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Sample records for active-site zinc ion

  1. 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

  2. Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily

    PubMed Central

    Baker, Patrick J.; Britton, K. Linda; Fisher, Martin; Esclapez, Julia; Pire, Carmen; Bonete, Maria Jose; Ferrer, Juan; Rice, David W.

    2009-01-01

    Despite being the subject of intensive investigations, many aspects of the mechanism of the zinc-dependent medium chain alcohol dehydrogenase (MDR) superfamily remain contentious. We have determined the high-resolution structures of a series of binary and ternary complexes of glucose dehydrogenase, an MDR enzyme from Haloferax mediterranei. In stark contrast to the textbook MDR mechanism in which the zinc ion is proposed to remain stationary and attached to a common set of protein ligands, analysis of these structures reveals that in each complex, there are dramatic differences in the nature of the zinc ligation. These changes arise as a direct consequence of linked movements of the zinc ion, a zinc-bound bound water molecule, and the substrate during progression through the reaction. These results provide evidence for the molecular basis of proton traffic during catalysis, a structural explanation for pentacoordinate zinc ion intermediates, a unifying view for the observed patterns of metal ligation in the MDR family, and highlight the importance of dynamic fluctuations at the metal center in changing the electrostatic potential in the active site, thereby influencing the proton traffic and hydride transfer events. PMID:19131516

  3. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase.

    PubMed

    Montagner, Caroline; Nigen, Michaël; Jacquin, Olivier; Willet, Nicolas; Dumoulin, Mireille; Karsisiotis, Andreas Ioannis; Roberts, Gordon C K; Damblon, Christian; Redfield, Christina; Matagne, André

    2016-07-29

    Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate-binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (ΔG(0)) of 32 ± 2 kJ·mol(-1) For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site, and the protein displays a well organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. Two-dimensional NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ΔG(0) value of 65 ± 1.4 kJ·mol(-1) These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well defined conformation for both active site loops to maintain enzymatic activity. PMID:27235401

  4. Accelerating degradation rate of pure iron by zinc ion implantation.

    PubMed

    Huang, Tao; Zheng, Yufeng; Han, Yong

    2016-12-01

    Pure iron has been considered as a promising candidate for biodegradable implant applications. However, a faster degradation rate of pure iron is needed to meet the clinical requirement. In this work, metal vapor vacuum arc technology was adopted to implant zinc ions into the surface of pure iron. Results showed that the implantation depth of zinc ions was about 60 nm. The degradation rate of pure iron was found to be accelerated after zinc ion implantation. The cytotoxicity tests revealed that the implanted zinc ions brought a slight increase on cytotoxicity of the tested cells. In terms of hemocompatibility, the hemolysis of zinc ion implanted pure iron was lower than 2%. However, zinc ions might induce more adhered and activated platelets on the surface of pure iron. Overall, zinc ion implantation can be a feasible way to accelerate the degradation rate of pure iron for biodegradable applications. PMID:27482462

  5. Accelerating degradation rate of pure iron by zinc ion implantation

    PubMed Central

    Huang, Tao; Zheng, Yufeng; Han, Yong

    2016-01-01

    Pure iron has been considered as a promising candidate for biodegradable implant applications. However, a faster degradation rate of pure iron is needed to meet the clinical requirement. In this work, metal vapor vacuum arc technology was adopted to implant zinc ions into the surface of pure iron. Results showed that the implantation depth of zinc ions was about 60 nm. The degradation rate of pure iron was found to be accelerated after zinc ion implantation. The cytotoxicity tests revealed that the implanted zinc ions brought a slight increase on cytotoxicity of the tested cells. In terms of hemocompatibility, the hemolysis of zinc ion implanted pure iron was lower than 2%. However, zinc ions might induce more adhered and activated platelets on the surface of pure iron. Overall, zinc ion implantation can be a feasible way to accelerate the degradation rate of pure iron for biodegradable applications. PMID:27482462

  6. Biosorption of zinc ion: a deep comprehension

    NASA Astrophysics Data System (ADS)

    Mishra, Vishal

    2014-12-01

    Massive industrialization and urbanization of civilization during the last few decades have made a thrust in heavy metal pollution in various water bodies. In past, various kinds of conventional metal ion remediation technologies, such as cementation, osmosis, reverse osmosis, ultrafiltration, etc., have been practised. However, most of these technologies are quite expensive, and lead to the generation of secondary chemical sludge. However, biosorption of heavy metal ions is significantly inexpensive and an eco-friendly technology. Among the series of heavy metals, zinc has gained the significant interest due to its toxicity and easy availability in water bodies. Biosorption of zinc in liquid phase by living, nonliving, conventional and non-conventional biosorbents has been practised extensively in the past. This literature review focuses on the recent trends practised in the field of biosorption of zinc from liquid phase. The present work provides deep insight into various aspects of biosorption of zinc by different mechanisms of biosorption, bioaccumulation, isotherm, kinetic and mechanistic modeling. An exhaustive comparison among different sorts of biomasses has also been given in the present work to enlist all the milestones of biosorption.

  7. 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

  8. Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

    PubMed

    Mir, Aamir; Golden, Barbara L

    2016-02-01

    The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid. PMID:26551631

  9. Zinc cysteine active sites of metalloproteins: A density functional theory and x-ray absorption fine structure study

    NASA Astrophysics Data System (ADS)

    Dimakis, Nicholas; Farooqi, Mohammed Junaid; Garza, Emily Sofia; Bunker, Grant

    2008-03-01

    Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)4-n(Cys)n sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.

  10. Abundance of zinc ions in synaptic terminals of mocha mutant mice: zinc transporter 3 immunohistochemistry and zinc sulphide autometallography.

    PubMed

    Stoltenberg, Meredin; Nejsum, Lene N; Larsen, Agnete; Danscher, Gorm

    2004-02-01

    The mocha mouse is an autosomal recessive pigment mutant on mouse chromosome 10 caused by a deletion in the gene for the delta subunit of the adaptor-like complex AP-3. Based on zinc transporter 3 (ZnT3) immunohistochemistry, zinc TSQ fluorescence and a modified Timm method, previous studies found a lack of histochemically-detectable zinc and a substantial reduction in the ZnT3 immunoreactivity. It has, therefore, been suggested that the mocha mouse could serve as a model for studies of the significance of zinc ions in zinc-enriched (ZEN) neurons. We have chosen the mocha-zinc-model in a study of the significance of ZEN neurons in hypoxia-caused damage in mouse brain. In order to establish that the model was either void of zinc ions or had a significantly decreased level of zinc ions in their ZEN terminals, we repeated the studies that had lead to the above assumption, the only methodology difference being that we used the zinc specific Neo-Timm method instead of the Timm method applied in the original study. We found that, although the ZnS autometallography (AMG) technique revealed a reduction in staining intensity as compared to the littermate controls, there were still plenty of zinc ions in the ZEN terminals, in particular visible in telencephalic structures like neocortex and hippocampus. At ultrastructural levels the zinc ions were found in a pool of vesicles of the ZEN terminals as in the control animals, but additionally zinc ions could be traced in ZEN neuronal somata in the neocortex and hippocampus. The mossy fibres in the hippocampus of mocha mice also bind with TSQ, though less than in the controls. We found ZnS AMG grains in ZEN neuronal somata, which were also immunoreactive for ZnT3. Our study confirmed the decreased ZnT3 immunoreactivity in ZEN terminals of the mocha mouse found in the original study. Based on these findings, we suggest that the mocha mouse may not be an ideal model for studies of the histochemically-detectable zinc ion pool of the

  11. 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

  12. Zinc ion availability--the determinant of efficacy in zinc lozenge treatment of common colds.

    PubMed

    Eby, G A

    1997-10-01

    This is a re-analysis of reports from 1984 to 1992 of double-blind, placebo-controlled, clinical trials of zinc lozenges in the treatment of common colds. This re-analysis was performed to test the hypothesis that major variations in daily zinc ion availability (ZIA) between chemically different lozenge formulations caused differing results in these clinical trials. Solution chemistry computations determined the bioavailability of Zn2+ ions at physiological pH from the lozenges used in these clinical trails. ZIA was derived from Fick's laws of diffusion in a bio-electric field. Lozenges that released Zn2+ ions at physiological pH (positive ZIAs) shortened colds. Lozenges that released negatively charged zinc species at physiological pH (negative ZIAs) lengthened colds. Lozenges having a zero ZIA had no effect on common colds. Lozenges with ZIA = 100 shortened colds by 7 days while ZIA = -55 lozenges lengthened colds by 4.4 days. A linear dose-response relationship exists between ZIAs of zinc lozenges and changes in duration of common colds. It is concluded that: prospective efficacy of zinc lozenges can be predicted based upon readily determined ZIA factors and ZIAs; chemically different zinc lozenge formulations having greatly different ZIAs resulted in greatly differing results in clinical trials; mast cell granule-derived Zn2+ ions are the foundation of the primary immune system; and high ZIA zinc acetate lozenges are beneficial for common colds. PMID:9372416

  13. Ion beam sputter deposited zinc telluride films

    NASA Technical Reports Server (NTRS)

    Gulino, D. A.

    1985-01-01

    Zinc telluride is of interest as a potential electronic device material, particularly as one component in an amorphous superlattice, which is a new class of interesting and potentially useful materials. Some structural and electronic properties of ZnTe films deposited by argon ion beam sputter depoairion are described. Films (up to 3000 angstroms thick) were deposited from a ZnTe target. A beam energy of 1000 eV and a current density of 4 mA/sq. cm. resulted in deposition rates of approximately 70 angstroms/min. The optical band gap was found to be approximately 1.1 eV, indicating an amorphous structure, as compared to a literature value of 2.26 eV for crystalline material. Intrinsic stress measurements showed a thickness dependence, varying from tensile for thicknesses below 850 angstroms to compressive for larger thicknesses. Room temperature conductivity measurement also showed a thickness dependence, with values ranging from 1.86 x to to the -6/ohm. cm. for 300 angstrom film to 2.56 x 10 to the -1/ohm. cm. for a 2600 angstrom film. Measurement of the temperature dependence of the conductivity for these films showed complicated behavior which was thickness dependent. Thinner films showed at least two distinct temperature dependent conductivity mechanisms, as described by a Mott-type model. Thicker films showed only one principal conductivity mechanism, similar to what might be expected for a material with more crystalline character.

  14. Ion beam sputter deposited zinc telluride films

    NASA Technical Reports Server (NTRS)

    Gulino, D. A.

    1986-01-01

    Zinc telluride is of interest as a potential electronic device material, particularly as one component in an amorphous superlattice, which is a new class of interesting and potentially useful materials. Some structural and electronic properties of ZnTe films deposited by argon ion beam sputter deposition are described. Films (up to 3000 angstroms thick) were deposited from a ZnTe target. A beam energy of 1000 eV and a current density of 4 mA/sq cm resulted in deposition rates of approximately 70 angstroms/min. The optical band gap was found to be approximately 1.1 eV, indicating an amorphous structure, as compared to a literature value of 2.26 eV for crystalline material. Intrinsic stress measurements showed a thickness dependence, varying from tensile for thicknesses below 850 angstroms to compressive for larger thicknesses. Room temperature conductivity measurement also showed a thickness dependence, with values ranging from 1.86 x 10 to the -6th/ohm cm for 300 angstrom film to 2.56 x 10 to the -1/ohm cm for a 2600 angstrom film. Measurement of the temperature dependence of the conductivity for these films showed complicated behavior which was thickness dependent. Thinner films showed at least two distinct temperature dependent conductivity mechanisms, as described by a Mott-type model. Thicker films showed only one principal conductivity mechanism, similar to what might be expected for a material with more crystalline character.

  15. Zinc as Allosteric Ion Channel Modulator: Ionotropic Receptors as Metalloproteins

    PubMed Central

    Peralta, Francisco Andrés; Huidobro-Toro, Juan Pablo

    2016-01-01

    Zinc is an essential metal to life. This transition metal is a structural component of many proteins and is actively involved in the catalytic activity of cell enzymes. In either case, these zinc-containing proteins are metalloproteins. However, the amino acid residues that serve as ligands for metal coordination are not necessarily the same in structural proteins compared to enzymes. While crystals of structural proteins that bind zinc reveal a higher preference for cysteine sulfhydryls rather than histidine imidazole rings, catalytic enzymes reveal the opposite, i.e., a greater preference for the histidines over cysteines for catalysis, plus the influence of carboxylic acids. Based on this paradigm, we reviewed the putative ligands of zinc in ionotropic receptors, where zinc has been described as an allosteric modulator of channel receptors. Although these receptors do not strictly qualify as metalloproteins since they do not normally bind zinc in structural domains, they do transitorily bind zinc at allosteric sites, modifying transiently the receptor channel’s ion permeability. The present contribution summarizes current information showing that zinc allosteric modulation of receptor channels occurs by the preferential metal coordination to imidazole rings as well as to the sulfhydryl groups of cysteine in addition to the carboxyl group of acid residues, as with enzymes and catalysis. It is remarkable that most channels, either voltage-sensitive or transmitter-gated receptor channels, are susceptible to zinc modulation either as positive or negative regulators. PMID:27384555

  16. Zinc as Allosteric Ion Channel Modulator: Ionotropic Receptors as Metalloproteins.

    PubMed

    Peralta, Francisco Andrés; Huidobro-Toro, Juan Pablo

    2016-01-01

    Zinc is an essential metal to life. This transition metal is a structural component of many proteins and is actively involved in the catalytic activity of cell enzymes. In either case, these zinc-containing proteins are metalloproteins. However, the amino acid residues that serve as ligands for metal coordination are not necessarily the same in structural proteins compared to enzymes. While crystals of structural proteins that bind zinc reveal a higher preference for cysteine sulfhydryls rather than histidine imidazole rings, catalytic enzymes reveal the opposite, i.e., a greater preference for the histidines over cysteines for catalysis, plus the influence of carboxylic acids. Based on this paradigm, we reviewed the putative ligands of zinc in ionotropic receptors, where zinc has been described as an allosteric modulator of channel receptors. Although these receptors do not strictly qualify as metalloproteins since they do not normally bind zinc in structural domains, they do transitorily bind zinc at allosteric sites, modifying transiently the receptor channel's ion permeability. The present contribution summarizes current information showing that zinc allosteric modulation of receptor channels occurs by the preferential metal coordination to imidazole rings as well as to the sulfhydryl groups of cysteine in addition to the carboxyl group of acid residues, as with enzymes and catalysis. It is remarkable that most channels, either voltage-sensitive or transmitter-gated receptor channels, are susceptible to zinc modulation either as positive or negative regulators. PMID:27384555

  17. Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

    PubMed Central

    Hermann, T; Auffinger, P; Scott, W G; Westhof, E

    1997-01-01

    In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH-ion is located between two Mg2+ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'- endo to the C2'- endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH-ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH-ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA. PMID:9254698

  18. Effects of Al(3+) Ions on Formation of Silica Framework and Surface Active Sites for SO4(2-) Ions.

    PubMed

    Sasahara, Shigeo; Ozeki, Sumio

    2016-07-19

    Al(3+) ions were introduced into silica framework at 318 K in order to make active Al sites for SO4(2-) by the addition of aqueous sodium silicate solution to aqueous sulfuric acid solution of Al2(SO4)3. The (27)Al and (29)Si NMR spectra of aluminosilicates were measured at 278 K with reaction time. (29)Si NMR spectra were analyzed by the multivariate curve resolution. The addition of Al(3+) ions to aqueous silicate solution promoted gel formation. Small amounts of Al(3+) ions were incorporated as a four-coordinated complex at early stage of polymerization reaction of silicates and during subsequent reaction six-coordinated Al complex increased, suggesting reversible conversion between 4- and 6-coordinated complexes. SO4(2-) ions interact with positive surfaces of aluminosilicates and are specifically adsorbed on the surface sites of 6-coordinated Al(3+) species, which may be stabilized on silicate surfaces as [Al(H2O)5SO4](+). PMID:27352046

  19. 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.

  20. GlmU (N-acetylglucosamine-1-phosphate uridyltransferase) bound to three magnesium ions and ATP at the active site

    PubMed Central

    Vithani, Neha; Bais, Vaibhav; Prakash, Balaji

    2014-01-01

    N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU), a bifunctional enzyme exclusive to prokaryotes, belongs to the family of sugar nucleotidyltransferases (SNTs). The enzyme binds GlcNAc-1-P and UTP, and catalyzes a uridyltransfer reaction to synthesize UDP-GlcNAc, an important precursor for cell-wall biosynthesis. As many SNTs are known to utilize a broad range of substrates, substrate specificity in GlmU was probed using biochemical and structural studies. The enzymatic assays reported here demonstrate that GlmU is specific for its natural substrates UTP and GlcNAc-1-P. The crystal structure of GlmU bound to ATP and GlcNAc-1-P provides molecular details for the inability of the enzyme to utilize ATP for the nucleotidyltransfer reaction. ATP binding results in an inactive pre-catalytic enzyme–substrate complex, where it adopts an unusual conformation such that the reaction cannot be catalyzed; here, ATP is shown to be bound together with three Mg2+ ions. Overall, this structure represents the binding of an inhibitory molecule at the active site and can potentially be used to develop new inhibitors of the enzyme. Further, similar to DNA/RNA polymerases, GlmU was recently recognized to utilize two metal ions, MgA 2+ and MgB 2+, to catalyze the uridyltransfer reaction. Interestingly, displacement of MgB 2+ from its usual catalytically competent position, as noted in the crystal structure of RNA polymerase in an inactive state, was considered to be a key factor inhibiting the reaction. Surprisingly, in the current structure of GlmU MgB 2+ is similarly displaced; this raises the possibility that an analogous inhibitory mechanism may be operative in GlmU. PMID:24915076

  1. 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

  2. An aqueous zinc-ion battery based on copper hexacyanoferrate.

    PubMed

    Trócoli, Rafael; La Mantia, Fabio

    2015-02-01

    A new zinc-ion battery based on copper hexacyanoferrate and zinc foil in a 20 mM solution of zinc sulfate, which is a nontoxic and noncorrosive electrolyte, at pH 6 is reported. The voltage of this novel battery system is as high as 1.73 V. The system shows cyclability, rate capability, and specific energy values near to those of lithium-ion organic batteries based on Li4 Ti5 O12 and LiFePO4 at 10 C. The effects of Zn(2+) intercalation and H2 evolution on the performance of the battery are discussed in detail. In particular, it has been observed that hydrogen evolution can cause a shift in pH near the surface of the zinc electrode, and favor the stabilization of zinc oxide, which decreases the performance of the battery. This mechanism is hindered when the surface of zinc becomes rougher. PMID:25510850

  3. Relative Penetration of Zinc Oxide and Zinc Ions into Human Skin after Application of Different Zinc Oxide Formulations.

    PubMed

    Holmes, Amy M; Song, Zhen; Moghimi, Hamid R; Roberts, Michael S

    2016-02-23

    Zinc oxide (ZnO) is frequently used in commercial sunscreen formulations to deliver their broad range of UV protection properties. Concern has been raised about the extent to which these ZnO particles (both micronized and nanoparticulate) penetrate the skin and their resultant toxicity. This work has explored the human epidermal skin penetration of zinc oxide and its labile zinc ion dissolution product that may potentially be formed after application of ZnO nanoparticles to human epidermis. Three ZnO nanoparticle formulations were used: a suspension in the oil, capric caprylic triglycerides (CCT), the base formulation commonly used in commercially available sunscreen products; an aqueous ZnO suspension at pH 6, similar to the natural skin surface pH; and an aqueous ZnO suspension at pH 9, a pH at which ZnO is stable and there is minimal pH-induced impairment of epidermal integrity. In each case, the ZnO in the formulations did not penetrate into the intact viable epidermis for any of the formulations but was associated with an enhanced increase in zinc ion fluorescence signal in both the stratum corneum and the viable epidermis. The highest labile zinc fluorescence was found for the ZnO suspension at pH 6. It is concluded that, while topically applied ZnO does not penetrate into the viable epidermis, these applications are associated with hydrolysis of ZnO on the skin surface, leading to an increase in zinc ion levels in the stratum corneum, thence in the viable epidermis and subsequently in the systemic circulation and the urine. PMID:26741484

  4. Rapid degradation of zinc oxide nanoparticles by phosphate ions

    PubMed Central

    García-García, F Javier; Reller, Armin

    2014-01-01

    Summary Zinc oxide nanoparticles are highly sensitive towards phosphate ions even at pH 7. Buffer solutions and cell culture media containing phosphate ions are able to destroy ZnO nanoparticles within a time span from less than one hour to one day. The driving force of the reaction is the formation of zinc phosphate of very low solubility. The morphology of the zinc oxide particles has only a minor influence on the kinetics of this reaction. Surface properties related to different production methods and the presence and absence of labelling with a perylene fluorescent dye are more important. Particles prepared under acidic conditions are more resistant than those obtained in basic or neutral reaction medium. Surprisingly, the presence of a SiO2 coating does not impede the degradation of the ZnO core. In contrast to phosphate ions, β-glycerophosphate does not damage the ZnO nanoparticles. These findings should be taken into account when assessing the biological effects or the toxicology of zinc oxide nanoparticles. PMID:25383310

  5. Fluorescence sensor for sequential detection of zinc and phosphate ions.

    PubMed

    An, Miran; Kim, Bo-Yeon; Seo, Hansol; Helal, Aasif; Kim, Hong-Seok

    2016-12-01

    A new, highly selective turn-on fluorescent chemosensor based on 2-(2'-tosylamidophenyl)thiazole (1) for the detection of zinc and phosphate ions in ethanol was synthesized and characterized. Sensor 1 showed a high selectivity for zinc compared to other cations and sequentially detected hydrogen pyrophosphate and hydrogen phosphate. The fluorescence mechanism can be explained by two different mechanisms: (i) the inhibition of excited-state intramolecular proton transfer (ESIPT) and (ii) chelation-induced enhanced fluorescence by binding with Zn(2+). The sequential detection of phosphate anions was achieved by the quenching and subsequent revival of ESIPT. PMID:27343439

  6. Fluorescence sensor for sequential detection of zinc and phosphate ions

    NASA Astrophysics Data System (ADS)

    An, Miran; Kim, Bo-Yeon; Seo, Hansol; Helal, Aasif; Kim, Hong-Seok

    2016-12-01

    A new, highly selective turn-on fluorescent chemosensor based on 2-(2‧-tosylamidophenyl)thiazole (1) for the detection of zinc and phosphate ions in ethanol was synthesized and characterized. Sensor 1 showed a high selectivity for zinc compared to other cations and sequentially detected hydrogen pyrophosphate and hydrogen phosphate. The fluorescence mechanism can be explained by two different mechanisms: (i) the inhibition of excited-state intramolecular proton transfer (ESIPT) and (ii) chelation-induced enhanced fluorescence by binding with Zn2 +. The sequential detection of phosphate anions was achieved by the quenching and subsequent revival of ESIPT.

  7. Osteogenic activity and antibacterial effect of zinc ion implanted titanium.

    PubMed

    Jin, Guodong; Cao, Huiliang; Qiao, Yuqin; Meng, Fanhao; Zhu, Hongqin; Liu, Xuanyong

    2014-05-01

    Titanium (Ti) and its alloys are widely used as orthopedic and dental implants. In this work, zinc (Zn) was implanted into oxalic acid etched titanium using plasma immersion ion implantation technology. Scanning electron microscopy and X-ray photoelectron spectroscopy were used to investigate the surface morphology and composition of Zn-implanted titanium. The results indicate that the depth profile of zinc in Zn-implanted titanium resembles a Gaussian distribution, and zinc exists in the form of ZnO at the surface whereas in the form of metallic Zn in the interior. The Zn-implanted titanium can significantly stimulate proliferation of osteoblastic MC3T3-E1 cells as well as initial adhesion, spreading activity, ALP activity, collagen secretion and extracellular matrix mineralization of the rat mesenchymal stem cells. The Zn-implanted titanium presents partly antibacterial effect on both Escherichia coli and Staphylococcus aureus. The ability of the Zn-implanted titanium to stimulate cell adhesion, proliferation and differentiation as well as the antibacterial effect on E. coli can be improved by increasing implantation time even to 2 h in this work, indicating that the content of zinc implanted in titanium can easily be controlled within the safe concentration using plasma immersion ion implantation technology. The Zn-implanted titanium with excellent osteogenic activity and partly antibacterial effect can serve as useful candidates for orthopedic and dental implants. PMID:24632388

  8. Improve the flame retardancy of cellulose fibers by grafting zinc ion.

    PubMed

    Zhang, KeKe; Zong, Lu; Tan, Yeqiang; Ji, Quan; Yun, Weicai; Shi, Ran; Xia, Yanzhi

    2016-01-20

    Zinc ion as the only flame retardant of cellulose fibers was successfully grafted onto cellulose fibers. Grafting maleic anhydride onto cellulose fibers via homogeneous acylation reaction between N,N-dimethyl formamide (DMF) as the first step. Then, graft zinc ion onto the formed cellulose fibers was conducted with zinc carbonate. The resulting copolymers were characterized by FTIR. Flame retardancy and thermal degradation of zinc-ion-modified cellulose fibers (cellulose-Zn fibers) was investigated by limiting oxygen index (LOI), cone calorimeter (CONE), XRD, TG and SEM. Zinc ion could effectively improve flame retardancy and thermal degradation when its content increases up to 4.96 wt%. PMID:26572337

  9. Analysis of cellular responses of macrophages to zinc ions and zinc oxide nanoparticles: a combined targeted and proteomic approach

    NASA Astrophysics Data System (ADS)

    Triboulet, Sarah; Aude-Garcia, Catherine; Armand, Lucie; Gerdil, Adèle; Diemer, Hélène; Proamer, Fabienne; Collin-Faure, Véronique; Habert, Aurélie; Strub, Jean-Marc; Hanau, Daniel; Herlin, Nathalie; Carrière, Marie; van Dorsselaer, Alain; Rabilloud, Thierry

    2014-05-01

    Two different zinc oxide nanoparticles, as well as zinc ions, are used to study the cellular responses of the RAW 264 macrophage cell line. A proteomic screen is used to provide a wide view of the molecular effects of zinc, and the most prominent results are cross-validated by targeted studies. Furthermore, the alteration of important macrophage functions (e.g. phagocytosis) by zinc is also investigated. The intracellular dissolution/uptake of zinc is also studied to further characterize zinc toxicity. Zinc oxide nanoparticles dissolve readily in the cells, leading to high intracellular zinc concentrations, mostly as protein-bound zinc. The proteomic screen reveals a rather weak response in the oxidative stress response pathway, but a strong response both in the central metabolism and in the proteasomal protein degradation pathway. Targeted experiments confirm that carbohydrate catabolism and proteasome are critical determinants of sensitivity to zinc, which also induces DNA damage. Conversely, glutathione levels and phagocytosis appear unaffected at moderately toxic zinc concentrations.Two different zinc oxide nanoparticles, as well as zinc ions, are used to study the cellular responses of the RAW 264 macrophage cell line. A proteomic screen is used to provide a wide view of the molecular effects of zinc, and the most prominent results are cross-validated by targeted studies. Furthermore, the alteration of important macrophage functions (e.g. phagocytosis) by zinc is also investigated. The intracellular dissolution/uptake of zinc is also studied to further characterize zinc toxicity. Zinc oxide nanoparticles dissolve readily in the cells, leading to high intracellular zinc concentrations, mostly as protein-bound zinc. The proteomic screen reveals a rather weak response in the oxidative stress response pathway, but a strong response both in the central metabolism and in the proteasomal protein degradation pathway. Targeted experiments confirm that carbohydrate

  10. Potentiometric Zinc Ion Sensor Based on Honeycomb-Like NiO Nanostructures

    PubMed Central

    Abbasi, Mazhar Ali; Ibupoto, Zafar Hussain; Hussain, Mushtaque; Khan, Yaqoob; Khan, Azam; Nur, Omer; Willander, Magnus

    2012-01-01

    In this study honeycomb-like NiO nanostructures were grown on nickel foam by a simple hydrothermal growth method. The NiO nanostructures were characterized by field emission electron microscopy (FESEM), high resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) techniques. The characterized NiO nanostructures were uniform, dense and polycrystalline in the crystal phase. In addition to this, the NiO nanostructures were used in the development of a zinc ion sensor electrode by functionalization with the highly selective zinc ion ionophore 12-crown-4. The developed zinc ion sensor electrode has shown a good linear potentiometric response for a wide range of zinc ion concentrations, ranging from 0.001 mM to 100 mM, with sensitivity of 36 mV/decade. The detection limit of the present zinc ion sensor was found to be 0.0005 mM and it also displays a fast response time of less than 10 s. The proposed zinc ion sensor electrode has also shown good reproducibility, repeatability, storage stability and selectivity. The zinc ion sensor based on the functionalized NiO nanostructures was also used as indicator electrode in potentiometric titrations and it has demonstrated an acceptable stoichiometric relationship for the determination of zinc ion in unknown samples. The NiO nanostructures-based zinc ion sensor has potential for analysing zinc ion in various industrial, clinical and other real samples. PMID:23202217

  11. Potentiometric zinc ion sensor based on honeycomb-like NiO nanostructures.

    PubMed

    Abbasi, Mazhar Ali; Ibupoto, Zafar Hussain; Hussain, Mushtaque; Khan, Yaqoob; Khan, Azam; Nur, Omer; Willander, Magnus

    2012-01-01

    In this study honeycomb-like NiO nanostructures were grown on nickel foam by a simple hydrothermal growth method. The NiO nanostructures were characterized by field emission electron microscopy (FESEM), high resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) techniques. The characterized NiO nanostructures were uniform, dense and polycrystalline in the crystal phase. In addition to this, the NiO nanostructures were used in the development of a zinc ion sensor electrode by functionalization with the highly selective zinc ion ionophore 12-crown-4. The developed zinc ion sensor electrode has shown a good linear potentiometric response for a wide range of zinc ion concentrations, ranging from 0.001 mM to 100 mM, with sensitivity of 36 mV/decade. The detection limit of the present zinc ion sensor was found to be 0.0005 mM and it also displays a fast response time of less than 10 s. The proposed zinc ion sensor electrode has also shown good reproducibility, repeatability, storage stability and selectivity. The zinc ion sensor based on the functionalized NiO nanostructures was also used as indicator electrode in potentiometric titrations and it has demonstrated an acceptable stoichiometric relationship for the determination of zinc ion in unknown samples. The NiO nanostructures-based zinc ion sensor has potential for analysing zinc ion in various industrial, clinical and other real samples. PMID:23202217

  12. Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations.

    PubMed

    Hladilkova, Jana; Prokop, Zbynek; Chaloupkova, Radka; Damborsky, Jiri; Jungwirth, Pavel

    2013-11-21

    Release of halide ions is an essential step of the catalytic cycle of haloalkane dehalogenases. Here we describe experimentally and computationally the process of release of a halide anion from the buried active site of the haloalkane dehalogenase LinB. Using stopped-flow fluorescence analysis and umbrella sampling free energy calculations, we show that the anion binding is ion-specific and follows the ordering I(-) > Br(-) > Cl(-). We also address the issue of the protonation state of the catalytic His272 residue and its effect on the process of halide release. While deprotonation of His272 increases binding of anions in the access tunnel, we show that the anionic ordering does not change with the switch of the protonation state. We also demonstrate that a sodium cation could relatively easily enter the active site, provided the His272 residue is singly protonated, and replace thus the missing proton. In contrast, Na(+) is strongly repelled from the active site containing the doubly protonated His272 residue. Our study contributes toward understanding of the reaction mechanism of haloalkane dehalogenase enzyme family. Determination of the protonation state of the catalytic histidine throughout the catalytic cycle remains a challenge for future studies. PMID:24151979

  13. Zinc-67 NMR study of zinc ions in water and in some nonaqueous and mixed solvents

    SciTech Connect

    Li, Z.; Popov, A.I.

    1982-01-01

    Solutions of zinc salts in water, methanol (MeOH), dimethylformamide (DMF) and binary mixtures of water with the two nonaqueous solvents were studied by zinc-67 MNR measurements. Anhydrous zinc nitrate solutions in DMF and MeOH show upfield, concentration independent, chemical shifts at -27 and -19 ppm, respectively, vs. the aqueous solution standard. Addition of DMF or MeOH to an aqueous solution of a zinc salt results in a diamagnetic shift but for the addition of acetonitrile a paramagnetic shift results. In all cases the signal was broadened very considerably, e.g., in ZnCl/sub 2/ solution the linewidth increased from --40 to --600 Hz in going from water to 35% aqueous MeOH. Both /sup 67/ Zn and /sup 13/ C NMR failed to show any complexation of Zn/sup 2/+ ion by crown ethers in aqueous solution. A gradual addition of EDTA, of diaza-18-crown-6 or of tetraazacyclotetradecane resulted in an immediate broadening of the /sup 67/ Zn signal which became undetectable when one equivalent of a ligand was added.

  14. Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.

    PubMed

    Ucisik, Melek N; Bevilacqua, Philip C; Hammes-Schiffer, Sharon

    2016-07-12

    The recently discovered twister ribozyme is thought to utilize general acid-base catalysis in its self-cleavage mechanism, but the roles of nucleobases and metal ions in the mechanism are unclear. Herein, molecular dynamics simulations of the env22 twister ribozyme are performed to elucidate the structural and equilibrium dynamical properties, as well as to examine the role of Mg(2+) ions and possible candidates for the general base and acid in the self-cleavage mechanism. The active site region and the ends of the pseudoknots were found to be less mobile than other regions of the ribozyme, most likely providing structural stability and possibly facilitating catalysis. A purported catalytic Mg(2+) ion and the closest neighboring Mg(2+) ion remained chelated and relatively immobile throughout the microsecond trajectories, although removal of these Mg(2+) ions did not lead to any significant changes in the structure or equilibrium motions of the ribozyme on the microsecond time scale. In addition, a third metal ion, a Na(+) ion remained close to A1(O5'), the leaving group atom, during the majority of the microsecond trajectories, suggesting that it might stabilize the negative charge on A1(O5') during self-cleavage. The locations of these cations and their interactions with key nucleotides in the active site suggest that they may be catalytically relevant. The P1 stem is partially melted at its top and bottom in the crystal structure and further unwinds in the trajectories. The simulations also revealed an interconnected network comprised of hydrogen-bonding and π-stacking interactions that create a relatively rigid network around the self-cleavage site. The nucleotides involved in this network are among the highly conserved nucleotides in twister ribozymes, suggesting that this interaction network may be important to structure and function. PMID:27295275

  15. Analysis of cellular responses of macrophages to zinc ions and zinc oxide nanoparticles: a combined targeted and proteomic approach.

    PubMed

    Triboulet, Sarah; Aude-Garcia, Catherine; Armand, Lucie; Gerdil, Adèle; Diemer, Hélène; Proamer, Fabienne; Collin-Faure, Véronique; Habert, Aurélie; Strub, Jean-Marc; Hanau, Daniel; Herlin, Nathalie; Carrière, Marie; Van Dorsselaer, Alain; Rabilloud, Thierry

    2014-06-01

    Two different zinc oxide nanoparticles, as well as zinc ions, are used to study the cellular responses of the RAW 264 macrophage cell line. A proteomic screen is used to provide a wide view of the molecular effects of zinc, and the most prominent results are cross-validated by targeted studies. Furthermore, the alteration of important macrophage functions (e.g. phagocytosis) by zinc is also investigated. The intracellular dissolution/uptake of zinc is also studied to further characterize zinc toxicity. Zinc oxide nanoparticles dissolve readily in the cells, leading to high intracellular zinc concentrations, mostly as protein-bound zinc. The proteomic screen reveals a rather weak response in the oxidative stress response pathway, but a strong response both in the central metabolism and in the proteasomal protein degradation pathway. Targeted experiments confirm that carbohydrate catabolism and proteasome are critical determinants of sensitivity to zinc, which also induces DNA damage. Conversely, glutathione levels and phagocytosis appear unaffected at moderately toxic zinc concentrations. PMID:24788578

  16. Influence of lead ions on the macromorphology of electrodeposited zinc

    SciTech Connect

    Tsuda, T.; Tobias, C.W.

    1981-09-01

    The morphology of zinc as it is electrodeposited from acid solutions demonstrates a remarkable imprint of electrolyte flow conditions. The development of macromorphology of zinc deposits has been investigated under galvanostatic conditions on a rotating plantinum disk electrode by use of photomacrography, scanning electron microscopy, electron probe microanalysis and Auger microprobe analysis. Logarithmic spiral markings, which reflect the hydrodynamic flow on a rotating disk, appear in a certain region of current density well below the limiting current density. Morphological observations revealed the major influence of trace lead ions on the amplifications of surface roughness through coalescence and preferred growth of initial protrusions. Results obtained from ultra-pure electrolyte suggest preferred crystal growth towards well-mixed orientation in the concentration field caused by slight differences in crystallization overpotential. A qualitative model involving a coupling mechanism between the evolving surface roughness and instability phenomena in the boundary layer is advanced to explain the formation of spiral patterns.

  17. Transient fluctuations of intracellular zinc ions in cell proliferation

    SciTech Connect

    Li, Yuan; Maret, Wolfgang

    2009-08-15

    Zinc is essential for cell proliferation, differentiation, and viability. When zinc becomes limited for cultured cells, DNA synthesis ceases and the cell cycle is arrested. The molecular mechanisms of actions of zinc are believed to involve changes in the availability of zinc(II) ions (Zn{sup 2+}). By employing a fluorescent Zn{sup 2+} probe, FluoZin-3 acetoxymethyl ester, intracellular Zn{sup 2+} concentrations were measured in undifferentiated and in nerve growth factor (NGF)-differentiated rat pheochromocytoma (PC12) cells. Intracellular Zn{sup 2+} concentrations are pico- to nanomolar in PC12 cells and are higher in the differentiated than in the undifferentiated cells. When following cellular Zn{sup 2+} concentrations for 48 h after the removal of serum, a condition that is known to cause cell cycle arrest, Zn{sup 2+} concentrations decrease after 30 min but, remarkably, increase after 1 h, and then decrease again to about one half of the initial concentration. Cell proliferation, measured by an MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, decreases after both serum starvation and zinc chelation. Two peaks of Zn{sup 2+} concentrations occur within one cell cycle: one early in the G1 phase and the other in the late G1/S phase. Thus, fluctuations of intracellular Zn{sup 2+} concentrations and established modulation of phosphorylation signaling, via an inhibition of protein tyrosine phosphatases at commensurately low Zn{sup 2+} concentrations, suggest a role for Zn{sup 2+} in the control of the cell cycle. Interventions targeted at these picomolar Zn{sup 2+} fluctuations may be a way of controlling cell growth in hyperplasia, neoplasia, and diseases associated with aberrant differentiation.

  18. Morphology-Dependent Electrochemical Performance of Zinc Hexacyanoferrate Cathode for Zinc-Ion Battery

    PubMed Central

    Zhang, Leyuan; Chen, Liang; Zhou, Xufeng; Liu, Zhaoping

    2015-01-01

    Zinc hexacyanoferrate (ZnHCF) which is a dimorphic (cubic or rhombohedral) Prussian blue analogue and can be intercalated by both monovalent and divalent ions,is a promising cathode material for rechargeable aqueous metal-ion batteries.In this paper, a simple co-precipitation method is developed to tune the particle morphology of ZnHCF by adjusting the dropping speed at room temperature. Three polyhedral ZnHCF particles, with cubooctahedral, truncated octahedral or octahedral shapes, are obtained at room temperature. Structural transformation from cubic phase of as-prepared ZnHCF to rhombohedral phase is observed by further dehydration of the sample at 70 °C, whereas the dehydrated ZnHCF crystals still hold the identical polyhedral shape as that of the cubic phase particles. Then the influence of shape and facets on electrochemical performance is studied for polyhedral ZnHCF with rhombohedral structure (RZnHCF). RZnHCF sample with cubooctahedral shape possesses the best rate capability and cyclic stability comparing with RZnHCF particles having truncated octahedral or octahedral shapes. Furthermore, the structure of cuboctahedron RZnHCF particles during electrochemical cycling has been monitored with ex situ X-ray diffraction to demonstrate the reversible zinc-ion intercalation mechanism. PMID:26669272

  19. Morphology-Dependent Electrochemical Performance of Zinc Hexacyanoferrate Cathode for Zinc-Ion Battery.

    PubMed

    Zhang, Leyuan; Chen, Liang; Zhou, Xufeng; Liu, Zhaoping

    2015-01-01

    Zinc hexacyanoferrate (ZnHCF) which is a dimorphic (cubic or rhombohedral) Prussian blue analogue and can be intercalated by both monovalent and divalent ions,is a promising cathode material for rechargeable aqueous metal-ion batteries.In this paper, a simple co-precipitation method is developed to tune the particle morphology of ZnHCF by adjusting the dropping speed at room temperature. Three polyhedral ZnHCF particles, with cubooctahedral, truncated octahedral or octahedral shapes, are obtained at room temperature. Structural transformation from cubic phase of as-prepared ZnHCF to rhombohedral phase is observed by further dehydration of the sample at 70 °C, whereas the dehydrated ZnHCF crystals still hold the identical polyhedral shape as that of the cubic phase particles. Then the influence of shape and facets on electrochemical performance is studied for polyhedral ZnHCF with rhombohedral structure (RZnHCF). RZnHCF sample with cubooctahedral shape possesses the best rate capability and cyclic stability comparing with RZnHCF particles having truncated octahedral or octahedral shapes. Furthermore, the structure of cuboctahedron RZnHCF particles during electrochemical cycling has been monitored with ex situ X-ray diffraction to demonstrate the reversible zinc-ion intercalation mechanism. PMID:26669272

  20. Relation of morphology of electrodeposited zinc to ion concentration profile

    NASA Technical Reports Server (NTRS)

    May, C. E.; Kautz, H. E.; Sabo, B. B.

    1977-01-01

    The morphology of electrodeposited zinc was studied with special attention to the ion concentration profile. The initial concentrations were 9M hydroxide ion and 1.21M zincate. Current densities were 6.4 to 64 mA/sq cm. Experiments were run with a horizontal cathode which was observed in situ using a microscope. The morphology of the zinc deposit was found to be a function of time as well as current density; roughly, the log of the transition time from mossy to large crystalline type deposit is inversely proportional to current density. Probe electrodes indicated that the electrolyte in the cathode chamber was mixed by self inducted convection. However, relatively large concentration gradients of the involved species existed across the boundary layer of the cathode. Analysis of the data suggests that the morphology converts from mossy to large crystalline when the hydroxide activity on the cathode surface exceeds about 12 M. Other experiments show that the pulse discharge technique had no effect on the morphology in the system where the bulk concentration of the electrolyte was kept homogeneous via self induced convection.

  1. 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

  2. Selective electrodiffusion of zinc ions in a Zrt-, Irt-like protein, ZIPB

    SciTech Connect

    Lin, W.; Fu, D.; Chai, J.; Love, J.

    2010-12-10

    All living cells need zinc ions to support cell growth. Zrt-, Irt-like proteins (ZIPs) represent a major route for entry of zinc ions into cells, but how ZIPs promote zinc uptake has been unclear. Here we report the molecular characterization of ZIPB from Bordetella bronchiseptica, the first ZIP homolog to be purified and functionally reconstituted into proteoliposomes. Zinc flux through ZIPB was found to be nonsaturable and electrogenic, yielding membrane potentials as predicted by the Nernst equation. Conversely, membrane potentials drove zinc fluxes with a linear voltage-flux relationship. Direct measurements of metal uptake by inductively coupled plasma mass spectroscopy demonstrated that ZIPB is selective for two group 12 transition metal ions, Zn{sup 2+} and Cd{sup 2+}, whereas rejecting transition metal ions in groups 7 through 11. Our results provide the molecular basis for cellular zinc acquisition by a zinc-selective channel that exploits in vivo zinc concentration gradients to move zinc ions into the cytoplasm.

  3. Ion imprinted polymeric nanoparticles for selective separation and sensitive determination of zinc ions in different matrices

    NASA Astrophysics Data System (ADS)

    Shamsipur, Mojtaba; Rajabi, Hamid Reza; Pourmortazavi, Seied Mahdi; Roushani, Mahmoud

    2014-01-01

    Preparation of Zn2+ ion-imprinted polymer (Zn-IIP) nanoparticles is presented in this report. The Zn-IIP nanoparticles are prepared by dissolving stoichiometric amounts of zinc nitrate and selected chelating ligand, 3,5,7,20,40-pentahydroxyflavone, in 15 mL ethanol-acetonitrile (2:1; v/v) mixture as a porogen solvent in the presence of ethylene glycol-dimethacrylate (EGDMA) as cross-linking, methacrylic acid (MAA) as functional monomer, and 2,2-azobisisobutyronitrile (AIBN) as initiator. After polymerization, Cavities in the polymer particles corresponding to the Zn2+ ions were created by leaching the polymer in HCl aqueous solution. The synthesized IIPs were characterized by scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, fluorescence spectroscopy and thermal analysis techniques. Also, the pH range for rebinding of Zn2+ ion on the IIP and equilibrium binding time were optimized, using flame atomic absorption spectrometry. In selectivity study, it was found that imprinting results increased affinity of the material toward Zn2+ ion over other competitor metal ions with the same charge and close ionic radius. The prepared IIPs were repeatedly used and regenerated for six times without any significant decrease in polymer binding affinities. Finally, the prepared sorbent was successfully applied to the selective recognition and determination of zinc ion in different real samples.

  4. Evidence for zinc ion sharing in metallothionein dimers provided by collision-induced dissociation

    NASA Astrophysics Data System (ADS)

    Afonso, Carlos; Hathout, Yetrib; Fenselau, Catherine

    2004-02-01

    Nanospray and collisionally-induced dissociation are used to evaluate the presence and absence of interstrand co-chelation of zinc ions in dimers of metallothionein. As was reported in a previous publication from this laboratory, co-chelation stabilizes the dimer to collisional activation, and facilitates asymmetrical zinc ion transfers during fragmentation. In the case of metallothionein, dimers of the holoprotein are found to share zinc ions, while dimers of metallothionein, in which one domain has been denatured, do not. Zinc ions are silent to most physicochemical probes, e.g., NMR and Mossbauer spectroscopies, and the capability of mass spectrometry to provide information on zinc complexes has widespread potential application in biochemistry.

  5. Preferential uptake of ammonium ions by zinc ferrocyanide

    NASA Technical Reports Server (NTRS)

    Braterman, P. S.; Arrhenius, G.; Hui, S.; Paplawsky, W.; Miller, S. L. (Principal Investigator)

    1995-01-01

    The concentration of ammonia from dilute aqueous solution could have facilitated many prebiotic reactions. This may be especially true if this concentration involves incorporation into an organized medium. We have shown that (unlike iron(III) ferrocyanide) zinc ferrocyanide,Zn2Fe(CN)6 xH2O, preferentially takes up ammonium ions from 0.01 M NH4Cl to give the known material Zn3(NH4)2[Fe(CN)6]2 xH2O, even in the presence of 0.01 M KCl. KCl alone gave Zn3K2[Fe(CN)6]2 xH2O. Products were characterized by elemental (CHN) analysis and powder X-ray diffraction (XRD). We attribute the remarkable specificity for the ammonium ion to the open framework of the product, which offers enough space for hydrogen-bonded ammonium ions, and infer that other inorganic materials with internal spaces rich in water may show a similar preference.

  6. Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica

    NASA Astrophysics Data System (ADS)

    Oboh, I.; Aluyor, E.; Audu, T.

    2015-03-01

    The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R2), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.

  7. Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica

    SciTech Connect

    Oboh, I.; Aluyor, E.; Audu, T.

    2015-03-30

    The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R{sup 2}), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.

  8. Zinc activates damage-sensing TRPA1 ion channels

    PubMed Central

    Hu, Hongzhen; Bandell, Michael; Petrus, Matt J.; Zhu, Michael X.; Patapoutian, Ardem

    2009-01-01

    Zinc is an essential biological trace element. It is required for the structure or function of over 300 proteins, and is increasingly recognized for its role in cell signaling. However, high concentrations of zinc have cytotoxic effects, and overexposure to zinc can cause pain and inflammation through unknown mechanisms. Here we show that zinc excites nociceptive somatosensory neurons and causes nociception in mice through TRPA1, a cation channel previously shown to mediate the pungency of wasabi and cinnamon through cysteine-modification. Zinc activates TRPA1 through a novel mechanism that requires zinc influx through TRPA1 channels and subsequent activation via specific intracellular cysteine and histidine residues. TRPA1 is highly sensitive to intracellular zinc, as low nanomolar concentrations activate TRPA1 and modulate its sensitivity. These findings identify TRPA1 as a major target for the sensory effects of zinc, and support an emerging role for zinc as a signaling molecule that can modulate sensory transmission. PMID:19202543

  9. ZINC

    EPA Science Inventory

    This report summarizes the available information on zinc as it relates to its effects on man and his environment. Zinc is found in most soils, but some areas are deficient in it. Metallurgic operations contribute to zinc contamination in air, water and soil. Trace amounts of zinc...

  10. Localization of ZnT7 and zinc ions in mouse retina-Immunohistochemistry and selenium autometallography

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Zinc transporter 7 (ZnT7, Slc30a7), a member of the Slc30 family, is involved in mobilizing zinc ions from the cytoplasm into the Golgi apparatus. In the present study, we examined the distribution and localization of ZnT7 and the labile zinc ions in the mouse retina using immunohistochemistry and i...

  11. Zinc-Permeable Ion Channels: Effects on Intracellular Zinc Dynamics and Potential Physiological/Pathophysiological Significance

    PubMed Central

    Inoue, Koichi; O'Bryant, Zaven; Xiong, Zhi-Gang

    2015-01-01

    Zinc (Zn2+) is one of the most important trace metals in the body. It is necessary for the normal function of a large number of proteins including enzymes and transcription factors. While extracellular fluid may contain up to micromolar Zn2+, intracellular Zn2+ concentration is generally maintained at a subnanomolar level; this steep gradient across the cell membrane is primarily attributable to Zn2+ extrusion by Zn2+ transporting systems. Interestingly, systematic investigation has revealed that activities, previously believed to be dependent on calcium (Ca2+), may be partially mediated by Zn2+. This is also supported by new findings that some Ca2+-permeable channels such as voltage-dependent calcium channels (VDCCs), N-methyl-D-aspartate receptors (NMDA), and amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors (AMPA-Rs) are also permeable to Zn2+. Thus, the importance of Zn2+ in physiological and pathophysiological processes is now more widely appreciated. In this review, we describe Zn2+-permeable membrane molecules, especially Zn2+-permeable ion channels, in intracellular Zn2+dynamics and Zn2+ mediated physiology/pathophysiology. PMID:25666796

  12. 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.

  13. A zinc-sensing receptor triggers the release of intracellular Ca2+ and regulates ion transport

    PubMed Central

    Hershfinkel, Michal; Moran, Arie; Grossman, Nili; Sekler, Israel

    2001-01-01

    Changes in extracellular zinc concentration participate in modulating fundamental cellular processes such as proliferation, secretion, and ion transport in a mechanism that is not well understood. Here, we show that a micromolar concentration of extracellular zinc triggers a massive release of calcium from thapsigargin-sensitive intracellular pools in the colonocytic cell line HT29. Calcium release was blocked by a phospholipase-C inhibitor, indicating that formation of inositol 1,4,5-triphosphate is required for zinc-dependent calcium release. Zinc influx was not observed, indicating that extracellular zinc triggered the release. The Cai2+ release was zinc specific and could not be triggered by other heavy metals. Furthermore, zinc failed to activate the Ca2+-sensing receptor heterologously expressed in HEK293 cells. The zinc-induced Cai2+ rise stimulated the activity of the Na+/H+ exchanger in HT29 cells. Our results indicate that a previously uncharacterized extracellular, G protein-coupled, Zn2+-sensing receptor is functional in colonocytes. Because Cai2+ rise is known to regulate key cellular and signal-transduction processes, the zinc-sensing receptor may provide the missing link between extracellular zinc concentration changes and the regulation of cellular processes. PMID:11573009

  14. Removal of lead and zinc ions from water by low cost adsorbents.

    PubMed

    Mishra, P C; Patel, R K

    2009-08-30

    In this study, activated carbon, kaolin, bentonite, blast furnace slag and fly ash were used as adsorbent with a particle size between 100 mesh and 200 mesh to remove the lead and zinc ions from water. The concentration of the solutions prepared was in the range of 50-100 mg/L for lead and zinc for single and binary systems which are diluted as required for batch experiments. The effect of contact time, pH and adsorbent dosage on removal of lead and zinc by adsorption was investigated. The equilibrium time was found to be 30 min for activated carbon and 3h for kaolin, bentonite, blast furnace slag and fly ash. The most effective pH value for lead and zinc removal was 6 for activated carbon. pH value did not effect lead and zinc removal significantly for other adsorbents. Adsorbent doses were varied from 5 g/L to 20 g/L for both lead and zinc solutions. An increase in adsorbent doses increases the percent removal of lead and zinc. A series of isotherm studies was undertaken and the data evaluated for compliance was found to match with the Langmuir and Freundlich isotherm models. To investigate the adsorption mechanism, the kinetic models were tested, and it follows second order kinetics. Kinetic studies reveals that blast furnace slag was not effective for lead and zinc removal. The bentonite and fly ash were effective for lead and zinc removal. PMID:19299083

  15. 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

  16. 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.

  17. Highly Reversible Zinc-Ion Intercalation into Chevrel Phase Mo6S8 Nanocubes and Applications for Advanced Zinc-Ion Batteries.

    PubMed

    Cheng, Yingwen; Luo, Langli; Zhong, Li; Chen, Junzheng; Li, Bin; Wang, Wei; Mao, Scott X; Wang, Chongmin; Sprenkle, Vincent L; Li, Guosheng; Liu, Jun

    2016-06-01

    This work describes the synthesis of Chevrel phase Mo6S8 nanocubes and its application as the anode material for rechargeable Zn-ion batteries. Mo6S8 can host Zn(2+) ions reversibly in both aqueous and nonaqueous electrolytes with specific capacities around 90 mAh/g, and exhibited remarkable intercalation kinetics and cyclic stability. In addition, we assembled full cells by integrating Mo6S8 anodes with zinc-polyiodide (I(-)/I3(-))-based catholytes, and demonstrated that such full cells were also able to deliver outstanding rate performance and cyclic stability. This first demonstration of a zinc-intercalating anode could inspire the design of advanced Zn-ion batteries. PMID:27182714

  18. Zinc

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Zinc was recognized as an essential trace metal for humans during the studies of Iranian adolescent dwarfs in the early 1960s. Zinc metal existing as Zn2+ is a strong electron acceptor in biological systems without risks of oxidant damage to cells. Zn2+ functions in the structure of proteins and is ...

  19. Zinc

    MedlinePlus

    ... Guidelines for Americans and the U.S. Department of Agriculture's MyPlate . Where can I find out more about ... on food sources of zinc: U.S. Department of Agriculture's (USDA’s) National Nutrient Database Nutrient List for zinc ( ...

  20. Inhibition of human acid-sensing ion channel 1b by zinc

    PubMed Central

    Jiang, Qian; Zha, Xiang-Ming; Chu, Xiang-Ping

    2012-01-01

    Acid-sensing ion channel 1b (ASIC1b) is expressed in peripheral sensory neurons and has been implicated in nociception. Understanding the modulation of ASIC1b will provide important insight into how ASIC1b contributes to pain sensation. In our previous study, we showed that zinc, an important modulator of pain sensation, reduces rat ASIC1b current. However, rat ASIC1b shows several important differences from its recently identified human homolog. Most noticeably, human ASIC1b (hASIC1b) has a sustained component, which may play a role in persistent pain. Therefore, we tested here the hypothesis that zinc modulates the current properties of hASIC1b. Bath application of zinc suppressed the peak amplitude of hASIC1b currents, with a half-maximum inhibitory concentration of 37 μM. However, zinc did not affect the sustained component of hASIC1b currents. The effect of zinc was independent of pH-dependent activation, steady-state desensitization, and extracellular Ca2+, suggesting noncompetitive mechanisms. Further, we found that extracellular site(s) of the hASIC1b subunit is important for the effect of zinc. Mutating cysteine 196, but not cysteine 309, in the extracellular domain of the hASIC1b abolished the zinc inhibition. These results suggest that, through modulating cysteine196, zinc may have a modulatory role in acute pain. PMID:22837807

  1. Solution NMR characterization of Sgf73(1-104) indicates that Zn ion is required to stabilize zinc finger motif

    SciTech Connect

    Lai, Chaohua; Wu, Minhao; Li, Pan; Shi, Chaowei; Tian, Changlin; Zang, Jianye

    2010-07-02

    Zinc finger motif contains a zinc ion coordinated by several conserved amino acid residues. Yeast Sgf73 protein was identified as a component of SAGA (Spt/Ada/Gcn5 acetyltransferase) multi-subunit complex and Sgf73 protein was known to contain two zinc finger motifs. Sgf73(1-104), containing the first zinc finger motif, was necessary to modulate the deubiquitinase activity of SAGA complex. Here, Sgf73(1-104) was over-expressed using bacterial expression system and purified for solution NMR (nuclear magnetic resonance) structural studies. Secondary structure and site-specific relaxation analysis of Sgf73(1-104) were achieved after solution NMR backbone assignment. Solution NMR and circular dichroism analysis of Sgf73(1-104) after zinc ion removal using chelation reagent EDTA (ethylene-diamine-tetraacetic acid) demonstrated that zinc ion was required to maintain stable conformation of the zinc finger motif.

