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Sample records for surface zinc binding

  1. Structural characterization of S100A15 reveals a novel zinc coordination site among S100 proteins and altered surface chemistry with functional implications for receptor binding

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    Murray Jill I

    2012-07-01

    Full Text Available Abstract Background S100 proteins are a family of small, EF-hand containing calcium-binding signaling proteins that are implicated in many cancers. While the majority of human S100 proteins share 25-65% sequence similarity, S100A7 and its recently identified paralog, S100A15, display 93% sequence identity. Intriguingly, however, S100A7 and S100A15 serve distinct roles in inflammatory skin disease; S100A7 signals through the receptor for advanced glycation products (RAGE in a zinc-dependent manner, while S100A15 signals through a yet unidentified G-protein coupled receptor in a zinc-independent manner. Of the seven divergent residues that differentiate S100A7 and S100A15, four cluster in a zinc-binding region and the remaining three localize to a predicted receptor-binding surface. Results To investigate the structural and functional consequences of these divergent clusters, we report the X-ray crystal structures of S100A15 and S100A7D24G, a hybrid variant where the zinc ligand Asp24 of S100A7 has been substituted with the glycine of S100A15, to 1.7 Å and 1.6 Å resolution, respectively. Remarkably, despite replacement of the Asp ligand, zinc binding is retained at the S100A15 dimer interface with distorted tetrahedral geometry and a chloride ion serving as an exogenous fourth ligand. Zinc binding was confirmed using anomalous difference maps and solution binding studies that revealed similar affinities of zinc for S100A15 and S100A7. Additionally, the predicted receptor-binding surface on S100A7 is substantially more basic in S100A15 without incurring structural rearrangement. Conclusions Here we demonstrate that S100A15 retains the ability to coordinate zinc through incorporation of an exogenous ligand resulting in a unique zinc-binding site among S100 proteins. The altered surface chemistry between S100A7 and S100A15 that localizes to the predicted receptor binding site is likely responsible for the differential recognition of distinct

  2. Zinc Binding by Lactic Acid Bacteria

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    Jasna Mrvčić

    2009-01-01

    Full Text Available Zinc is an essential trace element in all organisms. A common method for the prevention of zinc deficiency is pharmacological supplementation, especially in a highly available form of a metalloprotein complex. The potential of different microbes to bind essential and toxic heavy metals has recently been recognized. In this work, biosorption of zinc by lactic acid bacteria (LAB has been investigated. Specific LAB were assessed for their ability to bind zinc from a water solution. Significant amount of zinc ions was bound, and this binding was found to be LAB species-specific. Differences among the species in binding performance at a concentration range between 10–90 mg/L were evaluated with Langmuir model for biosorption. Binding of zinc was a fast process, strongly influenced by ionic strength, pH, biomass concentration, and temperature. The most effective metal-binding LAB species was Leuconostoc mesenteroides (27.10 mg of Zn2+ per gram of dry mass bound at pH=5 and 32 °C, during 24 h. FT-IR spectroscopy analysis and electron microscopy demonstrated that passive adsorption and active uptake of the zinc ions were involved.

  3. Zinc-induced oligomerization of zinc α2 glycoprotein reveals multiple fatty acid-binding sites.

    Science.gov (United States)

    Zahid, Henna; Miah, Layeque; Lau, Andy M; Brochard, Lea; Hati, Debolina; Bui, Tam T T; Drake, Alex F; Gor, Jayesh; Perkins, Stephen J; McDermott, Lindsay C

    2016-01-01

    Zinc α2 glycoprotein (ZAG) is an adipokine with a class I MHC protein fold and is associated with obesity and diabetes. Although its intrinsic ligand remains unknown, ZAG binds the dansylated C11 fatty acid 11-(dansylamino)undecanoic acid (DAUDA) in the groove between the α1 and α2 domains. The surface of ZAG has approximately 15 weak zinc-binding sites deemed responsible for precipitation from human plasma. In the present study the functional significance of these metal sites was investigated. Analytical ultracentrifugation (AUC) and CD showed that zinc, but not other divalent metals, causes ZAG to oligomerize in solution. Thus ZAG dimers and trimers were observed in the presence of 1 and 2 mM zinc. Molecular modelling of X-ray scattering curves and sedimentation coefficients indicated a progressive stacking of ZAG monomers, suggesting that the ZAG groove may be occluded in these. Using fluorescence-detected sedimentation velocity, these ZAG-zinc oligomers were again observed in the presence of the fluorescent boron dipyrromethene fatty acid C16-BODIPY (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-hexadecanoic acid). Fluorescence spectroscopy confirmed that ZAG binds C16-BODIPY. ZAG binding to C16-BODIPY, but not to DAUDA, was reduced by increased zinc concentrations. We conclude that the lipid-binding groove in ZAG contains at least two distinct fatty acid-binding sites for DAUDA and C16-BODIPY, similar to the multiple lipid binding seen in the structurally related immune protein CD1c. In addition, because high concentrations of zinc occur in the pancreas, the perturbation of these multiple lipid-binding sites by zinc may be significant in Type 2 diabetes where dysregulation of ZAG and zinc homoeostasis occurs.

  4. A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution.

    Science.gov (United States)

    Sharpe, Belinda K; Matthews, Jacqueline M; Kwan, Ann H Y; Newton, Anthea; Gell, David A; Crossley, Merlin; Mackay, Joel P

    2002-05-01

    Many different zinc binding modules have been identified. Their abundance and variety suggests that the formation of zinc binding folds might be relatively common. We have determined the structure of CH1(1), a 27-residue peptide derived from the first cysteine/histidine-rich region (CH1) of CREB binding protein (CBP). This peptide forms a highly ordered zinc-dependent fold that is distinct from known folds. The structure differs from a subsequently determined structure of a larger region from the CH3 region of CBP, and the CH1(1) fold probably represents a nonphysiologically active form. Despite this, the fold is thermostable and tolerant to both multiple alanine mutations and changes in the zinc-ligand spacing. Our data support the idea that zinc binding domains may arise frequently. Additionally, such structures may prove useful as scaffolds for protein design, given their stability and robustness.

  5. Predicting zinc binding at the proteome level

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    Rosato Antonio

    2007-02-01

    Full Text Available Abstract Background Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial. Results The present work reports on the development of a machine learning method for the prediction of the zinc-binding state of pairs of nearby amino-acids, using predictors based on support vector machines. The predictor was trained using chains containing zinc-binding sites and non-metalloproteins in order to provide positive and negative examples. Results based on strong non-redundancy tests prove that (1 zinc-binding residues can be predicted and (2 modelling the correlation between the binding state of nearby residues significantly improves performance. The trained predictor was then applied to the human proteome. The present results were in good agreement with the outcomes of previous, highly manually curated, efforts for the identification of human zinc-binding proteins. Some unprecedented zinc-binding sites could be identified, and were further validated through structural modelling. The software implementing the predictor is freely available at: http://zincfinder.dsi.unifi.it Conclusion The proposed approach constitutes a highly automated tool for the identification of metalloproteins, which provides results of comparable quality with respect to highly manually refined predictions. The ability to model correlations between pairwise residues allows it to obtain a significant improvement over standard 1D based approaches. In addition, the method permits the identification of unprecedented metal sites, providing important hints for the work of experimentalists.

  6. Chemical treatment of zinc surface and its corrosion inhibition studies

    Indian Academy of Sciences (India)

    S K Rajappa; T V Venkatesha; B M Praveen

    2008-02-01

    The surface treatment of zinc and its corrosion inhibition was studied using a product (BTSC) formed in the reaction between benzaldehyde and thiosemicarbozide. The corrosion behaviour of chemically treated zinc surface was investigated in aqueous chloride–sulphate medium using galvanostatic polarization technique. Zinc samples treated in BTSC solution exhibited good corrosion resistance. The measured electrochemical data indicated a basic modification of the cathode reaction during corrosion of treated zinc. The corrosion protection may be explained on the basis of adsorption and formation of BTSC film on zinc surface. The film was binding strongly to the metal surface through nitrogen and sulphur atoms of the product. The formation of film on the zinc surface was established by surface analysis techniques such as scanning electron microscopy (SEM–EDS) and Fourier transform infrared spectroscopy (FTIR).

  7. Zinc-induced oligomerization of zinc α2 glycoprotein reveals multiple fatty acid-binding sites

    OpenAIRE

    Zahid, Henna; Miah, Layeque; Lau, Andy; Brochard, Lea; Hati, Debolina; Bui, T. T.; Drake, A. F.; Gor, Jayesh; Perkins, Stephen J.; McDermott, Lindsay C.

    2016-01-01

    Zinc α2 glycoprotein (ZAG) is an adipokine with a class I MHC protein fold and is associated with obesity and diabetes. Although its intrinsic ligand remains unknown, ZAG binds the dansylated C11 fatty acid 11-(dansylamino)undecanoic acid (DAUDA) in the groove between the α1 and α2 domains. The surface of ZAG has approximately 15 weak zinc-binding sites deemed responsible for precipitation from human plasma. In the present study the functional significance of these metal sites was investigate...

  8. Zinc-regulated DNA binding of the yeast Zap1 zinc-responsive activator.

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    Avery G Frey

    Full Text Available The Zap1 transcription factor of Saccharomyces cerevisiae plays a central role in zinc homeostasis by controlling the expression of genes involved in zinc metabolism. Zap1 is active in zinc-limited cells and repressed in replete cells. At the transcriptional level, Zap1 controls its own expression via positive autoregulation. In addition, Zap1's two activation domains are regulated independently of each other by zinc binding directly to those regions and repressing activation function. In this report, we show that Zap1 DNA binding is also inhibited by zinc. DMS footprinting showed that Zap1 target gene promoter occupancy is regulated with or without transcriptional autoregulation. These results were confirmed using chromatin immunoprecipitation. Zinc regulation of DNA binding activity mapped to the DNA binding domain indicating other parts of Zap1 are unnecessary for this control. Overexpression of Zap1 overrode DNA binding regulation and resulted in constitutive promoter occupancy. Under these conditions of constitutive binding, both the zinc dose response of Zap1 activity and cellular zinc accumulation were altered suggesting the importance of DNA binding control to zinc homeostasis. Thus, our results indicated that zinc regulates Zap1 activity post-translationally via three independent mechanisms, all of which contribute to the overall zinc responsiveness of Zap1.

  9. Prediction of DNA-binding specificity in zinc finger proteins

    Indian Academy of Sciences (India)

    Sumedha Roy; Shayoni Dutta; Kanika Khanna; Shruti Singla; Durai Sundar

    2012-07-01

    Zinc finger proteins interact via their individual fingers to three base pair subsites on the target DNA. The four key residue positions −1, 2, 3 and 6 on the alpha-helix of the zinc fingers have hydrogen bond interactions with the DNA. Mutating these key residues enables generation of a plethora of combinatorial possibilities that can bind to any DNA stretch of interest. Exploiting the binding specificity and affinity of the interaction between the zinc fingers and the respective DNA can help to generate engineered zinc fingers for therapeutic purposes involving genome targeting. Exploring the structure–function relationships of the existing zinc finger–DNA complexes can aid in predicting the probable zinc fingers that could bind to any target DNA. Computational tools ease the prediction of such engineered zinc fingers by effectively utilizing information from the available experimental data. A study of literature reveals many approaches for predicting DNA-binding specificity in zinc finger proteins. However, an alternative approach that looks into the physico-chemical properties of these complexes would do away with the difficulties of designing unbiased zinc fingers with the desired affinity and specificity. We present a physico-chemical approach that exploits the relative strengths of hydrogen bonding between the target DNA and all combinatorially possible zinc fingers to select the most optimum zinc finger protein candidate.

  10. Influence of DNA-methylation on zinc homeostasis in myeloid cells: Regulation of zinc transporters and zinc binding proteins.

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    Kessels, Jana Elena; Wessels, Inga; Haase, Hajo; Rink, Lothar; Uciechowski, Peter

    2016-09-01

    The distribution of intracellular zinc, predominantly regulated through zinc transporters and zinc binding proteins, is required to support an efficient immune response. Epigenetic mechanisms such as DNA methylation are involved in the expression of these genes. In demethylation experiments using 5-Aza-2'-deoxycytidine (AZA) increased intracellular (after 24 and 48h) and total cellular zinc levels (after 48h) were observed in the myeloid cell line HL-60. To uncover the mechanisms that cause the disturbed zinc homeostasis after DNA demethylation, the expression of human zinc transporters and zinc binding proteins were investigated. Real time PCR analyses of 14 ZIP (solute-linked carrier (SLC) SLC39A; Zrt/IRT-like protein), and 9 ZnT (SLC30A) zinc transporters revealed significantly enhanced mRNA expression of the zinc importer ZIP1 after AZA treatment. Because ZIP1 protein was also enhanced after AZA treatment, ZIP1 up-regulation might be the mediator of enhanced intracellular zinc levels. The mRNA expression of ZIP14 was decreased, whereas zinc exporter ZnT3 mRNA was also significantly increased; which might be a cellular reaction to compensate elevated zinc levels. An enhanced but not significant chromatin accessibility of ZIP1 promoter region I was detected by chromatin accessibility by real-time PCR (CHART) assays after demethylation. Additionally, DNA demethylation resulted in increased mRNA accumulation of zinc binding proteins metallothionein (MT) and S100A8/S100A9 after 48h. MT mRNA was significantly enhanced after 24h of AZA treatment also suggesting a reaction of the cell to restore zinc homeostasis. These data indicate that DNA methylation is an important epigenetic mechanism affecting zinc binding proteins and transporters, and, therefore, regulating zinc homeostasis in myeloid cells.

  11. Zinc-protein from rat prostate fluid binds epididymal spermatozoa.

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    Sansone, G; Abrescia, P

    1991-09-01

    The detection and the isolation of a zinc-protein from the secretion of the rat dorsolateral prostate is described. The purification procedure, based on gel filtration and cationic exchange chromatography, allowed to separate a minor protein (Mr approximately 66,000) from free zinc ions and other secretory components. Two zinc ions were estimated to be associated with one molecule of isolated protein. The zinc-protein was labelled with 125I and then incubated at 37 degrees C with spermatozoa from rat epididymal cauda. Time-dependent in vitro binding of the radioactive protein to sperm cells was demonstrated. This binding was not affected by the presence of proteins from the seminal vesicle during the incubation, while it was blocked in the presence of an excess of unlabelled zinc-protein. After binding, the labelled spermatozoa were treated with a buffer containing 0.5% sodium deoxycholate and 40 mM EDTA; only very small amounts of label were removed from the cells, thus suggesting that the zinc-proteins were kept on the plasma membrane by interactions which do not involve merely hydrophobic bonds.

  12. Improvement in the UV resistance of baculoviruses by displaying nano-zinc oxide-binding peptides on the surfaces of their occlusion bodies.

