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Sample records for active-site zinc ion

  1. Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.

    PubMed

    Koca, Jaroslav; Zhan, Chang-Guo; Rittenhouse, Robert C; Ornstein, Rick L

    2003-02-01

    We have run several molecular dynamics (MD) simulations on zinc-containing phosphotriesterase (PTE) with two bound substrates, sarin and paraoxon, and with the substrate analog diethyl 4-methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa-coordinated. The hexa-coordination of this zinc ion was not seen in the deposited X-ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the hexa-coordinated zinc ion in PTE is only present in solution and not in the crystal; and the hexa-coordinated zinc ion in PTE is an artifact of the force field used. A charge of +1.5 leads to a coordination number (CN) of 5 on both zinc ions, which is consistent with the results from ab initio and DFT calculations and with the latest high resolution X-ray crystal structure. The commonly used charge of +2 produces a CN of 6 on the less buried zinc. The CN on the more buried zinc ion is 5 when the substrate/inhibitor is present in the simulation, and increases to 6 when the substrate/inhibitor is removed prior to the simulation. The results of both of the MD and quantum mechanical calculations lead to the conclusion that the zinc ions in the PTE active site are both penta-coordinated, and that the MD simulations performed with the charge of +2 overestimate the CN of the zinc ions in the PTE active site. The overall protein structures in the simulations remain unaffected by the

  2. 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

  3. Electron tunnelling through azurin is mediated by the active site Cu ion

    NASA Astrophysics Data System (ADS)

    Alessandrini, Andrea; Gerunda, Mimmo; Canters, G. W.; Verbeet, M. Ph.; Facci, Paolo

    2003-07-01

    Cu- and Zn-azurin chemisorbed on Au(1 1 1) have been comparatively investigated by electrochemical scanning tunnelling microscopy in buffer solution. Cu-azurin shows a marked tunnelling current resonance upon substrate potential at -0.21 V (vs SCE), whereas Zn counterparts do not. These data, discussed in terms of current theories on electron tunnelling through redox adsorbates, demonstrate the role of the electroactive metal ion present in the active site in assisting electron transfer via this metalloprotein.

  4. Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates.

    PubMed Central

    York, D M; Darden, T A; Pedersen, L G; Anderson, M W

    1993-01-01

    Human immunodeficiency virus type 1 protease is inhibited in vitro by zinc ions at neutral pH. The binding site of these ions is not known; however, experimental data suggest that binding may occur in the active site. To examine the possibility of zinc binding in the active site, molecular dynamics simulations in the presence and absence of zinc have been carried out to 200 psec. The results are compared with the 2.8-A crystallographic structures of a synthetic HIV-1 protease, and a zinc binding site at the catalytic aspartate residues (Asp-25, Asp-25') is proposed. Molecular dynamics simulations show that the zinc ion remains stably bound in this region, coordinating the carboxylate side chains of both aspartate residues. Interaction with zinc does not disrupt the dimeric structure of the protein or significantly alter the structure of the active site. These data are consistent with experimental studies of HIV-1 protease inhibition by zinc and give strong evidence that this is the binding site that leads to inactivation. Images p246-a Figure 1. Figure 2. Figure 3. PMID:8404763

  5. Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.

    PubMed

    Hadden, Jonathan M; Déclais, Anne-Cécile; Phillips, Simon E V; Lilley, David M J

    2002-07-01

    T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.

  6. 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

  7. 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

  8. 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.

  9. 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

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

    2015-12-15

    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 Mg(2+). 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 Mg(2+) from Ca(2+). 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.

  10. Inhibitory zinc sites in enzymes.

    PubMed

    Maret, Wolfgang

    2013-04-01

    Several pathways increase the concentrations of cellular free zinc(II) ions. Such fluctuations suggest that zinc(II) ions are signalling ions used for the regulation of proteins. One function is the inhibition of enzymes. It is quite common that enzymes bind zinc(II) ions with micro- or nanomolar affinities in their active sites that contain catalytic dyads or triads with a combination of glutamate (aspartate), histidine and cysteine residues, which are all typical zinc-binding ligands. However, for such binding to be physiologically significant, the binding constants must be compatible with the cellular availability of zinc(II) ions. The affinity of inhibitory zinc(II) ions for receptor protein tyrosine phosphatase β is particularly high (K i = 21 pM, pH 7.4), indicating that some enzymes bind zinc almost as strongly as zinc metalloenzymes. The competitive pattern of zinc inhibition for this phosphatase implicates its active site cysteine and nearby residues in the coordination of zinc. Quantitative biophysical data on both affinities of proteins for zinc and cellular zinc(II) ion concentrations provide the basis for examining the physiological significance of inhibitory zinc-binding sites in proteins and the role of zinc(II) ions in cellular signalling. Regulatory functions of zinc(II) ions add a significant level of complexity to biological control of metabolism and signal transduction and embody a new paradigm for the role of transition metal ions in cell biology.

  11. Mutagenesis of Zinc Ligand Residue Cys221 Reveals Plasticity in the IMP-1 Metallo-β-Lactamase Active Site

    PubMed Central

    Horton, Lori B.; Shanker, Sreejesh; Mikulski, Rose; Brown, Nicholas G.; Phillips, Kevin J.; Lykissa, Ernest; Venkataram Prasad, B. V.

    2012-01-01

    Metallo-β-lactamases catalyze the hydrolysis of a broad range of β-lactam antibiotics and are a concern for the spread of drug resistance. To analyze the determinants of enzyme structure and function, the sequence requirements for the subclass B1 IMP-1 β-lactamase zinc binding residue Cys221 were tested by saturation mutagenesis and evaluated for protein expression, as well as hydrolysis of β-lactam substrates. The results indicated that most substitutions at position 221 destabilized the enzyme. Only the enzymes containing C221D and C221G substitutions were expressed well in Escherichia coli and exhibited catalytic activity toward β-lactam antibiotics. Despite the lack of a metal-chelating group at position 221, the C221G enzyme exhibited high levels of catalytic activity in the presence of exogenous zinc. Molecular modeling suggests the glycine substitution is unique among substitutions in that the complete removal of the cysteine side chain allows space for a water molecule to replace the thiol and coordinate zinc at the Zn2 zinc binding site to restore function. Multiple methods were used to estimate the C221G Zn2 binding constant to be 17 to 43 μM. Studies of enzyme function in vivo in E. coli grown on minimal medium showed that both IMP-1 and the C221G mutant exhibited compromised activity when zinc availability was low. Finally, substitutions at residue 121, which is the IMP-1 equivalent of the subclass B3 zinc-chelating position, failed to rescue C221G function, suggesting the coordination schemes of subclasses B1 and B3 are not interchangeable. PMID:22908171

  12. Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis.

    PubMed

    Zalatan, Jesse G; Catrina, Irina; Mitchell, Rebecca; Grzyska, Piotr K; O'brien, Patrick J; Herschlag, Daniel; Hengge, Alvan C

    2007-08-01

    Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts, with the alterations presumably arising from interactions with active-site functional groups. In particular, the phosphate monoester hydrolysis reaction catalyzed by Escherichia coli alkaline phosphatase (AP) has been the subject of intensive scrutiny. Recent linear free energy relationship (LFER) studies suggest that AP catalyzes phosphate monoester hydrolysis through a loose transition state, similar to that in solution. To gain further insight into the nature of the transition state and active-site interactions, we have determined kinetic isotope effects (KIEs) for AP-catalyzed hydrolysis reactions with several phosphate monoester substrates. The LFER and KIE data together provide a consistent picture for the nature of the transition state for AP-catalyzed phosphate monoester hydrolysis and support previous models suggesting that the enzymatic transition state is similar to that in solution. Moreover, the KIE data provides unique information regarding specific interactions between the transition state and the active-site Zn2+ ions. These results provide strong support for a model in which electrostatic interactions between the bimetallo Zn2+ site and a nonbridging phosphate ester oxygen atom make a significant contribution to the large rate enhancement observed for AP-catalyzed phosphate monoester hydrolysis.

  13. Direct measurement of metal ion chelation in the active site of human ferrochelatase.

    PubMed

    Hoggins, M; Dailey, H A; Hunter, C N; Reid, J D

    2007-07-10

    The final step in heme biosynthesis, insertion of ferrous iron into protoporphyrin IX, is catalyzed by protoporphyrin IX ferrochelatase (EC 4.99.1.1). We demonstrate that pre-steady state human ferrochelatase (R115L) exhibits a stoichiometric burst of product formation and substrate consumption, consistent with a rate-determining step following metal ion chelation. Detailed analysis shows that chelation requires at least two steps, rapid binding followed by a slower (k approximately 1 s-1) irreversible step, provisionally assigned to metal ion chelation. Comparison with steady state data reveals that the rate-determining step in the overall reaction, conversion of free porphyrin to free metalloporphyrin, occurs after chelation and is most probably product release. We have measured rate constants for significant steps on the enzyme and demonstrate that metal ion chelation, with a rate constant of 0.96 s-1, is approximately 10 times faster than the rate-determining step in the steady state (kcat = 0.1 s-1). The effect of an additional E343D mutation is apparent at multiple stages in the reaction cycle with a 7-fold decrease in kcat and a 3-fold decrease in kchel. This conservative mutation primarily affects events occurring after metal ion chelation. Further evaluation of structure-function data on site-directed mutants will therefore require both steady state and pre-steady state approaches.

  14. 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.

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

    PubMed

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

    2008-03-21

    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.

  16. Effect of zinc ions on conformational stability of yeast alcohol dehydrogenase.

    PubMed

    Yang, Y; Zhou, H M

    2001-01-01

    Yeast alcohol dehydrogenase preparations were prepared with the conformational zinc ion removed (Apo-I YADH) and with both the conformational and catalytic zinc ions removed (Apo-II YADH). The unfolding of Apo-I YADH and Apo-II YADH during denaturation in urea solutions was then followed by fluorescence emission, circular dichroism, and second-derivative optical spectroscopies. Compared with the native enzyme, Apo-I YADH incurred some slight unfolding, and its stability against urea was markedly decreased, while Apo-II YADH incurred marked unfolding but contained residual ordered structure even at high urea concentrations. The results show that native YADH is more conformationally stable against urea denaturation than Apo-I YADH, indicating that the conformational Zn(2+) plays an important role in stabilizing the conformation of the YADH molecule. However, unfolding of the region around the conformational zinc ion is shown not to be the rate limited step in the unfolding of the molecule by the fact that the unfolding and inactivation rate constants of native and Apo-I YADH are the same. It is suggested that the catalytic zinc ion is more important in maintaining the structure of YADH. YADH lost its cooperative unfolding ability after the zinc ions were removed. The shape of the transition curves of Apo-I YADH suggests the existence of an unfolding intermediate. For both native and Apo-I YADH, inactivation occurs at much lower urea concentrations than that needed to produce significant conformational changes of the enzyme molecule. At urea concentration above 4 M, the inactivation rate constants are much higher than those of the fast phase of the reaction of unfolding. These results support the suggestion of flexibility at the active site of the enzyme (C. L. Tsou (1986) Trends Biochem. Sci., 11, 427-429; (1993) Science, 262, 308-381).

  17. 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.

  18. 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.

  19. Zinc finger peptide based optic sensor for detection of zinc ions.

    PubMed

    Verma, Neelam; Kaur, Gagandeep

    2016-12-15

    In the present work, polyacrylamide gel has been used as a matrix for the immobilization of zinc finger peptide and fluorescent dye acrydine orange on the micro well plate to fabricate the fluorescence based biosensor for the detection of zinc ions in milk samples. The fluorescent dye moves in the hydrophobic groove formed after folding of the peptide in the presence of zinc ions. Under optimized conditions, linear range was observed between 0.001µg/l to 10µg/l of Zinc ions, with a lowest detection limit of 0.001µg/l and response time of 5min. Presented biosensor has shown 20% decrease in fluorescent intensity values after 5 regenerations and stable for more than one month, stored at 4°C. Interference study with other metal ions like lead, cadmium and copper showed a negligible change in fluorescence intensity in comparison to zinc ions. Developed bio sensing system was found to be novel, quick, reliable, miniaturized, stable, reproducible and repeatable and specific for zinc ion, which has been applied to various milk samples.

  20. Zinc finger peptide based optic sensor for detection of zinc ions.

    PubMed

    Verma, Neelam; Kaur, Gagandeep

    2016-12-15

    In the present work, polyacrylamide gel has been used as a matrix for the immobilization of zinc finger peptide and fluorescent dye acrydine orange on the micro well plate to fabricate the fluorescence based biosensor for the detection of zinc ions in milk samples. The fluorescent dye moves in the hydrophobic groove formed after folding of the peptide in the presence of zinc ions. Under optimized conditions, linear range was observed between 0.001µg/l to 10µg/l of Zinc ions, with a lowest detection limit of 0.001µg/l and response time of 5min. Presented biosensor has shown 20% decrease in fluorescent intensity values after 5 regenerations and stable for more than one month, stored at 4°C. Interference study with other metal ions like lead, cadmium and copper showed a negligible change in fluorescence intensity in comparison to zinc ions. Developed bio sensing system was found to be novel, quick, reliable, miniaturized, stable, reproducible and repeatable and specific for zinc ion, which has been applied to various milk samples. PMID:27424265

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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](+).

  6. 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.

  7. Azamacrocycle activated quantum dot for zinc ion detection.

    PubMed

    Ruedas-Rama, Maria Jose; Hall, Elizabeth A H

    2008-11-01

    A new fluorescent nanosensor family for Zn (2+) determination is reported based on azamacrocycle derivatization of CdSe/ZnS core/shell quantum dot nanoparticles. They are the first zinc ion sensors using QD nanoparticles in a host-guest and receptor-fluorophore system. Three azamacrocycles are demonstrated as receptors: TACN (1,4,7-triazacyclononane), cyclen (1,4,7,10-tetraazacyclododecane), and cyclam (1,4,8,11-tetraazacyclotetradecane). Azamacrocycles conjugated to QDs via an amide link interact directly with one of the photoinduced QD charge carriers, probably transferring the hole in the QD to the azamacrocycle, thereby disrupting the radiative recombination process. When zinc ion enters the aza-crown, the lone pair electrons of the nitrogen atom become involved in the coordination and the energy level is no longer available for the hole-transfer mechanism, switching on the QD emission and a dramatic increase of the fluorescence intensity results, allowing the detection of low concentrations of zinc ions. Using this operating principle, three zinc ion sensors based on CdSe-ZnS core-shell QD nanoparticles showed a very good linearity in the range 5-500 microM, with detection limits lower than 2.4 microM and RSDs approximately 3% ( n = 10). In addition, the versatility of the sensors was demonstrated, since different sizes (and colors) of QDs can be employed and will respond to zinc in a similar way. In a study of interferences, the zinc-sensitive QDs showed good selectivity in comparison with other physiologically important cations and other transition metals tested. The results from fetal calf serum and samples mimicking physiological conditions suggested very good applicability in the determination of zinc ion in physiological samples.

  8. 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

  9. 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

  10. 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

  11. Motion of the Zinc Ions in Catalysis by a di-Zinc Metallo-beta-Lactamase

    SciTech Connect

    R Breece; Z Hu; M Crowder; D Tierney

    2011-12-31

    We report rapid-freeze-quench X-ray absorption spectroscopy of a dizinc metallo-beta-lactamase (MbetaL) reaction intermediate. The Zn(II) ions in the dinuclear active site of the S. maltophilia Class B3 MbetaL move away from each other, by approximately 0.3 A after 10 ms of reaction with nitrocefin, from 3.4 to 3.7 A. Together with our previous characterization of the resting enzyme and its nitrocefin product complex, where the Zn(II) ion separation relaxes to 3.6 A, these data indicate a scissoring motion of the active site that accompanies the ring-opening step. The average Zn(II) coordination number of 4.5 in the resting enzyme appears to be maintained throughout the reaction with nitrocefin. This is the first direct structural information available on early stage dizinc metallo-beta-lactamase catalysis.

  12. 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.

  13. Biomimetic ion nanochannels as a highly selective sequential sensor for zinc ions followed by phosphate anions.

    PubMed

    Han, Cuiping; Su, Haiyan; Sun, Zhongyue; Wen, Long; Tian, Demei; Xu, Kai; Hu, Junfeng; Wang, Aming; Li, Haibing; Jiang, Lei

    2013-07-01

    A novel biomimetic ion-responsive multi-nanochannel system is constructed by covalently immobilizing a metal-chelating ligand, 2,2'-dipicolylamine (DPA), in polyporous nanochannels prepared in a polymeric membrane. The DPA-modified multi-nanochannels show specific recognition of zinc ions over other common metal ions, and the zinc-ion-chelated nanochannels can be used as secondary sensors for HPO4(2-) anions. The immobilized DPA molecules act as specific-receptor binding sites for zinc ions, which leads to the highly selective zinc-ion response through monitoring of ionic current signatures. The chelated zinc ions can be used as secondary recognition elements for the capture of HPO4(2-) anions, thereby fabricating a sensing nanodevice for HPO4(2-) anions. The success of the DPA immobilization and ion-responsive events is confirmed by measurement of the X-ray photoelectron spectroscopy (XPS), contact angle (CA), and current-voltage (I-V) characteristics of the systems. The proposed nanochannel sensing devices display remarkable specificity, high sensitivity, and wide dynamic range. In addition, control experiments performed in complex matrices suggest that this sensing system has great potential applications in chemical sensing, biotechnology, and many other fields. PMID:23733212

  14. Inhibition of beta-amylase activity by calcium, magnesium and zinc ions determined by spectrophotometry and isothermal titration calorimetry.

    PubMed

    Dahot, M Umar; Saboury, A A; Moosavi-Movahedi, A A

    2004-04-01

    The inhibition effect of metal ions on beta amylase activity was studied. The inhibitor-binding constant (Ki) was determined by spectrophotometric and isothermal titration calorimetric (ITC) methods. The binding of calcium, magnesium and zinc ion as inhibitors at the active site of barley beta amylase was studied at pH = 4.8 (sodium acetate 16 mM) and T = 300K. The Ki and enthalpy of binding for calcium (13.4, 13.1 mM and -14.3 kJ/mol), magnesium (18.6, 17.8mM and -17.7 kJ/mol) and zinc (17.5, 17.7 mM and -20.0 kJ/mol) were found by spectrophotometric and ITC methods respectively.

  15. 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.

  16. Effectiveness of copper and zinc ions in preventing scaling of drinking water.

    PubMed

    Liu, Dan; Hui, Franck; Ledion, Jean; Li, Fengting

    2011-04-01

    This paper investigates the effectiveness of copper and zinc ions an economical and environmentally friendly method for inhibiting the scaling of drinking water, using the method of rapid controlled precipitation (RCP). The results indicated that zinc ions and copper ions, at low concentrations, were highly efficient inhibitors in a 300 mL solution (calcium ion concentration of 126.5 mg/L). To produce an inhibition efficiency of 100% (in 70 min), the concentration of the copper ion was 0.9 mg/L and that of the zinc ion was 0.4 mg/L. The analysis by SEM and infrared absorption spectrometry showed that copper and zinc ions could affect the calcium carbonate germination and change the crystal morphology, which indicated that copper and zinc ions had participated in the composition of the crystal; however, the quantity of copper or zinc ion in the precipitate was so small that it was difficult to observe them. PMID:21877541

  17. Effectiveness of copper and zinc ions in preventing scaling of drinking water.

    PubMed

    Liu, Dan; Hui, Franck; Ledion, Jean; Li, Fengting

    2011-04-01

    This paper investigates the effectiveness of copper and zinc ions an economical and environmentally friendly method for inhibiting the scaling of drinking water, using the method of rapid controlled precipitation (RCP). The results indicated that zinc ions and copper ions, at low concentrations, were highly efficient inhibitors in a 300 mL solution (calcium ion concentration of 126.5 mg/L). To produce an inhibition efficiency of 100% (in 70 min), the concentration of the copper ion was 0.9 mg/L and that of the zinc ion was 0.4 mg/L. The analysis by SEM and infrared absorption spectrometry showed that copper and zinc ions could affect the calcium carbonate germination and change the crystal morphology, which indicated that copper and zinc ions had participated in the composition of the crystal; however, the quantity of copper or zinc ion in the precipitate was so small that it was difficult to observe them.

  18. 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%.

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Ion Beam Layer Separation of Cadmium Zinc Telluride

    SciTech Connect

    Bhattacharya, Rabi S.; He, P.; Xu, Y.; Goorsky, M.

    2008-11-03

    We have investigated the approach of ion induced layer separation process for layer splitting from Cadmium Zinc Telluride (CZT) bulk single crystal and transferring and bonding the separated layers with Silicon (Si) wafers. Layer separation experiments have been carried out at UES using 1 MeV H{sup +} ions from the high energy accelerator (1.7 MV Tandetron). Ion dose and annealing temperature for complete separation of 1 cmx1 cm size layers have been optimized. Bonding of CZT with Si was accomplished using various IR transmitting chalcogenide glasses. Cracking of separated CZT films was occurring for chalcogenide glass bonded films. Optimization of thermal treatment has led to the minimization of such cracks. Detailed characterizations of the separated films will be presented.

  7. 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

  8. Biomimetic study of the Ca(2+)-Mg2+ and K(+)-Li+ antagonism on biologically active sites: new methodology to study potential dependent ion exchange.

    PubMed

    Paczosa-Bator, Beata; Stepien, Milena; Maj-Zurawska, Magdalena; Lewenstam, Andrzej

    2009-03-01

    Competitive divalent (magnesium and calcium) or monovalent (potassium, lithium and sodium) ion exchange and its influence on a membrane potential formation was studied at biological ligands (BL) such as adenosine triphosphate (ATP), asparagine (Asn) and glutamine (Gln) sites. The sites are dispersed electrochemically in membranes made of the conducting polymers (CPs)--poly(N-methylpyrrole) (PMPy) and poly(pyrrole) (PPy). The membranes are made sensitive to calcium and magnesium or to potassium, sodium and lithium by optimized electrodeposition and soaking procedures supported by the study of membrane topography and morphology. Distinctively different electrochemical responses, i.e. electrical potential transients or currents, are observed in the case of "antagonistic" calcium and magnesium or potassium and sodium/lithium ion pairs. Dissimilarity in the responses is ascribed to a difference between on site vs. bulk concentrations of ions, and is dictated by different transport properties of the ions, as shown by using the Nernst-Planck-Poisson (NPP) model and the diffusion-layer model (DLM). The method described allows inspecting potential-dependent competitive ion-exchange processes at the biologically active sites. It is suggested that this approach could be used as an auxiliary tool in study of potential dependent block in realistic membrane channels, such as Mg block in the N-methyl D-aspartate receptor channel (NMDA).

  9. 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.

  10. Solution NMR Structure of the Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site

    SciTech Connect

    Ramelot, Theresa A.; Cort, John R.; Goldsmith-Fischman, Sharon; Kornhaber, Greg J.; Xiao, Rong; Shastry, Ritu; Acton, Thomas; Honig, Barry; Montelione, Gaetano; Kennedy, Michael A.

    2004-11-19

    IscU is a highly conserved protein that serves as the scaffold for IscS-mediated assembly of iron-sulfur ([Fe-S]) clusters. We report the NMR solution structure of monomeric Haemophilus influenzae IscU with zinc bound at the [Fe-S] cluster assembly site. The compact core of the globular structure has an {alpha}-{beta} sandwich architecture with a three-stranded antiparallel {beta}-sheet and four {alpha}-helices. A nascent helix is located N-terminal to the core structure. The zinc is ligated by three cysteines and one histidine that are located in and near conformationally dynamic loops at one end of the IscU structure. Removal of the zinc metal by chelation results in widespread loss of structure in the apo form. The zinc-bound IscU may be a good model for iron-loaded IscU and may demonstrate structural features found in the iron-sulfur cluster bound form. Structural and functional similarities, genomic context in operons containing other homologous genes, and distributions of conserved surface residues support the hypothesis that IscU protein domains are homologous (i.e. derived from a common ancestor) with the SufE/YgdK family of iron sulfur cluster assembly proteins.

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

    PubMed

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

    2014-01-01

    Preparation of Zn(2+) 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 Zn(2+) 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 Zn(2+) 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 Zn(2+) 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.

  12. 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.

  13. Analyzing free zinc(II) ion concentrations in cell biology with fluorescent chelating molecules.

    PubMed

    Maret, Wolfgang

    2015-02-01

    Essential metal ions are tightly controlled in biological systems. An understanding of metal metabolism and homeostasis is being developed from quantitative information of the sizes, concentrations, and dynamics of cellular and subcellular metal ion pools. In the case of human zinc metabolism, minimally 24 proteins of two zinc transporter families and a dozen metallothioneins participate in cellular uptake, extrusion, and re-distribution among cellular compartments. Significantly, zinc(ii) ions are now considered signaling ions in intra- and intercellular communication. Such functions require transients of free zinc ions. It is experimentally quite challenging to distinguish zinc that is protein-bound from zinc that is not bound to proteins. Measurement of total zinc is relatively straightforward with analytical techniques such as atomic absorption/emission spectroscopy or inductively coupled plasma mass spectrometry. Total zinc concentrations of human cells are 200-300 μM. In contrast, the pool of non-protein bound zinc is mostly examined with fluorescence microscopy/spectroscopy. There are two widely applied fluorescence approaches, one employing low molecular weight chelating agents ("probes") and the other metal-binding proteins ("sensors"). The protein sensors, such as the CALWY, Zap/ZifCY, and carbonic anhydrase-based sensors, can be genetically encoded and have certain advantages in terms of controlling intracellular concentration, localization, and calibration. When employed correctly, both probes and sensors can establish qualitative differences in free zinc ion concentrations. However, when quantitative information is sought, the assumptions underlying the applications of probes and sensors must be carefully examined and even then measured pools of free zinc ions remain methodologically defined. A consensus is building that the steady-state free zinc ion concentrations in the cytosol are in the picomolar range but there is no consensus on their

  14. 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.