  2. Purification of proteins containing zinc finger domains using Immobilized Metal Ion Affinity Chromatography

    PubMed Central

    Voráčková, Irena; Suchanová, Šárka; Ulbrich, Pavel; Diehl, William E.; Ruml, Tomáš

    2011-01-01

    Heterologous proteins are frequently purified by Immobilized Metal Ion Affinity Chromatography (IMAC) based on their modification with a hexa-histidine affinity tag (His-tag). The terminal His-tag can, however, alter functional properties of the tagged protein. Numerous strategies for the tag removal have been developed including chemical treatment and insertion of protease target sequences in the protein sequence. Instead of using these approaches, we took an advantage of natural interaction of zinc finger domains with metal ions to purify functionally similar retroviral proteins from two different retroviruses. We found that these proteins exhibited significantly different affinities to the immobilized metal ions, despite that both contain the same type of zinc finger motif (i.e. CCHC). While zinc finger proteins may differ in biochemical properties, the multitude of IMAC platforms should allow relatively simple yet specific method for their isolation in native state. PMID:21600288

  3. Removal of Zinc Form Carbonic Anhydrase: A Kinetics Experiment for Upper-Level Chemistry Laboratories

    ERIC Educational Resources Information Center

    Williams, Kathryn R.; Adhyaru, Bhavin

    2004-01-01

    An experiment on kinetics of deactivation of carbonic anhydrase by removal of zinc is demonstrated. Carbonic anhydrase, the enzyme that catalyzes the interconversion of carbon dioxide and bicarbonate, requires on Zn(II) ion in its active site, and removal of the zinc cofactor by complexion to another ligand leaves the apoenzyme, which is totally…

  4. Zinc

    MedlinePlus

    ... women taking iron and folic acid supplements. Prostate cancer. Early research suggests that taking zinc along with other vitamins and minerals may prevent prostate cancer in some men. However, other research suggests that ...

  5. Zinc

    MedlinePlus

    ... by mouth does not improve sperm count or sperm movement in men with fertility problems. However, other early research suggests that zinc supplementation increases sperm count, testosterone levels, and pregnancy rates in infertile ...

  6. Nanosecond electric pulses deprive zinc ions of carboxypeptidase G2.

    PubMed

    Yu, Tinghe; Fu, Xiao

    2015-02-01

    Nanosecond electric pulses (nsEP, 10kV/cm with a pulse duration of 8, 16 or 24ns) inhibited the activity of carboxypeptidase G2 (CPG2), a zinc-dependent homodimer; the relative activity was <20% when the total exposure time was >120s. No alterations were detected in electrophoresis, chromatography, mass spectroscopy and circular dichroism, thus demonstrating intactness of the apoenzyme. Inductively coupled plasma-mass spectrometry indicated that zinc levels were 3.30μg/mg protein in control CPG2, and decreased to 0.40, 0.12 or 0.38μg/mg protein after 240s of 8-, 16- or 24-ns pulses, respectively. In CPG2 exposed to 240s of 8-, 16- and 24-ns pulses, the reloading of zinc with redialysis recovered the activity to 94.7±3.4%, 84.0±5.2% and 81.7±7.0%, respectively (p=0.0853, 0.0741, 0.0668). These data demonstrated that nsEP inhibited CPG2 via removal of zinc, and that nsEP can be used to modulate CPG2. PMID:25049063

  7. Active sites imaging for oxygen reduction at the La{sub 0.9}Sr{sub 0.1}MnO{sub 3{minus}x}/yttria-stabilized zirconia interface by secondary-ion mass spectrometry

    SciTech Connect

    Horita, Teruhisa; Yamaji, Katsuhiko; Ishikawa, Masahiko; Sakai, Natsuko; Yokokawa, Harumi; Kawada, Tatsuya; Kato, Tohru

    1998-09-01

    Active sites for oxygen reduction were investigated at the interface of O{sub 2}/La{sub 0.9}Sr{sub 0.1}MnO{sub 3{minus}x} (LSM)/yttria-stabilized zirconia (YSZ). Isotopic oxygen ({sup 16}O/{sup 18}O) exchange under cathodic polarization and secondary-ion mass spectrometry (SIMS) analysis were examined to visualize the oxygen reduction active sites. The LSM mesh pattern electrode was prepared to define the contact area of LSM/YSZ. Under cathodic polarization, oxygen can diffuse through the dense LSM via oxygen vacancy, which promotes the electrode reaction. By SIMS imaging technique, the active sites for oxygen reduction were clearly determined as spots around the O{sub 2}/LSM/YSZ three-phase boundary. The line analysis of the SIMS image enabled the authors to draw a contour map of the {sup 18}O concentration in the cross section of YSZ. The diffusion paths were clearly visualized in the contour map. The width of the active sites for oxygen reduction is estimated to be less than 1 {micro}m under the examined condition.

  8. VO2+ ions in zinc lead borate glasses studied by EPR and optical absorption techniques.

    PubMed

    Prakash, P Giri; Rao, J Lakshmana

    2005-09-01

    Electron paramagnetic resonance (EPR) and optical absorption spectra of vanadyl ions in zinc lead borate (ZnO-PbO-B2O3) glass system have been studied. EPR spectra of all the glass samples exhibit resonance signals characteristic of VO2+ ions. The values of spin-Hamiltonian parameters indicate that the VO2+ ions in zinc lead borate glasses were present in octahedral sites with tetragonal compression and belong to C4V symmetry. The spin-Hamiltonian parameters g and A are found to be independent of V2O5 content and temperature but changing with ZnO content. The decrease in Deltag( parallel)/Deltag( perpendicular) value with increase in ZnO content indicates that the symmetry around VO2+ ions is more octahedral. The decrease in intensity of EPR signal above 10 mol% of V2O5 is attributed to a fall in the ratio of the number of V4+ ions (N4) to the number of V5+ ions (N5). The number of spins (N) participating in resonance was calculated as a function of temperature for VO2+ doped zinc lead borate glass sample and the activation energy was calculated. From the EPR data, the paramagnetic susceptibility was calculated at various temperatures and the Curie constant was evaluated from the 1/chi-T graph. The optical absorption spectra show single absorption band due to VO2+ ions in tetragonally distorted octahedral sites. PMID:16043053

  9. Persistent ion beam induced conductivity in zinc oxide nanowires

    SciTech Connect

    Johannes, Andreas; Niepelt, Raphael; Gnauck, Martin; Ronning, Carsten

    2011-12-19

    We report persistently increased conduction in ZnO nanowires irradiated by ion beam with various ion energies and species. This effect is shown to be related to the already known persistent photo conduction in ZnO and dubbed persistent ion beam induced conduction. Both effects show similar excitation efficiency, decay rates, and chemical sensitivity. Persistent ion beam induced conduction will potentially allow countable (i.e., single dopant) implantation in ZnO nanostructures and other materials showing persistent photo conduction.

  10. Effect of Magnesium Ion on the Zinc Electrodeposition from Acidic Sulfate Electrolyte

    NASA Astrophysics Data System (ADS)

    Tian, Lin; Xie, Gang; Yu, Xiao-Hua; Li, Rong-Xing; Zeng, Gui-Sheng

    2012-02-01

    The effects of Mg2+ ion on the zinc electrodeposition were systematically investigated in sulfuric acid solution through the characterizations of current efficiency (CE), power consumption (PC), deposit morphology, cathodic polarization, and cyclic voltammetry. The results demonstrate that there is no significant influence on CE and PC in the Mg2+ concentration range of 1 to 10 g L-1, but with a drastic decrease of the CE and rapid increase of PC at Mg2+ ion concentration above 15 g L-1. Based on the morphology observation and polarization curves, the presence of Mg2+ ions could also induce the coarse surface on the electrodeposited zinc accompanying the enhancement of the cathodic polarization, which becomes more distinct at a high concentration above 15 g L-1. Furthermore, hydrogen evolution could be promoted with the existence of Mg2+ ions according to cyclic voltammograms.

  11. Functionalized Fe3O4 nanoparticles for detecting zinc ions in living cells and their cytotoxicity.

    PubMed

    Kang, Gyusik; Son, Hyunjong; Lim, Jung Mi; Kweon, Hee-Seek; Lee, In Soo; Kang, Dongmin; Jung, Jong Hwa

    2012-05-01

    The zinc tank: A new fluoro-chromogenic chemosensor based on BODIPY-functionalized Fe(3)O(4) nanoparticles (1) has been prepared. Chemoprobe 1 exhibits high selectivity for Zn(2+) over other competing metal ions tested. Moreover, confocal microscopy experiments established that 1 can be used for detecting Zn(2+) levels in living cells (see figure). PMID:22517629

  12. Synthesis and application of ion-imprinted polymer nanoparticles for the extraction and preconcentration of zinc ions.

    PubMed

    Roushani, Mahmoud; Abbasi, Shahryar; Khani, Hossein; Sahraei, Reza

    2015-04-15

    A new Zinc (II) ion-imprinted polymer (IIPs) nanoparticles was synthesised for the separation and recovery of trace Zn (II) ion from food and water sample. Zn (II) IIP was prepared by copolymerisation of methyl methacrylate (monomer) and ethylene glycol dimethacrylate (cross-linker) in the presence of Zn (II)-N,N'-o-phenylene bis (salicylideneimine) ternary complex wherein Zn (II) ion is the imprint ion and is used to form the imprinted polymer. Moreover, control polymer (NIP) particles were similarly prepared without the zinc (II) ions. The unleached and leached IIP particles were characterised by X-ray diffraction, Fourier transform infra-red spectroscopy and scanning electron microscopy. The preconcentration of Zn(2+) from aqueous solution was studied during rebinding with the leached IIP particles as a function of pH, the weight of the polymer material, the uptake and desorption times, the aqueous phase and the desorption volumes. Flame atomic absorption spectrometry was employed for determination of zinc in aqueous solution. PMID:25466022

  13. In vitro prominent bone regeneration by release zinc ion from Zn-modified implant

    SciTech Connect

    Yusa, Kazuyuki; Yamamoto, Osamu; Fukuda, Masayuki; Koyota, Souichi; Koizumi, Yukio; Sugiyama, Toshihiro

    2011-08-26

    Highlights: {yields} We isolated the Zn{sup 2+} ions (eluted Zn{sup 2+} ion; EZ) from zinc-incorporated titanium implant. {yields} The EZ promoted the cell viability in hBMCs. {yields} The EZ stimulated preosteoblast and osteoblast marker gene expression in hBMCs. {yields} The hBMCs supplemented with EZ showed typically cell morphology when osteoblast maturing. {yields} It is revealed that the EZ also stimulates the calcium deposition of hBMCs. -- Abstract: Zinc is one of the trace elements which induce the proliferation and the differentiation of the osteoblast. In the previous study, we found that zinc ions (Zn{sup 2+} ion)-releasing titanium implants had excellent bone fixation using a rabbit femurs model. In this study, we isolated the Zn{sup 2+} ions (eluted Zn{sup 2+} ion; EZ) released from the implant surface, and evaluated the effect of EZ on the osteogenesis of human bone marrow-derived mesenchymal cells (hBMCs). In the result, it was found that the EZ stimulated cell viability, osteoblast marker gene (type I collagen, osteocalcin (OC), alkaline phosphatase (ALP) and bone sialoprotein (BSP)) expressions and calcium deposition in hBMCs.

  14. Redox and zinc signalling pathways converging on protein tyrosine phosphatases.

    PubMed

    Bellomo, Elisa; Hogstrand, Christer; Maret, Wolfgang

    2014-10-01

    Zinc ions, though redox-inert, have either pro-antioxidant or pro-oxidant functions at critical junctures in redox metabolism and redox signalling. They are released from cells and in cells, e.g. from metallothionein, a protein that transduces redox signals into zinc signals (1). The released zinc ions inhibit enzymes such as protein tyrosine phosphatases (PTPs), key regulatory enzymes of cellular phosphorylation signalling. The Ki(Zn) value for inhibition of receptor PTPB is 21pM (2). The binding is about as tight as the binding of zinc to zinc metalloenzymes and suggests tonic zinc inhibition. PTP1-B (PTPN1), an enzyme regulating the insulin and leptin receptors and involved in cancer and diabetes pathobiochemistry, has a Ki(Zn) value of about 5nM (3). Zinc ions bind to the enzyme in the closed conformation when additional metal-binding ligands are brought into the vicinity of the active site. In contrast, redox reactions target cysteines in the active sites of PTPs in the open conformation. This work provides a molecular basis how hydrogen peroxide and free zinc ions generated by growth factor signalling stimulate phosphorylation signalling differentially. (Supported by the Biotechnology and Biological Sciences Research Council UK, grant BB/K001442/1.). PMID:26461422

  15. Laser Raman spectroscopy study of the zinc and bromide ion complex equilibrium in zinc/bromine battery electrolytes. [2M ZnBr/sub 2/ and 1M KBr solution

    SciTech Connect

    Grimes, P.G.; Larrabee, J.A.

    1985-01-01

    Laser Raman spectroscopy was used to study the zinc and bromide ion complex equilibrium in zinc bromine battery model electrolytes. Solutions of zinc bromide with added KBr, HBr and N-methyl, N-ethyl morpholinium (MEM) bromide were examined and compared. Solutions studied ranged from 1 to 3 molar in zinc and from 2.5 to 8 molar in bromide. A typical Raman spectrum of a zinc bromide solution is shown in Figure 1. Each of the zinc species is identified, Zn/sup + +/ (aq), ZnBr/sup +/, ZnBr/sub 2/ (aq), ZnBr/sub 3//sup -/ and ZnBr/sub 4//sup 2 -/. By the use of peak heights or deconvolution/integration along with published Raman cross sections, the amount of each zinc species could be quantitatively determined. The addition of bromide ions to the zinc bromide solutions will shift the equilibrium toward higher bromide complexes. The added cations will influence the shifts. It has been noted that the conductivity of the electrolyte decreases when the quaternary ammonium ions are present compared to cations such as potassium or hydrogen. Significantly more free zinc is present in zinc bromide solutions with added KBr than with either MEMBr or HBr. Shifts are also noted with the other zinc ion containing species. It appears that the quaternary ammonium ions and possibly the pH could have a stabilizing effect on zinc bromide complex ion formation. 2 figs.

  16. [Zinc].

    PubMed

    Couinaud, C

    1984-10-01

    Zinc is indispensable for life from bacteria to man. As a trace element it is included in numerous enzymes or serves as their activator (more than 80 zinc metallo-enzymes). It is necessary for nucleic acid and protein synthesis, the formation of sulphated molecules (insulin, growth hormone, keratin, immunoglobulins), and the functioning of carbonic anhydrase, aldolases, many dehydrogenases (including alcohol-dehydrogenase, retinal reductase indispensable for retinal rod function), alkaline phosphatase, T cells and superoxide dismutase. Its lack provokes distinctive signs: anorexia, diarrhea, taste, smell and vision disorders, skin lesions, delayed healing, growth retardation, delayed appearance of sexual characteristics, diminished resistance to infection, and it may be the cause of congenital malformations. Assay is now simplified by atomic absorption spectrophotometry in blood or hair. There is a latent lack prior to any disease because of the vices of modern eating habits, and this increases during stress, infections or tissue healing processes. Its lack is accentuated during long-term parenteral feeding or chronic gastrointestinal affections. Correction is as simple as it is innocuous, and zinc supplements should be given more routinely during surgical procedures. PMID:6210294

  17. Free zinc ion and dissolved orthophosphate effects on phytoplankton from Coeur d'Alene Lake, Idaho.

    PubMed

    Kuwabara, James S; Topping, Brent R; Woods, Paul F; Carter, James L

    2007-04-15

    Coeur d'Alene Lake in northern Idaho is fed by two major rivers: the Coeur d'Alene River from the east and the St. Joe River from the south, with the Spokane River as its outlet to the north. This phosphorus-limited lake has been subjected to decades of mining (primarily for zinc and silver) and other anthropogenic inputs. A 32 full-factorial experimental design was used to examine the interactive effects of free (uncomplexed) zinc ion and dissolved-orthophosphate concentrations on phytoplankton that were isolated from two sites along a longitudinal zinc-concentration gradient in Coeur d'Alene Lake. The two sites displayed different dominanttaxa. Chlorella minutissima, a dominant species near the southern St. Joe River inlet, exhibited greater sensitivity to free Zn ions than Asterionella formosa, collected nearer the Coeur d'Alene River mouth with elevated dissolved-zinc concentrations. Empirical phytoplankton-response models were generated to describe phytoplankton growth in response to remediation strategies in the surrounding watershed. If dissolved Zn can be reduced in the water column from >500 nM (i.e., current concentrations near and down stream of the Coeur d'Alene River plume) to <3 nM (i.e., concentrations near the southern St. Joe River inlet) such that the lake is truly phosphorus limited, management of phosphorus inputs by surrounding communities will ultimately determine the limnologic state of the lake. PMID:17533843

  18. Free zinc ion and dissolved orthophosphate effects on phytoplankton from Coeur d'Alene Lake, Idaho

    USGS Publications Warehouse

    Kuwabara, J.S.; Topping, B.R.; Woods, P.F.; Carter, J.L.

    2007-01-01

    Coeur d'Alene Lake in northern Idaho is fed by two major rivers: the Coeur d'Alene River from the east and the St. Joe River from the south, with the Spokane River as its outlet to the north. This phosphorus-limited lake has been subjected to decades of mining (primarily for zinc and silver) and other anthropogenic inputs. A 32 full-factorial experimental design was used to examine the interactive effects of free (uncomplexed) zinc ion and dissolved-orthophosphate concentrations on phytoplankton that were isolated from two sites along a longitudinal zinc-concentration gradient in Coeur d'Alene Lake. The two sites displayed different dominant taxa. Chlorella minutissima, a dominant species near the southern St. Joe River inlet, exhibited greater sensitivity to free Zn ions than Asterionella formosa, collected nearer the Coeur d'Alene River mouth with elevated dissolved-zinc concentrations. Empirical phytoplankton-response models were generated to describe phytoplankton growth in response to remediation strategies in the surrounding watershed. If dissolved Zn can be reduced in the water column from >500 nM (i.e., current concentrations near and down stream of the Coeur d'Alene River plume) to <3 nM (i.e., concentrations near the southern St. Joe River inlet) such that the lake is truly phosphorus limited, management of phosphorus inputs by surrounding communities will ultimately determine the limnologic state of the lake.

  19. Aqueous Rechargeable Zinc/Aluminum Ion Battery with Good Cycling Performance.

    PubMed

    Wang, Faxing; Yu, Feng; Wang, Xiaowei; Chang, Zheng; Fu, Lijun; Zhu, Yusong; Wen, Zubiao; Wu, Yuping; Huang, Wei

    2016-04-13

    Developing rechargeable batteries with low cost is critically needed for the application in large-scale stationary energy storage systems. Here, an aqueous rechargeable zinc//aluminum ion battery is reported on the basis of zinc as the negative electrode and ultrathin graphite nanosheets as the positive electrode in an aqueous Al2(SO4)3/Zn(CHCOO)2 electrolyte. The positive electrode material was prepared through a simple electrochemically expanded method in aqueous solution. The cost for the aqueous electrolyte together with the Zn negative electrode is low, and their raw materials are abundant. The average working voltage of this aqueous rechargeable battery is 1.0 V, which is higher than those of most rechargeable Al ion batteries in an ionic liquid electrolyte. It could also be rapidly charged within 2 min while maintaining a high capacity. Moreover, its cycling behavior is also very good, with capacity retention of nearly 94% after 200 cycles. PMID:26716878

  20. Improved corrosion resistance on biodegradable magnesium by zinc and aluminum ion implantation

    NASA Astrophysics Data System (ADS)

    Xu, Ruizhen; Yang, Xiongbo; Suen, Kai Wong; Wu, Guosong; Li, Penghui; Chu, Paul K.

    2012-12-01

    Magnesium and its alloys have promising applications as biodegradable materials, and plasma ion implantation can enhance the corrosion resistance by modifying the surface composition. In this study, suitable amounts of zinc and aluminum are plasma-implanted into pure magnesium. The surface composition, phases, and chemical states are determined, and electrochemical tests and electrochemical impedance spectroscopy (EIS) are conducted to investigate the surface corrosion behavior and elucidate the mechanism. The corrosion resistance enhancement after ion implantation is believed to stem from the more compact oxide film composed of magnesium oxide and aluminum oxide as well as the appearance of the β-Mg17Al12 phase.

  1. Surface nanostructuring by ion-induced localized plasma expansion in zinc oxide

    SciTech Connect

    El-Said, A. S. E-mail: a.s.el-said@hzdr.de; Moslem, W. M.; Djebli, M.

    2014-06-09

    Creation of hillock-like nanostructures on the surface of zinc oxide single crystals by irradiation with slow highly charged ions is reported. At constant kinetic energy, the nanostructures were only observed after irradiation with ions of potential energies above a threshold between 19.1 keV and 23.3 keV. The size of the nanostructures increases as a function of potential energy. A plasma expansion approach is used to explain the nanostructures creation. The calculations showed that the surface nanostructures became taller with the increase of ionic temperature. The influence of charged cluster formation and the relevance of their polarity are discussed.

  2. In situ analyses on negative ions in the indium-gallium-zinc oxide sputtering process

    SciTech Connect

    Jia, Junjun; Torigoshi, Yoshifumi; Shigesato, Yuzo

    2013-07-01

    The origin of negative ions in the dc magnetron sputtering process using a ceramic indium-gallium-zinc oxide target has been investigated by in situ analyses. The observed negative ions are mainly O{sup -} with energies corresponding to the target voltage, which originates from the target and barely from the reactive gas (O{sub 2}). Dissociation of ZnO{sup -}, GaO{sup -}, ZnO{sub 2}{sup -}, and GaO{sub 2}{sup -} radicals also contributes to the total negative ion flux. Furthermore, we find that some sputtering parameters, such as the type of sputtering gas (Ar or Kr), sputtering power, total gas pressure, and magnetic field strength at the target surface, can be used to control the energy distribution of the O{sup -} ion flux.

  3. Effect of Swift Heavy Ion Irradiation on Lithium Zinc Silicate Glasses: A Photoluminescence Study

    SciTech Connect

    Jogad, M. S.; Jogad, R. M.; Sudarsan, V.; Krishna, P. S. R.; Kothiyal, G. P.

    2011-07-15

    Lithium zinc silicate glasses with and without copper were prepared by melt-quench method and their luminescence characteristics after swift heavy ion irradiation has been investigated. Based on these studies it is established that both these glasses contain colour centres and the luminescence from such centres get significantly quenched once these samples get irradiated with 100 MeV swift heavy Ag{sup +} ions with a fluence of 10{sup 13} ions/cm{sup 2} at room temperature. Trapping of the charge carriers by the increased defect concentration brought about by irradiation is responsible for the decrease in the luminescence intensity from the irradiated samples. Copper in these glasses mainly exists as Cu{sup +} ions as revealed by the broad emission around 500 nm.

  4. p type doping of zinc oxide by arsenic ion implantation

    SciTech Connect

    Braunstein, G.; Muraviev, A.; Saxena, H.; Dhere, N.; Richter, V.; Kalish, R.

    2005-11-07

    p type doping of polycrystalline ZnO thin films, by implantation of arsenic ions, is demonstrated. The approach consisted of carrying out the implantations at liquid-nitrogen temperature ({approx}-196 deg. C), followed by a rapid in situ heating of the sample, at 560 deg. C for 10 min, and ex situ annealing at 900 deg. C for 45 min in flowing oxygen. p type conductivity with a hole concentration of 2.5x10{sup 13} cm{sup -2} was obtained using this approach, following implantation of 150 keV 5x10{sup 14} As/cm{sup 2}. A conventional room-temperature implantation of 1x10{sup 15} As/cm{sup 2}, followed by the same ex situ annealing, resulted in n type conductivity with a carrier concentration of 1.7x10{sup 12} cm{sup -2}.

  5. Spectroscopic investigation of zinc tellurite glasses doped with Yb(3+) and Er(3+) ions.

    PubMed

    Bilir, Gökhan; Kaya, Ayfer; Cinkaya, Hatun; Eryürek, Gönül

    2016-08-01

    This paper presents a detailed spectroscopic investigation of zinc tellurite glasses with the compositions (0.80-x-y) TeO2+(0.20) ZnO+xEr2O3+yYb2O3 (x=0, y=0; x=0.004, y=0; x=0, y=0.05 and x=0.004, y=0.05 per moles). The samples were synthesized by the conventional melt quenching method. The optical absorption and emission measurements were conducted at room temperature to determine the spectral properties of lanthanides doped zinc tellurite glasses and, to study the energy transfer processes between dopant lanthanide ions. The band gap energies for both direct and indirect possible transitions and the Urbach energies were measured from the absorption spectra. The absorption spectra of the samples were analyzed by using the Judd-Ofelt approach. The effect of the ytterbium ions on the emission properties of erbium ions was investigated and the energy transfer processes between dopant ions were studied by measuring the up-conversion emission properties of the materials. The color quality parameters of obtained visible up-conversion emission were also determined as well as possibility of using the Er(3+) glasses as erbium doped fiber amplifiers at 1.55μm in infrared emission region. PMID:27156100

  6. Spectroscopic investigation of zinc tellurite glasses doped with Yb3 + and Er3 + ions

    NASA Astrophysics Data System (ADS)

    Bilir, Gökhan; Kaya, Ayfer; Cinkaya, Hatun; Eryürek, Gönül

    2016-08-01

    This paper presents a detailed spectroscopic investigation of zinc tellurite glasses with the compositions (0.80 - x - y) TeO2 + (0.20) ZnO + xEr2O3 + yYb2O3 (x = 0, y = 0; x = 0.004, y = 0; x = 0, y = 0.05 and x = 0.004, y = 0.05 per moles). The samples were synthesized by the conventional melt quenching method. The optical absorption and emission measurements were conducted at room temperature to determine the spectral properties of lanthanides doped zinc tellurite glasses and, to study the energy transfer processes between dopant lanthanide ions. The band gap energies for both direct and indirect possible transitions and the Urbach energies were measured from the absorption spectra. The absorption spectra of the samples were analyzed by using the Judd-Ofelt approach. The effect of the ytterbium ions on the emission properties of erbium ions was investigated and the energy transfer processes between dopant ions were studied by measuring the up-conversion emission properties of the materials. The color quality parameters of obtained visible up-conversion emission were also determined as well as possibility of using the Er3 + glasses as erbium doped fiber amplifiers at 1.55 μm in infrared emission region.

  7. The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA-binding site

    SciTech Connect

    Min, Andrew B; Miallau, Linda; Sawaya, Michael R; Habel, Jeff; Cascio, Duilio; Eisenberg, David

    2013-01-10

    VapBC pairs account for 45 out of 88 identified toxin-antitoxin (TA) pairs in the Mycobacterium tuberculosis (Mtb) H37Rv genome. A working model suggests that under times of stress, antitoxin molecules are degraded, releasing the toxins to slow the metabolism of the cell, which in the case of VapC toxins is via their RNase activity. Otherwise the TA pairs remain bound to their promoters, autoinhibiting transcription. The crystal structure of Rv0301-Rv0300, an Mtb VapBC TA complex determined at 1.49 Å resolution, suggests a mechanism for these three functions: RNase activity, its inhibition by antitoxin, and its ability to bind promoter DNA. The Rv0301 toxin consists of a core of five parallel beta strands flanked by alpha helices. Three proximal aspartates coordinate a Mg2+ ion forming the putative RNase active site. The Rv0300 antitoxin monomer is extended in structure, consisting of an N-terminal beta strand followed by four helices. The last two helices wrap around the toxin and terminate near the putative RNase active site, but with different conformations. In one conformation, the C-terminal arginine interferes with Mg2+ ion coordination, suggesting a mechanism by which the antitoxin can inhibit toxin activity. At the N-terminus of the antitoxin, two pairs of Ribbon-Helix-Helix (RHH) motifs are related by crystallographic twofold symmetry. The resulting hetero-octameric complex is similar to the FitAB system, but the two RHH motifs are about 30 Å closer together in the Rv0301-Rv0300 complex, suggesting either a different span of the DNA recognition sequence or a conformational change.

  8. The chemical properties and functional role of a lysine residue within the active site of native sodium and potassium ion-activated adenosinetriphosphatase

    SciTech Connect

    Xu, K.Y.

    1988-01-01

    The peptide, HLLVMKGAPER, which contains Lysine 501 of the {alpha} polypeptide can be released from intact sodium and potassium ion activated adenosinetriphosphatase by tryptic digestion. An immunoadsorbent directed against the carboxy-terminal, -GAPER, has been constructed. Sealed, right-side-out vesicles, prepared from canine renal kidneys, were labeled with pyridoxal phosphate and sodium ({sup 3}H)borohydride in the absence or presence of saponin, respectively. Large increases in the incorporation of radioactivity into the peptides bound by the immunoadsorbent were observed in the digest obtained from the vesicles exposed to saponin. From the results of several control experiments examining the labeling reaction it could be concluded that the increase in the extent of modification was due to the cytoplasmic disposition of this segment in the native enzyme.

  9. Development of near-infrared fluorescent probes for nitric oxide and zinc ion

    NASA Astrophysics Data System (ADS)

    Kojima, Hirotatsu; Kiyose, Kazuki; Sasaki, Eita; Nishimatsu, Hiroaki; Hirata, Yasunobu; Nagano, Tetsuo

    2007-02-01

    In fluorescence imaging studies of biological mechanisms, cyanine dyes have been employed as fluorescent labels. In particular, tricarbocyanines have the advantage that light at their emission and absorption maxima in the near-infrared (NIR) region around 650-900 nm can penetrate deeply into tissues. We successfully developed two types of cyanine dyes whose fluorescence properties change upon specific reaction with nitric oxide (NO) or zinc ion. The mechanism of fluorescence modulation of the NO probes involves photoinduced electron transfer, and the fluorescent intensity can change at the same wavelengths. We synthesized a series of amine-substituted tricarbocyanines in order to examine the correlation between the electron-donating ability of the amine and the fluorescence peak wavelength. We found that changing the electron-donating ability of the amine substituent altered the absorption and emission wavelengths. Then, we synthesized dipicolylcyanine (DIPCY), consisting of tricarbocyanine as a fluorophore and dipicolylethylenediamine as a heavy metal chelator, and investigated its response to various heavy metal ions. DIPCY can work as a ratiometric fluorescent sensor for zinc ion. This fluorescence modulation of amine-substituted tricarbocyanines should be applicable to dual-wavelength measurement of various biomolecules or enzyme activities. Thus, we have established two mechanisms for modulating the fluorescence properties of cyanines.

  10. Selective zinc ion detection by functionalised ZnO nanorods with ionophore

    NASA Astrophysics Data System (ADS)

    Ibupoto, Z. H.; Usman Ali, Syed M.; Chey, C. O.; Khun, K.; Nur, O.; Willander, Magnus

    2011-11-01

    In this paper, highly dense and well aligned single-crystal zinc oxide nanorods were grown along the c-axis on a gold coated glass substrate using a low temperature aqueous chemical growth approach. The prepared ZnO nanorods were functionalized with plastic membrane coatings containing specific ionophore (12-crown-4) which is highly selective to zinc ions (Zn+2). The electrochemical response of the sensor was found to be linear over a relatively wide logarithmic concentration range from 1 μM to 100 mM. The proposed sensor showed a good linearity with a high sensitivity of ˜35 mV/decade for sensing Zn+2 ions. A fast response time of less than 5 s with a good selectivity, repeatability, reproducibility, and negligible response to common interferents ions such as calcium (Ca2+), magnesium (Mg2+), or potassium (K+), and iron (Fe+3) and copper (Cu+2) was also demonstrated. Moreover, the proposed sensor showed good stoichiometric results for potentiometric titration.

  11. Ion Microbeam Studies of Cadmium Zinc Telluride Radiation Detectors by IBICC

    SciTech Connect

    Brunett, B.A.; Doyle, B.L.; James, R.B.; Olsen, R.W.; Vizkelethy, G.; Walsh, D.S.

    1998-10-26

    Ion Beam Induced Charge Collection (IBICC) and Time Resolved IBICC (TRIBICC) techniques were e for imaging electronic properties of Cadmium Zinc Telluride (CZT) room temperature radiation detectors. The detectors were bombarded with a scanned 5.4 MeV He microbeam and the detector response was analyzed at each point. The electron mobility (A) and Metime (z.), and charge collection efficiency maps were calculated from the data. In order to determine the radiation damage to the detectors, the signal deteriomtion was measured as the function of dose.

  12. Measurement of valence band structure in boron-zinc-oxide films by making use of ion beams

    SciTech Connect

    Uhm, Han S.; Kwon, Gi C.; Choi, Eun H.

    2011-12-26

    Measurement of valence band structure in the boron-zinc oxide (BZO) films was developed using the secondary electron emission due to the Auger neutralization of ions. The energy distribution profile of the electrons emitted from boron-zinc-oxide films was measured and rescaled so that Auger self-convolution arose; thus, revealing the detailed structure of the valence band and suggesting that a high concentration of boron impurity in BZO films may enhance the transition of electrons and holes through the band gap from the valence to the conduction band in zinc oxide crystals; thereby improving the conductivity of the film.

  13. Luminescent zinc metal-organic framework (ZIF-90) for sensing metal ions, anions and small molecules.

    PubMed

    Liu, Chang; Yan, Bing

    2015-09-26

    We synthesize a zinc zeolite-type metal-organic framework, the zeolitic imidazolate framework (ZIF-90), which exhibits an intense blue luminescence excited under visible light. Luminescent studies indicate that ZIF-90 could be an efficient multifunctional fluorescence material for high sensitivity metal ions, anions and organic small molecules, especially for Cd(2+), Cu(2+), CrO4(2-) and acetone. The luminescence intensity of ZIF-90 increases with the concentration of Cd(2+) and decreases proportionally with the concentration of Cu(2+), while the same quenched experimental phenomena appear in the sensing of CrO4(2-). With the increase of the amount of acetone, the luminescence intensity decreases gradually in the emulsions of ZIF-90. The mechanism of the sensing properties is studied in detail as well. This study shows that ZIF-90 could be a useful luminescent sensor for metal ions, anions and organic small molecules. PMID:26123790

  14. Fluorescence Sensing of Zinc and Mercury Ions with Hydrophilic 1,2,3-Triazolyl Fluorene Probes

    PubMed Central

    Nguyen, Dao M.; Frazer, Andrew; Rodriguez, Luis

    2010-01-01

    The ability to rapidly detect biologically and environmentally significant metal ions such as zinc and mercury is important to study a number of important cellular and environmental processes. Hydrophilic bis(1,2,3-triazolyl)fluorene-based derivatives, containing a 1,2,3-triazole-based recognition moiety, were synthesized through Click chemistry and characterized by UV-vis absorption, fluorescence emission, and two-photon absorption as new fluorescence sensing probes, selective for Zn2+ and Hg2+ ions. The UV-vis absorption and fluorescence emission spectra of the complexes exhibited blue-shifted absorption and emission spectra upon chelation to Zn2+ and Hg2+ ions, resulting in ca. two-fold enhancement in fluorescence. Fluorometric titration revealed that 1:2 and 1:3 ligand to metal complexes formed with binding constants of 108 and 1016 for Zn2+ and Hg2+, respectively. The two-photon absorption cross sections for the probes and probe-metal ion complexes ranged from 200-350 GM at 800 nm. These novel fluorescent compounds may have potential as new metal ion sensors to probe cellular and biological environments. PMID:20577581

  15. Optical studies of Sm³⁺ ions doped zinc alumino bismuth borate glasses.

    PubMed

    Swapna, K; Mahamuda, Sk; Srinivasa Rao, A; Shakya, S; Sasikala, T; Haranath, D; Vijaya Prakash, G

    2014-05-01

    Zinc Alumino Bismuth Borate (ZnAlBiB) glasses doped with different concentrations of samarium (Sm(3+)) ions were prepared by using melt quenching technique and characterized for their lasing potentialities in visible region by using the techniques such as optical absorption, emission and emission decay measurements. Radiative properties for various fluorescent levels of Sm(3+) ions were estimated from absorption spectral information using Judd-Ofelt (JO) analysis. The emission spectra and con-focal photoluminescence images obtained by 410 nm laser excitation demonstrates very distinct and intense orange-red emission for all the doped glasses. The suitable concentration of Sm(3+) ions in these glasses to act as an efficient lasing material has been discussed by measuring the emission cross-section and branching ratios for the emission transitions. The quantum efficiencies were also been estimated from emission decay measurements recorded for the (4)G5/2 level of Sm(3+) ions. From the measured emission cross-sections, branching ratios, strong photoluminescence features and CIE chromaticity coordinates, it was found that 1 mol% of Sm(3+) ions doped ZnAlBiB glasses are most suitable for the development of visible orange-red lasers. PMID:24530709

  16. Optical studies of Sm3+ ions doped Zinc Alumino Bismuth Borate glasses

    NASA Astrophysics Data System (ADS)

    Swapna, K.; Mahamuda, Sk.; Srinivasa Rao, A.; Shakya, S.; Sasikala, T.; Haranath, D.; Vijaya Prakash, G.

    Zinc Alumino Bismuth Borate (ZnAlBiB) glasses doped with different concentrations of samarium (Sm3+) ions were prepared by using melt quenching technique and characterized for their lasing potentialities in visible region by using the techniques such as optical absorption, emission and emission decay measurements. Radiative properties for various fluorescent levels of Sm3+ ions were estimated from absorption spectral information using Judd-Ofelt (JO) analysis. The emission spectra and con-focal photoluminescence images obtained by 410 nm laser excitation demonstrates very distinct and intense orange-red emission for all the doped glasses. The suitable concentration of Sm3+ ions in these glasses to act as an efficient lasing material has been discussed by measuring the emission cross-section and branching ratios for the emission transitions. The quantum efficiencies were also been estimated from emission decay measurements recorded for the 4G5/2 level of Sm3+ ions. From the measured emission cross-sections, branching ratios, strong photoluminescence features and CIE chromaticity coordinates, it was found that 1 mol% of Sm3+ ions doped ZnAlBiB glasses are most suitable for the development of visible orange-red lasers.

  17. Pure zinc sulfide quantum dot as highly selective luminescent probe for determination of hazardous cyanide ion.

    PubMed

    Shamsipur, Mojtaba; Rajabi, Hamid Reza

    2014-03-01

    A rapid and simple fluorescence method is presented for selective and sensitive determination of hazardous cyanide ion in aqueous solution based on functionalized zinc sulfide (ZnS) quantum dot (QD) as luminescent prob. The ultra-small ZnS QDs were synthesized using a chemical co-precipitation method in the presence of 2-mercaptoethanol (ME) as an efficient capping agent. The prepared pure ZnS QDs was applied as an optical sensor for determination of cyanide ions in aqueous solutions. ZnS nanoparticles have exhibited a strong fluorescent emission at about 424 nm. The fluorescence intensity of QDs is linearly proportional to the cyanide ion concentration in the range 2.44×10(-6) to 2.59×10(-5)M with a detection limit of 1.70×10(-7)M at pH11. The designed fluorescent sensor possesses remarkable selectivity for cyanide ion over other anions such as Cl(-), Br(-), F(-), I(-), IO3(-), ClO4(-), BrO3(-), CO3(2-), NO2(-), NO3(-), SO4(2-), S2O4(2-), C2O4(2-), SCN(-), N3(-), citrate and tartarate with negligible influences on the cyanide detection by fluorescence spectroscopy. PMID:24433896

  18. QM/MM X-ray Refinement of Zinc Metalloenzymes

    PubMed Central

    Li, Xue; Hayik, Seth A.; Merz, Kenneth M.

    2010-01-01

    Zinc metalloenzymes play an important role in biology. However, due to the limitation of molecular force field energy restraints used in X-ray refinement at medium or low resolutions, the precise geometry of the zinc coordination environment can be difficult to distinguish from ambiguous electron density maps. Due to the difficulties involved in defining accurate force fields for metal ions, the QM/MM (Quantum-Mechanical /Molecular-Mechanical) method provides an attractive and more general alternative for the study and refinement of metalloprotein active sites. Herein we present three examples that indicate that QM/MM based refinement yields a superior description of the crystal structure based on R and Rfree values and on the inspection of the zinc coordination environment. It is concluded that QM/MM refinement is a useful general tool for the improvement of the metal coordination sphere in metalloenzyme active sites. PMID:20116858

  19. Bioabsorbable zinc ion induced biphasic cellular responses in vascular smooth muscle cells

    PubMed Central

    Ma, Jun; Zhao, Nan; Zhu, Donghui

    2016-01-01

    Bioabsorbable metal zinc (Zn) is a promising new generation of implantable scaffold for cardiovascular and orthopedic applications. In cardiovascular stent applications, zinc ion (Zn2+) will be gradually released into the surrounding vascular tissues from such Zn-containing scaffolds after implantation. However, the interactions between vascular cells and Zn2+ are still largely unknown. We explored the short-term effects of extracellular Zn2+ on human smooth muscle cells (SMCs) up to 24 h, and an interesting biphasic effect of Zn2+ was observed. Lower concentrations (<80 μM) of Zn2+ had no adverse effects on cell viability but promoted cell adhesion, cell spreading, cell proliferation, cell migration, and enhanced the expression of F-actin and vinculin. Cells treated with such lower concentrations of Zn2+ displayed an elongated shape compared to controls without any treatment. In contrast, cells treated with higher Zn2+ concentrations (80–120 μM) had opposite cellular responses and behaviors. Gene expression profiles revealed that the most affected functional genes were related to angiogenesis, inflammation, cell adhesion, vessel tone, and platelet aggregation. Results indicated that Zn has interesting concentration-dependent biphasic effects on SMCs with low concentrations being beneficial to cellular functions. PMID:27248371

  20. Bioabsorbable zinc ion induced biphasic cellular responses in vascular smooth muscle cells.

    PubMed

    Ma, Jun; Zhao, Nan; Zhu, Donghui

    2016-01-01

    Bioabsorbable metal zinc (Zn) is a promising new generation of implantable scaffold for cardiovascular and orthopedic applications. In cardiovascular stent applications, zinc ion (Zn(2+)) will be gradually released into the surrounding vascular tissues from such Zn-containing scaffolds after implantation. However, the interactions between vascular cells and Zn(2+) are still largely unknown. We explored the short-term effects of extracellular Zn(2+) on human smooth muscle cells (SMCs) up to 24 h, and an interesting biphasic effect of Zn(2+) was observed. Lower concentrations (<80 μM) of Zn(2+) had no adverse effects on cell viability but promoted cell adhesion, cell spreading, cell proliferation, cell migration, and enhanced the expression of F-actin and vinculin. Cells treated with such lower concentrations of Zn(2+) displayed an elongated shape compared to controls without any treatment. In contrast, cells treated with higher Zn(2+) concentrations (80-120 μM) had opposite cellular responses and behaviors. Gene expression profiles revealed that the most affected functional genes were related to angiogenesis, inflammation, cell adhesion, vessel tone, and platelet aggregation. Results indicated that Zn has interesting concentration-dependent biphasic effects on SMCs with low concentrations being beneficial to cellular functions. PMID:27248371

  1. 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

  2. Zinc-ion implanted and deposited titanium surfaces reduce adhesion of Streptococccus mutans

    NASA Astrophysics Data System (ADS)

    Xu, Juan; Ding, Gang; Li, Jinlu; Yang, Shenhui; Fang, Bisong; Sun, Hongchen; Zhou, Yanmin

    2010-10-01

    While titanium (Ti) is a commonly used dental implant material with advantageous biocompatible and mechanical properties, native Ti surfaces do not have the ability to prevent bacterial colonization. The objective of this study was to evaluate the chemical composition and bacterial adhesive properties of zinc (Zn) ion implanted and deposited Ti surfaces (Zn-PIIID-Ti) as potential dental implant materials. Surfaces of pure Ti (cp-Ti) were modified with increasing concentrations of Zn using plasma immersion ion implantation and deposition (PIIID), and elemental surface compositions were characterized by X-ray photoelectron spectrometry (XPS). To evaluate bacterial responses, Streptococcus mutans were seeded onto the modifiedTi surfaces for 48 h and subsequently observed by scanning electron microscopy. Relative numbers of bacteria on each surface were assessed by collecting the adhered bacteria, reculturing and counting colony forming units after 48 h on bacterial grade plates. Ti, oxygen and carbon elements were detected on all surfaces by XPS. Increased Zn signals were detected on Zn-PIIID-Ti surfaces, correlating with an increase of Zn-deposition time. Substantial numbers of S. mutans adhered to cp-Ti samples, whereas bacterial adhesion on Zn-PIIID-Ti surfaces signficantly decreased as the Zn concentration increased ( p < 0.01). In conclusion, PIIID can successfully introduce Zn onto a Ti surface, forming a modified surface layer bearing Zn ions that consequently deter adhesion of S. mutans, a common bacterium in the oral environment.

  3. A mitochondria-targeted ratiometric two-photon fluorescent probe for biological zinc ions detection.

    PubMed

    Ning, Peng; Jiang, Jiacheng; Li, Longchun; Wang, Shuxin; Yu, Haizhu; Feng, Yan; Zhu, Manzhou; Zhang, Buchang; Yin, Hang; Guo, Qingxiang; Meng, Xiangming

    2016-03-15

    A mitochondria-targeted ratiometric two-photon fluorescent probe (Mito-MPVQ) for biological zinc ions detection was developed based on quinolone platform. Mito-MPVQ showed large red shifts (68 nm) and selective ratiometric signal upon Zn(2+) binding. The ratio of emission intensity (I488 nm/I420 nm) increases dramatically from 0.45 to 3.79 (ca. 8-fold). NMR titration and theoretical calculation confirmed the binding of Mito-MPVQ and Zn(2+). Mito-MPVQ also exhibited large two-photon absorption cross sections (150 GM) at nearly 720 nm and insensitivity to pH within the biologically relevant pH range. Cell imaging indicated that Mito-MPVQ could efficiently located in mitochondria and monitor mitochondrial Zn(2+) under two-photon excitation with low cytotoxicity. PMID:26528806

  4. 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

  5. Zinc ion implantation-deposition technique improves the osteoblast biocompatibility of titanium surfaces

    PubMed Central

    LIANG, YONGQIANG; XU, JUAN; CHEN, JING; QI, MENGCHUN; XIE, XUEHONG; HU, MIN

    2015-01-01

    The plasma immersion ion implantation and deposition (PIIID) technique was used to implant zinc (Zn) ions into smooth surfaces of pure titanium (Ti) disks for investigation of tooth implant surface modification. The aim of the present study was to evaluate the surface structure and chemical composition of a modified Ti surface following Zn ion implantation and deposition and to examine the effect of such modification on osteoblast biocompatibility. Using the PIIID technique, Zn ions were deposited onto the smooth surface of pure Ti disks. The physical structure and chemical composition of the modified surface layers were characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS), respectively. In vitro culture assays using the MG-63 bone cell line were performed to determine the effects of Zn-modified Ti surfaces following PIIID on cellular function. Acridine orange staining was used to detect cell attachment to the surfaces and cell cycle analysis was performed using flow cytometry. SEM revealed a rough ‘honeycomb’ structure on the Zn-modified Ti surfaces following PIIID processing and XPS data indicated that Zn and oxygen concentrations in the modified Ti surfaces increased with PIIID processing time. SEM also revealed significantly greater MG-63 cell growth on Zn-modified Ti surfaces than on pure Ti surfaces (P<0.05). Flow cytometric analysis revealed increasing percentages of MG-63 cells in S phase with increasing Zn implantation and deposition, suggesting that MG-63 apoptosis was inhibited and MG-63 proliferation was promoted on Zn-PIIID-Ti surfaces. The present results suggest that modification with Zn-PIIID may be used to improve the osteoblast biocompatibility of Ti implant surfaces. PMID:25673139

  6. Zinc ion implantation‑deposition technique improves the osteoblast biocompatibility of titanium surfaces.

    PubMed

    Liang, Yongqiang; Xu, Juan; Chen, Jing; Qi, Mengchun; Xie, Xuehong; Hu, Min

    2015-06-01

    The plasma immersion ion implantation and deposition (PIIID) technique was used to implant zinc (Zn) ions into smooth surfaces of pure titanium (Ti) disks for investigation of tooth implant surface modification. The aim of the present study was to evaluate the surface structure and chemical composition of a modified Ti surface following Zn ion implantation and deposition and to examine the effect of such modification on osteoblast biocompatibility. Using the PIIID technique, Zn ions were deposited onto the smooth surface of pure Ti disks. The physical structure and chemical composition of the modified surface layers were characterized by scanning electron microscopy (SEM) and X‑ray photoelectron spectroscopy (XPS), respectively. In vitro culture assays using the MG‑63 bone cell line were performed to determine the effects of Zn‑modified Ti surfaces following PIIID on cellular function. Acridine orange staining was used to detect cell attachment to the surfaces and cell cycle analysis was performed using flow cytometry. SEM revealed a rough 'honeycomb' structure on the Zn‑modified Ti surfaces following PIIID processing and XPS data indicated that Zn and oxygen concentrations in the modified Ti surfaces increased with PIIID processing time. SEM also revealed significantly greater MG‑63 cell growth on Zn‑modified Ti surfaces than on pure Ti surfaces (P<0.05). Flow cytometric analysis revealed increasing percentages of MG‑63 cells in S phase with increasing Zn implantation and deposition, suggesting that MG‑63 apoptosis was inhibited and MG‑63 proliferation was promoted on Zn‑PIIID‑Ti surfaces. The present results suggest that modification with Zn‑PIIID may be used to improve the osteoblast biocompatibility of Ti implant surfaces. PMID:25673139

  7. 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.

  8. 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

  9. Preliminary evaluation of therapeutic ion release from Sr-doped zinc-silicate glass ceramics.

    PubMed

    Looney, Mark; O'Shea, Helen; Boyd, Daniel

    2013-01-01

    Bioactive and degradable porous bioceramics play an important role in many clinical situations. Porosity is essential to the performance of a material that is proposed to be used as an implantable osseous scaffold. Scaffolds provide a three dimensional support and template to osseous integration and vascularization. Combining the porosity of a scaffold with the ability of the scaffold material to deliver therapeutic ions to the site of implantation goes some way towards developing an ideal bone graft. A series of strontium-doped zinc silicate (Ca-Sr-Na-Zn-Si) glass ceramics scaffoldswere developed, whose porosity was measured to be between 93% and 96%, which is advantageous in terms of osseous integration and vascularization. The levels of Zn(2+) and Sr(2+) detected as a result of degradation of the crystalline phases were found to be 1.4-600 parts per million (ppm) and 0-583 ppm, respectively. The levels detected correlate well with the levels of Sr(2+) and Zn(2+)ions typically associated with clinical benefits, including antibacterial efficacy, osteoblastic differentiation and impaired osteoclastic resorption. PMID:21926151

  10. PTEN-inhibition by zinc ions augments interleukin-2-mediated Akt phosphorylation.

    PubMed

    Plum, Laura Marie; Brieger, Anne; Engelhardt, Gabriela; Hebel, Silke; Nessel, Andreas; Arlt, Marcus; Kaltenberg, Jennifer; Schwaneberg, Ulrich; Huber, Michael; Rink, Lothar; Haase, Hajo

    2014-07-01

    Free zinc ions (Zn(2+)) participate in several signaling pathways. The aim of the present study was to investigate a potential involvement of Zn(2+) in the PI3K/Akt pathway of interleukin (IL)-2 signaling in T-cells. The IL-2 receptor triggers three major pathways, ERK1/2, JAK/STAT5, and PI3K/Akt. We have previously shown that an IL-2-mediated release of lysosomal Zn(2+) into the cytoplasm activates ERK1/2, but not STAT5. In the present study, Akt phosphorylation in response to IL-2 was abrogated by the Zn(2+) chelator N,N,N',N'-tetrakis-2(pyridyl-methyl)ethylenediamine, and was induced by treatment with Zn(2+) and the ionophore pyrithione. The latter were ineffective in cells that were treated with siRNA against the phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a phosphatase that degrades the lipid second messenger PI(3,4,5)P3, which is produced by PI3K and leads to activation of Akt. Inhibition of recombinant PTEN by Zn(2+)in vitro yielded an IC50 of 0.59 nM. Considering a resting free cytoplasmic Zn(2+) level of 0.2 nM in the T-cell line CTLL-2, this seems ideally suited for dynamic regulation by cellular Zn(2+). Oxidation with H2O2 and supplementation with Zn(2+) led to similar changes in the CD spectrum of PTEN. Moreover, Zn(2+) partially prevented the oxidation of cysteines 71 and 124. Hence, we hypothesize that zinc signals affect the IL-2-dependent PI3K/Akt pathway by inhibiting the negative regulator PTEN through binding with a sub-nanomolar affinity to cysteine residues that are essential for its catalytic activity. PMID:24759986

  11. Structural Diversity Within the Mononuclear and Binuclear Active Sites of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase

    SciTech Connect

    Hall,R.; Brown, S.; Fedorov, A.; Fedorov, E.; Xu, C.; Babbitt, P.; Almo, S.; Raushel, F.

    2007-01-01

    NagA catalyzes the hydrolysis of N-acetyl-D-glucosamine-6-phosphate to D-glucosamine-6-phosphate and acetate. X-ray crystal structures of NagA from Escherichia coli were determined to establish the number and ligation scheme for the binding of zinc to the active site and to elucidate the molecular interactions between the protein and substrate. The three-dimensional structures of the apo-NagA, Zn-NagA, and the D273N mutant enzyme in the presence of a tight-binding N-methylhydroxyphosphinyl-D-glucosamine-6-phosphate inhibitor were determined. The structure of the Zn-NagA confirms that this enzyme binds a single divalent cation at the beta-position in the active site via ligation to Glu-131, His-195, and His-216. A water molecule completes the ligation shell, which is also in position to be hydrogen bonded to Asp-273. In the structure of NagA bound to the tight binding inhibitor that mimics the tetrahedral intermediate, the methyl phosphonate moiety has displaced the hydrolytic water molecule and is directly coordinated to the zinc within the active site. The side chain of Asp-273 is positioned to activate the hydrolytic water molecule via general base catalysis and to deliver this proton to the amino group upon cleavage of the amide bond of the substrate. His-143 is positioned to help polarize the carbonyl group of the substrate in conjunction with Lewis acid catalysis by the bound zinc. The inhibitor is bound in the {alpha}-configuration at the anomeric carbon through a hydrogen bonding interaction of the hydroxyl group at C-1 with the side chain of His-251. The phosphate group of the inhibitor attached to the hydroxyl at C-6 is ion paired with Arg-227 from the adjacent subunit. NagA from Thermotoga maritima was shown to require a single divalent cation for full catalytic activity.

  12. Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.