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    Li, Jin; Zhou, Yin; Lei, Chengfeng; Fang, Wei; Sun, Xiulian

    2015-08-01

    The sensitivity of baculoviruses to UV radiation severely limits their large-scale application as biological insecticides. The polyhedron envelope of a baculovirus, which is composed of carbohydrate and polyhedron envelope protein (PEP), is a significant structure for the stability and persistence of occlusion bodies (OBs) under environmental conditions. The results of this study revealed that the rough pitted surface phenotype of a pep-null Autographa californica multiple nucleopolyhedrovirus (AcMNPV) could not be rescued by any of its homologues, such as Helicoverpa armigera nucleopolyhedrovirus pep or Cydia pomonella granulovirus putative peps. In contrast, the N-terminal and middle flexible region (NM region, 1-167 aa) of AcMNPV PEP were able to form an intact OB envelope. Furthermore, this region was capable of carrying eGFP to the surfaces of the OBs. To improve the UV resistance of AcMNPV OBs, two peptides capable of specifically binding to nano-ZnO were separately fused to the NM region of PEP. Under laboratory conditions, infectivity of the recombinant viruses binding to nano-ZnO particles was about ninefold higher than that without the nano-ZnO particles after UV-B irradiation. Pot experiments revealed that the half-life of the recombinant baculovirus binding nano-ZnO particles was 3.3 ± 0.15 days, which was significantly longer than that of the control virus (0.49 ± 0.06 days). These results therefore represent a new approach for the protection the baculoviral insecticides against UV irradiation in the field.

  13. Zinc Blotting Assay for Detection of Zinc-Binding Prolamin in Barley (Hordeum vulgare) Grain

    DEFF Research Database (Denmark)

    Uddin, Mohammad Nasir; Langkilde, Ane; Vincze, Éva

    2014-01-01

    In plants, zinc is commonly found bound to proteins. In barley (Hordeum vulgare), major storage proteins are alcohol-soluble prolamins known as hordeins, and some of them have the potential to bind or store zinc. 65Zn overlay and blotting techniques have been widely used for detecting zinc...

  14. Zinc-induced interaction of the metal-binding domain of amyloid-β peptide with DNA.

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    Khmeleva, Svetlana A; Mezentsev, Yuri V; Kozin, Sergey A; Tsvetkov, Philipp O; Ivanov, Alexis S; Bodoev, Nikolay V; Makarov, Alexander A; Radko, Sergey P

    2013-01-01

    The interaction of the 16-mer synthetic peptide (Aβ16), which represents the metal-binding domain of the amyloid-β with DNA, was studied employing the surface plasmon resonance technique. It has been shown that Aβ16 binds to the duplex DNA in the presence of zinc ions and thus the metal-binding domain can serve as a zinc-dependent DNA-binding site of the amyloid-β. The interaction of Aβ16 with DNA most probably depends on oligomerization of the peptide and is dominated by interaction with phosphates of the DNA backbone.

  15. Characterization of the SUMO-binding activity of the myeloproliferative and mental retardation (MYM-type zinc fingers in ZNF261 and ZNF198.

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    Catherine M Guzzo

    Full Text Available SUMO-binding proteins interact with SUMO modified proteins to mediate a wide range of functional consequences. Here, we report the identification of a new SUMO-binding protein, ZNF261. Four human proteins including ZNF261, ZNF198, ZNF262, and ZNF258 contain a stretch of tandem zinc fingers called myeloproliferative and mental retardation (MYM-type zinc fingers. We demonstrated that MYM-type zinc fingers from ZNF261 and ZNF198 are necessary and sufficient for SUMO-binding and that individual MYM-type zinc fingers function as SUMO-interacting motifs (SIMs. Our binding studies revealed that the MYM-type zinc fingers from ZNF261 and ZNF198 interact with the same surface on SUMO-2 recognized by the archetypal consensus SIM. We also present evidence that MYM-type zinc fingers in ZNF261 contain zinc, but that zinc is not required for SUMO-binding. Immunofluorescence microscopy studies using truncated fragments of ZNF198 revealed that MYM-type zinc fingers of ZNF198 are necessary for localization to PML-nuclear bodies (PML-NBs. In summary, our studies have identified and characterized the SUMO-binding activity of the MYM-type zinc fingers in ZNF261 and ZNF198.

  16. Interaction of zinc and cobalt with dipeptides and their DNA binding studies

    Indian Academy of Sciences (India)

    P Rabindra Reddy; M Radhika; K Srinivas Rao

    2004-06-01

    Interactions of zinc and cobalt with peptides cysteinylglycine and histidylglycine have been studied. The binding modes were identified and geometry assigned. Stabilities of these complexes and their ability to bind DNA have been investigated. It is demonstrated that only zinc complexes bind DNA as compared to cobalt complexes.

  17. Arsenite binding-induced zinc loss from PARP-1 is equivalent to zinc deficiency in reducing PARP-1 activity, leading to inhibition of DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xi; Zhou, Xixi [Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 (United States); Du, Libo [Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Liu, Wenlan [Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 (United States); Liu, Yang [Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Hudson, Laurie G. [Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 (United States); Liu, Ke Jian, E-mail: kliu@salud.unm.edu [Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 (United States)

    2014-01-15

    Inhibition of DNA repair is a recognized mechanism for arsenic enhancement of ultraviolet radiation-induced DNA damage and carcinogenesis. Poly(ADP-ribose) polymerase-1 (PARP-1), a zinc finger DNA repair protein, has been identified as a sensitive molecular target for arsenic. The zinc finger domains of PARP-1 protein function as a critical structure in DNA recognition and binding. Since cellular poly(ADP-ribosyl)ation capacity has been positively correlated with zinc status in cells, we hypothesize that arsenite binding-induced zinc loss from PARP-1 is equivalent to zinc deficiency in reducing PARP-1 activity, leading to inhibition of DNA repair. To test this hypothesis, we compared the effects of arsenite exposure with zinc deficiency, created by using the membrane-permeable zinc chelator TPEN, on 8-OHdG formation, PARP-1 activity and zinc binding to PARP-1 in HaCat cells. Our results show that arsenite exposure and zinc deficiency had similar effects on PARP-1 protein, whereas supplemental zinc reversed these effects. To investigate the molecular mechanism of zinc loss induced by arsenite, ICP-AES, near UV spectroscopy, fluorescence, and circular dichroism spectroscopy were utilized to examine arsenite binding and occupation of a peptide representing the first zinc finger of PARP-1. We found that arsenite binding as well as zinc loss altered the conformation of zinc finger structure which functionally leads to PARP-1 inhibition. These findings suggest that arsenite binding to PARP-1 protein created similar adverse biological effects as zinc deficiency, which establishes the molecular mechanism for zinc supplementation as a potentially effective treatment to reverse the detrimental outcomes of arsenic exposure. - Highlights: • Arsenite binding is equivalent to zinc deficiency in reducing PARP-1 function. • Zinc reverses arsenic inhibition of PARP-1 activity and enhancement of DNA damage. • Arsenite binding and zinc loss alter the conformation of zinc finger

  18. Binding of free and protein-associated zinc to rat spermatozoa.

    Science.gov (United States)

    Sansone, G; Martino, M; Abrescia, P

    1991-01-01

    1. The zinc content of rat spermatozoa increases, upon ejaculation, from 0.035 to 1.055 micrograms/10(6) cells. 2. The rat seminal plasma holds zinc both as free ion and as protein-bound forms. 3. Zinc-free ions bind in vitro to rat epididymal spermatozoa. 4. Zinc-protein complexes can be isolated, by a chromatographic procedure, from the dorsolateral lobe of rat prostate. 5. The isolated zinc-protein complexes bind in vitro to rat epididymal spermatozoa.

  19. Oral zinc supplementation restore high molecular weight seminal zinc binding protein to normal value in Iraqi infertile men

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    Hadwan Mahmoud

    2012-11-01

    Full Text Available Abstract Background Zinc in human seminal plasma is divided into three types of ligands which are high (HMW, intermediate (IMW, and low molecular weight ligands (LMW. The present study was aimed to study the effect of Zn supplementation on the quantitative and qualitative characteristics of semen along with Zinc Binding Protein levels in the seminal plasma in asthenozoospermic patients. Methods Semen samples were obtained from 37 fertile and 37 asthenozoospermic infertile men with matched age. The subfertile group was treated with zinc sulfate, every participant took two capsules per day for three months (each one 220mg. Semen samples were obtained (before and after zinc sulfate supplementation. After liquefaction seminal fluid at room temperature, routine semen analyses were performed. For determination of the amount of zinc binding proteins, the gel filtration of seminal plasma on Sephadex G-75 was performed. All the fractions were investigated for protein and for zinc concentration by atomic absorption spectrophotometry. Evaluation of chromatograms was made directly from the zinc concentration in each fraction. Results A significant high molecular weight zinc binding ligands percentage (HMW-Zn % was observed in seminal plasma of fertile males compared with subfertile males. However, seminal low molecular weight ligands (LMW-Zn have opposite behavior. The mean value of semen volume, progressive sperm motility percentage and total normal sperm count were increased after zinc sulfate supplementation. Conclusions Zinc supplementation restores HMW-Zn% in seminal plasma of asthenozoospermic subjects to normal value. Zinc supplementation elevates LMW-Zn% in seminal plasma of asthenozoospermic subjects to more than normal value. Trial registration ClinicalTrials.gov identifier NCT01612403

  20. Identification of the human zinc transcriptional regulatory element (ZTRE): a palindromic protein-binding DNA sequence responsible for zinc-induced transcriptional repression

    NARCIS (Netherlands)

    Coneyworth, L.J.; Jackson, K.A.; Tyson, J.; Bosomworth, H.J.; Hagen, E.A.E. van der; Hann, G.M.; Ogo, O.A.; Swann, D.C.; Mathers, J.C.; Valentine, R.A.; Ford, D.

    2012-01-01

    Many genes with crucial roles in zinc homeostasis in mammals respond to fluctuating zinc supply through unknown mechanisms, and uncovering these mechanisms is essential to understanding the process at cellular and systemic levels. We detected zinc-dependent binding of a zinc-induced protein to a spe

  1. Zinc is sufficiently abundant within mammalian sperm nuclei to bind stoichiometrically with protamine 2.

    Science.gov (United States)

    Bench, G; Corzett, M H; Kramer, C E; Grant, P G; Balhorn, R

    2000-08-01

    Although studies have demonstrated that zinc can bind to sperm nuclear proteins, specifically protamine 2, it has not been shown that the metal is sufficiently abundant inside the sperm nucleus to interact stoichiometrically with these proteins. In this study proton-induced X-ray emission (PIXE) has been used to measure the amount of sulfur and zinc within the nuclei of individual sperm cells to infer the stoichiometry of zinc binding to protamine 2 in six species of mammal: bull, chinchilla, stallion, hamster, human, and mouse (protamine 2 comprises from 0% (bull) to 67% (mouse) of the protamine present in the sperm of these animals). Using the sulfur mass and electrophoretic data on the relative proportion of protamine 1 and protamine 2 in the sperm chromatin of these species, the protamine 1, protamine 2, and total protamine contents within each species sperm nuclei have been determined. The PIXE measurements reveal that the zinc content of the sperm nucleus varies proportionately with the protamine 2 content of sperm chromatin. PIXE analyses of hamster protamines extracted under conditions that appear to at least partially preserve zinc binding also confirm that the majority of the metal is bound to protamine. In five of the species examined, sufficient zinc is present for each protamine 2 molecule to bind one zinc. The results obtained for chinchilla sperm, conversely, indicate the chinchilla protamine 2 molecule may interact differently with zinc. Chinchilla sperm only contain enough zinc for one atom to be bound to two protamine 2 molecules.

  2. Binding of zinc and iron to wheat bread, wheat bran, and their components.

    Science.gov (United States)

    Ismail-Beigi, F; Faraji, B; Reinhold, J G

    1977-10-01

    Wholemeal wheat bread decreases the availability and intestinal absorption of divalent metals. To define this action further, binding of zinc in vitro to a wheat wholemeal bread (Tanok), dephytinized Tanok, and cellulose was determined at pH 5.0 to 7.5. Zinc binding by each was highly pH-dependent and reached a maximum at pH 6.5 to 7.5. Removal of phytate from Tanok did not reduce its binding capability. Wheat bran at pH 6.5 and 6.8 bound 72% of iron (0.5 microgram/ml of solution) and 82.5% of zinc (1.43 microgram/ml solution), respectively. Lignin and two of the hemicellulose fractions of wheat bran and high binding capabilities for zinc (85.6, 87.1, and 82.1%, respectively) whereas a third had a lower zinc-binding capability (38.7%). Binding of zinc to various celluloses and dextrans is also demonstrated. Formation of complexes of these metals with wheat fiber can explain, at least in part, the decreased availability of dietary iron and zinc in wholemeal wheat bread.

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

    Science.gov (United States)

    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).

  4. Spectroscopic characterization of copper(I) binding to apo and metal-reconstituted zinc finger peptides.

    Science.gov (United States)

    Doku, Reginald T; Park, Grace; Wheeler, Korin E; Splan, Kathryn E

    2013-08-01

    Cu(I) exhibits high affinity for thiolate ligands, suggesting that thiol-rich zinc or iron binding sites may be subject to disruption during copper stress conditions. Zinc fingers constitute a large class of metalloproteins that use a combination of cysteine and histidine residues that bind Zn(II) as a structural element. Despite the shared preference of both copper and zinc for thiolate and amine coordination, the susceptibility of zinc finger domains toward copper substitution is not well studied. We report spectroscopic studies that characterize the Cu(I) binding properties of the zinc finger consensus peptides CP-CCHH, CP-CCHC, and CP-CCCC and the C-terminal zinc finger domain of HIV-1 nucleocapsid protein p7 (NCp7_C). Cu(I) binds to both the apopeptides and the Co(II)-substituted peptides, and the stoichiometry of Cu(I) binding is dependent on the number of cysteine thiols at the metal binding site. Fluorescence studies of the Zn(II)-NCp7_C complex indicate that Cu(I) also effectively competes with Zn(II) at the metal binding site, despite the high affinity of Zn(II) for the CCHC binding motif. Circular dichroism studies on both CP-CCHC and NCp7_C show that the conformations of the Cu(I)-bound complexes differ substantially from those of the Zn(II) species, implying that Cu(I) substitution is likely to impact zinc finger function. These results show that for the peptides studied here, Cu(I) is the thermodynamically favored metal despite the known high Zn(II) affinity of zinc finger domains, suggesting that Cu(I)-substituted zinc finger domains might be relevant in the context of both copper toxicity mechanisms and copper-responsive transcription factors.