  15. 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.

  16. Direct measurement of metal-ion chelation in the active site of the AAA+ ATPase magnesium chelatase.

    PubMed

    Viney, Joanne; Davison, Paul A; Hunter, C Neil; Reid, James D

    2007-11-01

    Magnesium chelatase catalyzes the first committed step in chlorophyll biosynthesis. This complex enzyme has at least three substrates and couples ATP hydrolysis to the insertion of Mg2+ into protoporphyrin IX. We directly observed metal-ion chelation fluorometrically, providing the first data describing the on-enzyme reaction. We describe the transient-state kinetics of magnesium chelatase with direct observation of the evolution of an enzyme-product complex EMgDIX. We demonstrate that MgATP2- binding occurs after the rate-determining step. As nucleotide hydrolysis is essential for the overall reaction this must also occur after the rate-determining step. This provides the first evidence for the synchronization of the ATPase and chelatase pathways and suggests a mechanism where nucleotide binding acts to clamp the chelatase in a product complex. Comparison of rate constants for the slow step in the reaction with further transient kinetics under conditions where multiple turnovers can occur reveals that an additional activation step is required to explain the behavior of magnesium chelatase. These data provide a new view of the sequence of events occurring in the reaction catalyzed by magnesium chelatase.

  17. 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

  18. Effects of surface hydrophobicity on the catalytic iron ion retention in the active site of two catechol 1,2-dioxygenase isoenzymes.

    PubMed

    Di Nardo, Giovanna; Pessione, Enrica; Cavaletto, Maria; Anfossi, Laura; Vanni, Adriano; Briganti, Fabrizio; Giunta, Carlo

    2004-12-01

    The different behaviour of two isozymes (IsoA and IsoB) of catechol 1,2-dioxygenase (C 1,20) from Acinetobacter radioresistens S13 on a hydrophobic interaction, Phenyl-Sepharose chromatographic column, prompted us to investigate the role of superficial hydrophobicity on structural-functional aspects for such class of enzymes. The interaction of 8-anilino-1-naphtalenesulphonate (ANS), a fluorescent probe known to bind to hydrophobic sites in proteins, revealed that the two isoenzymes have a markedly different hydrophobicity degree although a similar number of hydrophobic superficial sites were estimated (2.65 for IsoA and 2.18 for IsoB). ANS is easily displaced by adding the substrates catechol or 3-methylcatechol to the adduct, suggesting that the binding sites are in the near surroundings of the catalytic clefts. The analysis of the hydropathy profiles and the possible superficial cavities allowed to recognize the most feasible region for ANS binding. The lower hydrophobicity detected in the near surroundings of the catalytic pocket of IsoB supports its peculiarity to lose the catalytic metal ions more easily than IsoA. As previously suggested for other metalloenzymes, the presence of more hydrophilic and/or smaller residues near to the active site of IsoB is expected to increase the metal ligands mobility thus increasing the metal ion dissociation rate constants, estimated to be 0.078 h(-1) and 0.670 h(-1) for IsoA and IsoB respectively.

  19. Zinc

    MedlinePlus

    ... ulcers and promoting weight gain in people with eating disorders such as anorexia nervosa. Some people use zinc ... is abnormal): 25-100 mg zinc. For the eating disorder anorexia nervosa: 100 mg of zinc gluconate daily. ...

  20. Probing the Protonation State and the Redox-Active Sites of Pendant Base Iron(II) and Zinc(II) Pyridinediimine Complexes.

    PubMed

    Delgado, Mayra; Sommer, Samantha K; Swanson, Seth P; Berger, Robert F; Seda, Takele; Zakharov, Lev N; Gilbertson, John D

    2015-08-01

    Utilizing the pyridinediimine ligand [(2,6-(i)PrC6H3)N═CMe)(N((i)Pr)2C2H4)N═CMe)C5H3N] (didpa), the zinc(II) and iron(II) complexes Zn(didpa)Cl2 (1), Fe(didpa)Cl2 (2), [Zn(Hdidpa)Cl2][PF6] (3), [Fe(Hdidpa)Cl2][PF6] (4), Zn(didpa)Br2 (5), and [Zn(Hdidpa)Br2][PF6] (6), Fe(didpa)(CO)2 (7), and [Fe(Hdidpa)(CO)2][PF6] (8) were synthesized and characterized. These complexes allowed for the study of the secondary coordination sphere pendant base and the redox-activity of the didpa ligand scaffold. The protonated didpa ligand is capable of forming metal halogen hydrogen bonds (MHHBs) in complexes 3, 4, and 6. The solution behavior of the MHHBs was probed via pKa measurements and (1)H NMR titrations of 3 and 6 with solvents of varying H-bond accepting strength. The H-bond strength in 3 and 6 was calculated in silico to be 5.9 and 4.9 kcal/mol, respectively. The relationship between the protonation state and the ligand-based redox activity was probed utilizing 7 and 8, where the reduction potential of the didpa scaffold was found to shift by 105 mV upon protonation of the reduced ligand in Fe(didpa)(CO)2.

  1. 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

  2. Separation of zinc and nickel ions in a strong acid through liquid-liquid extraction.

    PubMed

    Park, Young Jun; Fray, Derek J

    2009-04-15

    Many solid wastes contain both zinc and nickel at the same time. For recycling or recovery of metals, it is essential to separate materials. Among those materials, zinc and nickel are very difficult to be separated because there is not so much difference in the chemical and physical properties. This paper focuses on the separation of zinc and nickel ions in a diluted aqua regia solution. Liquid-liquid extraction by TBP, Cyanex 272 and Cyanex 301 was used and a distribution coefficient (D), a separation factor (S) and a relative purity (R) were induced to evaluate the degree of separation. All of the extractions were proportional to the concentration of the extractants, and zinc ions were extracted more easily than nickel ions. Among the extractants, Cyanex 301 showed the best characteristics regarding Zn/Ni separation. In particular, the extraction of zinc ions in the range of pHions was less than 20 wt.%, when 100 vol.% Cyanex 301 was used. The maximum S(Zn,Ni) value was about 21,700 at pH 6.0 and the highest relative purity (R) of zinc was about 99 wt.% without a pH control, pH -1.1. PMID:18675511

  3. Zinc.

    PubMed

    Barceloux, D G

    1999-01-01

    The use of zinc in metal alloys and medicinal lotions dates back before the time of Christ. Currently, most of the commercial production of zinc involves the galvanizing of iron and the manufacture of brass. Some studies support the use of zinc gluconate lozenges to treat the common cold, but there are insufficient data at this time to recommend the routine use of these lozenges. Zinc is an essential co-factor in a variety of cellular processes including DNA synthesis, behavioral responses, reproduction, bone formation, growth, and wound healing. Zinc is a relatively common metal with an average concentration of 50 mg/kg soil and a range of 10-300 mg/kg soil. Meat, seafood, dairy products, nuts, legumes, and whole grains contain relatively high concentrations of zinc. The mobility of zinc in anaerobic environments is poor and therefore severe zinc contamination occurs primarily near points sources of zinc release. The recommended daily allowance for adults is 15 mg zinc. The ingestion of 1-2 g zinc sulfate produces emesis. Zinc compounds can produce irritation and corrosion of the gastrointestinal tract, along with acute renal tubular necrosis and interstitial nephritis. Inhalation of high concentrations of zinc chloride from smoke bombs detonated in closed spaces may cause chemical pneumonitis and adult respiratory distress syndrome. In the occupational setting inhalation of fumes from zinc oxide is the most common cause of metal fume fever (fatigue, chills, fever, myalgias, cough, dyspnea, leukocytosis, thirst, metallic taste, salivation). Zinc compounds are not suspected carcinogens. Treatment of zinc toxicity is supportive. Calcium disodium ethylenediaminetetraacetate (CaNa2EDTA) is the chelator of choice based on case reports that demonstrate normalization of zinc concentrations, but there are few clinical data to confirm the efficacy of this agent. PMID:10382562

  4. Effect of zinc and iron ions on the electrochemistry of nickel oxide electrode: Slow cyclic voltammetry. Technical report

    SciTech Connect

    Krejci, I.; Vanysek, P.

    1993-04-07

    Porous sintered nickel oxide electrodes were prepared by cathodic electroprecipitation from metal nitrate solutions and characterized by slow (0.1 mV/s) voltammetry in 6 mol/l KOH. Presence of iron or zinc ions resulted in decrease of electrode charging ability and similar changes in voltammograms were observed for both ions. Removal of iron or zinc ions and introduction of lithium ions partially restored the electrode and corresponding voltammogram to original conditions. Presence of cobalt in the electrode material diminished substantially the influence of zinc ions on the electrode properties.... Storage batteries, Power sources, Membrane transport, Ion transport, Nafion.

  5. Tetrameric ZBRK1 DNA binding domain has affinity towards cognate DNA in absence of zinc ions.

    PubMed

    Yadav, Lumbini R; Biswal, Mahamaya N; Vikrant; Hosur, M V; Varma, Ashok K

    2014-07-18

    Zinc finger transcription regulatory proteins play crucial roles in cell-cycle regulation, DNA damage response and tumor genesis. Human ZBRK1 is a zinc-finger transcription repressor protein, which recognizes double helical DNA containing consensus sequences of 5'GGGXXXCAGXXXTTT3'. In the present study, we have purified recombinant DNA binding domain of ZBRK1, and studied binding with zinc ions and DNA, using biophysical techniques. The elution profile of the purified protein suggests that this ZBRK1 forms a homotetramer in solution. Dissociation and pull down assays also suggest that this domain forms a higher order oligomer. The ZBRK1-DNA binding domain acquires higher stability in the presence of zinc ions and DNA. The secondary structure of the ZBRK1-DNA complex is found to be significantly altered from the standard B-DNA conformation.

  6. 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.

  7. 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.

  8. 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

  9. Potential interaction between zinc ions and a cyclodextrin-based diclofenac formulation.

    PubMed

    Hamdan, Imad I; El-Sabawi, Dina; Abdel Jalil, Mariam

    2016-01-01

    Complexes of diclofenac sodium (DF-Na) with hydroxypropyl betacyclodextrin (HPβCD) were prepared by co-evaporation in a 1:1 ratio and characterized in light of previously reported data. Phase solubility diagrams were obtained for DF-Na with HPβCD in the presence and absence of zinc ions. Dissolution profiles were obtained for DF-Na and its HPβCD complex at acidic (pH 1.2) as well as in phosphate buffer (pH 6.8), in the presence and absence of zinc. HPβCD, as expected, was shown to improve the dissolution of DF-Na in acidic medium but not in phosphate buffer (pH 6.8). The presence of zinc ions decreased the in vitro dissolution of DF-HPβCD complex in acidic medium (pH 1.2) but not in phosphate buffer (pH 6.8). It was confirmed that the precipitate that was formed by zinc ions in the presence of HPβCD and DF-Na contained no cyclodextrin and most likely it was a mixture of the complexes: DF2-Zn and DF-Zn with some molecules of water. In vivo experiments on rats have shown that HPβCD has no statistically significant effect on absorption or bioavailability of DF-Na in spite of the observed improvement of its in vitro dissolution by HPβCD. Moreover, zinc ions were shown to decrease the absorption rate of DF-Na in rats model but did neither significantly alter the absorption nor bioavailability of DF-HPβCD complex. The zinc induced precipitates of DF were shown to have significantly different crystalline properties when HPβCD was present. Therefore, the pharmaceutical details of a DF-Na preparation should be considered when designing the formulation and predicting possible interaction between DF-Na (or other potential NSAIDs) and zinc metal.

  10. 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 ...

  11. 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…

  12. 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.

  13. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  14. 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.

  15. 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.

  16. Zinc

    MedlinePlus

    ... deficiency also causes hair loss, diarrhea, eye and skin sores and loss of appetite. Weight loss, problems ... pneumonia and other infections. Zinc also helps the skin stay healthy. Some people who have skin ulcers ...

  17. The relationship of sanguinaria extract concentration and zinc ion to plaque and gingivitis.

    PubMed

    Southard, G L; Parsons, L G; Thomas, L G; Boulware, R T; Woodall, I R; Jones, B J

    1987-07-01

    The effects of sanguinaria extract and zinc chloride on plaque growth and gingivitis inhibition were assessed on subjects with initially plaque-free tooth surfaces using a series of oral rinses in a single-blind, crossover, no-oral-hygiene study lasting 2 weeks. A placebo oral rinse containing no sanguinaria or zinc chloride (A), and test rinses containing 150 micrograms/ml sanguinaria and 0.2% zinc chloride (B), 300 micrograms/ml sanguinaria and no zinc chloride (C), and 300 micrograms/ml sanguinaria and 0.2% zinc chloride (D) were evaluated. Subjects using the higher concentration rinses C and D had significantly lower plaque scores than rinse A at 7 and 14 days (p less than 0.05 for C, p less than 0.01 for D). However, groups C and D were not significantly different from each other. Group D had significantly lower plaque (p less than 0.05) and gingivitis (p less than 0.01) scores than group B. Subjects who used rinse B and placebo rinse A had the highest plaque and gingivitis scores and comparison of these two groups revealed no significant difference. At the end of 14 days, the % distribution of 0 plaque and gingivitis scores was greatest among subjects using rinses C and D. Subjects in these 2 groups also had the lowest incidence of plaque and gingivitis scores of 2+. It is concluded that the effects of sanguinaria rinses on developing plaque and gingivitis are influenced more by sanguinaria concentrations than the presence or absence of zinc ion, but that zinc ion may provide a mild enhancement of sanguinaria effectiveness against gingivitis.

  18. Comparative effects of zinc oxide nanoparticles and dissolved zinc on zebrafish embryos and eleuthero-embryos: importance of zinc ions.

    PubMed

    Brun, Nadja Rebecca; Lenz, Markus; Wehrli, Bernhard; Fent, Karl

    2014-04-01

    The increasing use of zinc oxide nanoparticles (nZnO) and their associated environmental occurrence make it necessary to assess their potential effects on aquatic organisms. Upon water contact, nZnO dissolve partially to zinc (Zn(II)). To date it is not yet completely understood, whether effects of nZnO are solely or partly due to dissolved Zn(II). Here we compare potential effects of 0.2, 1 and 5mg/L nZnO and corresponding concentrations of released Zn(II) by water soluble ZnCl2 to two development stages of zebrafish, embryos and eleuthero-embryos, by analysing expressional changes by RT-qPCR. Another objective was to assess uptake and tissue distribution of Zn(II). Laser ablation-ICP-MS analysis demonstrated that uptake and tissue distribution of Zn(II) were identical for nZnO and ZnCl2 in eleuthero-embryos. Zn(II) was found particularly in the retina/pigment layer of eyes and brain. Both nZnO and dissolved Zn(II) derived from ZnCl2 had similar inhibiting effects on hatching, and they induced similar expressional changes of target genes. At 72hours post fertilization (hpf), both nZnO and Zn(II) delayed hatching at all doses, and inhibited hatching at 1 and 5 mg/L at 96 hpf. Both nZnO and Zn(II) lead to induction of metallothionein (mt2) in both embryos and eleuthero-embryos at all concentrations. Transcripts of oxidative stress related genes cat and Cu/Zn sod were also altered. Moreover, we show for the first time that nZnO exposure results in transcriptional changes of pro-inflammatory cytokines IL-1β and TNFα. Overall, transcriptional alterations were higher in embryos than eleuthero-embryos. The similarities of the effects lead to the conclusion that effects of nZnO are mainly related to the release of Zn(II).

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. The effect of exogenous zinc ions on the pattern of oxygen consumption of the hepatic mitochondria of albino rats.

    PubMed

    Kukoyi, B I; Costello, L C; Franklin, R B

    2004-12-01

    The effect of incubation of coupled liver mitochondria on varying concentration of zinc ion was determined. A low concentration of 6 microM zinc ion was found to inhibit the rate of oxygen consumption of the liver mitochondria significantly [P < 0.01]. There was uncoupling of the liver mitochondria when subjected to varying incubation periods. There was no change observed in the control experiment. Zinc-citrate inhibited the rate of oxygen consumption significantly [P < 0.01] when compare with the control. The changes observed in the Zn-aspartate were insignificant. Zn-EDTA had no inhibitory or stimulatory effect on the rate of liver mitochondrial oxygen consumption.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  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. 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.

  10. Optical properties of Sm3+ ions in zinc potassium fluorophosphate glasses

    NASA Astrophysics Data System (ADS)

    Thomas, Sunil; George, Rani; Nayab Rasool, Sk.; Rathaiah, M.; Venkatramu, V.; Joseph, Cyriac; Unnikrishnan, N. V.

    2013-12-01

    In the present work, different concentrations of Sm3+ ions doped zinc potassium fluorophosphate glasses (PKAMZFSm: P2O5 + K2O + MgO + Al2O3 + ZnF2 + Sm2O3) were synthesized via melt quench technique. Physical properties and refractive indices of the present glasses were evaluated. Optical characterization of Sm3+: PKAMZF glasses through absorption, excitation, emission and decay spectra had been carried out. Nephelauxetic ratios, bonding parameter and energy band gap of the 1.0 mol% Sm3+-doped PKAMZF glass were evaluated using absorption spectra. Judd-Ofelt (JO) intensity analysis had been presented and JO parameters were evaluated for 1.0 mol% Sm3+-doped zinc potassium fluorophosphate glass. Radiative properties such as transition probabilities, branching ratios and radiative lifetime were estimated by using JO parameters. Stimulated emission cross-sections and effective bandwidths of each transition were obtained from the luminescence spectra. The experimental lifetime, quantum efficiency and donor-acceptor interaction parameters were also estimated using decay curves of 4G5/2 level of Sm3+ ions in the present glasses. The influence of Sm3+ ion concentrations on the luminescence intensity, lifetime and energy transfer parameters for PKAMZFSm glasses was investigated. The results obtained have been compared with the other Sm3+-doped glasses.

  11. 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.

  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. Angiopoietin-1 blocks neurotoxic zinc entry into cortical cells via PIP2 hydrolysis-mediated ion channel inhibition.

    PubMed

    Lim, Joon Seo; Koh, Gou Young; Koh, Jae-Young

    2015-09-01

    Excessive entry of zinc ions into the soma of neurons and glial cells results in extensive oxidative stress and necrosis of cortical cells, which underlies acute neuronal injury in cerebral ischemia and epileptic seizures. Here, we show that angiopoietin-1 (Ang1), a potent angiogenic ligand for the receptor tyrosine kinase Tie2 and integrins, inhibits the entry of zinc into primary mouse cortical cells and exerts a substantial protective effect against zinc-induced neurotoxicity. The neuroprotective effect of Ang1 was mediated by the integrin/focal adhesion kinase (FAK) signaling axis, as evidenced by the blocking effects of a pan-integrin inhibitory RGD peptide and PF-573228, a specific chemical inhibitor of FAK. Notably, blockade of zinc-permeable ion channels by Ang1 was attributable to phospholipase C-mediated hydrolysis of phosphatidylinositol 4,5-bisphosphate. Collectively, these data reveal a novel role of Ang1 in regulating the activity of zinc-permeable ion channels, and thereby protecting cortical cells against zinc-induced neurotoxicity.

  14. 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.

  15. Calcium ions rescue human lung epithelial cells from the toxicity of zinc oxide nanoparticles.

    PubMed

    Hanagata, Nobutaka; Morita, Hiromi

    2015-01-01

    Contradictory results have been reported for in vitro evaluations of whether zinc oxide nanoparticles (ZnO NPs) are cytotoxic. Though there have been reports of ZnO NPs cytotoxicity due to Zn ions released from the nanoparticles, there have also been reports concluding that Zn ions are not cytotoxic. This inconsistency is mostly attributed to the types of cells used. In this research, we investigated the difference in the level of ZnO NPs cytotoxicity due to culturing conditions. The sensitivity of human lung epithelial cells to ZnO NPs cytotoxicity differed depending on the dispersing medium, physiological state of the cells resulting from their growth stage, and composition of the medium. Further, with regard to the toxicity of ZnO NPs, NPs internalized into cells had a greater cytotoxic effect than Zn ions released from ZnO NPs. Instead of inducing cell death, ZnO NPs internalized into cells slowed the rate of cell proliferation. Furthermore, the cytotoxicity of ZnO NPs depended greatly on the concentration of calcium ions (Ca2+) in the medium. When the concentration of Ca2+ was low, the cytotoxicity of ZnO NPs increased markedly. However, the toxicity of ZnO NPs was mitigated by the addition of CaCl2 to the medium. Global gene expression analysis revealed that Ca2+ -induced upregulation of cell cycle functions could be attributable to the mitigation of ZnO NP toxicity by Ca2+.

  16. 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.

  17. Computational characterization of ketone-ketal transformations at the active site of matrix metalloproteinases.

    PubMed

    Khrenova, Maria G; Nemukhin, Alexander V; Savitsky, Alexander P

    2014-04-24

    We modeled the first steps of hydrolysis reactions of a natural oligopeptide substrate of matrix metalloproteinase MMP-2 as well as of a substrate analogue. In the latter, the scissile amide group is substituted by a ketomethylene group which can be transformed to the ketal group upon binding of this compound to the enzyme active site. According to our quantum mechanical-molecular mechanical (QM/MM) calculations, the reaction of the ketone-ketal transformation proceeds with a low energy barrier (3.4 kcal/mol) and a high equilibrium constant (10(4)). The reaction product with the ketal group formed directly at the active site of the enzyme works as an inhibitor that chelates the zinc ion. On the other hand, the oligopeptide mimetic retains molecular groups responsible for binding of this compound to the enzyme active site. This example illustrates a strategy to design MMP inhibitors in situ by using data on binding specificity of substrates to a particular type of MMP and details of the reaction mechanism. PMID:24684684

  18. Visualization of calcium and zinc ions in Saccharomyces cerevisiae cells treated with PEFs (pulse electric fields) by laser confocal microscopy.

    PubMed

    Urszula, Pankiewicz; Jerzy, Jamroz; Sujka, Monika; Kowalski, Radosław

    2015-12-01

    The aim of the present work was to visualize the areas of increased concentration of calcium and zinc ions inside Saccharomyces cerevisiae cells with the use of confocal microscopy and to make an attempt to asses semi-quantitatively their concentration within the limits of the cells. Semi-quantitative analysis revealed that fluorescence inside cells from control samples was three-times lower than that observed for cells from the sample enriched with calcium. Differences in distribution of fluorescence intensity between cells originated from the samples enriched with zinc and control samples were also observed. On the basis of the optical sections, the 3D reconstructions of ion-rich areas distribution in the cell were made. The obtained results showed that confocal microscopy is a useful technique for visualization of the areas in S. cerevisiae cells which contain higher amount of calcium and zinc and it may be also used for semi-quantitative analysis.

  19. Effects of extracellular zinc ion on the rate of oxygen consumption of rat brain mitochondria.

    PubMed

    Kukoyi, B I

    2006-01-01

    The inhibitory effect of extracellular zinc ion on the rate of oxygen consumption of rat brain mitochondria pre-incubated in 1.0 mMol Ca(2+)EDTA were determined. There was a significant increase [P < 0.01] in the rate of oxygen consumption in the rat brain mitochondria pre-incubated in 1.0 mMol Ca(2+)EDTA in a succinate initiated reaction. The reverse was the case when the concentration of Ca(2+)EDTA was increased to 10 mMol. A 20 microMol zinc-aspartate was found to have no inhibitory effect on the rate of oxygen consumption of the brain mitochondria pre-incubated with 1.0 mMol Ca(2+)EDTA when compared with the control that lacked 1.0 mMol Ca(2+)EDTA, however there was a significant decrease [P < 0.01] in the rate of oxygen consumption of the rat brain mitochondria in the control experiment.

  20. 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

  1. 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.

  2. Structural and luminescence properties of Sm3+ ions in zinc fluorophosphate glasses

    NASA Astrophysics Data System (ADS)

    Lim, Ki-Soo; Vijaya, N.; Kesavulu, C. R.; Jayasankar, C. K.

    2013-06-01

    Sm3+-doped zinc fluorophosphate (PKAZLFSm) glasses have been prepared by conventional melt quenching technique and are characterized through thermal, Raman, absorption, emission and decay rate analysis. The Judd-Ofelt (JO) theory has been used to derive the spectroscopic properties of Sm3+:PKAZLFSm glasses. The decay rates for the 4G5/2 level of Sm3+ ions have been measured and are found to be single exponential at lower concentration (⩽0.1 mol% Sm2O3) and turns into non-exponential at higher concentrations (⩾0.5 mol% Sm2O3) due to energy transfer through cross-relaxation. The experimental lifetimes for 4G5/2 level of Sm3+ ions are found to decrease from 3.2 to 0.5 ms when the concentration increased from 0.01 to 4.0 mol% Sm2O3 due to energy transfer among Sm3+ ions. In order to know the nature of the energy transfer mechanism, the non-exponential decay rates are well fitted to Inokuti-Hirayama model for S = 6, indicating that the energy transfer process is of dipole-dipole type. The results obtained for the 4G5/2 → 6H7/2 transition indicate that the Sm3+:PKAZLFSm10 glass can be very much useful for the development of visible lasers in the reddish orange spectral region.