    PubMed

    Hall, Richard S; Brown, Shoshana; Fedorov, Alexander A; Fedorov, Elena V; Xu, Chengfu; Babbitt, Patricia C; Almo, Steven C; Raushel, Frank M

    2007-07-10

    NagA catalyzes the hydrolysis of N-acetyl-d-glucosamine-6-phosphate to d-glucosamine-6-phosphate and acetate. X-ray crystal structures of NagA from Escherichia coli were determined to establish the number and ligation scheme for the binding of zinc to the active site and to elucidate the molecular interactions between the protein and substrate. The three-dimensional structures of the apo-NagA, Zn-NagA, and the D273N mutant enzyme in the presence of a tight-binding N-methylhydroxyphosphinyl-d-glucosamine-6-phosphate inhibitor were determined. The structure of the Zn-NagA confirms that this enzyme binds a single divalent cation at the beta-position in the active site via ligation to Glu-131, His-195, and His-216. A water molecule completes the ligation shell, which is also in position to be hydrogen bonded to Asp-273. In the structure of NagA bound to the tight binding inhibitor that mimics the tetrahedral intermediate, the methyl phosphonate moiety has displaced the hydrolytic water molecule and is directly coordinated to the zinc within the active site. The side chain of Asp-273 is positioned to activate the hydrolytic water molecule via general base catalysis and to deliver this proton to the amino group upon cleavage of the amide bond of the substrate. His-143 is positioned to help polarize the carbonyl group of the substrate in conjunction with Lewis acid catalysis by the bound zinc. The inhibitor is bound in the alpha-configuration at the anomeric carbon through a hydrogen bonding interaction of the hydroxyl group at C-1 with the side chain of His-251. The phosphate group of the inhibitor attached to the hydroxyl at C-6 is ion paired with Arg-227 from the adjacent subunit. NagA from Thermotoga maritima was shown to require a single divalent cation for full catalytic activity. PMID:17567048

  13. Modification of optical and electrical properties of zinc oxide-coated porous silicon nanostructures induced by swift heavy ion

    PubMed Central

    2012-01-01

    Morphological and optical characteristics of radio frequency-sputtered zinc aluminum oxide over porous silicon (PS) substrates were studied before and after irradiating composite films with 130 MeV of nickel ions at different fluences varying from 1 × 1012 to 3 × 1013 ions/cm2. The effect of irradiation on the composite structure was investigated by scanning electron microscopy, X-ray diffraction (XRD), photoluminescence (PL), and cathodoluminescence spectroscopy. Current–voltage characteristics of ZnO-PS heterojunctions were also measured. As compared to the granular crystallites of zinc oxide layer, Al-doped zinc oxide (ZnO) layer showed a flaky structure. The PL spectrum of the pristine composite structure consists of the emission from the ZnO layer as well as the near-infrared emission from the PS substrate. Due to an increase in the number of deep-level defects, possibly oxygen vacancies after swift ion irradiation, PS-Al-doped ZnO nanocomposites formed with high-porosity PS are shown to demonstrate a broadening in the PL emission band, leading to the white light emission. The broadening effect is found to increase with an increase in the ion fluence and porosity. XRD study revealed the relative resistance of the film against the irradiation, i.e., the irradiation of the structure failed to completely amorphize the structure, suggesting its possible application in optoelectronics and sensing applications under harsh radiation conditions. PMID:22748164

  14. Relating cytotoxicity, zinc ions, and reactive oxygen in ZnO nanoparticle-exposed human immune cells.

    PubMed

    Shen, Cenchao; James, Simon A; de Jonge, Martin D; Turney, Terence W; Wright, Paul F A; Feltis, Bryce N

    2013-11-01

    Although zinc oxide (ZnO) nanoparticles (NPs) have been widely formulated in sunscreens, the relationship between reactive oxygen species (ROS) generation induced by these particles, zinc ions, and cytotoxicity is not clearly understood. This study explores whether these factors can be accurately quantified and related. The study demonstrates a strong correlation between ZnO NP-induced cytotoxicity and free intracellular zinc concentration (R (2) = .945) in human immune cells, indicating a requirement for NP dissolution to precede cytotoxicity. In addition, although direct exposure to ZnO NPs was found to induce cytotoxicity at relatively high concentrations, indirect exposure (via dialysis) was not cytotoxic, even at extremely high concentrations, highlighting a requirement for NP-to-cell contact. Elevated levels of ROS present in NP-exposed cells also correlated to both cytotoxicity and intracellular free zinc. Although the addition of antioxidant was able to reduce ROS, cytotoxicity to ZnO NPs was unaffected, suggesting ROS may be, in part, a result of cytotoxicity rather than a causal factor. This study highlights both the requirement and role of intracellular dissolution of zinc nanomaterials to elicit a cytotoxic response. This response is only partially ROS dependent, and therefore, modification of NP uptake and their intracellular solubility are key components in modulating the bioactivity of ZnO NPs. PMID:23997113

  15. Enhancing the Photostability of Arylvinylenebipyridyl Compounds as Fluorescent Indicators for Intracellular Zinc(II) Ions.

    PubMed

    Yuan, Zhao; Younes, Ali H; Allen, John R; Davidson, Michael W; Zhu, Lei

    2015-06-01

    Arylvinylenebipyridyl (AVB) ligands are bright, zinc(II)-sensitive fluoroionophores. The applicability of AVBs as fluorescent indicators for imaging cellular zinc(II), however, is limited by low photostability, partially attributable to the photoisomerization of the vinylene functionality. Two configurationally immobilized (i.e., "locked") AVB analogues are prepared in this work. The zinc(II)-sensitive photophysical properties and zinc(II) affinities of both AVBs and their locked analogues are characterized in organic and aqueous media. The zinc(II) sensitivity of the emission is attributed to the zinc(II)-dependent energies of the charge transfer excited states of these compounds. The configurationally locked ligands have improved photostability, while maintaining the brightness and zinc(II) sensibility of their AVB progenitors. The feasibility of the "locked" AVB analogues with improved photostability for imaging intracellular Zn(II) of eukaryotic cells using laser confocal fluorescence microscopy is demonstrated. PMID:25942357

  16. Enhancing the Photostability of Arylvinylenebipyridyl Compounds as Fluorescent Indicators for Intracellular Zinc(II) Ions

    PubMed Central

    Yuan, Zhao; Younes, Ali H.; Allen, John R.; Davidson, Michael W.; Zhu, Lei

    2015-01-01

    Arylvinylenebipyridyl (AVB) ligands are bright, zinc(II)-sensitive fluoroionophores. The applicability of AVBs as fluorescent indicators for imaging cellular zinc(II), however, is limited by low photostability, partially attributable to the photoisomerization of the vinylene functionality. Two configurationally immobilized (i.e., “locked”) AVB analogues are prepared in this work. The zinc(II)-sensitive photophysical properties and zinc(II) affinities of both AVBs and their locked analogues are characterized in organic and aqueous media. The zinc(II) sensitivity of the emission is attributed to the zinc(II)-dependent energies of the charge transfer excited states of these compounds. The configurationally locked ligands have improved photostability, while maintaining the brightness and zinc(II) sensibility of their AVB progenitors. The feasibility of the “locked” AVB analogues with improved photostability for imaging intracellular Zn(II) of eukaryotic cells using laser confocal fluorescence microscopy is demonstrated. PMID:25942357

  17. Coordination and ion-ion interactions of chromium centers in alkaline earth zinc borate glasses probed by electron paramagnetic resonance and optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Sumalatha, B.; Omkaram, I.; Rajavardana Rao, T.; Linga Raju, Ch

    2013-05-01

    Electron paramagnetic resonance (EPR), optical absorption and FT-IR studies have been carried out on chromium ions incorporated in alkaline earth zinc borate glasses. The EPR spectra exhibit two resonance signals with effective g values at g ≈ 1.99 and ≈1.97. The resonance signal at g ≈ 1.99 is attributed to the contribution from both the exchange coupled Cr3+-Cr3+ ion pairs and the isolated Cr3+ ions and the resonance signal at g ≈ 1.97 is due to Cr5+ ions. The paramagnetic susceptibility (χ) was calculated from the EPR data at various (123-303 K) temperatures and the Curie temperature (θp) was calculated from the 1/χ-T graph. The optical absorption spectra exhibit three bands at ˜360 nm, ˜440 nm and a broad band at ˜615 nm characteristic of Cr3+ ions in an octahedral symmetry. From the observed band positions, the crystal-field splitting parameter Dq and the Racah parameters (B and C) have been evaluated. From the ultraviolet edges, the optical band gap energies (Eopt) and Urbach energy (ΔE) are calculated. The theoretical optical basicity (Λth) of these glasses has also been evaluated. Chromium ions doped alkaline earth zinc borate glasses show BO3 and BO4 structural units in the FT-IR studies.

  18. Synergistic cytotoxic effects of ions released by zinc-aluminum bronze and the metallic salts on osteoblastic cells.

    PubMed

    Grillo, Claudia A; Morales, María L; Mirífico, María V; Fernández Lorenzo de Mele, Mónica A

    2013-07-01

    The use of copper-based alloys for fixed dental crowns and bridges is increasingly widespread in several countries. The aim of this work is to study the dissolution of a zinc-aluminum-bronze and the cytotoxic effects of the ions released on UMR-106 osteoblastic cell line. Two sources of ions were used: (1) ions released by the metal alloy immersed in the cell culture and (2) salts of the metal ions. Conventional electrochemical techniques, atomic absorption spectroscopy [to obtain the average concentration of ions (AC) in solution], and energy dispersive X-ray (EDX) spectroscopy analysis were used to study the corrosion process. Corrosion tests revealed a strong influence of the composition of the electrolyte medium and the immersion time on the electrochemical response. The cytotoxicity was evaluated with (a) individual ions, (b) combinations of two ions, and (c) the mixture of all the ions released by a metal disc of the alloy. Importantly, synergistic cytotoxic effects were found when Al-Zn ion combinations were used at concentration levels lower than the cytotoxic threshold values of the individual ions. Cytotoxic effects in cells in the vicinity of the metal disc were also found. These results were interpreted considering synergistic effects and a diffusion controlled mechanism that yields to concentration levels, in the metal surroundings, several times higher than the measured AC value. PMID:23596152

  19. Fabrication of Amorphous Indium Gallium Zinc Oxide Thin Film Transistor by using Focused Ion Beam

    NASA Astrophysics Data System (ADS)

    Zhu, Wencong

    Compared with other transparent semiconductors, amorphous indium gallium zinc oxide (a-IGZO) has both good uniformity and high electron mobility, which make it as a good candidate for displays or large-scale transparent circuit. The goal of this research is to fabricate alpha-IGZO thin film transistor (TFT) with channel milled by focused ion beam (FIB). TFTs with different channel geometries can be achieved by applying different milling strategies, which facilitate modifying complex circuit. Technology Computer-Aided Design (TCAD) was also introduced to understand the effect of trapped charges on the device performance. The investigation of the trapped charge at IGZO/SiO2 interface was performed on the IGZO TFT on p-Silicon substrate with thermally grown SiO2 as dielectric. The subgap density-of-state model was used for the simulation, which includes conduction band-tail trap states and donor-like state in the subgap. The result shows that the de-trapping and donor-state ionization determine the interface trapped charge density at various gate biases. Simulation of IGZO TFT with FIB defined channel on the same substrate was also applied. The drain and source were connected intentionally during metal deposition and separated by FIB milling. Based on the simulation, the Ga ions in SiO2 introduced by the ion beam was drifted by gate bias and affects the saturation drain current. Both side channel and direct channel transparent IGZO TFTs were fabricated on the glass substrate with coated ITO. Higher ion energy (30 keV) was used to etch through the substrate between drain and source and form side channels at the corner of milled trench. Lower ion energy (16 keV) was applied to stop the milling inside IGZO thin film and direct channel between drain and source was created. Annealing after FIB milling removed the residual Ga ions and the devices show switch feature. Direct channel shows higher saturation drain current (~10-6 A) compared with side channel (~10-7 A) because

  20. Goatpoxvirus ATPase activity is increased by dsDNA and decreased by zinc ion.

    PubMed

    Lee, Ming-Liang; Hsu, Wei-Li; Wang, Chi-Young; Chen, Hui-Yu; Lin, Fong-Yuan; Chang, Ming-Huang; Chang, Hong-You; Wong, Min-Liang; Chan, Kun-Wei

    2016-10-01

    Viral-encoded ATPase can act as a part of molecular motor in genome packaging of DNA viruses, such as vaccinia virus and adenovirus, by ATP hydrolysis and interaction with DNA. Poxviral ATPase (also called A32) is involved in genomic double-stranded DNA (dsDNA) encapsidation, and inhibition of the expression of A32 causes formation of immature virions lacking viral DNA. However, the role of A32 in goatpoxvirus genome packaging and its dsDNA binding property are not known. In this study, purified recombinant goatpoxvirus A32 protein (rA32) was examined for its dsDNA binding property as well as the effect of dsDNA on ATP hydrolysis. We found that rA32 could bind dsDNA, and its ATPase activity was significant increased with dsDNA binding. Effects of magnesium and calcium ions on ATP hydrolysis were investigated also. The ATPase activity was dramatically enhanced by dsDNA in the presence of Mg(2+); in contrast, ATPase function was not altered by Ca(2+). Furthermore, the enzyme activity of rA32 was completely blocked by Zn(2+). Regarding DNA-protein interaction, the rA32-ATP-Mg(2+) showed lower dsDNA binding affinity than that of rA32-ATP-Ca(2+). The DNA-protein binding was stronger in the presence of zinc ion. Our results implied that A32 may play a role in viral genome encapsidation and DNA condensation. PMID:27146321

  1. Zinc oxide nanolevel surface transformation for liquid crystal orientation by ion bombardment

    SciTech Connect

    Oh, Byeong-Yun; Lee, Won-Kyu; Kim, Young-Hwan; Seo, Dae-Shik

    2009-03-01

    This paper introduces the characteristics of the zinc oxide (ZnO) inorganic film deposited by radio-frequency magnetron sputtering as an alternative alignment layer for liquid crystal display (LCD) applications. The crystalline structure related to the texture formation of ZnO (1013) was observed with a tilt angle of approximately 28.1 deg. to the ZnO (0001) plane, leading to a smooth surface and high-density structure. Ion beam (IB) bombardment at various incident angles was used to induce liquid crystal (LC) alignment and cause the measured pretilt angle on ZnO films to assume a triangular contour. The orientation order of liquid crystal molecules was due to the van der Waals force for the vertical alignment of LCs with selective breaking of O-Zn bonds by IB bombardment. The contact angle contour as a function of the IB incident angle resembled the behavior of the pretilt angle. The pretilt angle is controllable by adjusting the surface features on ZnO films with IB bombardment. The electro-optic characteristics of vertically aligned (VA)-LCD based on ZnO film were comparable to those of VA-LCD based on polyimide, showing good potential of ZnO film as a LC alignment layer.

  2. A ratiometric fluorescent sensor for zinc ions based on covalently immobilized derivative of benzoxazole

    NASA Astrophysics Data System (ADS)

    Ma, Qiu-Juan; Zhang, Xiao-Bing; Zhao, Xu-Hua; Gong, Yi-Jun; Tang, Jian; Shen, Guo-Li; Yu, Ru-Qin

    2009-08-01

    In the present paper, we describe the fabrication and analytical characteristics of fluorescence-based zinc ion-sensing glass slides. To construct the sensor, a benzoxazole derivative 4-benzoxazol-2'-yl-3-hydroxyphenyl allyl ether (1) with a terminal double bond was synthesized and copolymerized with 2-hydroxyethyl methacrylate (HEMA) on the activated surface of glass slides by UV irradiation. In the absence of Zn 2+ at pH 7.24, the resulting optical sensor emitted fluorescence at 450 nm via excited-state intramolecular proton transfer (ESIPT). Upon binding with Zn 2+, the ESIPT process was inhibited resulting in a 46 nm blue-shift of fluorescence emission. Thus, the proposed sensor can behave as a ratiometric fluorescent sensor for the selective detection of Zn 2+. In addition, the sensor shows nice selectivity, good reproducibility and fast response time. Cd 2+ did not interfere with Zn 2+ sensing. The sensing membrane demonstrates a good stability with a lifetime of at least 3 months. The linear response range covers a concentration range of Zn 2+ from 8.0 × 10 -5 to 4.0 × 10 -3 mol/L and the detection limit is 4.0 × 10 -5 mol/L. The determination of Zn 2+ in both tap and river water samples shows satisfactory results.

  3. Optical characterization of Eu3+ and Tb3+ ions doped zinc lead borate glasses.

    PubMed

    Thulasiramudu, A; Buddhudu, S

    2007-02-01

    This paper reports on the spectral analysis of Eu3+ or Tb3+ ions (0.5 mol%) doped heavy metal oxide (HMO) based zinc lead borate glasses from the measurement of their absorption, emission spectra and also different physical properties. From the XRD, DSC profiles, the glass nature and glass thermal properties have been studied. The measured emission spectrum of Eu3+ glass has revealed five transitions (5D0-->7F0, 7F1, 7F2, 7F3 and 7F4) at 578, 591, 613, 654 and 702 nm, respectively, with lambdaexci=392 nm (7F0-->5L6). In the case of Tb3+:ZLB glass, four emission transitions such as (5D4-->7F6, 7F5, 7F4 and 7F3) that are located at 489, 542, 585 and 622 nm, respectively, have been measured with lambdaexci=374 nm. For all these emission bands decay curves have been plotted to evaluate their lifetimes and the emission processes that arise in the glasses have been explained in terms of energy level schemes. PMID:16843052

  4. Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

    PubMed

    Roston, Daniel; Demapan, Darren; Cui, Qiang

    2016-06-15

    A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care. PMID:27186960

  5. Structural and magnetic properties of zinc ferrite thin films irradiated by 90 keV neon ions

    NASA Astrophysics Data System (ADS)

    Gafton, E. V.; Bulai, G.; Caltun, O. F.; Cervera, S.; Macé, S.; Trassinelli, M.; Steydli, S.; Vernhet, D.

    2016-08-01

    The effects of 90 keV neon beam irradiation on the structure and magnetic properties of zinc ferrite thin films have been investigated through several methods, namely, X-ray diffraction technique, Vibrating Sample and SQUID magnetometers. Beforehand, the pristine have also been characterized using profilometry and microscopy techniques. In particular single-phase formation of the thin films deposited on monocrystalline Si (111) substrate by pulsed laser deposition technique was confirmed. Crystal lattice, coercivity, saturation magnetization have been studied for the first time, as a function of ion penetration depth and irradiation fluence. The chemical composition and the crystallinity of the films are not affected with the ion impact acting as a mechanical stress relief. On the contrary, both magnetization and coercivity are sensitive to Neq+ ion irradiation and exhibit different behaviours depending on the ion fluence range.

  6. An Optical Fiber-Based Sensor Array for the Monitoring of Zinc and Copper Ions in Aqueous Environments

    PubMed Central

    Kopitzke, Steven; Geissinger, Peter

    2014-01-01

    Copper and zinc are elements commonly used in industrial applications as aqueous solutions. Before the solutions can be discharged into civil or native waterways, waste treatment processes must be undertaken to ensure compliance with government guidelines restricting the concentration of ions discharged in solution. While currently there are methods of analysis available to monitor these solutions, each method has disadvantages, be it high costs, inaccuracy, and/or being time-consuming. In this work, a new optical fiber-based platform capable of providing fast and accurate results when performing solution analysis for these metals is described. Fluorescent compounds that exhibit a high sensitivity and selectivity for either zinc or copper have been employed for fabricating the sensors. These sensors demonstrated sub-part-per-million detection limits, 30-second response times, and the ability to analyze samples with an average error of under 10%. The inclusion of a fluorescent compound as a reference material to compensate for fluctuations from pulsed excitation sources has further increased the reliability and accuracy of each sensor. Finally, after developing sensors capable of monitoring zinc and copper individually, these sensors are combined to form a single optical fiber sensor array capable of simultaneously monitoring concentration changes in zinc and copper in aqueous environments. PMID:24549250

  7. Defect development and dopant location due to elevated temperature implantation of InP with MeV zinc ions

    NASA Astrophysics Data System (ADS)

    Krause, H.; Flagmeyer, R.-H.; Vogt, J.; Kling, A.; Butz, T.

    1996-06-01

    Zinc implantations in the MeV energy regime at temperatures of about 200°C within the dose range of 5 × 10 14-1 × 10 16 cm -2 were carried out. The investigations included RBS and PIXE measurements combined with ion channeling in the major crystallographic axes and additionally SNMS and XTEM. The implantation-induced damage is characterized by mobile point defects at the elevated implantation temperature. This results in damaged layers containing point-like defects, but far from amorphization. During rapid thermal annealing the surface up to about 0.6 Rp recovered channeling-perfect, while in a depth of (1-2) Rp a band of extrinsic dislocation loops was formed. Comparing the experimental with the calculated PIXE minimum yields, conclusions about the zinc positions were drawn: Due to the low ZnK aligned yield nearly all zinc atoms occupy substitutional lattice sites in the as-implanted samples. After annealing a remarkable diffusion of zinc combined with lattice site changes is observed.

  8. Binding of iron, zinc, and lead ions from aqueous solution by shea butter (Butyrospermun Parkii) seed husks

    SciTech Connect

    Eromosele, I.C.; Otitolaye, O.O. )

    1994-08-01

    Several workers have reported on the potential use of agricultural products as substrates for the removal of metal ions from aqueous solutions. These studies demonstrated that considerable amounts of metal ions can be removed from aqueous solutions by cellulosic materials. The merit in the use of the latter is their relative abundance and cheapness compared to conventional materials for the removal of toxic metal ions from waste-waters. In some of the studies, chemical modification of cellulosic materials significantly enhanced their ion-binding properties, providing greater flexibility in their applications to a wide range of heavy metal ions. Shea butter plant (Butyrospermun Parkii) normally grows in the wild within the guinea-savana zone of Nigeria. The seeds are a rich source of edible oils and the husks are usually discarded. The husk is thus available in abundance and, hence, there is reason to examine its ion-binding properties for its possible application in the removal of toxic metal ions from industrial waste-waters. This paper reports on preliminary studies of the sorption of iron, zinc and lead ions from aqueous solution by modified and unmodified shea butter seed husks. 8 refs., 5 figs., 1 tab.

  9. Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.

    PubMed

    Tsai, Yi-Chun Isabella; Fotinou, Constantina; Rana, Rohini; Yelland, Tamas; Frankel, Paul; Zachary, Ian; Djordjevic, Snezana

    2016-05-01

    Neuropilin-2 is a transmembrane receptor involved in lymphangiogenesis and neuronal development. In adults, neuropilin-2 and its homologous protein neuropilin-1 have been implicated in cancers and infection. Molecular determinants of the ligand selectivity of neuropilins are poorly understood. We have identified and structurally characterized a zinc ion binding site on human neuropilin-2. The neuropilin-2-specific zinc ion binding site is located near the interface between domains b1 and b2 in the ectopic region of the protein, remote from the neuropilin binding site for its physiological ligand, i.e. vascular endothelial growth factor. We also present an X-ray crystal structure of the neuropilin-2 b1 domain in a complex with the C-terminal sub-domain of VEGF-A. Zn(2+) binding to neuropilin-2 destabilizes the protein structure but this effect was counteracted by heparin, suggesting that modifications by glycans and zinc in the extracellular matrix may affect functional neuropilin-2 ligand binding and signalling activity. PMID:26991001

  10. A facile synthesis of zinc oxide/multiwalled carbon nanotube nanocomposite lithium ion battery anodes by sol-gel method

    NASA Astrophysics Data System (ADS)

    Köse, Hilal; Karaal, Şeyma; Aydın, Ali Osman; Akbulut, Hatem

    2015-11-01

    Free standing zinc oxide (ZnO) and multiwalled carbon nanotube (MWCNT) nanocomposite materials are prepared by a sol gel technique giving a new high capacity anode material for lithium ion batteries. Free-standing ZnO/MWCNT nanocomposite anodes with two different chelating agent additives, triethanolamine (TEA) and glycerin (GLY), yield different electrochemical performances. Field emission gun scanning electron microscopy (FEG-SEM), energy dispersive X-ray spectrometer (EDS), high resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) analyses reveal the produced anode electrodes exhibit a unique structure of ZnO coating on the MWCNT surfaces. Li-ion cell assembly using a ZnO/MWCNT/GLY free-standing anode and Li metal cathode possesses the best discharge capacity, remaining as high as 460 mAh g-1 after 100 cycles. This core-shell structured anode can offer increased energy storage and performance over conventional anodes in Li-ion batteries.

  11. The Influence of Doping with Transition Metal Ions on the Structure and Magnetic Properties of Zinc Oxide Thin Films

    PubMed Central

    2014-01-01

    Zn1−xNixO (x = 0.03 ÷ 0.10) and Zn1−xFexO (x = 0.03 ÷ 0.15) thin films were synthesized by sol-gel method. The structure and the surface morphology of zinc oxide thin films doped with transition metal (TM) ions have been investigated by X-ray diffraction (XRD) and atomic force microscopy (AFM). The magnetic studies were done using vibrating sample magnetometer (VSM) at room temperature. Experimental results revealed that the substitution of Ni ions in ZnO wurtzite lattice for the contents x = 0.03 ÷ 0.10 (Ni2+) leads to weak ferromagnetism of thin films. For Zn1−xFexO with x = 0.03 ÷ 0.05, the Fe3+ ions are magnetic coupling by superexchange interaction via oxygen ions in wurtzite structure. For x = 0.10 ÷ 0.15 (Fe3+) one can observe the increasing of secondary phase of ZnFe2O4 spinel. The Zn0.9Fe0.1O film shows a superparamagnetic behavior due to small crystallite sizes and the net spin magnetic moments arisen from the interaction between the iron ions through an oxygen ion in the spinel structure. PMID:24683324

  12. Electroreduction of nitrate ions in concentrated sodium hydroxide solutions at lead, zinc, nickel, and phthalocyanine-modified electrodes

    SciTech Connect

    Li, H. |; Chambers, J.Q.; Hobbs, D.T.

    1987-12-31

    The electrochemical reduction of nitrate in strongly alkaline solution has been studied using nickel, lead, zinc, and iron cathodes. Intermediate formation of nitrate ion and ammonia product was observed for all electrode materials. Coating a nickel sponge electrode with phthalocyanine renders it less active toward nitrate reduction, while iron electrodes appear to be activated. Electrolysis between a lead cathode and a nickel anode is an efficient means of removing nitrate from strongly alkaline solutions. Electrode pretreatment and solution conditions were chosen to correspond to those that might be encountered in practical applications, for example, the cleanup of radioactive waste solutions.

  13. Ion beam fabrication of aluminum-doped zinc oxide layer for high-performance liquid crystals alignment.

    PubMed

    Liu, Yang; Lee, Ju Hwan; Seo, Dae-Shik

    2016-07-25

    In this paper, a 1.8 keV ion beam (IB) sputtered thin layer of aluminum-doped zinc oxide (AZO) with columnar AZO bumps covering the surface working as an alignment layer for the homogeneous alignment of liquid crystals (LC) is investigated. Bumpy AZO alignment layers in twisted nematic (TN) cells generated larger LC pre-tilt angles and thus enabled accelerated switching of LC, and the highly conductive bumpy AZO thin layers allowed super-fast release of accumulated charges, and led to low residual DC performance. These results indicate the promising applications of AZO bumps layer as alignment layer in LC devices. PMID:27464189

  14. Raman and FTIR spectroscopic studies of 1-ethyl-3-methylimidazolium trifluoromethylsulfonate, its mixtures with water and the solvation of zinc ions.

    PubMed

    Liu, Zhen; El Abedin, Sherif Zein; Endres, Frank

    2015-04-01

    In this paper we report on the interactions of the ionic liquid 1-ethyl-3-methylimidazolium trifluoromethylsulfonate ([EMIm]TfO) with water and the solvation of zinc ions in neat [EMIm]TfO and [EMIm]TfO-water mixtures investigated by FTIR and Raman spectroscopy. The structures and physicochemical properties of the [EMIm]TfO-water mixtures are strongly dependent on the interaction between cations, anions, and water. The structure was changed from ionic-liquid-like to water-like solutions upon addition of water. In addition, zinc salts can precipitate in 0.2 M Zn(TfO)2/[EMIm]TfO upon addition of 10 % (v/v) water, presumably as a result of polarity change of the solution. The average coordination number of TfO(-) per zinc ion calculated from Raman spectra is 3.8 in neat [EMIm]TfO, indicating that [Zn(TfO)4](2-), and [Zn(TfO)3](-) complexes are present in the solution. However, in the presence of water, water interacts preferentially with the zinc ions, leading to aqueous zinc species. The solvation of zinc ions in 1-butyl-1-methylpyrrolidinium trifluoromethylsulfonate ([Py(1,4)]TfO) was also investigated. In [Py(1,4)]TfO, there are, on average, 4.5 TfO(-) anions coordinating each zinc ion, corresponding to the weak interaction between [Py(1,4)](+) cations and TfO(-) anions. The species present in [Py(1,4)]TfO are likely a mixture of [Zn(TfO)4](2-) and [Zn(TfO)5](3-). PMID:25630920

  15. 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

  16. Experimental phasing using zinc anomalous scattering

    SciTech Connect

    Cha, Sun-Shin; An, Young Jun; Jeong, Chang-Sook; Kim, Min-Kyu; Lee, Sung-Gyu; Lee, Kwang-Hoon; Oh, Byung-Ha

    2012-09-01

    The surface of proteins can be charged with zinc ions and the anomalous signals from these zinc ions can be used for structure determination of proteins. Zinc is a suitable metal for anomalous dispersion phasing methods in protein crystallography. Structure determination using zinc anomalous scattering has been almost exclusively limited to proteins with intrinsically bound zinc(s). Here, it is reported that multiple zinc ions can easily be charged onto the surface of proteins with no intrinsic zinc-binding site by using zinc-containing solutions. Zn derivatization of protein surfaces appears to be a largely unnoticed but promising method of protein structure determination.

  17. Zinc pyridinedicarboxylate micro-nanostructures: Promising anode materials for lithium-ion batteries with excellent cycling performance.

    PubMed

    Fei, Hailong; Lin, Yaqin

    2016-11-01

    It is important to discover new, cheap and environmental friendly coordination polymer electrode materials for lithium-ion batteries. Zinc 2,6-pyridilinedicarboxylate particles show better cycling stability and higher discharge capacity than 2,5-pyridilinedicarboxylate micro-platelets when they are firstly tested as anode materials for lithium-ion batteries. The former can steadily cycle at current densities of 750, 1000 and 2000mAg(-1). It is also stable in multiple insertion/extraction processes at current densities of 750, 1500, 2000, 2500, 3000, and 750mAg(-1), and the capacity retention is 77.9% after 60cycles. While the latter is apt to show good cycling performance at smaller discharge current density. PMID:27490195

  18. The requirement of zinc and calcium ions for functional MMP activity in demineralized dentin matrices

    PubMed Central

    Tezvergil-Mutluay, Arzu; Agee, Kelli A.; Hoshika, Tomohiro; Carrilho, Marcela; Breschi, Lorenzo; Tjäderhane, Leo; Nishitani, Yoshihiro; Carvalho, Ricardo M.; Looney, Stephen; Tay, Franklin R.; Pashley, David H.

    2010-01-01

    The progressive degradation of resin-dentin bonds is due, in part, to the slow degradation of collagen fibrils in the hybrid layer by endogenous matrix metalloproteinases (MMPs) of the dentin matrix. In in vitro durability studies, the storage medium composition might be important because the optimum activity of MMPs requires both zinc and calcium. Objective This study evaluated the effect of different storage media on changes in matrix stiffness, loss of dry weight or solubilization of collagen from demineralized dentin beams incubated in vitro for up to 60 days. Methods Dentin beams (1×2×6mm) were completely demineralized in 10% phosphoric acid. After baseline measurements of dry mass and elastic modulus (E) (3-point bending, 15% strain) the beams were divided into 5 groups (n=11/group) and incubated at 37°C in either media containing both zinc and calcium designated as complete medium(CM), calcium-free medium, zinc-free medium, a doubled-zinc medium or water. Beams were retested at 3, 7, 14, 30, and 60 days of incubation. The incubation media was hydrolyzed with HCl for the quantitation of hydroxyproline (HOP) as an index of solubilization of collagen by MMPs. Data were analyzed using repeated measures of ANOVA. Results Both the storage medium and storage time showed significant effects on E, mass loss and HOP release (p<0.05). The incubation in CM resulted in relatively rapid and significant (p<0.05) decreases in stiffness, and increasing amounts of mass loss. The HOP content of the experimental media also increased with incubation time but was significantly lower (p<0.05) than in the control CM medium, the recommended storage medium. Conclusions The storage solutions used to age resin-dentin bonds should be buffered solutions that contain both calcium and zinc. The common use of water as an aging medium may underestimate the hydrolytic activity of endogenous dentin MMPs. PMID:20688380

  19. MeV-ion microprobe analyses of whole Drosophila suggest that zinc and copper accumulation is regulated storage not deposit excretion.

    PubMed

    Schofield, R M; Postlethwait, J H; Lefevre, H W

    1997-12-01

    We examined Drosophila spp. using a penetrative ion microprobe technique that allows us to quantify element contents in whole organs and organisms. Comparatively non-penetrative techniques, such as electron microscopy, could not have been used to make many of these measurements because material is lost during sectioning. We found that zinc was accumulated predominantly within a single organ: in the main segments of both the anterior and posterior Malpighian tubules. In contrast to zinc, iron and copper were more generally distributed throughout the body. Zinc concentrations as high as 2.8 % of dry mass were measured in cell-sized volumes of the Malpighian tubules. The large quantities of zinc (approximately 2x10(-8) g in 8-day-old male adults) were sequestered by an unidentified mechanism. We found less than 1 % of the estimated amount of consumed zinc and copper in the abdomen of flies fed food containing several hundred parts per million dry mass of these metals. Our results are inconsistent with the detoxification hypothesis that predicts that a large proportion of the heavy metals passing through the gut are absorbed and stored permanently. We found for both zinc and copper that the quantity in the abdomen was not proportional to the concentration of these metals in the consumed food but was, instead, relatively invariant. For these reasons, we suggest that regulated biological availability, not detoxification, may be the primary benefit of zinc and copper storage. PMID:9364029

  20. 3,3'-Dihydroxyisorenieratene prevents UV-induced formation of reactive oxygen species and the release of protein-bound zinc ions in human skin fibroblasts.

    PubMed

    Lutter, Kaya; De Spirt, Silke; Kock, Sebastian; Kröncke, Klaus-Dietrich; Martin, Hans-Dieter; Wagener, Tanja; Stahl, Wilhelm

    2010-02-01

    3,3'-Dihydroxyisorenieratene (DHIR) is a structurally unusual carotenoid exhibiting bifunctional antioxidant properties. It is synthesized by Brevibacterium linens, used in dairy industry for the production of red smear cheeses. The compound protects cellular structures against photo-oxidative damage and inhibits the UV-dependent formation of thymidine dimers. Here we show that DHIR prevents a UV-induced intracellular release of zinc ions from proteins in human dermal fibroblasts. The effect is correlated with a decreased formation of intracellular reactive oxygen species. In contrast, zinc release from cellular proteins induced by hyperthermia is not affected by pretreatment of cells with the antioxidant DHIR. It is suggested that the intracellular zinc release upon UV irradiation is due to oxidative modifications of the zinc ligands in proteins (e.g. cysteine) and that protection by DHIR is due to intracellular scavenging of reactive oxygen species generated in photo-oxidation. PMID:19862772

  1. Kinetic effect of zinc(II) and cadmium(II) ions on configurational inversion of deltaLLL-fac(S)-tris(L-cysteinato-N,S)cobalt(III) complex.

    PubMed

    Aizawa, S; Ohishi, Y; Yamada, S; Nakamura, M

    2001-02-01

    It has been confirmed from circular dichroism (CD) spectral changes of aqueous solutions of deltaLLL-fac(S)-[Co(L-cys-N,S)3]3- that the absolute configurational inversion to the ALLL isomer is remarkably accelerated by zinc(II), while it is retarded by cadmium(II). In the diluted solutions of these metal ions containing excess deltaLLL-fac(S)-[Co(L-cys-N,S)3]3-, the observed inversion rate constant linearly depends on the zinc(II) concentration with an intercept, while it is not affected by the cadmium(II) concentration. The kinetic behavior has been explained by difference between zinc(II)- and cadmium(II)-interactions with lone pairs on sulfur donor atoms of fac(S)-[Co(L-cys-N,S)3]3-. It has also been proposed that concentrations of zinc(II) and cadmium(II) can be simultaneously determined by the kinetic measurements. PMID:11990552

  2. Benzimidazole Based 'Turn on' Fluorescent Chemodosimeter for Zinc Ions in Mixed Aqueous Medium.

    PubMed

    Sharma, Shilpa; Pradeep, Chullikkattil P; Dhir, Abhimanew

    2016-07-01

    Benzimidazole based compound 3 is designed and synthesized. The compound 3 is evaluated as fluorogenic sensor for metal ions in mixed aqueous solutions. Among all the metal ions tested, the compound 3 selectively senses Zn(2+) ions. The imine bond of 3 gets cleaved by Zn(2+) ions. Thus, 3 behave as 'turn on' fluorescent chemodosimeter for Zn(2+) ions with limit of detction in micromolar range. Furthurmore, we demonstated that 3 can detect Zn(2+) ions in cells of Allium cepa. Graphical Abstract Benzimidazole based ligand 3 is designed and synthesized which behave as chemodosimeter for Zn(2+) ions. We further demonstrated that 3 can detect Zn(2+) ions in cells of Allium cepa. PMID:27262442

  3. Zinc ion coordination as a modulating factor of the ZnuA histidine-rich loop flexibility: A molecular modeling and fluorescence spectroscopy study

    SciTech Connect

    Castelli, Silvia; Stella, Lorenzo; Petrarca, Patrizia; Battistoni, Andrea; Desideri, Alessandro; Falconi, Mattia

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer Fluorescence data indicate that the His-loop of ZnuA interacts with Zn{sup +2} ions. Black-Right-Pointing-Pointer The ZnuA structural model proposed validates these spectroscopic findings. Black-Right-Pointing-Pointer It is proposed that a zinc loaded His-loop may facilitate the ZnuA-ZnuB recognition. -- Abstract: ZnuA is the soluble component of the high-affinity ZnuABC zinc transporter belonging to the ATP-binding cassette-type periplasmic Zn-binding proteins. The zinc transporter ZnuABC is composed by three proteins: ZnuB, the membrane permease, ZnuC, the ATPase component and ZnuA, the soluble periplasmic metal-binding protein which captures Zn and delivers it to ZnuB. The ZnuA protein contains a charged flexible loop, rich in histidines and acidic residues, showing significant species-specific differences. Various studies have established that this loop contributes to the formation of a secondary zinc binding site, which has been proposed to be important in the acquisition of periplasmic Zn for its delivery to ZnuB or for regulation of zinc uptake. Due to its high mobility the structure of the histidine-rich loop has never been solved by X-ray diffraction studies. In this paper, through a combined use of molecular modeling, mutagenesis and fluorescence spectroscopy, we confirm the presence of two zinc binding sites characterized by different affinities for the metal ion and show that the flexibility of the loop is modulated by the binding of the zinc ions to the protein. The data obtained by fluorescence spectroscopy have then be used to validate a 3D model including the unsolved histidine-rich loop.

  4. 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

  5. Exploring zinc coordination in novel zinc battery electrolytes.

    PubMed

    Kar, Mega; Winther-Jensen, Bjorn; Forsyth, Maria; MacFarlane, Douglas R

    2014-06-14

    The coordination of zinc ions by tetraglyme has been investigated here to support the development of novel electrolytes for rechargeable zinc batteries. Zn(2+) reduction is electrochemically reversible from tetraglyme. The spectroscopic data, molar conductivity and thermal behavior as a function of zinc composition, between mole ratios [80 : 20] and [50 : 50] [tetraglyme : zinc chloride], all suggest that strong interactions take place between chloro-zinc complexes and tetraglyme. Varying the concentration of zinc chloride produces a range of zinc-chloro species (ZnClx)(2-x) in solution, which hinder full interaction between the zinc ion and tetraglyme. Both the [70 : 30] and [50 : 50] mixtures are promising electrolyte candidates for reversible zinc batteries, such as the zinc-air device. PMID:24760367

  6. Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.

    PubMed

    Flores, Jason F; Fisher, Charles R; Carney, Susan L; Green, Brian N; Freytag, John K; Schaeffer, Stephen W; Royer, William E

    2005-02-22

    Key to the remarkable ability of vestimentiferan tubeworms to thrive in the harsh conditions of hydrothermal vents are hemoglobins that permit the sequestration and delivery of hydrogen sulfide and oxygen to chemoautotrophic bacteria. Here, we demonstrate that zinc ions, not free cysteine residues, bind sulfide in vestimentiferan hemoglobins. The crystal structure of the C1 hemoglobin from the hydrothermal vent tubeworm Riftia pachyptila has been determined to 3.15 A and revealed the unexpected presence of 12 tightly bound Zn(2+) ions near the threefold axes of this D(3) symmetric hollow sphere. Chelation experiments on R. pachyptila whole-coelomic fluid and purified hemoglobins reveal a role for Zn(2+) ions in sulfide binding. Free cysteine residues, previously proposed as sulfide-binding sites in vestimentiferan hemoglobins, are found buried in surprisingly hydrophobic pockets below the surface of the R. pachyptila C1 molecule, suggesting that access of these residues to environmental sulfide is restricted. Attempts to reduce the sulfide-binding capacities of R. pachyptila hemoglobins by addition of a thiol inhibitor were also unsuccessful. These findings challenge the currently accepted paradigm of annelid hemoglobin evolution and adaptation to reducing environments. PMID:15710902

  7. The electrical properties of 60 keV zinc ions implanted into semi-insulating gallium arsenide

    NASA Technical Reports Server (NTRS)

    Littlejohn, M. A.; Anikara, R.

    1972-01-01

    The electrical behavior of zinc ions implanted into chromium-doped semiinsulating gallium arsenide was investigated by measurements of the sheet resistivity and Hall effect. Room temperature implantations were performed using fluence values from 10 to the 12th to 10 to the 15th power/sq cm at 60 keV. The samples were annealed for 30 minutes in a nitrogen atmosphere up to 800 C in steps of 200 C and the effect of this annealing on the Hall effect and sheet resistivity was studied at room temperature using the Van der Pauw technique. The temperature dependence of sheet resistivity and mobility was measured from liquid nitrogen temperature to room temperature. Finally, a measurement of the implanted profile was obtained using a layer removal technique combined with the Hall effect and sheet resistivity measurements.

  8. Effect of Aluminum, Iron, and Zinc Ions on the Assembly of Microtubules from Brain Microtubule Proteins.

    PubMed

    Shevtsov, P N; Shevtsova, E F; Burbaeva, G Sh

    2016-08-01

    Al(3+), Fe(3+), and Zn(2+) ions can disturb microtubule assembly from tubulin and microtubuleassociated proteins in rat brain. The main structural forms of these microtubules are rings and tangled bundles. These structures are formed only in the presence of Al(3+) and Fe(3+) ions. Therefore, Zn(2+) ions can be excluded from possible causes of structural abnormalities in microtubules during Alzheimer's disease. Al(3+) ions are the most probable etiological cause of Alzheimer's disease. The concentration of Al(3+) ions affecting the structure of microtubules is one order of magnitude lower than that of Fe(3+) ions (10 and 100 μM, respectively), which corresponds to their brain concentration reported in Alzheimer's disease. PMID:27591874

  9. Amphipathic Benzoic Acid Derivativies: Synthesis and Binding in the Hydrophobic Tunnel of the Zinc Deacetylase LpxC

    SciTech Connect

    Shin,H.; Gennadios, H.; Whittington, D.; Christianson, D.

    2007-01-01

    The first committed step in lipid A biosynthesis is catalyzed by uridine diphosphate-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase (LpxC), a zinc-dependent deacetylase, and inhibitors of LpxC may be useful in the development of antibacterial agents targeting a broad spectrum of Gram-negative bacteria. Here, we report the design of amphipathic benzoic acid derivatives that bind in the hydrophobic tunnel in the active site of LpxC. The hydrophobic tunnel accounts for the specificity of LpxC toward substrates and substrate analogues bearing a 3-O-myristoyl substituent. Simple benzoic acid derivatives bearing an aliphatic 'tail' bind in the hydrophobic tunnel with micromolar affinity despite the lack of a glucosamine ring like that of the substrate. However, although these benzoic acid derivatives each contain a negatively charged carboxylate 'warhead' intended to coordinate to the active site zinc ion, the 2.25 {angstrom} resolution X-ray crystal structure of LpxC complexed with 3-(heptyloxy)benzoate reveals 'backward' binding in the hydrophobic tunnel, such that the benzoate moiety does not coordinate to zinc. Instead, it binds at the outer end of the hydrophobic tunnel. Interestingly, these ligands bind with affinities comparable to those measured for more complicated substrate analogue inhibitors containing glucosamine ring analogues and hydroxamate 'warheads' that coordinate to the active site zinc ion. We conclude that the intermolecular interactions in the hydrophobic tunnel dominate enzyme affinity in this series of benzoic acid derivatives.

  10. 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

  11. Selective transport of copper(I, II), cadmium(II), and zinc(II) ions through a supported liquid membrane containing bathocuproine, neocuproine, or bathophenanthroline

    SciTech Connect

    Saito, Takashi )

    1994-06-01

    Some selective transport systems for heavy metallic ions through a supported liquid membrane (SLM) containing a 2,2[prime]-dipyridyl derivative ligand, 4,7-diphenyl-2,9-dimethyl-1, 10-phenanthroline (bathocuproine), 2,9-dimethyl-1,10-phenanthroline (neocuproine), or 4,7-diphenyl-1,10-phenanthroline (bathophenanthroline), were investigated. The transport of copper(I, II), cadmium(II), zinc(II), lead(II), and cobalt(II) ions was accomplished with a halogen ion such as chloride, bromide, or iodide ion as a pairing ion species for any SLM. The ranking of the permeability of the metallic ions was Cu[sup +,2+], Zn[sup 2+], Cd[sup 2+] [much gt] Pb[sup 2+], Co[sup 2+]. When the oxidation-reduction potential gradient was used as a driving force for metallic ions, the transport of Cu[sup +] ions was higher than those of Cd[sup 2+] and Zn[sup 2+] ions for any SLM containing bathocuproine, neocuproine, or bathophenanthroline. On the other hand, in the transport system which used the concentration gradient of pairing ion species, the permeability of the Cu[sup 2+] ion decreased whereas that of the Cd[sup 2+] ion increased. Moreover, it was found that the different selectivity for the transport of metallic ions is produced by using various pairing ion species. 18 refs., 9 figs.

  12. Effects of zinc and cadmium ions on cell growth and production of coumarins in cell suspension cultures of Angelica archangelica L.

    PubMed

    Siatka, Tomáš; Kašparová, Marie; Spilková, Jiřina

    2012-12-01

    The plant cell may respond to the excess of heavy metals in its environment by various mechanisms, including enhanced biosynthesis of secondary metabolites. In this study, zinc (0 to 1500 μM) and cadmium ions (0 to 100 μM) were tested as potential elicitors of the production of coumarins in angelica cell suspension cultures. In addition, the toxicity of both metals was assessed by evaluating their effect on cell growth (characterized by fresh and dry biomass at the end of a two-week subculture). It has been found that fresh biomass was not influenced up to zinc concentrations of 150 and 300 μM in the dark-grown and light-grown cultures, resp. Then it declined with an increasing zinc level. Zinc at 1500 μM diminished it by 54% and 24% in the dark-grown and light-grown cultures, resp. Dry biomass was influenced in a similar way. Zinc at 1500 μM reduced dry cell weight by 30% and 20% in cultures in the dark and in the light, resp. Cadmium ions did not affect fresh and dry weights of cells up to concentrations of 10 μM and 50 μM in cultures in the dark and in the light, resp. Toxic concentrations of cadmium are by an order of magnitude lower than those of zinc. Cadmium at 50 μM reduced fresh and dry cell weights by 66% and 59%, resp., in the dark-grown cultures. Cadmium at 100 μM caused a decrease in fresh and dry biomass by 40% and 44%, resp., in the light-grown cultures. Neither zinc nor cadmium improved production of coumarins. PMID:23387854

  13. Design and characterization of a novel sensor combined imaging and zinc ion sensing

    NASA Astrophysics Data System (ADS)

    Wang, Jian; Wang, Lili

    2012-05-01

    A novel fluorescent sensor for Zn(II) detection and imaging is developed by incorporating 1-(2-pyridylazo)-2-naphthol (PAN) and Rhodamine B (RB) in a sol-gel film on an end face of a gradient index (GRIN) lens rod which is tightly connected with an imaging fiber. This technique has high-quality imaging capabilities for observing remote sample while measuring Zn(II). The RB and PAN employed in combination as the indicator for zinc-sensing is much cheaper than that of the other zinc-sensitive fluorescent dyes. The sol is prepared by base catalyzed hydrolysis of tetraethylorthosilicate (TEOS) with the addition of 3-glycidyloxypropyltrimethoxysilane (GLYMO) and 3-aminopropyltriethoxysilane (APTES), which is more suitable for Zn(II) detection. The sensor has the linear range of Zn(II) from 0.1 to 1 mmol/L. Simultaneously, it has the capabilities of real-time imaging with the whole system's resolution of 18.73 line pairs/mm. This bi-functional sensor has potential applications in in situ biosensing and other remote measurements.

  14. Adsorption characteristics of copper, lead, zinc and cadmium ions by tourmaline.

    PubMed

    Jiang, Kan; Sun, Tie-heng; Sun, Li-na; Li, Hai-bo

    2006-01-01

    The adsorption characteristics of heavy metals: Cu(II), Pb(II), Zn(II) and Cd(II) ions on tourmaline were studied. Adsorption equilibrium was established. The adsorption isotherms of all the four metal ions followed well Langmuir equation. Tourmaline was found to remove heavy metal ions efficiently from aqueous solution with selectivity in the order of Pb(II)>Cu(II)>Cd(II)>Zn(II). The adsorption of metal ions by tourmaline increased with the initial concentration of metal ions increasing in the medium. Tourmaline could also increase pH value of metal solution. -The maximum heavy metal ions adsorbed by tourmaline was found to be 78.86, 154.08, 67.25, and 66.67 mg/g for Cu(II), Pb(II), Zn(II) and Cd(R), respectively. The temperature (25-55 degrees C) had a small effect on the adsorption capacity of tourmaline. Competitive adsorption of Cu(II), Pb(II), Zn(II) and Cd(II) ions was also studied. The adsorption capacity of tourmaline for single metal decreased in the order of Pb>Cu>Zn >Cd and inhibition dominance observed in two metal systems was Pb>Cu, Pb>Zn, Pb>Cd, Cu>Zn, Cu>Cd, and Cd>Zn. PMID:17294969

  15. Anionic clays as hosts for anchored synthesis: Interlayer bromination of maleate and fumarate ions in nickel zinc layered hydroxy double salt

    NASA Astrophysics Data System (ADS)

    Arulraj, James; Rajamathi, Jacqueline T.; Prabhu, Kandikere R.; Rajamathi, Michael

    2007-09-01

    Anionic clay-like nickel zinc hydroxyacetate, Ni 3Zn 2(OH) 8(OAc) 2·2H 2O was ion exchanged with maleate and fumarate ions. While the maleate enters as monoanion, fumarate enters as dianion. Also these anions take up different orientations in the interlayer region. The intercalated organic species could be reacted with bromine water in such a way that the brominated product remains intercalated making the reaction a true intracrystalline reaction. The stereochemistry of the reaction of the intercalated fumarate was identical to that of the free fumarate ion - both yielding only the anti addition product. While free maleate ion yielded only the anti addition product, the intercalated maleate ion yielded a small percentage of the syn addition product along with the anti addition product. The organic products could be quantitatively recovered by anion exchange with oxalate ions.

  16. Potential Interactions of Calcium-Sensitive Reagents with Zinc Ion in Different Cultured Cells

    PubMed Central

    Fujikawa, Koichi; Fukumori, Ryo; Nakamura, Saki; Kutsukake, Takaya; Takarada, Takeshi; Yoneda, Yukio

    2015-01-01

    Background Several chemicals have been widely used to evaluate the involvement of free Ca2+ in mechanisms underlying a variety of biological responses for decades. Here, we report high reactivity to zinc of well-known Ca2+-sensitive reagents in diverse cultured cells. Methodology/Principal Findings In rat astrocytic C6 glioma cells loaded with the fluorescent Ca2+ dye Fluo-3, the addition of ZnCl2 gradually increased the fluorescence intensity in a manner sensitive to the Ca2+ chelator EGTA irrespective of added CaCl2. The addition of the Ca2+ ionophore A23187 drastically increased Fluo-3 fluorescence in the absence of ZnCl2, while the addition of the Zn2+ ionophore pyrithione rapidly and additionally increased the fluorescence in the presence of ZnCl2, but not in its absence. In cells loaded with the zinc dye FluoZin-3 along with Fluo-3, a similarly gradual increase was seen in the fluorescence of Fluo-3, but not of FluoZin-3, in the presence of both CaCl2 and ZnCl2. Further addition of pyrithione drastically increased the fluorescence intensity of both dyes, while the addition of the Zn2+ chelator N,N,N',N'-tetrakis(2-pyridylmethyl)ethane-1,2-diamine (TPEN) rapidly and drastically decreased FluoZin-3 fluorescence. In cells loaded with FluoZin-3 alone, the addition of ZnCl2 induced a gradual increase in the fluorescence in a fashion independent of added CaCl2 but sensitive to EGTA. Significant inhibition was found in the vitality to reduce 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide in a manner sensitive to TPEN, EDTA and BAPTA in C6 glioma cells exposed to ZnCl2, with pyrithione accelerating the inhibition. Similar inhibition occurred in an EGTA-sensitive fashion after brief exposure to ZnCl2 in pluripotent P19 cells, neuronal Neuro2A cells and microglial BV2 cells, which all expressed mRNA for particular zinc transporters. Conclusions/Significance Taken together, comprehensive analysis is absolutely required for the demonstration of a

  17. Zinc(II)-Thiosemicarbazone Complexes Are Localized to the Lysosomal Compartment Where They Transmetallate with Copper Ions to Induce Cytotoxicity.

    PubMed

    Stacy, Alexandra E; Palanimuthu, Duraippandi; Bernhardt, Paul V; Kalinowski, Danuta S; Jansson, Patric J; Richardson, Des R

    2016-05-26

    As the di-2-pyridylketone thiosemicarbazone (DpT) and 2-acetylpyridine thiosemicarbazone (ApT) series show potent antitumor activity in vitro and in vivo, we synthesized their fluorescent zinc(II) complexes to assess their intracellular distribution. The Zn(II) complexes generally showed significantly greater cytotoxicity than the thiosemicarbazones alone in several tumor cell-types. Notably, specific structure-activity relationships demonstrated the importance of the di-2-pyridyl pharmacophore in their activity. Confocal fluorescence imaging and live cell microscopy showed that the Zn(II) complex of our lead compound, di-2-pyridylketone 4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC), which is scheduled to enter clinical trials, was localized to lysosomes. Under lysosomal conditions, the Zn(II) complexes were shown to transmetallate with copper ions, leading to redox-active copper complexes that induced lysosomal membrane permeabilization (LMP) and cytotoxicity. This is the first study to demonstrate direct lysosomal targeting of our novel Zn(II)-thiosemicarbazone complexes that mediate their activity via transmetalation with copper ions and LMP. PMID:27023111

  18. Judd-Ofelt analysis and spectral properties of Dy3+ ions doped niobium containing tellurium calcium zinc borate glasses

    NASA Astrophysics Data System (ADS)

    Ravi, O.; Reddy, C. Madhukar; Reddy, B. Sudhakar; Deva Prasad Raju, B.

    2014-02-01

    Niobium containing tellurium calcium zinc borate (TCZNB) glasses doped with different concentrations of Dy3+ ions were prepared by the melt quenching method and their optical properties have been studied. The Judd-Ofelt (J-O) intensity parameters Ωt (t=2, 4 and 6) were calculated using the least square fit method. Based on the magnitude of Ω2 parameter the hypersensitivity of 6H15/2→6F11/2 has also been discussed. From the evaluated J-O intensity parameters as well as from the emission and lifetime measurements, radiative transition properties such as radiative transition probability rates and branching ratios were calculated for 4F9/2 excited level. It is found that for Dy3+ ion, the transition 4F9/2→6H13/2 shows highest emission cross-section at 1.0 mol% TCZNB glass matrix. From the visible luminescence spectra, yellow to blue (Y/B) intensity ratios and chromaticity color coordinates were also estimated. The TCZNB glasses exhibit good luminescence properties and are suitable for generation of white light.

  19. The computed distribution of copper(II) and zinc(II) ions among seventeen amino acids present in human blood plasma

    PubMed Central

    Hallman, P. S.; Perrin, D. D.; Watt, Ann E.