  5. Molecular Basis of Transient Neonatal Zinc Deficiency: NOVEL ZnT2 MUTATIONS DISRUPTING ZINC BINDING AND PERMEATION.

    Science.gov (United States)

    Golan, Yarden; Itsumura, Naoya; Glaser, Fabian; Berman, Bluma; Kambe, Taiho; Assaraf, Yehuda G

    2016-06-24

    A gradually increasing number of transient neonatal zinc deficiency (TNZD) cases was recently reported, all of which were associated with inactivating ZnT2 mutations. Here we characterized the impact of three novel heterozygous ZnT2 mutations G280R, T312M, and E355Q, which cause TNZD in exclusively breastfed infants of Japanese mothers. We used the bimolecular fluorescence complementation (BiFC) assay to provide direct visual evidence for the in situ dimerization of these ZnT2 mutants, and to explore their subcellular localization. Moreover, using three complementary functional assays, zinc accumulation using BiFC-Zinquin and Zinpyr-1 fluorescence as well as zinc toxicity assay, we determined the impact of these ZnT2 mutations on vesicular zinc accumulation. Although all three mutants formed homodimers with the wild type (WT) ZnT2 and retained substantial vesicular localization, as well as vesicular zinc accumulation, they had no dominant-negative effect over the WT ZnT2. Furthermore, using advanced bioinformatics, structural modeling, and site-directed mutagenesis we found that these mutations localized at key residues, which play an important physiological role in zinc coordination (G280R and E355Q) and zinc permeation (T312M). Collectively, our findings establish that some heterozygous loss of function ZnT2 mutations disrupt zinc binding and zinc permeation, thereby suggesting a haploinsufficiency state for the unaffected WT ZnT2 allele in TNZD pathogenesis. These results highlight the burning need for the development of a suitable genetic screen for the early diagnosis of TNZD to prevent morbidity.

  6. Kv3 channel assembly, trafficking and activity are regulated by zinc through different binding sites.

    Science.gov (United States)

    Gu, Yuanzheng; Barry, Joshua; Gu, Chen

    2013-05-15

    Zinc, a divalent heavy metal ion and an essential mineral for life, regulates synaptic transmission and neuronal excitability via ion channels. However, its binding sites and regulatory mechanisms are poorly understood. Here, we report that Kv3 channel assembly, localization and activity are regulated by zinc through different binding sites. Local perfusion of zinc reversibly reduced spiking frequency of cultured neurons most likely by suppressing Kv3 channels. Indeed, zinc inhibited Kv3.1 channel activity and slowed activation kinetics, independent of its site in the N-terminal T1 domain. Biochemical assays surprisingly identified a novel zinc-binding site in the Kv3.1 C-terminus, critical for channel activity and axonal targeting, but not for the zinc inhibition. Finally, mutagenesis revealed an important role of the junction between the first transmembrane (TM) segment and the first extracellular loop in sensing zinc. Its mutant enabled fast spiking with relative resistance to the zinc inhibition. Therefore, our studies provide novel mechanistic insights into the multifaceted regulation of Kv3 channel activity and localization by divalent heavy metal ions.

  7. Zinc specifically stimulates the selective binding of a peptide analog of bindin to sulfated fucans.

    Science.gov (United States)

    DeAngelis, P L; Glabe, C G

    1990-01-01

    A synthetic nonapeptide (Leu-Arg-His-Leu-Arg-His-His-Ser-Asn) derived from the sequence of the sea urchin sperm adhesive protein, bindin, has been shown to bind sulfated fucans in high ionic strength (seawater) conditions. The binding is enhanced by approximately 100-fold in the presence of zinc ions, and no other transition metal tested demonstrates any enhancement. Bindin isolated from sperm contains zinc ion at roughly equimolar concentrations. In the presence of Zn++, the synthetic nonapeptide binds to eggs and inhibits fertilization with a half-maximal effective concentration of 300 microM. The polysaccharide binding selectivity of the peptide/Zn++ complex is similar to bindin but less stringent. Although the order of effectiveness of the inhibitory polysaccharides is the same for bindin and the synthetic peptide, polysaccharides that are only weak inhibitors of fucan binding to bindin show greater effectiveness against the peptide. The effect of chemical modification, pH, and amino acid substitution on the binding properties of the peptide suggest that arginine guanido moieties interact with the sulfated fucans, while histidine groups chelate zinc ions. Although the mechanism of zinc-specific stimulation of fucan binding is not yet clear, one potential explanation is that zinc may stabilize a peptide secondary structure that has a high affinity for fucans.

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

    Science.gov (United States)

    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. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Seeking for Non-Zinc-Binding MMP-2 Inhibitors: Synthesis, Biological Evaluation and Molecular Modelling Studies

    Science.gov (United States)

    Ammazzalorso, Alessandra; De Filippis, Barbara; Campestre, Cristina; Laghezza, Antonio; Marrone, Alessandro; Amoroso, Rosa; Tortorella, Paolo; Agamennone, Mariangela

    2016-01-01

    Matrix metalloproteinases (MMPs) are an important family of zinc-containing enzymes with a central role in many physiological and pathological processes. Although several MMP inhibitors have been synthesized over the years, none reached the market because of off-target effects, due to the presence of a zinc binding group in the inhibitor structure. To overcome this problem non-zinc-binding inhibitors (NZIs) have been recently designed. In a previous article, a virtual screening campaign identified some hydroxynaphtyridine and hydroxyquinoline as MMP-2 non-zinc-binding inhibitors. In the present work, simplified analogues of previously-identified hits have been synthesized and tested in enzyme inhibition assays. Docking and molecular dynamics studies were carried out to rationalize the activity data. PMID:27782083

  10. Seeking for Non-Zinc-Binding MMP-2 Inhibitors: Synthesis, Biological Evaluation and Molecular Modelling Studies

    Directory of Open Access Journals (Sweden)

    Alessandra Ammazzalorso

    2016-10-01

    Full Text Available Matrix metalloproteinases (MMPs are an important family of zinc-containing enzymes with a central role in many physiological and pathological processes. Although several MMP inhibitors have been synthesized over the years, none reached the market because of off-target effects, due to the presence of a zinc binding group in the inhibitor structure. To overcome this problem non-zinc-binding inhibitors (NZIs have been recently designed. In a previous article, a virtual screening campaign identified some hydroxynaphtyridine and hydroxyquinoline as MMP-2 non-zinc-binding inhibitors. In the present work, simplified analogues of previously-identified hits have been synthesized and tested in enzyme inhibition assays. Docking and molecular dynamics studies were carried out to rationalize the activity data.

  11. New chromate-free passivation treatments for zinc, zinc alloy, and zinc-containing coatings and surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Smith, C. J. E.; King, J. E.; Wright, D. G.; Erricker, S. L.; Wilcox, G.; Treacy, G.; Hovestad, A.; Woodhead, T.; Buckland, J.; Lindsey, L.; Eruli, M.; Koelewijn, H.; Shropshire, I. [Defence Evaluation and Research Agency, Farnborough, Hampshire (United Kingdom)

    2001-07-01

    Results of a series of experiments to develop chromate-free treatments which provide the same level of corrosion protection and promote adhesion of surface coatings and paint films are discussed. The initial phase of the project identified two different treatments which prompted the investigation of pH, temperature and immersion time, as part of the effort to optimize the processes. When subjected to accelerated corrosion tests, one of the two processes (the PTA process) compared favourably with conventional chromate filming when applied to electrodeposited zinc-nickel coatings. Further investigation revealed that the process also works effectively on brass and nickel substrates and provides an appropriate substrate for the application of lacquer. Development of an effective treatment for zinc coatings, particularly hot dip galvanized zinc, is in progress. This paper discusses the results of toxicological and environmental studies conducted in conjunction with the two processes and reviews lessons learned and opportunities for exploiting the findings. 5 refs., 6 tabs.

  12. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.

    Directory of Open Access Journals (Sweden)

    Florence Guillière

    Full Text Available While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.

  13. The large intracellular loop of hZIP4 is an intrinsically disordered zinc binding domain†

    Science.gov (United States)

    Bafaro, Elizabeth M.; Antala, Sagar; Nguyen, Tuong-Vi; Dzul, Stephen P.; Doyon, Brian; Stemmler, Timothy L.; Dempski, Robert E.

    2015-01-01

    The human (h) ZIP4 transporter is a plasma membrane protein which functions to increase the cytosolic concentration of zinc. hZIP4 transports zinc into intestinal cells and therefore has a central role in the absorption of dietary zinc. hZIP4 has eight transmembrane domains and encodes a large intracellular loop between transmembrane domains III and IV, M3M4. Previously, it has been postulated that this domain regulates hZIP4 levels in the plasma membrane in a zinc-dependent manner. The objective of this research was to examine the zinc binding properties of the large intracellular loop of hZIP4. Therefore, we have recombineantly expressed and purified M3M4 and showed that this domain binds two zinc ions. Using a combination of site-directed mutagenesis, metal binding affinity assays, and X-ray absorption spectroscopy, we demonstrated that the two Zn2+ ions bind sequentially, with the first Zn2+ binding to a CysHis3 site with a nanomolar binding affinity, and the second Zn2+ binding to a His4 site with a weaker affinity. Circular dichroism spectroscopy revealed that the M3M4 domain is intrinsically disordered, with only a small structural change induced upon Zn2+ coordination. Our data supports a model in which the intracellular M3M4 domain senses high cytosolic Zn2+ concentrations and regulates the plasma membrane levels of the hZIP4 transporter in response to Zn2+ binding. PMID:25882556

  14. The artificial zinc finger coding gene 'Jazz' binds the utrophin promoter and activates transcription.

    Science.gov (United States)

    Corbi, N; Libri, V; Fanciulli, M; Tinsley, J M; Davies, K E; Passananti, C

    2000-06-01

    Up-regulation of utrophin gene expression is recognized as a plausible therapeutic approach in the treatment of Duchenne muscular dystrophy (DMD). We have designed and engineered new zinc finger-based transcription factors capable of binding and activating transcription from the promoter of the dystrophin-related gene, utrophin. Using the recognition 'code' that proposes specific rules between zinc finger primary structure and potential DNA binding sites, we engineered a new gene named 'Jazz' that encodes for a three-zinc finger peptide. Jazz belongs to the Cys2-His2 zinc finger type and was engineered to target the nine base pair DNA sequence: 5'-GCT-GCT-GCG-3', present in the promoter region of both the human and mouse utrophin gene. The entire zinc finger alpha-helix region, containing the amino acid positions that are crucial for DNA binding, was specifically chosen on the basis of the contacts more frequently represented in the available list of the 'code'. Here we demonstrate that Jazz protein binds specifically to the double-stranded DNA target, with a dissociation constant of about 32 nM. Band shift and super-shift experiments confirmed the high affinity and specificity of Jazz protein for its DNA target. Moreover, we show that chimeric proteins, named Gal4-Jazz and Sp1-Jazz, are able to drive the transcription of a test gene from the human utrophin promoter.

  15. An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces

    Science.gov (United States)

    Persikov, Anton V.; Singh, Mona

    2011-06-01

    Cys2His2 zinc finger (C2H2-ZF) proteins comprise the largest class of eukaryotic transcription factors. The 'canonical model' for C2H2-ZF protein-DNA interaction consists of only four amino acid-nucleotide contacts per zinc finger domain, and this model has been the basis for several efforts for computationally predicting and experimentally designing protein-DNA interfaces. Here, we perform a systematic analysis of structural and experimental binding data and find that, in addition to the canonical contacts, several other amino acid and base pair combinations frequently play a role in C2H2-ZF protein-DNA binding. We suggest an expansion of the canonical C2H2-ZF model to include one to three additional contacts, and show that computational approaches including these additional contacts improve predictions of DNA targets of zinc finger proteins.

  16. Zinc uptake by brain cells: `surface' versus `bulk'

    Science.gov (United States)

    DeStasio, Gelsomina; Pochon, S.; Lorusso, G. F.; Tonner, B. P.; Mercanti, Delio; Ciotti, M. Teresa; Oddo, Nino; Galli, Paolo; Perfetti, P.; Margaritondo, G.

    1996-08-01

    The uptake of zinc by cerebellar rat cultures upon exposure to 0022-3727/29/8/023/img12 solutions was comparatively investigated using two well known condensed matter physics techniques: synchrotron photoelectron spectromicroscopy and inductively coupled plasma atomic emission spectroscopy. The objective was to apply a strategy - well known in surface physics - to distinguish between `surface' and `bulk' phenomena. The results clearly demonstrate that exposure significantly enhances the bulk (cell cytoplasm) Zn concentration with respect to the physiological level, whereas the effect on the surface (cell membrane) is negligible.

  17. Ligand binding and thermostability of different allosteric states of the insulin zinc-hexamer

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B

    2006-01-01

    The influence of ligand binding and conformation state on the thermostability of hexameric zinc-insulin was studied by differential scanning calorimetry (DSC). The insulin hexamer exists in equilibrium between the forms T6, T3R3, and R6. Phenolic ligands induce and stabilize the T3R3- and R6-states...

  18. Comparison of zinc complexation properties of dissolved organic matter from surface waters and wastewater treatment plant effluents

    Institute of Scientific and Technical Information of China (English)

    CHENG Tao

    2005-01-01

    Unlike natural organic matter(NOM), wastewater organic matter(WWOM) from wastewater treatment plant effluents has not been extensively studied with respect to complexation reactions with heavy metals such as copper or zinc. In this study, organic matter from surface waters and a wastewater treatment plant effluent were concentrated by reverse osmosis(RO) method. The samples were treated in the laboratory to remove trace metals and major cations. The zinc complexing properties of both NOM and the WWOM were studied by square wave anodic stripping voltammetry(SWASV). Experimental data were compared to predictions using the Windermere Humic Aqueous Model(WHAM) Version VI. We found that the zinc binding of WWOM was much stronger than that of NOM and not well predicted by WHAM. This suggests that in natural water bodies that receive wastewater treatment plant effluents the ratio of WWOM to NOM must be taken into account in order to accurately predict free zinc activities.

  19. Binding of nickel and zinc ions to bacitracin A.

    Science.gov (United States)

    Scogin, D A; Mosberg, H I; Storm, D R; Gennis, R B

    1980-07-08

    Bacitracin A is a cyclic dodecapeptide antibiotic produced by Bacillus licheniformis. Bacteriocidal activity requires the presence of divalent cations such as Zn2+. The metal-bacitracin A complex binds to bactoprenyl pyrophosphate, a lipid intermediate required for cell wall biosynsthesis which is found within the bacterial membrane. In this paper, the pH dependence of the metal binding to bacitracin A is investigated in an effort to define the sites of metal coordination. Most of the studies described in this report were performed with Ni2+ and Zn2+. Metal binding was monitored by observing changes in the ultraviolet absorption spectrum of bacitracin A and by monitoring the proton release which is concomitant with metal binding to the peptide. It was determined that both Ni2+ and Zn2+ form 1:1 complexes with bacitracin A in solution. These complexes are soluble in acidic solutions, but above approximately pH 5.5 they become insoluble. On the basis of the data reported as well as results previously reported from other laboratories, a model for divalent metal ion binding to bacitracin is suggested. It is proposed that the metal coordinates directly to the glutamate carboxyl, the histidine imidazole, and the thiazoline ring. The aspartate carboxyl and N-terminal amino group are not directly involved in metal binding. It is further proposed that due to the proximity of the metab, the pK of the N-terminal amino is shifted from 7.7 to 5.7 upon metal binding. Deprotonation of this group is suggested to cause precipitation of the bacitracin A-metal complex. This model is consistent with all the metal binding data and, furthermore, is consistent with the 1H NMR data presented in the accompanying paper [Mosberg, H. I., Scogin, D. A., Storm, D. R., & Gennis, R. B. (1980) Biochemistry (following paper in this issue)].