  3. Spectroscopic and radiative properties of Sm3+ ions in zinc borophosphate glasses

    NASA Astrophysics Data System (ADS)

    Hima Bindu, S.; Rajavardhana Rao, T.; Linga Raju, Ch

    2015-06-01

    The paper reports on the preparation and characterization of Sm3+ doped zinc borophosphate (ZBP) glasses. The density was measured and the corresponding molar volume was evaluated. The present glass system was investigated by the XRD, optical absorption, photoluminescence, decay curves and FTIR analysis. The Judd-Ofelt theory has been used to evaluate the JO intensity parameters (Ω2,4,6) and calculated oscillator strengths (ƒcal). Using JO intensity parameters, various radiative parameters such as transition probability (AR), radiative lifetime (τR), measured lifetime (τm), calculated branching ratios (βR), measured branching ratios (βm) have been calculated for the excited 4G5/2 level. The nature of the decay curves of 4G5/2 level for different Sm3+ ion concentration in all ZBP glasses has been analyzed and the lifetimes are noticed to decrease with increase of concentration.

  4. 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

  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.

  7. Inhibitory kinetics of beta-N-acetyl-D-glucosaminidase from green crab (Scylla serrata) by zinc ion.

    PubMed

    Zhang, Ji-Ping; Hu, Yong-Hua; Wang, Qin; Wang, Wei; Wang, Ye; Yan, Jiang-Hua; Chen, Qing-Xi

    2010-08-11

    Heavy metal pollution such as chromium and zinc in the seawater has been increasing in recent years in the China Sea. Marine shellfish such as prawn and crab are sensitive to this pollution. Beta-N-acetyl-d-glucosaminidase (NAGase, EC 3.2.1.52) catalyzes the cleavage the oligomers of N-acetylglucosamine (NAG) into the monomer. In this study, taking p-nitrophenyl-N-acetyl-beta-d-glucosaminide (pNP-NAG) as substrate, the effects of Zn(2+) on NAGase from green crab ( Scylla serrata ) have been studied. The results showed that appropriate concentrations of zinc could lead to reversible inhibition on the enzyme, and the IC(50) has been estimated to be 0.5 +/- 0.012 mM. Furthermore, it has been shown that Zn(2+) could reduce the thermal stability of NAGase depending on the concentration of Zn(2+). The inhibitory kinetics of zinc on the enzyme in the appropriate concentrations has been studied using the kinetic method of substrate reaction. The inhibition model has been set up, and the rate constants have been determined. The results showed that Zn(2+) was a mixed-type inhibitor of NAGase and that it could combine at the free enzyme and the enzyme-substrate active sites.

  8. 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.

  9. A conveniently prepared and hypersensitized small molecular fluorescent probe: Rapidly detecting free zinc ion in HepG2 cells and Arabidopsis.

    PubMed

    Gan, Xiaoping; Sun, Ping; Li, Hong; Tian, Xiaohe; Zhang, Baowei; Wu, Jieying; Tian, Yupeng; Zhou, Hongping

    2016-12-15

    In this paper, we reported a conveniently prepared fluorescent probe for zinc ions detection, which constructed by the condensation reaction between p-(benzothiazolyl)aniline with 4, 4- diethylaminesalicylaldehyde. The sensing ability of the probe toward zinc ions in vitro was tested by a series of UV-Vis and fluorescence spectroscopy studies, which showed that the probe possessed high sensitivity with a detection limit of 5.8nM and a rapid response time of 10s. We also carried out fluorescent bio-imaging of the probe for zinc ions in human liver hepatocellular carcinoma cells (HepG2), which showed that the probe could be utilized to detect the intracellular endogenous zinc ions visually without introducing external zinc sources. Meanwhile, co-staining experiment with organelle selective trackers was performed to illustrate that the probe could locate at endoplasmic reticulum. Finally, we successfully used it as a zinc ion developer in plant tissue, which clearly demonstrated the distribution of zinc ions in the growth stage of plant tissue. PMID:27414244

  10. 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

  11. 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

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

    PubMed

    Kumar, Yogesh; Herrera-Zaldivar, Manuel; Olive-Méndez, Sion Federico; Singh, Fouran; Mathew, Xavier; Agarwal, Vivechana

    2012-07-02

    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.

  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. 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.

  15. 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

  16. Competition of zinc ion for the [2Fe-2S] cluster binding site in the diabetes drug target protein mitoNEET.

    PubMed

    Tan, Guoqiang; Landry, Aaron P; Dai, Ruili; Wang, Li; Lu, Jianxin; Ding, Huangen

    2012-12-01

    Human mitochondrial protein mitoNEET is a novel target of type II diabetes drug pioglitazone, and contains a redox active [2Fe-2S] cluster that is hosted by a unique ligand arrangement of three cysteine and one histidine residues. Here we report that zinc ion can compete for the [2Fe-2S] cluster binding site in human mitoNEET and potentially modulate the physiological function of mitoNEET. When recombinant mitoNEET is expressed in Escherichia coli cells grown in M9 minimal media, purified mitoNEET contains very little or no iron-sulfur clusters. Addition of exogenous iron or zinc ion in the media produces mitoNEET bound with a [2Fe-2S] cluster or zinc, respectively. Mutations of the amino acid residues that hosting the [2Fe-2S] cluster in mitoNEET diminish the zinc binding activity, indicating that zinc ion and the [2Fe-2S] cluster may share the same binding site in mitoNEET. Finally, excess zinc ion effectively inhibits the [2Fe-2S] cluster assembly in mitoNEET in E. coli cells, suggesting that zinc ion may impede the function of mitoNEET by blocking the [2Fe-2S] cluster assembly in the protein.

  17. Synthesis of a highly Zn(2+)-selective cyanine-based probe and its use for tracing endogenous zinc ions in cells and organisms.

    PubMed

    Guo, Zhiqian; Kim, Gun-Hee; Yoon, Juyoung; Shin, Injae

    2014-01-01

    The zinc ion has a key role in a variety of physiological and pathological processes. As a consequence, the development of sensitive and reliable methods to monitor the presence of zinc ions in cells and organisms is of great importance to biological research and biomedical applications. This protocol describes detailed procedures for the five-stage synthesis of a zinc ion-selective, cyanine-based fluorescent probe, CTMPA, from 2,6-bis(hydroxymethyl)pyridine. In addition, we describe its applications in the detection of Zn(2+) released during apoptosis in cells and endogenous Zn(2+) in living zebrafish. Notably, the use of CTMPA enabled our research group to monitor for the first time the presence of zinc ions in neuromasts of zebrafish via fluorescence. The approximate time frame for the synthesis of CTMPA is 4-5 d, and for its use in bioimaging is 8-10 h for cells and 2 h for zebrafish.

  18. 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.

  19. 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.

  20. 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

  1. Reactivity of metallothioneins of frog Rana ridibunda treated by copper and zinc ions.

    PubMed

    Falfushynska, H I; Romanchuk, L D; Stoliar, O B

    2010-01-01

    The metal-buffering and stress proteins metallothioneins (MTs) of frog are characterised by unusually high content of copper as for vertebrate animals and instability that was shown in our previous studies. They easily lost copper and especially zinc under unfavourable conditions. The aim of this study was to examine the reactivity of SH groups in the MTs from the liver of frog Rana ridibunda after the effect of Cu2+ (0.01 mg/l) and Zn2+ (0.1 mg/l) ions on the organism during 14 days. The alpha- and beta-domains of MTs with molecular weights of about 4 kDa were separated by the size-exclusion chromatography on Sephadex G-50. Unlike higher vertebrates, frogs demonstrated higher reactivity of alpha-domain than beta-domain with the Ellman's reagent (DTNB). The signs of partial oxidations in beta-domain included the creation of by-products with molecular weight about 12 kDa, low reactivity of SH-groups, and typical of -S-S-bonds peculiarities of UV-spectra. The effect of both metal ions on frog provoked the elevation of SH-groups reactivity in a-domain with the appearance of by-product with molecular weight of 16 kDa and its reduction in beta-domain. The incubation of MTs of control animals with 0.5 and 5.0 mM of H2O2 did not affect its chromatographic characteristics. In the frogs loaded by Cu2+ and Zn2+ the effect of 5.0 mM H2O2 on MTs provoked the release of 4 kDa product. So the alpha-domain is responsible for the increased release of metals from injured MTs in frogs, whereas extremely high oxidizability of beta-domain makes its participation in the exchange of metals elusive and provokes the aggregation of MTs. PMID:21323122

  2. Zinc ions block H⁺/OH⁻ channels in Chara australis.

    PubMed

    Al Khazaaly, Sabah; Beilby, Mary J

    2012-08-01

    Chara australis cells exposed to media of pH 10 and above exhibit high conductance, arising from the opening of H⁺/OH⁻ channels in the plasma membrane. This high conductance can be totally inhibited by 1.0 mm ZnCl₂ and restored by 0.5 mm 2-mercaptoethanol (ME). Important for carbon fixation, H⁺/OH⁻ channels play a key role in cell pH banding. Banding was also shown to be abolished by 1.0 mm ZnCl₂ and restored in some cells by ME. The proton pump is also involved in banding, but was little affected by ZnCl₂ over the periods needed for the inhibition of H⁺/OH⁻ channels. Previously, we postulated that H⁺/OH⁻ channels open transiently at the onset of saline stress in salt-sensitive C. australis, causing membrane potential difference (PD) noise; and remain open in latter stages of saline stress, contributing to cell deterioration. ZnCl₂ totally inhibited the saline noise and the upwardly concave I/V characteristics associated with the putative H⁺/OH⁻ currents. Again, ME reversed both these effects. We discuss the mode of action of zinc ions and ME with reference to animal voltage-gated H⁺ channels and water channels.

  3. A two-dimensional coordination compound as a zinc ion selective luminescent probe for biological applications.

    PubMed

    Dhara, Koushik; Karan, Santanu; Ratha, Jagnyeswar; Roy, Partha; Chandra, Goutam; Manassero, Mario; Mallik, Biswanath; Banerjee, Pradyot

    2007-09-01

    A 2D coordination compound {[Cu2(HL)(N3)]ClO4}infinity (1; H3L = 2,6-bis(hydroxyethyliminoethyl)-4-methyl phenol) was synthesized and characterized by single-crystal X-ray diffraction to be a polymer in the crystalline state. Each [Cu2(HL)(N3)]+ species is connected to its adjacent unit by a bridging alkoxide oxygen atom of the ligand to form a helical propagation along the crystallographic a axis. The adjacent helical frameworks are connected by a ligand alcoholic oxygen atom along the crystallographic b axis to produce pleated 2D sheets. In solution, 1 dissociates into [Cu2(HL)2(H3L)]2H2O (2); the monomer displays high selectivity for Zn2+ and can be used in HEPES buffer (pH 7.4) as a zinc ion selective luminescent probe for biological application. The system shows a nearly 19-fold Zn2+-selective chelation-enhanced fluorescence response in the working buffer. Application of 2 to cultured living cells (B16F10 mouse melanoma and A375 human melanoma) and rat hippocampal slices was also studied by fluorescence microscopy.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. [Obtaining of bacterial bioluminescent strain Protobacterium phosphoreum B7071 (lux+) for the determination of zinc ion concentration].

    PubMed

    Gruzina, T G; Dybkova, S N; Chekhovskaia, T P; Vember, V V; Zadorozhniaia, A M; Ul'berg, Z R

    2006-01-01

    The transconjugate containing hybrid plasmid (Te(R)Zn(R)lux+) was obtained using the conjugation method on Pseudomonasfragi T2(5) (Te(R)ZnR) strain and bioluminescent strain Protobacterium phosphoreum B7071 (lux+). The expression regulation of lux-genes on the obtained plasmid is carried out by promotor-operational area conjointly with zinc resistance genes. The cells of the obtained genetically modified bacteria have the ability to specific induced luminescence, which is a respond to zinc ions' presence in the measuring medium. It was shown that the cells' bioluminescence intensity of trans-conjugate is linearly dependent on zinc ions' concentration within the range of 1-100 microM, that provides the opportunity of using biosensor as a strain for qualitative and quantitative detection of the metal. The low sensitivity limit of this method is 0.5 microM for the metal. Besides having high sensitivity, the developed lux-biosensor is highly specified. PMID:17147278

  10. Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins.

    PubMed

    Panina, Ekaterina M; Mironov, Andrey A; Gelfand, Mikhail S

    2003-08-19

    Zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. Thus its transport is regulated by zinc repressors ZUR of proteobacteria and Gram-positive bacteria from the Bacillus group and AdcR of bacteria from the Streptococcus group. Comparative computational analysis allowed us to identify binding signals of ZUR repressors GAAATGTTATANTATAACATTTC for gamma-proteobacteria, GTAATGTAATAACATTAC for the Agrobacterium group, GATATGTTATAACATATC for the Rhododoccus group, TAAATCGTAATNATTACGATTTA for Gram-positive bacteria, and TTAACYRGTTAA of the streptococcal AdcR repressor. In addition to known transporters and their paralogs, zinc regulons were predicted to contain a candidate component of the ATP binding cassette, zinT (b1995 in Escherichia coli and yrpE in Bacillus subtilis). Candidate AdcR-binding sites were identified upstream of genes encoding pneumococcal histidine triad (PHT) proteins from a number of pathogenic streptococci. Protein functional analysis of this family suggests that PHT proteins are involved in the invasion process. Finally, repression by zinc was predicted for genes encoding a variety of paralogs of ribosomal proteins. The original copies of all these proteins contain zinc-ribbon motifs and thus likely bind zinc, whereas these motifs are destroyed in zinc-regulated paralogs. We suggest that the induction of these paralogs in conditions of zinc starvation leads to their incorporation in a fraction of ribosomes instead of the original ribosomal proteins; the latter are then degraded with subsequent release of some zinc for the utilization by other proteins. Thus we predict a mechanism for maintaining zinc availability for essential enzymes. PMID:12904577

  11. Comparison on the molecular response profiles between nano zinc oxide (ZnO) particles and free zinc ion using a genome-wide toxicogenomics approach.

    PubMed

    Su, Guanyong; Zhang, Xiaowei; Giesy, John P; Musarrat, Javed; Saquib, Quaiser; Alkhedhairy, Abdulaziz A; Yu, Hongxia

    2015-11-01

    Increasing production and applications of nano zinc oxide particles (nano-ZnO) enhances the probability of its exposure in occupational and environmental settings, but toxicity studies are still limited. Taking the free Zn ion (Zn(2+)) as a control, cytotoxicity of a commercially available nano-ZnO was assessed with a 6-h exposure in Escherichia coli (E. coli). The fitted dose-cytotoxicity curve for ZnCl2 was significantly sharper than that from nano-ZnO. Then, a genome-wide gene expression profile following exposure to nano-ZnO was conducted by use of a live cell reporter assay system with library of 1820 modified green fluorescent protein (GFP)-expressing promoter reporter vectors constructed from E. coli K12 strains, which resulted in 387 significantly altered genes in bacterial (p < 0.001). These altered genes were enriched into ten biological processing and two cell components (p < 0.05) terms through statistical hypergeometric testing, strongly suggesting that exposure to nano-ZnO would result a great disturbance on the functional gene product synthesis processing, such as translation, gene expression, RNA modification, and structural constituent of ribosome. The pattern of expression of 37 genes altered by nano-ZnO (fold change>2) was different from the profile following exposure to 6 mg/L of free zinc ion. The result indicates that these two Zn forms might cause toxicity to bacterial in different modes of action. Our results underscore the importance of understanding the adverse effects elicited by nano-ZnO after entering aquatic environment. PMID:25940466

  12. Comparison on the molecular response profiles between nano zinc oxide (ZnO) particles and free zinc ion using a genome-wide toxicogenomics approach.

    PubMed

    Su, Guanyong; Zhang, Xiaowei; Giesy, John P; Musarrat, Javed; Saquib, Quaiser; Alkhedhairy, Abdulaziz A; Yu, Hongxia

    2015-11-01

    Increasing production and applications of nano zinc oxide particles (nano-ZnO) enhances the probability of its exposure in occupational and environmental settings, but toxicity studies are still limited. Taking the free Zn ion (Zn(2+)) as a control, cytotoxicity of a commercially available nano-ZnO was assessed with a 6-h exposure in Escherichia coli (E. coli). The fitted dose-cytotoxicity curve for ZnCl2 was significantly sharper than that from nano-ZnO. Then, a genome-wide gene expression profile following exposure to nano-ZnO was conducted by use of a live cell reporter assay system with library of 1820 modified green fluorescent protein (GFP)-expressing promoter reporter vectors constructed from E. coli K12 strains, which resulted in 387 significantly altered genes in bacterial (p < 0.001). These altered genes were enriched into ten biological processing and two cell components (p < 0.05) terms through statistical hypergeometric testing, strongly suggesting that exposure to nano-ZnO would result a great disturbance on the functional gene product synthesis processing, such as translation, gene expression, RNA modification, and structural constituent of ribosome. The pattern of expression of 37 genes altered by nano-ZnO (fold change>2) was different from the profile following exposure to 6 mg/L of free zinc ion. The result indicates that these two Zn forms might cause toxicity to bacterial in different modes of action. Our results underscore the importance of understanding the adverse effects elicited by nano-ZnO after entering aquatic environment.

  13. 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.

  14. Evaluation of layered zinc hydroxide nitrate and zinc/nickel double hydroxide salts in the removal of chromate ions from solutions

    NASA Astrophysics Data System (ADS)

    de Oliveira, Henrique Bortolaz; Wypych, Fernando

    2016-11-01

    Layered zinc hydroxide nitrate (ZnHN) and Zn/Ni layered double hydroxide salts were synthesized and used to remove chromate ions from solutions at pH 8.0. The materials were characterized by many instrumental techniques before and after chromate ion removal. ZnHN decomposed after contact with the chromate solution, whereas the layered structure of Zn/Ni hydroxide nitrate (Zn/NiHN) and Zn/Ni hydroxide acetate (Zn/NiHA) remained their layers intact after the topotactic anionic exchange reaction, only changing the basal distances. ZnHN, Zn/NiHN, and Zn/NiHA removed 210.1, 144.8, and 170.1 mg of CrO42-/g of material, respectively. Although the removal values obtained for Zn/NiHN and Zn/NiHA were smaller than the values predicted for the ideal formulas of the solids (194.3 and 192.4 mg of CrO42-/g of material, respectively), the measured capacities were higher than the values achieved with many materials reported in the literature. Kinetic experiments showed the removal reaction was fast. To facilitate the solid/liquid separation process after chromium removal, Zn/Ni layered double hydroxide salts with magnetic supports were also synthesized, and their ability to remove chromate was evaluated.

  15. 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.

  16. 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

  17. Dopamine-assisted one-pot synthesis of zinc ferrite-embedded porous carbon nanospheres for ultrafast and stable lithium ion batteries.

    PubMed

    Yao, Xiayin; Zhao, Chenyang; Kong, Junhua; Wu, Huiqing; Zhou, Dan; Lu, Xuehong

    2014-12-01

    Polydopamine-derived carbon (C-PDA) nanospheres embedded with zinc ferrite (ZnFe2O4) are synthesized by in situ polymerization of dopamine with zinc and iron species followed by carbonization. The composite nanospheres contain ZnFe2O4 nanoparticles ∼8 nm in size well dispersed in porous C-PDA. The unique structure and morphology endow the nanospheres with excellent rate capability and cycling stability for use as anodes in lithium-ion batteries.

  18. 68Zn isotope exchange experiments reveal an unusual kinetic lability of the metal ions in the di-zinc form of IMP-1 metallo-beta-lactamase.

    PubMed

    Siemann, Stefan; Badiei, Hamid R; Karanassios, Vassili; Viswanatha, Thammaiah; Dmitrienko, Gary I

    2006-02-01

    The apparently paradoxical behaviour of facile exchange (kinetic lability) of tightly bound (thermodynamic stability) zinc ions in the enzyme IMP-1 metallo-beta-lactamase with Zn-68 and cadmium ions, as indicated by in-torch vaporization inductively-coupled plasma mass spectrometry (ITV-ICP-MS) and electrospray-ionization mass spectrometry (ESI-MS), is consistent with the involvement of a third metal ion in promoting Lewis acid/base type exchange processes.

  19. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes.

    PubMed

    Jain, Tarun; Jayaram, B

    2007-06-01

    Zinc is one of the most important metal ions found in proteins performing specific functions associated with life processes. Coordination geometry of the zinc ion in the active site of the metalloprotein-ligand complexes poses a challenge in determining ligand binding affinities accurately in structure-based drug design. We report here an all atom force field based computational protocol for estimating rapidly the binding affinities of zinc containing metalloprotein-ligand complexes, considering electrostatics, van der Waals, hydrophobicity, and loss in conformational entropy of protein side chains upon ligand binding along with a nonbonded approach to model the interactions of the zinc ion with all the other atoms of the complex. We examined the sensitivity of the binding affinity predictions to the choice of Lennard-Jones parameters, partial atomic charges, and dielectric treatments adopted for system preparation and scoring. The highest correlation obtained was R2 = 0.77 (r = 0.88) for the predicted binding affinity against the experiment on a heterogenous dataset of 90 zinc containing metalloprotein-ligand complexes consisting of five unique protein targets. Model validation and parameter analysis studies underscore the robustness and predictive ability of the scoring function. The high correlation obtained suggests the potential applicability of the methodology in designing novel ligands for zinc-metalloproteins. The scoring function has been web enabled for free access at www.scfbio-iitd.res.in/software/drugdesign/bapplz.jsp as BAPPL-Z server (Binding Affinity Prediction of Protein-Ligand complexes containing Zinc metal ions).

  20. 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

  1. Accumulation of manganese superoxide dismutase under metal-depleted conditions: proposed role for zinc ions in cellular redox balance.

    PubMed Central

    Otsu, Kaoru; Ikeda, Yoshitaka; Fujii, Junichi

    2004-01-01

    A diet low in copper results in increased levels of MnSOD (manganese superoxide dismutase), a critical antioxidative enzyme conferring protection against oxidative stress, in rat liver mitochondria. The mechanism for this was investigated using cultured HepG2 cells, a human hepatocellular carcinoma-derived line. MnSOD activity increased 5-7-fold during incubation in a medium supplemented with metal-depleted fetal bovine serum, with a corresponding elevation of its mRNA levels. Metal depletion also decreased CuZnSOD and glutathione peroxidase levels to approx. 70-80% of baseline. When zinc ions were added to the medium at micromolar levels, MnSOD accumulation was suppressed; however, copper ions had essentially no effect on MnSOD expression. Since the intracellular redox status was shifted to a more oxidized state by metal depletion, we examined the DNA-binding activity of NF-kappaB (nuclear factor-kappaB), an oxidative stress-sensitive transactivating factor that plays a primary role in MnSOD induction. A gel shift assay indicated that the DNA-binding activity of NF-kappaB was increased in cells maintained in metal-depleted culture, suggesting the involvement of the transactivating function of NF-kappaB in this induction. This was further supported by the observation that curcumin suppressed both the DNA-binding activity of NF-kappaB and the induction of MnSOD mRNA in cells cultivated under metal-depleted conditions. These results suggest that the level of zinc, rather than copper, is a critical regulatory factor in MnSOD expression. It is possible that a deficiency of zinc in the low-copper diet may be primarily involved in MnSOD induction. PMID:14531733

  2. 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

  3. 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.

  4. Chelators for investigating zinc metalloneurochemistry.

    PubMed

    Radford, Robert J; Lippard, Stephen J

    2013-04-01

    The physiology and pathology of mobile zinc signaling has become an important topic in metalloneurochemistry. To study the action of mobile zinc effectively, specialized tools are required that probe the temporal and positional changes of zinc ions within live tissue and cells. In the present article we describe the design and implementation of selective zinc chelators as antagonists to interrogate the function of mobile zinc, with an emphasis on the pools of vesicular zinc in the terminals of hippocampal mossy fiber buttons.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  11. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  12. Electroanalytical investigation on the interaction between 6-mercaptopurine and zinc(II), lead(II), and cadmium(II) ions in nonaqueous solvents.

    PubMed

    Cinquantini, A; Cini, R; Zanello, P

    1980-04-01

    Different electroanalytical techniques have been employed in the study of the interaction between 6-mercaptopurine and zinc(II), lead(II), and cadmium(II) ions in ethanol, dimethylformamide, and dimethylsulfoxide. The stoichiometry of the formed complexes was determined as well as their instability constants. The kinetic parameters of the electrode processes have been also evaluated.