    1971-01-01

    The equilibrium distribution of copper(II) and zinc(II) ions among a mixture of 17 amino acids has been computed from stability-constant and blood-plasma-composition data. At pH7.4, 98% of the copper(II) in the simulated plasma solution is co-ordinated to histidine and cystine, predominantly as the mixed-ligand complexes [Cu·His·Cystine]− and [Cu·H·His·Cystine]. Approximately half of the zinc(II) is co-ordinated to cysteine and histidine, but appreciable complex-formation occurs with most of the other amino acids. Stability constants are given for copper(II) and zinc(II) amino acid complexes, including some mixed-ligand species, at 37°C and I=0.15m. PMID:5119792

  20. Calcium ion gradients modulate the zinc affinity and antibacterial activity of human calprotectin.

    PubMed

    Brophy, Megan Brunjes; Hayden, Joshua A; Nolan, Elizabeth M

    2012-10-31

    Calprotectin (CP) is an antimicrobial protein produced and released by neutrophils that inhibits the growth of pathogenic microorganisms by sequestering essential metal nutrients in the extracellular space. In this work, spectroscopic and thermodynamic metal-binding studies are presented to delineate the zinc-binding properties of CP. Unique optical absorption and EPR spectroscopic signatures for the interfacial His(3)Asp and His(4) sites of human calprotectin are identified by using Co(II) as a spectroscopic probe. Zinc competition titrations employing chromophoric Zn(II) indicators provide a 2:1 Zn(II):CP stoichiometry, confirm that the His(3)Asp and His(4) sites of CP coordinate Zn(II), and reveal that the Zn(II) affinity of both sites is calcium-dependent. The calcium-insensitive Zn(II) competitor ZP4 affords dissociation constants of K(d1) = 133 ± 58 pM and K(d2) = 185 ± 219 nM for CP in the absence of Ca(II). These values decrease to K(d1) ≤ 10 pM and K(d2) ≤ 240 pM in the presence of excess Ca(II). The K(d1) and K(d2) values are assigned to the His(3)Asp and His(4) sites, respectively. In vitro antibacterial activity assays indicate that the metal-binding sites and Ca(II)-replete conditions are required for CP to inhibit the growth of both Gram-negative and -positive bacteria. Taken together, these data provide a working model whereby calprotectin responds to physiological Ca(II) gradients to become a potent Zn(II) chelator in the extracellular space. PMID:23082970

  1. Zinc Inhibits Hedgehog Autoprocessing

    PubMed Central

    Xie, Jian; Owen, Timothy; Xia, Ke; Singh, Ajay Vikram; Tou, Emiley; Li, Lingyun; Arduini, Brigitte; Li, Hongmin; Wan, Leo Q.; Callahan, Brian; Wang, Chunyu

    2015-01-01

    Zinc is an essential trace element with wide-ranging biological functions, whereas the Hedgehog (Hh) signaling pathway plays crucial roles in both development and disease. Here we show that there is a mechanistic link between zinc and Hh signaling. The upstream activator of Hh signaling, the Hh ligand, originates from Hh autoprocessing, which converts the Hh precursor protein to the Hh ligand. In an in vitro Hh autoprocessing assay we show that zinc inhibits Hh autoprocessing with a Ki of 2 μm. We then demonstrate that zinc inhibits Hh autoprocessing in a cellular environment with experiments in primary rat astrocyte culture. Solution NMR reveals that zinc binds the active site residues of the Hh autoprocessing domain to inhibit autoprocessing, and isothermal titration calorimetry provided the thermodynamics of the binding. In normal physiology, zinc likely acts as a negative regulator of Hh autoprocessing and inhibits the generation of Hh ligand and Hh signaling. In many diseases, zinc deficiency and elevated level of Hh ligand co-exist, including prostate cancer, lung cancer, ovarian cancer, and autism. Our data suggest a causal relationship between zinc deficiency and the overproduction of Hh ligand. PMID:25787080

  2. Microstructured Optical Fiber-based Biosensors: Reversible and Nanoliter-Scale Measurement of Zinc Ions.

    PubMed

    Heng, Sabrina; McDevitt, Christopher A; Kostecki, Roman; Morey, Jacqueline R; Eijkelkamp, Bart A; Ebendorff-Heidepriem, Heike; Monro, Tanya M; Abell, Andrew D

    2016-05-25

    Sensing platforms that allow rapid and efficient detection of metal ions would have applications in disease diagnosis and study, as well as environmental sensing. Here, we report the first microstructured optical fiber-based biosensor for the reversible and nanoliter-scale measurement of metal ions. Specifically, a photoswitchable spiropyran Zn(2+) sensor is incorporated within the microenvironment of a liposome attached to microstructured optical fibers (exposed-core and suspended-core microstructured optical fibers). Both fiber-based platforms retains high selectivity of ion binding associated with a small molecule sensor, while also allowing nanoliter volume sampling and on/off switching. We have demonstrated that multiple measurements can be made on a single sample without the need to change the sensor. The ability of the new sensing platform to sense Zn(2+) in pleural lavage and nasopharynx of mice was compared to that of established ion sensing methodologies such as inductively coupled plasma mass spectrometry (ICP-MS) and a commercially available fluorophore (Fluozin-3), where the optical-fiber-based sensor provides a significant advantage in that it allows the use of nanoliter (nL) sampling when compared to ICP-MS (mL) and FluoZin-3 (μL). This work paves the way to a generic approach for developing surface-based ion sensors using a range of sensor molecules, which can be attached to a surface without the need for its chemical modification and presents an opportunity for the development of new and highly specific ion sensors for real time sensing applications. PMID:27152578

  3. Structural studies on the zinc-endopeptidase light chain of tetanus neurotoxin.

    PubMed

    De Filippis, V; Vangelista, L; Schiavo, G; Tonello, F; Montecucco, C

    1995-04-01

    Tetanus neurotoxin (TeNT) blocks neuroexocytosis via a zinc-endopeptidase activity highly specific for vescicle-associated membrane protein(VAMP)/synaptobrevin. TeNT is the prototype of clostridial neurotoxins, a new family of metalloproteinases. They consist of three domains and the proteolytic activity is displayed by the 50-kDa light chain (L chain). The L chain was isolated here in the native state from bacterial filtrates of Clostridium tetani and its structure was studied via circular dichroism (CD) and fluorescence spectroscopy. The secondary structure content (27% alpha-helix and 43% beta-sheet), estimated by far-ultraviolet CD measurements, was in reasonable agreement with that obtained by standard predictive methods (25% alpha-helix and 49% beta-sheet). Moreover, the hypothetical zinc-binding motif, encompassing residues His-Glu-Leu-Ile-His, was correctly predicted to be in alpha-helical conformation, as also expected on the basis of the geometrical requirements for a correct coordination of the zinc ion. Both near-ultraviolet CD and fluorescence data strongly suggest that the single Trp43 residue is buried and constrained in a hydrophobic environment, likely distant from the zinc ion located in the active-site cleft. The contribution of the bound zinc ion to the overall conformation of TeNT L chain was investigated by different and complementary techniques, including spectroscopic (far- and near-ultraviolet CD, fluorescence, second derivative absorption spectroscopy) as well as proteolytic probes. The results indicate that the zinc ion plays little, if any, role in determining the structural properties of the L chain molecule. Similarly, the metal-free apo-enzyme and the holo-protein share common stability features evaluated in respect to different physico-chemical parameters (pH, temperature and urea concentration). These results parallel those obtained on thermolysin, a zinc-dependent neutral endoprotease from Bacillus thermoproteolyticus, where both

  4. Shaping and compositional modification of zinc oxide nanowires under energetic manganese ion irradiation

    NASA Astrophysics Data System (ADS)

    Möller, Wolfhard; Johannes, Andreas; Ronning, Carsten

    2016-04-01

    For ZnO nanowires of 150 to 200 nm diameter standing on a flat substrate, the development of the surface contour/morphology and the local elemental composition under 175 keV Mn irradiation has been investigated both experimentally and by means of three-dimensional dynamic Monte Carlo computer simulation. The simulation results reveal a complex interplay of sputter erosion, implant incorporation, resputtering and atomic mixing, which is discussed in detail. The sputter-induced thinning of the wire is in good quantitative agreement with the experimental results obtained from pre- and post-irradiation scanning electron microscopy. The experiments also confirm the predicted sharpening of the tip, neck formation at the bottom interface, and ultimately the detachment of the nanowires from the substrate at high ion fluence. Additional good agreement with experimental results from nano-x-ray fluorescence is also obtained for the continuously increasing Mn/Zn atomic ratio within the nanowires as a function of ion fluence. The simulation yields a great deal of additional information that has not been accessible in the experiments. From this, preferential sputtering of O compared with Zn is deduced. A significant contamination of the wires with substrate material arises from ion mixing at the wire/substrate interface, rather than from redeposition of sputtered substrate atoms. Surprising hollow profiles are observed. Their formation is attributed to a special mechanism of collisional transport which is characteristic of the irradiation of nanowires at a suitable combination of wire diameter and ion energy.

  5. Shaping and compositional modification of zinc oxide nanowires under energetic manganese ion irradiation.

    PubMed

    Möller, Wolfhard; Johannes, Andreas; Ronning, Carsten

    2016-04-29

    For ZnO nanowires of 150 to 200 nm diameter standing on a flat substrate, the development of the surface contour/morphology and the local elemental composition under 175 keV Mn irradiation has been investigated both experimentally and by means of three-dimensional dynamic Monte Carlo computer simulation. The simulation results reveal a complex interplay of sputter erosion, implant incorporation, resputtering and atomic mixing, which is discussed in detail. The sputter-induced thinning of the wire is in good quantitative agreement with the experimental results obtained from pre- and post-irradiation scanning electron microscopy. The experiments also confirm the predicted sharpening of the tip, neck formation at the bottom interface, and ultimately the detachment of the nanowires from the substrate at high ion fluence. Additional good agreement with experimental results from nano-x-ray fluorescence is also obtained for the continuously increasing Mn/Zn atomic ratio within the nanowires as a function of ion fluence. The simulation yields a great deal of additional information that has not been accessible in the experiments. From this, preferential sputtering of O compared with Zn is deduced. A significant contamination of the wires with substrate material arises from ion mixing at the wire/substrate interface, rather than from redeposition of sputtered substrate atoms. Surprising hollow profiles are observed. Their formation is attributed to a special mechanism of collisional transport which is characteristic of the irradiation of nanowires at a suitable combination of wire diameter and ion energy. PMID:26978260

  6. Effect of F ions on physical and optical properties of fluorine substituted zinc arsenic tellurite glasses

    NASA Astrophysics Data System (ADS)

    Kareem Ahmmad, Shaik; kondaul, Edu; Rahman, Syed

    2015-02-01

    The effect of substitution of fluoride ions for oxide ions on the physical and optical properties of glass system (20-x) ZnO-xZnF2-40As2O3-40TeO2 where x = 0, 4, 8,12,16,20 mole % were investigated. The samples prepared by melt quenching method under controlled condition. The amorphous nature of these glasses was checked by X-ray diffraction technique. The density was measured according to Archimedes principle. The room temperature absorption spectra of all glass samples were determined using UV-Vis-NIR spectrometer. The thermal behaviour, glass transition temperature and stability of glass samples were studied by a differential scanning calorimetric (DSC). The density reduction of present glasses with ZnF2 concentrations may be due to the low density of ZnF2 compared with that of ZnO. Breaking the oxide network, the cross linking degree of the glass former could be reduced which results in decrease of both Tg and Tx. In the present glass system when F ions replaced by oxygen ions UV-Vis absorption cut-off wavelength decreases. This resulted form the conversion of structural unit in the glass from TeO4 to Te(O,F)4 and then to Te(O, F)3.

  7. Conformational Analysis on structural perturbations of the zinc finger NEMO

    NASA Astrophysics Data System (ADS)

    Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

    2014-03-01

    The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

  8. 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

  9. EFFECT OF LASER LIGHT ON MATTER. LASER PLASMAS: L spectra of zinc ions in the wavelength region 0.65-1.18 nm observed in a plasma heated by a Nd laser

    NASA Astrophysics Data System (ADS)

    Nilsen, J.; Pikuz, S. A.; Skobelev, I. Yu; Faenov, A. Ya; Khakhalin, S. Ya; Khabibulaev, B. K.; Érmatov, Sh A.

    1993-12-01

    A study has been made of the x-ray emission spectra of zinc ions (λ ~0.65-1.18 nm) excited in a plasma produced by the beam from a Nd laser. The wavelengths were measured within ±0.3 pm. The observed spectra have been identified. Detailed calculations have made it possible to identify, for the first time, some spectra lines due to the radiative decal of autoionizing states of Na-like zinc ions.

  10. 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

  11. Fluorescence properties of Eu3+ ions doped borate and fluoroborate glasses containing lithium, zinc and lead.

    PubMed

    Venkatramu, V; Babu, P; Jayasankar, C K

    2006-02-01

    The influence of glass composition on the fluorescence properties of Eu3+ ions doped borate and fluoroborate glasses modified with Li+, Zn2+ and Pb2+ cations have been investigated. The magnitude of splittings of 7F1 levels are analyzed using crystal-field (CF) analysis. The relative intensities of 5D0 --> 7F2 to 5D0 --> 7F1 transitions, crystal-field strength parameters and decay times of the 5D0 level have been determined and are found to be lower for Pb based glasses than those of Zn/Li based glasses. The lifetimes of 5D0 level are found to increase when borate glasses are modified with pure fluorides than with oxides and oxyfluorides. The fluorescence decay of 5D0 level fits perfect single exponential in the Eu3+:glass systems studied which indicates the absence of energy transfer between Eu3+ ions in these glasses. PMID:15979397

  12. Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site

    PubMed Central

    Stafford, Kate A.; Palmer III, Arthur G.

    2014-01-01

    Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold. PMID:25075292

  13. Binding of transition metal ions [cobalt, copper, nickel and zinc] with furanyl-, thiophenyl-, pyrrolyl-, salicylyl- and pyridyl-derived cephalexins as potent antibacterial agents.

    PubMed

    Chohan, Zahid H; Pervez, Humayun; Khan, Khalid Mohammed; Rauf, A; Supuran, Claudiu T

    2004-02-01

    A method is described for the preparation of novel cephalexin-derived furanyl-, thiophenyl-, pyrrolyl-, salicylyl- and pyridyl-containing compounds showing potent antibacterial activity. The binding of these newly synthesized antibacterial agents with metal ions such as cobalt(II), copper(II), nickel(II) and zinc(II) has been studied and their inhibitory properties against various bacterial species such as Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae are also reported. These results suggest that metal ions to possess an important role in the designing of metal-based antibacterials and that such complexes are more effective against infectious diseases compared to the uncomplexed drugs. PMID:15202493

  14. High-resolution structural study of zinc ion incorporation at the calcite cleavage surface.

    SciTech Connect

    Cheng, L.; Sturchio, N. C.; Woicik, J. C.; Kemner, K. M.; Lyman, P. F.; Bedzyk, M. J.; Northwestern Univ.; NIST

    1998-09-30

    The atomic-scale structure of Zn{sup 2+} incorporated at the CaCO{sub 3} (10{ovr 1}4) surface by adsorption from solution was determined by X-ray standing wave triangulation and surface extended X-ray absorption fine structure spectroscopy. At low coverage (approximately 0.1 ML), Zn{sup 2+} substitutes for Ca{sup 2+} in the surface layer. Structural relaxation of the adjacent in-plane CO{sup 2-}{sub 3} ions in the host surface is shown by the reduced nearest-neighbor distance of Zn-O relative to Ca-O. Relaxation of the Zn{sup 2+} ion in the out-of-plane direction is shown by the displacement of its lattice position from the ideal Ca{sup 2+} position. These relaxations, resulting in a local lattice buckling feature at the Zn{sup 2+} adsorption site, can be fully explained as the combined effect of the electrostatic relaxation of the nearest-neighbor anions in response to the smaller size of Zn{sup 2+}, and the bonding asymmetry due to surface truncation.

  15. Brain-Delivery of Zinc-Ions as Potential Treatment for Neurological Diseases: Mini Review

    PubMed Central

    Grabrucker, Andreas M.; Rowan, Magali; Garner, Craig C.

    2011-01-01

    Homeostasis of metal ions such as Zn2+ is essential for proper brain function. Moreover, the list of psychiatric and neurodegenerative disorders involving a dysregulation of brain Zn2+-levels is long and steadily growing, including Parkinson’s and Alzheimer’s disease as well as schizophrenia, attention deficit and hyperactivity disorder, depression, amyotrophic lateral sclerosis, Down's syndrome, multiple sclerosis, Wilson’s disease and Pick’s disease. Furthermore, alterations in Zn2+-levels are seen in transient forebrain ischemia, seizures, traumatic brain injury and alcoholism. Thus, the possibility of altering Zn2+-levels within the brain is emerging as a new target for the prevention and treatment of psychiatric and neurological diseases. Although the role of Zn2+ in the brain has been extensively studied over the past decades, methods for controlled regulation and manipulation of Zn2+ concentrations within the brain are still in their infancy. Since the use of dietary Zn2+ supplementation and restriction has major limitations, new methods and alternative approaches are currently under investigation, such as the use of intracranial infusion of Zn2+ chelators or nanoparticle technologies to elevate or decrease intracellular Zn2+ levels. Therefore, this review briefly summarizes the role of Zn2+ in psychiatric and neurodegenerative diseases and highlights key findings and impediments of brain Zn2+-level manipulation. Furthermore, some methods and compounds, such as metal ion chelation, redistribution and supplementation that are used to control brain Zn2+-levels in order to treat brain disorders are evaluated. PMID:22102982

  16. Substrate lattice relaxations, spectral distortions, and nanoparticle inclusions of ion implanted zinc oxide

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Ma, B.; Zhang, W.; Li, D.; Zhao, Y.; Finch, A. A.; Townsend, P. D.

    2015-09-01

    Low temperature radioluminescence and thermoluminescence spectra of ZnO track numerous changes produced by copper ion implantation into the surface layer. A significant, but unexpected, feature is that the bulk crystal becomes modified by the stress generated in the surface layer. This is reflected by the energy of intrinsic band gap emission. There are also differences in the spectra and peak temperatures of the thermoluminescence components, consistent with such a structural relaxation. The copper implant layer is both absorbing and reflective, so this introduces major distortions on the radioluminescence component from the bulk region, since the bulk luminescence signals are transmitted through, or reflected from, the implant layer. The temperature dependence of the spectra includes anomalies that are typical of changes driven by phase transitions of nanoparticle inclusions. Overall, the features of bulk relaxation, spectral distortion, and detection of nanoparticle inclusions are rarely considered for ion implanted luminescence studies, but the data suggest they are almost inevitable in a wide range of implanted materials.

  17. Iron sulfide attenuates the methanogenic toxicity of elemental copper and zinc oxide nanoparticles and their soluble metal ion analogs.

    PubMed

    Gonzalez-Estrella, Jorge; Gallagher, Sara; Sierra-Alvarez, Reyes; Field, Jim A

    2016-04-01

    Elemental copper (Cu(0)) and zinc oxide (ZnO) nanoparticle (NP) toxicity to methanogens has been attributed to the release of soluble metal ions. Iron sulfide (FeS) partially controls the soluble concentration of heavy metals and their toxicity in aquatic environments. Heavy metals displace the Fe from FeS forming poorly soluble metal sulfides in the FeS matrix. Therefore, FeS may be expected to attenuate the NP toxicity. This work assessed FeS as an attenuator of the methanogenic toxicity of Cu(0) and ZnO NPs and their soluble salt analogs. The toxicity attenuation capacity of fine (25-75μm) and coarse (500 to 1200μm) preparations of FeS (FeS-f and FeS-c respectively) was tested in the presence of highly inhibitory concentrations of CuCl2, ZnCl2 Cu(0) and ZnO NPs. FeS-f attenuated methanogenic toxicity better than FeS-c. The results revealed that 2.5× less FeS-f than FeS-c was required to recover the methanogenic activity to 50% (activity normalized to uninhibited controls). The results also indicated that a molar FeS-f/Cu(0) NP, FeS-f/ZnO NP, FeS-f/ZnCl2, and FeS-f/CuCl2 ratio of 2.14, 2.14, 4.28, and 8.56 respectively, was necessary to recover the methanogenic activity to >75%. Displacement experiments demonstrated that CuCl2 and ZnCl2 partially displaced Fe from FeS. As a whole, the results indicate that not all the sulfide in FeS was readily available to react with the soluble Cu and Zn ions which may explain the need for a large stoichiometric excess of FeS to highly attenuate Cu and Zn toxicity. Overall, this study provides evidence that FeS attenuates the toxicity caused by Cu(0) and ZnO NPs and their soluble ion analogs to methanogens. PMID:26803736

  18. Liquid Crystal Alignment on Solution Derived Zinc Oxide Films via Ion Beam Irradiation.

    PubMed

    Park, Hong-Gyu; Han, Jae-Jun; Seo, Dae-Shik

    2016-03-01

    A 75-nm-thick ZnO film was deposited by a sol-gel method on indium-tin oxide (ITO)-coated glass. This film served as a liquid crystal (LC) alignment layer. We report the fabrication and characteristics of this film after ion-beam (IB) irradiation. Uniform LC alignment was achieved at an IB incident energy above 2400 eV. The IB-treated ZnO surface was analyzed by X-ray photoelectron spectroscopy (XPS), monitoring the intensity of the Zn 2p and O 1s peaks as a function of IB-irradiation energy density. The electro-optical (EO) characteristics of a twisted nematic-liquid crystal display (TN-LCD) were comparable to rubbed polyimide. PMID:27455726

  19. Catalytic-Oxidative Leaching of Low-Grade Complex Zinc Ore by Cu (II) Ions Produced from Copper Ore in Ammonia-Ammonium Sulfate Solution

    NASA Astrophysics Data System (ADS)

    Liu, Zhi Xiong; Yin, Zhou Lan; Hu, Hui Ping; Chen, Qi Yuan

    2012-10-01

    The catalytic-oxidative leaching of a mixed ore, which consists of low-grade oxide copper ore and oxide zinc ore containing ZnS, was investigated in ammonia-ammonium sulfate solution. The effect of the main parameters, such as mass ratio of copper ore to zinc ore, liquid-to-solid ratio, concentration of lixivant, leaching time, and temperature, was studied. The optimal leaching conditions with a maximum extraction of Cu 92.6 pct and Zn 85.5 pct were determined as follows: the mass ratio of copper ore to zinc ore 4/10 g/g, temperature 323.15 K (50 °C), leaching time 6 hours, stirring speed 500 r/min, liquid-to-solid ratio 3.6/1 cm3/g, concentration of lixivant including ammonia 2.0 mol/dm3, ammonium sulfate 1.0 mol/dm3, and ammonium persulfate 0.3 mol/dm3. It was found that ZnS in the oxide zinc ore could be extracted with Cu(II) ion, which was produced from copper ore and was used as the catalyst in the presence of ammonium persulfate.

  20. Continuous flow analysis of iron in zinc electrowinning electrolyte using an iron chalcogenide glass ion-selective electrode Part I. Synthetic media.

    PubMed

    De Marco, Roland; Pejcic, Bobby; Loan, Mitch; Wilcox, Matthew

    2002-04-22

    It is shown that the iron(III) chalcogenide glass membrane ion-selective electrode (ISE) can be calibrated in continuous flow analysis (CFA) using acidified iron(III) nitrate standards, yielding a 60+/-3 mV per decade change in activity of Fe(3+) response in the range 10(-7)-10(-2) M total iron(III). Extended ageing of the iron(III) ISE in 2 M zinc(II) sulphate did not alter the potentiometric response characteristics of the electrode. Furthermore, electrochemical impedance spectroscopy and X-ray photoelectron spectroscopy in the presence and absence of zinc(II) sulphate failed to detect a zinc(II) interference on the iron(III) ISE. CFA/ISE determined activities of Fe(3+) in synthetic zinc electrolyte containing 2x10(-3)-2x10(-1) M total iron(III) yielded results falling within +/-0.2logaFe(3+) unit of the corresponding iron speciation data calculated using the minteqa2 program. PMID:18968611

  1. A new 3,5-bisporphyrinylpyridine derivative as a fluorescent ratiometric probe for zinc ions.

    PubMed

    Moura, Nuno M M; Núñez, Cristina; Santos, Sérgio M; Faustino, M Amparo F; Cavaleiro, José A S; Almeida Paz, Filipe A; Neves, M Graça P M S; Capelo, José Luis; Lodeiro, Carlos

    2014-05-26

    A new 3,5-disubstituted pyridine with two porphyrin moieties was prepared through an efficient synthetic approach involving 2-formyl-5,10,15,20-tetraphenylporphyrin (1), piperidine, and catalytic amounts of [La(OTf)3]. 3,5-Bis(5,10,15,20-tetraphenylporphyrin-2-ylmethyl)pyridine (2) was fully characterized and its sensing ability towards Zn(2+), Cu(2+), Hg(2+), Cd(2+), and Ag(+) was evaluated in solution by absorption and fluorescence spectroscopy and in gas phase by using matrix-assisted laser desorption/ionization (MALDI)-TOF mass spectrometry. Strong changes in the ground and excited state were detected in the case of the soft metal ions Zn(2+), Cd(2+), Hg(2+), and Cu(2+). A three-metal-per-ligand molar ratio was obtained in all cases and a significant ratiometric behavior was observed in the presence of Zn(2+) with the appearance of a new band at 608 nm, which can be assigned to a metal-to-ligand charge transfer. The system was able to quantify 79 ppb of Zn(2+) and the theoretical calculations are in accordance with the stoichiometry observed in solution. The gas-phase sensorial ability of compound 2 towards all metal ions was confirmed by using MALDI-TOF MS and in solid state by using polymeric films of polymethylmethacrylate (PMMA) doped with ligand 2. The results showed that compound 2 can be analytically used to develop new colorimetric molecular devices that are able to discriminate between Hg(2+) and Zn(2+) in solid phase. The crystal structure of Zn(II) complex of 3,5-bisporphyrinylpyridine was unequivocally elucidated by using single-crystal X-ray diffraction studies. PMID:24782336

  2. XRD and EPR structural investigation of some zinc borate glasses doped with iron ions

    NASA Astrophysics Data System (ADS)

    Stefan, Razvan; Pascuta, Petru; Popa, Adriana; Raita, Oana; Indrea, Emil; Culea, Eugen

    2012-02-01

    Glasses in the system xFe2O3·(100-x) [45ZnO·55B2O3] (0≤x≤10 mol%) have been prepared by melting at 1200 °C and rapidly cooling at room temperature. The obtained samples were submitted to an additional thermal treatment at 570 °C for 12 h in order to relax the glass structure as well as to improve the local order. The as cast and heat treated samples were investigated using X-ray diffraction (XRD) and electron paramagnetic resonance (EPR) measurements. The XRD patterns of all the studied samples show their vitreous nature. Structural modifications occurring in the heat treated samples compared to the untreated ones have been pointed out. EPR spectra of untreated and heat treated samples revealed resonance absorptions centered at g≈2.0, g≈4.3 and g≈6.4. The compositional variation of the line intensity and linewidth of the absorptions from g≈4.3 and g≈2.0 have been interpreted in terms of the variation in the concentration of the Fe3+ ions and the interaction between the iron ions. The EPR spectra of the untreated samples containing 5 mol% Fe2O3 have been studied at different temperatures (110-290 K). The line intensity of the resonance signals decreases with increase in temperature whereas the linewidth is found to be independent of temperature. It was also found that the temperature variation of reciprocal line intensity obeys the Boltzmann law.

  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. 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.

  5. Spectroscopic and dielectric investigations of tungsten ions doped zinc bismuth phosphate glass-ceramics

    NASA Astrophysics Data System (ADS)

    Srinivasa Rao, P.; Bala Murali Krishna, S.; Yusub, S.; Ramesh Babu, P.; Tirupataiah, Ch.; Krishna Rao, D.

    2013-03-01

    Pure and tungsten oxide doped ZnF2sbnd Bi2O3sbnd P2O5 glass-ceramics are prepared by the melt quenching and heat treatment techniques. These samples are characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), electron dispersive spectroscopy (EDS) and differential thermal analysis (DTA) techniques. The X-ray diffraction and the scanning electron microscopic studies have revealed the presence of BiPO4, α-Zn3(PO4)2, α-Zn(PO3)2, Zn3(PO4)2, WOF4, WOPO4, γ-Bi2WO6, Bi2W2O9, microcrystalline phases in these samples. FTIR and Raman studies exhibit bands due WO4 and WO6 units along with conventional phosphate groups. The optical absorption and electron spin resonance (ESR) spectra of present glass-ceramics indicate the co-existence of both W5+ and W6+ ions. The analysis of dielectric properties (dielectric constant, loss tan δ, a.c. conductivity) over a range of frequency and temperature suggests a gradual increase in semi conducting character with increase in the concentration of WO3. The studies on dielectric breakdown strength indicated the lowest insulating strength for 5.0 mol% of WO3 in the present samples.

  6. 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

  7. Computational design of zinc-ion-responsive two-photon fluorescent probes with conjugated multi-structures.

    PubMed

    Huang, Shuang; Yang, Bao-Zhu; Jiang, Xing-Fang; Ren, Ai-Min

    2016-01-01

    A series of conjugated multi-structured fluorescent probe molecules based on a salen ligand were designed and investigated in dimethyl sulfoxide solvent using a quantum-chemical method. The results indicate that the one-photon absorption and fluorescence emission spectra (λ (O) and λ (EM)) of these molecules generally show redshifts (of 23.1-74.5 and 22.7-116.6 nm, respectively) upon the coordination of the molecules to Zn(2+). Large Stokes shifts (1511.2-11744.1 cm(-1)) were found for the molecules, meaning that interference between λ (O) and λ (EM) can be avoided for these molecules. The two-photon absorption spectra of the molecules usually present blueshifts, but the two-photon absorption cross-section (δ) greatly increases (by 221.5-868.0 GM) upon the coordination of the molecules with Zn(2+). Most of the molecules show strong two-photon absorption peaks in the range 678.2-824.4 nm, i.e., in the near-infrared region. In a word, the expanded π-conjugated frameworks of these molecules lead to redshifted λ (O) and λ (EM) and enhanced δ values. Moreover, (L-phenyl)​2 and (L-phenyl-ethynyl)2 are the most suitable of the multi-structured molecules examined in this work for use as two-photon fluorescent probes for zinc ion detection in vivo. Graphical Abstract Scheme of the calculated transition energies (E0k and E0n) and the transition dipole moments (M0k and Mkn). NTO 109, NTO 197 and NTO 228 of Zn(L-phenyl-ethynyl), Zn2(L-phenyl-ethynyl)2 and Zn3(L-phenyl)3 for one-photon absorption, respectively. PMID:26781662

  8. A high surface area tunnel-type α-MnO2 nanorod cathode by a simple solvent-free synthesis for rechargeable aqueous zinc-ion batteries

    NASA Astrophysics Data System (ADS)

    Alfaruqi, Muhammad Hilmy; Islam, Saiful; Gim, Jihyeon; Song, Jinju; Kim, Sungjin; Pham, Duong Tung; Jo, Jeonggeun; Xiu, Zhiliang; Mathew, Vinod; Kim, Jaekook

    2016-04-01

    Tunnel-type α-MnO2 with a nanorod morphology was prepared via a simple solvent-free synthesis method for use in aqueous zinc-ion battery (ZIB). This synthesis method produced α-MnO2 with a high BET surface area of 153 m2 g-1. α-MnO2 electrode demonstrated remarkable zinc storage properties (first and second discharge capacities of 323 and 270 mAh g-1 at 16 mA g-1) with good capacity retentions and rate capability. After charging within only 60 s, the α-MnO2 nanorod cathode delivered a considerable discharge capacity of 115 mAh g-1 when cycled at current density of 16 mA g-1.

  9. 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

  10. 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

  11. The NS3 proteinase domain of hepatitis C virus is a zinc-containing enzyme.

    PubMed Central

    Stempniak, M; Hostomska, Z; Nodes, B R; Hostomsky, Z

    1997-01-01

    NS3 proteinase of hepatitis C virus (HCV), contained within the N-terminal domain of the NS3 protein, is a chymotrypsin-like serine proteinase responsible for processing of the nonstructural region of the HCV polyprotein. In this study, we examined the sensitivity of the NS3 proteinase to divalent metal ions, which is unusual behavior for this proteinase class. By using a cell-free coupled transcription-translation system, we found that HCV polyprotein processing can be activated by Zn2+ (and, to a lesser degree, by Cd2+, Pb2+, and Co2+) and inhibited by Cu2+ and Hg2+ ions. Elemental analysis of the purified NS3 proteinase domain revealed the presence of zinc in an equimolar ratio. The zinc content was unchanged in a mutated NS3 proteinase in which active-site residues His-57 and Ser-139 were replaced with Ala, suggesting that the zinc atom is not directly involved in catalysis but rather may have a structural role. Based on data from site-directed mutagenesis combined with zinc content determination, we propose that Cys-97, Cys-99, Cys-145, and His-149 coordinate the structural zinc in the HCV NS3 proteinase. A similar metal binding motif is found in 2A proteinases of enteroviruses and rhinoviruses, suggesting that these 2A proteinases and HCV NS3 proteinase are structurally related. PMID:9060645

  12. Zinc Enzymes.

    ERIC Educational Resources Information Center

    Bertini, I.; And Others

    1985-01-01

    Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)

  13. '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

  14. Crystal Structure of an Unusual Thioredoxin Protein with a Zinc Finger Domain

    SciTech Connect

    Ye, J.; Cho, S; Fuselier, J; Li, W; Beckwith, J; Rapoport, T

    2007-01-01

    Many Gram-negative bacteria have two cytoplasmic thioredoxins, thioredoxin-1 and -2, encoded by the trxA and trxC genes, respectively. Both thioredoxins have the highly conserved WCGPC motif and function as disulfide-bond reductases. However, thioredoxin-2 has unique features: it has an N-terminal motif that binds a zinc ion, and its transcription is under the control of OxyR, which allows it to be up-regulated under oxidative stress. Here, we report the crystal structure of thioredoxin-2 from Rhodobacter capsulatus. The C-terminal region of thioredoxin-2 forms a canonical thioredoxin fold with a central {beta}-sheet consisting of five strands and four flanking {alpha}-helices on either side. The N-terminal zinc finger is composed of four short {beta}-strands (S1-S4) connected by three short loops (L1-L3). The four cysteines are at loops L1 and L3 and form a tetragonal binding site for a zinc ion. The zinc finger is close to the first {beta}-strand and first {alpha}-helix of the thioredoxin fold. Nevertheless, the zinc finger may not directly affect the oxidoreductase activity of thioredoxin-2 because the zinc finger is not near the active site of a protomer and because thioredoxin-2 is a monomer in solution. On the basis of structural similarity to the zinc fingers in Npl4 and Vps36, we propose that the N-terminal zinc finger of thioredoxin-2 mediates protein-protein interactions, possibly with its substrates or chaperones.

  15. Leaching of zinc sulfide by Thiobacillus ferrooxidans: Bacterial oxidation of the sulfur product layer increases the rate of zinc sulfide dissolution at high concentrations of ferrous ions

    SciTech Connect

    Fowler, T.A.; Crundwell, F.K.

    1999-12-01

    This paper reports the results of leaching experiments conducted with and without Thiobacillus ferroxidans at the same conditions in solution. The extent of leaching of ZnS with Bacteria is significantly higher than that without bacteria at high concentrations of ferrous ions. A porous layer of elemental sulfur is present on the surfaces of the chemically leached particles, which no sulfur is present on the surfaces of the bacterially leached particles. The analysis of the data using the shrinking-core model shows that the chemical leaching of ZnS is limited by the diffusion of ferrous ions through the sulfur product layer at high concentrations of ferrous ions. The analysis of the data shows that diffusion through the product layer does not limit the rate of dissolution when bacteria are present. This suggests that the action of T.ferroxidans in oxidizing the sulfur formed on the particle surface is to remove the barrier to diffusion by ferrous ions.

  16. Leaching of zinc sulfide by Thiobacillus ferrooxidans: bacterial oxidation of the sulfur product layer increases the rate of zinc sulfide dissolution at high concentrations of ferrous ions.

    PubMed

    Fowler, T A; Crundwell, F K

    1999-12-01

    This paper reports the results of leaching experiments conducted with and without Thiobacillus ferrooxidans at the same conditions in solution. The extent of leaching of ZnS with bacteria is significantly higher than that without bacteria at high concentrations of ferrous ions. A porous layer of elemental sulfur is present on the surfaces of the chemically leached particles, while no sulfur is present on the surfaces of the bacterially leached particles. The analysis of the data using the shrinking-core model shows that the chemical leaching of ZnS is limited by the diffusion of ferrous ions through the sulfur product layer at high concentrations of ferrous ions. The analysis of the data shows that diffusion through the product layer does not limit the rate of dissolution when bacteria are present. This suggests that the action of T. ferrooxidans in oxidizing the sulfur formed on the particle surface is to remove the barrier to diffusion by ferrous ions. PMID:10583978

  17. Improving the cycle life of a high-rate, high-potential aqueous dual-ion battery using hyper-dendritic zinc and copper hexacyanoferrate

    NASA Astrophysics Data System (ADS)

    Gupta, Tanya; Kim, Andrew; Phadke, Satyajit; Biswas, Shaurjo; Luong, Thao; Hertzberg, Benjamin J.; Chamoun, Mylad; Evans-Lutterodt, Kenneth; Steingart, Daniel A.

    2016-02-01

    Prussian Blue Analogue (PBA)-Zn aqueous batteries are attractive because of the high potential of PBA against Zn (˜1.7 V), relative safety of the system, and high rate capability. But, despite the long cycle life of PBA half-cells, full PBA-Zn battery systems studied thus far have typically reported only up to 100 cycles and suffer significant capacity fade beyond that. In this work we demonstrate that the loss in capacity retention and cycle life is a combined effect of Zn2+ ion poisoning at the PBA cathode, as well as dendrite formation in the zinc anode. We address both these issues via the use of a dual ion (Na+ as the primary charge carrier) electrolyte and hyper-dendritic Zinc (HD Zn) as the anode. The copper hexacyanoferrate (CuHcf) vs. HD Zn system with Na+ ion electrolyte demonstrated herein exhibits 90% (83%) capacity retention after 300 (500) cycles at a 5C rate and a 3% reduction in usable capacity from 1C to 5C. Detailed characterization is done using in situ synchrotron energy-dispersive XRD (EDXRD), conventional XRD, XPS, SEM, TEM, and electrochemical techniques.

  18. Determination of Zinc(II) Ions Released into Artificial Digestive Juices from Culinary-Medicinal Button Mushroom, Agaricus bisporus (Agaricomycetidae), Biomass of In Vitro Cultures Using an Anodic Stripping Voltammetry Method.

    PubMed

    Kala, Katarzyna; Muszynska, Bozena; Zajac, Magdalena; Krezalek, Remigiusz; Opoka, Wlodzimierz

    2016-01-01

    Zinc is one of those microelements that are essential for the proper functioning of the human body and must be supplemented in our food at a daily dose of 15 mg. It is well known that mushrooms accumulate elements; thus, in order to determine the extent of accumulation and the level of zinc released from mushrooms, in vitro cultures of Agaricus bisporus were established. The cultures were run on a modified Oddoux medium (a control culture) as well as on the same medium with the addition of zinc hydroaspartate (100 and 200 mg/L) and zinc sulfate (87.23 and 174.47 mg/L). These compounds were chosen to help estimate which form, organic or inorganic, results in a better assimilation of zinc(II) ions by biomass. As the next step, the level of zinc(II) ions released from the lyophilized biomass of in vitro cultures to the digestive juices, under thermal conditions of the human body (37°C), was determined. For this purpose, artificial digestive juices, imitating the composition of human digestive juices, were used. For determination of zinc(II) ions in the digestive tract, an anodic stripping voltammetry method was employed. The amount of zinc released into artificial saliva over 1 minute varied from 0.15 mg/100 g d.w. in the control culture to 2.35 mg/100 g d.w. in the biomass in the medium to which 200 mg/L zinc hydroaspartate had been added. Values were higher in gastric juice and depended on incubation time (2.66 to 30.63 mg/100 g d.w.). In intestinal juice, the highest value of the released zinc grew to 24.20 mg/100 g d.w. (biomass of A. bisporus in vitro cultures in medium with the addition of 200 mg/L zinc hydroaspartate). Total average amount of zinc released into artificial digestive juices was the highest (56.26 mg/100 g d.w.) from A. bisporus biomass of in vitro cultures in the medium to which 200 mg/L zinc hydroaspartate had been added. PMID:27279537

  19. Zinc poisoning

    MedlinePlus

    ... other materials to make industrial items such as paint, dyes, and more. These combination substances can be ... Compounds used to make paint, rubber, dyes, wood preservatives, and ... Zinc chloride Zinc oxide (relatively nonharmful) Zinc ...

  20. Kinetic isotope effects for concerted multiple proton transfer: a direct dynamics study of an active-site model of carbonic anhydrase II.

    PubMed

    Smedarchina, Zorka; Siebrand, Willem; Fernández-Ramos, Antonio; Cui, Qiang

    2003-01-01

    The rate constant of the reaction catalyzed by the enzyme carbonic anhydrase II, which removes carbon dioxide from body fluids, is calculated for a model of the active site. The rate-determining step is proton transfer from a zinc-bound water molecule to a histidine residue via a bridge of two or more water molecules. The structure of the active site is known from X-ray studies except for the number and location of the water molecules. Model calculations are reported for a system of 58 atoms including a four-coordinated zinc ion connected to a methylimidazole molecule by a chain of two waters, constrained to reproduce the size of the active site. The structure and vibrational force field are calculated by an approximate density functional treatment of the proton-transfer step at the Self-Consistent-Charge Density Functional Tight Binding (SCC-DFTB) level. A single transition state is found indicating concerted triple proton transfer. Direct-dynamics calculations for proton and deuteron transfer and combinations thereof, based on the Approximate Instanton Method and on Variational Transition State Theory with Tunneling Corrections, are in fair agreement and yield rates that are considerably higher and kinetic isotope effects (KIEs) that are somewhat higher than experiment. Classical rate constants obtained from Transition State Theory are smaller than the quantum values but the corresponding KIEs are five times larger. For multiple proton transfer along water bridges classical KIEs are shown to be generally larger than quantum KIEs, which invalidates the standard method to distinguish tunneling and over-barrier transfer. In the present case, a three-way comparison of classical and quantum results with the observed data is necessary to conclude that proton transfer along the bridge proceeds by tunneling. The results suggest that the two-water bridge is present in low concentrations but makes a substantial contribution to proton transport because of its high

  1. Computational investigation of the histidine ammonia-lyase reaction: a modified loop conformation and the role of the zinc(II) ion.

    PubMed

    Seff, Amalia-Laura; Pilbák, Sarolta; Silaghi-Dumitrescu, Ioan; Poppe, László

    2011-07-01

    Possible reaction intermediates of the histidine ammonia-lyase (HAL) reaction were investigated within the tightly closed active site of HAL from Pseudomonas putida (PpHAL). The closed structure of PpHAL was derived from the crystal structure of PpHAL inhibited with L-cysteine, in which the 39-80 loop including the catalytically essential Tyr53 was replaced. This modified loop with closed conformation was modeled using the structure of phenylalanine ammonia-lyase from Anabaena variabilis (AvPAL) with a tightly closed active site as a template. Three hypothetical structures of the covalently bound intermediate in the PpHAL active site were investigated by conformational analysis. The distances between the acidic pro-S β-hydrogen of the ligand and the appropriate oxygen atoms of Tyr53, Ty280 and Glu414--which may act as enzymic bases--in the conformations of the three hypothetical intermediate structures were analyzed together with the substrate and product arrangements. The calculations indicated that the most plausible HAL reaction pathway involves the N-MIO intermediate structure in which the L-histidine substrate is covalently bound to the N-3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) prosthetic group of the apoenzyme via the amino group. Density functional theory (DFT) calculations--on a truncated model of the N-MIO intermediate containing a Zn²⁺ ion coordinated to the imidazole ring of the ligand and to His83, Met382 and a water molecule--indicated that Zn-complex formation plays a role in the reactivity and substrate specificity of HAL. PMID:20922445

  2. Biopharmaceutical characterisation of ciprofloxacin-metallic ion interactions: comparative study into the effect of aluminium, calcium, zinc and iron on drug solubility and dissolution.

    PubMed

    Stojković, Aleksandra; Tajber, Lidia; Paluch, Krzysztof J; Djurić, Zorica; Parojčić, Jelena; Corrigan, Owen I

    2014-03-01

    Ciprofloxacin bioavailability may be reduced when ciprofloxacin is co-administered with metallic ion containing preparations. In our previous study, physicochemical interaction between ciprofloxacin and ferrous sulphate was successfully simulated in vitro. In the present work, comparative in vitro ciprofloxacin solubility and dissolution studies were performed in the reactive media containing aluminium hydroxide, calcium carbonate or zinc sulphate. Solid phases collected from the dissolution vessel with aluminium hydroxide, calcium carbonate and zinc sulphate were investigated for their properties. The results obtained indicate that different types of adducts may form and retard ciprofloxacin solubility and dissolution. In the case of aluminium, no phase changes were observed. The solid phase generated in the presence of calcium carbonate was identified as hydrated ciprofloxacin base. Similarly to iron, a new complex consistent with Zn(SO4)2(Cl)2(ciprofloxacin)2 × nH2O stoichiometry was generated in the presence of relatively high concentrations of ciprofloxacin hydrochloride and zinc sulphate, indicating that small volume dissolution experiments can be useful for biorelevant dissolution tests. PMID:24670353

  3. Effect of chloride ion on the sedimentation volume and zeta potential of zinc insulin suspensions in neutral pH range.

    PubMed

    Kim, Y; Cuff, G W; Morris, R M

    1995-06-01

    When zinc insulin suspensions of different pH values were prepared in the presence of sodium chloride, an unusually high sedimentation volume was found at about pH 6.9. An experimental investigation was conducted in an effort to understand this phenomenon. The experiments involved measurements of electrophoretic mobilities to calculate zeta potentials and sedimentation volumes of zinc insulin suspensions prepared at different NaCl concentrations (0, 17, and 120 mM) and at various pH values from 5 to 8. The general trend observed was that the magnitude of the zeta potential increased with pH when it was higher than the isoelectric point of 5.3. When the sodium chloride concentration was 120 mM, a very rapid change in zeta potential was observed in the pH range of 6.6 to 7.2, with a maximum magnitude of zeta potential at about pH 6.9, the same pH that was observed to yield the largest sedimentation volume. Our experimental results indicate that the greatest adsorption of chloride ion on the zinc insulin suspension particles occurred in the same pH range, which appeared to be responsible for the rapid change of zeta potential in that pH range. The experimental data were interpreted by DLVO (Derjaguin, Landau, Vervey, and Overbeek) theory, which involves a comparison of the forces of electrostatic repulsion and of the van der Waals attraction. PMID:7562418

  4. 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.

  5. 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.

  6. Finding a Needle in the Haystack: Computational Modeling of Mg2+ Binding in the Active Site of Protein Farnesyltransferase

    PubMed Central

    Yang, Yue; Chakravorty, Dhruva K.; Merz, Kenneth M.

    2010-01-01

    Studies aimed at elucidating the unknown Mg2+ binding site in protein farnesyltransferase (FTase) are reported. FTase catalyzes the transfer of a farnesyl group to a conserved cysteine residue (Cys1p) on a target protein, an important step for proteins in the signal transduction pathways (e.g. Ras). Mg2+ ions accelerate the protein farnesylation reaction by up to 700-fold. The exact function of Mg2+ in catalysis and the structural characteristics of its binding remain unresolved to date. Molecular Dynamics (MD) simulations addressing the role of magnesium ions in FTase are presented, and relevant octahedral binding motifs for Mg2+ in wild type (WT) FTase and Dβ352A mutant are explored. Our simulations suggest that the addition of Mg2+ ions causes a conformational changes to occur in the FTase active site, breaking interactions known to keep FPP in its inactive conformation. Two relevant Mg2+ ion binding motifs were determined in WT FTase. In the first binding motif, WT1, the Mg2+ ion is coordinated to D352β, zinc-bound D297β, two water molecules, and one oxygen atoms from the α- and β-phosphates of farnesyl diphosphate (FPP). The second binding motif, WT2, is identical with the exception of the zinc-bound D297β being replaced by a water molecule in the Mg2+ coordination complex. In the Dβ352A mutant Mg2+ binding motif, D297β, three water molecules and one oxygen atom from the α- and β-phosphates of FPP complete the octahedral coordination sphere of Mg2+. Simulations of WT FTase, in which Mg2+ was replaced by water in the active site, re-created the salt bridges and hydrogen bonding patterns around FPP, validating these simulations. In all Mg2+ binding motifs, a key hydrogen bond was identified between a magnesium bound water and Cys1p, bridging the two metallic binding sites, and thereby, reducing the equilibrium distance between the reacting atoms of FPP Cys1p. The free energy profiles calculated for these systems provide a qualitative understanding of

  7. 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

  8. 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

  9. Photo-initiated ion formation from octaethyl-porphyrin and its zinc chelate as a model for electron transfer in reaction centers.

    PubMed Central

    Ballard, S G; Mauzerall, D

    1978-01-01

    Ion formation from the reaction of triplet (T) and ground state (P) octaethyl-porphyrin (OEP) and zinc octaethyl porphyrin (ZnOEP) and the corresponding cross-reactions have been measured in dry acetonitrile. A uniquely sensitive and fast conductance apparatus and a pulsed dye laser allowed the measurements to be made at the necessarily very low concentrations of T. The hemogeneous reaction of T (ZnOEP) and P (ZnOEP) occurs with rat constant k(1) = 2.0 x 10(8) M(-1)s(-1) and an ion yield of 67%. The similar homogeneous reaction of OEP has k(2) = 1.3 x 10(8)M(-1)s(-1) but an ion yield of only 3%. The cross-reaction of T (OEP) with P (ZnOEP) has k(3) = 1.5 x 10(8) M(-1)s(-1) and an ion yield of 27%, while the inverse cross-reaction of T (ZnOEP) with P (OEP) has k(4) = 3 x 10(8) M(-1)s(-1) and an ion yield of 20%. Thus, the rate constants are only slightly affected but the yields are sensitive to the porphyrin. The possible formation of the heterogeneous ions ZnOEP+ + OEP-, thermodynamically favored by 0.3 V over the homogeneous ions, has little influence on the observed yields. The data are explained by electron transfer and Coulomb field-electon spin-controlled escape of the initial ion-pair. PMID:708837

  10. Selective sorption of lead, cadmium and zinc ions by a polymeric cation exchanger containing nano-Zr(HPO3S)2.

    PubMed

    Zhang, Qingrui; Pan, Bingcai; Pan, Bingjun; Zhang, Weiming; Jia, Kun; Zhang, Quanxing

    2008-06-01

    A novel polymeric hybrid sorbent, namely ZrPS-001, was fabricated for enhanced sorption of heavy metal ions by impregnating Zr(HPO3S)2 (i.e., ZrPS) nanoparticles within a porous polymeric cation exchanger D-001. The immobilized negatively charged groups bound to the polymeric matrix D-001 would result in preconcentration and permeation enhancement of target metal ions prior to sequestration, and ZrPS nanoparticles are expected to sequester heavy metals selectively through an ion-exchange process. Highly effective sequestration of lead, cadmium, and zinc ions from aqueous solution can be achieved by ZrPS-001 even in the presence of competing calcium ion at concentration several orders of magnitude greater than the target species. The exhausted ZrPS-001 beads are amenable to regeneration with 6 M HCI solution for repeated use without any significant capacity loss. Fixed-bed column treatment of simulated waters containing heavy metals at high or trace levels was also performed. The content of heavy metals in treated effluent approached or met the WHO drinking water standard. PMID:18589978

  11. Zinc phosphate conversion coatings

    DOEpatents

    Sugama, T.

    1997-02-18

    Zinc phosphate conversion coatings for producing metals which exhibit enhanced corrosion prevention characteristics are prepared by the addition of a transition-metal-compound promoter comprising a manganese, iron, cobalt, nickel, or copper compound and an electrolyte such as polyacrylic acid, polymethacrylic acid, polyitaconic acid and poly-L-glutamic acid to a phosphating solution. These coatings are further improved by the incorporation of Fe ions. Thermal treatment of zinc phosphate coatings to generate {alpha}-phase anhydrous zinc phosphate improves the corrosion prevention qualities of the resulting coated metal. 33 figs.

  12. Zinc phosphate conversion coatings

    DOEpatents

    Sugama, Toshifumi

    1997-01-01

    Zinc phosphate conversion coatings for producing metals which exhibit enhanced corrosion prevention characteristics are prepared by the addition of a transition-metal-compound promoter comprising a manganese, iron, cobalt, nickel, or copper compound and an electrolyte such as polyacrylic acid, polymethacrylic acid, polyitaconic acid and poly-L-glutamic acid to a phosphating solution. These coatings are further improved by the incorporation of Fe ions. Thermal treatment of zinc phosphate coatings to generate .alpha.-phase anhydrous zinc phosphate improves the corrosion prevention qualities of the resulting coated metal.

  13. 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

  14. Active-site mutagenesis of tetanus neurotoxin implicates TYR-375 and GLU-271 in metalloproteolytic activity.

    PubMed

    Rossetto, O; Caccin, P; Rigoni, M; Tonello, F; Bortoletto, N; Stevens, R C; Montecucco, C

    2001-08-01

    Tetanus neurotoxin (TeNT) blocks neurotransmitter release by cleaving VAMP/synaptobrevin, a membrane associated protein involved in synaptic vesicle fusion. Such activity is exerted by the N-terminal 50kDa domain of TeNT which is a zinc-dependent endopeptidase (TeNT-L-chain). Based on the three-dimensional structure of botulinum neurotoxin serotype A (BoNT/A) and serotype B (BoNT/B), two proteins closely related to TeNT, and on X-ray scattering studies of TeNT, we have designed mutations at two active site residues to probe their involvement in activity. The active site of metalloproteases is composed of a primary sphere of residues co-ordinating the zinc atom, and a secondary sphere of residues that determines proteolytic specificity and activity. Glu-261 and Glu-267 directly co-ordinates the zinc atom in BoNT/A and BoNT/B respectively and the corresponding residue of TeNT was replaced by Asp or by the non conservative residue Ala. Tyr-365 is 4.3A away from zinc in BoNT/A, and the corresponding residue of TeNT was replaced by Phe or by Ala. The purified mutants had CD, fluorescence and UV spectra closely similar to those of the wild-type molecule. The proteolytic activity of TeNT-Asp-271 (E271D) is similar to that of the native molecule, whereas that of TeNT-Phe-375 (Y375F) is lower than the control. Interestingly, the two Ala mutants are completely devoid of enzymatic activity. These results demonstrate that both Glu-271 and Tyr-375 are essential for the proteolytic activity of TeNT. PMID:11306125

  15. Zinc Biochemistry: From a Single Zinc Enzyme to a Key Element of Life12

    PubMed Central

    Maret, Wolfgang

    2013-01-01

    The nutritional essentiality of zinc for the growth of living organisms had been recognized long before zinc biochemistry began with the discovery of zinc in carbonic anhydrase in 1939. Painstaking analytical work then demonstrated the presence of zinc as a catalytic and structural cofactor in a few hundred enzymes. In the 1980s, the field again gained momentum with the new principle of “zinc finger” proteins, in which zinc has structural functions in domains that interact with other biomolecules. Advances in structural biology and a rapid increase in the availability of gene/protein databases now made it possible to predict zinc-binding sites from metal-binding motifs detected in sequences. This procedure resulted in the definition of zinc proteomes and the remarkable estimate that the human genome encodes ∼3000 zinc proteins. More recent developments focus on the regulatory functions of zinc(II) ions in intra- and intercellular information transfer and have tantalizing implications for yet additional functions of zinc in signal transduction and cellular control. At least three dozen proteins homeostatically control the vesicular storage and subcellular distribution of zinc and the concentrations of zinc(II) ions. Novel principles emerge from quantitative investigations on how strongly zinc interacts with proteins and how it is buffered to control the remarkably low cellular and subcellular concentrations of free zinc(II) ions. It is fair to conclude that the impact of zinc for health and disease will be at least as far-reaching as that of iron. PMID:23319127

  16. The zinc repository of Cupriavidus metallidurans.

    PubMed

    Herzberg, Martin; Dobritzsch, Dirk; Helm, Stefan; Baginsky, Sacha; Nies, Dietrich H

    2014-11-01

    Zinc is a central player in the metalloproteomes of prokaryotes and eukaryotes. We used a bottom-up quantitative proteomic approach to reveal the repository of the zinc pools in the proteobacterium Cupriavidus metallidurans. About 60% of the theoretical proteome of C. metallidurans was identified, quantified, and the defect in zinc allocation was compared between a ΔzupT mutant and its parent strain. In both strains, the number of zinc-binding proteins and their binding sites exceeded that of the zinc ions per cell, indicating that the totality of the zinc proteome provides empty binding sites for the incoming zinc ions. This zinc repository plays a central role in zinc homeostasis in C. metallidurans and probably also in other organisms. PMID:25315396

  17. 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?

  18. Intracellular accumulation dynamics and fate of zinc ions in alveolar epithelial cells exposed to airborne ZnO nanoparticles at the air-liquid interface

    SciTech Connect

    Mihai, Cosmin; Chrisler, William B.; Xie, Yumei; Hu, Dehong; Szymanski, Craig J.; Tolic, Ana; Klein, Jessica; Smith, Jordan N.; Tarasevich, Barbara J.; Orr, Galya

    2015-02-01

    Airborne nanoparticles (NPs) that enter the respiratory tract are likely to reach the alveolar region. Accumulating observations support a role for zinc oxide (ZnO) NP dissolution in toxicity, but the majority of in vitro studies were conducted in cells exposed to NPs in growth media, where large doses of dissolved ions are shed into the exposure solution. To determine the precise intracellular accumulation dynamics and fate of zinc ions (Zn2+) shed by airborne NPs in the cellular environment, we exposed alveolar epithelial cells to aerosolized NPs at the air-liquid interface (ALI). Using a fluorescent indicator for Zn2+, together with organelle-specific fluorescent proteins, we quantified Zn2+ in single cells and organelles over time. We found that at the ALI, intracellular Zn2+ values peaked 3 h post exposure and decayed to normal values by 12 h, while in submersed cultures, intracellular Zn2+ values continued to increase over time. The lowest toxic NP dose at the ALI generated peak intracellular Zn2+ values that were nearly 3 folds lower than the peak values generated by the lowest toxic dose of NPs in submersed cultures, and 8 folds lower than the peak values generated by the lowest toxic dose of ZnSO4 or Zn2+. At the ALI, the majority of intracellular Zn2+ was found in endosomes and lysosomes as early as 1 h post exposure. In contrast, the majority of intracellular Zn2+ following exposures to ZnSO4 was found in other larger vesicles, with less than 10% in endosomes and lysosomes. Together, our observations indicate that low but critical levels of intracellular Zn2+ have to be reached, concentrated specifically in endosomes and lysosomes, for toxicity to occur, and point to the focal dissolution of the NPs in the cellular environment and the accumulation of the ions specifically in endosomes and lysosomes as the processes underlying the potent toxicity of airborne ZnO NPs.

  19. Active-Site Monovalent Cations Revealed in a 1.55 Å Resolution Hammerhead Ribozyme Structure

    PubMed Central

    Anderson, Michael; Schultz, Eric P.; Martick, Monika; Scott, William G.