  20. Amino Acid Derivatives as New Zinc Binding Groups for the Design of Selective Matrix Metalloproteinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Mariateresa Giustiniano

    2013-01-01

    Full Text Available A number of matrix metalloproteinases (MMPs are important medicinal targets for conditions ranging from rheumatoid arthritis to cardiomyopathy, periodontal disease, liver cirrhosis, multiple sclerosis, and cancer invasion and metastasis, where they showed to have a dual role, inhibiting or promoting important processes involved in the pathology. MMPs contain a zinc (II ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In an effort to devise new approaches to selective inhibitors, in this paper, we describe the synthesis and preliminary biological evaluation of amino acid derivatives as new zinc binding groups (ZBGs. The incorporation of selected metal-binding functions in more complex biphenyl sulfonamide moieties allowed the identification of one compound able to interact selectively with different MMP enzymatic isoforms.

  1. Perceptual-binding and persistent surface segregation.

    Science.gov (United States)

    Moradi, Farshad; Shimojo, Shinsuke

    2004-11-01

    Visual input is segregated in the brain into subsystems that process different attributes such as motion and color. At the same time, visual information is perceptually segregated into objects and surfaces. Here we demonstrate that perceptual segregation of visual entities based on a transparency cue precedes and affects perceptual binding of attributes. Adding an irrelevant transparency cue paradoxically improved the pairing of color and motion for rapidly alternating surfaces. Subsequent experiments show: (1) Attributes are registered over the temporal window defined by the perceptual persistence of segregation, resulting in asynchrony in binding, and (2) attention is necessary for correct registration of attributes in the presence of ambiguity.

  2. Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster.

    Science.gov (United States)

    Lee, Brian M; Buck-Koehntop, Bethany A; Martinez-Yamout, Maria A; Dyson, H Jane; Wright, Peter E

    2007-08-31

    Churchill is a zinc-containing protein that is involved in neural induction during embryogenesis. At the time of its discovery, it was thought on the basis of sequence alignment to contain two zinc fingers of the C4 type. Further, binding of an N-terminal GST-Churchill fusion protein to a particular DNA sequence was demonstrated by immunoprecipitation selection assay, suggesting that Churchill may function as a transcriptional regulator by sequence-specific DNA binding. We show by NMR solution structure determination that, far from containing canonical C4 zinc fingers, the protein contains three bound zinc ions in novel coordination sites, including an unusual binuclear zinc cluster. The secondary structure of Churchill is also unusual, consisting of a highly solvent-exposed single-layer beta-sheet. Hydrogen-deuterium exchange and backbone relaxation measurements reveal that Churchill is unusually dynamic on a number of time scales, with the exception of regions surrounding the zinc coordinating sites, which serve to stabilize the otherwise unstructured N terminus and the single-layer beta-sheet. No binding of Churchill to the previously identified DNA sequence could be detected, and extensive searches using DNA sequence selection techniques could find no other DNA sequence that was bound by Churchill. Since the N-terminal amino acids of Churchill form part of the zinc-binding motif, the addition of a fusion protein at the N terminus causes loss of zinc and unfolding of Churchill. This observation most likely explains the published DNA-binding results, which would arise due to non-specific interaction of the unfolded protein in the immunoprecipitation selection assay. Since Churchill does not appear to bind DNA, we suggest that it may function in embryogenesis as a protein-interaction factor.

  3. Characterization of the target DNA sequence for the DNA-binding domain of zinc finger protein 191

    Institute of Scientific and Technical Information of China (English)

    Haoyue Wang; Ruilin Sun; Guoxiang Liu; Minghui Yao; Jian Fei; Hebai Shen

    2008-01-01

    Studies on the DNA-binding properties of transcription factors are important in searching for the downstream genes regulated by these factors. In the present study, we report on the DNA-binding property of a Cys2His2-type transcription factor, zinc finger protein 191 (Zfp191), which has been newly found to play a significant role in mice.By constructing a fusion protein containing the DNA-binding domain of Zfp191,we characterized target DNA by determining the protein's binding specificity and dependence on zinc.The data showed that the DNA-binding domain of Zfp191can specifically bind to the TCAT repeat motif and that there is a cooperative effect among the target DNA's multiple binding sites.Furthermore,the binding reaction is dependent on zinc.This work provides a foundation for further studies on the role of Zfp191 in gene regulation and development.

  4. Perceptual-binding and persistent surface segregation

    OpenAIRE

    2004-01-01

    Visual input is segregated in the brain into subsystems that process different attributes such as motion and color. At the same time, visual information is perceptually segregated into objects and surfaces. Here we demonstrate that perceptual segregation of visual entities based on a transparency cue precedes and affects perceptual binding of attributes. Adding an irrelevant transparency cue paradoxically improved the pairing of color and motion for rapidly alternating surfaces. Subsequent ex...

  5. An azumamide C analogue without the zinc-binding functionality

    DEFF Research Database (Denmark)

    Villadsen, Jesper; Kitir, Betül; Wich, Kathrine;

    2014-01-01

    + - coordinating moiety. Herein, we describe the synthesis of an azumamide analogue lacking its native Zn 2+ -binding group and evaluation of its inhibitory activity against recombinant human HDAC1 – 11. Furthermore, kinetic investigation of the inhibitory mechanism of both parent natural product and synthetic...... analogue against HDAC3-NCoR2 is reported as well as their activity against Burkitt's lymphoma cell proliferation....

  6. Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model.

    Directory of Open Access Journals (Sweden)

    Thomas Stockner

    Full Text Available The high-resolution crystal structure of the leucine transporter (LeuT is frequently used as a template for homology models of the dopamine transporter (DAT. Although similar in structure, DAT differs considerably from LeuT in a number of ways: (i when compared to LeuT, DAT has very long intracellular amino and carboxyl termini; (ii LeuT and DAT share a rather low overall sequence identity (22% and (iii the extracellular loop 2 (EL2 of DAT is substantially longer than that of LeuT. Extracellular zinc binds to DAT and restricts the transporter's movement through the conformational cycle, thereby resulting in a decrease in substrate uptake. Residue H293 in EL2 praticipates in zinc binding and must be modelled correctly to allow for a full understanding of its effects. We exploited the high-affinity zinc binding site endogenously present in DAT to create a model of the complete transmemberane domain of DAT. The zinc binding site provided a DAT-specific molecular ruler for calibration of the model. Our DAT model places EL2 at the transporter lipid interface in the vicinity of the zinc binding site. Based on the model, D206 was predicted to represent a fourth co-ordinating residue, in addition to the three previously described zinc binding residues H193, H375 and E396. This prediction was confirmed by mutagenesis: substitution of D206 by lysine and cysteine affected the inhibitory potency of zinc and the maximum inhibition exerted by zinc, respectively. Conversely, the structural changes observed in the model allowed for rationalizing the zinc-dependent regulation of DAT: upon binding, zinc stabilizes the outward-facing state, because its first coordination shell can only be completed in this conformation. Thus, the model provides a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.

  7. Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model.

    Science.gov (United States)

    Stockner, Thomas; Montgomery, Therese R; Kudlacek, Oliver; Weissensteiner, Rene; Ecker, Gerhard F; Freissmuth, Michael; Sitte, Harald H

    2013-01-01

    The high-resolution crystal structure of the leucine transporter (LeuT) is frequently used as a template for homology models of the dopamine transporter (DAT). Although similar in structure, DAT differs considerably from LeuT in a number of ways: (i) when compared to LeuT, DAT has very long intracellular amino and carboxyl termini; (ii) LeuT and DAT share a rather low overall sequence identity (22%) and (iii) the extracellular loop 2 (EL2) of DAT is substantially longer than that of LeuT. Extracellular zinc binds to DAT and restricts the transporter's movement through the conformational cycle, thereby resulting in a decrease in substrate uptake. Residue H293 in EL2 praticipates in zinc binding and must be modelled correctly to allow for a full understanding of its effects. We exploited the high-affinity zinc binding site endogenously present in DAT to create a model of the complete transmemberane domain of DAT. The zinc binding site provided a DAT-specific molecular ruler for calibration of the model. Our DAT model places EL2 at the transporter lipid interface in the vicinity of the zinc binding site. Based on the model, D206 was predicted to represent a fourth co-ordinating residue, in addition to the three previously described zinc binding residues H193, H375 and E396. This prediction was confirmed by mutagenesis: substitution of D206 by lysine and cysteine affected the inhibitory potency of zinc and the maximum inhibition exerted by zinc, respectively. Conversely, the structural changes observed in the model allowed for rationalizing the zinc-dependent regulation of DAT: upon binding, zinc stabilizes the outward-facing state, because its first coordination shell can only be completed in this conformation. Thus, the model provides a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.

  8. Zinc complexes of the antibacterial drug oxolinic acid: structure and DNA-binding properties.

    Science.gov (United States)

    Tarushi, Alketa; Psomas, George; Raptopoulou, Catherine P; Kessissoglou, Dimitris P

    2009-06-01

    The neutral mononuclear zinc complexes with the quinolone antibacterial drug oxolinic acid in the absence or presence of a nitrogen donor heterocyclic ligand 2,2'-bipyridine or 1,10-phenanthroline have been synthesized and characterized. The experimental data suggest that oxolinic acid is on deprotonated mode acting as a bidentate ligand coordinated to the metal ion through the ketone and one carboxylato oxygen atoms. The crystal structures of (chloro)(oxolinato)(2,2'-bipyridine)zinc(II), 2, and bis(oxolinato)(1,10-phenanthroline)zinc(II), 3, have been determined with X-ray crystallography. The biological activity of the complexes has been evaluated by examining their ability to bind to calf-thymus DNA (CT DNA) with UV and fluorescence spectroscopies. UV studies of the interaction of the complexes with DNA have shown that they can bind to CT DNA and the DNA-binding constants have been calculated. Competitive studies with ethidium bromide (EB) have shown that complex 3 exhibits the ability to displace the DNA-bound EB indicating that it binds to DNA in strong competition with EB.

  9. THE EFFECTS OF COPPER AND ZINC IONS DURING THEIR BINDING WITH HUMAN SERUM γ-GLOBULIN

    Directory of Open Access Journals (Sweden)

    S. B. Cheknev

    2006-01-01

    Full Text Available Abstract. Conformational changes of human serum γ-globulin were studied during and after its binding with copper and zinc ions, using molecular ultrafiltration and differential spectrophotometry. The contents of nonbound metals in the filtrate were evaluated, resp., with sodium diethyl thyocarbamate and o-phenanthroline. It has been shown that copper and zinc exhibited common biological properties during their interactions with protein, but the binding differed sufficiently under similar experimental conditions. E.g., it was confirmed that copper was more active at the external sites of γ-globulin molecule, whereas zinc demonstrated tropicity for the areas of protein intraglobular compartments. The metal-binding sites have been described that differ in their parameters of interactions with cations and their spatial location within globular domains. Approaches are suggested for dynamic analysis of saturation for these differently located sites by the metal ions. We discuss the issues of altered conformational state of the γ-globulin molecule during the binding of cations, as well as potential usage of these data in clinical immunology.

  10. Design of a zinc finger protein binding a sequence upstream of the A20 gene

    Directory of Open Access Journals (Sweden)

    Cui Xiaoping

    2008-03-01

    Full Text Available Abstract Background Artificial transcription factors (ATFs are composed of DNA-binding and functional domains. These domains can be fused together to create proteins that can bind a chosen DNA sequence. To construct a valid ATF, it is necessary to design suitable DNA-binding and functional domains. The Cys2-His2 zinc finger motif is the ideal structural scaffold on which to construct a sequence-specific protein. A20 is a cytoplasmic zinc finger protein that inhibits nuclear factor kappa-B activity and tumor necrosis factor (TNF-mediated programmed cell death. A20 has been shown to prevent TNF-induced cytotoxicity in a variety of cell types including fibroblasts, B lymphocytes, WEHI 164 cells, NIH 3T3 cells and endothelial cells. Results In order to design a zinc finger protein (ZFP structural domain that binds specific target sequences in the A20 gene promoter region, the structure and sequence composition of this promoter were analyzed by bioinformatics methods. The target sequences in the A20 promoter were submitted to the on-line ZF Tools server of the Barbas Laboratory, Scripps Research Institute (TSRI, to obtain a specific 18 bp target sequence and also the amino acid sequence of a ZFP that would bind to it. Sequence characterization and structural modeling of the predicted ZFP were performed by bioinformatics methods. The optimized DNA sequence of this artificial ZFP was recombined into the eukaryotic expression vector pIRES2-EGFP to construct pIRES2-EGFP/ZFP-flag recombinants, and the expression and biological activity of the ZFP were analyzed by RT-PCR, western blotting and EMSA, respectively. The ZFP was designed successfully and exhibited biological activity. Conclusion It is feasible to design specific zinc finger proteins by bioinformatics methods.

  11. Controllable wettability and morphology of electrodeposited surfaces on zinc substrates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Binyan; Lu, Shixiang, E-mail: shixianglu@bit.edu.cn; Xu, Wenguo, E-mail: wenguoxu60@bit.edu.cn; Cheng, Yuanyuan

    2016-01-01

    Graphical abstract: Superhydrophobic surfaces combining hierarchical micro/nanostructures were fabricated on zinc substrates by etching, electrodeposition of ZnO coatings and annealing. Such superhydrophobic surfaces offer possibilities for chemical, biological, electronic and microfluidic applications. - Highlights: • Superhydrophobic surface was fabricated via electrodeposition of ZnO and annealing. • The ZnO hierarchical micro/nanostructures contribute to the surface superhydrophobicity. • Surface wettability and morphology can be controlled by varying process conditions. • The anti-icing properties and reversible wetting behaviors of the ZnO coatings were studied. - Abstract: Superhydrophobic surfaces combining hierarchical micro/nanostructures were fabricated on zinc substrates by etching in hydrochloric acid solution, electrodeposition of ZnO coatings and subsequent thermal annealing. The optimal coatings were electrodeposited at −1.25 V for 900 s on the etched zinc substrates and then annealed at 200 °C for 60 min, which could achieve a maximum water contact angle of 170 ± 2° and an ultra-low sliding angle of approximately 0°. By conducting SEM and water CA analysis, we found that the morphology and wettability of prepared samples were controllable by the fabrication process. Interestingly, even without any additional modification, the samples prepared under different electrodeposition conditions (including Zn(CH{sub 3}COO){sub 2} concentration from 5 mM to 40 mM and deposition time from 300 s to 1500 s) exhibited superhydrophobic character. The influences of the Zn(CH{sub 3}COO){sub 2} concentration, deposition time, annealing temperature and annealing time on the wetting behaviors were also discussed in detail. Such superhydrophobic surfaces possess long-term stability, and good corrosion resistance as well as self-cleaning ability. In addition, the anti-icing properties of the ZnO films were investigated. These surfaces could be rapidly and

  12. EOR-2 Is an Obligate Binding Partner of the BTB–Zinc Finger Protein EOR-1 in Caenorhabditis elegans

    OpenAIRE

    Howell, Kelly; Arur, Swathi; Schedl, Tim; Sundaram, Meera V.

