clinical use. Each inhibitor contains a pendant side chain thiol that coordinates to the active site Zn2+ ion, as observed in the X-ray crystal structure of the HDAC8–Largazole complex [Cole, K. E.; Dowling, D. P.; Boone, M. A.; Phillips, A. J.; Christianson, D. W. J. Am. Chem. Soc. 2011, 133, 12474]. Here, we report the X-ray crystal structures of HDAC8 complexed with three synthetic analogues of Largazole in which the depsipeptide ester is replaced with a rigid amide linkage. In two of these analogues, a 6-membered pyridine ring is also substituted (with two different orientations) for the 5-membered thiazole ring in the macrocycle skeleton. The side chain thiol group of each analogue coordinates to the active site Zn2+ ion with nearly ideal geometry, thereby preserving the hallmark structural feature of inhibition by Largazole. Surprisingly, in comparison with the binding of Largazole, these analogues trigger alternative conformational changes in the L1 and L2 loops flanking the active site. However, despite these structural differences, inhibitory potency is generally comparable to, or just moderately less than, the inhibitory potency of Largazole. Thus, this study reveals important new structure-affinity relationships for the binding of macrocyclic inhibitors to HDAC8. PMID:25793284

  20. Levels of asymmetry in Formica pratensis Retz. (Hymenoptera, Insecta) from a chronic metal-contaminated site

    SciTech Connect

    Rabitsch, W.B.

    1997-07-01

    Asymmetries of bilaterally symmetrical morphological traits in workers of the ant Formica pratensis Retzius were compared at sites with different levels of metal contamination and between mature and pre-mature colonies. Statistical analyses of the right-minus-left differences revealed that their distributions fit assumptions of fluctuating asymmetry (FA). No direct asymmetry or antisymmetry were present. Mean measurement error accounts for a third of the variation, but the maximum measurement error was 65%. Although significant differences of FA in ants were observed, the inconsistent results render uncovering a clear pattern difficult. Lead, cadmium, and zinc concentrations in the ants decreased with the distance from the contamination source, but no relation was found between FA and the heavy metal levels. Ants from the premature colonies were more asymmetrical than those from mature colonies but accumulated less metals. The use of asymmetry measures in ecotoxicology and biomonitoring is criticized, but should remain widely applicable if statistical assumptions are complemented by genetic and historical data.

  1. Hydrogen Storage and Selective, Reversible O2 Adsorption in a Metal-Organic Framework with Open Chromium(II) Sites.

    PubMed

    Bloch, Eric D; Queen, Wendy L; Hudson, Matthew R; Mason, Jarad A; Xiao, Dianne J; Murray, Leslie J; Flacau, Roxana; Brown, Craig M; Long, Jeffrey R

    2016-07-18

    A chromium(II)-based metal-organic framework Cr3 [(Cr4 Cl)3 (BTT)8 ]2 (Cr-BTT; BTT(3-) =1,3,5-benzenetristetrazolate), featuring coordinatively unsaturated, redox-active Cr(2+) cation sites, was synthesized and investigated for potential applications in H2 storage and O2 production. Low-pressure H2 adsorption and neutron powder diffraction experiments reveal moderately strong Cr-H2 interactions, in line with results from previously reported M-BTT frameworks. Notably, gas adsorption measurements also reveal excellent O2 /N2 selectivity with substantial O2 reversibility at room temperature, based on selective electron transfer to form Cr(III) superoxide moieties. Infrared spectroscopy and powder neutron diffraction experiments were used to confirm this mechanism of selective O2 binding. PMID:27249784

  2. Systematically biological prioritizing remediation sites based on datasets of biological investigations and heavy metals in soil

    NASA Astrophysics Data System (ADS)

    Lin, Wei-Chih; Lin, Yu-Pin; Anthony, Johnathen

    2015-04-01

    Heavy metal pollution has adverse effects on not only the focal invertebrate species of this study, such as reduction in pupa weight and increased larval mortality, but also on the higher trophic level organisms which feed on them, either directly or indirectly, through the process of biomagnification. Despite this, few studies regarding remediation prioritization take species distribution or biological conservation priorities into consideration. This study develops a novel approach for delineating sites which are both contaminated by any of 5 readily bioaccumulated heavy metal soil contaminants and are of high ecological importance for the highly mobile, low trophic level focal species. The conservation priority of each site was based on the projected distributions of 6 moth species simulated via the presence-only maximum entropy species distribution model followed by the subsequent application of a systematic conservation tool. In order to increase the number of available samples, we also integrated crowd-sourced data with professionally-collected data via a novel optimization procedure based on a simulated annealing algorithm. This integration procedure was important since while crowd-sourced data can drastically increase the number of data samples available to ecologists, still the quality or reliability of crowd-sourced data can be called into question, adding yet another source of uncertainty in projecting species distributions. The optimization method screens crowd-sourced data in terms of the environmental variables which correspond to professionally-collected data. The sample distribution data was derived from two different sources, including the EnjoyMoths project in Taiwan (crowd-sourced data) and the Global Biodiversity Information Facility (GBIF) ?eld data (professional data). The distributions of heavy metal concentrations were generated via 1000 iterations of a geostatistical co-simulation approach. The uncertainties in distributions of the heavy

  3. Ligational behavior of Schiff bases towards transition metal ion and metalation effect on their antibacterial activity.

    PubMed

    Devi, Jai; Batra, Nisha; Malhotra, Rajesh

    2012-11-01

    New Schiff bases pyrazine-2-carboxylicacid (phenyl-pyridin-2-yl-methylene)-hydrazide (Hpch-bp) HL(1) and pyrazine-2-carboxylicacid (pyridin-2-ylmethylene)-hydrazide (Hpch-pc) HL(2) derived from condensation of pyrazine carboxylic hydrazide (Hpch) with 2-benzoyl pyridine (bp) or pyridine 2-carbaldehyde (pc) and their transition metal complexes of type ML((1-2)2) have been synthesized, where M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). Characterization of ligands and their metal complexes was carried out by elemental analysis, conductimetric studies, magnetic susceptibility, spectroscopic techniques (IR, UV-VIS, NMR, ESR, Mass) and thermogravimetric analysis. The physico-chemical studies revealed octahedral geometry or distorted octahedral geometry around metal ion. These azomethine Schiff base ligands acted as tridentate coordinating through carbonyl, azomethine and pyridine nitrogen present in the ligand. The thermodynamic and thermal properties of the complexes have been investigated and it was observed on the basis of these studies that thermal stability of complexes follows the order Mnactivity at different concentrations against bacteria viz. Gram positive Bacillus subtilis, Micrococcus luteus and Gram negative Pseudomonas aeruginosa, Pseudomonas mendocina. A marked enhancement in biocidal activity of the ligands under similar experimental conditions was observed as a consequence of coordination with metal ions. The trend of growth inhibition in the complexes was found to be in the order: Cu>Mn>Ni>Co>Zn. PMID:22813991

  4. Pd-grafted open metal site copper-benzene-1,4-dicarboxylate metal organic frameworks (Cu-BDC MOF's) as promising interfacial catalysts for sustainable Suzuki coupling.

    PubMed

    Rostamnia, Sadegh; Alamgholiloo, Hassan; Liu, Xiao

    2016-05-01

    In this work, open metal site metal-organic framework of Cu-BDC was selected as a support for the multi-step grafting of palladium. The palladium ions was coordinated onto the Schiff base-decorated Cu-BDC pore cage, that this bifunctional Pd@Cu-BDC/Py-SI catalyst was successfully applied for Suzuki cross-coupling reaction. Recyclability test for the Pd@Cu-BDC/Py-SI catalyst showed a successful reusability for 7 runs. PMID:26897567

  5. Harnessing Lewis acidic open metal sites of metal-organic frameworks: the foremost route to achieve highly selective benzene sorption over cyclohexane.

    PubMed

    Mukherjee, Soumya; Manna, Biplab; Desai, Aamod V; Yin, Yuefeng; Krishna, Rajamani; Babarao, Ravichandar; Ghosh, Sujit K

    2016-07-01

    π-Complexation triggered Lewis acid-base interactions between open metal sites (OMS) of metal-organic frameworks (MOFs), and π-e(-) rich adsorptive benzene (Bz) is exploited to establish M-MOF-74 as the best Bz-selective MOF sorbent, marking the first report of utilizing OMS behind benzene/cyclohexane separation; a key advance from the energy-economy standpoint of industrial separation. PMID:27188914

  6. Scoping evaluation of the technical capabilities of DOE sites for disposal of hazardous metals in mixed low-level waste

    SciTech Connect

    Gruebel, M.M.; Waters, R.D.; Langkopf, B.S.

    1997-05-01

    A team of analysts designed and conducted a scoping evaluation to estimate the technical capabilities of fifteen Department of Energy sites for disposal of the hazardous metals in mixed low-level waste (i.e., waste that contains both low-level radioactive materials and hazardous constituents). Eight hazardous metals were evaluated: arsenic, barium, cadmium, chromium, lead, mercury, selenium, and silver. The analysis considered transport only through the groundwater pathway. The results are reported as site-specific estimates of maximum concentrations of each hazardous metal in treated mixed low-level waste that do not exceed the performance measures established for the analysis. Also reported are site-specific estimates of travel times of each hazardous metal to the point of compliance.

  7. Regulated incorporation of two different metal ions into programmed sites in a duplex by DNA polymerase catalyzed primer extension.

    PubMed

    Funai, Tatsuya; Nakamura, Junko; Miyazaki, Yuki; Kiriu, Risa; Nakagawa, Osamu; Wada, Shun-ichi; Ono, Akira; Urata, Hidehito

    2014-06-23

    Metal-mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag(I) ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C-Ag(I)-T base pair, as well as the previously reported C-Ag(I)-A base pair. The comparative susceptibility of dNTPs to Ag(I)-mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP≫dCTP. Furthermore, two kinds of metal ions, Ag(I) and Hg(II), selectively mediate the incorporation of thymidine 5'-triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved. PMID:24719384

  8. Bioaccumulation and translocation of heavy metals by nine native plant species grown at a sewage sludge dump site.

    PubMed

    Eid, Ebrahem M; Shaltout, Kamal H

    2016-11-01

    In the present study, nine native plant species were collected to determine their potential to clean up nine heavy metals from soil of a sewage sludge dump site. Almost all nine plant species grown at sewage sludge dump site showed multifold higher concentrations of heavy metals as compared to plants grown at the reference site. All the investigated species were characterized by a bioaccumulation factor (BF) > 1.0 for some heavy metals. BF was generally higher for Cd, followed by Pb, Co, Cr, Cu, Ni, Mn, Zn, and Fe. The translocation factor (TF) varied among plant species, and among heavy metals. For most studied heavy metals, TFs were <1.0. The present study proved that the concentrations of all heavy metals (except Cd, Co, and Pb) in most studied species were positively correlated with those in soil. Such correlations indicate that these species reflect the cumulative effects of environmental pollution from soil, and thereby suggesting their potential use in the biomonitoring of most heavy metals examined. In conclusion, all tissues of nine plant species could act as bioindicators, biomonitors, and remediates of most examined heavy metals. Moreover, Bassia indica, Solanum nigrum, and Pluchea dioscoridis are considered hyperaccumulators of Fe; Amaranthus viridis and Bassia indica are considered hyperaccumulators of Pb; and Portulaca oleracea is considered hyperaccumulator of Mn. PMID:27184987

  9. Identification of covalent active site inhibitors of dengue virus protease

    PubMed Central

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  10. Spatial variability of metal bioaccumulation in estuarine killifish (Fundulus heteroclitus) at the Callahan Mine Superfund site, Brooksville, ME

    PubMed Central

    Buckman, Kate L.; Bugge, Deenie M.; Chen, Celia Y.