    2013-01-01

    We have obtained a 1.55 Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni in conditions that permit detailed observations of Na+ ion binding in the ribozyme's active site. At least two such Na+ ions are observed. The first Na+ ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical to that previously observed for divalent cations. A second Na+ ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na+, but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na+ directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest resolution ribozyme structure in the protein data bank. PMID:23711504

  20. Fluidized beds in flow analysis: use with ion-exchange separation for spectrophotometric determination of zinc in plant digests.

    PubMed

    Ribeiro, Marta F T; Dias, Ana C B; Santos, João L M; Lima, José L F C; Zagatto, Elias A G

    2006-02-01

    A novel strategy for utilization of solid reagents in flow analysis is proposed. Establishment of diffuse and reproducible geometry enables the solid particles to be maintained in constant floating, reflux, and circulating motion inside a mini-chamber. This is efficiently accomplished with pulsed flows, a characteristic of multi-pumping flow systems. Drawbacks inherent in solid-phase packed columns, for example backpressure, preferential pathways, swelling, etc., and some limitations inherent in immobilized reagents are minimised. Spectrophotometric determination of zinc in plants was selected as an application of the technique. Dowex 1-X8 anionic resin was kept freely inside a mini-chamber. Zinc chloro-complexes were adsorbed on the moving particles and derivatization with zincon was performed after elution. Analytical figures of merit and the potential and limitations of the approach are discussed. PMID:16408216

  1. New beginnings for matrix metalloproteinase inhibitors: identification of high-affinity zinc-binding groups.

    PubMed

    Puerta, David T; Lewis, Jana A; Cohen, Seth M

    2004-07-14

    In an effort to identify promising non-hydroxamate inhibitors of matrix metalloproteinases (MMPs), several new zinc-binding groups (ZBGs) based on pyrone, pyrothione, hydroxypyridinone, and hydroxypyridinethione chelators have been examined. Structural studies with tris(pyrazolyl)borate model complexes show that these ligands bind to the MMP active site zinc(II) ion in a bidentate fashion, similar to that found with hydroxamate-based inhibitors. Fluorescence- and colorimetric-based enzyme assays have been used to determine the IC50 values for these ZBGs against MMP-3; mixed O,S-donor ligands were found to be remarkably potent, with IC50 values as much as 700-fold lower than that found for acetohydroxamic acid. Inhibitory activity was found to parallel metal binding affinity as determined in titrations with model complexes. These results demonstrate that MPIs based on new ZBGs are feasible and may indeed improve the overall performance of inhibitors designed against these important medicinal targets. PMID:15237990

  2. Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules

    SciTech Connect

    Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; Bae, Seong Hee; Hong, Seungwoo; Cho, Kyung-Bin; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo

    2015-06-19

    Here we report redox-inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. We describe the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn2+ ion in (TMC)FeIII-(O2)-Zn(CF3SO3)2 (1-Zn2+) decreases the Lewis acidity of the Zn2+ ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn2+. This further changes the reactivities of 1-Zn2+ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn2+, whereas 1-Zn2+ coordinating two water molecules, (TMC)FeIII-(O2)-Zn(CF3SO3)2-(OH2)2 [1-Zn2+-(OH2)2], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn2+ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn2+-(OH2)2. Finally, the present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates.

  3. Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules

    DOE PAGESBeta

    Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; Bae, Seong Hee; Hong, Seungwoo; Cho, Kyung-Bin; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo

    2015-06-19

    Here we report redox-inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. We describe the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn2+ ion in (TMC)FeIII-(O2)-Zn(CF3SO3)2 (1-Zn2+) decreases the Lewis acidity of the Zn2+ ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn2+. This further changes the reactivities of 1-Zn2+ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn2+, whereas 1-Zn2+ coordinatingmore » two water molecules, (TMC)FeIII-(O2)-Zn(CF3SO3)2-(OH2)2 [1-Zn2+-(OH2)2], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn2+ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn2+-(OH2)2. Finally, the present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates.« less

  4. Tuning the Redox Properties of a Nonheme Iron(III)–Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules

    PubMed Central

    Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; Bae, Seong Hee; Hong, Seungwoo; Cho, Kyung-Bin; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo

    2015-01-01

    Redox-inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. Herein we report the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn2+ ion in (TMC)FeIII-(O2)-Zn(CF3SO3)2 (1-Zn2+) decreases the Lewis acidity of the Zn2+ ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn2+. This further changes the reactivities of 1-Zn2+ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn2+, whereas 1-Zn2+ coordinating two water molecules, (TMC)FeIII-(O2)-Zn(CF3SO3)2-(OH2)2 [1-Zn2+-(OH2)2], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn2+ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn2+-(OH2)2. The present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates. PMID:26096281

  5. 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

  6. The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold.

    PubMed Central

    Carfi, A; Pares, S; Duée, E; Galleni, M; Duez, C; Frère, J M; Dideberg, O

    1995-01-01

    The 3-D structure of Bacillus cereus (569/H/9) beta-lactamase (EC 3.5.2.6), which catalyses the hydrolysis of nearly all beta-lactams, has been solved at 2.5 A resolution by the multiple isomorphous replacement method, with density modification and phase combination, from crystals of the native protein and of a specially designed mutant (T97C). The current model includes 212 of the 227 amino acid residues, the zinc ion and 10 water molecules. The protein is folded into a beta beta sandwich with helices on each external face. To our knowledge, this fold has never been observed. An approximate internal molecular symmetry is found, with a 2-fold axis passing roughly through the zinc ion and suggesting a possible gene duplication. The active site is located at one edge of the beta beta sandwich and near the N-terminal end of a helix. The zinc ion is coordinated by three histidine residues (86, 88 and 149) and a water molecule. A sequence comparison of the relevant metallo-beta-lactamases, based on this protein structure, highlights a few well-conserved amino acid residues. The structure shows that most of these residues are in the active site. Among these, aspartic acid 90 and histidine 210 participate in a proposed catalytic mechanism for beta-lactam hydrolysis. Images PMID:7588620

  7. Insights into the Effects of Zinc Doping on Structural Phase Transition of P2-Type Sodium Nickel Manganese Oxide Cathodes for High-Energy Sodium Ion Batteries.

    PubMed

    Wu, Xuehang; Xu, Gui-Liang; Zhong, Guiming; Gong, Zhengliang; McDonald, Matthew J; Zheng, Shiyao; Fu, Riqiang; Chen, Zonghai; Amine, Khalil; Yang, Yong

    2016-08-31

    P2-type sodium nickel manganese oxide-based cathode materials with higher energy densities are prime candidates for applications in rechargeable sodium ion batteries. A systematic study combining in situ high energy X-ray diffraction (HEXRD), ex situ X-ray absorption fine spectroscopy (XAFS), transmission electron microscopy (TEM), and solid-state nuclear magnetic resonance (SS-NMR) techniques was carried out to gain a deep insight into the structural evolution of P2-Na0.66Ni0.33-xZnxMn0.67O2 (x = 0, 0.07) during cycling. In situ HEXRD and ex situ TEM measurements indicate that an irreversible phase transition occurs upon sodium insertion-extraction of Na0.66Ni0.33Mn0.67O2. Zinc doping of this system results in a high structural reversibility. XAFS measurements indicate that both materials are almost completely dependent on the Ni(4+)/Ni(3+)/Ni(2+) redox couple to provide charge/discharge capacity. SS-NMR measurements indicate that both reversible and irreversible migration of transition metal ions into the sodium layer occurs in the material at the fully charged state. The irreversible migration of transition metal ions triggers a structural distortion, leading to the observed capacity and voltage fading. Our results allow a new understanding of the importance of improving the stability of transition metal layers. PMID:27494351

  8. Removal of zinc(II) ion by graphene oxide (GO) and functionalized graphene oxide-glycine (GO-G) as adsorbents from aqueous solution: kinetics studies

    NASA Astrophysics Data System (ADS)

    Najafi, F.

    2015-05-01

    The main purpose of this study is to explain the absorption of zinc from aqueous solution by grapheme oxide and functionalized grapheme oxide with glycine as the adsorbent surface. For confirmed functionalized graphene oxide, the glycine amino group was added to the surface of graphene oxide. The effects of the initial concentration of Zn(II) ions and contact time were studied. Results showed that with increasing initial concentration of Zn(II) ions, the adsorption capacity increased. The adsorption capacity did not show a large change after 50 min; therefore, for the study of kinetic parameters, the optimal time of 50 min was selected. The chemical structure of graphene oxide was confirmed by using FT-IR analysis. The adsorption process of Zn(II) ions graphene oxide and functionalized graphene oxide-glycine surfaces was fixed at 298 K and pH 6. The pseudo-first-order and the pseudo-second-order (types I, II, III and IV) kinetic models were tested for the adsorption process and the results showed that the kinetic parameters best fit type (I) of the pseudo-second-order model. A high R 2 was used to be the best match.

  9. Metal resistance-related genes are differently expressed in response to copper and zinc ion in six Acidithiobacillus ferrooxidans strains.

    PubMed

    Wu, Xueling; Zhang, Zhenzhen; Liu, Lili; Deng, Fanfan; Liu, Xinxing; Qiu, Guanzhou

    2014-12-01

    Metal resistance of acidophilic bacteria is very significant during bioleaching of copper ores since high concentration of metal is harmful to the growth of microorganisms. The resistance levels of six Acidithiobacillus ferrooxidans strains to 0.15 M copper and 0.2 M zinc were investigated, and eight metal resistance-related genes (afe-0022, afe-0326, afe-0329, afe-1143, afe-0602, afe-0603, afe-0604, and afe-1788) were sequenced and analyzed. The transcriptional expression levels of eight possible metal tolerance genes in six A. ferrooxidans strains exposed to 0.15 M Cu(2+) and 0.2 M Zn(2+) were determined by real-time quantitative PCR (RT-qPCR), respectively. The copper resistance levels of six A. ferrooxidans strains declined followed by DY26, DX5, DY15, GD-B, GD-0, and YTW. The zinc tolerance levels of six A. ferrooxidans strains exposed to 0.2 M Zn(2+) from high to low were YTW > GD-B > DY26 > GD-0 > DX5 > DY15. Seven metal tolerance-related genes all presented in the genome of six strains, except afe-0604. The metal resistance-related genes showed different transcriptional expression patterns in six A. ferrooxidans strains. The expression of gene afe-0326 and afe-0022 in six A. ferrooxidans strains in response to 0.15 M Cu(2+) showed the same trend with the resistance levels. The expression levels of genes afe-0602, afe-0603, afe-0604, and afe-1788 in six strains response to 0.2 M Zn(2+) did not show a clear correlation between the zinc tolerance levels of six strains. According to the results of RT-qPCR and bioinformatics analysis, the proteins encoded by afe-0022, afe-0326, afe-0329, and afe-1143 were related to Cu(2+) transport of A. ferrooxidans strains. PMID:25023638

  10. 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.

  11. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    SciTech Connect

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  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. Temperature-dependent toxicities of nano zinc oxide to marine diatom, amphipod and fish in relation to its aggregation size and ion dissolution.

    PubMed

    Wong, Stella W Y; Leung, Kenneth M Y

    2014-08-01

    This study, for the first time, concurrently investigated the influence of seawater temperature, exposure concentration and time on the aggregation size and ion dissolution of nano zinc oxides (nZnO) in seawater, and the interacting effect of temperature and waterborne exposure of nZnO to the marine diatom Skeletonema costatum, amphipod Melita longidactyla and fish Oryzias melastigma, respectively. Our results showed that aggregate size was jointly affected by seawater temperature, nZnO concentration and exposure time. Among the three factors, the concentration of nZnO was the most important and followed by exposure time, whereas temperature was less important as reflected by their F values in the three-way analysis of variance (concentration: F3, 300 = 247.305; time: F2, 300 = 20.923 and temperature: F4, 300 = 4.107; All p values <0.001). The aggregate size generally increased with increasing nZnO concentration and exposure time. The release of Zn ions from nZnO was significantly influenced by seawater temperature and exposure time; the ion dissolution rate generally increased with decreasing temperature and increasing exposure time. Growth inhibition of diatoms increased with increasing temperature, while temperature and nZnO had an interactional effect on their photosynthesis. For the amphipod, mortality was positively correlated with temperature. Fish larvae growth rate was only affected by temperature but not nZnO, while the two factors interactively modulated the expression of heat shock and metallothionein proteins. Evidently, temperature can influence aggregate size and ion dissolution and thus toxicity of nZnO to the marine organisms in a species-specific manner. PMID:24219175

  14. 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

  15. 46 CFR 148.330 - Zinc ashes; zinc dross; zinc residues; zinc skimmings.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Zinc ashes; zinc dross; zinc residues; zinc skimmings... Materials § 148.330 Zinc ashes; zinc dross; zinc residues; zinc skimmings. (a) The shipper must inform the cognizant Coast Guard Captain of the Port in advance of any cargo transfer operations involving zinc...

  16. 46 CFR 148.330 - Zinc ashes; zinc dross; zinc residues; zinc skimmings.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Zinc ashes; zinc dross; zinc residues; zinc skimmings... Materials § 148.330 Zinc ashes; zinc dross; zinc residues; zinc skimmings. (a) The shipper must inform the cognizant Coast Guard Captain of the Port in advance of any cargo transfer operations involving zinc...

  17. 46 CFR 148.330 - Zinc ashes; zinc dross; zinc residues; zinc skimmings.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Zinc ashes; zinc dross; zinc residues; zinc skimmings... Materials § 148.330 Zinc ashes; zinc dross; zinc residues; zinc skimmings. (a) The shipper must inform the cognizant Coast Guard Captain of the Port in advance of any cargo transfer operations involving zinc...

  18. 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

  19. Three-dimensional printed sample load/inject valves enabling online monitoring of extracellular calcium and zinc ions in living rat brains.

    PubMed

    Su, Cheng-Kuan; Hsia, Sheng-Chieh; Sun, Yuh-Chang

    2014-08-01

    We have developed a simple and low-cost flow injection system coupled to a quadruple ICP-MS for the direct and continuous determination of multi-element in microdialysates. To interface microdialysis sampling to an inductively coupled plasma mass spectrometer (ICP-MS), we employed 3D printing to manufacture an as-designed sample load/inject valve featuring an in-valve sample loop for precise handling of microliter samples with a dissolved solids content of 0.9% NaCl (w/v). To demonstrate the practicality of our developed on-line system, we applied the 3D printed valve equipped a 5-μL sample loop to minimize the occurrence of salt matrix effects and facilitate an online dynamic monitoring of extracellular calcium and zinc ions in living rat brains. Under the practical condition (temporal resolution: 10h(-1)), dynamic profiling of these two metal ions in living rat brain extracellular fluid after probe implantation (the basal values for Ca and Zn were 12.11±0.10mg L(-1) and 1.87±0.05μg L(-1), respectively) and real-time monitoring of the physiological response to excitotoxic stress elicited upon perfusing a solution of 2.5mM N-methyl-d-aspartate were performed. PMID:25064244

  20. Intracellular accumulation dynamics and fate of zinc ions in alveolar epithelial cells exposed to airborne ZnO nanoparticles at the air–liquid interface

    DOE PAGESBeta

    Mihai, Cosmin; Chrisler, William B.; Xie, Yumei; Hu, Dehong; Szymanski, Craig J.; Tolic, Ana; Klein, Jessica A.; Smith, Jordan N.; Tarasevich, Barbara J.; Orr, Galya

    2013-12-02

    Airborne nanoparticles (NPs) that enter the respiratory tract are likely to reach the alveolar region. Accumulating observations support a role for zinc oxide (ZnO) NP dissolution in toxicity, but the majority of in vitro studies were conducted in cells exposed to NPs in growth media, where large doses of dissolved ions are shed into the exposure solution. To determine the precise intracellular accumulation dynamics and fate of zinc ions (Zn2+) shed by airborne NPs in the cellular environment, we exposed alveolar epithelial cells to aerosolized NPs at the air-liquid interface (ALI). Using a fluorescent indicator for Zn2+, together with organelle-specificmore » fluorescent proteins, we quantified Zn2+ in single cells and organelles over time. We found that at the ALI, intracellular Zn2+ values peaked 3 h post exposure and decayed to normal values by 12 h, while in submersed cultures, intracellular Zn2+ values continued to increase over time. The lowest toxic NP dose at the ALI generated peak intracellular Zn2+ values that were nearly 3 folds lower than the peak values generated by the lowest toxic dose of NPs in submersed cultures, and 8 folds lower than the peak values generated by the lowest toxic dose of ZnSO4 or Zn2+. At the ALI, the majority of intracellular Zn2+ was found in endosomes and lysosomes as early as 1 h post exposure. In contrast, the majority of intracellular Zn2+ following exposures to ZnSO4 was found in other larger vesicles, with less than 10% in endosomes and lysosomes. In conclusion, together, our observations indicate that low but critical levels of intracellular Zn2+ have to be reached, concentrated specifically in endosomes and lysosomes, for toxicity to occur, and point to the focal dissolution of the NPs in the cellular environment and the accumulation of the ions specifically in endosomes and lysosomes as the processes underlying the potent toxicity of airborne ZnO NPs.« less

  1. Intracellular accumulation dynamics and fate of zinc ions in alveolar epithelial cells exposed to airborne ZnO nanoparticles at the air–liquid interface

    SciTech Connect

    Mihai, Cosmin; Chrisler, William B.; Xie, Yumei; Hu, Dehong; Szymanski, Craig J.; Tolic, Ana; Klein, Jessica A.; Smith, Jordan N.; Tarasevich, Barbara J.; Orr, Galya

    2013-12-02

    Airborne nanoparticles (NPs) that enter the respiratory tract are likely to reach the alveolar region. Accumulating observations support a role for zinc oxide (ZnO) NP dissolution in toxicity, but the majority of in vitro studies were conducted in cells exposed to NPs in growth media, where large doses of dissolved ions are shed into the exposure solution. To determine the precise intracellular accumulation dynamics and fate of zinc ions (Zn2+) shed by airborne NPs in the cellular environment, we exposed alveolar epithelial cells to aerosolized NPs at the air-liquid interface (ALI). Using a fluorescent indicator for Zn2+, together with organelle-specific fluorescent proteins, we quantified Zn2+ in single cells and organelles over time. We found that at the ALI, intracellular Zn2+ values peaked 3 h post exposure and decayed to normal values by 12 h, while in submersed cultures, intracellular Zn2+ values continued to increase over time. The lowest toxic NP dose at the ALI generated peak intracellular Zn2+ values that were nearly 3 folds lower than the peak values generated by the lowest toxic dose of NPs in submersed cultures, and 8 folds lower than the peak values generated by the lowest toxic dose of ZnSO4 or Zn2+. At the ALI, the majority of intracellular Zn2+ was found in endosomes and lysosomes as early as 1 h post exposure. In contrast, the majority of intracellular Zn2+ following exposures to ZnSO4 was found in other larger vesicles, with less than 10% in endosomes and lysosomes. In conclusion, together, our observations indicate that low but critical levels of intracellular Zn2+ have to be reached, concentrated specifically in endosomes and lysosomes, for toxicity to occur, and point to the focal dissolution of the NPs in the cellular environment and the accumulation of the ions specifically in endosomes and lysosomes as the processes

  2. High dose zinc supplementation induces hippocampal zinc deficiency and memory impairment with inhibition of BDNF signaling.

    PubMed

    Yang, Yang; Jing, Xiao-Peng; Zhang, Shou-Peng; Gu, Run-Xia; Tang, Fang-Xu; Wang, Xiu-Lian; Xiong, Yan; Qiu, Mei; Sun, Xu-Ying; Ke, Dan; Wang, Jian-Zhi; Liu, Rong

    2013-01-01

    Zinc ions highly concentrate in hippocampus and play a key role in modulating spatial learning and memory. At a time when dietary fortification and supplementation of zinc have increased the zinc consuming level especially in the youth, the toxicity of zinc overdose on brain function was underestimated. In the present study, weaning ICR mice were given water supplemented with 15 ppm Zn (low dose), 60 ppm Zn (high dose) or normal lab water for 3 months, the behavior and brain zinc homeostasis were tested. Mice fed high dose of zinc showed hippocampus-dependent memory impairment. Unexpectedly, zinc deficiency, but not zinc overload was observed in hippocampus, especially in the mossy fiber-CA3 pyramid synapse. The expression levels of learning and memory related receptors and synaptic proteins such as NMDA-NR2A, NR2B, AMPA-GluR1, PSD-93 and PSD-95 were significantly decreased in hippocampus, with significant loss of dendritic spines. In keeping with these findings, high dose intake of zinc resulted in decreased hippocampal BDNF level and TrkB neurotrophic signaling. At last, increasing the brain zinc level directly by brain zinc injection induced BDNF expression, which was reversed by zinc chelating in vivo. These results indicate that zinc plays an important role in hippocampus-dependent learning and memory and BDNF expression, high dose supplementation of zinc induces specific zinc deficiency in hippocampus, which further impair learning and memory due to decreased availability of synaptic zinc and BDNF deficit. PMID:23383172

  3. 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

  4. 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.

  5. 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

  6. Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase.

    PubMed

    Chen, Mengbin; Chou, Wayne K W; Al-Lami, Naeemah; Faraldos, Juan A; Allemann, Rudolf K; Cane, David E; Christianson, David W

    2016-05-24

    Aristolochene synthase (ATAS) is a high-fidelity terpenoid cyclase that converts farnesyl diphosphate exclusively into the bicyclic hydrocarbon aristolochene. Previously determined crystal structures of ATAS complexes revealed trapped active site water molecules that could potentially interact with catalytic intermediates: water "w" hydrogen bonds with S303 and N299, water molecules "w1" and "w2" hydrogen bond with Q151, and a fourth water molecule coordinates to the Mg(2+)C ion. There is no obvious role for water in the ATAS mechanism because the enzyme exclusively generates a hydrocarbon product. Thus, these water molecules are tightly controlled so that they cannot react with carbocation intermediates. Steady-state kinetics and product distribution analyses of eight ATAS mutants designed to perturb interactions with active site water molecules (S303A, S303H, S303D, N299A, N299L, N299A/S303A, Q151H, and Q151E) indicate relatively modest effects on catalysis but significant effects on sesquiterpene product distributions. X-ray crystal structures of S303A, N299A, N299A/S303A, and Q151H mutants reveal minimal perturbation of active site solvent structure. Seven of the eight mutants generate farnesol and nerolidol, possibly resulting from addition of the Mg(2+)C-bound water molecule to the initially formed farnesyl cation, but no products are generated that would suggest enhanced reactivity of other active site water molecules. However, intermediate germacrene A tends to accumulate in these mutants. Thus, apart from the possible reactivity of Mg(2+)C-bound water, active site water molecules in ATAS are not directly involved in the chemistry of catalysis but instead contribute to the template that governs the conformation of the flexible substrate and carbocation intermediates. PMID:27172425

  7. 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

  8. Adsorption of divalent copper, zinc, cadmium and lead ions from aqueous solution by waste tea and coffee adsorbents.

    PubMed

    Djati Utomo, H; Hunter, K A

    2006-01-01

    The adsorption of the divalent cations of Cu, Zn, Cd and Pb by tea leaves and coffee grounds from aqueous solutions is described. Both adsorbents exhibited strong affinity for these ions which could be described by a simple single-site equilibrium model. For coffee, the order of increasing adsorption equilibrium constant K was Cu < Pb < Zn < Cd, while for tea the opposite order was observed indicating that the adsorption sites on each adsorbent have a different chemical nature. Adsorption decreased at low pH < 4 through competition with H+ for adsorption sites, and for all metals except Cu, at high pH > 10, probably because of anion formation in the case of Zn2+ and also increased leaching of metal-binding soluble materials. The effect of metal ion concentration on the adsorptive equilibria indicated a threshold concentration above which overall adsorption became limited by saturation of the adsorption sites. Competition between two metal ions for the same sites was not observed with Cu(II) and Pb(II), however Zn(II) reacted competitively with Cd(II) binding sites on both tea and coffee. If fresh coffee or tea adsorbents were used, the fraction of metal ion taken up by the adsorbent was diminished by the competitive effects of soluble metal-binding ligands released by the tea or coffee. Experiments with coffee showed that roasting temperature controls the formation of metal ion adsorption sites for this adsorbent. PMID:16457172

  9. Probing the Effect of the Non-Active-Site Mutation Y229W in New Delhi Metallo-β-lactamase-1 by Site-Directed Mutagenesis, Kinetic Studies, and Molecular Dynamics Simulations

    PubMed Central

    Shi, Yun; Hu, Feng; Lao, Xingzhen; Gao, Xiangdong; Zheng, Heng; Yao, Wenbing

    2013-01-01

    New Delhi metallo-β-lactmase-1 (NDM-1) has attracted extensive attention for its high catalytic activities of hydrolyzing almost all β-lactam antibiotics. NDM-1 shows relatively higher similarity to subclass B1 metallo-β-lactmases (MβLs), but its residue at position 229 is identical to that of B2/B3 MβLs, which is a Tyr instead of a B1-MβL-conserved Trp. To elucidate the possible role of Y229 in the bioactivity of NDM-1, we performed mutagenesis study and molecular dynamics (MD) simulations. Although residue Y229 is spatially distant from the active site and not contacting directly with the substrate or zinc ions, the Y229W mutant was found to have higher kcat and Km values than those of wild-type NDM-1, resulting in 1∼7 fold increases in kcat/Km values against tested antibiotics. In addition, our MD simulations illustrated the enhanced flexibility of Loop 2 upon Y229W mutation, which could increase the kinetics of both substrate entrance (kon) and product egress (koff). The enhanced flexibility of Loop 2 might allow the enzyme to adjust the geometry of its active site to accommodate substrates with different structures, broadening its substrate spectrum. This study indicated the possible role of the residue at position 229 in the evolution of NDM-1. PMID:24339993

  10. Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies

    PubMed Central

    Fischer, Thomas; Riedl, Rainer

    2016-01-01

    Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91). PMID:26938528

  11. Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies.

    PubMed

    Fischer, Thomas; Riedl, Rainer

    2016-01-01

    Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91). PMID:26938528

  12. A Turn-on and Reversible Fluorescence Sensor for Zinc Ion Based on 4,5-Diazafluorene Schiff Base.

    PubMed

    Li, Hui; Zhang, ShuJiang; Gong, ChenLiang; Wang, JianZhi; Wang, Feng

    2016-09-01

    A new 4,5-diazafluorene-based fluorescent chemosensor has been synthesized by Schiff base condensation of 9,9-bis(3,5-dimethyl-4-aminophenyl)-4,5-diazafluorene with salicylaldehyde. The interaction of Schiff base with different metal ions has been studied over photofluorescent spectra. The results showed that Schiff base exhibited 194-fold enhancements in fluorescence at 465 nm after Zn(2+) ions. Such fluorescent responses could be detected by naked eye under UV-lamp. The complex solution (L-Zn(2+)) exhibited reversibility with EDTA. PMID:27430628

  13. 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.

  14. Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

    SciTech Connect

    R Daher; M Coincon; M Fonvielle; P Gest; M Guerin; M Jackson; J Sygusch; M Therisod

    2011-12-31

    We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very high selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.

  15. Zinc, magnesium, and calcium ion supplementation confers tolerance to acetic acid stress in industrial Saccharomyces cerevisiae utilizing xylose.

    PubMed

    Ismail, Ku Syahidah Ku; Sakamoto, Takatoshi; Hasunuma, Tomohisa; Zhao, Xin-Qing; Kondo, Akihiko

    2014-12-01

    Lignocellulosic biomass is a potential substrate for ethanol production. However, pretreatment of lignocellulosic materials produces inhibitory compounds such as acetic acid, which negatively affect ethanol production by Saccharomyces cerevisiae. Supplementation of the medium with three metal ions (Zn(2+) , Mg(2+) , and Ca(2+) ) increased the tolerance of S. cerevisiae toward acetic acid compared to the absence of the ions. Ethanol production from xylose was most improved (by 34%) when the medium was supplemented with 2 mM Ca(2+) , followed by supplementation with 3.5 mM Mg(2+) (29% improvement), and 180 μM Zn(2+) (26% improvement). Higher ethanol production was linked to high cell viability in the presence of metal ions. Comparative transcriptomics between the supplemented cultures and the control suggested that improved cell viability resulted from the induction of genes controlling the cell wall and membrane. Only one gene, FIT2, was found to be up-regulated in common between the three metal ions. Also up-regulation of HXT1 and TKL1 might enhance xylose consumption in the presence of acetic acid. Thus, the addition of ionic nutrients is a simple and cost-effective method to improve the acetic acid tolerance of S. cerevisiae. PMID:24924214

  16. 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure.

    PubMed

    Shaban, Nadine M; Shi, Ke; Li, Ming; Aihara, Hideki; Harris, Reuben S

    2016-06-01

    The APOBEC3 family of DNA cytosine deaminases is capable of restricting the replication of HIV-1 and other pathogens. Here, we report a 1.92 Å resolution crystal structure of the Vif-binding and catalytic domain of APOBEC3F (A3F). This structure is distinct from the previously published APOBEC and phylogenetically related deaminase structures, as it is the first without zinc in the active site. We determined an additional structure containing zinc in the same crystal form that allows direct comparison with the zinc-free structure. In the absence of zinc, the conserved active site residues that normally participate in zinc coordination show unique conformations, including a 90 degree rotation of His249 and disulfide bond formation between Cys280 and Cys283. We found that zinc coordination is influenced by pH, and treating the protein at low pH in crystallization buffer is sufficient to remove zinc. Zinc coordination and catalytic activity are reconstituted with the addition of zinc only in a reduced environment likely due to the two active site cysteines readily forming a disulfide bond when not coordinating zinc. We show that the enzyme is active in the presence of zinc and cobalt but not with other divalent metals. These results unexpectedly demonstrate that zinc is not required for the structural integrity of A3F and suggest that metal coordination may be a strategy for regulating the activity of A3F and related deaminases. PMID:27139641

  17. Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations.

    PubMed

    Sun, Zhizeng; Mehta, Shrenik C; Adamski, Carolyn J; Gibbs, Richard A; Palzkill, Timothy

    2016-01-01

    CphA is a Zn(2+)-dependent metallo-β-lactamase that efficiently hydrolyzes only carbapenem antibiotics. To understand the sequence requirements for CphA function, single codon random mutant libraries were constructed for residues in and near the active site and mutants were selected for E. coli growth on increasing concentrations of imipenem, a carbapenem antibiotic. At high concentrations of imipenem that select for phenotypically wild-type mutants, the active-site residues exhibit stringent sequence requirements in that nearly all residues in positions that contact zinc, the substrate, or the catalytic water do not tolerate amino acid substitutions. In addition, at high imipenem concentrations a number of residues that do not directly contact zinc or substrate are also essential and do not tolerate substitutions. Biochemical analysis confirmed that amino acid substitutions at essential positions decreased the stability or catalytic activity of the CphA enzyme. Therefore, the CphA active - site is fragile to substitutions, suggesting active-site residues are optimized for imipenem hydrolysis. These results also suggest that resistance to inhibitors targeted to the CphA active site would be slow to develop because of the strong sequence constraints on function. PMID:27616327

  18. 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

  19. New dinuclear copper(II) and zinc(II) complexes for the investigation of sugar-metal ion interactions.

    PubMed

    Bera, Manindranath; Patra, Ayan

    2011-10-18

    We have studied the binding interactions of biologically important carbohydrates (D-glucose, D-xylose and D-mannose) with the newly synthesized five-coordinate dinuclear copper(II) complex, [Cu(2)(hpnbpda)(μ-OAc)] (1) and zinc(II) complex, [Zn(2)(hpnbpda)(μ-OAc)] (2) [H(3)hpnbpda=N,N'-bis(2-pyridylmethyl)-2-hydroxy-1,3-propanediamine-N,N'-diacetic acid] in aqueous alkaline solution. The complexes 1 and 2 are fully characterized both in solid and solution using different analytical techniques. A geometrical optimization was made of the ligand H(3)hpnbpda and the complexes 1 and 2 by molecular mechanics (MM+) method in order to establish the stable conformations. All carbohydrates bind to the metal complexes in a 1:1 molar ratio. The binding events have been investigated by a combined approach of FTIR, UV-vis and (13)C NMR spectroscopic techniques. UV-vis spectra indicate a significant blue shift of the absorption maximum of complex 1 during carbohydrate coordination highlighting the sugar binding ability of complex 1. The apparent binding constants of the substrate-bound copper(II) complexes have been determined from the UV-vis titration experiments. The binding ability and mode of binding of these sugar substrates with complex 2 are indicated by their characteristic coordination induced shift (CIS) values in (13)C NMR spectra for carbon atoms C1, C2, and C3 of sugar substrates. PMID:21764045

  20. Expression of zinc transporter ZnT7 in mouse superior cervical ganglion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The superior cervical ganglion (SCG) neurons contain a considerable amount of zinc ions, but little is known about zinc homeostasis in the SCG. It is known that zinc transporter 7 (ZnT7, Slc30a7), a member of the Slc30 ZnT family, is involved in mobilizing zinc ions from the cytoplasm into the Golgi...

  1. The effect of metal ions on the activity and thermostability of the extracellular proteinase from a thermophilic Bacillus, strain EA.1.

    PubMed Central

    Coolbear, T; Whittaker, J M; Daniel, R M

    1992-01-01

    The proteinase from the extremely thermophilic Bacillus strain EA.1 exhibits maximum stability at a pH of approx. 6.5. In the presence of calcium ions the half-life at 95 degrees C of the enzyme at this pH was 17 min, and loss of activity followed first-order decay kinetics. The role of metal ions in the activity and stability of the enzyme was studied using the holoenzyme, the metal-depleted apoenzyme, and a zinc-enriched apoenzyme preparation. Zinc and calcium ions were the preferred bivalent cations for the active site and stabilization site(s) respectively. Stabilization by metal ions was not in itself a highly stringent process, but ions other than calcium which stabilized the enzyme generally had a concomitant inhibitory effect on activity. Inhibition and stabilization of the enzyme by cations were concentration-dependent effects and certain ions activated the apoenzyme but not the holoenzyme. Manganese(II) ions conferred some stability and also activated the enzyme, but in the latter case were not as effective as zinc ions. The results are discussed with reference to the ionic radii, co-ordination number and preferred ligand donors of the ions. Mercury(II) ions severely compromised enzyme activity and stability, and the effects of thiol-reactive agents suggest that thiol groups also have a role in enzyme integrity. PMID:1445196

  2. Highly sensitive and selective fluorescent sensor for zinc ion based on a new diarylethene with a thiocarbamide unit.

    PubMed

    Zhang, Congcong; Pu, Shouzhi; Sun, Zhiyuan; Fan, Congbin; Liu, Gang

    2015-04-01

    A new photochromic diarylethene has been synthesized by using thiocarbamide as a functional group and perfluordiarylethene as photoswitching trigger via a salicylidene Schiff base linkage. The diarylethene could be used as a multicontrollable fluorescence switch when triggered by base/acid, light, and metal ions. The results showed that the absorption and fluorescence characteristics of the diarylethene exhibited sequence-dependent responses through efficient interaction of specific salicylidene Schiff base-linked thiocarbamide unit with tetrabutylammonium hydroxide/trifluoroacetic acid and photoirradiation. Moreover, the diarylethene was highly selective toward Zn(2+) ion with obvious fluorescence change from light blue to bright yellow in acetonitrile. The deprotonated form of the diarylethene had typical photochromism, but it showed an irreversible photocyclization reaction after binding with Zn(2+). Finally, two logic circuits were constructed by using the fluorescence intensity as the output signal with the inputs of the combinational stimuli of light and chemical species. PMID:25760313

  3. Application of laboratory prepared and commercially available biochars to adsorption of cadmium, copper and zinc ions from water.

    PubMed

    Bogusz, Aleksandra; Oleszczuk, Patryk; Dobrowolski, Ryszard

    2015-11-01

    The goal of the presented work was the evaluation and comparison of two biochars (produced from Sida hermaphrodita - BCSH/laboratory produced and from wheatstraw - BCS/commercial available) to adsorb heavy metal ions (Cd(II), Cu(II) and Zn(II)) from water. Kinetics of the sorption as well as sorption isotherms, the influence of solution pH and interfering ions were investigated. Different physico-chemical properties of biochars had the great influence on adsorption capacity. The greater adsorption efficiency was observed for BCSH than for BCS in the case of all investigated metals. The adsorption efficiency of BCSH was correlated with higher content of carbon and oxygen, what is equal with higher content of polar-groups on the BCSH surface e.g., -COOH. Furthermore, the molar ratio of O/C as well as polarity index (which was higher for BCSH) was also important parameters. PMID:26295440

  4. Reevaluating the free-ion activity model of trace metal toxicity toward higher plants: experimental evidence with copper and zinc.

    PubMed

    Parker, D R; Pedler, J F; Ahnstrom, Z A; Resketo, M

    2001-04-01

    Across a diverse spectrum of organisms, the absorption and toxicity of trace elements are usually correlated with the activity of the free metal ion, but reported exceptions to this generalization are increasing. For the first time, we tested the validity of the free-ion activity model (FIAM) in the case of terrestrial plants and organic acids that may be abundant in the soil solution and rhizosphere. Short-term (48-h) root elongation of wheat (Triticum aestitvum L.) in a simple medium (2 mM CaCl2, pH 6.0) was used to probe the toxicity of Cu and Zn in the presence of malonate, malate, and citrate. Precautions were taken to prevent biodegradation of the organic acids, and its absence was confirmed by ion chromatography. Copper speciation was verified using a Cu-selective ion electrode, and published stability constants were modified to improve agreement between measured and calculated Cu2+ activities. With additions of both malonate and malate, Cu toxicity was alleviated but not to the extent predicted by the FIAM; the Cu-ligand complexes seemingly contributed to the toxicity. No such departures were observed with citrate and Cu nor with any of the three ligands in combination with Zn. Thus, exceptions to the FIAM occur with higher plants as well as with aquatic biota but do not seem to occur in a predictable or systematic fashion with respect to metal or organic acid under investigation. Several possible explanations for the observed departures from the FIAM are discussed, including the possibility of accidental cotransport of metal and ligand into the cytoplasm. PMID:11345467

  5. Modification of algae with zinc, copper and silver ions for usage as natural composite for antibacterial applications.

    PubMed

    Mahltig, B; Soltmann, U; Haase, H

    2013-03-01

    Nanometer sized metal particles are used in many applications as antimicrobial materials. However in public discussion nanoparticular materials are a matter of concern due to potential health risks. Hence there is a certain demand for alternative antimicrobial acting materials. For this, the aim of this work is to realize an antimicrobial active material based on the release of metal ions from a natural depot. By this, the use of elemental metal particles or metal oxide particles in nanometer or micrometer scale is avoided. As natural depot four different algae materials (gained from Ascophyllum nodosum, Fucus vesicolosus, Spirulina platensis and Nannochloropsis) are used and loaded by bioabsorption with metal ions Ag(+), Cu(2+) and Zn(2+). The amount of metal bound by biosorption differs strongly in the range of 0.8 to 5.4 mg/g and depends on type of investigated algae material and type of metal ion. For most samples a smaller release of biosorbed Ag(+) and Cu(2+) is observed compared to a strong release of Zn(2+). The antibacterial activity of the prepared composites is investigated with Escherichia coli. Algae material without biosorbed metal has only a small effect on E. coli. Also by modification of algae with Zn(2+) only a small antibacterial property can be observed. Only with biosorption of Ag(+), the algae materials gain a strong bactericidal effect, even in case of a small amount of released silver ions. These silver modified algae materials can be used as highly effective bactericidal composites which may be used in future applications for the production of antimicrobial textiles, papers or polymer materials. PMID:25427514

  6. Photocatalytic removal of Cu ions from aqueous Cu-EDTA solution using solution combusted zinc oxide nanopowder.

    PubMed

    Lee, Jae Chun; Kim, Hong-Sick; Lee, Ju-Hyeon; Park, Sung

    2008-10-01

    Nano-sized ZnO powder was prepared by "solution-combustion method (SCM)." The ZnO powder using Zn(OH)2 and glycine as an oxidant and a fuel (F/O = 0.8), showed good powder characteristics, such as average grain size of 30 nm and the specific surface area of 120 m2/g. and it was used as a semiconductor photocatalyst to remove Cu ions from aqueous Cu-EDTA solution. The result was then compared with other semiconductor photocatalyst powders such as titanium dioxide (TiO2) powder (P25, Degussa) and TiO2 powder prepared by homogeneous precipitation process at low temperature (HPPLT). The SCM ZnO nanopowder showed excellent photocatalytic properties. The Cu++ ions were completely removed from the solution within 90 min. However, for the other two powders, no complete removal of the ions was observed within the reaction time of 180 min. The ZnO powder synthesized at the fuel/oxidant ratio of 0.8, showed higher PL intensity at UV region than the other photocatalytic powders. The superior photoreduction ability of SCM ZnO nanopowder might be due to its excellent UV absorption capacity. PMID:19198439

  7. Selective Solid-Phase Extraction of Zinc(II) from Environmental Water Samples Using Ion Imprinted Activated Carbon.

    PubMed

    Moniri, Elham; Panahi, Homayon Ahmad; Aghdam, Khaledeh; Sharif, Amir Abdollah Mehrdad

    2015-01-01

    A simple ion imprinted amino-functionalized sorbent was synthesized by coupling activated carbon with iminodiacetic acid, a functional compound for metal chelating, through cyanoric chloride spacer. The resulting sorbent has been characterized using FTIR spectroscopy, elemental analysis, and thermogravimetric analysis and evaluated for the preconcentration and determination of trace Zn(II) in environmental water samples. The optimum pH value for sorption of the metal ion was 6-7.5. The sorption capacity of the functionalized sorbent was 66.6 mg/g. The chelating sorbent can be reused for 10 cycles of sorption-desorption without any significant change in sorption capacity. A recovery of 100% was obtained for the metal ion with 0.5 M nitric acid as the eluent. Compared with nonimprinted polymer particles, the prepared Zn-imprinted sorbent showed high adsorption capacity, significant selectivity, and good site accessibility for Zn(II). Scatchard analysis revealed that the homogeneous binding sites were formed in the polymer. The equilibrium sorption data of Zn(II) by modified resin were analyzed by Langmuir, Freundlich, Temkin, and Redlich-Peterson models. Based on equilibrium adsorption data, the Langmuir, Freundlich, and Temkin constants were determined as 0.139, 12.82, and 2.34, respectively, at 25°C. PMID:25857899

  8. 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.

  9. Ultrasensitive detection of lead ion sensor based on gold nanodendrites modified electrode and electrochemiluminescent quenching of quantum dots by electrocatalytic silver/zinc oxide coupled structures.

    PubMed

    Li, Meng; Kong, Qingkun; Bian, Zhaoquan; Ma, Chao; Ge, Shenguang; Zhang, Yan; Yu, Jinghua; Yan, Mei

    2015-03-15

    A signal-off electrochemiluminescence (ECL) DNA sensor based on gold nanodendrites (Au NDs) modified indium tin oxide (ITO) electrode for the detection of lead ion (Pb(2+)) was developed. Well-defined Au NDs were prepared on ITO electrode using low-potential synthesis, assisted by ethylenediamine. Based on Pb(2+)-specific deoxyribozyme, the silver/zinc oxide (Ag/ZnO) with coupled structure, prepared by one-pot method, was close to the surface of the electrode to catalyze the reduction of part of H2O2, the coreactant for cathodic ECL emission, leading to a decrease of ECL intensity. In addition, taking advantage of the larger surface area to capture a large amount of capture probe as well as excellent conductivity of Au NDs, the sensor could detect Pb(2+) quantitatively in a wider range, and performed excellent selectivity. Furthermore, such simple and sensitive DNA sensor was successfully applied for the detection of Pb(2+) in lake water and human serum samples, respectively. PMID:25461155

  10. Selective fluorescent probes based on C dbnd N isomerization and intramolecular charge transfer (ICT) for zinc ions in aqueous solution

    NASA Astrophysics Data System (ADS)

    Li, Lei; Liu, Feng; Li, Hong-Wei

    2011-09-01

    As the second most abundant transition-metal ion in the human body, Zn 2+ plays crucial roles in many important biological processes; while in the environment, an excessive concentration of Zn 2+ may reduce the soil microbial activity resulting in phytotoxic effects. Therefore, developing effective and sensitive detection method for Zn 2+ has become crucially important and necessary both in life and environment science. Two new fluorescence probes, 2-((2-hydroxynaphthalen-1-yl)methyleneamino)-3-(1H-imidazol-5-yl) propanoic acid ( 2) and 2-hydroxy-2-((2-hydroxynaphthalen-1-yl) methyleneamino) acetic acid ( 3), were easily prepared by a one step reaction between 2-hydroxy-1-naphthaldehyde with histidine and serine, respectively, in ethanol. The optical properties of them were investigated by fluorescence spectra, which displayed specific and sensitive recognition to Zn 2+ and especially avoided the interference of Cd 2+ when they were tested against a range of physiological and environmentally relevant metal ions in aqueous solution. The responsive mechanism of the two probes to Zn 2+ were involved both the C dbnd N isomerization and ICT, which were clarified by NBO charge analysis and the HOMO-LUMO energy gap calculation by using B3LYP/6-31G density functional theory.

  11. Selective fluorescent probes based on CN isomerization and intramolecular charge transfer (ICT) for zinc ions in aqueous solution.

    PubMed

    Li, Lei; Liu, Feng; Li, Hong-Wei

    2011-09-01

    As the second most abundant transition-metal ion in the human body, Zn2+ plays crucial roles in many important biological processes; while in the environment, an excessive concentration of Zn2+ may reduce the soil microbial activity resulting in phytotoxic effects. Therefore, developing effective and sensitive detection method for Zn2+ has become crucially important and necessary both in life and environment science. Two new fluorescence probes, 2-((2-hydroxynaphthalen-1-yl)methyleneamino)-3-(1H-imidazol-5-yl) propanoic acid (2) and 2-hydroxy-2-((2-hydroxynaphthalen-1-yl) methyleneamino) acetic acid (3), were easily prepared by a one step reaction between 2-hydroxy-1-naphthaldehyde with histidine and serine, respectively, in ethanol. The optical properties of them were investigated by fluorescence spectra, which displayed specific and sensitive recognition to Zn2+ and especially avoided the interference of Cd2+ when they were tested against a range of physiological and environmentally relevant metal ions in aqueous solution. The responsive mechanism of the two probes to Zn2+ were involved both the CN isomerization and ICT, which were clarified by NBO charge analysis and the HOMO-LUMO energy gap calculation by using B3LYP/6-31G density functional theory. PMID:21665525

  12. Characterization of Cr3+ doped mixed alkali ions effect in zinc borate glasses - Physical and spectroscopic investigations

    NASA Astrophysics Data System (ADS)

    Rama Sundari, G.; Pushpa Manjari, V.; Raghavendra Rao, T.; Satish, D. V.; Rama Krishna, Ch.; Venkata Reddy, Ch.; Ravikumar, R. V. S. S. N.

    2014-06-01

    The physical and structural properties of Cr3+ doped 19.9 ZnO + xLi2O + (30 - x) Na2O + 50B2O3 (5 ⩽ x ⩽ 25) (ZLNB) glasses have been studied. Powder X-ray diffraction patterns indicated the amorphous nature of the glass samples. The physical parameters of all the glasses were also evaluated with respect to the composition. They exhibit the non-linearity providing the evidence for mixed alkali ions effect. The infrared spectra of the glasses in the range 400-4000 cm-1 showed the presence of BO3 and BO4 local structures in all the glass systems. No boroxol ring formation was observed in the structure of these glasses. Optical absorption and electron paramagnetic resonance studies were carried out at room temperature. From the optical absorption data various optical parameters such as optical band gap, Urbach energy were evaluated. Crystal field and Racah parameters are evaluated from optical absorption spectra. The EPR spectra of Cr3+ doped ZLNB glasses exhibited resonance signals at g = 4.066 and g = 1.9779 characteristic of Cr3+ ions. The evaluated bonding parameters suggest the covalent nature.

  13. 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.

  14. 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…

  15. 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

  16. 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

  17. Mitochondrial-Targeted Two-Photon Fluorescent Probes for Zinc Ions, H2O2, and Thiols in Living Tissues

    PubMed Central

    Kim, Hwan Myung; Cho, Bong Rae

    2013-01-01

    Mitochondria provide the energy of the cells and are the primary site of oxygen consumption and the major source of reactive oxygen species. In mitochondria, metal ions and glutathione play vital roles in maintaining their structure and the redox environment. To understand their roles in mitochondria, it is crucial to monitor each of these chemical species in the mitochondria at the cell, tissue, and organism levels. An ideal tool for such purpose is the use of two-photon microscopy (TPM). Until recently, however, there has been no report on the two-photon (TP) probes suitable for such applications. In this paper, we summarize the mitochondria-targeted TP probes for Zn2+, H2O2, and thiols, as well as their bioimaging applications. PMID:23431410

  18. Electrical properties of Zinc-Tin diarsenide (ZnSnAs{sub 2}) irradiated with H{sup +} ions

    SciTech Connect

    Brudnyi, V. N. Vedernikova, T. V.

    2009-04-15

    The results of studying the electrical properties and isochronous annealing of p-ZnSnAs{sub 2} irradiated with H{sup +} ions (energy E = 5 MeV, dose D = 2 x 10{sup 16} cm{sup -2}) are reported. The limiting electrical characteristics of irradiated material (the Hall coefficient R{sub H} (D){sub lim} {approx} -4 x 10{sup 3} cm{sup 3} C{sup -1}, conductivity {sigma} (D){sub lim} {approx} 2.9 x 10{sup -2} {omega}{sup -1} cm{sup -1}, and the Fermi level position F{sub lim} {approx} 0.58 eV above the valence-band top at 300 K) are determined. The energy position of the 'neutral' point for the ZnSnAs{sub 2} compound is calculated.

  19. 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

  20. Arsenic doped zinc oxide

    SciTech Connect

    Volbers, N.; Lautenschlaeger, S.; Leichtweiss, T.; Laufer, A.; Graubner, S.; Meyer, B. K.; Potzger, K.; Zhou Shengqiang

    2008-06-15

    As-doping of zinc oxide has been approached by ion implantation and chemical vapor deposition. The effect of thermal annealing on the implanted samples has been investigated by using secondary ion mass spectrometry and Rutherford backscattering/channeling geometry. The crystal damage, the distribution of the arsenic, the diffusion of impurities, and the formation of secondary phases is discussed. For the thin films grown by vapor deposition, the composition has been determined with regard to the growth parameters. The bonding state of arsenic was investigated for both series of samples using x-ray photoelectron spectroscopy.

  1. 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

  2. Synthesis and characterization of three-dimensional transition metal ions doped zinc oxide based dilute magnetic semiconductor thin films

    NASA Astrophysics Data System (ADS)

    Samanta, Kousik

    Dilute magnetic semiconductors (DMS), especially 3d-transition metal (TM) doped ZnO based DMS materials are the most promising candidates for optoelectronics and spintronics applications; e.g. in spin light emitting diode (SLED), spin transistors, and spin field effect transistors (SFET), etc. In the present dissertation, thin films of Zn1-xTMxO (TM = Co2+, Cu2+, and Mn2+) were grown on (0001) oriented Al2O3 substrates by pulsed laser deposition (PLD) technique. The films were highly c-axis oriented, nearly single crystalline, and defects free for a limited concentration of the dilution of transition metal ions. In particular, we have obtained single crystalline phases of Zn1-xTMxO thin films for up to 10, 3, and 5 stoichiometric percentages of Co2+, Cu2+, and Mn2+ respectively. Raman micro-probe system was used to understand the structural and lattice dynamical properties at different physical conditions. The confinement of optical phonons in the disorder lattice was explained by alloy potential fluctuation (APF) using a spatial correlation (SC) model. The detailed analysis of the optical phonon behavior in disorder lattice confirmed the substitution of the transition metal ions in Zn 2+ site of the ZnO host lattice. The secondary phases of ZnCo 2O4, CuO, and ZnMn2O4 were detected in higher Co, Cu, and Mn doped ZnO thin films respectively; where as, XRD did not detect these secondary phases in the same samples. Room temperature ferromagnetism was observed in Co2+ and Cu2+ ions doped ZnO thin films with maximum saturation magnetization (Ms) of 1.0 and 0.76 muB respectively. The origin of the observed ferromagnetism in Zn1-xCoxO thin films was tested by the controlled introduction of shallow donors (Al) in Zn0.9-x Co0.1O:Alx (x = 0.005 and 0.01) thin films. The saturation magnetization for the 10% Co-doped ZnO (1.0 muB /Co) at 300K reduced (˜0.25 muB/Co) due to Al doping. The observed ferromagnetism and the reduction due to Al doping can be explained by the Bound

  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. Microwave and infrared dielectric response of monoclinic bismuth zinc niobate based pyrochlore ceramics with ion substitution in A site

    SciTech Connect

    Wang Hong; Kamba, Stanislav; Zhang Meiling; Yao Xi; Denisov, Sergey; Kadlec, Filip; Petzelt, Jan

    2006-08-01

    It is well known that the cubic pyrochlore Bi{sub 1.5}ZnNb{sub 1.5}O{sub 7} exhibits higher permittivity and dielectric loss than monoclinic Bi{sub 2}Zn{sub 2/3}Nb{sub 4/3}O{sub 7} due to structural disorder in the A sites of Bi{sub 1.5}ZnNb{sub 1.5}O{sub 7}. We have studied systematically the impact of the ion substitution in the A site of monoclinic Bi{sub 2}Zn{sub 2/3}Nb{sub 4/3}O{sub 7} on the structure and microwave dielectric properties. It is shown that the structure and permittivity of (Bi{sub 1.92}M{sub 0.08})(Zn{sub 0.64}Nb{sub 1.36})O{sub 7} (M=Zn,Ca,Cd,Sr,Ba) ceramics remain almost the same as in Bi{sub 2}Zn{sub 2/3}Nb{sub 4/3}O{sub 7}; only the Ba substituted ceramics have higher permittivity due to multiphase structure. Microwave dielectric properties were compared with complex dielectric response in terahertz and infrared frequency range of 0.1-100 THz, which allows us to estimate intrinsic and extrinsic contributions to microwave dielectric losses. The best microwave properties were obtained in (Bi{sub 1.92}Ca{sub 0.08})(Zn{sub 0.64}Nb{sub 1.36})O{sub 7} with {epsilon}=76, Qf{>=}5000 (sintered below 950 deg.C), which is promising for microwave low temperature cofiring ceramic application.

  5. 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.

  6. A turn-on fluorescence chemosensor based on a tripodal amine [tris(pyrrolyl-α-methyl)amine]-rhodamine conjugate for the selective detection of zinc ions.

    PubMed

    Balamurugan, Rathinam; Chang, Wen-I; Zhang, Yandison; Fitriyani, Sri; Liu, Jui-Hsiang

    2016-09-21

    A novel tetradendate ligand derived from a tris(pyrrolyl-α-methyl)amine (H3tpa) and rhodamine-based conjugate (PR) has been designed for use as a sensor, synthesized and characterized spectroscopically. PR {(tris(5-rhodamineiminopyrrol-2-ylmethyl)amine)} serves as a selective colorimetric as well as a fluorescent chemosensor for Zn(2+) in acetonitrile/water (1 : 1, v/v). In the presence of Zn(2+), PR exhibited obvious absorption (558 nm) and emission (577 nm) peaks whose intensity increased along with increasing Zn(2+) concentrations. Titration experiments revealed that a large excess of Zn(2+) was required to saturate the absorption (λmax) and emission intensities. Upon the addition of 1000 equivalents of Zn(2+), the fluorescence intensity of the PR underwent an ∼500-fold increase (Φf = 0.34) with the emission maximum at 580 nm. These kinetics studies demonstrated that the absorption and emission changes were proportional to the Zn(2+) concentration. The color of the solution changed from colorless to a dark pink color. The fluorescence of the PR-Zn(2+) complex can be reversibly restored by using ammonium water or by heating. Competitive ion tests revealed that the intensity of PR-Zn(2+) was not suppressed by excess amounts of other metal ions. The counter anions did not exert obvious influences on the absorption and emission profiles. (1)H-NMR and FT-IR spectroscopic investigations of PR and PR-Zn(2+) revealed that the pyrrole motifs, -C[double bond, length as m-dash]N- groups and spirolactam of rhodamine B are capable of coordinating cation guest species. Because each arm of the tripodal ligand tautomerizes independently, only moderate fluorescence enhancement could be seen until all three -C[double bond, length as m-dash]N- groups were coordinated by zinc, which may be due to the spirolactam ring opening mechanism of the rhodamine unit. Once all three -C[double bond, length as m-dash]N- groups were locked by coordinating with excess of Zn(2+), the

  7. Role of vanadium ions, oxygen vacancies, and interstitial zinc in room temperature ferromagnetism on ZnO-V2O5 nanoparticles

    PubMed Central

    2014-01-01

    In this work, we present the role of vanadium ions (V+5 and V+3), oxygen vacancies (VO), and interstitial zinc (Zni) to the contribution of specific magnetization for a mixture of ZnO-V2O5 nanoparticles (NPs). Samples were obtained by mechanical milling of dry powders and ethanol-assisted milling for 1 h with a fixed atomic ratio V/Zn?=?5% at. For comparison, pure ZnO samples were also prepared. All samples exhibit a room temperature magnetization ranging from 1.18?×?10−3 to 3.5?×?10−3 emu/gr. Pure ZnO powders (1.34?×?10−3 emu/gr) milled with ethanol exhibit slight increase in magnetization attributed to formation of Zni, while dry milled ZnO powders exhibit a decrease of magnetization due to a reduction of VO concentration. For the ZnO-V2O5 system, dry milled and thermally treated samples under reducing atmosphere exhibit a large paramagnetic component associated to the formation of V2O3 and secondary phases containing V+3 ions; at the same time, an increase of VO is observed with an abrupt fall of magnetization to σ?~?0.7?×?10−3 emu/gr due to segregation of V oxides and formation of secondary phases. As mechanical milling is an aggressive synthesis method, high disorder is induced at the surface of the ZnO NPs, including VO and Zni depending on the chemical environment. Thermal treatment restores partially structural order at the surface of the NPs, thus reducing the amount of Zni at the same time that V2O5 NPs segregate reducing the direct contact with the surface of ZnO NPs. Additional samples were milled for longer time up to 24 h to study the effect of milling on the magnetization; 1-h milled samples have the highest magnetizations. Structural characterization was carried out using X-ray diffraction and transmission electron microscopy. Identification of VO and Zni was carried out with Raman spectra, and energy-dispersive X-ray spectroscopy was used to verify that V did not diffuse into ZnO NPs as well to quantify O/Zn ratios. PMID:24708614

  8. Role of vanadium ions, oxygen vacancies, and interstitial zinc in room temperature ferromagnetism on ZnO-V2O5 nanoparticles.