    2010-01-01

    BTB-zinc finger transcription factors play many important roles in metazoan development. In these proteins, the BTB domain is critical for dimerization and for recruiting cofactors to target genes. Identification of these cofactors is important for understanding how BTB-zinc finger proteins influence transcription. Here we show that the novel but conserved protein EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans. EOR-1 and EOR-2 function toge...

  13. AztD, a Periplasmic Zinc Metallochaperone to an ATP-binding Cassette (ABC) Transporter System in Paracoccus denitrificans.

    Science.gov (United States)

    Handali, Melody; Roychowdhury, Hridindu; Neupane, Durga P; Yukl, Erik T

    2015-12-11

    Bacterial ATP-binding cassette (ABC) transporters of transition metals are essential for acquisition of necessary elements from the environment. A large number of Gram-negative bacteria, including human pathogens, have a fourth conserved gene of unknown function adjacent to the canonical permease, ATPase, and solute-binding protein (SBP) genes of the AztABC zinc transporter system. To assess the function of this putative accessory factor (AztD) from Paracoccus denitrificans, we have analyzed its transcriptional regulation, metal binding properties, and interaction with the SBP (AztC). Transcription of the aztD gene is significantly up-regulated under conditions of zinc starvation. Recombinantly expressed AztD purifies with slightly substoichiometric zinc from the periplasm of Escherichia coli and is capable of binding up to three zinc ions with high affinity. Size exclusion chromatography and a simple intrinsic fluorescence assay were used to determine that AztD as isolated is able to transfer bound zinc nearly quantitatively to apo-AztC. Transfer occurs through a direct, associative mechanism that prevents loss of metal to the solvent. These results indicate that AztD is a zinc chaperone to AztC and likely functions to maintain zinc homeostasis through interaction with the AztABC system. This work extends our understanding of periplasmic zinc trafficking and the function of chaperones in this process.

  14. Synthesis, characterization, thermal and DNA-binding properties of new zinc complexes with 2-hydroxyphenones.

    Science.gov (United States)

    Mrkalić, Emina; Zianna, Ariadni; Psomas, George; Gdaniec, Maria; Czapik, Agnieszka; Coutouli-Argyropoulou, Evdoxia; Lalia-Kantouri, Maria

    2014-05-01

    The neutral mononuclear zinc complexes with 2-hydroxyphenones (ketoH) having the formula [Zn(keto)2(H2O)2] and [Zn(keto)2(enR)], where enR stands for a N,N'-donor heterocyclic ligand such as 2,2'-bipyridine (bipy), 1,10-phenanthroline (phen) or 2,2'-dipyridylamine (dpamH), have been synthesized and characterized by IR, UV and (1)H NMR spectroscopies. The 2-hydroxyphenones are chelated to the metal ion through the phenolate and carbonyl oxygen atoms. The crystal structures of [bis(2-hydroxy-4-methoxy-benzophenone)(2,2'-bipyridine)zinc(II)] dimethanol solvate and [bis(2-hydroxy-benzophenone)(2,2'-bipyridine)zinc(II)] dimethanol solvate have been determined by X-ray crystallography. The thermal stability of the zinc complexes has been investigated by simultaneous TG/DTG-DTA technique. The ability of the complexes to bind to calf-thymus DNA (CT DNA) has been studied by UV-absorption and fluorescence emission spectroscopy as well as viscosity measurements. UV studies of the interaction of the complexes with DNA have shown that they can bind to CT DNA and the corresponding binding constants to DNA have been calculated and evaluated. The complexes most probably bind to CT DNA via intercalation as concluded by studying the viscosity of a DNA solution in the presence of the complexes. Competitive studies with ethidium bromide (EB) have shown that the reported complexes can displace the DNA-bound EB, suggesting strong competition with EB for the intercalation site.

  15. Leveraging zinc interstitials and oxygen vacancies for sensitive biomolecule detection through selective surface functionalization

    Science.gov (United States)

    Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Chaudhry, Shajee; Prasad, Shalini

    2015-03-01

    In this study, functionally engineered EIS technique was implemented to investigate the influence of surface functionalization on sensitivity of biomolecule detection using nanostructured ZnO platform. Organic molecules with thiol and carboxylic functional groups were chosen to control biomolecule immobilization on zinc and oxygen-terminated 2D planar and 1D nanostructured ZnO surfaces. The amount of functionalization and its influence on charge perturbations at the ZnO-electrolyte interface were studied using fluorescence and EIS measurements. We observed the dependence of charge transfer on both the polarity of platform and concentration of cross-linker molecules. Such selectively modified surfaces were used for detection of cortisol, a major stress indicator. Results demonstrated preferential binding of thiol groups to Zn terminations and thus leveraging ZnO interstitials increases the sensitivity of detection over larger dynamic range with detection limit at 10fg/mL.

  16. Surface treatment of zinc anodes to improve discharge capacity and suppress hydrogen gas evolution

    Science.gov (United States)

    Cho, Yung-Da; Fey, George Ting-Kuo

    The shape change and redistribution of zinc anode material over the electrode during repeated cycling have been identified as the main factors that can limit the life of alkaline zinc-air batteries. Li 2O-2B 2O 3 (lithium boron oxide, LBO) glass with high Li + conductivity and stability can be coated on the surface of zinc powders. The structures of the surface-treated and pristine zinc powders were characterized by XRD, SEM, TEM, ESCA and BET analyses. XRD patterns of LBO-coated zinc powders revealed that the coating did not affect the crystal structure. TEM images of LBO-coated on the zinc particles were compact with an average passivation layer of about 250 nm. The LBO layer can prevent zinc from coming into direct contact with the KOH electrolyte and minimize the side reactions within the batteries. The 0.1 wt.% LBO-coated zinc anode material provided an initial discharge capacity of 1.70 Ah at 0.5 V, while the pristine zinc electrode delivered only 1.57 Ah. A surface-treated zinc electrode can increase discharge capacity, decrease hydrogen evolution reaction, and reduce self-discharge. The results indicated that surface treatment should be effective for improving the comprehensive properties of anode materials for zinc-air batteries.

  17. [Effect of mutations and modifications of amino acid residues on zinc-induced interaction of the metal-binding domain of β-amyloid with DNA].

    Science.gov (United States)

    Khmeleva, S A; Mezentsev, Y V; Kozin, S A; Mitkevich, V A; Medvedev, A E; Ivanov, A S; Bodoev, N V; Makarov, A A; Radko, S P

    2015-01-01

    Interaction of intranuclear β-amyloid with DNA is considered to be a plausible mechanism of Alzheimer's disease pathogenesis. The interaction of single- and double-stranded DNA with synthetic peptides was analyzed using surface plasmon resonance. The peptides represent the metal-binding domain of β-amyloid (amino acids 1-16) and its variants with chemical modifications and point substitutions of amino acid residues which are associated with enhanced neurotoxicity of β-amyloid in cell tests. It has been shown that the presence of zinc ions is necessary for the interaction of the peptides with DNA in solution. H6R substitution has remarkably reduced the ability of domain 1-16 to bind DNA. This is in accordance with the supposition that the coordination of a zinc ion by amino acid residues His6, Glu11, His13, and His14 of the β-amyloid metal-binding domain results in the occurrence of an anion-binding site responsible for the interaction of the domain with DNA. Zinc-induced dimerization and oligomerization of domain 1-16 associated with phosphorylation of Ser8 and the presence of unblocked amino- and carboxy-terminal groups have resulted in a decrease of peptide concentrations required for detection of the peptide-DNA interaction. The presence of multiple anion-binding sites on the dimers and oligomers is responsible for the enhancement of the peptide-DNA interaction. A substitution of the negatively charged residue Asp7 for the neutral residue Asn in close proximity to the anion-binding site of the domain 1-16 of Aβ facilitates the electrostatic interaction between this site and phosphates of a polynucleotide chain, which enhances zinc-induced binding to DNA.

  18. Proteomic Characterization of Zinc-Binding Proteins of Canine Seminal Plasma.

    Science.gov (United States)

    Mogielnicka-Brzozowska, M; Kowalska, N; Fraser, L; Kordan, W

    2015-12-01

    The zinc-binding proteins (ZnBPs) of the seminal plasma are implicated in different processes related to sperm-egg fusion. The aim of this study was to characterize the ZnBPs of canine seminal plasma using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry. The ZnBPs were isolated from the ejaculates of five dogs by affinity chromatography and subjected to 2D-PAGE analysis. The acquired spots, detected across the gels, were analysed by mass spectrometry. Using 2D-PAGE analysis, it was shown that canine seminal plasma comprised about 46-57 zinc-binding polypeptides, with molecular mass ranging from 9.3 to 138.7 kDa and pI at pH 5.2-10.0. It was found that zinc-binding polypeptides of low molecular masses (9.3-19.0 kDa and pI at pH 6.1-10.0) were predominant in the seminal plasma, and seven polypeptides, with molecular masses ranging from 11.7 to 15.4 kDa and pI at pH 6.8-8.7, were characterized by high optical density values. In addition, analysis with mass spectrometry (LC-MS-MS/MS) revealed that the identified seven polypeptides are canine prostate-specific esterase (CPSE), which is the main proteolytic enzyme of the seminal plasma. The findings of this study indicate an important regulatory role of seminal plasma zinc ions in the functional activity of CPSE, which is of great significance for maintaining the normal function of canine prostate and the spermatozoa functions.

  19. EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans.

    Science.gov (United States)

    Howell, Kelly; Arur, Swathi; Schedl, Tim; Sundaram, Meera V

    2010-04-01

    BTB-zinc finger transcription factors play many important roles in metazoan development. In these proteins, the BTB domain is critical for dimerization and for recruiting cofactors to target genes. Identification of these cofactors is important for understanding how BTB-zinc finger proteins influence transcription. Here we show that the novel but conserved protein EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans. EOR-1 and EOR-2 function together to promote multiple Ras/ERK-dependent cell fates during development, and we show that EOR-1 is a robust substrate of ERK in vitro. A point mutation (L81F) in the EOR-1 BTB domain reduces both ERK phosphorylation and EOR-2 binding and eliminates all detectable biological function without affecting EOR-1 expression levels, localization, or dimerization. This point mutation lies near the predicted charged pocket region of the EOR-1 BTB dimer, a region that, in other BTB-zinc finger proteins, has been proposed to interact with corepressors or coactivators. We also show that a conserved zinc finger-like motif in EOR-2 is required for binding to EOR-1, that the interaction between EOR-1 and EOR-2 is direct, and that EOR-2 can bind to the human BTB-zinc finger protein PLZF. We propose that EOR-2 defines a new family of cofactors for BTB-zinc finger transcription factors that may have conserved roles in other organisms.

  20. EOR-2 Is an Obligate Binding Partner of the BTB–Zinc Finger Protein EOR-1 in Caenorhabditis elegans

    Science.gov (United States)

    Howell , Kelly; Arur , Swathi; Schedl , Tim; Sundaram , Meera V.

    2010-01-01

    BTB-zinc finger transcription factors play many important roles in metazoan development. In these proteins, the BTB domain is critical for dimerization and for recruiting cofactors to target genes. Identification of these cofactors is important for understanding how BTB-zinc finger proteins influence transcription. Here we show that the novel but conserved protein EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans. EOR-1 and EOR-2 function together to promote multiple Ras/ERK-dependent cell fates during development, and we show that EOR-1 is a robust substrate of ERK in vitro. A point mutation (L81F) in the EOR-1 BTB domain reduces both ERK phosphorylation and EOR-2 binding and eliminates all detectable biological function without affecting EOR-1 expression levels, localization, or dimerization. This point mutation lies near the predicted charged pocket region of the EOR-1 BTB dimer, a region that, in other BTB-zinc finger proteins, has been proposed to interact with corepressors or coactivators. We also show that a conserved zinc finger-like motif in EOR-2 is required for binding to EOR-1, that the interaction between EOR-1 and EOR-2 is direct, and that EOR-2 can bind to the human BTB-zinc finger protein PLZF. We propose that EOR-2 defines a new family of cofactors for BTB-zinc finger transcription factors that may have conserved roles in other organisms. PMID:20065070

  1. The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif.

    Science.gov (United States)

    Dathan, Nina; Zaccaro, Laura; Esposito, Sabrina; Isernia, Carla; Omichinski, James G; Riccio, Andrea; Pedone, Carlo; Di Blasio, Benedetto; Fattorusso, Roberto; Pedone, Paolo V

    2002-11-15

    The Arabidopsis SUPERMAN (SUP) gene has been shown to be important in maintaining the boundary between stamens and carpels, and is presumed to act by regulating cell proliferation. In this work, we show that the SUP protein, which contains a single Cys2-His2 zinc finger domain including the QALGGH sequence, highly conserved in the plant zinc finger proteins, binds DNA. Using a series of deletion mutants, it was determined that the minimal domain required for specific DNA binding (residues 15-78) includes the single zinc finger and two basic regions located on either side of this motif. Furthermore, amino acid substitutions in the zinc finger or in the basic regions, including a mutation that knocks out the function of the SUP protein in vivo (glycine 63 to aspartate), have been found to abolish the activity of the SUP DNA-binding domain. These results strongly suggest that the SUP protein functions in vivo by acting as a DNA-binding protein, likely involved in transcriptional regulation. The association of both an N-terminal and a C-terminal basic region with a single Cys2-His2 zinc finger represents a novel DNA-binding motif suggesting that the mechanism of DNA recognition adopted by the SUP protein is different from that described so far in other zinc finger proteins.