  13. Inhibition and active-site modelling of prolidase.

    PubMed

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  14. Integrated and Passive 1,2,3-Triazolyl Groups in Fluorescent Indicators for Zinc(II) Ions – Thermodynamic and Kinetic Evaluations

    PubMed Central

    Simmons, J. Tyler; Allen, John R.; Morris, Deborah R.; Clark, Ronald J.; Levenson, Cathy W.; Davidson, Michael W.; Zhu, Lei

    2013-01-01

    In addition to being a covalent linker in molecular conjugation chemistry, the function of a 1,2,3-triazolyl moiety resulting from the copper(I)-catalyzed azide-alkyne cycloaddition reaction as a ligand for metal ions is receiving considerable attention. In this work, we characterize the thermodynamic and kinetic effects of incorporating a 1,2,3-triazolyl group in a multidentate ligand scaffold on metal coordination in the context of fluorescent zinc(II) indicator development. Ligands L14, BrL14, and FL14 (1,4-isomers) contain the 1,4- disubstituted-1,2,3-triazolyl group that is capable of binding with zinc(II) in conjunction with a di(2-picolylamino) (DPA) moiety within a multidentate ligand scaffold. The 1,2,3-triazolyl in the 1,4-isomers is therefore “integrated” in chelation. The 1,5-isomers L15, BrL15, and FL15 contain 1,2,3-triazolyls that are excluded from participating in zinc(II) coordination. These 1,2,3- triazolyls are “passive linkers”. Zinc(II) complexes of 2:1 (ligand/metal) stoichiometry are identified in solution using 1H NMR spectroscopy and isothermal titration calorimetry (ITC), and in one case, characterized in the solid state. The 1:1 ligand/zinc(II) affinity ratio of L14 over L15, which is attributed to the affinity enhancement of a 1,2,3-triazolyl group to zinc(II) over that of the solvent acetonitrile, is quantified at 18 (−1.7 kcal/mol at 298 K) using an ITC experiment. Fluorescent ligands FL14 and FL15 are evaluated for their potential in zinc(II) sensing applications under pH neutral aqueous conditions. The 1,4-isomer FL14 binds zinc(II) both stronger and faster than the 1,5-isomer FL15. Visualization of free zinc(II) ion distribution in live HeLa cells is achieved using both FL14 and FL15. The superiority of FL14 in staining endogenous zinc(II) ions in live rat hippocampal slices is evident. In summation, this work is a fundamental study of 1,2,3-triazole coordination chemistry, with a demonstration of its utility in developing

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Structural and optical characteristics of Eu3+ ions in sodium-lead-zinc-lithium-borate glass system

    NASA Astrophysics Data System (ADS)

    Rajagukguk, J.; Kaewkhao, J.; Djamal, M.; Hidayat, R.; Suprijadi; Ruangtaweep, Y.

    2016-10-01

    Structural and optical properties of Eu3+-doped sodium-lead-zinc-lithium-borate glasses (65-x)B2O3sbnd 15Na2Osbnd 10PbOsbnd 5ZnOsbnd 5Li2Osbnd xEu2O3 (where x = 0, 0.05, 0.1, 0.5, 1.0, 2.0 and 4.0) have been measured and analyzed by varying the Eu3+ ion concentrations. The physical parameters such as polaron radius, field strength and inter nuclear distance have been determined from measurements of densities and refractive indices. The structural properties of the prepared borate glasses were analyzed based on X-ray diffraction (XRD) and FTIR instruments. The diffraction spectra show no characteristic peaks in these glasses, which indicates the amorphous nature of the glasses. The infrared spectrum of the Eu3+-doped sodium-lead-zinc-lithium-borate glass systems show three disparate regions for active absorption band around 830-860 cm-1, 1020-1040 cm-1 and 1170-1180 cm-1. The electronic transitions in the UV-vis and NIR regions are assigned to the 7F0 → 5D4, 7F0 → 5G2, 7F0 → 5L6, 7F0 → 5D3, 7F0 → 5D2, 7F0 → 5D1, 7F0 → 5D07F1 → 5D07F0 → 7F6 and 7F1 → 7F6 levels centered at 362 nm, 380 nm, 395 nm, 414 nm, 465 nm, 533 nm, 583 nm, 590 nm 2092 nm and 2202 nm respectively. Five transition bands of luminescence spectra have been observed by using an excited wavelength of 395 nm. The luminescence intensity ratio (R) of 5D0 → 7F2 (electric dipole) transition to 5D0 → 7F1 (magnetic dipole) transition has been determined to obtain the strength of the covalent/ionic bond between the Eu3+ ions and the surrounding ligands. Radiative life time and emission color of the glasses were estimated and compared with other literature data by varying Eu3+ concentrations. The experimental lifetime of the 5D0 level was found to increase with increasing Eu3+ ion content, suggesting higher non-radiative energy transfer among Eu3+ ions in the glasses.

  20. 5-Arylvinyl-2,2′-bipyridyls: Bright “push–pull” dyes as components in fluorescent indicators for zinc ions

    PubMed Central

    Zhu, Lei; Younes, Ali H.; Yuan, Zhao; Clark, Ronald J.

    2015-01-01

    This article reviews the zinc(II)-dependent photophysical properties of arylvinylbipyridines (AVBs), a class of fluoroionophores in which 2,2′-bipyridyl and an aryl moiety are electronically conjugated. Zinc(II) binding of an AVB may lead to an emission bathochromic shift of the fluoroionophore without diminishing its fluorescence quantum yield. This observation can be explained using the excited state model of electron donor–π bridge–electron acceptor “push–pull” fluorophores, in which the bipy moiety acts as an electron acceptor, and zinc(II)-coordination strengthens its electron affinity. The spectral sensitivity of bipy-containing fluoroionophores, such as AVBs, to zinc(II) can be exploited to prepare fluorescent indicators for this ion. In several cases, AVB moieties are incorporated in fluorescent heteroditopic ligands, so that the variation of zinc(II) concentration over a relatively large range can be correlated to fluorescence changes in either intensity or color. AVB fluoroionophores are also used to introduce an intramolecular Förster resonance energy transfer (FRET) strategy for creating zinc(II) indicators with high photostability and a narrow emission band, two desired characteristics of dyes used in fluorescence microscopy. PMID:26190906

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Thermodynamics of zinc binding to hepatitis C virus NS3 protease: a folding by binding event.

    PubMed

    Abian, Olga; Neira, Jose Luis; Velazquez-Campoy, Adrian

    2009-11-15

    The hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease is responsible for the processing of the non-structural region of the viral precursor polyprotein in infected hepatic cells. HCV NS3 is a zinc-dependent serine protease. The zinc ion, which is bound far away from the active site and considered to have a structural role, is essential for the structural integrity of the protein; furthermore, the ion is required for the hydrolytic activity. Consequently, the NS3 zinc binding site has been considered for a long time as a possible target for drug discovery. As a first step towards this goal, the energetics of the NS3-zinc interaction and its effect on the NS3 conformation must be established and discussed. The thermodynamic characterization of zinc binding to NS3 protease by isothermal titration calorimetry and spectroscopy is presented here. Spectroscopic and calorimetric results suggest that a considerable conformational change in the protein is coupled to zinc binding. The energetics of the conformational change is comparable to that of the folding of a protein of similar size. Therefore, zinc binding to NS3 protease can be considered as a "folding by binding" event.

  9. 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

  10. 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

  11. Bioavailability of cadmium and zinc to the common carp, Cyprinus carpio, in complexing environments: A test for the validity of the free ion activity model

    SciTech Connect

    Ginneken, L. Van; Chowdhury, M.J.; Blust, R.

    1999-10-01

    The uptake of cadmium and zinc by the common carp, Cyprinus carpio, was studied in chemically defined freshwater in the presence of different organic ligands (i.e., citrate, glycine, histidine, ethylenediaminetetraacetic acid, and nitrilotriacetic acid). In most cases, metal complexation decreased Cd and Zn uptake by reducing the free Cd and Zn ion activity. However, Cd and Zn uptake did not increase linearly with the free Cd and Zn ion activity in the solution. A good fit to the data was obtained when the observations were fitted to a Michaelis-Menten-like model for carrier-mediated transport of the metal ions across the biological interface. In addition, the uptake of Cd in the presence of citrate, glycine, and histidine was markedly higher than expected on the basis of the free Cd ion activity. It was concluded that cadmium complexes of these low molecular weight, hydrophilic ligands contributed to the Cd bioavailability, probably by direct uptake of these complexes. Zinc uptake in the presence of the complexing agents could be predicted on the basis of the ambient free Zn ion activity, although uptake in the presence of citrate was lower than expected on the basis of the free Zn ion activity. These results provide a challenging test for the free ion activity model.

  12. 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

  13. Sorbitol dehydrogenase is a zinc enzyme.

    PubMed Central

    Jeffery, J; Chesters, J; Mills, C; Sadler, P J; Jörnvall, H

    1984-01-01

    Evidence is given that tetrameric sorbitol dehydrogenase from sheep liver contains one zinc atom per subunit, most probably located at the active site, and no other specifically bound zinc or iron atom. In alcohol dehydrogenases that are structurally related to sorbitol dehydrogenase, more than one zinc atom per subunit can complicate investigations of zinc atom function. Therefore, sorbitol dehydrogenase will be particularly valuable for defining the precise roles of zinc in alcohol and polyol dehydrogenases, and for establishing correlations of structure and function with other important zinc-containing proteins. PMID:6370679

  14. Evidence for surface Ag + complexes as the SERS-active sites on Ag electrodes

    NASA Astrophysics Data System (ADS)

    Watanabe, T.; Kawanami, O.; Honda, K.; Pettinger, B.

    1983-12-01

    Evidence is given that SERS-active sites at Ag electrodes are associated with Ag + ions, forming sparingly soluble surface complexes with ligands such as pyridine molecules and halide ions. Such surface Ag + complexes contribute a factor of >800 to the overall (10 7-fold) enhancement, possibly via a resonance Raman effect.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. [Unification of methods for determining the trace quantities of lead, zinc, sodium and potassium ions in the assessment of drinking water adn transfusion fluid quality].

    PubMed

    Popkov, V A; Golovina, N V; Evgrafov, A A

    2001-01-01

    The results of long-term studies made by the Department of General Chemistry, I. M. Sechenov Moscow Medical Academy, that deals with unification of methods for determining some ions of metals (lead, zinc, sodium, and potassium) in the assessment of the quality of drinking water and transfusion fluids are summarized. A procedure was developed to determine the trace impurities of zinc, lead, and silver by atomic absorption spectrometry (AAS) by using sorption concentration. C-80-2-aminothiazole, a new sorbent synthesized at the Research Institute of Polymers, was used to detect these ions in the drinking water. With regards to the chosen optimal conditions, drinking water samples were analyzed via their direct spraying in the air-acetylene flame. The prior sorption concentration determined drinking water zinc and lead ions in the concentrations equal to or less than their permissible dose concentrations. The studies indicated that the used methods to determine the trace quantities of metals in the drinking water and aqueous solutions show a high sensitivity, rapidity, simplicity of sample preparation.

  1. Copper and Zinc Ions Specifically Promote Nonamyloid Aggregation of the Highly Stable Human γ-D Crystallin.

    PubMed

    Quintanar, Liliana; Domínguez-Calva, José A; Serebryany, Eugene; Rivillas-Acevedo, Lina; Haase-Pettingell, Cameron; Amero, Carlos; King, Jonathan A

    2016-01-15

    Cataract is the leading cause of blindness in the world. It results from aggregation of eye lens proteins into high-molecular-weight complexes, causing light scattering and lens opacity. Copper and zinc concentrations in cataractous lens are increased significantly relative to a healthy lens, and a variety of experimental and epidemiological studies implicate metals as potential etiological agents for cataract. The natively monomeric, β-sheet rich human γD (HγD) crystallin is one of the more abundant proteins in the core of the lens. It is also one of the most thermodynamically stable proteins in the human body. Surprisingly, we found that both Cu(II) and Zn(II) ions induced rapid, nonamyloid aggregation of HγD, forming high-molecular-weight light-scattering aggregates. Unlike Zn(II), Cu(II) also substantially decreased the thermal stability of HγD and promoted the formation of disulfide-bridged dimers, suggesting distinct aggregation mechanisms. In both cases, however, metal-induced aggregation depended strongly on temperature and was suppressed by the human lens chaperone αB-crystallin (HαB), implicating partially folded intermediates in the aggregation process. Consistently, distinct site-specific interactions of Cu(II) and Zn(II) ions with the protein and conformational changes in specific hinge regions were identified by nuclear magnetic resonance. This study provides insights into the mechanisms of metal-induced aggregation of one of the more stable proteins in the human body, and it reveals a novel and unexplored bioinorganic facet of cataract disease. PMID:26579725

  2. Revisiting zinc coordination in human carbonic anhydrase II.

    PubMed

    Song, He; Wilson, David L; Farquhar, Erik R; Lewis, Edwin A; Emerson, Joseph P

    2012-10-15

    Carbonic anhydrase (CA, general abbreviation for human carbonic anhydrase II) is a well-studied, zinc-dependent metalloenzyme that catalyzes hydrolysis of carbon dioxide to the bicarbonate ion. The apo-form of CA (apoCA, CA where Zn(2+) ion has been removed) is relatively easy to generate, and reconstitution of the human erythrocyte CA has been initially investigated. In the past, these studies have continually relied on equilibrium dialysis measurements to ascertain an extremely strong association constant (K(a) ≈ 1.2 × 10(12)) for Zn(2+). However, new reactivity data and isothermal titration calorimetry (ITC) data reported herein call that number into question. As shown in the ITC experiments, the catalytic site binds a stoichiometric quantity of Zn(2+) with a strong equilibrium constant (K(a) ≈ 2 × 10(9)) that is 3 orders of magnitude lower than the previously established value. Thermodynamic parameters associated with Zn(2+) binding to apoCA are unraveled from a series of complex equilibria associated with the in vitro metal binding event. This in-depth analysis adds clarity to the complex ion chemistry associated with zinc binding to carbonic anhydrase and validates thermochemical methods that accurately measure association constants and thermodynamic parameters for complex-ion and coordination chemistry observed in vitro. Additionally, the zinc sites in both the as-isolated and the reconstituted ZnCA (active CA containing a mononuclear Zn(2+) center) were probed using X-ray absorption spectroscopy. Both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses indicate the zinc center in the reconstituted carbonic anhydrase is nearly identical to that of the as-isolated protein and confirm the notion that the metal binding data reported herein is the reconstitution of the zinc active site of human CA II. PMID:23030313

  3. 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.

  4. Carboxylated dithiafulvenes and tetrathiafulvalene vinylogues: synthesis, electronic properties, and complexation with zinc ions

    PubMed Central

    Wang, Yunfei

    2015-01-01

    Summary A class of carboxyl and carboxylate ester-substituted dithiafulvene (DTF) derivatives and tetrathiafulvalene vinylogues (TTFVs) has been synthesized and their electronic and electrochemical redox properties were characterized by UV–vis spectroscopic and cyclic voltammetric analyses. The carboxyl-TTFV was applied as a redox-active ligand to complex with Zn(II) ions, forming a stable Zn-TTFV coordination polymer. The structural, electrochemical, and thermal properties of the coordination polymer were investigated by infrared spectroscopy, cyclic voltammetry, powder X-ray diffraction, and differential scanning calorimetric analyses. Furthermore, the microscopic porosity and surface area of the Zn-TTFV coordination polymer were measured by nitrogen gas adsorption analysis, showing a BET surface of 148.2 m2 g−1 and an average pore diameter of 10.2 nm. PMID:26124898

  5. EPR Study of Vanadium Ion in Zinc-Boro-Vanadate Glasses

    SciTech Connect

    Renuka, C.; Gowda, V. C. Veeranna; Chakradhar, R. P. S.; Reddy, C. Narayana

    2011-07-15

    This paper describes EPR studies on x V{sub 2}O{sub 5}-(40-x)ZnO-60B{sub 2}O{sub 3}(where x 5, 10, 15 and 20 mol %) glass system. These studies indicate a strong compositional dependent trend and existence of characteristic boro-vanadate groups in these glasses. The EPR spectra show a distinct hyperfine structure of {sup 51}V. Spectral analysis shows that the vanadium is present in the glass as vanadyl ion [VO]{sup 2+} at tetragonally distorted octahedral site. The decrease of A{sub ||} and A{sub perpendicular} with increase of V{sub 2}O{sub 5} concentration suggests an increase in the covalence between the central atom and the surrounding oxygen ligands.

  6. 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

  7. 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

  8. Improving the porosity and catalytic capacity of a zinc paddlewheel metal-organic framework (MOF) through metal-ion metathesis in a single-crystal-to-single-crystal fashion.

    PubMed

    Yang, Jie; Wang, Xiaoqing; Dai, Fangna; Zhang, Liangliang; Wang, Rongming; Sun, Daofeng

    2014-10-01

    Zinc paddlewheel metal-organic frameworks (MOFs) frequently exhibit low stability or complete collapse upon the removal of axial ligands. Hence, there are very few reports on gas adsorption of zinc paddlewheel MOFs. In this work, the N2 and H2 adsorption measurements were carried out for a zinc MOF (namely, SDU-1) based on two types of paddlewheel secondary building units (SBUs): [Zn2(COO)3] and [Zn2(COO)4]. Because of the existence of inherent surface instability upon removal of solvates in zinc paddlewheel SBU, SDU-1 possesses a very low surface area. Through metal-ion metathesis in a single-crystal-to-single-crystal fashion, the Zn(2+) ions in SDU-1 were exchanged by Cu(2+) ions to generate Cu-SDU-1. Through the measurements of gas adsorption and catalytic test, the porosity and catalytic capacity of Cu-SDU-1 have been improved significantly, compared to SDU-1.

  9. 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

  10. 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.

  11. Competitive adsorption of copper and zinc ions in two natural soils

    NASA Astrophysics Data System (ADS)

    Bianchi Janetti, E.; Riva, M.; Guadagnini, A.; Dror, I.; Berkowitz, B.

    2010-12-01

    We studied the competitive adsorption of Cu and Zn ions in different natural soils. We considered two Israeli soils, Bet Dagan and Yatir, both of which are slightly alkaline but with substantially different adsorption capacities (1.2% and 3.7% organic matter, and 16.2% and 36.9% clay content, respectively). Experiments under batch conditions were performed in single- and double-component systems to obtain adsorption isotherms. The equilibrium adsorption data were collected after 48 h contact time, with a soil-solution ratio of 1:50, initial soil pH=7, by varying the initial ion concentrations in the range 20-200 mg/l for Bet Dagan soil and 20-800 mg/l for Yatir soil. Experimental mono-component adsorption isotherms showed similar nonlinear behavior for Cu and Zn in both Bet Dagan and Yatir soils. The latter had maximum adsorption capacity about 4 times larger than the former. Cu and Zn exhibited almost the same affinity for both types of soils in single-component systems, while in competitive systems Cu adsorption increased significantly as compared to Zn. Experimental data obtained in single-component systems were analyzed with Langmuir, Freundlich and Redlich-Peterson (R-P) models. Measurements of adsorption behavior under double-component conditions were interpreted using different competitive models: unmodified, modified and extended Langmuir, unmodified and modified R-P models, and the Sheindorf-Rebuhn-Sheintuch (SRS) model. The results were examined using formal model quality criteria. These allow discrimination among different models on the basis on their goodness-of-fit to available observations, number of parameters, and quality of the available data and parameter estimates. The analysis suggested that for both soils, single-component data were better represented by Freundlich or R-P models. In double- component systems, the modified R-P model was identified as best in the case of Bet Dagan soil while the SRS model best described the behavior of the Yatir

  12. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  13. Endogenous zinc in neurological diseases.

    PubMed

    Koh, Jae-Yong

    2005-10-01

    The use of zinc in medicinal skin cream was mentioned in Egyptian papyri from 2000 BC (for example, the Smith Papyrus), and zinc has apparently been used fairly steadily throughout Roman and modern times (for example, as the American lotion named for its zinc ore, 'Calamine'). It is, therefore, somewhat ironic that zinc is a relatively late addition to the pantheon of signal ions in biology and medicine. However, the number of biological functions, health implications and pharmacological targets that are emerging for zinc indicate that it might turn out to be 'the calcium of the twenty-first century'. Here neurobiological roles of endogenous zinc is summarized.

  14. Endogenous Zinc in Neurological Diseases

    PubMed Central

    2005-01-01

    The use of zinc in medicinal skin cream was mentioned in Egyptian papyri from 2000 BC (for example, the Smith Papyrus), and zinc has apparently been used fairly steadily throughout Roman and modern times (for example, as the American lotion named for its zinc ore, 'Calamine'). It is, therefore, somewhat ironic that zinc is a relatively late addition to the pantheon of signal ions in biology and medicine. However, the number of biological functions, health implications and pharmacological targets that are emerging for zinc indicate that it might turn out to be 'the calcium of the twenty-first century'. Here neurobiological roles of endogenous zinc is summarized. PMID:20396459

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Metals in the active site of native protein phosphatase-1.

    PubMed

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

  3. [Zinc and autophagy].

    PubMed

    Qiaoyun, Liu; Hanming, Shen; Dajing, Xia

    2016-05-25

    Autophagy refers to a catabolic process,in which the damaged organelles or biological macromolecules, such as protein aggregates, are degraded via lysosome. The completion of autophagy depends on a series of autophagy-related genes (Atgs) and many upstream regulatory molecules. Zinc is an essential trace element, and plays an important role in the process of autophagy as a component of enzymes and structural proteins like zinc transporters or zinc finger protein. The regulation of autophagy is closely associated with the zinc ion homeostasis. In addition, many studies suggest that the protective effects of zinc on cells are likely to be done by autophagy. This review aims to summarize the current research progress and discuss the reciprocal regulation mechanism between zinc and autophagy, which may provide insights into the intricate roles of autophagy in diseases and find novel strategies for treatment and prevention of human diseases. PMID:27651198

  4. 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

  5. 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.

  6. 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.

  7. Control of zinc transfer between thionein, metallothionein, and zinc proteins

    PubMed Central

    Jacob, Claus; Maret, Wolfgang; Vallee, Bert L.

    1998-01-01

    Metallothionein (MT), despite its high metal binding constant (KZn = 3.2 × 1013 M−1 at pH 7.4), can transfer zinc to the apoforms of zinc enzymes that have inherently lower stability constants. To gain insight into this paradox, we have studied zinc transfer between zinc enzymes and MT. Zinc can be transferred in both directions—i.e., from the enzymes to thionein (the apoform of MT) and from MT to the apoenzymes. Agents that mediate or enhance zinc transfer have been identified that provide kinetic pathways in either direction. MT does not transfer all of its seven zinc atoms to an apoenzyme, but apparently contains at least one that is more prone to transfer than the others. Modification of thiol ligands in MT zinc clusters increases the total number of zinc ions released and, hence, the extent of transfer. Aside from disulfide reagents, we show that selenium compounds are potential cellular enhancers of zinc transfer from MT to apoenzymes. Zinc transfer from zinc enzymes to thionein, on the other hand, is mediated by zinc-chelating agents such as Tris buffer, citrate, or glutathione. Redox agents are asymmetrically involved in both directions of zinc transfer. For example, reduced glutathione mediates zinc transfer from enzymes to thionein, whereas glutathione disulfide oxidizes MT with enhanced release of zinc and transfer of zinc to apoenzymes. Therefore, the cellular redox state as well as the concentration of other biological chelating agents might well determine the direction of zinc transfer and ultimately affect zinc distribution. PMID:9520393

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

    PubMed

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

    2014-04-01

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

  9. 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

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

    PubMed

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

    2015-07-20

    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 Zn(2+) ion in (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 (1-Zn(2+) ) decreases the Lewis acidity of the Zn(2+) ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn(2+) . This further changes the reactivities of 1-Zn(2+) in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn(2+) , whereas 1-Zn(2+) coordinating two water molecules, (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 -(OH2 )2 [1-Zn(2+) -(OH2 )2 ], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn(2+) 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-Zn(2+) -(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

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

    PubMed

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

    2015-07-20

    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 Zn(2+) ion in (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 (1-Zn(2+) ) decreases the Lewis acidity of the Zn(2+) ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn(2+) . This further changes the reactivities of 1-Zn(2+) in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn(2+) , whereas 1-Zn(2+) coordinating two water molecules, (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 -(OH2 )2 [1-Zn(2+) -(OH2 )2 ], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn(2+) 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-Zn(2+) -(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.

  12. 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.

  13. 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)

  14. 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

  15. 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.

  16. 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

  17. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  18. 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.

  19. 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

  20. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  1. 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 ...

  2. 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

  3. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy

    PubMed Central

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-01-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides. PMID:27704049

  4. 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.

  5. 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.

  6. 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

  7. Spectroscopic definition of the copper active sites in mordenite: selective methane oxidation.

    PubMed

    Vanelderen, Pieter; Snyder, Benjamin E R; Tsai, Ming-Li; Hadt, Ryan G; Vancauwenbergh, Julie; Coussens, Olivier; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2015-05-20

    Two distinct [Cu-O-Cu](2+) sites with methane monooxygenase activity are identified in the zeolite Cu-MOR, emphasizing that this Cu-O-Cu active site geometry, having a ∠Cu-O-Cu ∼140°, is particularly formed and stabilized in zeolite topologies. Whereas in ZSM-5 a similar [Cu-O-Cu](2+) active site is located in the intersection of the two 10 membered rings, Cu-MOR provides two distinct local structures, situated in the 8 membered ring windows of the side pockets. Despite their structural similarity, as ascertained by electronic absorption and resonance Raman spectroscopy, the two Cu-O-Cu active sites in Cu-MOR clearly show different kinetic behaviors in selective methane oxidation. This difference in reactivity is too large to be ascribed to subtle differences in the ground states of the Cu-O-Cu sites, indicating the zeolite lattice tunes their reactivity through second-sphere effects. The MOR lattice is therefore functionally analogous to the active site pocket of a metalloenzyme, demonstrating that both the active site and its framework environment contribute to and direct reactivity in transition metal ion-zeolites.