    PubMed

    Olive-Méndez, Sion F; Santillán-Rodríguez, Carlos R; González-Valenzuela, Ricardo A; Espinosa-Magaña, Francisco; Matutes-Aquino, José A

    2014-01-01

    In this work, we present the role of vanadium ions (V+5 and V+3), oxygen vacancies (VO), and interstitial zinc (Zni) to the contribution of specific magnetization for a mixture of ZnO-V2O5 nanoparticles (NPs). Samples were obtained by mechanical milling of dry powders and ethanol-assisted milling for 1 h with a fixed atomic ratio V/Zn?=?5% at. For comparison, pure ZnO samples were also prepared. All samples exhibit a room temperature magnetization ranging from 1.18?×?10-3 to 3.5?×?10-3 emu/gr. Pure ZnO powders (1.34?×?10-3 emu/gr) milled with ethanol exhibit slight increase in magnetization attributed to formation of Zni, while dry milled ZnO powders exhibit a decrease of magnetization due to a reduction of VO concentration. For the ZnO-V2O5 system, dry milled and thermally treated samples under reducing atmosphere exhibit a large paramagnetic component associated to the formation of V2O3 and secondary phases containing V+3 ions; at the same time, an increase of VO is observed with an abrupt fall of magnetization to σ?~?0.7?×?10-3 emu/gr due to segregation of V oxides and formation of secondary phases. As mechanical milling is an aggressive synthesis method, high disorder is induced at the surface of the ZnO NPs, including VO and Zni depending on the chemical environment. Thermal treatment restores partially structural order at the surface of the NPs, thus reducing the amount of Zni at the same time that V2O5 NPs segregate reducing the direct contact with the surface of ZnO NPs. Additional samples were milled for longer time up to 24 h to study the effect of milling on the magnetization; 1-h milled samples have the highest magnetizations. Structural characterization was carried out using X-ray diffraction and transmission electron microscopy. Identification of VO and Zni was carried out with Raman spectra, and energy-dispersive X-ray spectroscopy was used to verify that V did not diffuse into ZnO NPs as well to quantify O/Zn ratios. PMID:24708614

  9. 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.

  10. 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.

  11. 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

  12. The Role of an Active Site Mg2+ in HDV Ribozyme Self-Cleavage: Insights from QM/MM Calculations

    PubMed Central

    Mlýnský, Vojtěch; Šponer, Jiří

    2014-01-01

    The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H+ in the active site, which acts as the general acid, and a partially hydrated Mg2+ ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with distinct position and coordination of the catalytically important active site Mg2+ ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal/mol, indicating that the specific position of the Mg2+ ion in the active site is predicted to strongly affect the kinetics of self-cleavage. The deprotonation of the U-1(2′-OH) nucleophile and the nucleophilic attack of the resulting U-1(2′-O−) on the scissile phosphodiester are found to be separate steps, as deprotonation precedes the nucleophilic attack. This sequential mechanism of the HDV ribozyme differs from the concerted nucleophilic activation and attack suggested for the hairpin ribozyme. We estimated the pKa of the U-1(2′-OH) group to range from 8.8 to 11.2, suggesting that the pKa is lowered by several units from that of a free ribose, comparable to and most likely smaller than the pKa of the solvated active site Mg2+ ion. Our results thus support the notion that the structure of the HDV ribozyme, and particularly the positioning of the active site Mg2+ ion, facilitates deprotonation and activation of the 2′-OH nucleophile. PMID:25412464

  13. Symptomatic zinc deficiency in experimental zinc deprivation.

    PubMed Central

    Taylor, C M; Goode, H F; Aggett, P J; Bremner, I; Walker, B E; Kelleher, J

    1992-01-01

    An evaluation of indices of poor zinc status was undertaken in five male subjects in whom dietary zinc intake was reduced from 85 mumol d-1 in an initial phase of the study to 14 mumol d-1. One of the subjects developed features consistent with zinc deficiency after receiving the low zinc diet for 12 days. These features included retroauricular acneform macullo-papular lesions on the face, neck, and shoulders and reductions in plasma zinc, red blood cell zinc, neutrophil zinc and plasma alkaline phosphatase activity. Alcohol induced hepatitis, which was suspected in this subject, may have caused a predisposition to altered zinc metabolism and possible zinc deficiency which was exacerbated by subsequent zinc deprivation. The report supports the value of neutrophil zinc concentration as an indicator of poor zinc status. PMID:1740525

  14. Structure of HIV-1 Reverse Transcriptase with the Inhibitor -thujaplicinol Bound at the RNase H Active Site

    SciTech Connect

    Himmel, D.; Maegley, K; Pauly, T; Bauman, J; Das, K; Dharia, C; Clark, Jr., A; Ryan, K; Hickey, M; et al.

    2009-01-01

    Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. Inhibitors that act against new targets, such as RNH, should be effective against all of the current drug-resistant variants. Here, we present 2.80 {angstrom} and 2.04 {angstrom} resolution crystal structures of an RNH inhibitor, {beta}-thujaplicinol, bound at the RNH active site of both HIV-1 RT and an isolated RNH domain. {beta}-thujaplicinol chelates two divalent metal ions at the RNH active site. We provide biochemical evidence that {beta}-thujaplicinol is a slow-binding RNH inhibitor with noncompetitive kinetics and suggest that it forms a tropylium ion that interacts favorably with RT and the RNA:DNA substrate.

  15. 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

  16. Long Wavelength Fluorescence Ratiometric Zinc Biosensor

    PubMed Central

    Zeng, Hui Hui; Matveeva, Evgenia; Stoddard, Andrea K.; Fierke, Carol A.; Thompson, Richard B.

    2013-01-01

    A protein-based emission ratiometric fluorescence biosensor is described that exhibits sensitivity to free zinc ion solutions down to picomolar concentrations. Ratiometric measurements are widely used to assure accurate quantitation, and emission ratios are preferred for laser scanning microscopes such as confocal fluorescence microscopes. The relatively long emission wavelengths used are well suited to studies in tissues and other matrices which exhibit significant fluorescence background, and the apo-carbonic anhydrase moiety recognizes zinc ion with high and controllable specificity. PMID:23345045

  17. Active site nanospace of aminoacyl tRNA synthetase: difference between the class I and class II synthetases.

    PubMed

    Dutta, Saheb; Choudhury, Kaberi; Banik, Sindrila Dutta; Nandi, Nilashis

    2014-03-01

    The present work is aimed at understanding the origin of the difference in the molecular organization of the active site nanospaces of the class I and class II aminoacyl tRNA synthetases (aaRSs) which are tunnel-like structures. The active site encloses the cognate amino acid (AA) and the adenosine triphosphate (ATP) to carry out aminoacylation reaction. Comparison of the structures of the active site of the class I and class II (aaRSs) shows that the nanodimensional tunnels are curved in opposite directions in the two classes. We investigated the origin of this difference using quantum mechanical computation of electrostatic potential (ESP) of substrates, surrounding residues and ions, using Atoms in Molecule (AIM) Theory and charge population analysis. We show that the difference is principally due to the variation in the spatial charge distribution of ATP in the two classes which correspond to extended and bent conformations of ATP. The present computation shows that the most feasible pathway for nucleophilic attack to alphaP is oppositely directed for class I and class II aaRSs. The available crystal structures show that the cognate AA is indeed located along the channel favorable for nucleophilic attack as predicted by the ESP analysis. It is also shown that the direction of the channel changes its orientation when the orientation of ATP is changed from extended to a bent like structure. We further used the AIM theory to confirm the direction of the approach of AA in each case and the results corroborate the results from the ESP analysis. The opposite curvatures of the active site nanospaces in class I and class II aaRSs are related with the influence of the charge distributions of the extended and bent conformations of ATP, respectively. The results of the computation of electrostatic potential by successive addition of active site residues show that their roles on the reaction are similar in both classes despite the difference in the organization of the

  18. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex.

    PubMed

    Fugmann, S D; Villey, I J; Ptaszek, L M; Schatz, D G

    2000-01-01

    During V(D)J recombination, the RAG1 and RAG2 proteins cooperate to catalyze a series of DNA bond breakage and strand transfer reactions. The structure, location, and number of active sites involved in RAG-mediated catalysis have as yet not been determined. Using protein secondary structure prediction algorithms, we have identified a region of RAG1 with possible structural similarities to the active site regions of transposases and retroviral integrases. Based on this information, we have identified two aspartic acid residues in RAG1 (D600 and D708) that function specifically in catalysis. The results support a model in which RAG1 contains a single, divalent metal ion binding active site structurally related to the active sites of transposases/integrases and responsible for all catalytic functions of the RAG protein complex. PMID:10678172

  19. 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.

  20. 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.

  1. Affinity labeling and characterization of the active site histidine of glucosephosphate isomerase

    SciTech Connect

    Gibson, D.R.; Gracy, R.W.; Hartman, F.C.

    1980-10-10

    N-bromoacetylethanolamine phosphate was found to act as a specific affinity label for the active center of glucosephosphate isomerase. The inactivation process followed pseudo-first order kinetics, was irreversible, and exhibited rate saturation kinetics with minimal half-lives of inactivation of 4.5 and 6.3 min for the enzyme isolated from human placenta and rabbit muscle, respectively. The pH dependence of the inactivation process closely paralleled the pH dependence of the overall catalytic process with pK/sub a/ values at pH 6.4 and 9.0. The stoichiometry of labeling of either enzyme, as determined with N-bromo(/sup 14/C/sub 2/)acetylethanolamine phosphate, was 1 eq of the affinity label/subunit of enzyme. After acid hydrolysis and amino acid analysis of the radioactive affinity-labeled human enzyme, only radioactive 3-carboxymethyl histidine was found. In the case of the rabbit enzyme, the only radioactive derivative obtained was 1-carboxymethyl histidine. Active site tryptic peptides were isolated by solvent extraction, thin layer peptide fingerprinting, and ion exchange chromatography before and after removal of the phosphate from the active site peptide. Amino acid analysis of the labeled peptides from the two species were very similar. Using high sensitivity methods for sequence analysis, the primary structure of the active site was established as Val-Leu-His-Ala-Glu-Asn-Val-Asp (Gly,Thr,Ser) Glu-Ile (Thr-Gly-His-Lys-Glx)-Tyr-Phe. Apparent sequence homology between the catalytic center of glucosephosphate isomerase and triosephosphate isomerase suggest that the two enzymes may have evolved from a common ancestral gene.

  2. 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.

  3. 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

  4. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

    PubMed Central

    Bonneau, Eric; Girard, Nicolas; Boisbouvier, Jérôme; Legault, Pascale

    2011-01-01

    The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme. PMID:21266483

  5. Zinc cyanide

    Integrated Risk Information System (IRIS)

    Zinc cyanide ; CASRN 557 - 21 - 1 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effe

  6. Zinc phosphide

    Integrated Risk Information System (IRIS)

    Zinc phoshide ; CASRN 1314 - 84 - 7 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Ef

  7. Zinc interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The most common and probably the most harmful micronutrient deficiency of commercial pecan enterprises is zinc deficiency. A review is presented of how orchard nutrient element management practices potentially influence tree Zn nutrition. Findings provide background information on how to reduce th...

  8. 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

  9. 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

  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. Enhancement in ion adsorption rate and desalination efficiency in a capacitive deionization cell through improved electric field distribution using electrodes composed of activated carbon cloth coated with zinc oxide nanorods.

    PubMed

    Laxman, Karthik; Myint, Myo Tay Zar; Bourdoucen, Hadj; Dutta, Joydeep

    2014-07-01

    Electrodes composed of activated carbon cloth (ACC) coated with zinc oxide (ZnO) nanorods are compared with plain ACC electrodes, with respect to their desalination efficiency of a 17 mM NaCl solution at different applied potentials. Polarization of the ZnO nanorods increased the penetration depth and strength of the electric field between the electrodes, leading to an increase in the capacitance and charge efficiency at reduced input charge ratios. Uniform distribution of the electric field lines between two electrodes coated with ZnO nanorods led to faster ion adsorption rates, reduced the electrode saturation time, and increased the average desalination efficiency by ∼45% for all applied potentials. The electrodes were characterized for active surface area, capacitance from cyclic voltammetry, theoretical assessment of surface area utilization, and the magnitude of electric field force acting on an ion of unit charge for each potential. PMID:24940607

  12. On the binding mode of urease active site inhibitors: A density functional study

    NASA Astrophysics Data System (ADS)

    Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M.

    The way with which boric acid, a rapid reversible competitive inhibitor, binds the urease active site was explored at density functional B3LYP level of theory. The catalytic core of the enzyme was simulated by two models of different size. In both cases, amino acid residues belonging to the inner and to the outer coordination spheres of nickel ions were replaced by smaller molecular species. Contrary to the experimental indication that attributes the inhibitory ability of this acid to the lack of a nucleophilic attack by the enzyme to the boron atom, we instead found that another possibility exists based on the presence of a strong covalent sigma bond between boron and urease that we think can be hardly broken to allow any course of the reaction.

  13. ZnuA and zinc homeostasis in Pseudomonas aeruginosa

    PubMed Central

    Pederick, Victoria G.; Eijkelkamp, Bart A.; Begg, Stephanie L.; Ween, Miranda P.; McAllister, Lauren J.; Paton, James C.; McDevitt, Christopher A.

    2015-01-01

    Pseudomonas aeruginosa is a ubiquitous environmental bacterium and a clinically significant opportunistic human pathogen. Central to the ability of P. aeruginosa to colonise both environmental and host niches is the acquisition of zinc. Here we show that P. aeruginosa PAO1 acquires zinc via an ATP-binding cassette (ABC) permease in which ZnuA is the high affinity, zinc-specific binding protein. Zinc uptake in Gram-negative organisms predominantly occurs via an ABC permease, and consistent with this expectation a P. aeruginosa ΔznuA mutant strain showed an ~60% reduction in cellular zinc accumulation, while other metal ions were essentially unaffected. Despite the major reduction in zinc accumulation, minimal phenotypic differences were observed between the wild-type and ΔznuA mutant strains. However, the effect of zinc limitation on the transcriptome of P. aeruginosa PAO1 revealed significant changes in gene expression that enable adaptation to low-zinc conditions. Genes significantly up-regulated included non-zinc-requiring paralogs of zinc-dependent proteins and a number of novel import pathways associated with zinc acquisition. Collectively, this study provides new insight into the acquisition of zinc by P. aeruginosa PAO1, revealing a hitherto unrecognized complexity in zinc homeostasis that enables the bacterium to survive under zinc limitation. PMID:26290475

  14. 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

  15. 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.

  16. 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.

  17. Effects of zinc on particulate methane monooxygenase activity and structure.

    PubMed

    Sirajuddin, Sarah; Barupala, Dulmini; Helling, Stefan; Marcus, Katrin; Stemmler, Timothy L; Rosenzweig, Amy C

    2014-08-01

    Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Zinc is a known inhibitor of pMMO, but the details of zinc binding and the mechanism of inhibition are not understood. Metal binding and activity assays on membrane-bound pMMO from Methylococcus capsulatus (Bath) reveal that zinc inhibits pMMO at two sites that are distinct from the copper active site. The 2.6 Å resolution crystal structure of Methylocystis species strain Rockwell pMMO reveals two previously undetected bound lipids, and metal soaking experiments identify likely locations for the two zinc inhibition sites. The first is the crystallographic zinc site in the pmoC subunit, and zinc binding here leads to the ordering of 10 previously unobserved residues. A second zinc site is present on the cytoplasmic side of the pmoC subunit. Parallels between these results and zinc inhibition studies of several respiratory complexes suggest that zinc might inhibit proton transfer in pMMO. PMID:24942740

  18. Effects of Zinc on Particulate Methane Monooxygenase Activity and Structure*

    PubMed Central

    Sirajuddin, Sarah; Barupala, Dulmini; Helling, Stefan; Marcus, Katrin; Stemmler, Timothy L.; Rosenzweig, Amy C.

    2014-01-01

    Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Zinc is a known inhibitor of pMMO, but the details of zinc binding and the mechanism of inhibition are not understood. Metal binding and activity assays on membrane-bound pMMO from Methylococcus capsulatus (Bath) reveal that zinc inhibits pMMO at two sites that are distinct from the copper active site. The 2.6 Å resolution crystal structure of Methylocystis species strain Rockwell pMMO reveals two previously undetected bound lipids, and metal soaking experiments identify likely locations for the two zinc inhibition sites. The first is the crystallographic zinc site in the pmoC subunit, and zinc binding here leads to the ordering of 10 previously unobserved residues. A second zinc site is present on the cytoplasmic side of the pmoC subunit. Parallels between these results and zinc inhibition studies of several respiratory complexes suggest that zinc might inhibit proton transfer in pMMO. PMID:24942740

  19. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site.

    PubMed

    Iyer, Shalini; La-Borde, Penelope J; Payne, Karl A P; Parsons, Mark R; Turner, Anthony J; Isaac, R Elwyn; Acharya, K Ravi

    2015-01-01

    Eukaryotic aminopeptidase P1 (APP1), also known as X-prolyl aminopeptidase (XPNPEP1) in human tissues, is a cytosolic exopeptidase that preferentially removes amino acids from the N-terminus of peptides possessing a penultimate N-terminal proline residue. The enzyme has an important role in the catabolism of proline containing peptides since peptide bonds adjacent to the imino acid proline are resistant to cleavage by most peptidases. We show that recombinant and catalytically active Caenorhabditis elegans APP-1 is a dimer that uses dinuclear zinc at the active site and, for the first time, we provide structural information for a eukaryotic APP-1 in complex with the inhibitor, apstatin. Our analysis reveals that C. elegans APP-1 shares similar mode of substrate binding and a common catalytic mechanism with other known X-prolyl aminopeptidases. PMID:25905034

  20. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site

    PubMed Central

    Iyer, Shalini; La-Borde, Penelope J.; Payne, Karl A.P.; Parsons, Mark R.; Turner, Anthony J.; Isaac, R. Elwyn; Acharya, K. Ravi

    2015-01-01

    Eukaryotic aminopeptidase P1 (APP1), also known as X-prolyl aminopeptidase (XPNPEP1) in human tissues, is a cytosolic exopeptidase that preferentially removes amino acids from the N-terminus of peptides possessing a penultimate N-terminal proline residue. The enzyme has an important role in the catabolism of proline containing peptides since peptide bonds adjacent to the imino acid proline are resistant to cleavage by most peptidases. We show that recombinant and catalytically active Caenorhabditis elegans APP-1 is a dimer that uses dinuclear zinc at the active site and, for the first time, we provide structural information for a eukaryotic APP-1 in complex with the inhibitor, apstatin. Our analysis reveals that C. elegans APP-1 shares similar mode of substrate binding and a common catalytic mechanism with other known X-prolyl aminopeptidases. PMID:25905034

  1. Aluminium compound additives to reduce zinc corrosion in anodes of electrochemical cells

    SciTech Connect

    Jacus, R.J.

    1991-07-23

    This patent describes an electrochemical cell. It comprises an alkaline anode/electrolyte mixture, the anode/electrolyte mixture comprising zinc anode material containing less than 1% mercury by weight of zinc and a source of aluminum ions.

  2. Zinc in diet

    MedlinePlus

    Animal proteins are a good source of zinc. Beef, pork, and lamb contain more zinc than fish. The ... use by the body as the zinc from animal proteins. Therefore, low-protein diets and vegetarian diets tend ...

  3. Recent advances in zinc-air batteries.

    PubMed

    Li, Yanguang; Dai, Hongjie

    2014-08-01

    Zinc-air is a century-old battery technology but has attracted revived interest recently. With larger storage capacity at a fraction of the cost compared to lithium-ion, zinc-air batteries clearly represent one of the most viable future options to powering electric vehicles. However, some technical problems associated with them have yet to be resolved. In this review, we present the fundamentals, challenges and latest exciting advances related to zinc-air research. Detailed discussion will be organized around the individual components of the system - from zinc electrodes, electrolytes, and separators to air electrodes and oxygen electrocatalysts in sequential order for both primary and electrically/mechanically rechargeable types. The detrimental effect of CO2 on battery performance is also emphasized, and possible solutions summarized. Finally, other metal-air batteries are briefly overviewed and compared in favor of zinc-air. PMID:24926965

  4. 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.

  5. Characterization of active site residues of nitroalkane oxidase.

    PubMed

    Valley, Michael P; Fenny, Nana S; Ali, Shah R; Fitzpatrick, Paul F

    2010-06-01

    The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Ser171 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by approximately 5-fold and decreases in the rate constant for product release of approximately 2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. PMID:20056514

  6. 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.

  7. 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.

  8. Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations

    SciTech Connect

    Spraggon, Glen; Hornsby, Michael; Shipway, Aaron; Tully, David C.; Bursulaya, Badry; Danahay, Henry; Harris, Jennifer L.; Lesley, Scott A.

    2010-01-12

    Prostasin or human channel-activating protease 1 has been reported to play a critical role in the regulation of extracellular sodium ion transport via its activation of the epithelial cell sodium channel. Here, the structure of the extracellular portion of the membrane associated serine protease has been solved to high resolution in complex with a nonselective d-FFR chloromethyl ketone inhibitor, in an apo form, in a form where the apo crystal has been soaked with the covalent inhibitor camostat and in complex with the protein inhibitor aprotinin. It was also crystallized in the presence of the divalent cation Ca{sup +2}. Comparison of the structures with each other and with other members of the trypsin-like serine protease family reveals unique structural features of prostasin and a large degree of conformational variation within specificity determining loops. Of particular interest is the S1 subsite loop which opens and closes in response to basic residues or divalent ions, directly binding Ca{sup +2} cations. This induced fit active site provides a new possible mode of regulation of trypsin-like proteases adapted in particular to extracellular regions with variable ionic concentrations such as the outer membrane layer of the epithelial cell.

  9. Porous capsules with a large number of active sites: nucleation/growth under confined conditions.

    PubMed

    Garai, Somenath; Rubčić, Mirta; Bögge, Hartmut; Gouzerh, Pierre; Müller, Achim

    2015-03-01

    This work deals with the generation of large numbers of active sites and with ensuing nucleation/ growth processes on the inside wall of the cavity of porous nanocapsules of the type (pentagon)12(linker)30≡{(Mo(VI))Mo(VI)5}12{Mo(V)2(ligand)}30. A first example refers to sulfur dioxide capture through displacement of acetate ligands, while the grafted sulfite ligands are able to trap {MoO3H}(+) units thereby forming unusual {(O2SO)3MoO3H}(5-) assemblies. A second example relates to the generation of open coordination sites through release of carbon dioxide upon mild acidification of a carbonate-type capsule. When the reaction is performed in the presence of heptamolybdate ions, MoO4(2-) ions enter the cavity where they bind to the inside wall while forming new types of polyoxomolybdate architectures, thereby extending the molybdenum oxide skeleton of the capsule. Parallels can be drawn with Mo-storage proteins and supported MoO3 catalysts, making the results relevant to molybdenum biochemistry and to catalysis. PMID:25653204

  10. 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

  11. The Essential Toxin: Impact of Zinc on Human Health

    PubMed Central

    Plum, Laura M.; Rink, Lothar; Haase, Hajo

    2010-01-01

    Compared to several other metal ions with similar chemical properties, zinc is relatively harmless. Only exposure to high doses has toxic effects, making acute zinc intoxication a rare event. In addition to acute intoxication, long-term, high-dose zinc supplementation interferes with the uptake of copper. Hence, many of its toxic effects are in fact due to copper deficiency. While systemic homeostasis and efficient regulatory mechanisms on the cellular level generally prevent the uptake of cytotoxic doses of exogenous zinc, endogenous zinc plays a significant role in cytotoxic events in single cells. Here, zinc influences apoptosis by acting on several molecular regulators of programmed cell death, including caspases and proteins from the Bcl and Bax families. One organ where zinc is prominently involved in cell death is the brain, and cytotoxicity in consequence of ischemia or trauma involves the accumulation of free zinc. Rather than being a toxic metal ion, zinc is an essential trace element. Whereas intoxication by excessive exposure is rare, zinc deficiency is widespread and has a detrimental impact on growth, neuronal development, and immunity, and in severe cases its consequences are lethal. Zinc deficiency caused by malnutrition and foods with low bioavailability, aging, certain diseases, or deregulated homeostasis is a far more common risk to human health than intoxication. PMID:20617034

  12. Zinc supplementation or regulation of its homeostasis: advantages and threats.

    PubMed

    Tubek, Sławomir

    2007-10-01

    To accomplish its multifunctional biological roles, zinc requires precise homeostatic mechanisms. There are efficient mechanisms that regulate zinc absorption from the alimentary tract and its excretion by the kidney depending on the organism demands. The regulatory mechanisms of cellular zinc inflow, distribution, and zinc outflow are so efficient that symptoms of zinc deficiency are rare, and symptoms connected with its massive accumulation are even more rare. The efficiency of homeostatic mechanisms that prevent zinc deficiency or excessive zinc accumulation in the organism is genetically conditioned. It seems that an essential element of zinc homeostasis is the efficiency of zinc transmembrane exchange mechanisms. Intracellular free zinc concentration is higher than in extracellular space. Physiologically, the active outflow of zinc ions from the cell depends on the increase of its concentration in extracellular space. The ion pumps activity depends on the efficiency by which the cell manages energy. Considering the fact that zinc deficiency accelerates apoptosis and that excessive zinc accumulation inside cells results in a toxic effect that forces its death brings about several questions: Is intensification and acceleration of changes in zinc metabolism with age meaningful? Is there a real zinc deficiency occurring with age or in connection with the aforementioned pathological processes, or is it just a case of tissue and cell redistribution? When discussing factors that influence zinc homeostasis, can we consider zinc supplementation or regulation of zinc balance in the area of its redistribution? To clarify these aspects, an essential element will also be the clear understanding of the nomenclature used to describe changes in zinc balance. Zinc homeostasis can be different in different age groups and depends on sex, thus zinc dyshomeostasis refers to changes in its metabolism that deviate from the normal rates for a particular age group and sex. This

  13. 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

  14. 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

  15. 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.

  16. 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

  17. Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1.

    PubMed

    Martinez, Salette; Wu, Rui; Krzywda, Karoline; Opalka, Veronika; Chan, Hei; Liu, Dali; Holz, Richard C

    2015-07-01

    A strictly conserved active site arginine residue (αR157) and two histidine residues (αH80 and αH81) located near the active site of the Fe-type nitrile hydratase from Comamonas testosteroni Ni1 (CtNHase), were mutated. These mutant enzymes were examined for their ability to bind iron and hydrate acrylonitrile. For the αR157A mutant, the residual activity (k cat = 10 ± 2 s(-1)) accounts for less than 1% of the wild-type activity (k cat = 1100 ± 30 s(-1)) while the K m value is nearly unchanged at 205 ± 10 mM. On the other hand, mutation of the active site pocket αH80 and αH81 residues to alanine resulted in enzymes with k cat values of 220 ± 40 and 77 ± 13 s(-1), respectively, and K m values of 187 ± 11 and 179 ± 18 mM. The double mutant (αH80A/αH81A) was also prepared and provided an enzyme with a k cat value of 132 ± 3 s(-1) and a K m value of 213 ± 61 mM. These data indicate that all three residues are catalytically important, but not essential. X-ray crystal structures of the αH80A/αH81A, αH80W/αH81W, and αR157A mutant CtNHase enzymes were solved to 2.0, 2.8, and 2.5 Å resolutions, respectively. In each mutant enzyme, hydrogen-bonding interactions crucial for the catalytic function of the αCys(104)-SOH ligand are disrupted. Disruption of these hydrogen bonding interactions likely alters the nucleophilicity of the sulfenic acid oxygen and the Lewis acidity of the active site Fe(III) ion. PMID:26077812

  18. Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B.

    PubMed

    Ozcan, Ahmet; Olmez, Elif Ozkirimli; Alakent, Burak

    2013-05-01

    In protein tyrosine phosphatase 1B (PTP1B), the flexible WPD loop adopts a closed conformation (WPDclosed ) in the active state of PTP1B, bringing the catalytic Asp181 close to the active site pocket, while WPD loop is in an open conformation (WPDopen ) in the inactive state. Previous studies showed that Asp181 may be protonated at physiological pH, and ordered water molecules exist in the active site. In the current study, molecular dynamics simulations are employed at different Asp181 protonation states and initial positions of active site water molecules, and compared with the existing crystallographic data of PTP1B. In WPDclosed conformation, the active site is found to maintain its conformation only in the protonated state of Asp181 in both free and liganded states, while Asp181 is likely to be deprotonated in WPDopen conformation. When the active site water molecule network that is a part of the free WPDclosed crystal structure is disrupted, intermediate WPD loop conformations, similar to that in the PTPRR crystal structure, are sampled in the MD simulations. In liganded PTP1B, one active site water molecule is found to be important for facilitating the orientation of Cys215 and the phosphate ion, thus may play a role in the reaction. In conclusion, conformational stability of WPD loop, and possibly catalytic activity of PTP1B, is significantly affected by the protonation state of Asp181 and position of active site water molecules, showing that these aspects should be taken into consideration both in MD simulations and inhibitor design. PMID:23239271

  19. Production of zinc pellets

    SciTech Connect

    Cooper, J.F.

    1996-11-26

    Uniform zinc pellets are formed for use in batteries having a stationary or moving slurry zinc particle electrode. The process involves the cathodic deposition of zinc in a finely divided morphology from battery reaction product onto a non-adhering electrode substrate. The mossy zinc is removed from the electrode substrate by the action of gravity, entrainment in a flowing electrolyte, or by mechanical action. The finely divided zinc particles are collected and pressed into pellets by a mechanical device such as an extruder, a roller and chopper, or a punch and die. The pure zinc pellets are returned to the zinc battery in a pumped slurry and have uniform size, density and reactivity. Applications include zinc-air fuel batteries, zinc-ferricyanide storage batteries, and zinc-nickel-oxide secondary batteries. 6 figs.

  20. Update on zinc biology.

    PubMed

    Solomons, Noel W

    2013-01-01

    Zinc has become a prominent nutrient of clinical and public health interest in the new millennium. Functions and actions for zinc emerge as increasingly ubiquitous in mammalian anatomy, physiology and metabolism. There is undoubtedly an underpinning in fundamental biology for all of the aspects of zinc in human health (clinical and epidemiological) in pediatric and public health practice. Unfortunately, basic science research may not have achieved a full understanding as yet. As a complement to the applied themes in the companion articles, a selection of recent advances in the domains homeostatic regulation and transport of zinc is presented; they are integrated, in turn, with findings on genetic expression, intracellular signaling, immunity and host defense, and bone growth. The elements include ionic zinc, zinc transporters, metallothioneins, zinc metalloenzymes and zinc finger proteins. In emerging basic research, we find some plausible mechanistic explanations for delayed linear growth with zinc deficiency and increased infectious disease resistance with zinc supplementation. PMID:23689109

  1. Production of zinc pellets

    DOEpatents

    Cooper, John F.

    1996-01-01

    Uniform zinc pellets are formed for use in batteries having a stationary or moving slurry zinc particle electrode. The process involves the cathodic deposition of zinc in a finely divided morphology from battery reaction product onto a non-adhering electrode substrate. The mossy zinc is removed from the electrode substrate by the action of gravity, entrainment in a flowing electrolyte, or by mechanical action. The finely divided zinc particles are collected and pressed into pellets by a mechanical device such as an extruder, a roller and chopper, or a punch and die. The pure zinc pellets are returned to the zinc battery in a pumped slurry and have uniform size, density and reactivity. Applications include zinc-air fuel batteries, zinc-ferricyanide storage batteries, and zinc-nickel-oxide secondary batteries.

  2. Kinetic analysis of zinc metabolism and its regulation in normal humans

    SciTech Connect

    Wastney, M.E.; Aamodt, R.L.; Rumble, W.F.; Henkin, R.I.

    1986-08-01

    Zinc metabolism was studied in 32 normal volunteers after oral or intravenous administration of WVZn. Data were collected from the blood, urine, feces, whole body, and over the liver and thigh regions for 9 mo while the subjects consumed their regular diets (containing 10 mg Zn ion/day) and for an additional 9 mo while the subjects received an exogenous oral supplement of 100 mg Zn ion/day. Data from each subject were fitted by a compartmental model for zinc metabolism that was developed previously for patients with taste and smell dysfunction. These data from normal subjects were used to determine the absorption, distribution, and excretion of zinc and the mass of zinc in erythrocytes, liver, thigh, and whole body. By use of additional data obtained from the present study, the model was refined further such that a large compartment, which was previously determined to contain 90% of the body zinc, was subdivided into two compartments to represent zinc in muscle and bone. When oral zinc intake was increased 11-fold three new sites of regulation of zinc metabolism were identified in addition to the two sites previously defined in patients with taste and smell dysfunction (absorption of zinc from gut and excretion of zinc in urine). The three new sites are exchange of zinc with erythrocytes, release of zinc by muscle, and secretion of zinc into gut. Regulation at these five sites appears to maintain some tissue concentrations of zinc when dietary zinc increases.

  3. Phosphorescent Sensor for Biological Mobile Zinc

    PubMed Central

    You, Youngmin; Lee, Sumin; Kim, Taehee; Ohkubo, Kei; Chae, Weon-Sik; Fukuzumi, Shunichi; Jhon, Gil-Ja; Nam, Wonwoo; Lippard, Stephen J.

    2011-01-01

    A new phosphorescent zinc sensor (ZIrF) was constructed based on an Ir(III) complex bearing two 2-(2,4-difluorophenyl)pyridine (dfppy) cyclometalating ligands and a neutral 1,10-phenanthroline (phen) ligand. A zinc-specific di(2-picolyl)amino (DPA) receptor was introduced at the 4-position of the phen ligand via a methylene linker. The cationic Ir(III) complex exhibited dual phosphorescence bands in CH3CN solutions originating from blue and yellow emission of the dfppy and phen ligands, respectively. Zinc coordination selectively enhanced the latter, affording a phosphorescence ratiometric response. Electrochemical techniques, quantum chemical calculations, and steady-state and femtosecond spectroscopy were employed to establish a photophysical mechanism for this phosphorescence response. The studies revealed that zinc coordination perturbs nonemissive processes of photoinduced electron transfer (PeT) and intraligand charge transfer (ILCT) transition occurring between DPA and phen. ZIrF can detect zinc ions in a reversible and selective manner in buffered solution (pH 7.0, 25 mM PIPES) with Kd = 11 nM and pKa = 4.16. Enhanced signal-to-noise ratios were achieved by time-gated acquisition of long-lived phosphorescence signals. The sensor was applied to image biological free zinc ions in live A549 cells by confocal laser scanning microscopy. A fluorescence lifetime imaging microscope (FLIM) detected an increase in photoluminescence lifetime for zinc-treated A549 cells as compared to controls. ZIrF is the first successful phosphorescent sensor that detects zinc ions in biological samples. PMID:22023085

  4. Complexation of copper and zinc ions with proteins of a light-harvesting complex (LHC-II) of chloroplast thylakoid membranes studied by FT-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Tajmir-Riahi, H. A.; Ahmed, A.

    1993-08-01

    The interaction of Zn(II) and Cu(II) ions with the light-harvesting proteins (LHC-II) of chloroplast thylakoid membranes was studied in aqueous solution with metal ion concentrations of 0.01 to 20mM, using Fourier transform-infrared (FT-IR) spectroscopy. Analyses of the metal ion binding mode and protein conformational variations were carried out and correlations between spectral changes and metal—protein complexation were established. Infrared difference spectroscopic results revealed the presence of a strong metal—protein interaction at high metal ion concentrations, while at low concentrations complexation was negligible. The binding of Zn and Cu ions was found to be with the protein carbonyl groups at low metal ion concentrations, whereas CO and CN groups were the main coordination sites at higher concentrations. A major conformational variation from α-helix to β-sheet and turn structures was observed in the presence of a concentrated metal ion solution.

  5. Molecular mechanisms of the epithelial transport of toxic metal ions, particularly mercury, cadmium, lead, arsenic, zinc and copper. Progress report, January 1, 1980-December 31, 1980

    SciTech Connect

    Wasserman, R H

    1980-01-01

    Investigations were continued to elucidate the mode of transepithelial transport of toxic metal ions across the gastrointestinal tract, as well as their interactions with biological processes and other metal ions. All experimental details that are either published, submitted for publication or in press during this report period are included in the Appendix. Primary attention for this report has been given to the intestinal absorption of lead and its interaction with other biological moieties.

  6. Transient neonatal zinc deficiency.

    PubMed

    Krieger, I; Alpern, B E; Cunnane, S C

    1986-06-01

    We report an infant who developed clinical manifestations of zinc deficiency during the first month of life although the diet was adequate for zinc and no other causes could be ascertained. The diagnosis was confirmed by low plasma-zinc concentrations and a positive response to zinc treatment. The fatty acid profile of plasma phospholipids was typical of zinc deficiency (ie, arachidonic acid was markedly decreased). The transient nature of this disorder was evident when no relapse occurred after cessation of zinc therapy and plasma-zinc and arachidonic acid concentrations remained normal. Several explanations for the development of transient neonatal zinc deficiency are offered. The observation demonstrates that occasional infants may have requirements for zinc that are beyond the intakes of the conventional RDA. PMID:3717070

  7. A zinc protein isolated from human parotid saliva.

    PubMed Central

    Henkin, R I; Lippoldt, R E; Bilstad, J; Edelhoch, H

    1975-01-01

    A zinc protein has been isolated and purified to apparent homogeneity from subjects with normal taste acuity by gel filtration and ion-exchange chromatography. The protein has a molecular weight of 37,000 and does not appear to have subunits. It is composed of 8% histidine residues and has 2 moles of zinc per mole of protein. Images PMID:1054831

  8. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    DOE PAGESBeta

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with themore » metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.« less

  9. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    SciTech Connect

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with the metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.

  10. 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

  11. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    SciTech Connect

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with the metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.

  12. Measurements of plasma zinc

    PubMed Central

    Davies, I. J. T.; Musa, M.; Dormandy, T. L.

    1968-01-01

    Zinc is an essential trace element. Previous methods of measuring zinc in clinical material have been difficult and reported findings must be treated with caution. Using atomic absorption spectroscopy it has been established that plasma zinc is one of the most uniform biochemical characteristics of normal adult blood. Sex and age differences in adult life are insignificant. Increased metabolic activity, on the other hand, induces a marked, immediate fall in plasma zinc level. The possible implications of this are discussed. Zinc levels in patients with diabetes mellitus, cardiovascular disease, and anaemia due to acute blood loss have been within normal limits. Plasma zinc is low in certain types of liver disease. PMID:5303355

  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. Signal Amplification of Bioassay Using Zinc Nanomaterials

    NASA Astrophysics Data System (ADS)

    Cowles, Chad L.

    bioassay signal tranducers. To overcome the limitations associated with zinc-based nanomaterials, a novel signal transduction approach was developed that relies on zinc ion release from nanoparticle labels during an immunoassay. The development of an innovative method for zinc ion detection and the description of a previously undescribed zinc-based nanomaterial are also described in this work. There are three major contributions to science in this work: (1) The development of an original and innovative signal transduction approach for immunoassays that adopts fluorescence detection of zinc ions released from ZnS nanoparticle labels; (2) The discovery and development of dual signal amplification for immunoassay signal transduction using ion release and subsequent activation of a zinc dependent metallozyme; (3) The synthesis and characterization of a novel zinc-based nanomaterial and its biosensing application using both single and dual signal amplification strategies.

  15. Deletion of the zupT gene for a zinc importer influences zinc pools in Cupriavidus metallidurans CH34.

    PubMed

    Herzberg, M; Bauer, L; Nies, D H

    2014-03-01

    Cupriavidus metallidurans strain CH34 accomplishes a high level of transition metal resistance by a combination of rather unspecific transition metal import and controlled efflux of surplus metals. Using the plasmid-free mutant strain AE104 that possesses only a limited number of metal efflux systems, cellular metal pools were identified as counterparts of these transport reactions. At low zinc concentrations strain AE104 took up Zn(II) until the zinc content reached an optimum level of 70,000 Zn(II) per cell in the exponential phase of growth, whereas a ΔzupT mutant lacking the zinc importer ZupT contained only 20,000 Zn(II)/cell, possibly the minimum zinc content. Mutant and parent cells accumulated up to 125,000 Zn(II) per cell at high (100 μM) external zinc concentrations (optimum zinc content). When the mutant strain Δe4, which has all the known genes for zinc efflux systems deleted, was cultivated in the presence of zinc concentrations close to its upper tolerance level (10 μM), these cells contained 250,000 Zn(II) per cell, probably the maximum zinc content. Instead of zinc, 120,000 cobalt or cadmium ions could also fill-up parts of this zinc pool, showing that it is in fact an undefined pool of divalent transition metal cations bound with low substrate specificity. Even when the cells contained sufficient numbers of total zinc, the zinc importer ZupT was required for important cellular processes, indicating the presence of a pool of tightly bound zinc ions, which depends on ZupT for efficient replenishment. The absence of ZupT led to the formation of inclusion bodies, perturbed oxidative stress resistance and decreased efficiency in the synthesis of the zinc-dependent subunit RpoC of the RNA polymerase, leading to RpoC accumulation. Moreover, when a czc allele for a zinc-exporting transenvelope efflux system CzcCBA was constitutively expressed in a ΔzupT mutant, this led to the disappearance of the CzcA protein and the central subunit of the protein

  16. Unexpected reactivity of 2-fluorolinalyl diphosphate in the active site of crystalline 2-methylisoborneol synthase

    PubMed Central

    Köksal, Mustafa; Chou, Wayne K. W.; Cane, David E.; Christianson, David W.

    2013-01-01

    The crystal structure of 2-methylisoborneol synthase (MIBS) from Streptomyces coelicolor A3(2) has been determined in its unliganded state and in complex with 2 Mg2+ ions and cis-2-fluorogeranyl diphosphate at 1.85 Å and 2.00 Å resolution, respectively. Under normal circumstances, MIBS catalyzes the cyclization of the naturally-occurring, non-canonical 11-carbon isoprenoid substrate, 2-methylgeranyl diphosphate, which first undergoes an ionization-isomerization-ionization sequence through the tertiary diphosphate intermediate 2-methyllinalyl diphosphate to enable subsequent cyclization chemistry. MIBS does not exhibit catalytic activity with 2-fluorogeranyl diphosphate, and we recently reported the crystal structure of MIBS complexed with this unreactive substrate analogue [Köksal, M., Chou, W. K. W., Cane, D. E., Christianson, D. W. (2012) Biochemistry 51, 3011–3020]. However, cocrystallization of MIBS with the fluorinated analogue of the tertiary allylic diphosphate intermediate, 2-fluorolinalyl diphosphate, reveals unexpected reactivity for the intermediate analogue and yields the crystal structure of the complex with the primary allylic diphosphate, 2-fluoroneryl diphosphate. Comparison with the structure of the unliganded enzyme reveals that the crystalline enzyme active site remains partially open, presumably due to the binding of only 2 Mg2+ ions. Assays in solution indicate that MIBS catalyzes the generation of (1R)-(+)-camphor from the substrate 2-fluorolinalyl diphosphate, suggesting that both 2-fluorolinalyl diphosphate and 2-methyllinalyl diphosphate follow the identical cyclization mechanism leading to 2-substituted isoborneol products; however, the initially generated 2-fluoroisoborneol cyclization product is unstable and undergoes elimination of hydrogen fluoride to yield (1R)-(+)-camphor. PMID:23844678

  17. Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites.

    PubMed

    Munch, Henrik K; Nygaard, Jesper; Christensen, Niels Johan; Engelbrekt, Christian; Østergaard, Mads; Porsgaard, Trine; Hoeg-Jensen, Thomas; Zhang, Jingdong; Arleth, Lise; Thulstrup, Peter W; Jensen, Knud J

    2016-02-12

    Controlled self-assembly (SA) of proteins offers the possibility to tune their properties or to create new materials. Herein, we present the synthesis of a modified human insulin (HI) with two distinct metal-ion binding sites, one native, the other abiotic, enabling hierarchical SA through coordination with two different metal ions. Selective attachment of an abiotic 2,2'-bipyridine (bipy) ligand to HI, yielding HI-bipy, enabled Zn(II)-binding hexamers to SA into trimers of hexamers, [[HI-bipy]6]3, driven by octahedral coordination to a Fe(II)  ion. The structures were studied in solution by small-angle X-ray scattering and on surfaces with AFM. The abiotic metal ligand had a higher affinity for Fe(II) than Zn(II)  ions, enabling control of the hexamer formation with Zn(II) and the formation of trimers of hexamers with Fe(II)  ions. This precise control of protein SA to give oligomers of oligomers provides nanoscale structures with potential applications in nanomedicine. PMID:26762534

  18. The active sites of supported silver particle catalysts in formaldehyde oxidation.

    PubMed

    Chen, Yaxin; Huang, Zhiwei; Zhou, Meijuan; Hu, Pingping; Du, Chengtian; Kong, Lingdong; Chen, Jianmin; Tang, Xingfu

    2016-08-01

    Surface silver atoms with upshifted d-orbitals are identified as the catalytically active sites in formaldehyde oxidation by correlating their activity with the number of surface silver atoms, and the degree of the d-orbital upshift governs the catalytic performance of the active sites. PMID:27406403

  19. Ultrafast ligand binding dynamics in the active site of native bacterial nitric oxide reductase.

    PubMed

    Kapetanaki, Sofia M; Field, Sarah J; Hughes, Ross J L; Watmough, Nicholas J; Liebl, Ursula; Vos, Marten H

    2008-01-01

    The active site of nitric oxide reductase from Paracoccus denitrificans contains heme and non-heme iron and is evolutionarily related to heme-copper oxidases. The CO and NO dynamics in the active site were investigated using ultrafast transient absorption spectroscopy. We find that, upon photodissociation from the active site heme, 20% of the CO rebinds in 170 ps, suggesting that not all the CO transiently binds to the non-heme iron. The remaining 80% does not rebind within 4 ns and likely migrates out of the active site without transient binding to the non-heme iron. Rebinding of NO to ferrous heme takes place in approximately 13 ps. Our results reveal that heme-ligand recombination in this enzyme is considerably faster than in heme-copper oxidases and are consistent with a more confined configuration of the active site. PMID:18420024

  20. 2,2‧-[Benzene-1,2-diylbis(iminomethanediyl)]diphenol derivative bearing two amine and hydroxyl groups as fluorescent receptor for Zinc(II) ion

    NASA Astrophysics Data System (ADS)

    Tayade, Kundan; Sahoo, Suban K.; Patil, Rahul; Singh, Narinder; Attarde, Sanjay; Kuwar, Anil

    A new non-natural receptor 2,2‧-[benzene-1,2-diylbis(iminomethanediyl)]diphenol (4) was synthesized, and it is fluorogenic behaviour toward various metal ions were investigated. Receptor 4 exhibited pronounced fluorescence enhancement in the presence of Zn2+, which can visually be discernible by an orchid fluorescence in compared to other metal ions. The receptor 4 shows high sensitivity and selectivity for Zn2+ through changes in the fluorescence intensity based on chelation-enhanced fluorescence (CHEF). The binding modes of the complexes were investigated by Job’s plot and density functional theory (DFT).

  1. Electrochemical synthesis and characterization of zinc carbonate and zinc oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Pourmortazavi, Seied Mahdi; Marashianpour, Zahra; Karimi, Meisam Sadeghpour; Mohammad-Zadeh, Mohammad

    2015-11-01

    Zinc oxide and its precursor i.e., zinc carbonate is widely utilized in various fields of industry, especially in solar energy conversion, optical, and inorganic pigments. In this work, a facile and clean electrodeposition method was utilized for the synthesis of zinc carbonate nanoparticles. Also, zinc oxide nanoparticles were produced by calcination of the prepared zinc carbonate powder. Zinc carbonate nanoparticles with different sizes were electrodeposited by electrolysis of a zinc plate as anode in the solution of sodium carbonate. It was found that the particle size of zinc carbonate might be tuned by process parameters, i.e., electrolysis voltage, carbonate ion concentration, solvent composition and stirring rate of the electrolyte solution. An orthogonal array design was utilized to identify the optimum experimental conditions. The experimental results showed that the minimum size of the electrodeposited ZnCO3 particles is about 24 nm whereas the maximum particle size is around 40 nm. The TG-DSC studies of the nanoparticles indicated that the main thermal degradation of ZnCO3 occurs in two steps over the temperature ranges of 150-250 and 350-400 °C. The electrosynthesized ZnCO3 nanoparticles were calcined at the temperature of 600 °C to prepare ZnO nanoparticles. The prepared ZnCO3 and ZnO nanoparticles were characterized by SEM, X-ray diffraction (XRD), and FT-IR techniques.

  2. Zinc Transporters and Zinc Signaling: New Insights into Their Role in Type 2 Diabetes

    PubMed Central

    Myers, Stephen A.

    2015-01-01

    Zinc is an essential trace element that plays a vital role in many biological processes including growth and development, immunity, and metabolism. Recent studies have highlighted zinc's dynamic role as a “cellular second messenger” in the control of insulin signaling and glucose homeostasis. Accordingly, mechanisms that contribute to dysfunctional zinc signaling are suggested to be associated with metabolic disease states including cancer, cardiovascular disease, Alzheimer's disease, and diabetes. The actions of the proteins that control the uptake, storage, and distribution of zinc, the zinc transporters, are under intense investigation due to their emerging role in type 2 diabetes. The synthesis, secretion, and action of insulin are dependent on zinc and the transporters that make this ion available to cellular processes. This suggests that zinc plays a previously unidentified role where changes in zinc status over time may affect insulin activity. This previously unexplored concept would raise a whole new area of research into the pathophysiology of insulin resistance and introduce a new class of drug target with utility for diabetes pharmacotherapy. PMID:25983752

  3. Total zinc in zinc battery plates by EDTA titration

    SciTech Connect

    Hammersley, V.L.

    1995-07-01

    At present, zinc battery plate electrodes are analyzed for zinc oxide, zinc chloride, zinc fluoride, zinc carbonate, zinc oxychloride, total zinc, zinc as the metal, and trace metals. A variety of methods are used to determine each of these components. The amount of zinc in each of the zinc compounds is determined by multiplying the percent of the compound by the ratio of the molecular weights of zinc to the zinc compound. This percent zinc is subtracted from percent total zinc and the operation is performed for every zinc compound determined. The remaining zinc value after these subtractions represents zinc as the metal. Zinc metal is the charged state on the anode. Percent total zinc is required in all these calculations. The importance of these components cannot be overemphasized. The presence, or absence, of certain components in the zinc electrode can influence its behavior in a zinc-silver oxide primary battery. Passivation layers, tendency to dendritic growth, corrosion rates, voltage rise times, current density, porosity, surface area, electrochemical capacity, and other considerations make it imperative that the chemical composition of the zinc electrode be known. The focus of this project was to evaluate the present method for total zinc and to develop a better method.

  4. Bacitracin zinc overdose

    MedlinePlus

    ... Small amounts of bacitracin zinc are dissolved in petroleum jelly to create antibiotic ointments. Bacitracin zinc overdose ... is accredited by URAC, also known as the American Accreditation HealthCare Commission (www.urac.org). URAC's accreditation ...

  5. Zinc oxide overdose

    MedlinePlus

    Zinc oxide is an ingredient in many products. Some of these are certain creams and ointments used ... prevent or treat minor skin burns and irritation. Zinc oxide overdose occurs when someone eats one of ...

  6. Bacitracin zinc overdose

    MedlinePlus

    Bacitracin zinc is a medicine that is used on cuts and other skin wounds to help prevent infection. Bacitracin ... medicine that kills germs. Small amounts of bacitracin zinc are dissolved in petroleum jelly to create antibiotic ...

  7. Zinc and gastrointestinal disease

    PubMed Central

    Skrovanek, Sonja; DiGuilio, Katherine; Bailey, Robert; Huntington, William; Urbas, Ryan; Mayilvaganan, Barani; Mercogliano, Giancarlo; Mullin, James M

    2014-01-01

    This review is a current summary of the role that both zinc deficiency and zinc supplementation can play in the etiology and therapy of a wide range of gastrointestinal diseases. The recent literature describing zinc action on gastrointestinal epithelial tight junctions and epithelial barrier function is described. Zinc enhancement of gastrointestinal epithelial barrier function may figure prominently in its potential therapeutic action in several gastrointestinal diseases. PMID:25400994

  8. ZINC ABSORPTION BY INFANTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Zinc is a vital mineral in human nutrition, and rare cases of overt zinc deficiency are well described in term and preterm infants. A variety of methods have been developed to assess zinc absorption, retention, and balance in humans, either using mass (metabolic) balance or stable isotope-based METH...

  9. Atomically-thin two-dimensional sheets for understanding active sites in catalysis.

    PubMed

    Sun, Yongfu; Gao, Shan; Lei, Fengcai; Xie, Yi

    2015-02-01

    Catalysis can speed up chemical reactions and it usually occurs on the low coordinated steps, edges, terraces, kinks and corner atoms that are often called "active sites". However, the atomic level interplay between active sites and catalytic activity is still an open question, owing to the large difference between idealized models and real catalysts. This stimulates us to pursue a suitable material model for studying the active sites-catalytic activity relationship, in which the atomically-thin two-dimensional sheets could serve as an ideal model, owing to their relatively simple type of active site and the ultrahigh fraction of active sites that are comparable to the overall atoms. In this tutorial review, we focus on the recent progress in disclosing the factors that affect the activity of reactive sites, including characterization of atomic coordination number, structural defects and disorder in ultrathin two-dimensional sheets by X-ray absorption fine structure spectroscopy, positron annihilation spectroscopy, electron spin resonance and high resolution transmission electron microscopy. Also, we overview their applications in CO catalytic oxidation, photocatalytic water splitting, electrocatalytic oxygen and hydrogen evolution reactions, and hence highlight the atomic level interplay among coordination number, structural defects/disorder, active sites and catalytic activity in the two-dimensional sheets with atomic thickness. Finally, we also present the major challenges and opportunities regarding the role of active sites in catalysis. We believe that this review provides critical insights for understanding the catalysis and hence helps to develop new catalysts with high catalytic activity. PMID:25382246

  10. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  11. Inhibition of cyclin-dependent kinase CDK1 by oxindolimine ligands and corresponding copper and zinc complexes.

    PubMed

    Miguel, Rodrigo Bernardi; Petersen, Philippe Alexandre Divina; Gonzales-Zubiate, Fernando A; Oliveira, Carla Columbano; Kumar, Naresh; do Nascimento, Rafael Rodrigues; Petrilli, Helena Maria; da Costa Ferreira, Ana Maria

    2015-10-01

    Oxindolimine-copper(II) and zinc(II) complexes that previously have shown to induce apoptosis, with DNA and mitochondria as main targets, exhibit here significant inhibition of kinase CDK1/cyclin B protein. Copper species are more active than the corresponding zinc, and the free ligand shows to be less active, indicating a major influence of coordination in the process, and a further modulation by the coordinated ligand. Molecular docking and classical molecular dynamics provide a better understanding of the effectiveness and kinase inhibition mechanism by these compounds, showing that the metal complex provides a stronger interaction than the free ligand with the ATP-binding site. The metal ion introduces charge in the oxindole species, giving it a more rigid conformation that then becomes more effective in its interactions with the protein active site. Analogous experiments resulted in no significant effect regarding phosphatase inhibition. These results can explain the cytotoxicity of these metal complexes towards different tumor cells, in addition to its capability of binding to DNA, and decreasing membrane potential of mitochondria. PMID:26411703

  12. Regional interrelationships of zinc, copper, and lead in the brain following lead intoxication. [Rabbits

    SciTech Connect

    Rehman, S.; Chandra, O.