    2013-01-01

    The former Callahan Mine Site in Brooksville, ME is an open-pit, hardrock mine site in an intertidal system, providing a unique opportunity to evaluate how metal-enriched sediments and overlying water impact estuarine food webs. Cu, Zn, Cd, and Pb concentrations in sediment, whole water, and Atlantic killifish (Fundulus heteroclitus) were evaluated at sites in Goose Pond (the Callahan Mine Site) and at reference sites. The metal concentrations of sediment, water, and fish were spatially distinct and significantly higher at the Mine Site than in the reference estuary. Sediment concentrations were particularly elevated and were above probable effects levels (PEL) for all four metals adjacent to the tailings pile. Even in this well-mixed system, water metal concentrations were significantly elevated adjacent to the tailings pile and the concentrations of Cu and Zn were above ambient water quality criteria (AWQC) for chronic marine exposure. Neither organic matter in the sediment nor salinity or pH of the water explained the metal concentrations. Adjacent to the tailings pile, killifish body burdens were elevated and were significantly related to both sediment and aqueous concentrations. In conclusion, (1) the contaminated sediment and seepage from the tailings impoundment and waste rock pile 3 create a continual flux of metals into the water column, (2) the metals are bioavailable and are bioconcentrating as evident in the killifish tissue concentrations, and (3) Callahan Mine is directly affecting metal bioaccumulation in fauna residing in the Goose Pond estuary and, potentially, in Penobscot Bay via the ‘trophic nekton relay.’ PMID:24022459

  11. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer.

    PubMed

    Dinpajooh, Mohammadhasan; Martin, Daniel R; Matyushov, Dmitry V

    2016-01-01

    Enzymes in biology's energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  12. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  13. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  14. Active Interrogation Observables for Enrichment Determination of DU Shielded HEU Metal Assemblies with Limited Geometrical Information

    SciTech Connect

    Pena, Kirsten E; McConchie, Seth M; Crye, Jason Michael; Mihalczo, John T

    2011-01-01

    Determining the enrichment of highly enriched uranium (HEU) metal assemblies shielded by depleted uranium (DU) proves a unique challenge to currently employed measurement techniques. Efforts to match time-correlated neutron distributions obtained through active interrogation to Monte Carlo simulations of the assemblies have shown promising results, given that the exact geometries of both the HEU metal assemblies and DU shields are known from imaging and fission site mapping. In certain situations, however, it is desirable to obtain enrichment with limited or no geometrical information of the assemblies being measured. This paper explores the possibility that the utilization of observables in the interrogation of assemblies by time-tagged D-T neutrons, including time-correlated distribution of neutrons and gammas using liquid scintillators operating on the fission chain time scale, can lead to enrichment determination without a complete set of geometrical information.

  15. Vertical Extent of 100 Area Vadose Zone Contamination of Metals at the Hanford Site

    NASA Astrophysics Data System (ADS)

    Khaleel, R.; Mehta, S.

    2012-12-01

    The 100 Area is part of the U.S. Department of Energy Hanford Site in southeastern Washington and borders the Columbia River. The primary sources of contamination in the area are associated with the operation of nine former production reactors, the last one shutting down in 1988. The area is undergoing a CERCLA remedial investigation (RI) that will provide data to support final cleanup decisions. During reactor operations, cooling water contaminated with radioactive and hazardous chemicals was discharged to both the adjacent Columbia River and infiltration cribs and trenches. Contaminated solid wastes were disposed of in burial grounds; the estimated Lead-Cadmium used as "reactor poison" and disposed of in 100 Area burial grounds is 1103 metric tons, of which up to 1059 metric tons are Lead and 44 metric tons are Cadmium. We summarize vadose zone site characterization data for the recently drilled boreholes, including the vertical distribution of concentration profiles for metals (i.e., Lead, Arsenic and Mercury) under the near neutral pH and oxygenated conditions. The deep borehole measurements targeted in the RI work plan were identified with a bias towards locating contaminants throughout the vadose zone and targeted areas at or near the waste sites; i.e., the drilling as well as the sampling was biased towards capturing contamination within the "hot spots." Unlike non-reactive contaminants such as tritium, Arsenic, Mercury and Lead are known to have a higher distribution coefficient (Kd), expected to be relatively immobile, and have a long residence time within the vadose zone. However, a number of sediment samples located close to the water table exceed the background concentrations for Lead and Arsenic. Three conceptual models are postulated to explain the deeper than expected penetration for the metals.

  16. The Structural Basis for the Metal Selective Activation of the Manganese Transport Regulator of Bacillus subtilis†,§

    PubMed Central

    Kliegman, Joseph I.; Griner, Sarah L.; Helmann, John D.; Brennan, Richard G.; Glasfeld, Arthur

    2008-01-01

    The manganese transport regulator (MntR) of Bacillus subtilis is activated by Mn2+ to repress transcription of genes encoding transporters involved in the uptake of manganese. MntR is also strongly activated by cadmium, both in vivo and in vitro, but it is poorly activated by other metal cations, including calcium and zinc. The previously published MntR•Mn2+ structure revealed a binuclear complex of manganese ions with a metal-metal separation of 3.3 Å (herein designated the AB conformer). Analysis of four additional crystal forms of MntR•Mn2+ reveals that the AB conformer is only observed in monoclinic crystals at 100 K, suggesting that this conformation may be stabilized by crystal packing forces. In contrast, monoclinic crystals analyzed at room temperature (at either pH 6.5 or 8.5), and a second hexagonal crystal form (analyzed at 100 K), all reveal the shift of one manganese ion by 2.5 Å thereby leading to a newly identified conformation (the AC conformer) with an internuclear distance of 4.4 Å. Significantly, the cadmium and calcium complexes of MntR also contain binuclear complexes with a 4.4 Å internuclear separation. In contrast, the zinc complex of MntR contains only one metal ion per subunit, in the A site. Isothermal titration calorimetry confirms the stoichiometry of Mn2+, Cd2+ and Zn2+ binding to MntR. We propose that the specificity of MntR activation is tied to productive binding of metal ions at two sites; the A site appears to act as a selectivity filter, determining whether the B or C site will be occupied and thereby fully activate MntR. PMID:16533030

  17. [Study on pollution evaluation of heavy metal in surface soil of the original site of Qingdao North Station].

    PubMed

    Zhu, Lei; Jia, Yong-gang; Pan, Yu-ying

    2013-09-01

    The determination of pollution extent and health risk assessment are the premise of heavy metal contaminated site remediation. The content of Cu, Cr, Pb, Cd, Zn, Ni in Qingdao North Station was detected, and the correlation of the 6 kinds of heavy metal content was analyzed. The pollution extent in excess of background values was characterized by anthropogenic influence multiple, and the pollution of heavy metal in soil was evaluated using geoaccumulation index and a new method which connects geoaccumulation index with Nemero index. Finally, human health risk assessment was carried out with health risk assessment model for heavy metal content. The results showed that Qingdao North Station soil were polluted by heavy metals. Six heavy metal pollution levels were: Cd > Cu > Ni > Pb > Cr > Zn, and Cd had reached the severity pollution level, Cu and Ni followed by, Cr, Pb and Zn were in minor pollution level. The order of coefficient variation in all heavy metals was: Cd > Ni > Cr > Zn > Pb > Cu. Within the study area soil heavy metal distribution was different, but overall discrepancy was small. The order of non-cancer hazards of heavy metals in soil was Cr > Pb > Cu > Ni > Cd > Zn, and the order of carcinogen risks of heavy metals was Ni > Cd. The non-cancer hazard and carcinogen risks values of metals were both lower than that their threshold values. They were not the direct threats to human health. PMID:24289020

  18. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  19. Biofilms Versus Activated Sludge: Considerations in Metal and Metal Oxide Nanoparticle Removal from Wastewater.

    PubMed

    Walden, Connie; Zhang, Wen

    2016-08-16

    The increasing application of metal and metal oxide nanoparticles [Me(O)NPs] in consumer products has led to a growth in concentration of these nanoparticles in wastewater as emerging contaminants. This may pose a threat to ecological communities (e.g., biological nutrient removal units) within treatment plants and those subject to wastewater effluents. Here, the toxicity, fate, and process implications of Me(O)NPs within wastewater treatment, specifically during activated sludge processing and biofilm systems are reviewed and compared. Research showed activated sludge achieves high removal rate of Me(O)NPs by the formation of aggregates through adsorption. However, recent literature reveals evidence that inhibition is likely for nutrient removal capabilities such as nitrification. Biofilm systems were much less studied, but show potential to resist Me(O)NP inhibition and achieve removal through possible retention by sorption. Implicating factors during bacteria-Me(O)NP interactions such as aggregation, surface functionalization, and the presence of organics are summarized. At current modeled levels, neither activated sludge nor biofilm systems can achieve complete removal of Me(O)NPs, thus allowing for long-term environmental exposure of diverse biological communities to Me(O)NPs in streams receiving wastewater effluents. Future research directions are identified throughout in order to minimize the impact of these nanoparticles released. PMID:27437755

  20. Differential Active Site Loop Conformations Mediate Promiscuous Activities in the Lactonase SsoPox

    PubMed Central

    Elias, Mikael; Chabriere, Eric

    2013-01-01

    Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263) that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability. PMID:24086491

  1. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  2. Evidence for segmental mobility in the active site of pepsin

    SciTech Connect

    Pohl, J.; Strop, P.; Senn, H.; Foundling, S.; Kostka, V.