  8. 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?

  9. 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

  10. 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

  11. 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

  12. 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.

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

    DOE PAGES

    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

  14. In vitro evaluation of cellular responses induced by ZnO nanoparticles, zinc ions and bulk ZnO in fish cells.

    PubMed

    Fernández, Dolores; García-Gómez, Concepción; Babín, Mar

    2013-05-01

    Zinc oxide nanoparticles (ZnO-NPs) are inevitably released into the environment and are potentially dangerous for aquatic life. However, the potential mechanisms of cytotoxicity of zinc nanoparticles remain unclear. Studying the toxicity of ZnO-NPs with In vitro systems will help to determine their interactions with cellular biomolecules. The aim of this study was to evaluate the cytotoxic potentials of ZnO-NPs in established fish cell lines (RTG-2, RTH-149 and RTL-W1) and compare them with those of bulk ZnO and Zn(2+) ions. Membrane function (CFDA-AM assay), mitochondrial function (MTT assay), cell growth (KBP assay), cellular stress (β-galactosidase assay), reductase enzyme activity (AB assay), reactive oxygen species (ROS), total glutathione cellular content (tGSH assay) and glutathione S-transferase (GST) activities were assessed for all cell lines. ZnO-NPs cytotoxicity was greater than those of bulk ZnO and Zn(2+). ZnO-NPs induced oxidative stress is dependent on their dose. Low cost tests, such as CFDA-AM, ROS, GST activity and tGSH cell content test that use fish cell lines, may be used to detect oxidative stress and redox status changes. Particle dissolution of the ZnO-NPs did not appear to play an important role in the observed toxicity in this study.

  15. Application of micro-segmented flow for two-dimensional characterization of the combinatorial effect of zinc and copper ions on metal-tolerant Streptomyces strains.

    PubMed

    Cao, Jialan; Kürsten, Dana; Krause, Katrin; Kothe, Erika; Martin, Karin; Roth, Martin; Köhler, J Michael

    2013-10-01

    The cultivation and growth behavior of metal-tolerant strains of Streptomyce acidiscabies E13 and Streptomyces sp. F4 were studied under droplet-based microfluidics conditions. It was shown that the technique of micro segmented flow is well suited for the investigation of dependence of bacterial growth on different concentrations of either single metal ions or combinations of them. This study confirms higher tolerance to Zn than to Cu by our test organism. The highly resolved dose-response curves reflect two transitions between the different growth behaviors, separating initial responses to Cu concentration ranges into those with (a) intense growth, (b) moderate growth, and (c) growth inhibition. For Streptomyces sp. F4, an initial stimulation was shown in the sublethal range of zinc sulfate. Two-dimensional screenings using computer-controlled fluid actuation and in situ micro flow-through fluorimetry reflected a strong growth stimulation of strain F4 by zinc sulfate in the presence of sublethal Cu concentrations. This stimulatory effect on binary mixtures may be useful in providing optimal growth conditions in bioremediation procedures.

  16. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  17. 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.

  18. 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.

  19. 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

  20. [Zinc signaling-mediated regulation of dentin and periodontal tissues].

    PubMed

    Fukada, Toshiyuki; Idaira, Yayoi; Shimoda, Shinji; Asada, Yoshinobu

    2015-12-01

    An essential trace element zinc is required for variety of cellular functions and physiological responses, therefore, downregulation of zinc homeostasis cause serious problems in health, such as growth retardation and abnormal bone formation. Recent technical advances contributed to reveal that zinc ion regulated by zinc transporters acts as a signaling mediator, called zinc signaling that involves in mammalian physiology and pathogenesis. This review will address the current understanding of the roles of zinc signaling in regulation of dentin formation and periodontal tissues homeostasis.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Immobilization of alkaline phosphatase on solid surface through self-assembled monolayer and by active-site protection.

    PubMed

    Gao, En-Feng; Kang, Kyung Lhi; Kim, Jeong Hee

    2014-06-01

    Retaining biological activity of a protein after immobilization is an important issue and many studies reported to enhance the activity of proteins after immobilization. We recently developed a new immobilization method of enzyme using active-site protection and minimization of the cross-links between enzyme and surface with a DNA polymerase as a model system. In this study, we extended the new method to an enzyme with a small mono-substrate using alkaline phosphatase (AP) as another model system. A condition to apply the new method is that masking agents, in this case its own substrate needs to stay at the active-site of the enzyme to be immobilized in order to protect the active-site during the harsh immobilization process. This could be achieved by removal of essential divalent ion, Zn2+ that is required for full enzyme activity of AP from the masking solution while active-site of AP was protected with p-nitrophenyl phosphate (pNPP). Approximately 40% of the solution-phase activity was acquired with active-site protected immobilized AP. In addition to protection active-site of AP, the number of immobilization links was kinetically controlled. When the mole fraction of the activated carboxyl group of the linker molecule in self-assembled monolayer (SAM) of 12-mercaptododecanoic acid and 6-mercapto-1-ethanol was varied, 10% of 12-mercaptododecanoic acid gave the maximum enzyme activity. Approximately 51% increase in enzyme activity of the active-site protected AP was observed compared to that of the unprotected group. It was shown that the concept of active-site protection and kinetic control of the number of covalent immobilization bonds can be extended to enzymes with small mono-substrates. It opens the possibility of further extension of the new methods of active-site protection and kinetic control of immobilization bond to important enzymes used in research and industrial fields. PMID:24738440

  6. 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

  7. Growth, optical, mechanical and dielectric studies on NLO active pure and metal ion doped single crystals of bis-thiourea zinc chloride

    NASA Astrophysics Data System (ADS)

    Parasuraman, K.; Sakthi Murugesan, K.; Uthrakumar, R.; Jerome Das, S.; Milton Boaz, B.

    2011-10-01

    Good quality single crystals of pure and metal ion (Ni 2+) doped bis-thiourea zinc chloride (BTZC) possessing excellent nonlinear optical properties have been grown from aqueous solution by the slow solvent evaporation technique. The lattice parameters of the grown crystals are determined by single crystal X-ray analysis. The well defined sharp peaks in the powder X-ray diffraction pattern reveals the crystalline perfection and the EDAX spectrum confirms the presence of dopant in the lattice of the parent crystal. The DRS UV-visible spectral study reveals improved transparency for the doped crystal, ascertaining the inclusion of metal ion in the lattice. The optical band gap of the pure and doped crystals was calculated to be 4.8 and 5.2 eV respectively from the UV transmission spectrum. The vickers hardness test brings forth higher hardness value for Ni 2+doped BTZC as compared to pure BTZC crystal. The dielectric measurement exhibits very low dielectric constant and dielectric loss at higher frequencies for both the pure and Ni 2+doped BTZC. The existence of second harmonic generation signals in the crystal also has been confirmed by performing the Kurtz powder test.

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

    DOE PAGES

    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

  9. 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

  10. 175 MeV Au{sup +13} ion irradiation induced structural and morphological modifications in zinc oxide thin films

    SciTech Connect

    Singh, Devendra; Sharma, Aditya; Varshney, Mayora; Verma, K. D.; Kumar, Shalendra

    2013-02-05

    Thin films of ZnO were deposited, on Si substrates, using the RF-sputtering technique and irradiated by the 175 MeV Au{sup +13} beams. The structural changes were investigated by x-ray diffraction (XRD) measurements. The particle size found to increase with the increasing ion fluence up to 1 Multiplication-Sign 10{sup 12} ion/cm{sup 2}. At highest irradiation fluence of 5 Multiplication-Sign 10{sup 12} ion/cm{sup 2} the average particle size decreases. The Raman spectroscopy measurements were performed to understand the local phonon mode of the samples. The surface morphology of the as-deposited and irradiated thin films is measured by the Atomic Force Microscopy (AFM).

  11. Correlation between the distribution of lignin and pectin and distribution of sorbed metal ions (lead and zinc) on coir (Cocos nucifera L.).

    PubMed

    Conrad, Kathrine

    2008-11-01

    Plant fibres are capacious for sorption of metal ions, and can be used in water cleaning. Knowledge about the sorption will help in selection of the fibre and optimisation of its chemical modification, if any. The aim of this paper is to investigate the connection, if any, between the distribution of lignin and pectin and the loading of Pb and Zn on coir (mesocarp fibres from Cocos nucifera L.). The coir consisted mainly of xylem and a fibre sheath. The lignin was evenly distributed in the cell walls of the fibre sheath, but in the xylem, there was no detectable content in the compound middle lamella, and a smaller content of lignin in the secondary walls than in the walls of the fibre sheath. The only detectable content of pectin in the fibre sheath walls was in the middle lamella, cell corners and extracellular matrix, while in the xylem, the pectin was almost evenly distributed in the wall, with a higher concentration in the middle lamella and cell corners. All cell walls facing the lacuna had a high content of pectin. The metal ions were mainly loaded on the xylem and cell walls facing the lacuna, maybe with an additional trend to be loaded on the large fibres. Lead was distributed on and across the whole secondary wall. Zinc was loaded on the secondary walls, but there was no information about the distribution across the wall. If there is a simple correlation between the loading of metal ions and the distribution of lignin or pectin, these investigations point at no correlation with lignin and a positive correlation with pectin. It has to be stressed that these conclusions are made on limited material and are therefore preliminary in nature.

  12. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  13. 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.

  14. 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

  15. 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.

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

    PubMed Central

    Herschlag, Daniel

    2016-01-01

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

  17. 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. 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...

  19. 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...

  20. Characterization and sequencing of the active site of 1-aminocyclopropane-1-carboxylate synthase

    SciTech Connect

    Yip, Wing-Kin; Dong, Jian-Guo; Yang, S.F. ); Kenny, J.W.; Thompson, G.A. )

    1990-10-01

    The pyridoxal phosphate (PLP)-dependent 1-aminocyclopropane-1-carboxylic acid (ACC) synthase the key enzyme in ethylene biosynthesis, is inactivated by its substrate S-adenosylmethionine (AdoMet). Apple ACC synthase was purified with an immunoaffinity gel, and its active site was probed with NaB{sup 3}H{sub 4} or Ado({sup 14}C)Met. Peptide sequencing of both {sup 3}H- and {sup 14}C-labeled peptides revealed a common dodecapeptide of Ser-Leu-Ser-Xaa-Asp-Leu-Gly-Leu-Pro-Gly-Phe-Arg, where Xaa was the modified, radioactive residue in each case. Acid hydrolysis of the {sup 3}H-labeled enzyme released radioactive N-pyridoxyllysine, indicating that the active-site peptide contained lysine at position 4. Mass spectrometry of the {sup 14}C-labeled peptide indicated a protonated molecular ion at m/z 1390.6, from which the mass of Xaa was calculated to be 229, a number that is equivalent to the mass of a lysine residue alkylated by the 2-aminobutyrate portion of AdoMet, as we previously proposed. These results indicate that the same active-site lysine binds the PLP and convalently links to the 2-aminobutyrate portion of AdoMet during inactivation. The active site of tomato ACC synthase was probed in the same manner with Ado ({sup 14}C)Met. Sequencing of the tomato active-site peptide revealed two highly conserved dodecapeptides; the minor peptide possessed a sequence identical to that of the apple enzyme, whereas the major peptide differed from the minor peptide in that methionine replaced leucine at position 6.

  1. 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

  2. Active sites and mechanisms for direct oxidation of benzene to phenol over carbon catalysts.

    PubMed

    Wen, Guodong; Wu, Shuchang; Li, Bo; Dai, Chunli; Su, Dang Sheng

    2015-03-23

    The direct oxidation of benzene to phenol with H2 O2 as the oxidizer, which is regarded as an environmentally friendly process, can be efficiently catalyzed by carbon catalysts. However, the detailed roles of carbon catalysts, especially what is the active site, are still a topic of debate controversy. Herein, we present a fundamental consideration of possible mechanisms for this oxidation reaction by using small molecular model catalysts, Raman spectra, static secondary ion mass spectroscopy (SIMS), DFT calculations, quasi in situ ATR-IR and UV spectra. Our study indicates that the defects, being favorable for the formation of active oxygen species, are the active sites for this oxidation reaction. Furthermore, one type of active defect, namely the armchair configuration defect was successfully identified.

  3. Sorption of cadmium(II) and zinc(II) ions from aqueous solutions by cassava waste biomass (Manihot sculenta Cranz).

    PubMed

    Horsfall, M; Abia, A A

    2003-12-01

    The sorption of two divalent metal ions, Cd(II) and Zn(II), onto untreated and differentially acid-treated cassava waste biomass over a wide range of reaction conditions was studied at 30 degrees C. The metal ion removal from the spent biomass was also measured. The batch experiments show that pH 4.5-5.5 was the best range for the sorption of the metal ions for untreated and acid-treated biomass. Time-dependent experiments for the metal ions showed that for the two metals examined, binding to the cassava waste biomass was rapid and occurred within 30 min and completed within 1h. High sorption capacities were observed for the two metals. The binding capacity experiments revealed the following amounts of metal ions bound per gram of biomass: 86.68 mg/g Cd, 55.82 mg/g Zn and 647.48 mg/g Cd, 559.74 mg/g Zn for untreated and acid-treated biomass, respectively. It was further found that the rate of sorption was particle-diffusion controlled, and the sorption rate coefficients were determined to be 2.30 x 10(-1)min(-1) (Cd(2+)), 4.0 x 10(-3)min(-1) (Zn(2+)) and 1.09 x 10(-1)min(-1) (Cd(2+)), 3.67 x 10(-2)min(-1) (Zn(2+)) for 0.5 and 1.00 M differential acid treatment, respectively. Desorption studies showed that acid treatment inhibited effective recovery of metal ions already bound to the biomass as a result of stronger sulfhydryl-metal bonds formed. Less than 25% of both metals were desorbed as concentration of acid treating reagent increases. However, over 60% Cd and 40% Zn were recovered from untreated biomass during the desorption study. The results from these studies indicated that both untreated and acid-treated cassava waste biomass could be employed in the removal of toxic and valuable metals from industrial effluents.

  4. 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

  5. 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.

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

    PubMed Central

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

    2016-01-01

    CphA is a Zn2+-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

  7. 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

  8. 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

  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.

  10. 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...

  11. Identification of glutamic acid 646 as a zinc-coordinating residue in endopeptidase-24.11.

    PubMed

    Le Moual, H; Devault, A; Roques, B P; Crine, P; Boileau, G

    1991-08-25

    Neutral endopeptidase (EC 3.424.11, NEP) is a membrane-bound zinc-metallopeptidase. The substrate specificity and catalytic activity of NEP resemble those of thermolysin, a bacterial zinc-metalloprotease. Comparison of the primary structure of both enzymes suggests that several amino acids present in the active site of thermolysin are also found in NEP. Using site-directed mutagenesis of the cDNA encoding the NEP sequence, we have already shown that His residues 583 and 587 are two of the three zinc ligands. In order to identify the third zinc ligand, we have substituted Val or Asp for Glu616 or Glu646. Val616 NEP showed the same kinetic parameters as the non-mutated NEP. In contrast, the mutant Val646 NEP was almost completely devoid of catalytic activity and unable to bind the tritiated inhibitor [3H]N-[2(R,S)-3-hydroxyaminocarbonyl-2-benzyl-1-oxypropyl]gl ycine, the binding of which is dependent on the presence of the zinc ion. Replacing Glu for Asp at position 646 conserved the negative charge, and the mutant enzyme exhibited the same Km value as the non-mutated enzyme, but kCat was decreased to less than 3% of the value of the non-mutated enzyme. When compared to the non-mutated enzyme Asp646 NEP showed a higher susceptibility to chelating agents, but bound the tritiated inhibitor with the same affinity. Taken together, these observations strongly suggest that Glu646 of NEP is the third zinc-coordinating residue and is equivalent to Glu166 in thermolysin.

  12. 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.

  13. 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

  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. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  16. 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.

  17. 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

  18. Diethyldithiocarbamate-mediated zinc ion chelation reveals role of Cav2.3 channels in glucagon secretion.

    PubMed

    Drobinskaya, Irina; Neumaier, Felix; Pereverzev, Alexey; Hescheler, Jürgen; Schneider, Toni

    2015-05-01

    Peptide-hormone secretion is partially triggered by Ca2+ influx through voltage-gated Ca2+ channels (VGCCs) and gene inactivation of Zn2+-sensitive Cav2.3-type VGCCs is associated with disturbed glucose homeostasis in mice. Zn2+ has been implicated in pancreatic islet cell crosstalk and recent findings indicate that sudden cessation of Zn2+ supply during hypoglycemia triggers glucagon secretion in rodents. Here we show that diethyldithiocarbamate (DEDTC), a chelating agent for Zn2+ and other group IIB metal ions, differentially affects blood glucose and serum peptide hormone level in wild-type mice and mice lacking the Cav2.3-subunit. Fasting glucose and glucagon level were significantly higher in Cav2.3-deficient compared to wild-type mice, while DEDTC Zn2+-chelation produced a significant and correlated increase of blood glucose and serum glucagon concentration in wild-type but not Cav2.3-deficient mice. Glucose tolerance tests revealed severe glucose intolerance in Zn2+-depleted Cav2.3-deficient but not vehicle-treated Cav2.3-deficient or Zn2+-depleted wildtype mice. Collectively, these findings indicate that Cav2.3 channels are critically involved in the Zn2+-mediated suppression of glucagon secretion during hyperglycemia. Especially under conditions of Zn2+ deficiency, ablation or dysfunction of Cav2.3 channels may lead to severe disturbances in glucose homeostasis. PMID:25603538

  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. Study of the interactions of cadmium and zinc ions with cellular calcium homoeostasis using 19F-NMR spectroscopy.

    PubMed Central

    Benters, J; Flögel, U; Schäfer, T; Leibfritz, D; Hechtenberg, S; Beyersmann, D

    1997-01-01

    The effects of the heavy-metal ions Cd2+ and Zn2+ on the homoeostasis of intracellular free Ca2+ in E367 neuroblastoma cells were examined using 19F-NMR spectroscopy with the fluorinated chelator probe 1,2-bis-(2-amino-5-fluorophenoxy)ethane-N,N,N', N'-tetra-acetic acid (5F-BAPTA). First, the technique was used to quantify the uptake and intracellular free concentrations of the heavy metals after treatment of the cells with 20 microM CdCl2 or 100 microM ZnCl2. Secondly, metal-induced transients in intracellular free Ca2+ were recorded. Addition of 20 microM CdCl2, but not 100 microM ZnCl2, evoked a transient increase in Ca2+ from a resting level of 84 nM to approx. 190 nM within 15 min after addition of the metal. Zn2+ at 20 microM completely prevented the induction of a Ca2+ transient by Cd2+. Ca2+ was mobilized by Cd2+ from intracellular organelles, since depletion of these stores by thapsigargin abolished the effect of the toxic metal. Furthermore, 20 microM Cd2+ evoked a transient rise in cellular Ins(1,4,5)P3, reaching a maximum level within 5 min after addition of the metal. These results demonstrate that perturbation of the Ins(1,4,5)P3/Ca2+ messenger system is an early and discrete cellular effect of Cd2+. PMID:9148751

  1. Batch sorption dynamics and equilibrium for the removal of lead ions from aqueous phase using activated carbon developed from coffee residue activated with zinc chloride.

    PubMed

    Boudrahem, F; Aissani-Benissad, F; Aït-Amar, H

    2009-07-01

    Lignocellulosic materials are good precursors for the production of activated carbon. In this work, coffee residue has been used as raw material in the preparation of powder activated carbon by the method of chemical activation with zinc chloride for the sorption of Pb(II) from dilute aqueous solutions. The influence of impregnation ratio (ZnCl2/coffee residue) on the physical and chemical properties of the prepared carbons was studied in order to optimize this parameter. The optimum experimental condition for preparing predominantly microporous activated carbons with high pore surface area (890 m2/g) and micropore volume (0.772 cm3/g) is an impregnation ratio of 100%. The developed activated carbon shows substantial capability to sorb lead(II) ions from aqueous solutions and for relative impregnation ratios of 75 and 100%, the maximum uptake is practically the same. Thus, 75% represents the optimal impregnation ratio. Batch experiments were conducted to study the effects of the main parameters such as contact time, initial concentration of Pb(II), solution pH, ionic strength and temperature. The maximum uptake of lead(II) at 25 degrees C was about 63 mg/g of adsorbent at pH 5.8, initial Pb(II) concentration of 10 mg/L, agitation speed of 200 rpm and ionic strength of 0.005 M. The kinetic data were fitted to the models of pseudo-first order and pseudo-second order, and follow closely the pseudo-second order model. Equilibrium sorption isotherms of Pb(II) were analyzed by the Langmuir, Freundlich and Temkin isotherm models. The Freundlich model gives a better fit than the others. Results from this study suggest that activated carbon produced from coffee residue is an effective adsorbent for the removal of lead from aqueous solutions and that ZnCl2 is a suitable activating agent for the preparation of high-porosity carbons. PMID:19447542

  2. Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase.

    PubMed

    Martí-Arbona, Ricardo; Thoden, James B; Holden, Hazel M; Raushel, Frank M

    2005-12-01

    Isoaspartyl dipeptidase (IAD) is a binuclear metalloenzyme and a member of the amidohydrolase superfamily. This enzyme catalyzes the hydrolytic cleavage of beta-aspartyl dipeptides. The pH-rate profiles for the hydrolysis of beta-Asp-Leu indicates that catalysis is dependent on the ionization of two groups; one that ionizes at a pH approximately 6 and the other approximately 9. The group that must be ionized for catalysis is directly dependent on the identity of the metal ion bound to the active site. This result is consistent with the ionization of the hydroxide that bridges the two divalent cations. In addition to the residues that interact directly with the divalent cations there are two other residues that are highly conserved and found within the active site: Glu-77 and Tyr-137. Mutation of Tyr-137 to phenylalanine reduced the rate of catalysis by three orders of magnitude. The three dimensional X-ray structure of the Y137F mutant did not show any significant conformation changes relative to the three dimensional structure of the wild-type enzyme. The positioning of the side-chain phenolic group of Tyr-137 in the active site of IAD is consistent with the stabilization of the tetrahedral adduct concomitant with nucleophilic attack by the hydroxide that bridges the two divalent cations. Mutation of Glu-77 resulted in the reduction of catalytic activity by five orders of magnitude. The three dimensional structure of the E77Q mutant did not show any significant conformational changes in the mutant relative to the three dimensional structure of the wild-type enzyme. The positioning of the side-chain carboxylate of Glu-77 is consistent with the formation of an ion pair interaction with the free alpha-amino group of the substrate.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. Binding of Mn-deoxyribonucleoside triphosphates to the active site of the DNA polymerase of bacteriophage T7

    PubMed Central

    Akabayov, Barak; Richardson, Charles C.

    2013-01-01

    Divalent metal ions are crucial as cofactors for a variety of intracellular enzymatic activities. Mg2+, 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 Mg2+ to an active site because Mg2+ is spectroscopically silent and Mg2+ binds with low affinity to the active site of an enzyme. Therefore, we substituted Mg2+ with Mn2+:Mn2+ 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 Mn2+ 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 Mn2+ that is free in solution and Mn2+ 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. PMID:23761703

  8. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  9. 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.

  10. Zinc metalloproteins as medicinal targets.

    PubMed

    Anzellotti, A I; Farrell, N P

    2008-08-01

    Zinc bioinorganic chemistry has emphasized the role of the metal ion on the structure and function of the protein. There is, more recently, an increasing appreciation of the role of zinc proteins in a variety of human diseases. This critical review, aimed at both bioinorganic and medicinal chemists, shows how apparently widely-diverging diseases share the common mechanistic approaches of targeting the essential function of the metal ion to inhibit activity. Protein structure and function is briefly summarized in the context of its clinical relevance. The status of current and potential inhibitors is discussed along with the prospects for future developments (162 references).

  11. 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.

  12. 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.

  13. 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

  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. 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

  16. 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.

  17. 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.

  18. Role of arginine-304 in the diphosphate-triggered active site closure mechanism of trichodiene synthase.

    PubMed

    Vedula, L Sangeetha; Cane, David E; Christianson, David W

    2005-09-27

    The X-ray crystal structures of R304K trichodiene synthase and its complexes with inorganic pyrophosphate (PP(i)) and aza analogues of the bisabolyl carbocation intermediate are reported. The R304K substitution does not cause large changes in the overall structure in comparison with the wild-type enzyme. The complexes with (R)- and (S)-azabisabolenes and PP(i) bind three Mg2+ ions, and each undergoes a diphosphate-triggered conformational change that caps the active site cavity. This conformational change is only slightly attenuated compared to that of the wild-type enzyme complexed with Mg2+(3)-PP(i), in which R304 donates hydrogen bonds to PP(i) and D101. In R304K trichodiene synthase, K304 does not engage in any hydrogen bond interactions in the unliganded state and it donates a hydrogen bond to only PP(i) in the complex with (R)-azabisabolene; K304 makes no hydrogen bond contacts in its complex with PP(i) and (S)-azabisabolene. Thus, although the R304-D101 hydrogen bond interaction stabilizes diphosphate-triggered active site closure, it is not required for Mg2+(3)-PP(i) binding. Nevertheless, since R304K trichodiene synthase generates aberrant cyclic terpenoids with a 5000-fold reduction in kcat/KM, it is clear that a properly formed R304-D101 hydrogen bond is required in the enzyme-substrate complex to stabilize the proper active site contour, which in turn facilitates cyclization of farnesyl diphosphate for the exclusive formation of trichodiene. Structural analysis of the R304K mutant and comparison with the monoterpene cyclase (+)-bornyl diphosphate synthase suggest that the significant loss in activity results from compromised activation of the PP(i) leaving group. PMID:16171386

  19. Role of Arginine-304 in the Diphosphate-Triggered Active Site Closure Mechanism of Trichodiene Synthase

    SciTech Connect

    Vedula,L.; Cane, D.; Christianson, D.