    1984-02-01

    Among heavy metals of industrial and toxicological importance, lead, zinc and copper have probably the widest distribution in the human environment. These metal ions have a non-homogeneous pattern of distribution in the central nervous system (CNS). It has been shown that the normal concentration of these metal ions in the CNS is disturbed following zinc-intoxication. In the present study, the authors have demonstrated the effect of lead alone and in combination with zinc or copper on the regional concentration of zinc, copper and lead ions in the CNS and blood.

  13. Zinc oxyfluoride transparent conductor

    DOEpatents

    Gordon, Roy G.

    1991-02-05

    Transparent, electrically conductive and infrared-reflective films of zinc oxyfluoride are produced by chemical vapor deposition from vapor mixtures of zinc, oxygen and fluorine-containing compounds. The substitution of fluorine for some of the oxygen in zinc oxide results in dramatic increases in the electrical conductivity. For example, diethyl zinc, ethyl alcohol and hexafluoropropene vapors are reacted over a glass surface at 400.degree. C. to form a visibly transparent, electrically conductive, infrared reflective and ultraviolet absorptive film of zinc oxyfluoride. Such films are useful in liquid crystal display devices, solar cells, electrochromic absorbers and reflectors, energy-conserving heat mirrors, and antistatic coatings.

  14. Trace elements in human physiology and pathology: zinc and metallothioneins.

    PubMed

    Tapiero, Haim; Tew, Kenneth D

    2003-11-01

    Zinc is one of the most abundant nutritionally essential elements in the human body. It is found in all body tissues with 85% of the whole body zinc in muscle and bone, 11% in the skin and the liver and the remaining in all the other tissues. In multicellular organisms, virtually all zinc is intracellular, 30-40% is located in the nucleus, 50% in the cytoplasm, organelles and specialized vesicles (for digestive enzymes or hormone storage) and the remainder in the cell membrane. Zinc intake ranges from 107 to 231 micromol/d depending on the source, and human zinc requirement is estimated at 15 mg/d. Zinc has been shown to be essential to the structure and function of a large number of macromolecules and for over 300 enzymic reactions. It has both catalytic and structural roles in enzymes, while in zinc finger motifs, it provides a scaffold that organizes protein sub-domains for the interaction with either DNA or other proteins. It is critical for the function of a number of metalloproteins, inducing members of oxido-reductase, hydrolase ligase, lyase family and has co-activating functions with copper in superoxide dismutase or phospholipase C. The zinc ion (Zn(++)) does not participate in redox reactions, which makes it a stable ion in a biological medium whose potential is in constant flux. Zinc ions are hydrophilic and do not cross cell membranes by passive diffusion. In general, transport has been described as having both saturable and non-saturable components, depending on the Zn(II) concentrations involved. Zinc ions exist primarily in the form of complexes with proteins and nucleic acids and participate in all aspects of intermediary metabolism, transmission and regulation of the expression of genetic information, storage, synthesis and action of peptide hormones and structural maintenance of chromatin and biomembranes. PMID:14652165

  15. [Zinc and gastrointestinal disorders].

    PubMed

    Higashimura, Yasuki; Takagi, Tomohisa; Naito, Yuji

    2016-07-01

    Zinc, an essential trace element, affects immune responses, skin metabolism, hormone composition, and some sensory function, so that the deficiency presents various symptoms such as immunodeficiency and taste obstacle. Further, the zinc deficiency also considers as a risk of various diseases. Recent reports demonstrated that -20% of the Japanese population was marginally zinc deficiency, and over 25% of the global population is at high risk of zinc deficiency. In gastrointestinal disorders, zinc plays an important role in the healing of mucosal and epithelial damage. In fact, polaprezinc, a chelate compound of zinc and L-carnosine, has been used for the treatment of gastric ulcer and gastritis. We describe here the therapeutic effect of zinc on gastrointestinal disorders. PMID:27455800

  16. Cadmium and zinc relationships.

    PubMed Central

    Elinder, C G; Piscator, M

    1978-01-01

    Cadmium and zinc concentrations in kidney and liver have been measured under different exposure situations in different species including man. The results show that zinc increases almost equimolarly with cadmium in kidney after long-term low-level exposure to cadmium, e.g., in man, horse, pig, and lamb. In contrast, the increase of zinc follows that of cadmium to only a limited extent, e.g., in guinea pig, rabbit, rat, mouse, and chicks. In liver, the cadmium--zinc relationship seems to be reversed in such a way that zinc increases with cadmium more markedly in laboratory animals than in higher mammals. These differences between cadmium and zinc relationships in humans and large farm animals and those in commonly used laboratory animals must be considered carefully before experimental data on cadmium and zinc relationships in laboratory animals can be extrapolated to humans. PMID:720298

  17. Highly Ordered Mesoporous Cobalt-Containing Oxides: Structure, Catalytic Properties, and Active Sites in Oxidation of Carbon Monoxide.

    PubMed

    Gu, Dong; Jia, Chun-Jiang; Weidenthaler, Claudia; Bongard, Hans-Josef; Spliethoff, Bernd; Schmidt, Wolfgang; Schüth, Ferdi

    2015-09-01

    Co3O4 with a spinel structure is a very active oxide catalyst for the oxidation of CO. In such catalysts, octahedrally coordinated Co(3+) is considered to be the active site, while tetrahedrally coordinated Co(2+) is assumed to be basically inactive. In this study, a highly ordered mesoporous CoO has been prepared by H2 reduction of nanocast Co3O4 at low temperature (250 °C). The as-prepared CoO material, which has a rock-salt structure with a single Co(2+) octahedrally coordinated by lattice oxygen in Fm3̅m symmetry, exhibited unexpectedly high activity for CO oxidation. Careful investigation of the catalytic behavior of mesoporous CoO catalyst led to the conclusion that the oxidation of surface Co(2+) to Co(3+) causes the high activity. Other mesoporous spinels (CuCo2O4, CoCr2O4, and CoFe2O4) with different Co species substituted with non/low-active metal ions were also synthesized to investigate the catalytically active site of cobalt-based catalysts. The results show that not only is the octahedrally coordinated Co(3+) highly active but also the octahedrally coordinated Co(2+) species in CoFe2O4 with an inverse spinel structure shows some activity. These results suggest that the octahedrally coordinated Co(2+) species is easily oxidized and shows high catalytic activity for CO oxidation. PMID:26301797

  18. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2

    PubMed Central

    Aglietti, Robin A.; Floor, Stephen N.; McClendon, Chris L.; Jacobson, Matthew P.; Gross, John D.

    2013-01-01

    Summary Removal of the 5′ cap structure by Dcp2 is a major step in several 5′–3′ mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using NMR and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators. PMID:23911090

  19. The Zinc Dyshomeostasis Hypothesis of Alzheimer's Disease

    PubMed Central

    Craddock, Travis J. A.; Tuszynski, Jack A.; Chopra, Deepak; Casey, Noel; Goldstein, Lee E.; Hameroff, Stuart R.; Tanzi, Rudolph E.

    2012-01-01

    Alzheimer's disease (AD) is the most common form of dementia in the elderly. Hallmark AD neuropathology includes extracellular amyloid plaques composed largely of the amyloid-β protein (Aβ), intracellular neurofibrillary tangles (NFTs) composed of hyper-phosphorylated microtubule-associated protein tau (MAP-tau), and microtubule destabilization. Early-onset autosomal dominant AD genes are associated with excessive Aβ accumulation, however cognitive impairment best correlates with NFTs and disrupted microtubules. The mechanisms linking Aβ and NFT pathologies in AD are unknown. Here, we propose that sequestration of zinc by Aβ-amyloid deposits (Aβ oligomers and plaques) not only drives Aβ aggregation, but also disrupts zinc homeostasis in zinc-enriched brain regions important for memory and vulnerable to AD pathology, resulting in intra-neuronal zinc levels, which are either too low, or excessively high. To evaluate this hypothesis, we 1) used molecular modeling of zinc binding to the microtubule component protein tubulin, identifying specific, high-affinity zinc binding sites that influence side-to-side tubulin interaction, the sensitive link in microtubule polymerization and stability. We also 2) performed kinetic modeling showing zinc distribution in extra-neuronal Aβ deposits can reduce intra-neuronal zinc binding to microtubules, destabilizing microtubules. Finally, we 3) used metallomic imaging mass spectrometry (MIMS) to show anatomically-localized and age-dependent zinc dyshomeostasis in specific brain regions of Tg2576 transgenic, mice, a model for AD. We found excess zinc in brain regions associated with memory processing and NFT pathology. Overall, we present a theoretical framework and support for a new theory of AD linking extra-neuronal Aβ amyloid to intra-neuronal NFTs and cognitive dysfunction. The connection, we propose, is based on β-amyloid-induced alterations in zinc ion concentration inside neurons affecting stability of polymerized

  20. A metallothionein containing a zinc finger within a four-metal cluster protects a bacterium from zinc toxicity

    PubMed Central

    Blindauer, Claudia A.; Harrison, Mark D.; Parkinson, John A.; Robinson, Andrea K.; Cavet, Jennifer S.; Robinson, Nigel J.; Sadler, Peter J.

    2001-01-01

    Zinc is essential for many cellular processes, including DNA synthesis, transcription, and translation, but excess can be toxic. A zinc-induced gene, smtA, is required for normal zinc-tolerance in the cyanobacterium Synechococcus PCC 7942. Here we report that the protein SmtA contains a cleft lined with Cys-sulfur and His-imidazole ligands that binds four zinc ions in a Zn4Cys9His2 cluster. The thiolate sulfurs of five Cys ligands provide bridges between the two ZnCys4 and two ZnCys3His sites, giving two fused six-membered rings with distorted boat conformations. The inorganic core strongly resembles the Zn4Cys11 cluster of mammalian metallothionein, despite different amino acid sequences, a different linear order of the ligands, and presence of histidine ligands. Also, SmtA contains elements of secondary structure not found in metallothioneins. One of the two Cys4-coordinated zinc ions in SmtA readily exchanges with exogenous metal (111Cd), whereas the other is inert. The thiolate sulfur ligands bound to zinc in this site are buried within the protein. Regions of β-strand and α-helix surround the inert site to form a zinc finger resembling the zinc fingers in GATA and LIM-domain proteins. Eukaryotic zinc fingers interact specifically with other proteins or DNA and an analogous interaction can therefore be anticipated for prokaryotic zinc fingers. SmtA now provides structural proof for the existence of zinc fingers in prokaryotes, and sequences related to the zinc finger motif can be identified in several bacterial genomes. PMID:11493688

  1. HEPARIN-BINDING EGF CLEAVAGE MEDIATES ZINC-INDUCED EGF RECEPTOR PHOSPHORYLATION

    EPA Science Inventory

    We have previously shown that exposure to zinc ions can activate epidermal growth factor (EGF) receptor (EGFR) signaling in murine fibroblasts and A431 cells through a mechanism involving Src kinase. While studying the effects of zinc ions in normal human bronchial epithelial cel...

  2. The conserved active-site loop residues of ferrochelatase induce porphyrin conformational changes necessary for catalysis.

    SciTech Connect

    Haddad, Raid Edward; Shelnutt, John Allen; Shi, Zhen; Ferreira, Gloria C.; Franco, Ricardo T.

    2005-05-01

    Binding of porphyrin to murine ferrochelatase, the terminal enzyme of the heme biosynthetic pathway, is investigated by employing a set of variants harboring mutations in a putative porphyrin-binding loop. Using resonance Raman (RR) spectroscopy, the structural properties of the ferrochelatase-bound porphyrins are examined, especially with respect to the porphyrin deformation occurring in the environment of the active site. This deformation is thought to be a key step in the enzymatic insertion of ferrous iron into the porphyrin ring to make heme. Our previous RR spectroscopic studies of binding of porphyrin to murine ferrochelatase led us to propose that the wild-type enzyme induces porphyrin distortion even in the absence of the metal ion substrate. Here, we broaden this view by presenting evidence that the degree of a specific nonplanar porphyrin deformation contributes to the catalytic efficiency of ferrochelatase and its variants. The results also suggest that the conserved Trp256 (murine ferrochelatase numbering) is partially responsible for the observed porphyrin deformation. Binding of porphyrin to the ferrochelatase variants causes a decrease in the intensity of RR out-of-plane vibrational mode {gamma}{sub 15}, a saddling-like mode that is strong in the wild-type enzyme. In particular, the variant with a catalytic efficiency 1 order of magnitude lower than that of the wild-type enzyme is estimated to produce less than 30% of the wild-type saddling deformation. These results suggest that specific conserved loop residues (especially Trp256) are directly involved in the saddling of the porphyrin substrate.

  3. A bicarbonate ion as a general base in the mechanism of peptide hydrolysis by dizinc leucine aminopeptidase

    PubMed Central

    Sträter, Norbert; Sun, Lee; Kantrowitz, E. R.; Lipscomb, William N.

    1999-01-01

    The active sites of aminopeptidase A (PepA) from Escherichia coli and leucine aminopeptidase from bovine lens are isostructural, as shown by x-ray structures at 2.5 Å and 1.6 Å resolution, respectively. In both structures, a bicarbonate anion is bound to an arginine side chain (Arg-356 in PepA and Arg-336 in leucine aminopeptidase) very near two catalytic zinc ions. It is shown that PepA is activated about 10-fold by bicarbonate when l-leucine p-nitroanilide is used as a substrate. No activation by bicarbonate ions is found for mutants R356A, R356K, R356M, and R356E of PepA. In the suggested mechanism, the bicarbonate anion is proposed to facilitate proton transfer from a zinc-bridging water nucleophile to the peptide leaving group. Thus, the function of the bicarbonate ion as a general base is similar to the catalytic role of carboxylate side chains in the presumed mechanisms of other dizinc or monozinc peptidases. A mutational analysis shows that Arg-356 influences activity by binding the bicarbonate ion but is not essential for activity. Mutation of the catalytic Lys-282 reduces kcat/Km about 10,000-fold. PMID:10500145

  4. Influence of zinc on the calcium carbonate biomineralization of Halomonas halophila

    PubMed Central

    2012-01-01

    Background The salt tolerance of halophilic bacteria make them promising candidates for technical applications, like isolation of salt tolerant enzymes or remediation of contaminated saline soils and waters. Furthermore, some halophilic bacteria synthesize inorganic solids resulting in organic–inorganic hybrids. This process is known as biomineralization, which is induced and/or controlled by the organism. The adaption of the soft and eco-friendly reaction conditions of this formation process to technical syntheses of inorganic nano materials is desirable. In addition, environmental contaminations can be entrapped in biomineralization products which facilitate the subsequent removal from waste waters. The moderately halophilic bacteria Halomonas halophila mineralize calcium carbonate in the calcite polymorph. The biomineralization process was investigated in the presence of zinc ions as a toxic model contaminant. In particular, the time course of the mineralization process and the influence of zinc on the mineralized inorganic materials have been focused in this study. Results H. halophila can adapt to zinc contaminated medium, maintaining the ability for biomineralization of calcium carbonate. Adapted cultures show only a low influence of zinc on the growth rate. In the time course of cultivation, zinc ions accumulated on the bacterial surface while the medium depleted in the zinc contamination. Intracellular zinc concentrations were below the detection limit, suggesting that zinc was mainly bound extracellular. Zinc ions influence the biomineralization process. In the presence of zinc, the polymorphs monohydrocalcite and vaterite were mineralized, instead of calcite which is synthesized in zinc-free medium. Conclusions We have demonstrated that the bacterial mineralization process can be influenced by zinc ions resulting in the modification of the synthesized calcium carbonate polymorph. In addition, the shape of the mineralized inorganic material is chancing

  5. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes. PMID:25449264

  6. Active sites in Cu-SSZ-13 deNOx catalyst under reaction conditions: a XAS/XES perspective

    NASA Astrophysics Data System (ADS)

    Lomachenko, Kirill A.; Borfecchia, Elisa; Bordiga, Silvia; Soldatov, Alexander V.; Beato, Pablo; Lamberti, Carlo

    2016-05-01

    Cu-SSZ-13 is a highly active catalyst for the NH3-assisted selective catalytic reduction (SCR) of the harmful nitrogen oxides (NOx, x=1, 2). Since the catalytically active sites for this reaction are mainly represented by isolated Cu ions incorporated into the zeolitic framework, element-selective studies of Cu local environment are crucial to fully understand the enhanced catalytic properties of this material. Herein, we highlight the recent advances in the characterization of the most abundant Cu-sites in Cu-SSZ-13 upon different reaction-relevant conditions made employing XAS and XES spectroscopies, complemented by computational analysis. A concise review of the most relevant literature is also presented.

  7. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase

    PubMed Central

    Seibold, Steve A.; Singh, Badri Nath; Zhang, Chunfen; Kireeva, Maria; Domecq, Céline; Bouchard, Annie; Nazione, Anthony M.; Feig, Michael; Cukier, Robert I.; Coulombe, Benoit; Kashlev, Mikhail; Hampsey, Michael; Burton, Zachary F.

    2010-01-01

    Molecular dynamics simulation of Thermus thermophilus (Tt) RNA polymerase (RNAP) in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. In silico mutant β R428A RNAP, which was designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae (Sc) RNAP II, was used as a reference structure to compare to Tt RNAP in simulations. Long range conformational coupling linking a dynamic segment of the bridge α-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in β R428A RNAP. Furthermore, bridge helix bending is detected in the catalytic structure, indicating that bridge helix dynamics may regulate phosphodiester bond synthesis as well as translocation. An active site “latch” assembly that includes a key trigger helix residue Tt β’ H1242 and highly conserved active site residues β E445 and R557 appears to help regulate active site hydration/dehydration. The potential relevance of these observations in understanding RNAP and DNAP induced fit and fidelity is discussed. PMID:20478425

  8. Zap1p, a metalloregulatory protein involved in zinc-responsive transcriptional regulation in Saccharomyces cerevisiae.

    PubMed

    Zhao, H; Eide, D J

    1997-09-01

    Zinc ion homeostasis in Saccharomyces cerevisiae is controlled primarily through the transcriptional regulation of zinc uptake systems in response to intracellular zinc levels. A high-affinity uptake system is encoded by the ZRT1 gene, and its expression is induced more than 30-fold in zinc-limited cells. A low-affinity transporter is encoded by the ZRT2 gene, and this system is also regulated by zinc. We used a genetic approach to isolate mutants whose ZRT1 expression is no longer repressed in zinc-replete cells, and a new gene, ZAP1, was identified. ZAP1 encodes a 93-kDa protein with sequence similarity to transcriptional activators; the C-terminal 174 amino acids contains five C2H2 zinc finger domains, and the N terminus (residues 1 to 706) has two potential acidic activation domains. The N-terminal region also contains 12% histidine and cysteine residues. The mutant allele isolated, ZAP1-1up, is semidominant and caused high-level expression of ZRT1 and ZRT2 in both zinc-limited and zinc-replete cells. This phenotype is the result of a mutation that substitutes a serine for a cysteine residue in the N-terminal region. A zap1 deletion mutant grew well on zinc-replete media but poorly on zinc-limiting media. This mutant had low-level ZRT1 and ZRT2 expression in zinc-limited as well as zinc-replete cells. These data indicate that Zap1p plays a central role in zinc ion homeostasis by regulating transcription of the zinc uptake system genes in response to zinc. Finally, we present evidence that Zap1p regulates transcription of its own promoter in response to zinc through a positive autoregulatory mechanism. PMID:9271382

  9. The active site of hydroxynitrile lyase from Prunus amygdalus: Modeling studies provide new insights into the mechanism of cyanogenesis

    PubMed Central

    Dreveny, Ingrid; Kratky, Christoph; Gruber, Karl

    2002-01-01

    The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R-mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction—the enantiospecific formation of α-hydroxynitriles—is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C–C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident. PMID:11790839

  10. The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis.

    PubMed

    Dreveny, Ingrid; Kratky, Christoph; Gruber, Karl

    2002-02-01

    The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R-mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction-the enantiospecific formation of alpha-hydroxynitriles--is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C-C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident. PMID:11790839

  11. Potential antidiabetic drug involving a zinc anionic complex of dipic and metformin as counter ions: Synthesis, characterization, crystal structure and electrochemical studies

    NASA Astrophysics Data System (ADS)

    Ghasemi, Khaled; Rezvani, Ali Reza; Rosli, Mohd Mustaqim; Abdul Razak, Ibrahim; Moghimi, Abolghasem; Ghasemi, Fatemeh

    2014-09-01

    The new complex [H2Met][Zn(dipic)2]·3H2O (1) (dipicH2 = 2,6-pyridinedicarboxylic acid) and Met = metformin (N,N-dimethylebiguanidine), was synthesized and characterized by elemental analysis, FTIR, 1H NMR, 13C NMR and UV-Vis spectroscopy and single crystal X-ray method. The crystal system is triclinic with space group Pī. The unit cell dimensions for ZnII complex is a = 9.3817(5), b = 10.0714(5), c = 12.4917(6). In this complex, metformin is diprotonated and acts as counter ion. The intra and intermolecular hydrogen bonds stabilize the crystal structure of compound. The redox behavior of the complex was investigated by cyclic voltammetry.

  12. The galvanization of biology: a growing appreciation for the roles of zinc.

    PubMed

    Berg, J M; Shi, Y

    1996-02-23

    Zinc ions are key structural components of a large number of proteins. The binding of zinc stabilizes the folded conformations of domains so that they may facilitate interactions between the proteins and other macromolecules such as DNA. The modular nature of some of these zinc-containing proteins has allowed the rational design of site-specific DNA binding proteins. The ability of zinc to be bound specifically within a range of tetrahedral sites appears to be responsible for the evolution of the side range of zinc-stabilized structural domains now known to exist. The lack of redox activity for the zinc ion and its binding and exchange kinetics also may be important in the use of zinc for specific functional roles. PMID:8599083

  13. EPR and 1H-NMR spectroscopic studies on the paramagnetic iron at the active site of phenylalanine hydroxylase and its interaction with substrates and inhibitors.

    PubMed

    Martínez, A; Andersson, K K; Haavik, J; Flatmark, T

    1991-06-15

    The paramagnetic iron at the active site of highly purified, catalytically active phenylalanine hydroxylase was studied by EPR at 3.6 K and one-dimensional 1H-NMR spectroscopy at 293 K. The EPR-detectable iron of the bovine enzyme was found to be present as a high-spin form (S = 5/2) in different ligand field symmetries depending on medium conditions (buffer ions) and the presence of ligands known to bind at the active site. At 3.6 K and in phosphate buffer, the paramagnetic iron is coordinated in an environment of rhombic symmetry (g = 4.3), whereas Tris buffer favours an environment of axial ligand field symmetry (g = 6.7, 5.3 and 2.0). The latter axial type of signals resembles those observed at g = 7.0, 5.2 and 1.9 for the enzyme in phosphate buffer when L-noradrenaline is added as an active-site ligand (inhibitor). The same proportion of iron that coordinates to L-noradrenaline seems to be reduced by the pterin cofactor and participate in catalysis. Experimental evidence is presented that Tris inhibits the enzyme by interacting with the enzyme-bound ferric iron and decreases its rate of reduction by the tetrahydropterin cofactor. Preincubation with dithiothreitol also inhibits the enzyme activity and prevents the reduction of its catalytically active ferric iron by pterin cofactors as well as binding of catecholamines to the enzyme. 1H-NMR spectroscopy revealed that the substrate (L-phenylalanine) and L-noradrenaline bind close to the paramagnetic iron, and that the catecholamine displaces the substrate from its binding at the active site. The results support our recently proposed model for the cooperative binding of inhibitor and substrate at the active site [Martínez, A. et al. (1990) Eur. J. Biochem. 193, 211-219]. PMID:1646718

  14. Improved zinc electrode and rechargeable zinc-air battery

    SciTech Connect

    Ross, P.N. Jr.

    1988-06-21

    The invention comprises an improved rechargeable zinc-air cell/battery having recirculating alkaline electrolyte and a zinc electrode comprising a porous foam support material which carries the active zinc electrode material. 5 figs.

  15. The metzincins--topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.

    PubMed Central

    Stöcker, W.; Grams, F.; Baumann, U.; Reinemer, P.; Gomis-Rüth, F. X.; McKay, D. B.; Bode, W.

    1995-01-01

    The three-dimensional structures of the zinc endopeptidases human neutrophil collagenase, adamalysin II from rattle snake venom, alkaline proteinase from Pseudomonas aeruginosa, and astacin from crayfish are topologically similar, with respect to a five-stranded beta-sheet and three alpha-helices arranged in typical sequential order. The four proteins exhibit the characteristic consensus motif HEXXHXXGXXH, whose three histidine residues are involved in binding of the catalytically essential zinc ion. Moreover, they all share a conserved methionine residue beneath the active site metal as part of a superimposable "Met-turn." This structural relationship is supported by a sequence alignment performed on the basis of topological equivalence showing faint but distinct sequential similarity. The alkaline proteinase is about equally distant (26% sequence identity) to both human neutrophil collagenase and astacin and a little further away from adamalysin II (17% identity). The pairs astacin/adamalysin II, astacin/human neutrophil collagenase, and adamalysin II/human neutrophil collagenase exhibit sequence identities of 16%, 14%, and 13%, respectively. Therefore, the corresponding four distinct families of zinc peptidases, the astacins, the matrix metalloproteinases (matrixins, collagenases), the adamalysins/reprolysins (snake venom proteinases/reproductive tract proteins), and the serralysins (large bacterial proteases from Serratia, Erwinia, and Pseudomonas) appear to have originated by divergent evolution from a common ancestor and form a superfamily of proteolytic enzymes for which the designation "metzincins" has been proposed. There is also a faint but significant structural relationship of the metzincins to the thermolysin-like enzymes, which share the truncated zinc-binding motif HEXXH and, moreover, similar topologies in their N-terminal domains. PMID:7663339

  16. Zinc electrode and rechargeable zinc-air battery

    SciTech Connect

    Ross, P.N. Jr.

    1989-06-27

    This patent describes an improved zinc electrode for a rechargeable zinc-air battery comprising an outer frame and a porous foam electrode support within the frame which is treated prior to the deposition of zinc thereon to inhibit the formation of zinc dendrites on the external surface thereof. The outer frame is provided with passageways for circulating an alkaline electrolyte through the treated zinc-coated porous foam. A novel rechargeable zinc-air battery system is also disclosed.

  17. Morphological Control of Metal Oxide-Doped Zinc Oxide and Application to Cosmetics

    NASA Astrophysics Data System (ADS)

    Goto, Takehiro; Yin, Shu; Sato, Tsugio; Tanaka, Takumi

    2012-06-01

    Zinc oxide shows excellent transparency and ultraviolet radiation shielding ability, and is used for various cosmetics.1-3 However, it possesses high catalytic activity and lower dispersibility. Therefore, spherical particles of zinc oxide have been synthesized by soft solution reaction using zinc nitrate, ethylene glycol, sodium hydroxide and triethanolamine as starting materials. After dissolving these compounds in water, the solution was heated at 90°C for 1 h to form almost mono-dispersed spherical zinc oxide particles. The particle size changed depending on zinc ion concentration, ethylene glycol concentration and so on. Furthermore, with doping some metal ions, the phtocatalytic activity could be decreased. The obtained monodispersed metal ion-doped spherical zinc oxides showed excellent UV shielding ability and low photocatalytic activity. Therefore, they are expected to be used as cosmetics ingredients.

  18. Zinc in Entamoeba invadens.

    NASA Technical Reports Server (NTRS)

    Morgan, R. S.; Sattilaro, R. F.

    1972-01-01

    Atomic absorption spectroscopy, electron microprobe analysis, and dithizone staining of trophozoites and cysts of Entamoeba invadens demonstrate that these cells have a high concentration of zinc (approximately one picogram per cell or 1% of their dry weight). In the cysts of this organism, the zinc is confined to the chromatoid bodies, which previous work has shown to contain crystals of ribosomes. The chemical state and function of this zinc are unknown.

  19. A moonlighting function of Mycobacterium smegmatis Ku in zinc homeostasis?

    PubMed

    Kushwaha, Ambuj K; Deochand, Dinesh K; Grove, Anne

    2015-02-01

    Ku protein participates in DNA double-strand break repair via the nonhomologous end-joining pathway. The three-dimensional structure of eukaryotic Ku reveals a central core consisting of a β-barrel domain and pillar and bridge regions that combine to form a ring-like structure that encircles DNA. Homologs of Ku are encoded by a subset of bacterial species, and they are predicted to conserve this core domain. In addition, the bridge region of Ku from some bacteria is predicted from homology modeling and sequence analyses to contain a conventional HxxC and CxxC (where x is any residue) zinc-binding motif. These potential zinc-binding sites have either deteriorated or been entirely lost in Ku from other organisms. Using an in vitro metal binding assay, we show that Mycobacterium smegmatis Ku binds two zinc ions. Zinc binding modestly stabilizes the Ku protein (by ∼3°C) and prevents cysteine oxidation, but it has little effect on DNA binding. In vivo, zinc induces significant upregulation of the gene encoding Ku (∼sixfold) as well as a divergently oriented gene encoding a predicted zinc-dependent MarR family transcription factor. Notably, overexpression of Ku confers zinc tolerance on Escherichia coli. We speculate that zinc-binding sites in Ku proteins from M. smegmatis and other mycobacterial species have been evolutionarily retained to provide protection against zinc toxicity without compromising the function of Ku in DNA double-strand break repair. PMID:25450225

  20. Zinc Modulates Nanosilver-Induced Toxicity in Primary Neuronal Cultures.

    PubMed

    Ziemińska, Elżbieta; Strużyńska, Lidia

    2016-02-01

    Silver nanoparticles (NAg) have recently become one of the most commonly used nanomaterials. Since the ability of nanosilver to enter the brain has been confirmed, there has been a need to investigate mechanisms of its neurotoxicity. We previously showed that primary neuronal cultures treated with nanosilver undergo destabilization of calcium homeostasis via a mechanism involving glutamatergic NMDA receptors. Considering the fact that zinc interacts with these receptors, the aim of the present study was to examine the role of zinc in mechanisms of neuronal cell death in primary cultures. In cells treated with nanosilver, we noted an imbalance between extracellular and intracellular zinc levels. Thus, the influence of zinc deficiency and supplementation on nanosilver-evoked cytotoxicity was investigated by treatment with TPEN (a chelator of zinc ions), or ZnCl(2), respectively. Elimination of zinc leads to complete death of nanosilver-treated CGCs. In contrast, supplementation with ZnCl(2) increases viability of CGCs in a dose-dependent manner. Addition of zinc provided protection against the extra/intracellular calcium imbalance in a manner similar to MK-801, an antagonist of NMDA receptors. Zinc chelation by TPEN decreases the mitochondrial potential and dramatically increases the rate of production of reactive oxygen species. Our results indicate that zinc supplementation positively influences nanosilver-evoked changes in CGCs. This is presumed to be due to an inhibitory effect on NMDA-sensitive calcium channels. PMID:26690781

  1. Zinc: An Essential Micronutrient

    PubMed Central

    SAPER, ROBERT B.; RASH, REBECCA

    2009-01-01

    Zinc is an essential micronutrient for human metabolism that catalyzes more than 100 enzymes, facilitates protein folding, and helps regulate gene expression. Patients with malnutrition, alcoholism, inflammatory bowel disease, and malabsorption syndromes are at an increased risk of zinc deficiency. Symptoms of zinc deficiency are nonspecific, including growth retardation, diarrhea, alopecia, glossitis, nail dystrophy, decreased immunity, and hypogonadism in males. In developing countries, zinc supplementation may be effective for the prevention of upper respiratory infection and diarrhea, and as an adjunct treatment for diarrhea in malnourished children. Zinc in combination with antioxidants may be modestly effective in slowing the progression of intermediate and advanced age-related macular degeneration. Zinc is an effective treatment for Wilson disease. Current data do not support zinc supplementation as effective for upper respiratory infection, wound healing, or human immunodeficiency virus. Zinc is well tolerated at recommended dosages. Adverse effects of long-term high-dose zinc use include suppressed immunity, decreased high-density lipoprotein cholesterol levels, anemia, copper deficiency, and possible genitourinary complications. PMID:20141096

  2. Zinc and Chlamydia trachomatis

    SciTech Connect

    Sugarman, B.; Epps, L.R.

    1985-07-01

    Zinc was noted to have significant effects upon the infection of McCoy cells by each of two strains of Chlamydia trachomatis. With a high or low Chlamydia inoculant, the number of infected cells increased up to 200% utilizing supplemental zinc (up to 1 x 10/sup -4/ M) in the inoculation media compared with standard Chlamydia cultivation media (8 x 10/sup -6/ M zinc). Ferric chloride and calcium chloride did not effect any such changes. Higher concentrations of zinc, after 2 hr of incubation with Chlamydia, significantly decreased the number of inclusions. This direct effect of zinc on the Chlamydia remained constant after further repassage of the Chlamydia without supplemental zinc, suggesting a lethal effect of the zinc. Supplemental zinc (up to 10/sup -4/ M) may prove to be a useful addition to inoculation media to increase the yield of culturing for Chlamydia trachomatis. Similarly, topical or oral zinc preparations used by people may alter their susceptibility to Chamydia trachomatis infections.

  3. Dissolution and corrosion inhibition of copper, zinc, and their alloys

    SciTech Connect

    Jinturkar, P.; Guan, Y.C.; Han, K.N.

    1998-02-01

    The corrosion behavior of copper, zinc, and their alloys in sulfuric acid (H{sub 2}SO{sub 4}) solutions with oxygen and ferric ions (Fe{sup 3+}) was studied using a potentiostat. Oxygen and Fe{sup 3+} ions were shown to play an important role in corrosion of copper and copper-zinc alloys. Cathodic reduction of oxygen mainly was controlled by chemical reaction, and that of Fe{sup 3+} ions was controlled by diffusion. The overall cathodic process was the summation of the reduction of oxygen and Fe{sup 3+} ions. Corrosion of zinc was controlled mainly by reduction of water. Corrosion inhibition using benzotriazole (BTAH) also was investigated in aerated and deaerated solutions. BTAH was found to be a useful inhibitor, and the inhibition layer was shown to be stable and persistent. Morphology of the surface of copper, zinc, and brasses after corrosion in the presence and absence of BTAH was examined by scanning electron microscopy. BTAH formed a protective layer on the surface, thereby inhibiting corrosion. Solution analysis of the dissolution of brasses showed that zinc dissolved preferentially in the initial stages, followed by simultaneous dissolution of copper and zinc.

  4. Simultaneous Automatic Electrochemical Detection of Zinc, Cadmium, Copper and Lead Ions in Environmental Samples Using a Thin-Film Mercury Electrode and an Artificial Neural Network

    PubMed Central

    Kudr, Jiri; Nguyen, Hoai Viet; Gumulec, Jaromir; Nejdl, Lukas; Blazkova, Iva; Ruttkay-Nedecky, Branislav; Hynek, David; Kynicky, Jindrich; Adam, Vojtech; Kizek, Rene

    2015-01-01

    In this study a device for automatic electrochemical analysis was designed. A three electrodes detection system was attached to a positioning device, which enabled us to move the electrode system from one well to another of a microtitre plate. Disposable carbon tip electrodes were used for Cd(II), Cu(II) and Pb(II) ion quantification, while Zn(II) did not give signal in this electrode configuration. In order to detect all mentioned heavy metals simultaneously, thin-film mercury electrodes (TFME) were fabricated by electrodeposition of mercury on the surface of carbon tips. In comparison with bare electrodes the TMFEs had lower detection limits and better sensitivity. In addition to pure aqueous heavy metal solutions, the assay was also performed on mineralized rock samples, artificial blood plasma samples and samples of chicken embryo organs treated with cadmium. An artificial neural network was created to evaluate the concentrations of the mentioned heavy metals correctly in mixture samples and an excellent fit was observed (R2 = 0.9933). PMID:25558996

  5. Redox magnetohydrodynamics enhancement of stripping voltammetry of lead(II), cadmium(II) and zinc(II) ions using 1,4-benzoquinone as an alternative pumping species.

    PubMed

    Ensafi, Ali A; Nazari, Z; Fritsch, I

    2012-01-21

    Differential pulse anodic stripping voltammetry (DPASV) coupled with redox-magnetohydrodynamics (MHD) is used to enhance the anodic stripping voltammetry (ASV) response using a mercury thin film-glassy carbon electrode. The sensitivity increased to at least a factor of two (at 1.2 T) and is facilitated by using 20.0 mmol L(-1) 1,4-benzoquinone as an alternative pumping species to enhance ASV by redox-MHD. The MHD force formed by the cross-product of ion flux with magnetic field induces solution convection during the deposition step, enhancing mass transport of the analytes to the electrode surface and increasing their preconcentrated quantity in the mercury thin film. Therefore, larger ASV peaks and improved sensitivities are obtained, compared with analyses performed without a magnet. The influence of pH, 1,4-benzoquinone concentration, accumulation potential, and time are also investigated. Detection limits of 0.05, 0.09 and 2.2 ng mL(-1) Cd(II), Pb(II) and Zn(II) were established with an accumulation time of 65 s. The method is used for the analysis of Cd(II), Pb(II) and Zn(II) in different water samples, certified reference materials, and saliva samples with satisfactory results. PMID:22116833

  6. Sol-Gel Derived Mg-Based Ceramic Scaffolds Doped with Zinc or Copper Ions: Preliminary Results on Their Synthesis, Characterization, and Biocompatibility.

    PubMed

    Theodorou, Georgios S; Kontonasaki, Eleana; Theocharidou, Anna; Bakopoulou, Athina; Bousnaki, Maria; Hadjichristou, Christina; Papachristou, Eleni; Papadopoulou, Lambrini; Kantiranis, Nikolaos A; Chrissafis, Konstantinos; Paraskevopoulos, Konstantinos M; Koidis, Petros T

    2016-01-01

    Glass-ceramic scaffolds containing Mg have shown recently the potential to enhance the proliferation, differentiation, and biomineralization of stem cells in vitro, property that makes them promising candidates for dental tissue regeneration. An additional property of a scaffold aimed at dental tissue regeneration is to protect the regeneration process against oral bacteria penetration. In this respect, novel bioactive scaffolds containing Mg(2+) and Cu(2+) or Zn(2+), ions known for their antimicrobial properties, were synthesized by the foam replica technique and tested regarding their bioactive response in SBF, mechanical properties, degradation, and porosity. Finally their ability to support the attachment and long-term proliferation of Dental Pulp Stem Cells (DPSCs) was also evaluated. The results showed that conversely to their bioactive response in SBF solution, Zn-doped scaffolds proved to respond adequately regarding their mechanical strength and to be efficient regarding their biological response, in comparison to Cu-doped scaffolds, which makes them promising candidates for targeted dental stem cell odontogenic differentiation and calcified dental tissue engineering. PMID:26981124

  7. Sol-Gel Derived Mg-Based Ceramic Scaffolds Doped with Zinc or Copper Ions: Preliminary Results on Their Synthesis, Characterization, and Biocompatibility

    PubMed Central

    Theodorou, Georgios S.; Kontonasaki, Eleana; Theocharidou, Anna; Bakopoulou, Athina; Bousnaki, Maria; Hadjichristou, Christina; Papachristou, Eleni; Papadopoulou, Lambrini; Kantiranis, Nikolaos A.; Chrissafis, Konstantinos; Paraskevopoulos, Konstantinos M.; Koidis, Petros T.

    2016-01-01

    Glass-ceramic scaffolds containing Mg have shown recently the potential to enhance the proliferation, differentiation, and biomineralization of stem cells in vitro, property that makes them promising candidates for dental tissue regeneration. An additional property of a scaffold aimed at dental tissue regeneration is to protect the regeneration process against oral bacteria penetration. In this respect, novel bioactive scaffolds containing Mg2+ and Cu2+ or Zn2+, ions known for their antimicrobial properties, were synthesized by the foam replica technique and tested regarding their bioactive response in SBF, mechanical properties, degradation, and porosity. Finally their ability to support the attachment and long-term proliferation of Dental Pulp Stem Cells (DPSCs) was also evaluated. The results showed that conversely to their bioactive response in SBF solution, Zn-doped scaffolds proved to respond adequately regarding their mechanical strength and to be efficient regarding their biological response, in comparison to Cu-doped scaffolds, which makes them promising candidates for targeted dental stem cell odontogenic differentiation and calcified dental tissue engineering. PMID:26981124

  8. Runoff rates and ecotoxicity of zinc induced by atmospheric corrosion.

    PubMed

    Karlén, C; Wallinde, I O; Heijerick, D; Leygraf, C; Janssen, C R

    2001-09-28

    Initiated by regulatory restrictions on the use of zinc for various building and construction applications, together with a lack of knowledge related to the release of zinc induced by atmospheric corrosion, a major interdisciplinary research project was implemented to generate data to be used in future risk assessment. Runoff rates from a large number of commercially available zinc-based materials have been determined on panels inclined 45 degrees from the horizon, facing south, during a 1-year atmospheric exposure in an urban environment in Sweden. Possible environmental effects of runoff water immediately after leaving the surface of the various materials have been evaluated during two different sampling periods of varying season and zinc concentration, using the standard growth inhibition test with algae. Raphidocelis subcapitata (formerly Selenastrum capricornutum). Zinc-specific biosensors with the bacterial strain of Alcaligenes eutrophus, and computer modeling using the water-ligand model MINTEQA2 and the humic aquatic model WHAM, have been used to assess the bioavailability and chemical speciation of zinc in the runoff water. An excellent consistency between the different methods was observed. The results show considerably lower runoff rates of zinc (0.07-3.5 g m(-2) year(-1)) than previously being used for regulatory restrictions, and the concentration of zinc to be predominantly responsible for the observed toxicity of the runoff water towards the green algae. The majority of the released zinc quantity was found to be present as free hydrated zinc ions and, hence, bioavailable. The data do not consider changes in bioavailability and chemical speciation or dilution effects during entry into the environment, and should therefore only be used as an initial assessment of the potential environmental effect of zinc runoff from building applications. This interdisciplinary approach has the potential for studies on the environmental fate of zinc in soil or

  9. Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents.

    PubMed

    Hudson, Elton P; Eppler, Ross K; Beaudoin, Julianne M; Dordick, Jonathan S; Reimer, Jeffrey A; Clark, Douglas S

    2009-04-01

    The enzyme subtilisin Carlsberg was surfactant-solubilized into two organic solvents, isooctane and tetrahydrofuran, and hydrated through stepwise changes in the thermodynamic water activity, a(w). The apparent turnover number k(cat)(app) in these systems ranged from 0.2 to 80 s(-1) and increased 11-fold in isooctane and up to 50-fold in tetrahydrofuran with increasing a(w). (19)F NMR relaxation experiments employing an active-site inhibitor were used to assess the dependence of active-site motions on a(w). The rates of NMR-derived fast (k > 10(7) s(-1)) and slow (k < 10(4) s(-1)) active-site motions increased in both solvents upon hydration, but only the slow motions correlated with k(cat). The (19)F chemical shift was a sensitive probe of the local electronic environment and provided an empirical measure of the active-site dielectric constant epsilon(as), which increased with hydration to epsilon(as) approximately 13 in each solvent. In both solvents, the transition state free energy data and epsilon(as) followed Kirkwood's model for the continuum solvation of a dipole, indicating that water also enhanced catalysis by altering the active-site's electronic environment and increasing its polarity to better stabilize the transition state. These results reveal that favorable dynamic and electrostatic effects both contribute to accelerated catalysis by solubilized subtilisin Carlsberg upon hydration in organic solvents. PMID:19317505

  10. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    NASA Astrophysics Data System (ADS)

    Qi, Jian-Xun; Jiang, Fan

    2011-05-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  11. Active Site Inhibitors Protect Protein Kinase C from Dephosphorylation and Stabilize Its Mature Form*

    PubMed Central

    Gould, Christine M.; Antal, Corina E.; Reyes, Gloria; Kunkel, Maya T.; Adams, Ryan A.; Ziyar, Ahdad; Riveros, Tania; Newton, Alexandra C.

    2011-01-01

    Conformational changes acutely control protein kinase C (PKC). We have previously shown that the autoinhibitory pseudosubstrate must be removed from the active site in order for 1) PKC to be phosphorylated by its upstream kinase phosphoinositide-dependent kinase 1 (PDK-1), 2) the mature enzyme to bind and phosphorylate substrates, and 3) the mature enzyme to be dephosphorylated by phosphatases. Here we show an additional level of conformational control; binding of active site inhibitors locks PKC in a conformation in which the priming phosphorylation sites are resistant to dephosphorylation. Using homogeneously pure PKC, we show that the active site inhibitor Gö 6983 prevents the dephosphorylation by pure protein phosphatase 1 (PP1) or the hydrophobic motif phosphatase, pleckstrin homology domain leucine-rich repeat protein phosphatase (PHLPP). Consistent with results using pure proteins, treatment of cells with the competitive inhibitors Gö 6983 or bisindolylmaleimide I, but not the uncompetitive inhibitor bisindolylmaleimide IV, prevents the dephosphorylation and down-regulation of PKC induced by phorbol esters. Pulse-chase analyses reveal that active site inhibitors do not affect the net rate of priming phosphorylations of PKC; rather, they inhibit the dephosphorylation triggered by phorbol esters. These data provide a molecular explanation for the recent studies showing that active site inhibitors stabilize the phosphorylation state of protein kinases B/Akt and C. PMID:21715334

  12. Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site*

    PubMed Central

    Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

    2014-01-01

    Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser105 residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T5015, the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability. PMID:24448805

  13. Chelating ionic liquids for reversible zinc electrochemistry.

    PubMed

    Kar, Mega; Winther-Jensen, Bjorn; Forsyth, Maria; MacFarlane, Douglas R

    2013-05-21

    Advanced, high energy-density, metal-air rechargeable batteries, such as zinc-air, are of intense international interest due to their important role in energy storage applications such as electric and hybrid vehicles, and to their ability to deal with the intermittency of renewable energy sources such as solar and wind. Ionic liquids offer a number of ideal thermal and physical properties as potential electrolytes in such large-scale energy storage applications. We describe here the synthesis and characterisation of a family of novel "chelating" ILs designed to chelate and solubilize the zinc ions to create electrolytes for this type of battery. These are based on quaternary alkoxy alkyl ammonium cations of varying oligo-ether side chains and anions such as p-toluene sulfonate, bis(trifluoromethylsulfonyl)amide and dicyanoamides. This work shows that increasing the ether chain length in the cation from two to four oxygens can increase the ionic conductivity and reduce the melting point from 67 °C to 15 °C for the tosylate system. Changing the anion also plays a significant role in the nature of the zinc deposition electrochemistry. We show that zinc can be reversibly deposited from [N(222(20201))][NTf2] and [N(222(202020201))][NTf2] beginning at -1.4 V and -1.7 V vs. SHE, respectively, but not in the case of tosylate based ILs. This indicates that the [NTf2] is a weaker coordinating anion with the zinc cation, compared to the tosylate anion, allowing the coordination of the ether chain to dominate the behavior of the deposition and stripping of zinc ions. PMID:23558696

  14. Zinc deficiency and eating disorders.

    PubMed

    Humphries, L; Vivian, B; Stuart, M; McClain, C J

    1989-12-01

    Decreased food intake, a cyclic pattern of eating, and weight loss are major manifestations of zinc deficiency. In this study, zinc status was evaluated in 62 patients with bulimia and 24 patients with anorexia nervosa. Forty percent of patients with bulimia and 54% of those with anorexia nervosa had biochemical evidence of zinc deficiency. The authors suggest that for a variety of reasons, such as lower dietary intake of zinc, impaired zinc absorption, vomiting, diarrhea, and binging on low-zinc foods, patients with eating disorders may develop zinc deficiency. This acquired zinc deficiency could then add to the chronicity of altered eating behavior in those patients. PMID:2600063

  15. Influence of cation substitution and activator site exchange on the photoluminescence properties of Eu3+-doped quaternary pyrochlore oxides.

    PubMed

    Mahesh, S K; Rao, P Prabhakar; Thomas, Mariyam; Francis, T Linda; Koshy, Peter

    2013-12-01

    Stannate-based pyrochlore-type red phosphors CaGd(1-x)SnNbO7:xEu(3+), Ca(1-y)Sr(y)Gd(1-x)SnNbO7:xEu(3+), and Ca(0.8-x)Sr0.2GdSnNbO(7+δ): xEu(3+) were prepared via conventional solid-state method. Influence of cation substitution and activator site control on the photoluminescence properties of these phosphors are elucidated using powder X-ray diffraction, Rietveld analysis, Raman spectrum analysis, and photoluminescence excitation and emission spectra. The Eu(3+) luminescence in quaternary pyrochlore lattice exemplifies as a very good structural probe for the detection of short-range disorder in the lattice, which otherwise is not detected by normal powder X-ray diffraction technique. The Eu(3+) emission due to magnetic dipole transition ((5)D0-(7)F1 MD) is modified with the increase in europium concentration in the quaternary pyrochlore red phosphors. (5)D0-(7)F1 MD transition splitting is not observable for low Eu(3+) doping because of the short-range disorder in the pyrochlore lattice. Appearance of narrow peaks in Raman spectra confirms that short-range disorder in the crystal lattice disappears with progressive europium doping. By using Sr as a network modifier ion in place of Ca we were able to increase the f-f transition intensities and europium quenching concentration. The influence of effective positive charge of the central Eu(3+) ions when it replaces a metal ion having lower oxidation state such as Ca(2+) was also investigated. The relative intensities of A1g (∼500 cm(-1)) and F2g (∼330 cm(-1)) Raman vibrational modes get inverted when Eu(3+) ions replaces Ca(2+) ions instead of Gd(3+) as trivalent europium ions can attract the electron cloud of oxygen ions strongly in comparison with divalent calcium ions. The influence of positive charge effect of Eu(3+) in Ca0.7Sr0.2GdSnNbO7+δ:0.1Eu(3+) phosphor is greatly strengthened the charge transfer band and (7)F0-(5)L6 transition intensities than that of the Ca0.8Sr0.2Gd0.9SnNbO7:0.1Eu(3+) phosphor. Our

  16. Preparation of zinc orthotitanate

    NASA Technical Reports Server (NTRS)

    Gates, D. W.; Gilligan, J. E.; Harada, Y.; Logan, W. R.

    1977-01-01

    Use of decomposable precursors to enhance zinc oxide-titanium dioxide reaction and rapid fixing results in rapid preparation of zinc orthotitanate powder pigment. Preparation process allows production under less stringent conditions. Elimination of powder grinding results in purer that is less susceptible to color degradation.

  17. Denaturation studies of active-site labeled papain using electron paramagnetic resonance and fluorescence spectroscopy.

    PubMed Central

    Ping, Z A; Butterfiel, D A

    1991-01-01

    A spin-labeled p-chloromercuribenzoate (SL-PMB) and a fluorescence probe, 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan), both of which bind to the single SH group located in the active site of papain, were used to investigate the interaction of papain (EC 3.4.22.2) with two protein denaturants. It was found that the active site of papain was highly stable in urea solution, but underwent a large conformational change in guanidine hydrochloride solution. Electron paramagnetic resonance and fluorescence results were in agreement and both paralleled enzymatic activity of papain with respect to both the variation in pH and denaturation. These results strongly suggest that SL-PMB and Acrylodan labels can be used to characterize the physical state of the active site of the enzyme. PMID:1657229

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    SciTech Connect

    Carra,J.; McHugh, C.; Mulligan, S.; Machiesky, L.; Soares, A.; Millard, C.

    2007-01-01

    We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding to a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.

  3. 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.

  4. 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

  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. Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

    PubMed Central

    Wang, Lu; Fried, Stephen D.; Boxer, Steven G.; Markland, Thomas E.

    2014-01-01

    Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds. PMID:25503367

  7. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    SciTech Connect

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  8. Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite By Small Molecules

    SciTech Connect

    Tocheva, E.I.; Eltis, L.D.; Murphy, M.E.P.

    2009-05-26

    The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

  9. 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

  10. 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

  11. Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications

    PubMed Central

    2015-01-01

    We report the parametrization of the approximate density functional theory, DFTB3, for magnesium and zinc for chemical and biological applications. The parametrization strategy follows that established in previous work that parametrized several key main group elements (O, N, C, H, P, and S). This 3OB set of parameters can thus be used to study many chemical and biochemical systems. The parameters are benchmarked using both gas-phase and condensed-phase systems. The gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization (MIO). The results indicate that DFTB3/3OB is particularly successful at predicting structures, including rather complex dinuclear metalloenzyme active sites, while being semiquantitative (with a typical mean absolute deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point calculations with high-level quantum mechanics (QM) methods generally lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic properties. DFTB3/MM simulations for solution and two enzyme systems also lead to encouraging structural and energetic properties in comparison to available experimental data. The remaining limitations of DFTB3, such as the treatment of interaction between metal ions and highly charged/polarizable ligands, are also discussed. PMID:25178644

  12. Zinc pyrithione impairs zinc homeostasis and upregulates stress response gene expression in reconstructed human epidermis

    PubMed Central

    Lamore, Sarah D.

    2014-01-01

    Zinc ion homeostasis plays an important role in human cutaneous biology where it is involved in epidermal differentiation and barrier function, inflammatory and antimicrobial regulation, and wound healing. Zinc-based compounds designed for topical delivery therefore represent an important class of cutaneous therapeutics. Zinc pyrithione (ZnPT) is an FDA-approved microbicidal agent used worldwide in over-the-counter topical antimicrobials, and has also been examined as an investigational therapeutic targeting psoriasis and UVB-induced epidermal hyperplasia. Recently, we have demonstrated that cultured primary human skin keratinocytes display an exquisite sensitivity to nanomolar ZnPT concentrations causing induction of heat shock response gene expression and poly(ADP-ribose) polymerase (PARP)-dependent cell death (Cell Stress Chaperones 15:309–322, 2010). Here we demonstrate that ZnPT causes rapid accumulation of intracellular zinc in primary keratinocytes as observed by quantitative fluorescence microscopy and inductively coupled plasma mass spectrometry (ICP-MS), and that PARP activation, energy crisis, and genomic impairment are all antagonized by zinc chelation. In epidermal reconstructs (EpiDerm™) exposed to topical ZnPT (0.1–2% in Vanicream™), ICP-MS demonstrated rapid zinc accumulation, and expression array analysis demonstrated upregulation of stress response genes encoding metallothionein-2A (MT2A), heat shock proteins (HSPA6, HSPA1A, HSPB5, HSPA1L, DNAJA1, HSPH1, HSPD1, HSPE1), antioxidants (SOD2, GSTM3, HMOX1), and the cell cycle inhibitor p21 (CDKN1A). IHC analysis of ZnPT-treated EpiDerm™ confirmed upregulation of Hsp70 and TUNEL-positivity. Taken together our data demonstrate that ZnPT impairs zinc ion homeostasis and upregulates stress response gene expression in primary keratinocytes and reconstructed human epidermis, activities that may underlie therapeutic and toxicological effects of this topical drug. PMID:21424779

  13. 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.

  14. 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

  15. LiZIP3 is a cellular zinc transporter that mediates the tightly regulated import of zinc in Leishmania infantum parasites

    PubMed Central

    Carvalho, Sandra; da Silva, Rosa Barreira; Shawki, Ali; Castro, Helena; Lamy, Márcia; Eide, David; Costa, Vítor; Mackenzie, Bryan; Tomás, Ana M.

    2016-01-01

    Summary Cellular zinc homeostasis ensures that the intracellular concentration of this element is kept within limits that enable its participation in critical physiological processes without exerting toxic effects. We report here the identification and characterization of the first mediator of zinc homeostasis in Leishmania infantum, LiZIP3, a member of the ZIP family of divalent metal-ion transporters. The zinc transporter activity of LiZIP3 was first disclosed by its capacity to rescue the growth of Saccharomyces cerevisiae strains deficient in zinc acquisition. Subsequent expression of LiZIP3 in Xenopus laevis oocytes was shown to stimulate the uptake of a broad range of metal ions, among which Zn2+ was the preferred LiZIP3 substrate (K0.5 ≈ 0.1 μM). Evidence that LiZIP3 functions as a zinc importer in L. infantum came from the observations that the protein locates to the cell membrane and that its overexpression leads to augmented zinc internalization. Importantly, expression and cell-surface location of LiZIP3 are lost when parasites face high zinc bioavailability. LiZIP3 decline in response to zinc is regulated at the mRNA level in a process involving (a) short-lived protein(s). Collectively, our data reveal that LiZIP3 enables L. infantum to acquire zinc in a highly regulated manner, hence contributing to zinc homeostasis. PMID:25644708

  16. Bioavailability of zinc in runoff water from roofing materials.

    PubMed

    Heijerick, D G; Janssen, C R; Karlèn, C; Wallinder, I Odnevall; Leygraf, C

    2002-06-01

    Corrosion and runoff from zinc-coated materials and outdoor structures is an important source for the dispersion of zinc in the environment. Being part of a large inter-disciplinary research project, this study presents the bioavailability of zinc in runoff water immediately after release from the surface of 15 different commercially available zinc-based materials exposed to the urban environment of Stockholm, Sweden. Runoff water was analysed chemically and evaluated for its possible environmental impact, using both a biosensor test with the bacteria Alcaligenes eutrophus (Biomet) and the conventional 72 h growth inhibition test with the green alga Raphidocelis subcapitata. Chemical speciation modelling revealed that most zinc (94.3-99.9%) was present as the free Zn ion, the most bioavailable speciation form. These findings were confirmed by the results of the biosensor test (Biomet) which indicated that all zinc was indeed bioavailable. Analysis of the ecotoxicity data also suggested that the observed toxic effects were due to the presence of Zn2+ ions. Finally, regression analysis showed that, for this type of runoff samples, the rapid screening biosensor was capable of predicting (a) the total amount of zinc present in the runoff samples (R2 of 0.93-0.98; p < 0.05) and (b) the observed 72 h-EbC50s (R2 of 0.69-0.97; p < 0.05). PMID:12137040

  17. An Enlarged, Adaptable Active Site in CYP164 Family P450 Enzymes, the Sole P450 in Mycobacterium leprae

    PubMed Central

    Agnew, Christopher R. J.; Warrilow, Andrew G. S.; Burton, Nicholas M.; Lamb, David C.; Kelly, Steven L.