    1986-05-01

    The low hydrolytic activity (k/sub cat/ < 0.001 s/sup -1/) of chicken pepsin (CP) towards tri- and tetrapeptides is enhanced at least 100 times by modification of its single sulfhydryl group of Cys-115, with little effect on K/sub m/-values. Modification thus simulates the effect of secondary substrate binding on pepsin catalysis. The rate of Cys-115 modification is substantially decreased in the presence of some competitive inhibitors, suggesting its active site location. Experiments with CP alkylated at Cys-115 with Acrylodan as a fluorescent probe or with N-iodoacetyl-(4-fluoro)-aniline as a /sup 19/F-nmr probe suggest conformation change around Cys-115 to occur on substrate or substrate analog binding. The difference /sup 1/H-nmr spectra (500 MHz) of unmodified free and inhibitor-complexed CP reveal chemical shifts almost exclusively in the aromatic region. The effects of Cu/sup + +/ on /sup 19/F- and /sup 1/H-nmr spectra have been studied. Examination of a computer graphics model of CP based on E. parasitica pepsin-inhibitor complex X-ray coordinates suggests that Cys-115 is located near the S/sub 3//S/sub 5/ binding site. The results are interpreted in favor of segmental mobility of this region important for pepsin substrate binding and catalysis.

  3. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  4. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

  5. Development of structure-activity relationship for metal oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Zhang, Hai Yuan; Ji, Zhao Xia; Rallo, Robert; Xia, Tian; Chang, Chong Hyun; Nel, Andre; Cohen, Yoram

    2013-05-01

    Nanomaterial structure-activity relationships (nano-SARs) for metal oxide nanoparticles (NPs) toxicity were investigated using metrics based on dose-response analysis and consensus self-organizing map clustering. The NP cellular toxicity dataset included toxicity profiles consisting of seven different assays for human bronchial epithelial (BEAS-2B) and murine myeloid (RAW 264.7) cells, over a concentration range of 0.39-100 mg L-1 and exposure time up to 24 h, for twenty-four different metal oxide NPs. Various nano-SAR building models were evaluated, based on an initial pool of thirty NP descriptors. The conduction band energy and ionic index (often correlated with the hydration enthalpy) were identified as suitable NP descriptors that are consistent with suggested toxicity mechanisms for metal oxide NPs and metal ions. The best performing nano-SAR with the above two descriptors, built with support vector machine (SVM) model and of validated robustness, had a balanced classification accuracy of ~94%. An applicability domain for the present data was established with a reasonable confidence level of 80%. Given the potential role of nano-SARs in decision making, regarding the environmental impact of NPs, the class probabilities provided by the SVM nano-SAR enabled the construction of decision boundaries with respect to toxicity classification under different acceptance levels of false negative relative to false positive predictions.Nanomaterial structure-activity relationships (nano-SARs) for metal oxide nanoparticles (NPs) toxicity were investigated using metrics based on dose-response analysis and consensus self-organizing map clustering. The NP cellular toxicity dataset included toxicity profiles consisting of seven different assays for human bronchial epithelial (BEAS-2B) and murine myeloid (RAW 264.7) cells, over a concentration range of 0.39-100 mg L-1 and exposure time up to 24 h, for twenty-four different metal oxide NPs. Various nano-SAR building models were

  6. Identification of catalytic sites for oxygen reduction and oxygen evolution in N-doped graphene materials: Development of highly efficient metal-free bifunctional electrocatalyst

    PubMed Central

    Yang, Hong Bin; Miao, Jianwei; Hung, Sung-Fu; Chen, Jiazang; Tao, Hua Bing; Wang, Xizu; Zhang, Liping; Chen, Rong; Gao, Jiajian; Chen, Hao Ming; Dai, Liming; Liu, Bin

    2016-01-01

    Oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are critical to renewable energy conversion and storage technologies. Heteroatom-doped carbon nanomaterials have been reported to be efficient metal-free electrocatalysts for ORR in fuel cells for energy conversion, as well as ORR and OER in metal-air batteries for energy storage. We reported that metal-free three-dimensional (3D) graphene nanoribbon networks (N-GRW) doped with nitrogen exhibited superb bifunctional electrocatalytic activities for both ORR and OER, with an excellent stability in alkaline electrolytes (for example, KOH). For the first time, it was experimentally demonstrated that the electron-donating quaternary N sites were responsible for ORR, whereas the electron-withdrawing pyridinic N moieties in N-GRW served as active sites for OER. The unique 3D nanoarchitecture provided a high density of the ORR and OER active sites and facilitated the electrolyte and electron transports. As a result, the as-prepared N-GRW holds great potential as a low-cost, highly efficient air cathode in rechargeable metal-air batteries. Rechargeable zinc-air batteries with the N-GRW air electrode in a two-electrode configuration exhibited an open-circuit voltage of 1.46 V, a specific capacity of 873 mAh g−1, and a peak power density of 65 mW cm−2, which could be continuously charged and discharged with an excellent cycling stability. Our work should open up new avenues for the development of various carbon-based metal-free bifunctional electrocatalysts of practical significance. PMID:27152333

  7. Identification of catalytic sites for oxygen reduction and oxygen evolution in N-doped graphene materials: Development of highly efficient metal-free bifunctional electrocatalyst.

    PubMed

    Yang, Hong Bin; Miao, Jianwei; Hung, Sung-Fu; Chen, Jiazang; Tao, Hua Bing; Wang, Xizu; Zhang, Liping; Chen, Rong; Gao, Jiajian; Chen, Hao Ming; Dai, Liming; Liu, Bin

    2016-04-01

    Oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are critical to renewable energy conversion and storage technologies. Heteroatom-doped carbon nanomaterials have been reported to be efficient metal-free electrocatalysts for ORR in fuel cells for energy conversion, as well as ORR and OER in metal-air batteries for energy storage. We reported that metal-free three-dimensional (3D) graphene nanoribbon networks (N-GRW) doped with nitrogen exhibited superb bifunctional electrocatalytic activities for both ORR and OER, with an excellent stability in alkaline electrolytes (for example, KOH). For the first time, it was experimentally demonstrated that the electron-donating quaternary N sites were responsible for ORR, whereas the electron-withdrawing pyridinic N moieties in N-GRW served as active sites for OER. The unique 3D nanoarchitecture provided a high density of the ORR and OER active sites and facilitated the electrolyte and electron transports. As a result, the as-prepared N-GRW holds great potential as a low-cost, highly efficient air cathode in rechargeable metal-air batteries. Rechargeable zinc-air batteries with the N-GRW air electrode in a two-electrode configuration exhibited an open-circuit voltage of 1.46 V, a specific capacity of 873 mAh g(-1), and a peak power density of 65 mW cm(-2), which could be continuously charged and discharged with an excellent cycling stability. Our work should open up new avenues for the development of various carbon-based metal-free bifunctional electrocatalysts of practical significance. PMID:27152333

  8. Factors influencing the heavy metal bioaccessibility in soils were site dependent from different geographical locations.

    PubMed

    Zhu, Xiaodong; Yang, Fen; Wei, Chaoyang

    2015-09-01

    A soil survey was conducted in urban areas from five sites, including Beijing, Baotou, Datong, Fuyang, and Xiantao in China. The objective was to explore the most significant factors that may impact the bioaccessibility of heavy metals (Bio-HMs), including As, Cr, Cu, Pb, and Zn, in soils. Twenty to 30 composite soil samples were collected at each site. The various soil properties, including pH, particle size, Fe/Mn, and organic matter contents, were analyzed. The chemical operated forms of HMs in soils were measured by the Bureau of Reference (BCR) sequential extraction scheme, while the Bio-HMs were determined by the simple bioaccessibility extraction test (SBET) procedure. The concentrations of total heavy metals (T-HMs) in soils from different sites (cities) were in the range as As (5.69-9.86), Cr (77.42-230.20), Cu (15.68-36.54), Pb (14.12-58.93), and Zn (38.66-183.46) mg/kg. Cu and Pb had higher relative bioaccessibilities (48-70%) than those of As and Cr (6-15%), indicating higher health risks of the former than the latter two HMs. The Bio-HMs for various HMs were comparable to the first two or three combined BCR extracted fractions, with an exception of Cu, whose Bio-HMs were larger than the combined three BCR fractions, indicating that Cu was highly accessible in soils as compared with other HMs. Factor analysis showed that all variables, including soil property parameters and BCR extracted fractions, could be represented by three common factors extracted with higher than 0.5 loadings and ∼80% cumulative contribution to the total variance. Among the three common factors, factor 1, containing mainly pH, texture, and Fe/Mn variables, and factor 3, containing mainly organic matter variable, could be attributed to geographical regions, while factor 2, containing mainly BCR extracted fractions, could be ascribed to relative bioaccessibility of HMs (R-Bio-HMs). Interactive mapping of the main factors and cluster analysis were consistent, which supported the

  9. Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.

    PubMed

    Debela, Mekdes; Magdolen, Viktor; Grimminger, Valerie; Sommerhoff, Christian; Messerschmidt, Albrecht; Huber, Robert; Friedrich, Rainer; Bode, Wolfram; Goettig, Peter

    2006-10-01

    Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition. PMID:16950394

  10. Modelling metal centres, acid sites and reaction mechanisms in microporous catalysts.

    PubMed

    O'Malley, Alexander J; Logsdail, A J; Sokol, A A; Catlow, C R A

    2016-07-01

    We discuss the role of QM/MM (embedded cluster) computational techniques in catalytic science, in particular their application to microporous catalysis. We describe the methodologies employed and illustrate their utility by briefly summarising work on metal centres in zeolites. We then report a detailed investigation into the behaviour of methanol at acidic sites in zeolites H-ZSM-5 and H-Y in the context of the methanol-to-hydrocarbons/olefins process. Studying key initial steps of the reaction (the adsorption and subsequent methoxylation), we probe the effect of framework topology and Brønsted acid site location on the energetics of these initial processes. We find that although methoxylation is endothermic with respect to the adsorbed system (by 17-56 kJ mol(-1) depending on the location), there are intriguing correlations between the adsorption/reaction energies and the geometries of the adsorbed species, of particular significance being the coordination of methyl hydrogens. These observations emphasise the importance of adsorbate coordination with the framework in zeolite catalysed conversions, and how this may vary with framework topology and site location, particularly suited to investigation by QM/MM techniques. PMID:27136967

  11. Transition metal activation and functionalization of carbon-hydrogen bonds

    SciTech Connect

    Jones, W.D.