    2005-01-01

    The X-ray crystal structures of R304K trichodiene synthase and its complexes with inorganic pyrophosphate (PPi) and aza analogues of the bisabolyl carbocation intermediate are reported. The R304K substitution does not cause large changes in the overall structure in comparison with the wild-type enzyme. The complexes with (R)- and (S)-azabisabolenes and PPi bind three Mg2+ ions, and each undergoes a diphosphate-triggered conformational change that caps the active site cavity. This conformational change is only slightly attenuated compared to that of the wild-type enzyme complexed with Mg{sup 2+}{sub 3-}PP{sub i}, in which R304 donates hydrogen bonds to PP{sub i} and D101. In R304K trichodiene synthase, K304 does not engage in any hydrogen bond interactions in the unliganded state and it donates a hydrogen bond to only PP{sub i} in the complex with (R)-azabisabolene; K304 makes no hydrogen bond contacts in its complex with PP{sub i} and (S)-azabisabolene. Thus, although the R304-D101 hydrogen bond interaction stabilizes diphosphate-triggered active site closure, it is not required for Mg{sup 2+}{sub 3-}PP{sub i} binding. Nevertheless, since R304K trichodiene synthase generates aberrant cyclic terpenoids with a 5000-fold reduction in kcat/KM, it is clear that a properly formed R304-D101 hydrogen bond is required in the enzyme-substrate complex to stabilize the proper active site contour, which in turn facilitates cyclization of farnesyl diphosphate for the exclusive formation of trichodiene. Structural analysis of the R304K mutant and comparison with the monoterpene cyclase (+)-bornyl diphosphate synthase suggest that the significant loss in activity results from compromised activation of the PP{sub i} leaving group.

  20. 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.

  1. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  2. 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.

  3. 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

  4. Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase.

    PubMed

    Batt, C A; Jamieson, A C; Vandeyar, M A

    1990-01-01

    Two conserved histidine residues (His-101 and His-271) appear to be essential components in the active site of the enzyme xylose (glucose) isomerase (EC 5.3.1.5). These amino acid residues were targeted for mutagenesis on the basis of sequence homology among xylose isomerases isolated from Escherichia coli, Bacillus subtilis, Ampullariella sp. strain 3876, and Streptomyces violaceus-niger. Each residue was selectively replaced by site-directed mutagenesis and shown to be essential for activity. No measurable activity was observed for any mutations replacing either His-101 or His-271. Circular dichroism measurements revealed no significant change in the overall conformation of the mutant enzymes, and all formed dimers similar to the wild-type enzyme. Mutations at His-271 could be distinguished from those at His-101, since the former resulted in a thermolabile protein whereas no significant change in heat stability was observed for the latter. Based upon these results and structural data recently reported, we speculate that His-101 is the catalytic base mediating the reaction. Replacement of His-271 may render the enzyme thermolabile, since this residue appears to be a ligand for one of the metal ions in the active site of the enzyme. PMID:2405386

  5. 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

  6. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  7. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  8. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

  9. 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.

  10. Further aspects of ochratoxin A-cation interactions: complex formation with zinc ions and a novel analytical application of ochratoxin A-magnesium interaction in the HPLC-FLD system.

    PubMed

    Poór, Miklós; Kuzma, Mónika; Matisz, Gergely; Li, Yin; Perjési, Pál; Kunsági-Máté, Sándor; Kőszegi, Tamás

    2014-04-10

    Ochratoxin A (OTA) is a mycotoxin produced by different Aspergillus and Penicillium species. Since its mechanism of action is not fully understood yet, it is important to gain further insight into different interactions of OTA at the molecular level. OTA is found worldwide in many foods and drinks. Moreover, it can also be detected in human and animal tissues and body fluids, as well. Therefore, the development of highly sensitive quantitative methods for the determination of OTA is of utmost importance. OTA most likely forms complexes with divalent cations, both in cells and body fluids. In the present study, the OTA-zinc interaction was investigated and compared to OTA-magnesium complex formation using fluorescence spectroscopy and molecular modeling. Our results show that zinc(II) ion forms a two-fold higher stable complex with OTA than magnesium(II) ion. In addition, based on the enhanced fluorescence emission of OTA in its magnesium-bound form, a novel RP-HPLC-fluorescence detector (FLD) method was also established. Our results highlight that the application of magnesium chloride in alkaline eluents results in an approximately two-fold increase in sensitivity using the HPLC-FLD technique.

  11. Key active site residues in the inhibition of acetylcholinesterases by soman.

    PubMed

    Qian, N; Kovach, I M

    1993-12-27

    Molecular modeling (GEMM 7.3) and molecular mechanics calculations (YETI V 5.3) using the X-ray coordinates for acetylcholinesterase (AChE) from Torpedo californica indicate electrostatic stabilization by the active site, Glu-199, of the developing positive charge on the incipient carbonium ion in the dealkylation in the adducts of AChE with PSCR and PSCS diastereomers of 2-(3,3-dimethylbutyl) methylphosphonofluoridate (soman). His-440 is indispensable as a general acid catalyst of C-O bond breaking in the dealkylation reaction and that of bond breaking to the Ser gamma-O in reactivation. This demand for catalysis seems to be satisfied for the reactivation of enzyme from the PSCS diastereomer of soman, but not from the P(S)C(R) diastereomer.

  12. 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

  13. 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

  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. Regulation of S100A8/A9 (Calprotectin) Binding to Tumor Cells by Zinc Ion and Its Implication for Apoptosis-Inducing Activity

    PubMed Central

    Nakatani, Yuichi; Yamazaki, Masatoshi; J. Chazin, Walter; Yui, Satoru

    2005-01-01

    S100A8/A9 (calprotectin), which is released by neutrophils under inflammatory conditions, has the capacity to induce apoptosis in various cells. We previously reported that S100A8/A9 induces apoptosis of EL-4 lymphoma cells via the uptake of extracellular zinc in a manner similar to DTPA, a membrane-impermeable zinc chelator. In this study, S100A8/A9-induced apoptosis was examined in several cell lines that are weakly sensitive to DTPA, suggesting S100A8/A9 is directly responsible for apoptosis in these cells. Since zinc inhibits apoptosis of MM46, one of these cells, the regulation by zinc of the capacity of S100A8/A9 to bind MM46 cells was studied. When MM46 cells were incubated with S100A8/A9 in standard or zinc-depleted medium, the amounts of S100A8/A9 bound to cells was markedly lower at 3 h than at 1 h. In contrast, when MM46 cells were incubated with S100A8/A9 in the presence of high levels of zinc, binding to cells was the same at 1 and 3 h. When the cells were permeabilized with saponin prior to analysis, a larger amount of cell-associated S100A8/A9 was detected at 3 h. The amount was further increased in cells treated with chloroquine, suggesting that S100A8/A9 was internalized and degraded in lysosomes. Although it has been reported that S100A8/A9 binds to heparan sulfate on cell membranes, the amount of S100A8/A9 bound to MM46 cells was not reduced by heparinase treatment, but was reduced by trypsin treatment. These results suggest that S100A8/A9 induces apoptosis by direct binding to MM46 cells, and that this activity is regulated by zinc. PMID:16258195

  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. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

  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. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

  20. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

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

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, 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. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

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

    SciTech Connect

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

    1992-02-01

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

  2. 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.

  3. The neurobiology of zinc in health and disease.

    PubMed

    Frederickson, Christopher J; Koh, Jae-Young; Bush, Ashley I

    2005-06-01

    The use of zinc in medicinal skin cream was mentioned in Egyptian papyri from 2000 BC (for example, the Smith Papyrus), and zinc has apparently been used fairly steadily throughout Roman and modern times (for example, as the American lotion named for its zinc ore, 'Calamine'). It is, therefore, somewhat ironic that zinc is a relatively late addition to the pantheon of signal ions in biology and medicine. However, the number of biological functions, health implications and pharmacological targets that are emerging for zinc indicate that it might turn out to be 'the calcium of the twenty-first century'.

  4. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

  5. Antimicrobial properties of zeolite-X and zeolite-A ion-exchanged with silver, copper, and zinc against a broad range of microorganisms.

    PubMed

    Demirci, Selami; Ustaoğlu, Zeynep; Yılmazer, Gonca Altın; Sahin, Fikrettin; Baç, Nurcan

    2014-02-01

    Zeolites are nanoporous alumina silicates composed of silicon, aluminum, and oxygen in a framework with cations, water within pores. Their cation contents can be exchanged with monovalent or divalent ions. In the present study, the antimicrobial (antibacterial, anticandidal, and antifungal) properties of zeolite type X and A, with different Al/Si ratio, ion exchanged with Ag(+), Zn(2+), and Cu(2+) ions were investigated individually. The study presents the synthesis and manufacture of four different zeolite types characterized by scanning electron microscopy and X-ray diffraction. The ion loading capacity of the zeolites was examined and compared with the antimicrobial characteristics against a broad range of microorganisms including bacteria, yeast, and mold. It was observed that Ag(+) ion-loaded zeolites exhibited more antibacterial activity with respect to other metal ion-embedded zeolite samples. The results clearly support that various synthetic zeolites can be ion exchanged with Ag(+), Zn(2+), and Cu(2+) ions to acquire antimicrobial properties or ion-releasing characteristics to provide prolonged or stronger activity. The current study suggested that zeolite formulations could be combined with various materials used in manufacturing medical devices, surfaces, textiles, or household items where antimicrobial properties are required.

  6. 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.

  7. 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

  8. Studies of removal of platinum(IV) ion microquantities from the model solutions of aluminium, copper, iron, nickel and zinc chloride macroquantities on the anion exchanger Duolite S 37.

    PubMed

    Hubicki, Z; Wójcik, G

    2006-08-25

    Platinum has been widely applied in catalytic industry and the recovery of noble metals from industrial wastes becomes an economic issue. The laboratory studies of platinum(IV) microquantities removal from 1M aluminium, copper, iron, nickel and zinc chloride solutions in 0.1M hydrochloric acid solutions on the anion exchanger Duolite S 37 of the functional secondary and tertiary amine groups were carried out. For this anion exchanger the fraction extracted values (%E, Pt(IV)) as well as the sorption isotherms were determined depending on the kind of aqueous phase and phase contact time. Moreover, the bed and weight distribution coefficients as well as working and total ion-exchange capacities were calculated from the platinum(IV) breakthrough curves. Kinetic parameters were determined. PMID:16469435

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: mechanistic insights from DFT calculations.

    PubMed

    Liao, Rong-Zhen; Himo, Fahmi; Yu, Jian-Guo; Liu, Ruo-Zhuang

    2010-01-01

    The reaction mechanism of the dinuclear zinc enzyme human renal dipeptidase is investigated using hybrid density functional theory. This enzyme catalyzes the hydrolysis of dipeptides and beta-lactam antibiotics. Two different protonation states in which the important active site residue Asp288 is either neutral or ionized were considered. In both cases, the bridging hydroxide is shown to be capable of performing the nucleophilic attack on the substrate carbonyl carbon from its bridging position, resulting in the formation of a tetrahedral intermediate. This step is followed by protonation of the dipeptide nitrogen, coupled with C-N bond cleavage. The calculations establish that both cases have quite feasible energy barriers. When the Asp288 is neutral, the hydrolytic reaction occurs with a large exothermicity. However, the reaction becomes very close to thermoneutral with an ionized Asp288. The two zinc ions are shown to play different roles in the reaction. Zn1 binds the amino group of the substrate, and Zn2 interacts with the carboxylate group of the substrate, helping in orienting it for the nucleophilic attack. In addition, Zn2 stabilizes the oxyanion of the tetrahedral intermediate, thereby facilitating the nucleophilic attack.

  15. Application of mechanosynthesized azine-decorated zinc(II) metal-organic frameworks for highly efficient removal and extraction of some heavy-metal ions from aqueous samples: a comparative study.

    PubMed

    Tahmasebi, Elham; Masoomi, Mohammad Yaser; Yamini, Yadollah; Morsali, Ali

    2015-01-20

    The three zinc(II) metal-organic frameworks [Zn2(oba)2(4-bpdb)]·(DMF)x (TMU-4), [Zn(oba)(4-bpdh)0.5]n·(DMF)y (TMU-5), and [Zn(oba)(4-bpmb)0.5]n·(DMF)z (TMU-6) [DMF = dimethylformamide, H2oba = 4,4'-oxybisbenzoic acid, 4-bpdb = 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene, 4-bpdh = 2,5-bis(4-pyridyl)-3,4-diaza-2,4-hexadiene, and 4-bpmb = N(1),N(4)-bis((pyridin-4-yl)methylene)benzene-1,4-diamine], which contain azine-functionalized pores, have been successfully synthesized by mechanosynthesis as a convenient, rapid, low-cost, solventless, and green process. These MOFs were studied for the removal and extraction of some heavy-metal ions from aqueous samples, and the effects of the basicity and void space of these MOFs on adsorption efficiency were evaluated. The results showed that, for trace amounts of metal ions, the basicity of the N-donor ligands in the MOFs determines the adsorption efficiency of the MOFs for the metal ions. In contrast, at high concentrations of metal ions, the void space of the MOFs plays a main role in the adsorption process. The studies conducted revealed that, among the three MOFs, TMU-6 had a lower adsorption efficiency for metal ions than the other two MOFs. This result can be attributed to the greater basicity of the azine groups on the TMU-4 and TMU-5 pore walls as compared to the imine groups on the N-donor ligands on the TMU-6 pore walls. Subsequently, TMU-5 was chosen as an efficient sorbent for the extraction and preconcentration of trace amounts of some heavy-metal ions including Cd(II), Co(II), Cr(III), Cu(II), and Pb(II), followed by their determination by flow injection inductively coupled plasma optical emission spectrometry. Several variables affecting the extraction efficiency of the analytes were investigated and optimized. The optimized methodology exhibits a good linearity between 0.05 and 100 μg L(-1) (R(2) > 0.9935) and detection limits in the range of 0.01-1.0 μg L(-1). The method has enhancement factors between 42

  16. Zinc ion acts as a cofactor for serine/threonine kinase MST3 and has a distinct role in autophosphorylation of MST3.

    PubMed

    Lu, Te-Jung; Huang, Chi-Ying F; Yuan, Chiun-Jye; Lee, Yuan-Chii; Leu, Tzeng-Horng; Chang, Wen-Chang; Lu, Te-Ling; Jeng, Wen-Yih; Lai, Ming-Derg

    2005-06-01

    We examined the metal ion cofactor preference for MST3 (mammalian Ste20-like kinase 3) of the Ste20 serine/threonine kinase family. Four metal ions (Mg(+2), Mn(+2), Zn(2+), and Co(2+)) activate endogenous, exogenous, and baculovirus-expressed recombinant MST3 within the physiological concentration range. In contrast, Fe(+2) and Ca(+2) do not function as MST3 cofactors. Mn(2+), Co(2+), and Mg(2+)-dependent autophosphorylation of MST3 is mainly on threonine residue while Zn(2+)-stimulated MST3 autophosphorylation is on both serine and threonine residues. The distinct autophosphorylation pattern on MST3 suggests that MST3 may exert various types of kinase reactions depending on the type of metal ion cofactor used. To our knowledge, this is the first report showing Zn(2+) as the metal ion cofactor of a recombinant serine/threonine kinase.

  17. 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.

  18. Design and synthesis of a new terbium complex-based luminescent probe for time-resolved luminescence sensing of zinc ions.

    PubMed

    Ye, Zhiqiang; Xiao, Yunna; Song, Bo; Yuan, Jingli

    2014-09-01

    Luminescent probes/chemosensors based on lanthanide complexes have shown great potentials in various bioassays due to their unique long-lived luminescence property for eliminating short-lived autofluorescence with time-resolved detection mode. In this work, we designed and synthesized a new dual-chelating ligand {4'-[N,N-bis(2-picolyl)amino]methylene-2,2':6',2'-terpyridine-6,6'-diyl} bis(methylenenitrilo) tetrakis(acetic acid) (BPTTA), and investigated the performance of its Tb(3+) complex (BPTTA-Tb(3+)) for the time-resolved luminescence sensing of Zn(2+) ions in aqueous media. Weakly luminescent BPTTA-Tb(3+) can rapidly react with Zn(2+) ions to display remarkable luminescence enhancement with high sensitivity and selectivity, and such luminescence response can be realized repeatedly. Laudably, the dose-dependent luminescence enhancement shows a good linear response to the concentration of Zn(2+) ions with a detection limit of 4.1 nM. To examine the utility of the new probe for detecting intracellular Zn(2+) ions, the performance of BPTTA-Tb(3+) in the time-resolved luminescence imaging of Zn(2+) ions in living HeLa cells was investigated. The results demonstrated the applicability of BPTTA-Tb(3+) as a probe for the time-resolved luminescence sensing of intracellular Zn(2+) ions.

  19. Zinc and zinc transporters in prostate carcinogenesis

    PubMed Central

    Kolenko, Vladimir; Teper, Ervin; Kutikov, Alexander; Uzzo, Robert

    2013-01-01

    The healthy human prostate accumulates the highest level of zinc of any soft tissue in the body. This unique property is retained in BPH, but is lost in prostatic malignancy, which implicates changes in zinc and its transporters in carcinogenesis. Indeed, zinc concentrations diminish early in the course of prostate carcinogenesis, preceding histopathological changes, and continue to decline during progression toward castration-resistant disease. Numerous studies suggest that increased zinc intake might protect against progression of prostatic malignancy. Despite increased dietary intake, zinc accumulation might be limited by the diminished expression of zinc uptake transporters, resulting in decreased intratumoural zinc levels. This finding can explain the conflicting results of various epidemiological studies evaluating the role of zinc supplementation on primary and secondary prostate cancer prevention. Overall, more research into the mechanisms of zinc homeostasis are needed to fully understand its impact on prostate carcinogenesis. Only then can the potential of zinc and zinc transport proteins be harnessed in the diagnosis and treatment of men with prostate cancer. PMID:23478540

  20. 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.

  1. Production of zinc pellets

    DOEpatents

    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.

  2. 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

  3. Distinct Roles of the Active-site Mg2+ Ligands, Asp882 and Asp705, of DNA Polymerase I (Klenow Fragment) during the Prechemistry Conformational Transitions*

    PubMed Central

    Bermek, Oya; Grindley, Nigel D. F.; Joyce, Catherine M.

    2011-01-01

    DNA polymerases catalyze the incorporation of deoxynucleoside triphosphates into a growing DNA chain using a pair of Mg2+ ions, coordinated at the active site by two invariant aspartates, whose removal by mutation typically reduces the polymerase activity to barely detectable levels. Using two stopped-flow fluorescence assays that we developed previously, we have investigated the role of the carboxylate ligands, Asp705 and Asp882, of DNA polymerase I (Klenow fragment) in the early prechemistry steps that prepare the active site for catalysis. We find that neither carboxylate is required for an early conformational transition, reported by a 2-aminopurine probe, that takes place in the open ternary complex after binding of the complementary dNTP. However, the subsequent fingers-closing step requires Asp882; this step converts the open ternary complex into the closed conformation, creating the active-site geometry required for catalysis. Crystal structures indicate that the Asp882 position changes very little during fingers-closing; this side chain may therefore serve as an anchor point to receive the dNTP-associated metal ion as the nucleotide is delivered into the active site. The Asp705 carboxylate is not required until after the fingers-closing step, and we suggest that its role is to facilitate the entry of the second Mg2+ into the active site. The two early prechemistry steps that we have studied take place normally at very low Mg2+ concentrations, although higher concentrations are needed for covalent nucleotide addition, consistent with the second metal ion entering the ternary complex after fingers-closing. PMID:21084297

  4. 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.

  5. 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

  6. 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.

  7. Sensitivity of Anabaena spiroides to zinc and cobalt

    SciTech Connect

    Kostyayev, V. Ya.; Yagodka, S.N.; Sokolov, V.A.

    1980-01-01

    The influence of zinc and cobalt chlorous salts on destruction, nitrogen fixation photosynthesis, and Na/sup +/ and K/sup +/-ion concentrations in the cells was studied for the blue-green alga Anabaena spiroides. Stability of A. spiroides depends on the developmental stage. The algae are most sensitive to cobalt at the beginning of the growth lag-phase, and they are least sensitive to it at the end of this phase. Cobalt ions are more toxic for A. spiroides than zinc ions. Salts of heavy metals inhibit active ion transport, which results in a sharp decrease of K and Na ions concentration in the algae cells.

  8. 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.

  9. 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

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

    DOE PAGES

    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

  11. Practical 4′-Phosphopantetheine Active Site Discovery from Proteomic Samples

    PubMed Central

    Meier, Jordan L.; Patel, Anand D.; Niessen, Sherry; Meehan, Michael; Kersten, Roland; Yang, Jane Y.; Rothmann, Michael; Cravatt, Benjamin F.; Dorrestein, Pieter

    2011-01-01

    Polyketide and nonribosomal peptides constitute important classes of small molecule natural products. Due to the proven biological activities of these compounds, novel methods for discovery and study of the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymes responsible for their production remains an area of intense interest, and proteomic approaches represent a relatively unexplored avenue. While these enzymes may be distinguished from the proteomic milieu by their use of the 4′-phosphopantetheine (PPant) posttranslational modification, proteomic detection of PPant peptides is hindered by their low abundance and labile nature which leaves them unassigned using traditional database searching. Here we address key experimental and computational challenges to facilitate practical discovery of this important posttranslational modification during shotgun proteomics analysis using low-resolution ion-trap mass spectrometers. Activity-based enrichment maximizes MS input of PKS/NRPS peptides, while targeted fragmentation detects putative PPant active sites. An improved data analysis pipeline allows experimental identification and validation of these PPant peptides directly from MS2 data. Finally, a machine learning approach is developed to directly detect PPant peptides from only MS2 fragmentation data. By providing new methods for analysis of an often cryptic posttranslational modification, these methods represent a first step towards the study of natural product biosynthesis in proteomic settings. PMID:21067235

  12. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  13. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  14. Dietary phytate, zinc and hidden zinc deficiency.

    PubMed

    Sandstead, Harold H; Freeland-Graves, Jeanne H

    2014-10-01

    Epidemiological data suggest at least one in five humans are at risk of zinc deficiency. This is in large part because the phytate in cereals and legumes has not been removed during food preparation. Phytate, a potent indigestible ligand for zinc prevents it's absorption. Without knowledge of the frequency of consumption of foods rich in phytate, and foods rich in bioavailable zinc, the recognition of zinc deficiency early in the illness may be difficult. Plasma zinc is insensitive to early zinc deficiency. Serum ferritin concentration≤20μg/L is a potential indirect biomarker. Early effects of zinc deficiency are chemical, functional and may be "hidden". The clinical problem is illustrated by 2 studies that involved US Mexican-American children, and US premenopausal women. The children were consuming home diets that included traditional foods high in phytate. The premenopausal women were not eating red meat on a regular basis, and their consumption of phytate was mainly from bran breakfast cereals. In both studies the presence of zinc deficiency was proven by functional responses to controlled zinc treatment. In the children lean-mass, reasoning, and immunity were significantly affected. In the women memory, reasoning, and eye-hand coordination were significantly affected. A screening self-administered food frequency questionnaire for office might help caregiver's identify patients at risk of zinc deficiency.

  15. 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).

  16. 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

  17. Identification of ice nucleation active sites on feldspar dust particles.

    PubMed

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-03-19

    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

  18. 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

  19. 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

  20. Zinc and vegetarian diets.

    PubMed

    Saunders, Angela V; Craig, Winston J; Baines, Surinder K

    2013-08-19

    Well planned vegetarian diets can provide adequate amounts of zinc from plant sources. Vegetarians appear to adapt to lower zinc intakes by increased absorption and retention of zinc. Good sources of zinc for vegetarians include whole grains, tofu, tempeh, legumes, nuts and seeds, fortified breakfast cereals and dairy products. The inhibitory effects of phytate on absorption of zinc can be minimised by modern food-processing methods such as soaking, heating, sprouting, fermenting and leavening. Absorption of zinc can be improved by using yeast-based breads and sourdough breads, sprouts, and presoaked legumes. Studies show vegetarians have similar serum zinc concentrations to, and no greater risk of zinc deficiency than, non-vegetarians (despite differences in zinc intake).