    2012-01-01

    CYP164 family P450 enzymes are found in only a subset of mycobacteria and include CYP164A1, which is the sole P450 found in Mycobacterium leprae, the causative agent of leprosy. This has previously led to interest in this enzyme as a potential drug target. Here we describe the first crystal structure of a CYP164 enzyme, CYP164A2 from Mycobacterium smegmatis. CYP164A2 has a distinctive, enlarged hydrophobic active site that extends above the porphyrin ring toward the access channels. Unusually, we find that CYP164A2 can simultaneously bind two econazole molecules in different regions of the enlarged active site and is accompanied by the rearrangement and ordering of the BC loop. The primary location is through a classic interaction of the azole group with the porphyrin iron. The second econazole molecule is bound to a unique site and is linked to a tetracoordinated metal ion complexed to one of the heme carboxylates and to the side chains of His 105 and His 364. All of these features are preserved in the closely homologous M. leprae CYP164A1. The computational docking of azole compounds to a homology model of CYP164A1 suggests that these compounds will form effective inhibitors and is supported by the correlation of parallel docking with experimental binding studies of CYP164A2. The binding of econazole to CYP164A2 occurs primarily through the high-spin “open” conformation of the enzyme (Kd [dissociation constant] of 0.1 μM), with binding to the low-spin “closed” form being significantly hindered (Kd of 338 μM). These studies support previous suggestions that azole derivatives may provide an effective strategy to improve the treatment of leprosy. PMID:22037849

  18. Interfacial reactivity studies between epoxy-type or alcohol-type molecules and zinc oxide surfaces by vibrational spectroscopy

    SciTech Connect

    Szumilo, C. |; Dubot, P.; Verchere, D.; Hocquaux, H.; Rei-Vilar, M.; Dumas, P. |

    1996-01-01

    We report the interaction of 1,2-epoxypropane with polycrystalline zinc substrates. This system is evidenced as a model for epoxy-type polymers/zinc-covered substrates assemblies. Gas-solid interaction was followed by infrared spectroscopy in a time-resolved mode. Comparison with methanol adsorption is also reported. The interfacial species produced upon the interaction process, and the corresponding surface active sites are discussed. General trends are emphasized. Finally, adhesion and durability properties promotion are suggested in such prepared epoxy-type polymers/zinc-based substrates assemblies. {copyright} {ital 1996 American Institute of Physics.}

  19. Zinc sulphate attenuates chloride secretion in human colonic mucosae in vitro.

    PubMed

    Medani, Mekki; Bzik, Victoria A; Rogers, Ailin; Collins, Danielle; Kennelly, Rory; Winter, Des C; Brayden, David J; Baird, Alan W

    2012-12-01

    Zinc's usefulness in the treatment of diarrhoea is well established as an addition to oral rehydration. Mechanisms of action of zinc have been explored in intestinal epithelia from rodents and in cell lines. The aim was to examine how zinc alters ion transport and signal transduction in human colon in vitro. Voltage clamped colonic sheets obtained at the time of surgical resection were used to quantify ion transport responses to established secretagogues. Nystatin permeabilisation was used to study basolaterally-sited ion channels. Direct actions of zinc were determined using preparations of colonic crypts isolated from human mucosal sheets. Electrophysiological measurements revealed zinc to be an inhibitor of electrogenic ion transport stimulated by forskolin, PGE(2), histamine and carbachol in isolated human colonic epithelium. Basolateral addition of zinc sulphate had no direct effect on the epithelium. To further outline the mechanism of action, levels of secondary intracellular messengers (3', 5'-cyclic adenosine monophosphate; cAMP) were determined in isolated colonic crypts, and were found to be reduced by zinc sulphate. Finally, indirect evidence from nystatin-permeabilised mucosae further suggested that zinc inhibits basolateral K(+) channels, which are critical for transepithelial Cl(-) secretion linked to water flux. Anti-secretory, and therefore anti-diarrhoeal, actions of exogenous zinc are due, at least in part, to direct basolateral epithelial K(+) channel inhibition. PMID:23022335

  20. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri.

    PubMed

    Dutta, Saheb; Nandi, Nilashis

    2015-08-27

    Aminoacyl tRNA synthetases (aaRSs) carry out the first step of protein biosynthesis. Several aaRSs are multimeric, and coordination between the dynamics of active sites present in each monomer is a prerequisite for the fast and accurate aminoacylation. However, important lacunae of understanding exist concerning the conformational dynamics of multimeric aaRSs. Questions remained unanswered pertaining to the dynamics of the active site. Little is known concerning the conformational dynamics of the active sites in response to the substrate binding, reorganization of the catalytic residues around reactants, time-dependent changes at the reaction center, which are essential for facilitating the nucleophilic attack, and interactions at the interface of neighboring monomers. In the present work, we carried out all-atom molecular dynamics simulation of dimeric (mk)SerRS from Methanopyrus kandleri bound with tRNA using an explicit solvent system. Two dimeric states of seryl tRNA synthetase (open, substrate bound, and adenylate bound) and two monomeric states (open and substrate bound) are simulated with bound tRNA. The aim is to understand the conformational dynamics of (mk)SerRS during its reaction cycle. While the present results provide a clear dynamical perspective of the active sites of (mk)SerRS, they corroborate with the results from the time-averaged experimental data such as crystallographic and mutation analysis of methanogenic SerRS from M. kandleri and M. barkeri. It is observed from the present simulation that the motif 2 loop gates the active site and its Glu351 and Arg360 stabilizes ATP in a bent state favorable for nucleophilic attack. The flexibility of the walls of the active site gradually reduces near reaction center, which is a more organized region compared to the lid region. The motif 2 loop anchors Ser and ATP using Arg349 in a hydrogen bonded geometry crucial for nucleophilic attack and favorably influences the electrostatic potential at the

  1. Radioisotopic studies concerning the efficacy of standard washing procedures for the cleansing of hair before zinc analysis

    SciTech Connect

    Buckley, R.A.; Dreosti, I.E.

    1984-10-01

    Various standard procedures were investigated in relation to the removal of exogenously applied 65Zn from human hair and endogenously incorporated 65Zn from rat hair. Human hair was found to adsorb zinc and a variety of other metal ions from aqueous solutions in a manner which suggested some ion-exchange capacity. Uptake of zinc varied considerably between human hair samples, but in most cases accumulation of zinc occurred rapidly and often resulted in hair zinc levels several-fold higher than found in control samples. Extraction of zinc and other metal ions was greatest after treatment with disodium EDTA and sodium lauryl sulfate than after washing with water or aqueous Triton X-100. However, no procedure effectively removed all exogenous zinc, while all treatments extracted varying proportions of the endogenous zinc component. Because of the inability of standard washing procedures to remove exogenous zinc without reducing endogenous or indicator zinc levels, use of hair zinc analyses to indicate nutritional zinc status are inadvisable if hair zinc contamination is likely to have occurred.

  2. A new class of potent reversible inhibitors of metallo-proteinases: C-terminal thiol-peptides as zinc-coordinating ligands.

    PubMed

    Peters, K; Jahreis, G; Kotters, E M

    2001-10-01

    A number of substrate analogous peptides containing a phosphoramidate, phosphonate ester, hydroxamate, carboxylate or sulfhydryl group are known to be inhibitors of thermolysin and other metalloproteinases. According to the specificity, most of the inhibitors mimic the prime site of the active center. Hitherto, peptidyl derivatives with a thiol group at the C-terminus have not been described. We have synthesized the protected cysteamides Ac-Ala-Ala-CA-SH and Z-Aa1-Aa2-CA-SH (Aa1: Ala, Pro; Aa2: Ala, Leu). The binding of these thiol peptide inhibitors to the metalloproteinases is characterized first by the coordination of the thiolate group of the inhibitor to the catalytic zinc ion and second by the subsite interaction of the peptide ligand in the active site of the enzyme. All peptide derivatives were competitive inhibitors of the zinc metalloproteinase thermolysin. The strongest inhibition was found with Z-Pro-Leu-CA-SH (Ki = 30 microM). Substitution of the N-protecting benzyloxycarbonyl residue towards the acetyl group in the peptide inhibitor, the inhibition constant decreased about 25 times. PMID:11916139

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

    PubMed

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

    2016-04-26

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

  4. The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase.

    PubMed

    Sharma, Vivek; Wikström, Mårten

    2016-08-01

    The active site of cytochrome c oxidase (CcO) comprises an oxygen-binding heme, a nearby copper ion (CuB), and a tyrosine residue that is covalently linked to one of the histidine ligands of CuB. Two proton-conducting pathways are observed in CcO, namely the D- and the K-channels, which are used to transfer protons either to the active site of oxygen reduction (substrate protons) or for pumping. Proton transfer through the D-channel is very fast, and its role in efficient transfer of both substrate and pumped protons is well established. However, it has not been fully clear why a separate K-channel is required, apparently for the supply of substrate protons only. In this work, we have analysed the available experimental and computational data, based on which we provide new perspectives on the role of the K-channel. Our analysis suggests that proton transfer in the K-channel may be gated by the protonation state of the active-site tyrosine (Tyr244) and that the neutral radical form of this residue has a more general role in the CcO mechanism than thought previously. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi. PMID:26898520

  5. Zinc acquisition: a key aspect in Aspergillus fumigatus virulence.

    PubMed

    Amich, Jorge; Calera, José Antonio

    2014-12-01

    Zinc is an essential micronutrient required for the growth of all microorganisms. To grow in the lungs of a susceptible patient Aspergillus fumigatus must obtain zinc from the surrounding tissues. The concentration of Zn(2+) ions in living tissues is much lower than that required for optimal fungal growth in vitro because most of them are tightly bound to proteins at the physiological pH. However, A. fumigatus has several zinc transporters (ZrfA, ZrfB and ZrfC) that enable it to uptake zinc efficiently under the extreme zinc-limiting conditions provided by a susceptible host. The ZafA transcriptional regulator induces the expression of these transporters and is essential for virulence. ZrfC is required for fungal growth within the host tissues, whereas ZrfA and ZrfB play an accessory role. The zinc-scavenging capacity of ZrfC relies on its unusually long N-terminus. In addition, ZrfC also enables A. fumigatus to overcome the inhibitory effect of calprotectin, which is an antimicrobial Zn/Mn-chelating protein synthesized in high amounts by neutrophils, even in immunosuppressed non-leucopenic animals. In summary, the regulation of zinc homeostasis and zinc acquisition could be promising targets for the discovery and development of a new generation of antifungals for the treatment of invasive pulmonary aspergillosis. PMID:24947168

  6. Zinc recovery and waste sludge minimization from chromium passivation baths.

    PubMed

    Diban, Nazely; Mediavilla, Rosa; Urtiaga, Ane; Ortiz, Inmaculada

    2011-08-30

    This work reports the feasibility of applying emulsion pertraction technology (EPT) aiming at zinc recovery and waste minimization in the zinc electroplating processes that include Cr (III) passivation. The assessment consists of firstly the lifetime extension of the passivation baths by selective removal of the tramp ions zinc and iron, and secondly, the recovery of zinc for further reuse. Spent passivation baths from a local industry were tested, being the major metallic content: Cr(3+) 9000mg L(-1), Zn(2+) 12,000mg L(-1), Fe(3+) 100mg L(-1). Working in a Liqui-Cel hollow fiber membrane contactor and using the extractant bis(2,4,4-trimethylpentyl) phosphinic acid, reduction of zinc and iron concentrations below 60mg L(-1) and 2mg L(-1), respectively were obtained, while trivalent chromium, the active metal that generates the passivation layer, was retained in the baths. Zinc was selectively transferred to an acidic stripping phase that in the experimental time reached a concentration of 157,000mg L(-1). Zinc recovery by electrowinning from the acidic stripping phase without any pretreatment of the electrolyte solution provided a purity of 98.5%, matching the lower commercial zinc grade. As a result of the extension of the life time of the passivation bath, significant environmental advantages are derived such as minimization of the volume of hazardous wastes and savings in the consumption of raw materials. PMID:21704452

  7. Interstitial zinc clusters in zinc oxide

    NASA Astrophysics Data System (ADS)

    Gluba, M. A.; Nickel, N. H.; Karpensky, N.

    2013-12-01

    Doped zinc oxide (ZnO) exhibits anomalous Raman modes in the range of 270 to 870 cm-1. Commonly, the resonance at 275 cm-1 is attributed to the local vibration of Zn atoms in the vicinity of extrinsic dopants. We revisit this assignment by investigating the influence of isotopically purified zinc oxide thin films on the frequency of the vibrational mode around 275 cm-1. For this purpose, undoped and nitrogen-doped ZnO thin-films with Zn isotope compositions of natural Zn, 64Zn, 68Zn, and a 1:1 mixture of 64Zn and 68Zn were grown by pulsed laser deposition. The isotopic shift and the line shape of the Raman resonance around 275 cm-1 are analyzed in terms of three different microscopic models, which involve the vibration of (i) interstitial zinc atoms bound to extrinsic defects, (ii) interstitial diatomic Zn molecules, and (iii) interstitial zinc clusters. The energy diagram of interstitial Zn-Zn bonds in a ZnO matrix is derived from density functional theory calculations. The interstitial Zn-Zn bond is stabilized by transferring electrons from the antibonding orbital into the ZnO conduction band. This mechanism facilitates the formation of interstitial Zn clusters and fosters the common n-type doping asymmetry of ZnO.

  8. Designing Hydrolytic Zinc Metalloenzymes

    PubMed Central

    2015-01-01

    Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up. PMID:24506795

  9. Identification of active sites in gold-catalyzed hydrogenation of acrolein.

    PubMed

    Mohr, Christian; Hofmeister, Herbert; Radnik, Jörg; Claus, Peter

    2003-02-19

    The active sites of supported gold catalysts, favoring the adsorption of C=O groups of acrolein and subsequent reaction to allyl alcohol, have been identified as edges of gold nanoparticles. After our recent finding that this reaction preferentially occurs on single crystalline particles rather than multiply twinned ones, this paper reports on a new approach to distinguish different features of the gold particle morphology. Elucidation of the active site issue cannot be simply done by varying the size of gold particles, since the effects of faceting and multiply twinned particles may interfere. Therefore, modification of the gold particle surface by indium has been used to vary the active site characteristics of a suitable catalyst, and a selective decoration of gold particle faces has been observed, leaving edges free. This is in contradiction to theoretical predictions, suggesting a preferred occupation of the low-coordinated edges of the gold particles. On the bimetallic catalyst, the desired allyl alcohol is the main product (selectivity 63%; temperature 593 K, total pressure p(total) = 2 MPa). From the experimentally proven correlation between surface structure and catalytic behavior, the edges of single crystalline gold particles have been identified as active sites for the preferred C=O hydrogenation. PMID:12580618

  10. Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents

    PubMed Central

    Hudson, Elton P; Eppler, Ross K; Beaudoin, Julianne M; Dordick, Jonathan S; Reimer, Jeffrey A; Clark, Douglas S

    2009-01-01

    The enzyme subtilisin Carlsberg was surfactant-solubilized into two organic solvents, isooctane and tetrahydrofuran, and hydrated through stepwise changes in the thermodynamic water activity, aw. The apparent turnover number kcatapp in these systems ranged from 0.2 to 80 s−1 and increased 11-fold in isooctane and up to 50-fold in tetrahydrofuran with increasing aw. 19F-NMR relaxation experiments employing an active-site inhibitor were used to assess the dependence of active-site motions on aw. The rates of NMR-derived fast (k > 107 s−1) and slow (k < 104 s−1) active-site motions increased in both solvents upon hydration, but only the slow motions correlated with kcat. The 19F chemical shift was a sensitive probe of the local electronic environment and provided an empirical measure of the active-site dielectric constant εas, which increased with hydration to εas ≈ 13 in each solvent. In both solvents the transition state free energy data and εas followed Kirkwood’s model for the continuum solvation of a dipole, indicating that water also enhanced catalysis by altering the active-site’s electronic environment and increasing its polarity to better stabilize the transition state. These results reveal that favorable dynamic and electrostatic effects both contribute to accelerated catalysis by solubilized subtilisin Carlsberg upon hydration in organic solvents. PMID:19317505

  11. A caspase active site probe reveals high fractional inhibition needed to block DNA fragmentation.

    PubMed

    Méthot, Nathalie; Vaillancourt, John P; Huang, JingQi; Colucci, John; Han, Yongxin; Ménard, Stéphane; Zamboni, Robert; Toulmond, Sylvie; Nicholson, Donald W; Roy, Sophie

    2004-07-01

    Apoptotic markers consist of either caspase substrate cleavage products or phenotypic changes that manifest themselves as a consequence of caspase-mediated substrate cleavage. We have shown recently that pharmacological inhibitors of caspase activity prevent the appearance of two such apoptotic manifestations, alphaII-spectrin cleavage and DNA fragmentation, but that blockade of the latter required a significantly higher concentration of inhibitor. We investigated this phenomenon through the use of a novel radiolabeled caspase inhibitor, [(125)I]M808, which acts as a caspase active site probe. [(125)I]M808 bound to active caspases irreversibly and with high sensitivity in apoptotic cell extracts, in tissue extracts from several commonly used animal models of cellular injury, and in living cells. Moreover, [(125)I]M808 detected active caspases in septic mice when injected intravenously. Using this caspase probe, an active site occupancy assay was developed and used to measure the fractional inhibition required to block apoptosis-induced DNA fragmentation. In thymocytes, occupancy of up to 40% of caspase active sites had no effect on DNA fragmentation, whereas inhibition of half of the DNA cleaving activity required between 65 and 75% of active site occupancy. These results suggest that a high and persistent fractional inhibition will be required for successful caspase inhibition-based therapies. PMID:15067000

  12. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

    PubMed

    Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

    2012-05-01

    Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds. PMID:21877154

  13. Cyclic silicate active site and stereochemical match for apatite nucleation on pseudowollastonite bioceramic-bone interfaces.

    PubMed

    Sahai, Nita; Anseau, Michel

    2005-10-01

    Hydroxyapatite (Ca5(PO4)3(OH)) forms on pseudowollastonite (psW) (alpha-CaSiO3) in vitro in simulated body fluid, human parotid saliva and cell-culture medium, and in vivo in implanted rat tibias. We used crystallographic constraints with ab initio molecular orbital calculations to identify the active site and reaction mechanism for heterogeneous nucleation of the earliest calcium phosphate oligomer/phase. The active site is the planar, cyclic, silicate trimer (Si3O9) on the (001) face of psW. The trimer has three silanol groups (>SiOH) arranged at 60 degrees from each other, providing a stereochemical match for O atoms bonded to Ca2+ on the (001) face of hydroxyapatite. Calcium phosphate nucleation is modeled in steps as hydrolysis of surface Ca-O bonds with leaching of Ca2+ into solution, protonation of the surface Si-O groups to form silanols, calcium sorption as an inner-sphere surface complex and, attachment of HPO4(2-). Our model explains the experimental solution and high resolution transmission electron microscopy data for epitaxial hydroxyapatite growth on psW in vitro and in vivo. We propose that the cyclic silicate trimer is the universal active site for heterogeneous, stereochemically promoted nucleation on silicate-based bioactive ceramics. A critical active site-density and a point of zero charge of the bioceramic less than physiological pH are required for bioactivity. PMID:15949543

  14. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    SciTech Connect

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  15. 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

  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. Acylpeptide hydrolase: inhibitors and some active site residues of the human enzyme.

    PubMed

    Scaloni, A; Jones, W M; Barra, D; Pospischil, M; Sassa, S; Popowicz, A; Manning, L R; Schneewind, O; Manning, J M

    1992-02-25

    Acylpeptide hydrolase may be involved in N-terminal deacetylation of nascent polypeptide chains and of bioactive peptides. The activity of this enzyme from human erythrocytes is sensitive to anions such as chloride, nitrate, and fluoride. Furthermore, blocked amino acids act as competitive inhibitors of the enzyme. Acetyl leucine chloromethyl ketone has been employed to identify one active site residue as His-707. Diisopropylfluorophosphate has been used to identify a second active site residue as Ser-587. Chemical modification studies with a water-soluble carbodiimide implicate a carboxyl group in catalytic activity. These results and the sequence around these active site residues, especially near Ser-587, suggest that acylpeptide hydrolase contains a catalytic triad. The presence of a cysteine residue in the vicinity of the active site is suggested by the inactivation of the enzyme by sulfhydryl-modifying agents and also by a low amount of modification by the peptide chloromethyl ketone inhibitor. Ebelactone A, an inhibitor of the formyl aminopeptidase, the bacterial counterpart of eukaryotic acylpeptide hydrolase, was found to be an effective inhibitor of this enzyme. These findings suggest that acylpeptidase hydrolase is a member of a family of enzymes with extremely diverse functions. PMID:1740429

  18. A novel hydrothermal method for zinc extraction and separation from zinc ferrite and electric arc furnace dust

    NASA Astrophysics Data System (ADS)

    Wang, Hui-gang; Li, Yang; Gao, Jian-ming; Zhang, Mei; Guo, Min

    2016-02-01

    A novel hydrothermal process was developed to extract zinc from pure zinc ferrite (ZnFe2O4) nanopowder and zinc-containing electric arc furnace (EAF) dust using hexahydrated ferric chloride (FeCl3·6H2O) as a decomposing agent. The effects of solid FeCl3·6H2O to ZnFe2O4 ratio by mass ( R F/Z), hydrothermal reaction temperature, and time on zinc extraction were systematically investigated. In the results, when the hydrothermal reaction is conducted at 150°C for 2 h with R F/Z of 15:20, the efficiency of zinc extraction from ZnFe2O4 reaches 97.2%, and the concentration of ferric ions (Fe3+) in the leaching solution is nearly zero, indicating a high selectivity for zinc. In addition, the zinc extraction efficiency from the EAF dust reaches 94.5% in the case of the hydrothermal reaction performed at 200°C for 10 h with the solid FeCl3·6H2O to EAF dust ratio by mass ( R F/EAF dust) of 15:10. Zinc and iron separation is achieved by adjusting the pH value of the leaching solution according to the different precipitation pH values of metal hydroxides.

  19. Application of Polymeric Nanoparticles for CNS Targeted Zinc Delivery In Vivo.

    PubMed

    Chhabra, Resham; Ruozi, Barbara; Vilella, Antonietta; Belletti, Daniela; Mangus, Katharina; Pfaender, Stefanie; Sarowar, Tasnuva; Boeckers, Tobias Maria; Zoli, Michele; Forni, Flavio; Vandelli, Maria Angela; Tosi, Giovanni; Grabrucker, Andreas Martin

    2015-01-01

    A dyshomeostasis of zinc ions has been reported for many psychiatric and neurodegenerative disorders including schizophrenia, attention deficit hyperactivity disorder, depression, autism, Parkinson's and Alzheimer's disease. Furthermore, alterations in zinc-levels have been associated with seizures and traumatic brain injury. Thus, altering zinclevels within the brain is emerging as a new target for the prevention and treatment of psychiatric and neurological diseases. However, given the restriction of zinc uptake into the brain by the blood-brain barrier, methods for controlled regulation and manipulation of zinc concentrations within the brain are rare. Here, we performed in vivo studies investigating the possibility of brain targeted zinc delivery using zinc-loaded nanoparticles which are able to cross the blood-brain barrier. After injecting these nanoparticles, we analyzed the regional and time-dependent distribution of zinc and nanoparticles within the brain. Moreover, we evaluated whether the presence of zinc-loaded nanoparticles alters the expression of zinc sensitive genes and proteins such as metallothioneins and zinc transporters and quantified possible toxic effects. Our results show that zinc loaded g7 nanoparticles offer a promising approach as a novel non - invasive method to selectively enrich zinc in the brain within a small amount of time. PMID:26295815

  20. Kinetics of cobalt cementation on zinc powder

    SciTech Connect

    Polcaro, A.M.; Palmas, S.; Dernini, S.

    1995-09-01

    The cementation process may be considered an interesting method to treat dilute solutions containing metal ions. The aim of the process may be either the removal of pollutant metals or the recovery of economically valuable metals such as Ag from spent photographic liquors. The kinetics of cobalt cementation on Zn powder from zinc sulfate concentrated solutions in the presence of copper and antimony ions was investigated in stirred tank reactors. The composition of the solutions was in the range usually utilized in industrial zinc electrowinning plants. The results showed that the reaction occurs by means of the formation of crystallization nuclei of noble metals on the zinc powder, followed by the cementation of cobalt ions on these newly-formed nuclei. Mass transfer to the reaction surface is shown to be the controlling step in copper and antimony reduction, and an equation correlating mass transfer coefficients has been determined. A kinetic equation, which interprets the influence of stirring speed and solution composition on cobalt cementation, has also been proposed.

  1. 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.

  2. Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site.

    PubMed

    Whittington, D A; Lippard, S J

    2001-02-01

    The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme. PMID:11456616

  3. Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

    PubMed Central

    Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

    2015-01-01

    The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

  4. A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

    PubMed

    Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

    2007-10-01

    Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase. PMID:17850513

  5. A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase

    SciTech Connect

    Somarowthu, Srinivas; Brodkin, Heather R.; D’Aquino, J. Alejandro; Ringe, Dagmar; Ondrechen, Mary Jo; Beuning, Penny J.

    2012-07-11

    Understanding the catalytic efficiency and specificity of enzymes is a fundamental question of major practical and conceptual importance in biochemistry. Although progress in biochemical and structural studies has enriched our knowledge of enzymes, the role in enzyme catalysis of residues that are not nearest neighbors of the reacting substrate molecule is largely unexplored experimentally. Here computational active site predictors, THEMATICS and POOL, were employed to identify functionally important residues that are not in direct contact with the reacting substrate molecule. These predictions then guided experiments to explore the active sites of two isomerases, Pseudomonas putida ketosteroid isomerase (KSI) and human phosphoglucose isomerase (PGI), as prototypes for very different types of predicted active sites. Both KSI and PGI are members of EC 5.3 and catalyze similar reactions, but they represent significantly different degrees of remote residue participation, as predicted by THEMATICS and POOL. For KSI, a compact active site of mostly first-shell residues is predicted, but for PGI, an extended active site in which residues in the first, second, and third layers around the reacting substrate are predicted. Predicted residues that have not been previously tested experimentally were investigated by site-directed mutagenesis and kinetic analysis. In human PGI, single-point mutations of the predicted second- and third-shell residues K362, H100, E495, D511, H396, and Q388 show significant decreases in catalytic activity relative to that of the wild type. The results of these experiments demonstrate that, as predicted, remote residues are very important in PGI catalysis but make only small contributions to catalysis in KSI.

  6. Sealed nickel-zinc battery

    SciTech Connect

    Gibbard, H. F.; Menard, C. J.; Murray Jr., R. C.; Putt, R. A.; Valentine, T. W.

    1985-11-12

    A sealed, rechargeable nickel-zinc cell includes a zinc electrode active mass essentially free of zinc metal when at full discharge, a carboxylated styrene-butadiene binder retaining the zinc electrode mixture in a coherent structure, a predetermined amount of cadmium being included in the zinc electrode mixture, a separator preferably comprising at least two layers of material free of any adhesive binding the layers together and a wicking layer positioned between the nickel positive electrode and the separator.

  7. Zinc asparaginate supplementation induces redistribution of toxic trace elements in rat tissues and organs.

    PubMed

    Skalny, Andrey A; Tinkov, Alexey A; Medvedeva, Yulia S; Alchinova, Irina B; Karganov, Mikhail Yu; Ajsuvakova, Olga P; Skalny, Anatoly V; Nikonorov, Alexandr A

    2015-09-01

    The primary objective of the current study was the investigation of the influence of zinc asparaginate supplementation for 7 and 14 days on toxic metal and metalloid content in rat organs and tissues. Rats obtained zinc asparaginate in doses of 5 and 15 mg/kg/day for 7 and 14 days. At the end of the experiment rat tissues and organs (liver, kidney, heart, m. gastrocnemius, serum, and hair) were collected for subsequent analysis. Estimation of Zn, Al, As, Li, Ni, Sn, Sr content in the harvested organs was performed using inductively coupled plasma mass spectrometry at NexION 300D. The obtained data showed that intragastric administration of zinc significantly increased liver, kidney and serum zinc concentrations. Seven-day zinc treatment significantly affected the toxic trace element content in the animals' organs. Zinc supplementation significantly decreased particularly liver aluminium, nickel, and tin content, whereas lead tended to increase. Zinc-induced changes in kidney metal content were characterized by elevated lithium and decreased nickel concentration. Zinc-induced alteration of myocardical toxic element content was multidirectional. Muscle aluminium and lead concentration were reduced in response to zinc supplementation. At the same time, serum and hair toxic element concentrations remained relatively stable after 7-day zinc treatment. Zinc asparaginate treatment of 14 days significantly depressed liver and elevated kidney lithium content, whereas a significant zinc-associated decrease was detected in kidney strontium content. Zinc supplementation for 14 days resulted also in multidirectional changes in the content of heart toxic elements. At the same time, significant zinc-associated decrease in muscle lithium and nickel levels was observed. Fourteen-day zinc treatment resulted in significantly increased serum arsenic and tin concentrations, whereas hair trace element content remained relatively stable. Generally, the obtained data indicate a

  8. Zinc asparaginate supplementation induces redistribution of toxic trace elements in rat tissues and organs

    PubMed Central

    Skalny, Andrey A.; Medvedeva, Yulia S.; Alchinova, Irina B.; Karganov, Mikhail Yu.; Ajsuvakova, Olga P.; Skalny, Anatoly V.; Nikonorov, Alexandr A.

    2015-01-01

    The primary objective of the current study was the investigation of the influence of zinc asparaginate supplementation for 7 and 14 days on toxic metal and metalloid content in rat organs and tissues. Rats obtained zinc asparaginate in doses of 5 and 15 mg/kg/day for 7 and 14 days. At the end of the experiment rat tissues and organs (liver, kidney, heart, m. gastrocnemius, serum, and hair) were collected for subsequent analysis. Estimation of Zn, Al, As, Li, Ni, Sn, Sr content in the harvested organs was performed using inductively coupled plasma mass spectrometry at NexION 300D. The obtained data showed that intragastric administration of zinc significantly increased liver, kidney and serum zinc concentrations. Seven-day zinc treatment significantly affected the toxic trace element content in the animals’ organs. Zinc supplementation significantly decreased particularly liver aluminium, nickel, and tin content, whereas lead tended to increase. Zinc-induced changes in kidney metal content were characterized by elevated lithium and decreased nickel concentration. Zinc-induced alteration of myocardical toxic element content was multidirectional. Muscle aluminium and lead concentration were reduced in response to zinc supplementation. At the same time, serum and hair toxic element concentrations remained relatively stable after 7-day zinc treatment. Zinc asparaginate treatment of 14 days significantly depressed liver and elevated kidney lithium content, whereas a significant zinc-associated decrease was detected in kidney strontium content. Zinc supplementation for 14 days resulted also in multidirectional changes in the content of heart toxic elements. At the same time, significant zinc-associated decrease in muscle lithium and nickel levels was observed. Fourteen-day zinc treatment resulted in significantly increased serum arsenic and tin concentrations, whereas hair trace element content remained relatively stable. Generally, the obtained data indicate a

  9. Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.

    PubMed

    Yang, G; Sandalova, T; Lohman, K; Lindqvist, Y; Rendina, A R

    1997-04-22

    41A, S41C, K37Q, and K37L, showed that the crystals were essentially isomorphous to that of the wild-type DTBS. The models of these mutant enzymes were well refined (1.9 -2.6 A) and showed good similarity to the wild-type enzyme (rmsd of C alpha atoms: 0.16-0.24 A). The crystal structure of S41C complexed with DAPA, Mn2+/Mg2+, and AMPPCP revealed a localized conformational change (rotations of side chains of Cys41 and Thr11) which can account for the changes in the kinetic parameters observed for S41C. The crystal structures of the Lys37 mutant enzymes showed that the positive charge of the side chain of Lys37 is indispensable. Mutations of Lys37 to either glutamine or leucine resulted in a shift of the metal ion (up to 0.5 A) together with side chains of other active site residues which could disrupt the subtle balance between the positive and negative charges in the active site. The conformational change of the phosphate binding loop (Gly8-X-X-X-X-X-Gly14-Lys15-Thr16) upon nucleotide binding observed previously [Huang, W., Jia, J., Gibson, K. J., Taylor, W. S., Rendina, A. R., Schneider, G., & Lindqvist, Y. (1995) Biochemistry 34, 10985] appears to be important to attain the proper active site scaffold. PMID:9125495

  10. Oral zinc therapy for zinc deficiency-related telogen effluvium.

    PubMed

    Karashima, Tadashi; Tsuruta, Daisuke; Hamada, Takahiro; Ono, Fumitake; Ishii, Norito; Abe, Toshifumi; Ohyama, Bungo; Nakama, Takekuni; Dainichi, Teruki; Hashimoto, Takashi

    2012-01-01

    Zinc is crucial for maintaining human body homeostasis and is one of the major components of hormones, signal molecules, and enzymes. Zinc deficiency is caused by insufficient uptake of zinc from food, or caused by malabsorption syndromes, increased gastrointestinal and urinary losses, and administration of various medications. In order to test whether oral zinc administration can successfully improve zinc deficiency-related alopecia, we treated five patients with zinc deficiency-related telogen effluvium with oral zinc administration in the form of polaprezinc (Promac®). In all patients, hair loss was cured or improved. The administration of zinc for zinc deficiency-related alopecia may recover appropriate activities of metalloenzymes, hedgehog signaling, and immunomodulation, all of which are required for normal control of hair growth cycle. PMID:22741940

  11. Zinc electrode and rechargeable zinc-air battery

    DOEpatents

    Ross, Jr., Philip N.

    1989-01-01

    An improved zinc electrode is disclosed for a rechargeable zinc-air battery comprising an outer frame and a porous foam electrode support within the frame which is treated prior to the deposition of zinc thereon to inhibit the formation of zinc dendrites on the external surface thereof. The outer frame is provided with passageways for circulating an alkaline electrolyte through the treated zinc-coated porous foam. A novel rechargeable zinc-air battery system is also disclosed which utilizes the improved zinc electrode and further includes an alkaline electrolyte within said battery circulating through the passageways in the zinc electrode and an external electrolyte circulation means which has an electrolyte reservoir external to the battery case including filter means to filter solids out of the electrolyte as it circulates to the external reservoir and pump means for recirculating electrolyte from the external reservoir to the zinc electrode.

  12. Zinc wired rebar

    SciTech Connect

    Zhang, X.G.; Hwang, J.

    1997-02-01

    A novel method for corrosion protection of rebar in concrete is reported wherein it is galvanically protected by attaching a zinc wire along its length. The self-corrosion and galvanic-corrosion loss of the zinc wire is dependent on the water/cement ratio, the size of the cathode, and the concrete cover thickness. The wire acts as a sacrificial anode when the rebar embedded in concrete is exposed to corrosive environments.

  13. Rechargeable battery which combats shape change of the zinc anode

    NASA Technical Reports Server (NTRS)

    Cohn, E. M. (Inventor)

    1976-01-01

    A rechargeable cell or battery is provided in which shape change of the zinc anode is combatted by profiling the ionic conductivity of the paths between the electrodes. The ion flow is greatest at the edges of the electrodes and least at the centers, thereby reducing migration of the zinc ions from edges to the center of the anode. A number of embodiments are disclosed in which the strength and/or amount of electrolyte, and/or the number and/or size of the paths provided by the separator between the electrodes, are varied to provide the desired ionic conductivity profile.

  14. Crystallographic Analysis of Active Site Contributions to Regiospecificity in the Diiron Enzyme Toluene 4-Monooxygenase

    SciTech Connect

    Bailey, Lucas J.; Acheson, Justin F.; McCoy, Jason G.; Elsen, Nathaniel L.; Phillips, Jr., George N.; Fox, Brian G.

    2014-10-02

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric {mu}-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH{sub 2}-benzoate and p-Br-benzoate showed a {mu}-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a {pi}-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 {angstrom}) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential

  15. Electrochemical Aging of Thermal-Sprayed Zinc Anodes on Concrete

    SciTech Connect

    Holcomb, G.R.; Bullard, S.J.; Covino, B.S. Jr.; Cramer, S.D.; Cryer, C.B.; McGill, G.E.

    1996-10-01

    Thermal-sprayed zinc anodes are used in impressed current cathodic protection systems for some of Oregon's coastal reinforced concrete bridges. Electrochemical aging of zinc anodes results in physical and chemical changes at the zinc-concrete interface. Concrete surfaces heated prior to thermal-spraying had initial adhesion strengths 80 pct higher than unheated surfaces. For electrochemical aging greater than 200 kC/m{sup 2} (5.2 A h/ft{sup 2}), there was no difference in adhesion strengths for zinc on preheated and unheated concrete. Adhesion strengths decreased monotonically after about 400 to 600 kC/m{sup 2} (10.4 to 15.6 A-h/ft{sup 2}) as a result of the reaction zones at the zinc-concrete interface. A zone adjacent to the metallic zinc (and originally part of the zinc coating) was primarily zincite (ZnO), with minor constituents of wulfingite (Zn(OH){sub 2}), simonkolleite (Zn{sub 5}(OH) {sub 8}C{sub l2}{sup .}H{sub 2}O), and hydrated zinc hydroxide sulfates (Zn{sub 4}SO{sub 4}(OH){sub 6}{sup .}xH{sub 2}O). This zone is the locus for cohesive fracture when the zinc coating separates from the concrete during adhesion tests. Zinc ions substitute for calcium in the cement paste adjacent to the coating as the result of secondary mineralization. The initial estimate of the coating service life based on adhesion strength measurements in accelerated impressed current cathodic protection tests is about 27 years.

  16. Zinc deficiency in elderly patients.

    PubMed

    Prasad, A S; Fitzgerald, J T; Hess, J W; Kaplan, J; Pelen, F; Dardenne, M

    1993-01-01

    Zinc is needed for growth and development, DNA synthesis, neurosensory functions, and cell-mediated immunity. Although zinc intake is reduced in elderly people, its deficiency and effects on cell-mediated immunity of the elderly have not been established. Subjects enrolled in "A Model Health Promotion and Intervention Program for Urban Middle Aged and Elderly Americans" were assessed for nutrition and zinc status. One hundred eighty healthy subjects were randomly selected for the study. Their mean dietary zinc intake was 9.06 mg/day, whereas the recommended dietary allowance is 15 mg/day. Plasma zinc was normal, but zinc in granulocytes and lymphocytes were decreased compared with younger control subjects. Of 118 elderly subjects in whom zinc levels in both granulocytes and lymphocytes were available, 36 had deficient levels. Plasma copper was increased, and interleukin 1 (IL-1) production was significantly decreased. Reduced response to the skin-test antigen panel and decreased taste acuity were observed. Thirteen elderly zinc-deficient subjects were supplemented with zinc, and various variables were assessed before and after zinc supplementation. Zinc supplementation corrected zinc deficiency and normalized plasma copper levels. Serum thymulin activity, IL-1 production, and lymphocyte ecto-5'-nucleotidase increased significantly after supplementation. Improvement in response to skin-test antigens and taste acuity was observed after zinc supplementation. A mild zinc deficiency appears to be a significant clinical problem in free-living elderly people. PMID:8353362

  17. The cellular and subcellular localization of zinc transporter 7 in the mouse spinal cord

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The present work addresses the cellular and subcellular localization of the zinc transporter 7 (ZNT7, SLC30a7) protein and the distribution of zinc ions (Zn2+) in the mouse spinal cord. Our results indicated that the ZNT7 immunoreactive neurons were widely distributed in the Rexed’s laminae of the g...

  18. Influence Of pH On The Transport Of Nanoscale Zinc Oxide In Saturated Porous Media

    EPA Science Inventory

    Widespread use of nanoscale zinc oxide (nZnO) in various fields causes subsurface environment contamination. Even though the transport of dissolved zinc ions in subsurface environments such as soils and sediments has been widely studied, the transport mechanism of nZnO in such e...

  19. Determination of hydroxide and carbonate contents of alkaline electrolytes containing zinc

    NASA Technical Reports Server (NTRS)

    Otterson, D. A.

    1975-01-01

    A method to prevent zinc interference with the titration of OH- and CO3-2 ions in alkaline electrolytes with standard acid is presented. The Ba-EDTA complex was tested and shown to prevent zinc interference with acid-base titrations without introducing other types of interference. Theoretical considerations indicate that this method can be used to prevent interference by other metals.

  20. Redox-coupled substrate water reorganization in the active site of Photosystem II-The role of calcium in substrate water delivery.

    PubMed

    Ugur, Ilke; Rutherford, A William; Kaila, Ville R I

    2016-06-01

    Photosystem II (PSII) catalyzes light-driven water splitting in nature and is the key enzyme for energy input into the biosphere. Important details of its mechanism are not well understood. In order to understand the mechanism of water splitting, we perform here large-scale density functional theory (DFT) calculations on the active site of PSII in different oxidation, spin and ligand states. Prior to formation of the O-O bond, we find that all manganese atoms are oxidized to Mn(IV) in the S3 state, consistent with earlier studies. We find here, however, that the formation of the S3 state is coupled to the movement of a calcium-bound hydroxide (W3) from the Ca to a Mn (Mn1 or Mn4) in a process that is triggered by the formation of a tyrosyl radical (Tyr-161) and its protonated base, His-190. We find that subsequent oxidation and deprotonation of this hydroxide on Mn1 result in formation of an oxyl-radical that can exergonically couple with one of the oxo-bridges (O5), forming an O-O bond. When O(2) leaves the active site, a second Ca-bound water molecule reorients to bridge the gap between the manganese ions Mn1 and Mn4, forming a new oxo-bridge for the next reaction cycle. Our findings are consistent with experimental data, and suggest that the calcium ion may control substrate water access to the water oxidation sites. PMID:26826591

  1. Chemical modification studies on arginine kinase: essential cysteine and arginine residues at the active site.

    PubMed

    Zhu, Wen-Jing; Li, Miao; Wang, Xiao-Yun

    2007-12-01

    Chemical modification was used to elucidate the essential amino acids in the catalytic activity of arginine kinase (AK) from Migratoria manilensis. Among six cysteine (Cys) residues only one Cys residue was determined to be essential in the active site by Tsou's method. Furthermore, the AK modified by DTNB can be fully reactivated by dithiothreitol (DTT) in a monophasic kinetic course. At the same time, this reactivation can be slowed down in the presence of ATP, suggesting that the essential Cys is located near the ATP binding site. The ionizing groups at the AK active site were studied and the standard dissociation enthalpy (DeltaH degrees ) was 12.38kcal/mol, showing that the dissociation group may be the guanidino of arginine (Arg). Using the specific chemical modifier phenylglyoxal (PG) demonstrated that only one Arg, located near the ATP binding site, is essential for the activity of AK. PMID:17765964

  2. Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites.

    PubMed

    Wang, P-H; De Sancho, D; Best, R B; Blumberger, J

    2016-01-01

    The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently developed methodology for calculation of rate constants for diffusion and binding of small molecules to buried protein active sites. The diffusive dynamics of the ligand obtained from molecular dynamics simulation is coarse grained and described by a Markov state model. Diffusion and binding rate constants are then obtained either from the reactive flux formalism or by fitting the time-dependent population of the Markov state model to a phenomenological rate law. The method is illustrated by applications to diffusion of substrate and inhibitors in [NiFe] hydrogenase, CO-dehydrogenase, and myoglobin. We also discuss a recently developed sensitivity analysis that allows one to identify hot spots in proteins, where mutations are expected to have the strongest effects on ligand diffusion rates. PMID:27497172

  3. 13C-Methyl isocyanide as an NMR probe for cytochrome P450 active sites.

    PubMed

    McCullough, Christopher R; Pullela, Phani Kumar; Im, Sang-Choul; Waskell, Lucy; Sem, Daniel S

    2009-03-01

    The cytochromes P450 (CYPs) play a central role in many biologically important oxidation reactions, including the metabolism of drugs and other xenobiotic compounds. Because they are often assayed as both drug targets and anti-targets, any tools that provide: (a) confirmation of active site binding and (b) structural data, would be of great utility, especially if data could be obtained in reasonably high throughput. To this end, we have developed an analog of the promiscuous heme ligand, cyanide, with a (13)CH(3)-reporter attached. This (13)C-methyl isocyanide ligand binds to bacterial (P450cam) and membrane-bound mammalian (CYP2B4) CYPs. It can be used in a rapid 1D experiment to identify binders, and provides a qualitative measure of structural changes in the active site. PMID:19199046

  4. Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction.

    PubMed

    Zeymer, Cathleen; Werbeck, Nicolas D; Zimmermann, Sabine; Reinstein, Jochen; Hansen, D Flemming

    2016-09-12

    States along the phosphoryl transfer reaction catalyzed by the nucleoside monophosphate kinase UmpK were captured and changes in the conformational heterogeneity of conserved active site arginine side-chains were quantified by NMR spin-relaxation methods. In addition to apo and ligand-bound UmpK, a transition state analog (TSA) complex was utilized to evaluate the extent to which active site conformational entropy contributes to the transition state free energy. The catalytically essential arginine side-chain guanidino groups were found to be remarkably rigid in the TSA complex, indicating that the enzyme has evolved to restrict the conformational freedom along its reaction path over the energy landscape, which in turn allows the phosphoryl transfer to occur selectively by avoiding side reactions. PMID:27534930

  5. 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.

  6. Extreme electric fields power catalysis in the active site of ketosteroid isomerase

    PubMed Central

    Fried, Stephen D.; Bagchi, Sayan; Boxer, Steven G.

    2015-01-01

    Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI’s rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme’s catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems. PMID:25525245

  7. Dynamics and Mechanism of Efficient DNA Repair Reviewed by Active-Site Mutants

    NASA Astrophysics Data System (ADS)

    Tan, Chuang; Liu, Zheyun; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2010-06-01

    Photolyases repair the UV-induced pyrimidine dimers in damage DNA via a photoreaction which includes a series of light-driven electron transfers between the two-electron-reduced flavin cofactor FADH^- and the dimer. We report here our systematic studies of the repair dynamics in E. coli photolyase with mutation of several active-site residues. With femtosecond resolution, we observed the significant change in the forward electron transfer from the excited FADH^- to the dimer and the back electron transfer from the repaired thymines by mutation of E274A, R226A, R342A, N378S and N378C. We also found that the mutation of E274A accelerates the bond-breaking of the thymine dimer. The dynamics changes are consistent with the quantum yield study of these mutants. These results suggest that the active-site residues play a significant role, structurally and chemically, in the DNA repair photocycle.

  8. 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).

  9. Active site hydrophobicity is critical to the bioluminescence activity of Vibrio harveyi luciferase.

    PubMed

    Li, Chi-Hui; Tu, Shiao-Chun

    2005-10-01

    Vibrio harveyi luciferase is an alphabeta heterodimer containing a single active site, proposed earlier to be at a cleft in the alpha subunit. In this work, six conserved phenylalanine residues at this proposed active site were subjected to site-directed mutations to investigate their possible functional roles and to delineate the makeup of luciferase active site. After initial screening of Phe --> Ala mutants, alphaF46, alphaF49, alphaF114, and alphaF117 were chosen for additional mutations to Asp, Ser, and Tyr. Comparisons of the general kinetic properties of wild-type and mutated luciferases indicated that the hydrophobic nature of alphaF46, alphaF49, alphaF114, and alphaF117 was important to luciferase V(max) and V(max)/K(m), which were reduced by 3-5 orders of magnitude for the Phe --> Asp mutants. Both alphaF46 and alphaF117 also appeared to be involved in the binding of reduced flavin substrate. Additional studies on the stability and yield of the 4a-hydroperoxyflavin intermediate II and measurements of decanal substrate oxidation by alphaF46D, alphaF49D, alphaF114D, and alphaF117D revealed that their marked reductions in the overall quantum yield (phi( degrees )) were a consequence of diminished yields of luciferase intermediates and, with the exception of alphaF114D, emission quantum yield of the excited emitter due to the replacement of the hydrophobic Phe by the anionic Asp. The locations of these four critical Phe residues in relation to other essential and/or hydrophobic residues are depicted in a refined map of the active site. Functional implications of these residues are discussed. PMID:16185065

  10. Systematic mutagenesis of the active site omega loop of TEM-1 beta-lactamase.

    PubMed Central

    Petrosino, J F; Palzkill, T

    1996-01-01

    Beta-Lactamase is a bacterial protein that provides resistance against beta-lactam antibiotics. TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Normally, this enzyme has high levels of hydrolytic activity for penicillins, but mutant beta-lactamases have evolved with activity toward a variety of beta-lactam antibiotics. It has been shown that active site substitutions are responsible for changes in the substrate specificity. Since mutant beta-lactamases pose a serious threat to antimicrobial therapy, the mechanisms by which mutations can alter the substrate specificity of TEM-1 beta-lactamase are of interest. Previously, screens of random libraries encompassing 31 of 55 active site amino acid positions enabled the identification of the residues responsible for maintaining the substrate specificity of TEM-1 beta-lactamase. In addition to substitutions found in clinical isolates, many other specificity-altering mutations were also identified. Interestingly, many nonspecific substitutions in the N-terminal half of the active site omega loop were found to increase ceftazidime hydrolytic activity and decrease ampicillin hydrolytic activity. To complete the active sight study, eight additional random libraries were constructed and screened for specificity-altering mutations. All additional substitutions found to alter the substrate specificity were located in the C-terminal half of the active site loop. These mutants, much like the N-terminal omega loop mutants, appear to be less stable than the wild-type enzyme. Further analysis of a 165-YYG-167 triple mutant, selected for high levels of ceftazidime hydrolytic activity, provides an example of the correlation which exists between enzyme instability and increased ceftazidime hydrolytic activity in the ceftazidime-selected omega loop mutants. PMID:8606154

  11. Controlling activation site density by low-energy far-field stimulation in cardiac tissue

    NASA Astrophysics Data System (ADS)

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites (“virtual electrodes”) in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  12. Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements

    PubMed Central

    Sumner, Isaiah; Iyengar, Srinivasan S.

    2010-01-01

    We build on our earlier quantum wavepacket study of hydrogen transfer in the biological enzyme, soybean lipoxygenase-1, by using von Neumann quantum measurement theory to gain qualitative insights into the transfer event. We treat the enzyme active site as a measurement device which acts on the tunneling hydrogen nucleus via the potential it exerts at each configuration. A series of changing active site geometries during the tunneling process effects a sequential projection of the initial, reactant state onto the final, product state. We study this process using several different kinds of von Neumann measurements and show how a discrete sequence of such measurements not only progressively increases the projection of the hydrogen nuclear wavepacket onto the product side but also favors proton over deuteron transfer. Several qualitative features of the hydrogen tunneling problem found in wavepacket dynamics studies are also recovered here. These include the shift in the “transition state” towards the reactant as a result of nuclear quantization, greater participation of excited states in the case of deuterium, and presence of critical points along the reaction coordinate that facilitate hydrogen and deuterium transfer and coincide with surface crossings. To further “tailor” the dynamics, we construct a perturbation to the sequence of measurements, that is a perturbation to the dynamical sequence of active site geometry evolution, which leads us to insight on the existence of sensitive regions of the reaction profile where subtle changes to the dynamics of the active site can have an effect on the hydrogen and deuterium transfer process. PMID:22933858

  13. Electrochemical synthesis and characterization of zinc oxalate nanoparticles

    SciTech Connect

    Shamsipur, Mojtaba; Roushani, Mahmoud; Pourmortazavi, Seied Mahdi

    2013-03-15

    Highlights: ► Synthesis of zinc oxalate nanoparticles via electrolysis of a zinc plate anode in sodium oxalate solutions. ► Design of a Taguchi orthogonal array to identify the optimal experimental conditions. ► Controlling the size and shape of particles via applied voltage and oxalate concentration. ► Characterization of zinc oxalate nanoparticles by SEM, UV–vis, FT-IR and TG–DTA. - Abstract: A rapid, clean and simple electrodeposition method was designed for the synthesis of zinc oxalate nanoparticles. Zinc oxalate nanoparticles in different size and shapes were electrodeposited by electrolysis of a zinc plate anode in sodium oxalate aqueous solutions. It was found that the size and shape of the product could be tuned by electrolysis voltage, oxalate ion concentration, and stirring rate of electrolyte solution. A Taguchi orthogonal array design was designed to identify the optimal experimental conditions. The morphological characterization of the product was carried out by scanning electron microscopy. UV–vis and FT-IR spectroscopies were also used to characterize the electrodeposited nanoparticles. The TG–DTA studies of the nanoparticles indicated that the main thermal degradation occurs in two steps over a temperature range of 350–430 °C. In contrast to the existing methods, the present study describes a process which can be easily scaled up for the production of nano-sized zinc oxalate powder.

  14. Zinc in calcium phosphate mediates bone induction: in vitro and in vivo model.

    PubMed

    Luo, Xiaoman; Barbieri, Davide; Davison, Noel; Yan, Yonggang; de Bruijn, Joost D; Yuan, Huipin

    2014-01-01

    Zinc-containing tricalcium phosphate (Zn-TCP) was synthesized to investigate the role of zinc in osteoblastogenesis, osteoclastogenesis and in vivo bone induction in an ectopic implantation model. Zinc ions were readily released in the culture medium. Zn-TCP with the highest zinc content enhanced the alkaline phosphatase activity of human bone marrow stromal cells and tartrate-resistant acid phosphatase activity, as well as multinuclear giant cell formation of RAW264.7 monocyte/macrophages. RAW264.7 cultured with different dosages of zinc supplements in medium with or without zinc-free TCP showed that zinc could influence both the activity and the formation of multinuclear giant cells. After a 12-week implantation in the paraspinal muscle of canines, de novo bone formation and bone incidence increased with increasing zinc content in Zn-TCP - up to 52% bone in the free space. However, TCP without zinc induced no bone formation. Although the observed bone induction cannot be attributed to zinc release alone, these results indicate that zinc incorporated in TCP can modulate bone metabolism and render TCP osteoinductive, indicating to a novel way to enhance the functionality of this synthetic bone graft material. PMID:24140609

  15. Evidence for the Role of Active Site Residues in the Hairpin Ribozyme from Molecular Simulations along the Reaction Path

    PubMed Central

    2015-01-01

    The hairpin ribozyme accelerates a phosphoryl transfer reaction without catalytic participation of divalent metal ions. Residues A38 and G8 have been implicated as playing roles in general acid and base catalysis, respectively. Here we explore the structure and dynamics of key active site residues using more than 1 μs of molecular dynamics simulations of the hairpin ribozyme at different stages along the catalytic pathway. Analysis of results indicates hydrogen bond interactions between the nucleophile and proR nonbridging oxygen are correlated with active inline attack conformations. Further, the simulation results suggest a possible alternative role for G8 to promote inline fitness and facilitate activation of the nucleophile by hydrogen bonding, although this does not necessarily exclude an additional role as a general base. Finally, we suggest that substitution of G8 with N7- or N3-deazaguanosine which have elevated pKa values, both with and without thio modifications at the 5′ leaving group position, would provide valuable insight into the specific role of G8 in catalysis. PMID:24842535

  16. Locating active-site hydrogen atoms in d-xylose isomerase: Time-of-flight neutron diffraction

    PubMed Central

    Katz, Amy K.; Li, Xinmin; Carrell, H. L.; Hanson, B. Leif; Langan, Paul; Coates, Leighton; Schoenborn, Benno P.; Glusker, Jenny P.; Bunick, Gerard J.

    2006-01-01

    Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of d-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 Å) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which d-xylose is converted to d-xylulose or d-glucose to d-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an −NH2-terminal group (rather than NH3+). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 Å) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms. PMID:16707576

  17. The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction.

    PubMed Central

    Cavarelli, J; Eriani, G; Rees, B; Ruff, M; Boeglin, M; Mitschler, A; Martin, F; Gangloff, J; Thierry, J C; Moras, D

    1994-01-01

    The crystal structures of the various complexes formed by yeast aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of the active site corresponding to different steps of the aminoacylation reaction. Native crystals of the binary complex tRNA-AspRS were soaked in solutions containing the two other substrates, ATP (or its analog AMPPcP) and aspartic acid. When all substrates are present in the crystal, this leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA. A class II-specific pathway for the aminoacylation reaction is proposed which explains the known functional differences between the two classes while preserving a common framework. Extended signature sequences characteristic of class II aaRS (motifs 2 and 3) constitute the basic functional unit. The ATP molecule adopts a bent conformation, stabilized by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the pyrophosphate group and to two class-invariant acidic residues. The aspartic acid substrate is positioned by a class II invariant acidic residue, Asp342, interacting with the amino group