    1992-06-01

    We are investigating the fundamental thermodynamic and kinetic factors that influence carbon-hydrogen bond activation at homogeneous transition metal centers and the conversion of hydrocarbons into functionalized products of potential use to the chemical industry. Advances have been made in both understanding the interactions of hydrocarbons with metals and in the functionalization of hydrocarbons. We have found that RhCl(PR{sub 3}){sub 2}(CNR) complexes can catalyze the insertion of isonitriles into the C-H bonds or arenes upon photolysis. The mechanism of these reactions was found to proceed by way of initial phosphine dissociation, followed by C-H activation and isonitrile insertion. We have also examined reactions of a series of arenes with (C{sub 5}Me{sub 5})Rh(PMe{sub 3})PhH and begun to map out the kinetic and thermodynamic preferences for arene coordination. The effects of resonance, specifically the differences in the Hueckel energies of the bound vs free ligand, are now believed to fully control the C-H activation/{eta}{sup 2}-coordination equilibria. We have begun to examine the reactions of rhodium isonitrile pyrazolylborates for alkane and arene C-H bond activation. A new, labile, carbodiimide precursor has been developed for these studies. We have completed studies of the reactions of (C{sub 5}Me{sub 5})Rh(PMe{sub 3})H{sub 2} with D{sub 2} and PMe{sub 3} that indicate that both {eta}{sup 5} {yields} {eta}{sup 3} ring slippage and metal to ring hydride migration occur more facilely than thermal reductive elimination of H{sub 2}. We have examined the reactions of heterocycles with (C{sub 5}Me{sub 5})Rh(PMe{sub 3})PhH and found that pyrrole and furan undergo C-H or N-H activation. Thiophene, however, undergoes C-S bond oxidative addition, and the mechanism of activation has been shown to proceed through sulfur coordination prior to C-S insertion.

  12. Microbiological-enhanced mixing across scales during in-situ bioreduction of metals and radionuclides at Department of Energy Sites

    SciTech Connect

    Valocchi, Albert; Werth, Charles; Liu, Wen-Tso; Sanford, Robert; Nakshatrala, Kalyan

    2015-10-20

    Bioreduction is being actively investigated as an effective strategy for subsurface remediation and long-term management of DOE sites contaminated by metals and radionuclides (i.e. U(VI)). These strategies require manipulation of the subsurface, usually through injection of chemicals (e.g., electron donor) which mix at varying scales with the contaminant to stimulate metal reducing bacteria. There is evidence from DOE field experiments suggesting that mixing limitations of substrates at all scales may affect biological growth and activity for U(VI) reduction. Although current conceptual models hold that biomass growth and reduction activity is limited by physical mixing processes, a growing body of literature suggests that reaction could be enhanced by cell-to-cell interaction occurring over length scales extending tens to thousands of microns. Our project investigated two potential mechanisms of enhanced electron transfer. The first is the formation of single- or multiple-species biofilms that transport electrons via direct electrical connection such as conductive pili (i.e. ‘nanowires’) through biofilms to where the electron acceptor is available. The second is through diffusion of electron carriers from syntrophic bacteria to dissimilatory metal reducing bacteria (DMRB). The specific objectives of this work are (i) to quantify the extent and rate that electrons are transported between microorganisms in physical mixing zones between an electron donor and electron acceptor (e.g. U(IV)), (ii) to quantify the extent that biomass growth and reaction are enhanced by interspecies electron transport, and (iii) to integrate mixing across scales (e.g., microscopic scale of electron transfer and macroscopic scale of diffusion) in an integrated numerical model to quantify these mechanisms on overall U(VI) reduction rates. We tested these hypotheses with five tasks that integrate microbiological experiments, unique micro-fluidics experiments, flow cell experiments, and

  13. Stabilization of dissolved trace metals at hydrothermal vent sites: Impact on their marine biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Sander, Sylvia G.; Powell, Zach D.; Koschinsky, Andrea; Kuzmanovski, Stefan; Kleint, Charlotte

    2014-05-01

    Hydrothermal vents have long been neglected as a significant source of several bioactive trace metals as it was assumed that elements such as Fe, Mn, and Cu etc., precipitate in extensor forming poly-metallic sulfide and oxy-hydroxy sediments in the relative vicinity of the emanation site. However, recently this paradigm has been reviewed since the stabilization of dissolved Fe and Cu from hydrothermal vents was observed [1, 2] and increased concentrations of trace metals can be traced from their hydrothermal source thousands of kilometres through the ocean basins [3]. Furthermore several independent modelling attempts have shown that not only a stabilization of dissolved hydrothermal Fe and Cu is possible [4] but also that hydrothermalism must be a significant source of Fe to be able to balance the Fe-biogeochemical cycle [5]. Here we present new data that gives further evidence of the presence of copper stabilising organic and inorganic compounds in samples characterized by hydrothermal input. We can show that there are systematic differences in copper-complexing ligands at different vent sites such as 5°S on the Mid Atlantic Ridge, Brother Volcano on the Kermadec Arc, and some shallow hydrothermal CO2 seeps in the Bay of Plenty, New Zealand and the Mediterranean Sea. Quantitative and qualitative voltammetric data convincingly indicates that inorganic sulphur and organic thiols form the majority of the strong copper-complexing ligand pool in many of these hydrothermal samples. On average, the high temperature vents had a significantly higher copper binding capacity than the diffuse vents due to higher inorganic sulphur species concentrations. References: [1] Sander, S. G., et al. 2007. Organic complexation of copper in deep-sea hydrothermal vent systems. Environmental Chemistry 4: 81-89 [2] Bennett, S. A., et al. 2008. The distribution and stabilisation of dissolved Fe in deep-sea hydrothermal plumes. Earth and Planetary Science Letters 270: 157-167. [3] Wu J

  14. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

    Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; Udell, Hannah S.; Yik, Eric J.; Bergeman, Lai F.; Fox, Brian G.

    2015-01-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100–10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  15. Active site and laminarin binding in glycoside hydrolase family 55.

    PubMed

    Bianchetti, Christopher M; Takasuka, Taichi E; Deutsch, Sam; Udell, Hannah S; Yik, Eric J; Bergeman, Lai F; Fox, Brian G

    2015-05-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  16. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  17. In Situ Detection of Active Edge Sites in Single-Layer MoS2 Catalysts.

    PubMed

    Bruix, Albert; Füchtbauer, Henrik Gøbel; Tuxen, Anders K; Walton, Alexander S; Andersen, Mie; Porsgaard, Søren; Besenbacher, Flemming; Hammer, Bjørk; Lauritsen, Jeppe V

    2015-09-22

    MoS2 nanoparticles are proven catalysts for processes such as hydrodesulfurization and hydrogen evolution, but unravelling their atomic-scale structure under catalytic working conditions has remained significantly challenging. Ambient pressure X-ray Photoelectron Spectroscopy (AP-XPS) allows us to follow in situ the formation of the catalytically relevant MoS2 edge sites in their active state. The XPS fingerprint is described by independent contributions to the Mo 3d core level spectrum whose relative intensity is sensitive to the thermodynamic conditions. Density Functional Theory (DFT) is used to model the triangular MoS2 particles on Au(111) and identify the particular sulphidation state of the edge sites. A consistent picture emerges in which the core level shifts for the edge Mo atoms evolve counterintuitively toward higher binding energies when the active edges are reduced. The shift is explained by a surprising alteration in the metallic character of the edge sites, which is a distinct spectroscopic signature of the MoS2 edges under working conditions. PMID:26203593

  18. Stepwise magnetic-geochemical approach for efficient assessment of heavy metal polluted sites

    NASA Astrophysics Data System (ADS)

    Appel, E.; Rösler, W.; Ojha, G.

    2012-04-01

    Previous studies have shown that magnetometry can outline the distribution of fly ash deposition in the surroundings of coal-burning power plants and steel industries. Especially the easy-to-measure magnetic susceptibility (MS) is capable to act as a proxy for heavy metal (HM) pollution caused by such kind of point source pollution. Here we present a demonstration project around the coal-burning power plant complex "Schwarze Pumpe" in eastern Germany. Before reunification of West and East Germany huge amounts of HM pollutants were emitted from the "Schwarze Pumpe" into the environment by both fly ash emission and dumped clinker. The project has been conducted as part of the TASK Centre of Competence which aims at bringing new innovative techniques closer to the market. Our project combines in situ and laboratory MS measurements and HM analyses in order to demonstrate the efficiency of a stepwise approach for site assessment of HM pollution around point sources of fly-ash emission and deposition into soil. The following scenario is played through: We assume that the "true" spatial distribution of HM pollution (given by the pollution load index PLI comprising Fe, Zn, Pb, and Cu) is represented by our entire set of 85 measured samples (XRF analyses) from forest sites around the "Schwarze Pumpe". Surface MS data (collected with a Bartington MS2D) and in situ vertical MS sections (logged by an SM400 instrument) are used to determine a qualitative overview of potentially higher and lower polluted areas. A suite of spatial HM distribution maps obtained by random selections of 30 out of the 85 analysed sites is compared to the HM map obtained from a targeted 30-sites-selection based on pre-information from the MS results. The PLI distribution map obtained from the targeted 30-sites-selection shows all essential details of the "true" pollution map, while the different random 30-sites-selections miss important features. This

  19. Metal and precursor effect during 1-heptyne selective hydrogenation using an activated carbon as support.

    PubMed

    Lederhos, Cecilia R; Badano, Juan M; Carrara, Nicolas; Coloma-Pascual, Fernando; Almansa, M Cristina; Liprandi, Domingo; Quiroga, Mónica

    2013-01-01

    Palladium, platinum, and ruthenium supported on activated carbon were used as catalysts for the selective hydrogenation of 1-heptyne, a terminal alkyne. All catalysts were characterized by temperature programmed reduction, X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy. TPR and XPS suggest that the metal in all catalysts is reduced after the pretreatment with H2 at 673 K. The TPR trace of the PdNRX catalyst shows that the support surface groups are greatly modified as a consequence of the use of HNO3 during the catalyst preparation. During the hydrogenation of 1-heptyne, both palladium catalysts were more active and selective than the platinum and ruthenium catalysts. The activity order of the catalysts is as follows: PdClRX>PdNRX>PtClRX≫RuClRX. This superior performance of PdClRX was attributed in part to the total occupancy of the d electronic levels of the Pd metal that is supposed to promote the rupture of the H2 bond during the hydrogenation reaction. The activity differences between PdClRX and PdNRX catalysts could be attributed to a better accessibility of the substrate to the active sites, as a consequence of steric and electronic effects of the superficial support groups. The order for the selectivity to 1-heptene is as follows: PdClRX=PdNRX>RuClRX>PtClRX, and it can be mainly attributed to thermodynamic effects. PMID:24348168

  20. Effective removal of field-emitting sites from metallic surfaces by dry ice cleaning

    SciTech Connect

    Dangwal, Arti; Mueller, Guenter; Reschke, Detlef; Floettmann, Klaus; Singer, Xenia

    2007-08-15

    Systematic results of the field emission properties of polycrystalline copper and niobium and single-crystal Nb are reported. Dry ice cleaning (DIC) is found to suppress enhanced field emission from metallic surfaces. The cleaning effect on the emitting sites was investigated by means of field emission scanning microscopy up to fields of 250 MV/m and high-resolution scanning electron microscopy with energy dispersive x-ray analysis. The number density of emitters at given fields was drastically reduced by dry ice cleaning. Current-voltage measurements and derived Fowler-Nordheim parameters are partially discussed with respect to the morphology and impurity content of localized emitters. No emission from grain boundaries on large-grain Nb samples was observed. The microscopy results prove the effective removal of field-emitting particulates down to 400 nm as well as the partial smoothing of surface protrusions by DIC.