  1. 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

  2. Zinc: the neglected nutrient.

    PubMed

    Shambaugh, G E

    1989-03-01

    Zinc was first recognized as essential for animals at the University of Illinois School of Agriculture in 1916, when it was found that zinc-deficient baby pigs were runty, developed dermatitis on their legs, and were sterile. Zinc deficiency was first recognized in man by Dr. Ananda Prasad of Detroit 26 years ago when he measured serum and hair zinc levels in young male Egyptian dwarfs who had failed to mature and were small in stature. By simply adding zinc to their regular diet, they grew in height and became sexually mature. It is now recognized that dwarfism in males is frequent around the Mediterranean, where wheat is the staple of life and has been grown for 4,000 years on the same soil, thereby resulting in the depletion of zinc. Professor Robert Henkin first suggested that zinc deficiency might cause hearing-nerve impairment. Assay of the soft tissues of the cochlea and vestibule revealed a zinc level higher than that of any other part of the body. Previously, the eye was considered to have the highest level of zinc of any organ. To diagnose zinc deficiency clinically, we use serum zinc assays made at the Mayo Clinic Trace Element Laboratory. With zinc supplementation in patients who are marginally zinc deficient, there has been improvement in tinnitus and sensorineural hearing loss in about one-third of elderly adults. We believe zinc deficiency is one causation of presbycusis; by recognizing and correcting it, a progressive hearing loss can be arrested.

  3. Zinc: the neglected nutrient.

    PubMed

    Shambaugh, G E

    1989-03-01

    Zinc was first recognized as essential for animals at the University of Illinois School of Agriculture in 1916, when it was found that zinc-deficient baby pigs were runty, developed dermatitis on their legs, and were sterile. Zinc deficiency was first recognized in man by Dr. Ananda Prasad of Detroit 26 years ago when he measured serum and hair zinc levels in young male Egyptian dwarfs who had failed to mature and were small in stature. By simply adding zinc to their regular diet, they grew in height and became sexually mature. It is now recognized that dwarfism in males is frequent around the Mediterranean, where wheat is the staple of life and has been grown for 4,000 years on the same soil, thereby resulting in the depletion of zinc. Professor Robert Henkin first suggested that zinc deficiency might cause hearing-nerve impairment. Assay of the soft tissues of the cochlea and vestibule revealed a zinc level higher than that of any other part of the body. Previously, the eye was considered to have the highest level of zinc of any organ. To diagnose zinc deficiency clinically, we use serum zinc assays made at the Mayo Clinic Trace Element Laboratory. With zinc supplementation in patients who are marginally zinc deficient, there has been improvement in tinnitus and sensorineural hearing loss in about one-third of elderly adults. We believe zinc deficiency is one causation of presbycusis; by recognizing and correcting it, a progressive hearing loss can be arrested. PMID:2786676

  4. 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.

  5. 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

  6. Steady state fluorescence studies of wild type recombinant cinnamoyl CoA reductase (Ll-CCRH1) and its active site mutants.

    PubMed

    Sonawane, Prashant; Vishwakarma, Rishi Kishore; Singh, Somesh; Gaikwad, Sushama; Khan, Bashir M

    2014-05-01

    Fluorescence quenching and time resolved fluorescence studies of wild type recombinant cinnamoyl CoA reductase (Ll-CCRH1), a multitryptophan protein from Leucaena leucocephala and 10 different active site mutants were carried out to investigate tryptophan environment. The enzyme showed highest affinity for feruloyl CoA (K(a)  = 3.72 × 10(5) M(-1)) over other CoA esters and cinnamaldehydes, as determined by fluorescence spectroscopy. Quenching of the fluorescence by acrylamide for wild type and active site mutants was collisional with almost 100% of the tryptophan fluorescence accessible under native condition and remained same after denaturation of protein with 6 M GdnHCl. In wild type Ll-CCRH1, the extent of quenching achieved with iodide (f(a) = 1.0) was significantly higher than cesium ions (f(a) = 0.33) suggesting more density of positive charge around surface of trp conformers under native conditions. Denaturation of wild type protein with 6 M GdnHCl led to significant increase in the quenching with cesium (f(a) = 0.54), whereas quenching with iodide ion was decreased (f(a) = 0.78), indicating reorientation of charge density around trp from positive to negative and heterogeneity in trp environment. The Stern-Volmer plots for wild type and mutants Ll-CCRH1 under native and denatured conditions, with cesium ion yielded biphasic quenching profiles. The extent of quenching for cesium and iodide ions under native and denatured conditions observed in active site mutants was significantly different from wild type Ll-CCRH1 under the same conditions. Thus, single substitution type mutations of active site residues showed heterogeneity in tryptophan microenvironment and differential degree of conformation of protein under native or denatured conditions. PMID:24322526

  7. 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

  8. Is zinc a neuromodulator?

    PubMed

    Kay, Alan R; Tóth, Katalin

    2008-01-01

    The vesicles of certain glutamatergic terminals in the mammalian forebrain are replete with ionic zinc. It is believed that during synaptic transmission zinc is released, binds to receptors on the pre- or postsynaptic membranes, and hence acts as a neuromodulator. Although exogenous zinc modulates a wide variety of channels, whether synaptic zinc transits across the synaptic cleft and alters the response of channels has been difficult to establish. We will review the evidence for zinc as a neuromodulator and propose diagnostic criteria for establishing whether it is indeed one. Moreover, we will delineate alternative ways in which zinc might act at synapses.

  9. Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase.

    PubMed

    Bueno, Amy N; Shrestha, Rashmi K; Ronau, Judith A; Babar, Aditya; Sheedlo, Michael J; Fuchs, Julian E; Paul, Lake N; Das, Chittaranjan

    2015-10-01

    The endosome-associated deubiquitinase (DUB) AMSH is a member of the JAMM family of zinc-dependent metallo isopeptidases with high selectivity for Lys63-linked polyubiquitin chains, which play a key role in endosomal-lysosomal sorting of activated cell surface receptors. The catalytic domain of the enzyme features a flexible flap near the active site that opens and closes during its catalytic cycle. Structural analysis of its homologues, AMSH-LP (AMSH-like protein) and the fission yeast counterpart, Sst2, suggests that a conserved Phe residue in the flap may be critical for substrate binding and/or catalysis. To gain insight into the contribution of this flap in substrate recognition and catalysis, we generated mutants of Sst2 and characterized them using a combination of enzyme kinetics, X-ray crystallography, molecular dynamics simulations, and isothermal titration calorimetry (ITC). Our analysis shows that the Phe residue in the flap contributes key interactions during the rate-limiting step but not to substrate binding, since mutants of Phe403 exhibit a defect only in kcat but not in KM. Moreover, ITC studies show Phe403 mutants have similar KD for ubiquitin compared to the wild-type enzyme. The X-ray structures of both Phe403Ala and the Phe403Trp, in both the free and ubiquitin bound form, reveal no appreciable structural change that might impair substrate or alter product binding. We observed that the side chain of the Trp residue is oriented identically with respect to the isopeptide moiety of the substrate as the Phe residue in the wild-type enzyme, so the loss of activity seen in this mutant cannot be explained by the absence of a group with the ability to provide van der Waals interactions that facilitate the hyrdolysis of the Lys63-linked diubiquitin. Molecular dynamics simulations indicate that the flap in the Trp mutant is quite flexible, allowing almost free rotation of the indole side chain. Therefore, it is possible that these different dynamic

  10. Lewis acid properties of zinc(II) in Its cyclen complex. The structure of [Zn(cyclen)(S=C(NH2)2](ClO4)2 and the bonding of thiourea to metal ions. Some implications for zinc metalloenzymes.

    PubMed

    Salter, Michael H; Reibenspies, Joseph H; Jones, S Bart; Hancock, Robert D

    2005-04-18

    cyclen complex, and softer still in tridentate N-donor ligands in model complexes, and in the Zn(II) active site of carbonic anhydrase as representative of Zn(II) metalloenzymes in general, is discussed in terms of the role of such effects in the functioning of metalloenzymes. PMID:15819567

  11. Mechanism of the antihypoxic action of zinc compounds

    SciTech Connect

    Uryupov, O.Y.; Sumina, E.N.

    1985-10-01

    This paper studies the mechanism of the protective action of zinc compound in acute carbon monoxide poisoning. The survival rate of animals receiving a preliminary injection of bis (1-vinylimidazole) zinc sulfate before exposure to hypobaric and mormobaric hypoxia was 60% respectively compared with 10 and 15% in the control groups. During CO poisoning the rise of the HbCO level in the blood of mice receiving prophylactic zinc complex was delayed. It is suggested that the antihypoxic effect of the zinc ion is connected with changes in the functional properties of the hemoglobin molecule.

  12. A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations.

    PubMed

    O'Farrell, Norah; Kreiner, Michaela; Moore, Barry D; Parker, Marie-Claire

    2006-11-01

    We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

  13. 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 ...

  14. 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 ...

  15. Enhanced in vitro regeneration and change in photosynthetic pigments, biomass and proline content in Withania somnifera L. (Dunal) induced by copper and zinc ions.

    PubMed

    Fatima, Nigar; Ahmad, Naseem; Anis, Mohammad

    2011-12-01

    In the present study the effect of inorganic nutrients (CuSO₄ & ZnSO₄) on morphogenic and biochemical responses from nodal explants in Withania somnifera L. was investigated. Incorporation of either Copper sulphate (25-200 μM) or Zinc sulphate (50-500 μM) in the optimized Murashige and Skoog (MS) medium highly influenced the shoot bud formation and subsequent elongation, which induced maximum percentage (95%) regeneration, number (61.7 ± 0.25) of shoots with shoot length (5.46 ± 0.16 cm) on CuSO₄ (100 μM) and maximum percentage regeneration (100%), number of shoots (66.1 ± 0.96) with shoot length (6.24 ± 0.21 cm) on ZnSO₄ (300 μM) after 12 weeks of culture. Healthy growing in vitro microshoots rooted efficiently on ½ MS medium supplemented with NAA (0.5 μM), which induced (16.2 ± 0.12) roots with root length (3.30 ± 0.12 cm) after 4 weeks. Pigment content increased with increasing concentration of Cu and Zn and the maximum Chl. a (0.47), (0.41); Chl. b (0.52), (0.42); total Chl. (0.99), (0.83) and Carotenoid (0.16), (0.16) mg/g FW contents in regenerants were found on CuSO₄ (100 μM) and ZnSO₄ (300 μM), respectively. Maximum proline content (0.17), (0.16) μg/g FW was observed on high concentrations of CuSO₄ (200 μM) and ZnSO₄ (500 μM) respectively, in the basal medium. Regenerated plantlets were acclimatized successfully in soilrite with a survival rate of 95%. No morphological variations were detected among the micropropagated plants when compared with seedling raised plants of the same age.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. Gamma Radiation-Induced Damage in the Zinc Finger of the Transcription Factor IIIA

    PubMed Central

    Miao, YuJi; Hu, XiaoDan; Min, Rui; Liu, PeiDang; Zhang, HaiQian

    2016-01-01

    A zinc finger motif is an element of proteins that can specifically recognize and bind to DNA. Because they contain multiple cysteine residues, zinc finger motifs possess redox properties. Ionizing radiation generates a variety of free radicals in organisms. Zinc finger motifs, therefore, may be a target of ionizing radiation. The effect of gamma radiation on the zinc finger motifs in transcription factor IIIA (TFIIIA), a zinc finger protein, was investigated. TFIIIA was exposed to different gamma doses from 60Co sources. The dose rates were 0.20 Gy/min and 800 Gy/h, respectively. The binding capacity of zinc finger motifs in TFIIIA was determined using an electrophoretic mobility shift assay. We found that 1000 Gy of gamma radiation impaired the function of the zinc finger motifs in TFIIIA. The sites of radiation-induced damage in the zinc finger were the thiol groups of cysteine residues and zinc (II) ions. The thiol groups were oxidized to form disulfide bonds and the zinc (II) ions were indicated to be reduced to zinc atoms. These results indicate that the zinc finger motif is a target domain for gamma radiation, which may decrease 5S rRNA expression via impairment of the zinc finger motifs in TFIIIA. PMID:27803644

  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. Zinc oxyfluoride transparent conductor

    SciTech Connect

    Gordon, R.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 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. 8 figures.

  3. 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.

  4. 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.

  5. 2,6-Bis(2-Benzimidazolyl)Pyridine Fluorescent Red-Shifted Sensor for Recognition of Zinc(II) and a Calorimetric Sensor for Iron Ions.

    PubMed

    Vosough Razavi, Bita; Badiei, Alireza; Lashgari, Negar; Mohammadi Ziarani, Ghodsi

    2016-09-01

    The ability of 2,6-bis(2-benzimidazolyl)pyridine (bbp) as an optical sensor was studied by fluorescence spectroscopy, colorimetric and UV-visible techniques. The fluorescence spectra of bbp demonstrated a red-shifted upon addition of Zn(2+) ion, whereas rest of the cations did not induce any shift. Selectivity of the sensor was examined toward Zn(2+) in the presence of a wide range of cations, as interfering agents, that showed no disruption in its function. In addition, the pH effect was tested on the fluorescence response of bbp; which showed the efficiency of the sensor in a wide pH range. The limit of detection for Zn(2+) was estimated as 2.1 μM. Furthermore, the colorimetric studies were carried out and the observations showed a color change from colorless to purple by the addition of Fe(2+) ion and from colorless to yellow by the addition of Fe(3+). The UV-visible studies were carried out to confirm the colorimetric observations. The color changes occurred when Fe(2+) and Fe(3+) were added to the sensors solution, respectively. The detection limits were calculated as 2.8 × 10(-7) M and 3.5 × 10(-6) M for Fe(2+) and Fe(3+), respectively. Hence, bbp can be used as a dual mode optical sensor for detection of Zn(2+) by fluorescence and discriminately detection of Fe(2+) and Fe(3+) visually.

  6. 2,6-Bis(2-Benzimidazolyl)Pyridine Fluorescent Red-Shifted Sensor for Recognition of Zinc(II) and a Calorimetric Sensor for Iron Ions.

    PubMed

    Vosough Razavi, Bita; Badiei, Alireza; Lashgari, Negar; Mohammadi Ziarani, Ghodsi

    2016-09-01

    The ability of 2,6-bis(2-benzimidazolyl)pyridine (bbp) as an optical sensor was studied by fluorescence spectroscopy, colorimetric and UV-visible techniques. The fluorescence spectra of bbp demonstrated a red-shifted upon addition of Zn(2+) ion, whereas rest of the cations did not induce any shift. Selectivity of the sensor was examined toward Zn(2+) in the presence of a wide range of cations, as interfering agents, that showed no disruption in its function. In addition, the pH effect was tested on the fluorescence response of bbp; which showed the efficiency of the sensor in a wide pH range. The limit of detection for Zn(2+) was estimated as 2.1 μM. Furthermore, the colorimetric studies were carried out and the observations showed a color change from colorless to purple by the addition of Fe(2+) ion and from colorless to yellow by the addition of Fe(3+). The UV-visible studies were carried out to confirm the colorimetric observations. The color changes occurred when Fe(2+) and Fe(3+) were added to the sensors solution, respectively. The detection limits were calculated as 2.8 × 10(-7) M and 3.5 × 10(-6) M for Fe(2+) and Fe(3+), respectively. Hence, bbp can be used as a dual mode optical sensor for detection of Zn(2+) by fluorescence and discriminately detection of Fe(2+) and Fe(3+) visually. PMID:27365126

  7. 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

  8. 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.

  9. Locating Active-site Hydrogen Atoms in D-Xylose Isomerase: Time-of-Flight Neutron Diffraction.

    SciTech Connect

    Bunick, G 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 ) 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 was also determined.

  10. 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

  11. 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.

  12. [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

  13. 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

  14. 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

  15. 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

  16. 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

    Kudr, Jiri; Nguyen, Hoai Viet; Gumulec, Jaromir; Nejdl, Lukas; Blazkova, Iva; Ruttkay-Nedecky, Branislav; Hynek, David; Kynicky, Jindrich; Adam, Vojtech; Kizek, Rene

    2014-12-30

    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).

  17. 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

  18. 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

  19. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

    PubMed

    Fafarman, Aaron T; Sigala, Paul A; Schwans, Jason P; Fenn, Timothy D; Herschlag, Daniel; Boxer, Steven G

    2012-02-01

    Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.

  20. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  1. Elevated zinc induces siderophore biosynthesis genes and a zntA-like gene in Pseudomonas fluorescens.

    PubMed

    Rossbach, S; Wilson, T L; Kukuk, M L; Carty, H A

    2000-10-01

    Zinc-regulated genes were analyzed in Pseudomonas fluorescens employing mutagenesis with a reporter gene transposon. Six mutants responded with increased gene expression to elevated concentrations of zinc. Genetic and biochemical analysis revealed that in four of the six mutants the transposon had inserted into genes essential for the biosynthesis of the siderophore pyoverdine. The growth of one of the mutants was severely impaired in the presence of elevated concentrations of cadmium and zinc ions. In this mutant, the transposon had inserted in a gene with high similarity to P-type ATPases involved in zinc and cadmium ion transport. Four mutants reacted with reduced gene expression to elevated concentrations of zinc. One of these mutants was sensitive to zinc, cadmium and copper ions. The genetic region targeted in this mutant did not show similarity to any known gene. PMID:11004401

  2. 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

  3. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge.

    PubMed

    Tara, S; Elcock, A H; Kirchhoff, P D; Briggs, J M; Radic, Z; Taylor, P; McCammon, J A

    1998-12-01

    It is known that anionic surface residues play a role in the long-range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant kon, for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.

  4. Improved zinc electrode and rechargeable zinc-air battery

    DOEpatents

    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.

  5. Memo is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-Derived Phosphopeptide in its Vestigial Active Site

    SciTech Connect

    Qiu,C.; Lienhard, S.; Hynes, N.; Badache, A.; Leahy, D.

    2008-01-01

    Memo (mediator of ErbB2-driven cell motility) is a 297-amino-acid protein recently shown to co-precipitate with the C terminus of ErbB2 and be required for ErbB2-driven cell motility. Memo is not homologous to any known signaling proteins, and how it mediates ErbB2 signals is not known. To provide a molecular basis for understanding Memo function, we have determined and report here the 2.1A crystal structure of human Memo and show it be homologous to class III nonheme iron-dependent dioxygenases, a structural class that now includes a zinc-binding protein of unknown function. No metal binding or enzymatic activity can be detected for Memo, but Memo does bind directly to a specific ErbB2-derived phosphopeptide encompassing Tyr-1227 using its vestigial enzymatic active site. Memo thus represents a new class of phosphotyrosine-binding protein.

  6. 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.

  7. 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.

  8. Molecular dynamics explorations of active site structure in designed and evolved enzymes.

    PubMed

    Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

    2015-04-21

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. The depletion and regeneration of dissolution-active sites at the mineral-water interface: II. regeneration of active sites on α-Fe 2O 3 at pH 3 and pH 6

    NASA Astrophysics Data System (ADS)

    Samson, Sherry D.; Eggleston, Carrick M.

    2000-11-01

    Periods of transient nonsteady state dissolution can contain much information about dissolution mechanisms. Here, pH-jump-induced dissolution transients are used to explore the kinetics of production, at pH 3 and pH 6, of α-Fe 2O 3 surface sites active for dissolution at pH 1. We find that such sites are generated in a matter of minutes or less at higher pH. The steady state dissolution rate of hematite at pH 1 is ≤10.7 pmol m -2 s -1, whereas the rate of active site production at pH 6 in the first 30 min. of aging is at least 119 pmol m -2 s -1. Apparently, active sites are produced relatively slowly at low pH and relatively rapidly at circumneutral pH, despite the fact that dissolution rates are near a minimum at circumneutral pH. Using aqueous water exchange rates as a proxy for surface ligand exchange rates, this is qualitatively consistent with relatively slow water exchange by aqueous Fe 3+ ions at low pH and relatively rapid water exchange by Fe 3+ hydrolysis products (e.g., Fe(OH) 2+) at circumneutral pH. Consequently, the highest overall dissolution rates are achieved not at steady state at low pH, but by cycling between neutral and low pH. Our results call into question the assumption that oxide mineral surfaces, particularly those of iron and aluminum oxides, are inert on the time scale of proton or ligand adsorption (e.g., during the acid-base titrations typically used to measure oxide surface charge due to proton adsorption).

  17. Limitations of the potentiometric titration technique in determining the proton active site density of goethite surfaces

    NASA Astrophysics Data System (ADS)

    Lützenkirchen, Johannes; Boily, Jean-François; Lövgren, Lars; Sjöberg, Staffan

    2002-10-01

    these studies are restricted to goethite, those studies in which titrations with excess acid and base have been used for the determination of proton active site concentrations of sorbents should be reconsidered.

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

    SciTech Connect

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

    2008-01-01

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

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

    SciTech Connect

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

    2011-12-31

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

  20. 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.

  1. 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

  2. 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.

  3. 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.

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

    PubMed

    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.

  6. 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

  7. 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

  8. Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin

    SciTech Connect

    Dey, A.; Francis, E.J.; Adams, M.W.W.; Babini, E.; Takahashi, Y.; Fukuyama, K.; Hodgson, K.O.; Hedman, B.; Solomon, E.I.; /Stanford U., Chem. Dept. /Georgia U. /Bologna U. /Osaka U. /SLAC, SSRL

    2009-04-29

    A persistent puzzle in the field of biological electron transfer is the conserved iron-sulfur cluster motif in both high potential iron-sulfur protein (HiPIP) and ferredoxin (Fd) active sites. Despite this structural similarity, HiPIPs react oxidatively at physiological potentials, whereas Fds are reduced. Sulfur K-edge x-ray absorption spectroscopy uncovers the substantial influence of hydration on this variation in reactivity. Fe-S covalency is much lower in natively hydrated Fd active sites than in HiPIPs but increases upon water removal; similarly, HiPIP covalency decreases when unfolding exposes an otherwise hydrophobically shielded active site to water. Studies on model compounds and accompanying density functional theory calculations support a correlation of Fe-S covalency with ease of oxidation and therefore suggest that hydration accounts for most of the difference between Fd and HiPIP reduction potentials.

  9. 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.

  10. Additive agent for zinc alloy electrolyte and process

    SciTech Connect

    Bammel, B.D.

    1986-07-01

    An aqueous acidic electrolyte is described suitable for electrodepositing zinc alloys on a substrate comprising zinc ions and at least one additional metal ion selected from the group consisting nickel, cobalt, iron and mixtures thereof present in an amount sufficient to electrodeposit a zinc alloy, and, for providing improved grain-refinement and enhancing the codeposition of the alloying metals in the zinc alloy deposit. An effective amount of an additive agent consists of a bath-soluble anionic carboxylated polyoxyalkylene compound derived from the carboxylation of: (a) the polymerization of alkylene oxides selected from the group consisting of ethylene oxide, propylene oxide, glycidol, butylene oxide and mixtures thereof; and (b) the alkoxylation of mono and polyhydroxy compounds selected from the group consisting of hydroxyl containing alkyl, alkenyl, alkynyl, aryl, as well as mixtures thereof.

  11. Role of zinc in chronic gastritis.

    PubMed

    Marjanović, Ksenija; Dovhanj, Jasna; Kljaić, Ksenija; Sakić, Katarina; Kondza, Goran; Tadzić, Refmir; Vcev, Aleksandar

    2010-06-01

    Oxidative stress occurs in inflammation of gastric mucosa. The role of zinc in modulating oxidative stress has recently been recognized. Zn deficiency results in an increased sensitivity to oxidative stress and have a higher risk of musoca damage in inflammation. The aim of this study was to determine wheather chronic inflammation affects on the concentration of Zn2+ ions in gastric mucosa of patients with chronic gastritis. Forthy-three patients with chronic gastitis were enrolled. Patients were endoscoped. Histology and scoring of gastritis was performed following the guidelines of the updated Sydney system. Endoscopic finding of mucosa were scored according to a Lanza scoring system. The diagnosis of Helicobacter pylori (H. pylori) infection, histopathologic changes, intensity of inflammation and zinc concentration were determined from biopsies of gastric mucosa. The atomic absorption spectrophotometer was used to determine tissue concentrations of zinc. Twenty of 43 patients with chronic gastritis were uninfected by H. pylori. There was no statistically significant difference in tissue concentrations of zinc between H. pylori-positive and H. pylori-negative patients. From those infected patients 53.3% had chronic active gastritis. There was no statistically significant difference in tissue concentrations of zinc between patients with chronic active gastritis and patients with chronic inactive gastritis (p = 0.966). Zn in antrum showed positive correlation with density of H. pylori in antrum (Spearman' rho = 0.481, p = 0.020), negative correlation with density of H. pylori in corpus (Spearman' rho = -0.492, p = 0.017) and with zinc in corpus (Spearman' rho = 0.631, p =0.001). Tissue concentration of zinc was not affected by chronic inflammation of gastric mucosa in patients with chronic gastritis.

  12. 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.

  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. Structural Analysis of the Active Site Geometry of N[superscript 5]-Carboxyaminoimidazole Ribonucleotide Synthetase from Escherichia coli

    SciTech Connect

    Thoden, James B.; Holden, Hazel M.; Firestine, Steven M.

    2009-09-11

    N{sub 5}-Carboxyaminoimidazole ribonucleotide synthetase (N{sub 5}-CAIR synthetase) converts 5-aminoimidazole ribonucleotide (AIR), MgATP, and bicarbonate into N{sub 5}-CAIR, MgADP, and P{sub i}. The enzyme is required for de novo purine biosynthesis in microbes yet is not found in humans suggesting that it represents an ideal and unexplored target for antimicrobial drug design. Here we report the X-ray structures of N{sub 5}-CAIR synthetase from Escherichia coli with either MgATP or MgADP/P{sub i} bound in the active site cleft. These structures, determined to 1.6-{angstrom} resolution, provide detailed information regarding the active site geometry before and after ATP hydrolysis. In both structures, two magnesium ions are observed. Each of these is octahedrally coordinated, and the carboxylate side chain of Glu238 bridges them. For the structure of the MgADP/P{sub i} complex, crystals were grown in the presence of AIR and MgATP. No electron density was observed for AIR, and the electron density corresponding to the nucleotide clearly revealed the presence of ADP and P{sub i} rather than ATP. The bound P{sub i} shifts by approximately 3 {angstrom} relative to the {gamma}-phosphoryl group of ATP and forms electrostatic interactions with the side chains of Arg242 and His244. Since the reaction mechanism of N{sub 5}-CAIR synthetase is believed to proceed via a carboxyphosphate intermediate, we propose that the location of the inorganic phosphate represents the binding site for stabilization of this reactive species. Using the information derived from the two structures reported here, coupled with molecular modeling, we propose a catalytic mechanism for N{sub 5}-CAIR synthetase.