  2. Analysis of zinc oxide nanoparticles binding proteins in rat blood and brain homogenate

    Directory of Open Access Journals (Sweden)

    Shim KH

    2014-12-01

    Full Text Available Kyu Hwan Shim,1 John Hulme,1 Eun Ho Maeng,2 Meyoung-Kon Kim,3 Seong Soo A An1 1Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnam-si, Gyeonggi-do, South Korea; 2Department of Analysis, KTR, Kimpo, Gyeonggi-do, South Korea; 3Department of Biochemistry and Molecular Biology, Korea University Medical School and College, Seoul, South Korea Abstract: Nanoparticles (NPs are currently used in chemical, cosmetic, pharmaceutical, and electronic products. Nevertheless, limited safety information is available for many NPs, especially in terms of their interactions with various binding proteins, leading to potential toxic effects. Zinc oxide (ZnO NPs are included in the formulation of new products, such as adhesives, batteries, ceramics, cosmetics, cement, glass, ointments, paints, pigments, and supplementary foods, resulting in increased human exposures to ZnO. Hence, we investigated the potential ZnO nanotoxic pathways by analyzing the adsorbed proteins, called protein corona, from blood and brain from four ZnO NPs, ZnOSM20(-, ZnOSM20(+, ZnOAE100(-, and ZnOAE100(+, in order to understand their potential mechanisms in vivo. Through this study, liquid chromatography–mass spectroscopy/mass spectroscopy technology was employed to identify all bound proteins. Totals of 52 and 58 plasma proteins were identified as being bound to ZnOSM20(- and ZnOSM20(+, respectively. For ZnOAE100(- and ZnOAE100(+, 58 and 44 proteins were bound, respectively. Similar numbers of proteins were adsorbed onto ZnO irrespective of size or surface charge of the nanoparticle. These proteins were further analyzed with ClueGO, a Cytoscape plugin, which provided gene ontology and the biological interaction processes of identified proteins. Interactions between diverse proteins and ZnO nanoparticles could result in an alteration of their functions, conformation, and clearance, eventually affecting many biological processes. Keywords: brain

  3. Zinc Oxide Surface Flashover Triggering of Pseudospark Switch

    Institute of Scientific and Technical Information of China (English)

    谢建民; 邱毓昌

    2003-01-01

    Accurate and reliable triggering is one of the most important issues with high powerpseudospark switch, because it not only has an impact on the design of discharge chamber ofswitch, but also has an influence on the dynamic range of operation voltage, repetition frequenciesand lifetime of switch. The unique feature of pseudospark switch is its hollow cathode geometry.The hollow cathode effect produced by the hollow cathode provides the protection of the switchfor the triggering unit from erosion by high discharge plasma. In this paper, a zinc oxide (ZnO)surface flashover triggering is presented. This trigger unit possesses an excellent time delay (80 ns~ 360 ns) and jitter (20 ns ~ 50 ns) at the switch voltage of 30 kV ~ 2 kV. The emitted plasmaelectron density is high enough to trigger switch reliably down to switch voltage of 440 V.

  4. Zinc

    Science.gov (United States)

    ... slow wound healing, poor sense of taste and smell, diarrhea, and nausea. Moderate zinc deficiency is associated ... nose, as it might cause permanent loss of smell. In June 2009, the US Food and Drug ...

  5. Zinc surface complexes on birnessite: A density functional theory study

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Kideok D.; Refson, Keith; Sposito, Garrison

    2009-01-05

    Biogeochemical cycling of zinc is strongly influenced by sorption on birnessite minerals (layer-type MnO2), which are found in diverse terrestrial and aquatic environments. Zinc has been observed to form both tetrahedral (Zn{sup IV}) and octahedral (Zn{sup VI}) triple-corner-sharing surface complexes (TCS) at Mn(IV) vacancy sites in hexagonal birnessite. The octahedral complex is expected to be similar to that of Zn in the Mn oxide mineral, chalcophanite (ZnMn{sub 3}O{sub 7} {center_dot} 3H{sub 2}O), but the reason for the occurrence of the four-coordinate Zn surface species remains unclear. We address this issue computationally using spin-polarized Density Functional Theory (DFT) to examine the Zn{sub IV}-TCS and Zn{sup VI}-TCS species. Structural parameters obtained by DFT geometry optimization were in excellent agreement with available experimental data on Zn-birnessites. Total energy, magnetic moments, and electron-overlap populations obtained by DFT for isolated Zn{sup IV}-TCS revealed that this species is stable in birnessite without a need for Mn(III) substitution in the octahedral sheet and that it is more effective in reducing undersaturation of surface O at a Mn vacancy than is Zn{sub VI}-TCS. Comparison between geometry-optimized ZnMn{sub 3}O{sub 7} {center_dot} 3H{sub 2}O (chalcophanite) and the hypothetical monohydrate mineral, ZnMn{sub 3}O{sub 7} {center_dot} H{sub 2}O, which contains only tetrahedral Zn, showed that the hydration state of Zn significantly affects birnessite structural stability. Finally, our study also revealed that, relative to their positions in an ideal vacancy-free MnO{sub 2}, Mn nearest to Zn in a TCS surface complex move toward the vacancy by 0.08-0.11 {angstrom}, while surface O bordering the vacancy move away from it by 0.16-0.21 {angstrom}, in agreement with recent X-ray absorption spectroscopic analyses.

  6. Severe Zinc Depletion of Escherichia coli: ROLES FOR HIGH AFFINITY ZINC BINDING BY ZinT, ZINC TRANSPORT AND ZINC-INDEPENDENT PROTEINS*

    OpenAIRE

    Graham, A.I.; Hunt, S; Stokes, S.L.; Bramall, N.; Bunch, J.; Cox, A G; McLeod, C.W.; Poole, R K

    2009-01-01

    Zinc ions play indispensable roles in biological chemistry. However, bacteria have an impressive ability to acquire Zn2+ from the environment, making it exceptionally difficult to achieve Zn2+ deficiency, and so a comprehensive understanding of the importance of Zn2+ has not been attained. Reduction of the Zn2+ content of Escherichia coli growth medium to 60 nM or less is reported here for the first time, without recourse to chelators of poor specificity. Cells grown in Zn2+-deficient medium ...

  7. Comparison and analysis on the serum-binding characteristics of aspirin-zinc complex and aspirin.

    Science.gov (United States)

    Zhang, Hua-Xin; Zhang, Qun; Wang, Hong-Lin; Li, Li-Wei

    2017-09-01

    This study was designed to compare the protein-binding characteristics of aspirin-zinc complex (AZN) with those of aspirin itself. AZN was synthesized and interacted with a model transport protein, human serum albumin (HSA). Three-dimensional fluorescence, ultraviolet-visible and circular dichroism (CD) spectra were used to characterize the interaction of AZN with HSA under physiological conditions. The interaction mechanism was explored using a fluorescence quenching method and thermodynamic calculation. The binding site and binding locality of AZN on HSA were demonstrated using a fluorescence probe technique and Förster non-radiation energy transfer theory. Synchronous fluorescence and CD spectra were employed to reveal the effect of AZN on the native conformation of the protein. The HSA-binding results for AZN were compared with those for aspirin under consistent experimental conditions, and indicated that aspirin acts as a guide in AZN when binding to Sudlow's site I, in subdomain IIA of the HSA molecule. Moreover, compared with aspirin, AZN showed greater observed binding constants with, but smaller changes in the α-helicity of, HSA, which proved that AZN might be easier to transport and have less toxicity in vivo. Copyright © 2017 John Wiley & Sons, Ltd.

  8. Growth-inhibitory and metal-binding proteins in Chlorella vulgaris exposed to cadmium or zinc

    Energy Technology Data Exchange (ETDEWEB)

    Huang Zhiyong [College of Bioengineering, Jimei University, Xiamen, 361021 (China)], E-mail: zhyhuang@jmu.edu.cn; Li Lianping; Huang Gaoling [College of Bioengineering, Jimei University, Xiamen, 361021 (China); Yan Qingpi [College of fisheries, Jimei University, Xiamen, 361021 (China); Shi Bing; Xu Xiaoqin [Xiamen Products Quality Inspection Institute, Xiamen, 361004 (China)

    2009-01-18

    Phytochelatins, with the general structure of ({gamma}-Glu-Cys)n-Gly (n = 2-11), are usually recognized as being strongly induced by metals in microalgae and play an important role in the detoxification of heavy metals in environment. However, there have been few studies on metallothionein (MT) synthesis in Chlorella vulgaris (C. vulgaris) exposed to heavy metals. The present study describes the growth inhibition of C. vulgaris exposed to different concentrations of cadmium and zinc, and the induction of metal-binding MT-like proteins in the cells. The amounts of metal-binding proteins, induced in the alga exposed to different concentrations of Cd and Zn, were analyzed with a size-exclusion HPLC coupled to ICP-MS. After being purified with a gel filtration column (Sephadex G-75, 3.5 cm x 80 cm) and a desalting column (G-25, 1.5 cm x 30 cm), the isoforms and sub-isoforms of Zn-binding protein were characterized by a reverse phase-HPLC coupled to electrospray ionization and a triple quadrupole mass spectrometer (HPLC-ESI-MS/MS). In addition, the ultraviolet spectra of purified Zn-binding proteins were analyzed in media with different pH values. The results showed that the significant inhibitory effects (at p < 0.05) on the cell growth were observed when excessive metals such as 80 {mu}mol l{sup -1} of Cd, and 60 and 80 {mu}mol l{sup -1} of Zn were added. The Cd/Zn-binding proteins induced in C. vulgaris exposed to Cd and Zn were referred to as Cd/Zn-MT-like proteins in which the mean molecular mass of the apo-MT-like was 6152 Da. The induced Cd/Zn-MT-like proteins might be involved in the detoxification of heavy metals, such as cadmium and zinc, by the alga.

  9. A Rac1-GDP Trimer Complex Binds Zinc with Tetrahedral and Octahedral Coordination, Displacing Magnesium

    Energy Technology Data Exchange (ETDEWEB)

    Prehna,G.; Stebbins, E.

    2007-01-01

    The Rho family of small GTPases represent well characterized signaling molecules that regulate many cellular functions such as actin cytoskeletal arrangement and the cell cycle by acting as molecular switches. A Rac1-GDP-Zn complex has been crystallized in space group P3{sub 2}21 and its crystal structure has been solved at 1.9 {angstrom} resolution. These trigonal crystals reveal the unexpected ability of Rac1 to coordinate Zn atoms in a tetrahedral fashion by use of its biologically relevant switch I and switch II regions. Upon coordination of zinc, the switch I region is stabilized in the GDP-bound conformation and contributes to a Rac1 trimer in the asymmetric unit. Zinc coordination causes switch II to adopt a novel conformation with a symmetry-related molecule. Additionally, zinc was found to displace magnesium from its octahedral coordination at switch I, although GDP binding remained stable. This structure represents the first reported Rac1-GDP-Zn complex, which further underscores the conformational flexibility and versatility of the small GTPase switch regions.

  10. A Rac1--GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium

    Energy Technology Data Exchange (ETDEWEB)

    Prehna, G.; Stebbins, C

    2007-01-01

    The Rho family of small GTPases represent well characterized signaling molecules that regulate many cellular functions such as actin cytoskeletal arrangement and the cell cycle by acting as molecular switches. A Rac1-GDP-Zn complex has been crystallized in space group P3221 and its crystal structure has been solved at 1.9 {angstrom} resolution. These trigonal crystals reveal the unexpected ability of Rac1 to coordinate Zn atoms in a tetrahedral fashion by use of its biologically relevant switch I and switch II regions. Upon coordination of zinc, the switch I region is stabilized in the GDP-bound conformation and contributes to a Rac1 trimer in the asymmetric unit. Zinc coordination causes switch II to adopt a novel conformation with a symmetry-related molecule. Additionally, zinc was found to displace magnesium from its octahedral coordination at switch I, although GDP binding remained stable. This structure represents the first reported Rac1-GDP-Zn complex, which further underscores the conformational flexibility and versatility of the small GTPase switch regions.

  11. From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces.

    Science.gov (United States)

    Shazman, Shula; Elber, Gershon; Mandel-Gutfreund, Yael

    2011-09-01

    Protein nucleic acid interactions play a critical role in all steps of the gene expression pathway. Nucleic acid (NA) binding proteins interact with their partners, DNA or RNA, via distinct regions on their surface that are characterized by an ensemble of chemical, physical and geometrical properties. In this study, we introduce a novel methodology based on differential geometry, commonly used in face recognition, to characterize and predict NA binding surfaces on proteins. Applying the method on experimentally solved three-dimensional structures of proteins we successfully classify double-stranded DNA (dsDNA) from single-stranded RNA (ssRNA) binding proteins, with 83% accuracy. We show that the method is insensitive to conformational changes that occur upon binding and can be applicable for de novo protein-function prediction. Remarkably, when concentrating on the zinc finger motif, we distinguish successfully between RNA and DNA binding interfaces possessing the same binding motif even within the same protein, as demonstrated for the RNA polymerase transcription-factor, TFIIIA. In conclusion, we present a novel methodology to characterize protein surfaces, which can accurately tell apart dsDNA from an ssRNA binding interfaces. The strength of our method in recognizing fine-tuned differences on NA binding interfaces make it applicable for many other molecular recognition problems, with potential implications for drug design.

  12. DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger

    DEFF Research Database (Denmark)

    Danielsen, Jannie Michaela Rendtlew; Povlsen, Lou Klitgaard; Villumsen, Bine Hare

    2012-01-01

    Nonproteolytic ubiquitylation of chromatin surrounding deoxyribonucleic acid (DNA) double-strand breaks (DSBs) by the RNF8/RNF168/HERC2 ubiquitin ligases facilitates restoration of genome integrity by licensing chromatin to concentrate genome caretaker proteins near the lesions. In parallel......, SUMOylation of so-far elusive upstream DSB regulators is also required for execution of this ubiquitin-dependent chromatin response. We show that HERC2 and RNF168 are novel DNA damage-dependent SUMOylation targets in human cells. In response to DSBs, both HERC2 and RNF168 were specifically modified with SUMO1...... at DSB sites in a manner dependent on the SUMO E3 ligase PIAS4. SUMOylation of HERC2 was required for its DSB-induced association with RNF8 and for stabilizing the RNF8-Ubc13 complex. We also demonstrate that the ZZ Zinc finger in HERC2 defined a novel SUMO-specific binding module, which together...

  13. A Surface Acoustic Wave Ethanol Sensor with Zinc Oxide Nanorods

    Directory of Open Access Journals (Sweden)

    Timothy J. Giffney

    2012-01-01

    Full Text Available Surface acoustic wave (SAW sensors are a class of piezoelectric MEMS sensors which can achieve high sensitivity and excellent robustness. A surface acoustic wave ethanol sensor using ZnO nanorods has been developed and tested. Vertically oriented ZnO nanorods were produced on a ZnO/128∘ rotated Y-cut LiNbO3 layered SAW device using a solution growth method with zinc nitrate, hexamethylenetriamine, and polyethyleneimine. The nanorods have average diameter of 45 nm and height of 1 μm. The SAW device has a wavelength of 60 um and a center frequency of 66 MHz at room temperature. In testing at an operating temperature of 270∘C with an ethanol concentration of 2300 ppm, the sensor exhibited a 24 KHz frequency shift. This represents a significant improvement in comparison to an otherwise identical sensor using a ZnO thin film without nanorods, which had a frequency shift of 9 KHz.