  1. Role of electrostatics at the catalytic metal binding site in xylose isomerase action: Ca(2+)-inhibition and metal competence in the double mutant D254E/D256E.

    PubMed

    Fuxreiter, M; Böcskei, Z; Szeibert, A; Szabó, E; Dallmann, G; Naray-Szabo, G; Asboth, B

    1997-06-01

    The catalytic metal binding site of xylose isomerase from Arthrobacter B3728 was modified by protein engineering to diminish the inhibitory effect of Ca2+ and to study the competence of metals on catalysis. To exclude Ca2+ from Site 2 a double mutant D254E/D256E was designed with reduced space available for binding. In order to elucidate structural consequences of the mutation the binary complex of the mutant with Mg2+ as well as ternary complexes with bivalent metal ions and the open-chain inhibitor xylitol were crystallized for x-ray studies. We determined the crystal structures of the ternary complexes containing Mg2+, Mn2+, and Ca2+ at 2.2 to 2.5 A resolutions, and refined them to R factors of 16.3, 16.6, and 19.1, respectively. We found that all metals are liganded by both engineered glutamates as well as by atoms O1 and O2 of the inhibitor. The similarity of the coordination of Ca2+ to that of the cofactors as well as results with Be2+ weaken the assumption that geometry differences should account for the catalytic noncompetence of this ion. Kinetic results of the D254E/D256E mutant enzyme showed that the significant decrease in Ca2+ inhibition was accompanied by a similar reduction in the enzymatic activity. Qualitative argumentation, based on the protein electrostatic potential, indicates that the proximity of the negative side chains to the substrate significantly reduces the electrostatic stabilization of the transition state. Furthermore, due to the smaller size of the catalytic metal site, no water molecule, coordinating the metal, could be observed in ternary complexes of the double mutant. Consequently, the proton shuttle step in the overall mechanism should differ from that in the wild type. These effects can account for the observed decrease in catalytic efficiency of the D254E/D256E mutant enzyme. PMID:9188736

  2. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  3. Catalytic Activity of Supported Metal Particles for Sulfuric Acid Decomposition Reaction

    SciTech Connect

    Sergey N. Rashkeev; Daniel M. Ginosar; Lucia M. Petkovic; Helen H. Farrell

    2007-08-01

    Production of hydrogen by splitting water in thermochemical water-splitting cycles, such as the sulfur-based group that employs the catalytic decomposition of sulfuric acid into SO2 and O2 is of considerable interest. Most of these processes occur at high temperatures (T = 1,000 K) and exposes catalysts to the extreme conditions such as steam, oxygen, and acid vapor that severely damage these catalysts within a short time. To develop an understanding of the factors that cause catalyst deactivation, we performed density-functional-theory (DFT)-based first-principles calculations and computer simulations for transition metal (TM) particles positioned on the two types of substrate (?-alumina and TiO2-rutile). The catalytic activity of the considered systems is defined by several factors, namely: (i) The efficiency of detaching oxygen atoms from the sulfur-containing species SOn (n = 1,2,3). The breaking of the S-O bonds may occur at both the substrate and the transition metal cluster. However, the bond-breaking at the substrate is endothermic (and takes about 1.5 eV per bond) while at low-coordinated metal atom of a cluster it is exothermic (with energy gain of about 0.5 eV per bond). This explains why the presence of transition metal clusters is necessary for catalytic activity; (ii) The ability of the cluster to “clean” itself, i.e., to eliminate oxygen from its surface, in order to regain the catalytically active sites and to continue the process. We found that the clusters of Pd and Pt with the size = 2-3 nm are more efficient in this process (at T = 1,000 K) than the clusters of other TM’s considered (Rh, Ir, Ru, and Os); (iii) The ability of the cluster to keep its size to avoid sintering (that reduces the number of low-coordinated catalytically active sites at the surface of the cluster). We found that the sintering of Rh, Ir, Ru, and Os clusters is significantly suppressed in comparison with the sintering of Pd and Pt clusters of the same size (the

  4. Metal contamination at a wood preservation site: characterisation and experimental studies on remediation.

    PubMed

    Bhattacharya, Prosun; Mukherjee, Arun B; Jacks, Gunnar; Nordqvist, Sune

    2002-05-01

    The aim of this investigation was to determine the occurrence of As, Cu, Cr and Zn in the soil at an abandoned wood preservation unit and to examine some possible extractants for the contaminants in the soil. The mean As content of the contaminated surface soils (0-10 cm) was 186 mg kg(-1), where as the mean concentrations of Cu, Cr and Zn in soils from the contaminated area were 26, 29 and 91 mg kg(-1), respectively. The elevated As content in the mineral soils is related to adsorption of inorganic As phases in the fine grained fractions, which are characterised by large surface area and high positive surface charge under the current acidic conditions. Cu and Cr were found to be rather mobile, which is reflected in their lower abundance in soils and significant accumulation in sediments in the drainage leaving the area. The fine fraction of the soil (<0.125 mm) has an average metal content increased by nearly 34% as compared to the <2-mm fraction conventionally used for the analysis and assessment of soil contamination. The <2-mm fraction constitutes approximately 65% of the total weight while the fine fraction (<0.125 mm) constitutes approximately 10%. These facts, taken together, are essential for the choice of remediation measures. Oxalate solutions have been tested as extractants for soil remediation. Dark acid oxalate extraction dissolves the amorphous Al- and Fe-oxides and hydroxides and mobilises the adsorbed inorganic As species. Oxalate also acts as a ligand for the cationic heavy metals, releasing them from exchangeable sites. With a three-step sequential leaching, up to 98-99% of the metals could be removed. At lower concentrations and higher pH, the leaching decreased to approximately 70%. PMID:12083708

  5. Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism

    SciTech Connect

    Gallagher, D.T.; Robinson, H.; Kim, S.-K.; Reddy, P. T.

    2011-01-21

    Adenylyl cyclases (ACs) belonging to three nonhomologous classes (II, III, and IV) have been structurally characterized, enabling a comparison of the mechanisms of cyclic adenosine 3',5'-monophosphate biosynthesis. We report the crystal structures of three active-site complexes for Yersinia pestis class IV AC (AC-IV)-two with substrate analogs and one with product. Mn{sup 2+} binds to all three phosphates, and to Glu12 and Glu136. Electropositive residues Lys14, Arg63, Lys76, Lys111, and Arg113 also form hydrogen bonds to phosphates. The conformation of the analogs is suitable for in-line nucleophilic attack by the ribose O3' on {alpha}-phosphate (distance {approx} 4 {angstrom}). In the product complex, a second Mn ion is observed to be coordinated to both ribose 2' oxygen and ribose 3' oxygen. Observation of both metal sites, together with kinetic measurements, provides strong support for a two-cation mechanism. Eleven active-site mutants were also made and kinetically characterized. These findings and comparisons with class II and class III enzymes enable a detailed transphyletic analysis of the AC mechanism. Consistent with its lack of coordination to purine, Y. pestis AC-IV cyclizes both ATP and GTP. As in other classes of AC, the ribose is loosely bound, and as in class III, no base appears to ionize the O3' nucleophile. Different syn/anti conformations suggest that the mechanism involves a conformational transition, and further evidence suggests a role for ribosyl pseudorotation. With resolutions of 1.6-1.7 {angstrom}, these are the most detailed active-site ligand complexes for any class of this ubiquitous signaling enzyme.

  6. Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism

    SciTech Connect

    D Gallagher; S Kim; H Robinson; P Reddy

    2011-12-31

    Adenylyl cyclases (ACs) belonging to three nonhomologous classes (II, III, and IV) have been structurally characterized, enabling a comparison of the mechanisms of cyclic adenosine 3',5'-monophosphate biosynthesis. We report the crystal structures of three active-site complexes for Yersinia pestis class IV AC (AC-IV) - two with substrate analogs and one with product. Mn{sup 2+} binds to all three phosphates, and to Glu12 and Glu136. Electropositive residues Lys14, Arg63, Lys76, Lys111, and Arg113 also form hydrogen bonds to phosphates. The conformation of the analogs is suitable for in-line nucleophilic attack by the ribose O3' on {alpha}-phosphate (distance {approx} 4 {angstrom}). In the product complex, a second Mn ion is observed to be coordinated to both ribose 2' oxygen and ribose 3' oxygen. Observation of both metal sites, together with kinetic measurements, provides strong support for a two-cation mechanism. Eleven active-site mutants were also made and kinetically characterized. These findings and comparisons with class II and class III enzymes enable a detailed transphyletic analysis of the AC mechanism. Consistent with its lack of coordination to purine, Y. pestis AC-IV cyclizes both ATP and GTP. As in other classes of AC, the ribose is loosely bound, and as in class III, no base appears to ionize the O3' nucleophile. Different syn/anti conformations suggest that the mechanism involves a conformational transition, and further evidence suggests a role for ribosyl pseudorotation. With resolutions of 1.6-1.7 {angstrom}, these are the most detailed active-site ligand complexes for any class of this ubiquitous signaling enzyme.

  7. ECOLOGICAL EFFECTS OF METALS IN STREAMS ON A DEFENSE MATERIALS PROCESSING SITE IN SOUTH CAROLINA, USA

    SciTech Connect

    Paller, M.; Dyer, S.