  16. 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

  17. The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction.

    PubMed Central

    Derbyshire, V; Grindley, N D; Joyce, C M

    1991-01-01

    We have used site-directed mutagenesis to change amino acid side chains that have been shown crystallographically to be in close proximity to a DNA 3' terminus bound at the 3'-5' exonuclease active site of Klenow fragment. Exonuclease assays of the resulting mutant proteins indicate that the largest effects on exonuclease activity result from mutations in a group of carboxylate side chains (Asp355, Asp424 and Asp501) anchoring two divalent metal ions that are essential for exonuclease activity. Another carboxylate (Glu357) within this cluster seems to be less important as a metal ligand, but may play a separate role in catalysis of the exonuclease reaction. A second group of residues (Leu361, Phe473 and Tyr497), located around the terminal base and ribose positions, plays a secondary role, ensuring correct positioning of the substrate in the active site and perhaps also facilitating melting of a duplex DNA substrate by interacting with the frayed 3' terminus. The pH-dependence of the 3'-5' exonuclease reaction is consistent with a mechanism in which nucleophilic attack on the terminal phosphodiester bond is initiated by a hydroxide ion coordinated to one of the enzyme-bound metal ions. PMID:1989882

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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).

  3. Reversible zinc-induced injuries to erythrocyte membrane nanostructure.

    PubMed

    Chernysh, A M; Kozlova, E K; Moroz, V V; Sergunova, V A; Gudkova, O Ye; Fedorova, M S

    2012-11-01

    Zinc-induced injuries to red blood cell membrane nanostructures at different zinc concentrations were studied by atomic force microscopy. In order to distinguish the intrinsic characteristics of membrane nanostructures, the membrane surfaces were represented by three orders using 3D Fourier transform. Increasing the concentrations of zinc ions modified the pattern of induced injuries: their depths and diameters and their number on the membrane surface test area increased. The injuries and their distribution for each order of membrane surface were analyzed. Albumin restored membrane nanosurface.

  4. Merging Allosteric and Active Site Binding Motifs: De novo Generation of Target Selectivity and Potency via Natural-Product-Derived Fragments

    PubMed Central

    Lanz, Jan; Riedl, Rainer

    2015-01-01

    The de novo design of molecules from scratch with tailored biological activity is still the major intellectual challenge in chemical biology and drug discovery. Herein we validate natural-product-derived fragments (NPDFs) as excellent molecular seeds for the targeted de novo discovery of lead structures for the modulation of therapeutically relevant proteins. The application of this de novo approach delivered, in synergy with the combination of allosteric and active site binding motifs, highly selective and ligand-efficient non-zinc-binding (3: 4-{[5-(2-{[(3-methoxyphenyl)methyl]carbamoyl}eth-1-yn-1-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl]methyl}benzoic acid) as well as zinc-binding (4: 4-({5-[2-({[3-(3-carboxypropoxy)phenyl]methyl}carbamoyl)eth-1-yn-1-yl]-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl}methyl)benzoic acid) uracil-based MMP-13 inhibitors presenting IC50 values of 11 nm (3: LE=0.35) and 6 nm (4: LE=0.31). PMID:25487909

  5. Merging allosteric and active site binding motifs: de novo generation of target selectivity and potency via natural-product-derived fragments.

    PubMed

    Lanz, Jan; Riedl, Rainer

    2015-03-01

    The de novo design of molecules from scratch with tailored biological activity is still the major intellectual challenge in chemical biology and drug discovery. Herein we validate natural-product-derived fragments (NPDFs) as excellent molecular seeds for the targeted de novo discovery of lead structures for the modulation of therapeutically relevant proteins. The application of this de novo approach delivered, in synergy with the combination of allosteric and active site binding motifs, highly selective and ligand-efficient non-zinc-binding (3: 4-{[5-(2-{[(3-methoxyphenyl)methyl]carbamoyl}eth-1-yn-1-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl]methyl}benzoic acid) as well as zinc-binding (4: 4-({5-[2-({[3-(3-carboxypropoxy)phenyl]methyl}carbamoyl)eth-1-yn-1-yl]-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl}methyl)benzoic acid) uracil-based MMP-13 inhibitors presenting IC50 values of 11 nM (3: LE=0.35) and 6 nM (4: LE=0.31).

  6. 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

  7. 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.

  8. Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

    SciTech Connect

    Phillips, J.; Warby, C; Whitby, F; Kushner, J; Hill, C

    2009-01-01

    Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.

  9. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    PubMed

    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.

  10. Active site of tripeptidyl peptidase II from human erythrocytes is of the subtilisin type.

    PubMed Central

    Tomkinson, B; Wernstedt, C; Hellman, U; Zetterqvist, O

    1987-01-01

    The present report presents evidence that the amino acid sequence around the serine of the active site of human tripeptidyl peptidase II is of the subtilisin type. The enzyme from human erythrocytes was covalently labeled at its active site with [3H]diisopropyl fluorophosphate, and the protein was subsequently reduced, alkylated, and digested with trypsin. The labeled tryptic peptides were purified by gel filtration and repeated reversed-phase HPLC, and their amino-terminal sequences were determined. Residue 9 contained the radioactive label and was, therefore, considered to be the active serine residue. The primary structure of the part of the active site (residues 1-10) containing this residue was concluded to be Xaa-Thr-Gln-Leu-Met-Asx-Gly-Thr-Ser-Met. This amino acid sequence is homologous to the sequence surrounding the active serine of the microbial peptidases subtilisin and thermitase. These data demonstrate that human tripeptidyl peptidase II represents a potentially distinct class of human peptidases and raise the question of an evolutionary relationship between the active site of a mammalian peptidase and that of the subtilisin family of serine peptidases. PMID:3313395

  11. 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

  12. 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.

  13. Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors.

    PubMed

    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

    2010-08-01

    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.

  14. 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

  15. A modular treatment of molecular traffic through the active site of cholinesterase

    PubMed Central

    Botti, SA; Felder, CE; Lifson, S; Sussman, JL; Silman, I

    1999-01-01

    We present a model for the molecular traffic of ligands, substrates, and products through the active site of cholinesterases (ChEs). First, we describe a common treatment of the diffusion to a buried active site of cationic and neutral species. We then explain the specificity of ChEs for cationic ligands and substrates by introducing two additional components to this common treatment. The first module is a surface trap for cationic species at the entrance to the active-site gorge that operates through local, short-range electrostatic interactions and is independent of ionic strength. The second module is an ionic-strength-dependent steering mechanism generated by long-range electrostatic interactions arising from the overall distribution of charges in ChEs. Our calculations show that diffusion of charged ligands relative to neutral isosteric analogs is enhanced approximately 10-fold by the surface trap, while electrostatic steering contributes only a 1.5- to 2-fold rate enhancement at physiological salt concentration. We model clearance of cationic products from the active-site gorge as analogous to the escape of a particle from a one-dimensional well in the presence of a linear electrostatic potential. We evaluate the potential inside the gorge and provide evidence that while contributing to the steering of cationic species toward the active site, it does not appreciably retard their clearance. This optimal fine-tuning of global and local electrostatic interactions endows ChEs with maximum catalytic efficiency and specificity for a positively charged substrate, while at the same time not hindering clearance of the positively charged products. PMID:10545346

  16. 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

  17. 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

  18. 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.

  19. SABER: A computational method for identifying active sites for new reactions

    PubMed Central

    Nosrati, Geoffrey R; Houk, K N

    2012-01-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  20. SABER: a computational method for identifying active sites for new reactions.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  1. [Effect of Zinc Doped Calcium Phosphate Coating on Bone Formation and the Underlying Biological Mechanism].

    PubMed

    Luo, Wenjing; Zhao, Jinghui; Meng, Xing; Ma, Shanshan; Sun, Qianyue; Guo, Tianqi; Wang, Yufeng; Zhou, Yanmin

    2015-12-01

    Implant surface modified coating can improve its osteoinductivity, about which simple calcium phosphate coating has been extensively studied. But it has slow osteointegration speed and poor antibacterial property, while other metal ions added, such as nano zinc ion, can compensate for these deficiencies. This paper describes the incorporation form, the effect on physical and chemical properties of the material and the antibacterial property of nano zinc, and summarizes the material's biological property given by calcium ion, zinc ion and inorganic phosphate (Pi), mainly focusing on the influence of these three inorganic ions on osteoblast proliferation, differentiation, protein synthesis and matrix mineralization in order to present the positive function of zinc doped calcium phosphate in the field of bone formation.

  2. Polymerization of UDMA using zinc particles and 4-META with and without BPO.

    PubMed

    Wanichacheva, N; Miyagawa, Y; Ogura, H

    2000-06-01

    The polymerization phenomena of zinc particles moistened with a small amount of water, 4-META, and UDMA without amine in the presence and absence of BPO were investigated. The effects of 4-META and BPO on the setting time and the degree of conversion (DC) were studied. Moreover, the effect of zinc ion amount on the setting time was investigated. As-received zinc particles could induce the polymerization either with or without BPO. A higher concentration of 4-META shortened the setting time and increased DC when BPO was absent. However, the presence of BPO generally retarded the setting time and decreased DC, although its effect was dependent on the 4-META concentration. A higher amount of zinc ion retarded the setting reaction in the presence of 4-META. The zinc particles mixed with 10% zinc sulfate and acetic acid solutions could induce the polymerization of UDMA containing BPO when the amine and 4-META were absent.

  3. Importance of the structural zinc atom for the stability of yeast alcohol dehydrogenase.

    PubMed Central

    Magonet, E; Hayen, P; Delforge, D; Delaive, E; Remacle, J

    1992-01-01

    Yeast alcohol dehydrogenase is a tetrameric enzyme containing zinc. Initially we confirmed the presence of two zinc atoms per subunit. Incubation of the enzyme with increasing concentrations of dithiothreitol, a method for partial chelation, allowed first the reduction of four disulphide bridges per enzyme, but eventually was sufficient to chelate the structural zinc atom without having any effect on the zinc located in the active site. The enzyme activity was not affected but the enzyme became very sensitive to heat denaturation. Chelation by EDTA was also performed. Given its location at an external position in the globular protein, protected in each subunit by one disulphide bridge, the results establish that the second zinc atom present on each enzymic subunit plays a prominent conformational role, probably by stabilizing the tertiary structure of yeast alcohol dehydrogenase. Recovery experiments were performed by incubation of the native enzyme, or the dithiothreitol-treated enzyme, with a small amount of Zn2+. A stabilization effect was found when the structural zinc was re-incorporated after its removal by dithiothreitol. In all cases a large increase in activity was also observed, which was much greater than that expected based on the amount of re-incorporated zinc atom, suggesting the re-activation of some inactive commercial enzyme which had lost some of its original catalytic zinc atoms. PMID:1445195

  4. 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.

  5. 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.

  6. 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.

  7. Designing hydrolytic zinc metalloenzymes.

    PubMed

    Zastrow, Melissa L; Pecoraro, Vincent L

    2014-02-18

    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

  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. The interactive roles of zinc and calcium in mitochondrial dysfunction and neurodegeneration

    PubMed Central

    Pivovarova, Natalia B.; Stanika, Ruslan I.; Kazanina, Galina; Villanueva, Idalis; Andrews, S. Brian

    2013-01-01

    Zinc has been implicated in neurodegeneration following ischemia. In analogy to calcium, zinc has been proposed to induce toxicity via mitochondrial dysfunction, but the relative role of each cation in mitochondrial damage is unclear. Here we report that under conditions mimicking ischemia in hippocampal neurons — normal (2 mM) calcium plus elevated (>100 μM) exogenous zinc — mitochondrial dysfunction evoked by glutamate, kainate or direct depolarization is, despite significant zinc uptake, primarily governed by calcium. Thus, robust mitochondrial ion accumulation, swelling, depolarization and ROS generation were only observed after toxic stimulation in calcium-containing media. This contrasts with the lack of any mitochondrial response in zinc-containing but calcium-free medium, even though zinc uptake and toxicity were strong under these conditions. Indeed, abnormally high, ionophore-induced zinc uptake was necessary to elicit any mitochondrial depolarization. In calcium- and zinc-containing media, depolarization-induced zinc uptake facilitated cell death and enhanced accumulation of mitochondrial calcium, which localized to characteristic matrix precipitates. Some of these contained detectable amounts of zinc. Together these data indicate that zinc uptake is generally insufficient to trigger mitochondrial dysfunction, so that mechanism(s) of zinc toxicity must be different from that of calcium. PMID:24127746

  10. The interactive roles of zinc and calcium in mitochondrial dysfunction and neurodegeneration.

    PubMed

    Pivovarova, Natalia B; Stanika, Ruslan I; Kazanina, Galina; Villanueva, Idalis; Andrews, S Brian

    2014-02-01

    Zinc has been implicated in neurodegeneration following ischemia. In analogy with calcium, zinc has been proposed to induce toxicity via mitochondrial dysfunction, but the relative role of each cation in mitochondrial damage remains unclear. Here, we report that under conditions mimicking ischemia in hippocampal neurons - normal (2 mM) calcium plus elevated (> 100 μM) exogenous zinc - mitochondrial dysfunction evoked by glutamate, kainate or direct depolarization is, despite significant zinc uptake, primarily governed by calcium. Thus, robust mitochondrial ion accumulation, swelling, depolarization, and reactive oxygen species generation were only observed after toxic stimulation in calcium-containing media. This contrasts with the lack of any mitochondrial response in zinc-containing but calcium-free medium, even though zinc uptake and toxicity were strong under these conditions. Indeed, abnormally high, ionophore-induced zinc uptake was necessary to elicit any mitochondrial depolarization. In calcium- and zinc-containing media, depolarization-induced zinc uptake facilitated cell death and enhanced accumulation of mitochondrial calcium, which localized to characteristic matrix precipitates. Some of these contained detectable amounts of zinc. Together these data indicate that zinc uptake is generally insufficient to trigger mitochondrial dysfunction, so that mechanism(s) of zinc toxicity must be different from that of calcium.

  11. 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

  12. 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

  13. Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase.

    PubMed

    Mládková, Jana; Hladílková, Jana; Diamond, Carrie E; Tryon, Katherine; Yamada, Kazuhiro; Garrow, Timothy A; Jungwirth, Pavel; Koutmos, Markos; Jiráček, Jiří

    2014-10-01

    Betaine-homocysteine S-methyltransferase (BHMT) is a zinc-dependent methyltransferase that uses betaine as the methyl donor for the remethylation of homocysteine to form methionine. This reaction supports S-adenosylmethionine biosynthesis, which is required for hundreds of methylation reactions in humans. Herein we report that BHMT is activated by potassium ions with an apparent K(M) for K⁺ of about 100 µM. The presence of potassium ions lowers the apparent K(M) of the enzyme for homocysteine, but it does not affect the apparent K(M) for betaine or the apparent k(cat) for either substrate. We employed molecular dynamics (MD) simulations to theoretically predict and protein crystallography to experimentally localize the binding site(s) for potassium ion(s). Simulations predicted that K⁺ ion would interact with residues Asp26 and/or Glu159. Our crystal structure of BHMT bound to homocysteine confirms these sites of interaction and reveals further contacts between K⁺ ion and BHMT residues Gly27, Gln72, Gln247, and Gly298. The potassium binding residues in BHMT partially overlap with the previously identified DGG (Asp26-Gly27-Gly28) fingerprint in the Pfam 02574 group of methyltransferases. Subsequent biochemical characterization of several site-specific BHMT mutants confirmed the results obtained by the MD simulations and crystallographic data. Together, the data herein indicate that the role of potassium ions in BHMT is structural and that potassium ion facilitates the specific binding of homocysteine to the active site of the enzyme.

  14. 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

  15. 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

  16. Zinc fingers, zinc clusters, and zinc twists in DNA-binding protein domains.

    PubMed Central

    Vallee, B L; Coleman, J E; Auld, D S

    1991-01-01

    We now recognize three distinct motifs of DNA-binding zinc proteins: (i) zinc fingers, (ii) zinc clusters, and (iii) zinc twists. Until very recently, x-ray crystallographic or NMR three-dimensional structure analyses of DNA-binding zinc proteins have not been available to serve as standards of reference for the zinc binding sites of these families of proteins. Those of the DNA-binding domains of the fungal transcription factor GAL4 and the rat glucocorticoid receptor are the first to have been determined. Both proteins contain two zinc binding sites, and in both, cysteine residues are the sole zinc ligands. In GAL4, two zinc atoms are bound to six cysteine residues which form a "zinc cluster" akin to that of metallothionein; the distance between the two zinc atoms of GAL4 is approximately 3.5 A. In the glucocorticoid receptor, each zinc atom is bound to four cysteine residues; the interatomic zinc-zinc distance is approximately 13 A, and in this instance, a "zinc twist" is represented by a helical DNA recognition site located between the two zinc atoms. Zinc clusters and zinc twists are here recognized as two distinctive motifs in DNA-binding proteins containing multiple zinc atoms. For native "zinc fingers," structural data do not exist as yet; consequently, the interatomic distances between zinc atoms are not known. As further structural data become available, the structural and functional significance of these different motifs in their binding to DNA and other proteins participating in the transmission of the genetic message will become apparent. Images PMID:1846973

  17. 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

  18. Zinc and inflammatory/immune response in aging.

    PubMed

    Vasto, Sonya; Mocchegiani, Eugenio; Malavolta, Marco; Cuppari, Irene; Listì, Florinda; Nuzzo, Domenico; Ditta, Vito; Candore, Giuseppina; Caruso, Calogero

    2007-04-01

    Life-long antigenic burden determines a condition of chronic inflammation, with increased lymphocyte activation and proinflammatory cytokine production. A large number of studies have documented changes in zinc metabolism in experimental animal models of acute and chronic inflammation and in human chronic inflammatory conditions. In particular, modification of zinc plasma concentration, as well as intracellular disturbance of antioxidant intracellular pathways, has been found in aging and in some age-related diseases. Zinc deficiency is diffused in aged individuals in order to avoid meat and other high zinc content foods due to fear of cholesterol. Rather, they increase the consumption of refined wheat products that lack zinc and other critical nutrients as a consequence of the refining process. On the other hand, plasma zinc concentration is influenced by proinflammatory cytokines (IL-6 and TNF-alpha) and by metallothioneins (MT) homeostasis, which is in turn affected by proinflammatory cytokines. MT increase in aging and chronic inflammation allowing a continuous sequestration of intracellular zinc with subsequent low zinc ion availability against stressor agents and inflammation. This phenomenon leads to an impaired inflammatory/immune response in the elderly. A major target of zinc is NF-kappaB, a transcription factor critical for the expression of proinflammatory cytokines whose production is regulated by extra- and intracellular activating and inhibiting factors interacting with the regulatory elements on cytokine genes. Effects of zinc on translocation of NF-kappaB have been attributed to the suppression of phosphorylation and degradation of the inhibitory proteins (A20) that normally sequester it in the cytoplasm. Moreover, this factor and A20 are regulated by specific genes involved in inflammation and by intracellular zinc ion availability. So, it is not so surprising that zinc deficiency is constantly observed in chronic inflammation, such as in old

  19. Zinc and inflammatory/immune response in aging.

    PubMed

    Vasto, Sonya; Mocchegiani, Eugenio; Malavolta, Marco; Cuppari, Irene; Listì, Florinda; Nuzzo, Domenico; Ditta, Vito; Candore, Giuseppina; Caruso, Calogero

    2007-04-01

    Life-long antigenic burden determines a condition of chronic inflammation, with increased lymphocyte activation and proinflammatory cytokine production. A large number of studies have documented changes in zinc metabolism in experimental animal models of acute and chronic inflammation and in human chronic inflammatory conditions. In particular, modification of zinc plasma concentration, as well as intracellular disturbance of antioxidant intracellular pathways, has been found in aging and in some age-related diseases. Zinc deficiency is diffused in aged individuals in order to avoid meat and other high zinc content foods due to fear of cholesterol. Rather, they increase the consumption of refined wheat products that lack zinc and other critical nutrients as a consequence of the refining process. On the other hand, plasma zinc concentration is influenced by proinflammatory cytokines (IL-6 and TNF-alpha) and by metallothioneins (MT) homeostasis, which is in turn affected by proinflammatory cytokines. MT increase in aging and chronic inflammation allowing a continuous sequestration of intracellular zinc with subsequent low zinc ion availability against stressor agents and inflammation. This phenomenon leads to an impaired inflammatory/immune response in the elderly. A major target of zinc is NF-kappaB, a transcription factor critical for the expression of proinflammatory cytokines whose production is regulated by extra- and intracellular activating and inhibiting factors interacting with the regulatory elements on cytokine genes. Effects of zinc on translocation of NF-kappaB have been attributed to the suppression of phosphorylation and degradation of the inhibitory proteins (A20) that normally sequester it in the cytoplasm. Moreover, this factor and A20 are regulated by specific genes involved in inflammation and by intracellular zinc ion availability. So, it is not so surprising that zinc deficiency is constantly observed in chronic inflammation, such as in old

  20. 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.

  1. 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

  2. Zinc in diet

    MedlinePlus

    ... Zinc is also needed for the senses of smell and taste. During pregnancy, infancy, and childhood the ... sense of taste Problems with the sense of smell Skin sores Slow growth Trouble seeing in the ...

  3. 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.

  4. Docking and molecular dynamics studies at trypanothione reductase and glutathione reductase active sites.

    PubMed

    Iribarne, Federico; Paulino, Margot; Aguilera, Sara; Murphy, Miguel; Tapia, Orlando

    2002-05-01

    A theoretical docking study on the active sites of trypanothione reductase (TR) and glutathione reductase (GR) with the corresponding natural substrates, trypanothione disulfide (T[S]2) and glutathione disulfide (GSSG), is reported. Molecular dynamics simulations were carried out in order to check the robustness of the docking results. The energetic results are in agreement with previous experimental findings and show the crossed complexes have lower stabilization energies than the natural ones. To test DOCK3.5, four nitro furanic compounds, previously designed as potentially active anti-chagasic molecules, were docked at the GR and TR active sites with the DOCK3.5 procedure. A good correlation was found between differential inhibitory activity and relative interaction energy (affinity). The results provide a validation test for the use of DOCK3.5 in connection with the design of anti-chagasic drugs.

  5. 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

  6. 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

  7. 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).

  8. 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.

  9. 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.

  10. 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.

  11. Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction

    PubMed Central

    Zeymer, Cathleen; Werbeck, Nicolas D.; Zimmermann, Sabine

    2016-01-01

    Abstract 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

  12. 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

  13. 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...

  14. 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.

  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. 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

  17. Controlling activation site density by low-energy far-field stimulation in cardiac tissue.

    PubMed

    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.

  18. 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.

  19. 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

  20. ttm-1 encodes CDF transporters that excrete zinc from intestinal cells of C. elegans and act in a parallel negative feedback circuit that promotes homeostasis.

    PubMed

    Roh, Hyun Cheol; Collier, Sara; Deshmukh, Krupa; Guthrie, James; Robertson, J David; Kornfeld, Kerry

    2013-05-01

    Zinc is an essential metal involved in a wide range of biological processes, and aberrant zinc metabolism is implicated in human diseases. The gastrointestinal tract of animals is a critical site of zinc metabolism that is responsible for dietary zinc uptake and distribution to the body. However, the role of the gastrointestinal tract in zinc excretion remains unclear. Zinc transporters are key regulators of zinc metabolism that mediate the movement of zinc ions across membranes. Here, we identified a comprehensive list of 14 predicted Cation Diffusion Facilitator (CDF) family zinc transporters in Caenorhabditis elegans and demonstrated that zinc is excreted from intestinal cells by one of these CDF proteins, TTM-1B. The ttm-1 locus encodes two transcripts, ttm-1a and ttm-1b, that use different transcription start sites. ttm-1b expression was induced by high levels of zinc specifically in intestinal cells, whereas ttm-1a was not induced by zinc. TTM-1B was localized to the apical plasma membrane of intestinal cells, and analyses of loss-of-function mutant animals indicated that TTM-1B promotes zinc excretion into the intestinal lumen. Zinc excretion mediated by TTM-1B contributes to zinc detoxification. These observations indicate that ttm-1 is a component of a negative feedback circuit, since high levels of cytoplasmic zinc increase ttm-1b transcript levels and TTM-1B protein functions to reduce the level of cytoplasmic zinc. We showed that TTM-1 isoforms function in tandem with CDF-2, which is also induced by high levels of cytoplasmic zinc and reduces cytoplasmic zinc levels by sequestering zinc in lysosome-related organelles. These findings define a parallel negative feedback circuit that promotes zinc homeostasis and advance the understanding of the physiological roles of the gastrointestinal tract in zinc