  14. Phosphorylation of Ser8 promotes zinc-induced dimerization of the amyloid-β metal-binding domain.

    Science.gov (United States)

    Kulikova, Alexandra A; Tsvetkov, Philipp O; Indeykina, Maria I; Popov, Igor A; Zhokhov, Sergey S; Golovin, Andrey V; Polshakov, Vladimir I; Kozin, Sergey A; Nudler, Evgeny; Makarov, Alexander A

    2014-10-01

    Zinc-induced aggregation of the amyloid-β peptide (Aβ) is a hallmark molecular feature of Alzheimer's disease (AD). Recently it was shown that phosphorylation of Aβ at Ser8 promotes the formation of toxic aggregates. In this work, we have studied the impact of Ser8 phosphorylation on the mode of zinc interaction with the Aβ metal-binding domain 1-16 using isothermal titration calorimetry, electrospray ionization mass spectrometry and NMR spectroscopy. We have discovered a novel zinc binding site ((6)HDpS(8)) in the phosphorylated peptide, in which the zinc ion is coordinated by the imidazole ring of His6, the phosphate group attached to Ser8 and a backbone carbonyl group of His6 or Asp7. Interaction of the zinc ion with this site involves His6, thereby withdrawing it from the interaction pattern observed in the non-modified peptide. This event was found to stimulate dimerization of peptide chains through the (11)EVHH(14) site, where the zinc ion is coordinated by the two pairs of Glu11 and His14 in the two peptide subunits. The proposed molecular mechanism of zinc-induced dimerization could contribute to the understanding of initiation of pathological Aβ aggregation, and the (11)EVHH(14) tetrapeptide can be considered as a promising drug target for the prevention of amyloidogenesis.

  15. Zinc binding to RNA recognition motif of TDP-43 induces the formation of amyloid-like aggregates.

    Science.gov (United States)

    Garnier, Cyrille; Devred, François; Byrne, Deborah; Puppo, Rémy; Roman, Andrei Yu; Malesinski, Soazig; Golovin, Andrey V; Lebrun, Régine; Ninkina, Natalia N; Tsvetkov, Philipp O

    2017-07-28

    Aggregation of TDP-43 (transactive response DNA binding protein 43 kDa) is a hallmark of certain forms of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Moreover, intracellular TDP-43-positive inclusions are often found in other neurodegenerative diseases. Recently it was shown that zinc ions can provoke the aggregation of endogenous TDP-43 in cells, allowing to assume a direct interaction of TDP-43 with zinc ions. In this work, we investigated zinc binding to the 102-269 TDP-43 fragment, which comprise the two RNA recognition motifs. Using isothermal titration calorimetry, mass spectrometry, and differential scanning fluorimetry, we showed that zinc binds to this TDP-43 domain with a dissociation constant in the micromolar range and modifies its tertiary structure leading to a decrease of its thermostability. Moreover, the study by dynamic light scattering and negative stain electron microscopy demonstrated that zinc ions induce auto-association process of this TDP-43 fragment into rope-like structures. These structures are thioflavin-T-positive allowing to hypothesize the direct implication of zinc ions in pathological aggregation of TDP-43.

  16. The Characterization And Role of Zinc Binding in Yeast Cox4

    Energy Technology Data Exchange (ETDEWEB)

    Coyne, H.J., III; Ciofi-Baffoni, S.; Banci, L.; Bertini, I.; Zhang, L.; George, G.N.; Winge, D.R.; /Utah U. /Florence U. /Saskatchewan U.

    2007-07-09

    Yeast Cox4 is a zinc binding subunit of cytochrome c oxidase. Cox4 is the only cofactor-containing subunit that is not directly part of the catalytic core of the enzyme located in the mitochondrial inner membrane. The Zn(II) site is shown to be distinct from the bovine ortholog, as it results from the x-ray structure of the entire cytochrome c oxidase in having a single histidyl residue and three conserved cysteines residues in the coordination sphere. Substitutions at the Cys ligand positions result in non-functional Cox4 proteins that fail to lead to cytochrome oxidase assembly. Limited function exists in His-119 mutants when overexpressed. Zn(II) binding in Cox4 is, therefore, important for the stability of the complex. The solution structure of yeast Cox4 elucidated by multidimensional NMR reveals a C-terminal globular domain consisting of two {beta} sheets analogous to the bovine ortholog except the loop containing the coordinating His in the yeast protein and the fourth Cys in the bovine protein are in different positions in the two structures. The conformation of this loop is dictated by the different sequence position of the fourth coordinating zinc ligand. The Zn(II) ion is buried within the domain, consistent with its role in structural stability. Potential functions of this matrix-facing subunit are discussed.

  17. Stereoselective HDAC inhibition from cysteine-derived zinc-binding groups.

    Science.gov (United States)

    Butler, Kyle V; He, Rong; McLaughlin, Kathryn; Vistoli, Giulio; Langley, Brett; Kozikowski, Alan P

    2009-08-01

    A series of small-molecule histone deacetylase (HDAC) inhibitors, which feature zinc binding groups derived from cysteine, were synthesized. These inhibitors were tested against multiple HDAC isoforms, and the most potent, compound 10, was determined to have IC(50) values below 1 microM. The compounds were also tested in a cellular assay of oxidative stress-induced neurodegeneration. Many of the inhibitors gave near-complete protection against cell death at 10 microM without the neurotoxicity seen with hydroxamic acid-based inhibitors, and were far more neuroprotective than HDAC inhibitors currently in clinical trials. Both enantiomers of cysteine were used in the synthesis of a variety of novel zinc-binding groups (ZBGs). Derivatives of L-cysteine were active in the HDAC inhibition assays, while the derivatives of D-cysteine were inactive. Notably, the finding that both the D- and L-cysteine derivatives were active in the neuroprotection assays suggests that multiple mechanisms are working to protect the neurons from cell death. Molecular modeling was employed to investigate the differences in inhibitory activity between the HDAC inhibitors generated from the two enantiomeric forms of cysteine.

  18. The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model

    Science.gov (United States)

    Oiwa, Nestor; Cordeiro, Claudette; Heermann, Dieter

    2016-05-01

    Instead of ATCG letter alignments, typically used in bioinformatics, we propose a new alignment method using the probability distribution function of the bottom of the occupied molecular orbital (BOMO), highest occupied molecular orbital (HOMO) and lowest unoccupied orbital (LUMO). We apply the technique to transcription factors with Cys2His2 zinc fingers. These transcription factors search for binding sites, probing for the electronic patterns at the minor and major DNA groves. The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains. They are responsible for gene regulation and the spatial organization of DNA. To study and understand these zinc finger DNA-protein interactions, we use the extended ladder in the DNA model proposed by Zhu, Rasmussen, Balatsky & Bishop (2007) te{Zhu-2007}. Considering one single spinless electron in each nucleotide π-orbital along a double DNA chain (dDNA), we find a typical pattern for the bottom of BOMO, HOMO and LUMO along the binding sites. We specifically looked at two members of zinc finger protein family: specificity protein 1 (SP1) and early grown response 1 transcription factors (EGR1). When the valence band is filled, we find electrons in the purines along the nucleotide sequence, compatible with the electric charges of the binding amino acids in SP1 and EGR1 zinc finger.

  19. Protein-folding location can regulate manganese-binding versus copper- or zinc-binding.

    Science.gov (United States)

    Tottey, Steve; Waldron, Kevin J; Firbank, Susan J; Reale, Brian; Bessant, Conrad; Sato, Katsuko; Cheek, Timothy R; Gray, Joe; Banfield, Mark J; Dennison, Christopher; Robinson, Nigel J

    2008-10-23

    Metals are needed by at least one-quarter of all proteins. Although metallochaperones insert the correct metal into some proteins, they have not been found for the vast majority, and the view is that most metalloproteins acquire their metals directly from cellular pools. However, some metals form more stable complexes with proteins than do others. For instance, as described in the Irving-Williams series, Cu(2+) and Zn(2+) typically form more stable complexes than Mn(2+). Thus it is unclear what cellular mechanisms manage metal acquisition by most nascent proteins. To investigate this question, we identified the most abundant Cu(2+)-protein, CucA (Cu(2+)-cupin A), and the most abundant Mn(2+)-protein, MncA (Mn(2+)-cupin A), in the periplasm of the cyanobacterium Synechocystis PCC 6803. Each of these newly identified proteins binds its respective metal via identical ligands within a cupin fold. Consistent with the Irving-Williams series, MncA only binds Mn(2+) after folding in solutions containing at least a 10(4) times molar excess of Mn(2+) over Cu(2+) or Zn(2+). However once MncA has bound Mn(2+), the metal does not exchange with Cu(2+). MncA and CucA have signal peptides for different export pathways into the periplasm, Tat and Sec respectively. Export by the Tat pathway allows MncA to fold in the cytoplasm, which contains only tightly bound copper or Zn(2+) (refs 10-12) but micromolar Mn(2+) (ref. 13). In contrast, CucA folds in the periplasm to acquire Cu(2+). These results reveal a mechanism whereby the compartment in which a protein folds overrides its binding preference to control its metal content. They explain why the cytoplasm must contain only tightly bound and buffered copper and Zn(2+).

  20. Surface analysis of zinc-porphyrin functionalized carbon nano-onions.

    Science.gov (United States)

    Spampinato, Valentina; Ceccone, Giacomo; Giordani, Silvia

    2015-03-10

    Multishell fullerenes, known as carbon nano-onions (CNOs), are an interesting class of carbon-based nanomaterials. They display several unique properties, such as a large surface area to volume ratio, a low density, and a graphitic multilayer morphology, which have made them appealing for several applications in many fields, including biology. Chemical functionalization of CNOs dramatically enhances their solubility and attenuates their inflammatory properties, thereby increasing their applicability especially in the fields of biology and medicine. CNOs functionalized with fluorescent probes can be used for cellular imaging. In this article, detailed surface characterization of CNOs functionalized with a zinc porphyrin (ZnTPP) as the fluorescent probe is presented. In particular, time-of-flight secondary ion mass spectrometry and x-ray photoelectron spectroscopy provide a detailed surface characterization of the organic functionalities introduced via "click chemistry" and clearly demonstrate the success of the CNOs functionalization process. XPS data reveal the presence of Zn and N, whilst ToF-SIMS is able to identify specific fragments related to the presence of the ZnTPP, such as the quasimolecular mass peak [C32N4H20Zn](+) and the molecular mass peak [C44N4H28Zn](+). Moreover, ions fragments deriving from the triazole ring formed by the click chemistry reaction have been identified by ToF-SIMS analysis, proving unambiguously the covalent binding of the fluorescent molecules to the CNOs surfaces.

  1. [Zinc].

    Science.gov (United States)

    Couinaud, C

    1984-10-01

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

  2. Direct binding of specific AUF1 isoforms to tandem zinc finger domains of tristetraprolin (TTP) family proteins.

    Science.gov (United States)

    Kedar, Vishram P; Zucconi, Beth E; Wilson, Gerald M; Blackshear, Perry J

    2012-02-17

    Tristetraprolin (TTP) is the prototype of a family of CCCH tandem zinc finger proteins that can bind to AU-rich elements in mRNAs and promote their decay. TTP binds to mRNA through its central tandem zinc finger domain; it then promotes mRNA deadenylation, considered to be the rate-limiting step in eukaryotic mRNA decay. We found that TTP and its related family members could bind to certain isoforms of another AU-rich element-binding protein, HNRNPD/AUF1, as well as a related protein, laAUF1. The interaction domain within AUF1p45 appeared to be a C-terminal "GY" region, and the interaction domain within TTP was the tandem zinc finger domain. Surprisingly, binding of AUF1p45 to TTP occurred even with TTP mutants that lacked RNA binding activity. In cell extracts, binding of AUF1p45 to TTP potentiated TTP binding to ARE-containing RNA probes, as determined by RNA gel shift assays; AUF1p45 did not bind to the RNA probes under these conditions. Using purified, recombinant proteins and a synthetic RNA target in FRET assays, we demonstrated that AUF1p45, but not AUF1p37, increased TTP binding affinity for RNA ∼5-fold. These data suggest that certain isoforms of AUF1 can serve as "co-activators" of TTP family protein binding to RNA. The results raise interesting questions about the ability of AUF1 isoforms to regulate the mRNA binding and decay-promoting activities of TTP and its family members as well as the ability of AUF1 proteins to serve as possible physical links between TTP and other mRNA decay proteins and structures.

  3. Localized frustration and binding-induced conformational change in recognition of 5S RNA by TFIIIA zinc finger.

    Science.gov (United States)

    Tan, Cheng; Li, Wenfei; Wang, Wei

    2013-12-19

    Protein TFIIIA is composed of nine tandemly arranged Cys2His2 zinc fingers. It can bind either to the 5S RNA gene as a transcription factor or to the 5S RNA transcript as a chaperone. Although structural and biochemical data provided valuable information on the recognition between the TFIIIIA and the 5S DNA/RNA, the involved conformational motions and energetic factors contributing to the binding affinity and specificity remain unclear. In this work, we conducted MD simulations and MM/GBSA calculations to investigate the binding-induced conformational changes in the recognition of the 5S RNA by the central three zinc fingers of TFIIIA and the energetic factors that influence the binding affinity and specificity at an atomistic level. Our results revealed drastic interdomain conformational changes between these three zinc fingers, involving the exposure/burial of several crucial DNA/RNA binding residues, which can be related to the competition between DNA and RNA for the binding of TFIIIA. We also showed that the specific recognition between finger 4/finger 6 and the 5S RNA introduces frustrations to the nonspecific interactions between finger 5 and the 5S RNA, which may be important to achieve optimal binding affinity and specificity.

  4. Dye-Sensitized Solar Cells Based on High Surface Area Nanocrystalline Zinc Oxide Spheres

    Directory of Open Access Journals (Sweden)

    Pavuluri Srinivasu

    2011-01-01

    Full Text Available High surface area nanocrystalline zinc oxide material is fabricated using mesoporous nanostructured carbon as a sacrificial template through combustion process. The resulting material is characterized by XRD, N2 adsorption, HR-SEM, and HR-TEM. The nitrogen adsorption measurement indicates that the materials possess BET specific surface area ca. 30 m2/g. Electron microscopy images prove that the zinc oxide spheres possess particle size in the range of 0.12 μm–0.17 μm. The nanocrystalline zinc oxide spheres show 1.0% of energy conversion efficiency for dye-sensitized solar cells.

  5. Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins

    Science.gov (United States)

    Patel, A.; Hashimoto, H.; Zhang, X.; Cheng, X.