    2009-09-01

    The Savannah River Site (SRS) is a 780 km{sup 2} U.S. Department of Energy facility near Aiken SC established in 1950 to produce nuclear materials. SRS streams are 'integrators' that potentially receive water transportable contaminants from all sources within their watersheds necessitating a GIS-based watershed approach to organize contaminant distribution data and accurately characterize the effects of multiple contaminant sources on aquatic organisms. Concentrations of metals in sediments, fish, and water were elevated in streams affected by SRS operations, but contaminant exposure models for Lontra Canadensis and Ceryle alcyon indicated that toxicological reference values were exceeded only by Hg and Al. Macroinvertebrate community structure was unrelated to sediment metal concentrations. This study indicated that (1) modeling studies and field bioassessments provide a complementary basis for addressing the individual and cumulative effects of contaminants, (2) habitat effects must be controlled when assessing contaminant impacts, (3) sensitivity analyses of contaminant exposure models are helpful in apportioning sampling effort, and (4) contaminants released during fifty years of industrial operations have not resulted in demonstrable harm to aquatic organisms in SRS streams.

  8. Effects of organic and inorganic amendments on heavy metal fractionation in soils from the "Cartagena-La Union" mining site (Spain)

    NASA Astrophysics Data System (ADS)

    Clemente, Rafael; de La Fuente, Carlos; Alburquerque, José Antonio; Martínez-Alcalá, Isabel; Pardo, Tania; Bernal, María. Pilar

    2010-05-01

    The intensive mining activity carried out in the "Cartagena-La Union" district has led to the contamination with heavy metals of the surrounding area. Our aim was to evaluate the heavy metal solubility in soils from this area, in order to optimize the use of different soil amendments for the improvement of soil conditions that would favour plant establishment. Soils collected from abandoned mine sites (n = 8) showed a high heterogeneity in both soil pH (2.5-7.7) and electrical conductivity (1.2-3.1 dS m-1) and they presented low organic matter contents (0.2-2.0%). These soils showed high pseudo-total concentrations of heavy metals, especially Zn and Pb (Zn: 966-10103, Pb: 1572-11426, Cd:

  9. Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with Its Metal Ion Effectors and DNA Binding Site

    PubMed Central

    Corbett, John; Cornacchione, Louis; Daly, William; Galan, Diego; Wysota, Michael; Tivnan, Patrick; Collins, Justin; Nye, Dillon; Levitz, Talya; Breyer, Wendy A.; Glasfeld, Arthur

    2015-01-01

    ABSTRACT Streptococcus mutans is the causative agent of dental caries, a significant concern for human health, and therefore an attractive target for therapeutics development. Previous work in our laboratory has identified a homodimeric, manganese-dependent repressor protein, SloR, as an important regulator of cariogenesis and has used site-directed mutagenesis to map functions to specific regions of the protein. Here we extend those studies to better understand the structural interaction between SloR and its operator and its effector metal ions. The results of DNase I assays indicate that SloR protects a 42-bp region of DNA that overlaps the sloABC promoter on the S. mutans UA159 chromosome, while electrophoretic mobility shift and solution binding assays indicate that each of two SloR dimers binds to this region. Real-time semiquantitative reverse transcriptase PCR (real-time semi-qRT-PCR) experiments were used to determine the individual base pairs that contribute to SloR-DNA binding specificity. Solution studies indicate that Mn2+ is better than Zn2+ at specifically activating SloR to bind DNA, and yet the 2.8-Å resolved crystal structure of SloR bound to Zn2+ provides insight into the means by which selective activation by Mn2+ may be achieved and into how SloR may form specific interactions with its operator. Taken together, these experimental observations are significant because they can inform rational drug design aimed at alleviating and/or preventing S. mutans-induced caries formation. IMPORTANCE This report focuses on investigating the SloR protein as a regulator of essential metal ion transport and virulence gene expression in the oral pathogen Streptococcus mutans and on revealing the details of SloR binding to its metal ion effectors and binding to DNA that together facilitate this expression. We used molecular and biochemical approaches to characterize the interaction of SloR with Mn2+ and with its SloR recognition element to gain a clearer picture

  10. Metavanadate at the active site of the phosphatase VHZ.

    PubMed

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  11. Metal bioavailability and bioaccumulation in the polychaete Nereis (Alitta) virens (Sars): The effects of site-specific sediment characteristics.

    PubMed

    Pini, J M; Richir, J; Watson, G J

    2015-06-30

    The present study investigates the relationships between copper (Cu) and zinc (Zn) concentrations in sediment, pore water and their bioaccumulation in the polychaete Nereis (Alitta) virens, as well as the importance of site-specific sediment characteristics in that process. Sediment, pore water and N. virens were sampled from seven sites with different pollution histories along the English Channel coast. Results showed that site-specific metal levels and sediment characteristics were important in determining the bioavailability of metals to worms. Significant correlations were found between Cu in the sediment and in the pore water and between Zn in the pore water and in N. virens. Zn from the pore water was thus more readily available from a dissolved source to N. virens than Cu. Data also showed that metal concentrations in N. virens were lower than those found in other closely related polychaetes, indicating that it may regulate tissue concentrations of Cu and Zn. PMID:25935802

  12. DEVELOPMENT OF LOCOMOTOR ACTIVITY OF RAT PUPS EXPOSED TO HEAVY METALS

    EPA Science Inventory

    Cadmium (Cd), triethyltin (TET), and trimethyltin (TMT) are heavy metals which are neurotoxic to developing animals. In the present experiment, preweaning assessment of locomotor activity was used to detect and differentiate between the developmental toxicity of these metals. On ...

  13. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    DOE PAGESBeta

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active sitemore » metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.« less

  14. Metal Nanoparticles Catalyzed Selective Carbon-Carbon Bond Activation in the Liquid Phase.

    PubMed

    Ye, Rong; Yuan, Bing; Zhao, Jie; Ralston, Walter T; Wu, Chung-Yeh; Unel Barin, Ebru; Toste, F Dean; Somorjai, Gabor A

    2016-07-13

    Understanding the C-C bond activation mechanism is essential for developing the selective production of hydrocarbons in the petroleum industry and for selective polymer decomposition. In this work, ring-opening reactions of cyclopropane derivatives under hydrogen catalyzed by metal nanoparticles (NPs) in the liquid phase were studied. 40-atom rhodium (Rh) NPs, encapsulated by dendrimer molecules and supported in mesoporous silica, catalyzed the ring opening of cyclopropylbenzene at room temperature under hydrogen in benzene, and the turnover frequency (TOF) was higher than other metals or the Rh homogeneous catalyst counterparts. Comparison of reactants with various substitution groups showed that electron donation on the three-membered ring boosted the TOF of ring opening. The linear products formed with 100% selectivity for ring opening of all reactants catalyzed by the Rh NP. Surface Rh(0) acted as the active site in the NP. The capping agent played an important role in the ring-opening reaction kinetics. Larger particle size tended to show higher TOF and smaller reaction activation energy for Rh NPs encapsulated in either dendrimer or poly(vinylpyrrolidone). The generation/size of dendrimer and surface group also affected the reaction rate and activation energy. PMID:27322570

  15. Phytochelatin synthase activity as a marker of metal pollution.

    PubMed

    Zitka, Ondrej; Krystofova, Olga; Sobrova, Pavlina; Adam, Vojtech; Zehnalek, Josef; Beklova, Miroslava; Kizek, Rene

    2011-08-30

    The synthesis of phytochelatins is catalyzed by γ-Glu-Cys dipeptidyl transpeptidase called phytochelatin synthase (PCS). Aim of this study was to suggest a new tool for determination of phytochelatin synthase activity in the tobacco BY-2 cells treated with different concentrations of the Cd(II). After the optimization steps, an experiment on BY-2 cells exposed to different concentrations of Cd(NO(3))(2) for 3 days was performed. At the end of the experiment, cells were harvested and homogenized. Reduced glutathione and cadmium (II) ions were added to the cell suspension supernatant. These mixtures were incubated at 35°C for 30min and analysed using high performance liquid chromatography coupled with electrochemical detector (HPLC-ED). The results revealed that PCS activity rises markedly with increasing concentration of cadmium (II) ions. The lowest concentration of the toxic metal ions caused almost three fold increase in PCS activity as compared to control samples. The activity of PCS (270fkat) in treated cells was more than seven times higher in comparison to control ones. K(m) for PCS was estimated as 2.3mM. PMID:21715087

  16. Bactericidal activity of metal-mediated peroxide-ascorbate systems.

    PubMed

    Drath, D B; Karnovsky, M L

    1974-11-01

    Model systems containing ascorbate, hydrogen peroxide, and divalent copper or cobalt have been shown to possess marked bactericidal activity. At equivalent concentrations, copper-containing systems were more bactericidal than the corresponding mixtures containing cobalt. Cobalt at concentrations below 10(-4) M did not appreciably augment microbicidal activity, whereas systems containing copper at concentrations as low as 5 x 10(-6) M were still capable of causing some bacterial death. Manganese was inactive. None of these systems was as potent as the well known myeloperoxidase-peroxide-halide system. The mechanisms of action of these systems are not as yet clear. The possibility that they function through the generation of superoxide (O(2) (-)), hydroxyl radical (OH.), or other free radicals was explored through the use of superoxide dismutase and several free radical scavengers. It seems likely at present that the two active metal-mediated systems function via separate mechanisms. The copper system acts with dehydroascorbate, whereas the cobalt system does not. Activity in the cobalt system appears to depend upon the generation of free radicals. PMID:16558093

  17. Heavy metal concentrations and enzymatic activities in the functional zone sediments of Haizhou Bay, Lianyungang, Jiangsu, China.

    PubMed

    Li, Yu; Liu, Fu-cheng

    2015-11-01

    Surface sediments were collected at 31 sites covering five functional zones of Haizhou Bay, Lianyungang, Jiangsu, China. Heavy metal concentrations and enzymatic activity of phosphatase and urease were determined on a dry-weight basis of sediments. Metal concentrations in sediments were comparable to the Chinese National Standard of Marine Sediment Quality and were as follows: Cu, 8.60-55.8 mg kg(-1); Zn, 107-384 mg kg(-1); Pb, 33.6-200 mg kg(-1); Cd, 0.24-2.57 mg kg(-1); Cr, 30.3-92.1 mg kg(-1); As, 12.9-110 mg kg(-1); Ni, 15.8-49.6 mg kg(-1); Mn, 379-1272 mg kg(-1); and Fe, 13,790-38,240 mg kg(-1). A geoaccumulation index (I geo) was calculated to help researchers understand the status of pollutants in the sediments. I geo showed that Cd and As contamination existed in the study area. The mobility of the metals and the relationship between heavy metal concentrations of chemical fractions and enzymatic activities were also investigated. Results showed that Cd and Mn had higher mobility than other metals, and enzymatic activities may play an important role in controlling the bioavailability and transformation trend of heavy metals from one fraction to another in sediments. PMID:26431704

  18. Identification of carbon-encapsulated iron nanoparticles as active species in non-precious metal oxygen reduction catalysts

    PubMed Central

    Varnell, Jason A.; Tse, Edmund C. M.; Schulz, Charles E.; Fister, Tim T.; Haasch, Richard T.; Timoshenko, Janis; Frenkel, Anatoly I.; Gewirth, Andrew A.

    2016-01-01

    The widespread use of fuel cells is currently limited by the lack of efficient and cost-effective catalysts for the oxygen reduction reaction. Iron-based non-precious metal catalysts exhibit promising activity and stability, as an alternative to state-of-the-art platinum catalysts. However, the identity of the active species in non-precious metal catalysts remains elusive, impeding the development of new catalysts. Here we demonstrate the reversible deactivation and reactivation of an iron-based non-precious metal oxygen reduction catalyst achieved using high-temperature gas-phase chlorine and hydrogen treatments. In addition, we observe a decrease in catalyst heterogeneity following treatment with chlorine and hydrogen, using Mössbauer and X-ray absorption spectroscopy. Our study reveals that protected sites adjacent to iron nanoparticles are responsible for the observed activity and stability of the catalyst. These findings may allow for the design and synthesis of enhanced non-precious metal oxygen reduction catalysts with a higher density of active sites. PMID:27538720

  19. Identification of carbon-encapsulated iron nanoparticles as active species in non-precious metal oxygen reduction catalysts.

    PubMed

    Varnell, Jason A; Tse, Edmund C M; Schulz, Charles E; Fister, Tim T; Haasch, Richard T; Timoshenko, Janis; Frenkel, Anatoly I; Gewirth, Andrew A

    2016-01-01

    The widespread use of fuel cells is currently limited by the lack of efficient and cost-effective catalysts for the oxygen reduction reaction. Iron-based non-precious metal catalysts exhibit promising activity and stability, as an alternative to state-of-the-art platinum catalysts. However, the identity of the active species in non-precious metal catalysts remains elusive, impeding the development of new catalysts. Here we demonstrate the reversible deactivation and reactivation of an iron-based non-precious metal oxygen reduction catalyst achieved using high-temperature gas-phase chlorine and hydrogen treatments. In addition, we observe a decrease in catalyst heterogeneity following treatment with chlorine and hydrogen, using Mössbauer and X-ray absorption spectroscopy. Our study reveals that protected sites adjacent to iron nanoparticles are responsible for the observed activity and stability of the catalyst. These findings may allow for the design and synthesis of enhanced non-precious metal oxygen reduction catalysts with a higher density of active sites. PMID:27538720

  20. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas

    DOE PAGESBeta

    Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D.; Kropat, Janette; Dodani, Sheel C.; Chan, Jefferson; Barupala, Dulmini; Domaille, Dylan W.; Shirasaki, Dyna I.; Loo, Joseph A.; et al

    2014-10-26

    Here we identified a Cu-accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulates Cu, a process dependent on the nutritional Cu sensor CRR1, but it is functionally Cu deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. Nano-secondary ion MS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labelingmore » demonstrated that sequestered Cu+ became bioavailable for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mismetallation during Zn deficiency and enabling efficient cuproprotein metallation or remetallation upon Zn resupply.« less

  1. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas

    SciTech Connect

    Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D.; Kropat, Janette; Dodani, Sheel C.; Chan, Jefferson; Barupala, Dulmini; Domaille, Dylan W.; Shirasaki, Dyna I.; Loo, Joseph A.; Weber, Peter K.; Pett-Ridge, Jennifer; Stemmler, Timothy L.; Chang, Christopher J.; Merchant, Sabeeha S.

    2014-10-26

    Here we identified a Cu-accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulates Cu, a process dependent on the nutritional Cu sensor CRR1, but it is functionally Cu deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. Nano-secondary ion MS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu+ became bioavailable for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mismetallation during Zn deficiency and enabling efficient cuproprotein metallation or remetallation upon Zn resupply.

  2. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas.

    PubMed

    Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D; Kropat, Janette; Dodani, Sheel C; Chan, Jefferson; Barupala, Dulmini; Domaille, Dylan W; Shirasaki, Dyna I; Loo, Joseph A; Weber, Peter K; Pett-Ridge, Jennifer; Stemmler, Timothy L; Chang, Christopher J; Merchant, Sabeeha S

    2014-12-01

    We identified a Cu-accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulates Cu, a process dependent on the nutritional Cu sensor CRR1, but it is functionally Cu deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. Nano-secondary ion MS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy was consistent with Cu(+) accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu(+) became bioavailable for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mismetallation during Zn deficiency and enabling efficient cuproprotein metallation or remetallation upon Zn resupply. PMID:25344811

  3. Released polysaccharides (RPS) from Cyanothece sp. CCY 0110 as biosorbent for heavy metals bioremediation: interactions between metals and RPS binding sites.

    PubMed

    Mota, Rita; Rossi, Federico; Andrenelli, Luisa; Pereira, Sara Bernardes; De Philippis, Roberto; Tamagnini, Paula

    2016-09-01

    Bioremediation of heavy metals using microorganisms can be advantageous compared to conventional physicochemical methods due to the use of renewable resources and efficiencies of removal particularly cations at low concentrations. In this context, cyanobacteria/cyanobacterial extracellular polymeric substances (EPS) emerge as a valid alternative due to the anionic nature and particular composition of these polymers. In this work, various culture fractions of the unicellular cyanobacterium Cyanothece sp. CCY 0110 were employed in bioremoval assays using three of the most common heavy metal pollutants in water bodies-copper, cadmium, and lead-separately or in combined systems. Our study showed that the released polysaccharides (RPS) were the most efficient fraction, removing the metal(s) by biosorption. Therefore, this polymer was subsequently used to evaluate the interactions between the metals/RPS binding sites using SEM-EDX, ICP-OES, and FTIR. Acid and basic pretreatments applied to the polymer further improve the process efficiency, and the exposure to an alkaline solution seems to alter the RPS conformation. The differences observed in the specific metal bioremoval seem to be mainly due to the RPS organic functional groups available, mainly carboxyl and hydroxyl, than to an ion exchange mechanism. Considering that Cyanothece is a highly efficient RPS-producer and that RPS can be easily separated from the culture, immobilized or confined, this polymer can be advantageous for the establishment/improvement of heavy metal removal systems. PMID:27188779

  4. Active Site Dependent Reaction Mechanism over Ru/CeO2 Catalyst toward CO2 Methanation.

    PubMed

    Wang, Fei; He, Shan; Chen, Hao; Wang, Bin; Zheng, Lirong; Wei, Min; Evans, David G; Duan, Xue

    2016-05-18

    Oxygen vacancy on the surface of metal oxides is one of the most important defects which acts as the reactive site in a variety of catalytic reactions. In this work, operando spectroscopy methodology was employed to study the CO2 methanation reaction catalyzed by Ru/CeO2 (with oxygen vacancy in CeO2) and Ru/α-Al2O3 (without oxygen vacancy), respectively, so as to give a thorough understanding on active site dependent reaction mechanism. In Ru/CeO2 catalyst, operando XANES, IR, and Raman were used to reveal the generation process of Ce(3+), surface hydroxyl, and oxygen vacancy as well as their structural evolvements under practical reaction conditions. The steady-state isotope transient kinetic analysis (SSITKA)-type in situ DRIFT infrared spectroscopy undoubtedly substantiates that CO2 methanation undergoes formate route over Ru/CeO2 catalyst, and the formate dissociation to methanol catalyzed by oxygen vacancy is the rate-determining step. In contrast, CO2 methanation undergoes CO route over Ru surface in Ru/α-Al2O3 with the absence of oxygen vacancy, demonstrating active site dependent catalytic mechanism toward CO2 methanation. In addition, the catalytic activity evaluation and the oscillating reaction over Ru/CeO2 catalyst further prove that the oxygen vacancy catalyzes the rate-determining step with a much lower activation temperature compared with Ru surface in Ru/α-Al2O3 (125 vs 250 °C). PMID:27135417

  5. Remedial actions at the former Vitro Rare Metals plant site, Canonsburg, Washington County, Pennsylvania. Final Environmental Impact Statement. Volume I

    SciTech Connect

    Not Available

    1983-07-01

    The environmental impacts associated with remedial actions in connection with residual radioactive materials remaining at the inactive uranium processing site located in Canonsburg, Washington County, Pennsylvania are evaluated. The Canonsburg site is an 18.5-acre property that was formerly owned by the Vitro Rare Metals Company. The expanded Canonsburg site would be 30-acre property that would include the Canonsburg site (the former Vitro Rare Metals plant), seven adjacent private houses, and the former Georges Pottery property. During the period 1942 through 1957 the Vitro Manufacturing Company and its successor, the Vitro Corporation of America, processed onsite residues and ores, and government-owned ores, concentrates, and scraps to extract uranium and other rare metals. The Canonsburg site is now the Canon Industrial Park. In addition to storing the residual radioactive materials of this process at the Canonsburg site, about 12,000 tons of radioactively contaminated materials were transferred to a railroad landfill in Burrell Township, Indiana County, Pennsylvania. This Canonsburg FEIS evaluates five alternatives for removing the potential public health hazard associated with the radioactively contaminated materials. In addition to no action, these alternatives involve various combinations of stabilization of the radioactively contaminated materials in place or decontamination of the Canonsburg and Burrell sites by removing the radioactively contaminated materials to another location. In addition to the two sites mentioned, a third site located in Hanover Township, Washington County, Pennsylvania has been considered as a disposal site to which the radioactively contaminated materials presently located at either of the other two sites might be moved.

  6. Characterization and metal sorptive properties of oxidized active carbon.

    PubMed

    Strelko, Vladimir; Malik, Danish J

    2002-06-01

    A commercial activated carbon Chemviron F 400 has been oxidized using nitric acid in order to introduce a variety of acidic surface functional groups. Both unoxidized and oxidized carbon samples were characterized using nitrogen porosimetry, elemental analysis, pH titration, Boehm's titration, and electrophoretic mobility measurements. Results show that oxidation treatment reduced surface area and pore volume. However, the carbon surface acquires an acidic character with carboxylic groups being the dominant surface functional groups. The modified sample displays cation-exchange properties over a wide range of pH values and exhibits polyfunctional nature. Both carbon samples were challenged for the removal of transition metals such as copper(II), nickel(II), cobalt(II), zinc(II), and manganese(II). The affinity series Mn2+Zn2+ has been found to coincide with the general stability sequence of metal complexes (the Irving-Williams series). The higher preference displayed by carbons toward copper(II) is a consequence of the fact that copper(II) often forms distorted and more stable octahedral complexes. PMID:16290653

  7. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  8. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  9. Surface sites on spinel-type and corundum-type metal oxide powders

    SciTech Connect

    Busca, G.; Lorenzelli, V.; Ramis, G. |; Willey, R.J.

    1993-06-01

    The surface sites on isostructural metal oxides containing Al{sup 3+}, Fe{sup 3+}, and Cr{sup 3+} have been investigated by IR spectroscopy. The IR spectra of surface hydroxy groups and of pyridine coordinated on Lewis acidic surface cationic sites on the defective spinel-type sesquioxides {gamma}-Al{sub 2}O{sub 3}, {theta}-Al{sub 2}O{sub 3}, and {gamma}-Fe{sub 2}O{sub 3}, on the spinels MgAl{sub 2}O{sub 4}, MgFe{sub 2}O{sub 4}, MgCr{sub 2}O{sub 4}, ZnAl{sub 2}O{sub 4}, ZnFe{sub 2}O{sub 4}, and ZnCr{sub 2}O{sub 4}, as well as on the corundum-type sesquioxides {alpha}-Al{sub 2}O{sub 3}, {alpha}-Fe{sub 2}O{sub 3}, and {alpha}-Cr{sub 2}O{sub 3}, have been compared. Some Co{sup 2+} and Ni{sup 2+} spinel-type compounds have also been considered. An extension of the criteria previously proposed for the identification of the surface sites on aluminum-based materials to ferrites and chromites is suggested. The OH stretchings of surface hydroxy groups are indicative of the nature and the coordination of the cations to which they are bonded. Pyridine species bonded to tetrahedrally- and octahedrally-coordinated trivalent cations are well distinguishable on aluminates, while the distiction is more difficult for ferrites. 41 refs., 9 figs., 3 tabs.

  10. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

    PubMed

    Sengupta, Raghuvir N; Van Schie, Sabine N S; Giambaşu, George; Dai, Qing; Yesselman, Joseph D; York, Darrin; Piccirilli, Joseph A; Herschlag, Daniel

    2016-01-01

    Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. PMID:26567314

  11. Influence of Traffic Activity on Heavy Metal Concentrations of Roadside Farmland Soil in Mountainous Areas

    PubMed Central

    Zhang, Fan; Yan, Xuedong; Zeng, Chen; Zhang, Man; Shrestha, Suraj; Devkota, Lochan Prasad; Yao, Tandong

    2012-01-01

    Emission of heavy metals from traffic activities is an important pollution source to roadside farmland ecosystems. However, little previous research has been conducted to investigate heavy metal concentrations of roadside farmland soil in mountainous areas. Owing to more complex roadside environments and more intense driving conditions on mountainous highways, heavy metal accumulation and distribution patterns in farmland soil due to traffic activity could be different from those on plain highways. In this study, design factors including altitude, roadside distance, terrain, and tree protection were considered to analyze their influences on Cu, Zn, Cd, and Pb concentrations in farmland soils along a mountain highway around Kathmandu, Nepal. On average, the concentrations of Cu, Zn, Cd, and Pb at the sampling sites are lower than the tolerable levels. Correspondingly, pollution index analysis does not show serious roadside pollution owing to traffic emissions either. However, some maximum Zn, Cd, and Pb concentrations are close to or higher than the tolerable level, indicating that although average accumulations of heavy metals pose no hazard in the region, some spots with peak concentrations may be severely polluted. The correlation analysis indicates that either Cu or Cd content is found to be significantly correlated with Zn and Pb content while there is no significant correlation between Cu and Cd. The pattern can be reasonably explained by the vehicular heavy metal emission mechanisms, which proves the heavy metals’ homology of the traffic pollution source. Furthermore, the independent factors show complex interaction effects on heavy metal concentrations in the mountainous roadside soil, which indicate quite a different distribution pattern from previous studies focusing on urban roadside environments. It is found that the Pb concentration in the downgrade roadside soil is significantly lower than that in the upgrade soil while the Zn concentration in the

  12. Anomalous scattering analysis of Agrobacterium radiobacter phosphotriesterase: the prominent role of iron in the heterobinuclear active site

    PubMed Central

    Jackson, Colin J.; Carr, Paul D.; Kim, Hye-Kyung; Liu, Jian-Wei; Herrald, Paul; Mitić, Nataša; Schenk, Gerhard; Smith, Clyde A.; Ollis, David L.

    2006-01-01

    Bacterial phosphotriesterases are binuclear metalloproteins for which the catalytic mechanism has been studied with a variety of techniques, principally using active sites reconstituted in vitro from apoenzymes. Here, atomic absorption spectroscopy and anomalous X-ray scattering have been used to determine the identity of the metals incorporated into the active site in vivo. We have recombinantly expressed the phosphotriesterase from Agrobacterium radiobacter (OpdA) in Escherichia coli grown in medium supplemented with 1 mM CoCl2 and in unsupplemented medium. Anomalous scattering data, collected from a single crystal at the Fe–K, Co–K and Zn–K edges, indicate that iron and cobalt are the primary constituents of the two metal-binding sites in the catalytic centre (α and β) in the protein expressed in E. coli grown in supplemented medium. Comparison with OpdA expressed in unsupplemented medium demonstrates that the cobalt present in the supplemented medium replaced zinc at the β-position of the active site, which results in an increase in the catalytic efficiency of the enzyme. These results suggest an essential role for iron in the catalytic mechanism of bacterial phosphotriesterases, and that these phosphotriesterases are natively heterobinuclear iron–zinc enzymes. PMID:16686603

  13. Transition Metals Catalyzed Element-Cyano Bonds Activations

    PubMed Central

    Wang, Rui; Falck, John R.

    2014-01-01

    Cyano group as a versatile functionalized intermediate has been explored for several decades, as it readily transfers to many useful functionalization groups such as amine, amide, acid, etc., which make it possess high popularization and use value in organic synthesis. Reactions involved with element-cyano bond cleavage can provide not only a new cyano group but also a freshly functionalized skeleton in one-pot, consequently making it of high importance. The highlights reviewed herein include H-CN, Si-CN, C-CN, B-CN, Sn-CN, Ge-CN, S-CN, Halo-CN, N-CN, and O-CN bonds cleavages and will summarize progress in such an important research area. This review article will focus on transition metal catalyzed reactions involving element-cyano bond activation. PMID:25558119

  14. Pomegranate-Inspired Design of Highly Active and Durable Bifunctional Electrocatalysts for Rechargeable Metal-Air Batteries.

    PubMed

    Li, Ge; Wang, Xiaolei; Fu, Jing; Li, Jingde; Park, Moon Gyu; Zhang, Yining; Lui, Gregory; Chen, Zhongwei

    2016-04-11

    Rational design of highly active and durable electrocatalysts for oxygen reactions is critical for rechargeable metal-air batteries. Herein, we report the design and development of composite electrocatalysts based on transition metal oxide nanocrystals embedded in a nitrogen-doped, partially graphitized carbon framework. Benefiting from the unique pomegranate-like architecture, the composite catalysts possess abundant active sites, strong synergetic coupling, enhanced electron transfer, and high efficiencies in the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). The Co3O4-based composite electrocatalyst exhibited a high half-wave potential of 0.842 V for ORR, and a low overpotential of only 450 mV at the current density of 10 mA cm(-2) for OER. A single-cell zinc-air battery was also fabricated with superior durability, holding great promise in the practical implementation of rechargeable metal-air batteries. PMID:26970076

  15. Phase-Transfer Activation of Transition Metal Catalysts.

    PubMed

    Tuba, Robert; Xi, Zhenxing; Bazzi, Hassan S; Gladysz, John A

    2015-11-01

    With metal-based catalysts, it is quite common that a ligand (L) must first dissociate from a catalyst precursor (L'n M-L) to activate the catalyst. The resulting coordinatively unsaturated active species (L'n M) can either back react with the ligand in a k-1 step, or combine with the substrate in a k2 step. When dissociation is not rate determining and k-1 [L] is greater than or comparable to k2 [substrate], this slows the rate of reaction. By introducing a phase label onto the ligand L and providing a suitable orthogonal liquid or solid phase, dramatic rate accelerations can be achieved. This phenomenon is termed "phase-transfer activation". In this Concept, some historical antecedents are reviewed, followed by successful applications involving fluorous/organic and aqueous/organic liquid/liquid biphasic catalysis, and liquid/solid biphasic catalysis. Variants that include a chemical trap for the phase-labeled ligands are also described. PMID:26338471

  16. The activity of calcium in calcium-metal-fluoride fluxes

    NASA Astrophysics Data System (ADS)

    Ochifuji, Yuichiro; Tsukihashi, Fumitaka; Sano, Nobuo

    1995-08-01

    The standard Gibbs energy of reaction Ca (1) + O (mass pct, in Zr) = CaO (s) has been determined as follows by equilibrating molten calcium with solid zirconium in a CaO crucible: Δ G° = -64,300(±700) + 19.8(±3.5) T J/mol (1373 to 1623 K) The activities of calcium in the CaOsatd-Ca- MF2 ( M: Ca, Ba, Mg) and CaOsatd-Ca-NaF systems were measured as a function of calcium composition at high calcium contents at 1473 K on the basis of the standard Gibbs energy. The activities of calcium increase in the order of CaF2, BaF2, and MgF2 at the same calcium fraction of these fluxes. The observed activities are compared with those estimated by using the Temkin model for ionic solutions. Furthermore, the possibility of the removal of tramp elements such as tin, arsenic, antimony, bismuth, and lead from carbon-saturated iron by using calcium-metal-fluoride fluxes is discussed.

  17. The activity of calcium in calcium-metal-fluoride fluxes

    SciTech Connect

    Ochifuji, Yuichiro; Tsukihashi, Fumitaka; Sano, Nobuo

    1995-08-01

    The standard Gibbs energy of reaction Ca (1) + {und O} (mass pct, in Zr) = CaO (s) has been determined as follows by equilibrating molten calcium with solid zirconium in a CaO crucible: {Delta}G{degree} = {minus}64,300({+-}700) + 19.8({+-}3.5)T J/mol (1,373 to 1,623 K). The activities of calcium in the CaO{sub satd.}-Ca-MF{sub 2} (M: Ca, Ba, Mg) and CaO{sub satd.}-Ca-NaF systems were measured as a function of calcium composition at high calcium contents at 1,473 K on the basis of the standard Gibbs energy. The activities of calcium increase in the order of CaF{sub 2}, BaF{sub 2}, and MgF{sub 2} at the same calcium fraction of these fluxes. The observed activities are compared with those estimated by using the Temkin model for ionic solutions. Furthermore, the possibility of the removal of tramp elements such as tin, arsenic, antimony, bismuth, and lead from carbon