    2016-01-01

    Much is known about vertebrate DNA methylation and oxidation; however, much less is known about how modified cytosine residues within particular sequences are recognized. Among the known methylated DNA-binding domains, the Cys2-His2 zinc finger (ZnF) protein superfamily is the largest with hundreds of members, each containing tandem ZnFs ranging from 3 to >30 fingers. We have begun to biochemically and structurally characterize these ZnFs not only on their sequence specificity but also on their sensitivity to various DNA modifications. Rather than following published methods of refolding insoluble ZnF arrays, we have expressed and purified soluble forms of ZnFs, ranging in size from a tandem array of two to six ZnFs, from seven different proteins. We also describe a fluorescence polarization assay to measure ZnFs affinity with oligonucleotides containing various modifications and our approaches for cocrystallization of ZnFs with oligonucleotides. PMID:27372763

  6. 3-Hydroxypyridin-2-thione as novel zinc binding group for selective histone deacetylase inhibition.

    Science.gov (United States)

    Patil, Vishal; Sodji, Quaovi H; Kornacki, James R; Mrksich, Milan; Oyelere, Adegboyega K

    2013-05-09

    Small molecules bearing hydroxamic acid as the zinc binding group (ZBG) have been the most effective histone deacetylase inhibitors (HDACi) to date. However, concerns about the pharmacokinetic liabilities of the hydroxamic acid moiety have stimulated research efforts aimed at finding alternative nonhydroxamate ZBGs. We have identified 3-hydroxypyridin-2-thione (3-HPT) as a novel ZBG that is compatible with HDAC inhibition. 3-HPT inhibits HDAC 6 and HDAC 8 with an IC50 of 681 and 3675 nM, respectively. Remarkably, 3-HPT gives no inhibition of HDAC 1. Subsequent optimization led to several novel 3HPT-based HDACi that are selective for HDAC 6 and HDAC 8. Furthermore, a subset of these inhibitors induces apoptosis in various cancer cell lines.

  7. Predicting copper-, iron- and zinc-binding proteins in pathogenic species of the Paracoccidioides genus

    Directory of Open Access Journals (Sweden)

    Gabriel B Tristao

    2015-01-01

    Full Text Available Approximately one-third of all proteins have been estimated to contain at least one metal cofactor, and these proteins are referred to as metalloproteins. These represent one of the most diverse classes of proteins, containing metal ions that bind to specific sites to perform catalytic, regulatory and structural functions. Bioinformatic tools have been developed to predict metalloproteins encoded by an organism based only on its genome sequence. Its function and the type of metal binder can also be predicted via a bioinformatics approach. Paracoccidioides complex includes termodimorphic pathogenic fungi that are found as saprobic mycelia in the environment and as yeast, the parasitic form, in host tissues. They are the etiologic agents of Paracoccidioidomycosis, a prevalent systemic mycosis in Latin America. Many metalloproteins are important for the virulence of several pathogenic microorganisms. Accordingly, the present work aimed to predict the cooper, iron and zinc proteins encoded by the genomes of three phylogenetic species of Paracoccidioides (Pb01, Pb03 and Pb18. The metalloproteins were identified using bioinformatics approaches based on structure, annotation and domains. Cu-, Fe- and Zn-binding proteins represent 7% of the total proteins encoded by Paracoccidioides spp. genomes. Zinc proteins were the most abundant metalloproteins, representing 5.7% of the fungus proteome, whereas copper and iron proteins represent 0.3% and 1.2%, respectively. Functional classification revealed that metalloproteins are related to many cellular processes. Furthermore, it was observed that many of these metalloproteins serve as virulence factors in the biology of the fungus. Thus, it is concluded that the Cu, Fe and Zn metalloproteomes of the Paracoccidioides spp. are of the utmost importance for the biology and virulence of these particular human pathogens.

  8. A poxvirus protein with a RING finger motif binds zinc and localizes in virus factories.

    Science.gov (United States)

    Upton, C; Schiff, L; Rice, S A; Dowdeswell, T; Yang, X; McFadden, G

    1994-07-01

    Shope fibroma virus (SFV) is a Leporipoxvirus closely related to the highly virulent myxoma virus. The DNA sequence of the BamHI N fragment of the SFV DNA genome was determined, and the single complete open reading frame (N1R) was characterized. The protein encoded by the N1R gene was found to contain a C3HC4 RING finger motif at the C terminus. This C3HC4 motif is the hallmark of a growing family of proteins, many of which are involved in regulation of gene expression, DNA repair, or DNA recombination. Complete homologs of the SFV N1R gene were also detected in variola virus, myxoma virus, and vaccinia virus strain IHD-W. In contrast, the gene is completely absent from vaccinia virus strain Copenhagen, and in vaccinia virus strain WR, the open reading frame is truncated prior to the zinc binding domain because of an 11-bp deletion, thus producing a frameshift and premature stop codon. Recombinant N1R protein from SFV was expressed in Escherichia coli and shown to bind zinc in a specific manner. Using fluorescence microscopy to visualize a peptide epitope tag (derived from ICP27 of herpes simplex virus) fused to the N terminus of the poxvirus proteins, we observed that the N1R protein of SFV and its homologs in myxoma virus and vaccinia virus IHD-W were localized primarily to the virus factories in the cytoplasm of infected cells and, to a lesser degree, the host cell nucleus. The truncated protein of vaccinia virus strain WR failed to localize in this manner but instead was observed throughout the cytoplasm.

  9. Crystal Structure of the Zinc-Binding Transport Protein ZnuA from Escherichia coli Reveals an Unexpected Variation in Metal Coordination

    Energy Technology Data Exchange (ETDEWEB)

    Li,H.; Jogl, G.

    2007-01-01

    Bacterial ATP-binding cassette transport systems for high-affinity uptake of zinc and manganese use a cluster 9 solute-binding protein. Structures of four cluster 9 transport proteins have been determined previously. However, the structural determinants for discrimination between zinc and manganese remain under discussion. To further investigate the variability of metal binding sites in bacterial transporters, we have determined the structure of the zinc-bound transport protein ZnuA from Escherichia coli to 1.75 {angstrom} resolution. The overall structure of ZnuA is similar to other solute-binding transporters. A scaffolding {alpha}-helix forms the backbone for two structurally related globular domains. The metal-binding site is located at the domain interface. The bound zinc ion is coordinated by three histidine residues (His78, His161 and His225) and one glutamate residue (Glu77). The functional role of Glu77 for metal binding is unexpected, because this residue is not conserved in previously determined structures of zinc and manganese-specific transport proteins. The observed metal coordination by four protein residues differs significantly from the zinc-binding site in the ZnuA transporter from Synechocystis 6803, which binds zinc via three histidine residues. In addition, the E. coli ZnuA structure reveals the presence of a disulfide bond in the C-terminal globular domain that is not present in previously determined cluster 9 transport protein structures.

  10. Surface Modification With Zinc and Zn-Ni Alloy Compositionally Modulated Multilayer Coatings

    Institute of Scientific and Technical Information of China (English)

    FEI Jing-yin; LIANG Guo-zheng; XIN Wen-li; WANG Wei-kang

    2006-01-01

    Zinc and Zn-Ni alloy compositionally modulated multilayer (CMM) coatings were electrodeposited on to a steel substrate by the successive deposition of zinc and Zn-Ni alloy sublayers from dual baths. The coated samples were evaluated in terms of the surface appearance, surface and cross-sectional morphologies, as well as corrosion resistance. The microstructural characteristics that were examined using the field emission gun scanning electron microscopy (FEGSEM) confirmed the layered structure, grain refinement of the zinc and Zn-Ni alloy CMM coatings, and revealed the existence of microcracks caused by the internal stress in the thick Zn-Ni alloy sublayers. The corrosion resistance that was evaluated by means of the salt spray test shows that the zinc and Zn-Ni alloy CMM coatings were more corrosion-resistant than the monolithic coatings of zinc or Zn-Ni alloy of the same thickness. The possible reasons for the better protective performance of Zn-Ni/Zn CMM coatings were given on the basis of the analysis on the micrographic features of zinc and Zn-Ni alloy CMM coatings after the corrosion test. A probable corrosion mechanism of zinc and Zn-Ni alloy CMM coatings was also proposed.

  11. Soybean extracts increase cell surface ZIP4 abundance and cellular zinc levels: a potential novel strategy to enhance zinc absorption by ZIP4 targeting.

    Science.gov (United States)

    Hashimoto, Ayako; Ohkura, Katsuma; Takahashi, Masakazu; Kizu, Kumiko; Narita, Hiroshi; Enomoto, Shuichi; Miyamae, Yusaku; Masuda, Seiji; Nagao, Masaya; Irie, Kazuhiro; Ohigashi, Hajime; Andrews, Glen K; Kambe, Taiho

    2015-12-01

    Dietary zinc deficiency puts human health at risk, so we explored strategies for enhancing zinc absorption. In the small intestine, the zinc transporter ZIP4 functions as an essential component of zinc absorption. Overexpression of ZIP4 protein increases zinc uptake and thereby cellular zinc levels, suggesting that food components with the ability to increase ZIP4 could potentially enhance zinc absorption via the intestine. In the present study, we used mouse Hepa cells, which regulate mouse Zip4 (mZip4) in a manner indistinguishable from that in intestinal enterocytes, to screen for suitable food components that can increase the abundance of ZIP4. Using this ZIP4-targeting strategy, two such soybean extracts were identified that were specifically able to decrease mZip4 endocytosis in response to zinc. These soybean extracts also effectively increased the abundance of apically localized mZip4 in transfected polarized Caco2 and Madin-Darby canine kidney cells and, moreover, two apically localized mZip4 acrodermatitis enteropathica mutants. Soybean components were purified from one extract and soyasaponin Bb was identified as an active component that increased both mZip4 protein abundance and zinc levels in Hepa cells. Finally, we confirmed that soyasaponin Bb is capable of enhancing cell surface endogenous human ZIP4 in human cells. Our results suggest that ZIP4 targeting may represent a new strategy to improve zinc absorption in humans.

  12. Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1.

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    Carina Frauer

    Full Text Available Several mammalian proteins involved in chromatin and DNA modification contain CXXC zinc finger domains. We compared the structure and function of the CXXC domains in the DNA methyltransferase Dnmt1 and the methylcytosine dioxygenase Tet1. Sequence alignment showed that both CXXC domains have a very similar framework but differ in the central tip region. Based on the known structure of a similar MLL1 domain we developed homology models and designed expression constructs for the isolated CXXC domains of Dnmt1 and Tet1 accordingly. We show that the CXXC domain of Tet1 has no DNA binding activity and is dispensable for catalytic activity in vivo. In contrast, the CXXC domain of Dnmt1 selectively binds DNA substrates containing unmethylated CpG sites. Surprisingly, a Dnmt1 mutant construct lacking the CXXC domain formed covalent complexes with cytosine bases both in vitro and in vivo and rescued DNA methylation patterns in dnmt1⁻/⁻ embryonic stem cells (ESCs just as efficiently as wild type Dnmt1. Interestingly, neither wild type nor ΔCXXC Dnmt1 re-methylated imprinted CpG sites of the H19a promoter in dnmt1⁻/⁻ ESCs, arguing against a role of the CXXC domain in restraining Dnmt1 methyltransferase activity on unmethylated CpG sites.

  13. Laser fluorescence spectroscopy of zinc neutrals originating from laser-irradiated and ion-bombarded zinc sulfide and zinc surfaces

    Science.gov (United States)

    Arlinghaus, H. F.; Calaway, W. F.; Young, C. E.; Pellin, M. J.; Gruen, D. M.; Chase, L. L.

    Time-of-flight (TOF) measurements, employing high-resolution laser-induced fluorescence spectroscopy (LFS) as a probe, have been used to measure the yield and velocity distribution of Zn atoms ejected from a ZnS single crystal under irradiation by 308 nm photons. By comparison with the known ion sputtering yield for pure zinc, the absolute yield was determined to be 10 to the 10th power atoms/pulse at a laser fluence of 30 mJ/sq cm. The velocity distribution of the Zn atoms could be fitted by a Maxwell-Boltzmann distribution, having characteristic temperature of approx 2300 K. In addition, Doppler-shift techniques have been combined with TOF measurements in order to separate prompt from delayed emission of ablated atoms, as well as to probe possible molecular or cluster fragmentation. The results obtained suggest the possibility of molecular or cluster emission from ZnS.

  14. Controlling Multivalent Binding through Surface Chemistry: Model Study on Streptavidin

    Science.gov (United States)

    2017-01-01

    Although multivalent binding to surfaces is an important tool in nanotechnology, quantitative information about the residual valency and orientation of surface-bound molecules is missing. To address these questions, we study streptavidin (SAv) binding to commonly used biotinylated surfaces such as supported lipid bilayers (SLBs) and self-assembled monolayers (SAMs). Stability and kinetics of SAv binding are characterized by quartz crystal microbalance with dissipation monitoring, while the residual valency of immobilized SAv is quantified using spectroscopic ellipsometry by monitoring binding of biotinylated probes. Purpose-designed SAv constructs having controlled valencies (mono-, di-, trivalent in terms of biotin-binding sites) are studied to rationalize the results obtained on regular (tetravalent) SAv. We find that divalent interaction of SAv with biotinylated surfaces is a strict requirement for stable immobilization, while monovalent attachment is reversible and, in the case of SLBs, leads to the extraction of biotinylated lipids from the bilayer. The surface density and lateral mobility of biotin, and the SAv surface coverage are all found to influence the average orientation and residual valency of SAv on a biotinylated surface. We demonstrate how the residual valency can be adjusted to one or two biotin binding sites per immobilized SAv by choosing appropriate surface chemistry. The obtained results provide means for the rational design of surface-confined supramolecular architectures involving specific biointeractions at tunable valency. This knowledge can be used for the development of well-defined bioactive coatings, biosensors and biomimetic model systems. PMID:28234007

  15. Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins.

    Science.gov (United States)

    Giachini, Lisa; Veronesi, Giulia; Francia, Francesco; Venturoli, Giovanni; Boscherini, Federico

    2010-01-01

    In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple-scattering EXAFS analysis performed within the rigid-body refinement scheme, non-muffin-tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye-Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K-edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.

  16. Novel glyoxalase-I inhibitors possessing a “zinc-binding feature” as potential anticancer agents

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    Al-Balas QA

    2016-08-01

    Full Text Available Qosay A Al-Balas,1 Mohammad A Hassan,1 Nizar A Al-Shar’i,1 Nizar M Mhaidat,2 Ammar M Almaaytah,3 Fatima M Al-Mahasneh,1 Israa H Isawi1 1Department of Medicinal Chemistry and Pharmacognosy, 2Department of Clinical Pharmacy, 3Department of Pharmaceutical Technology, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan Background: The glyoxalase system including two thiol-dependent enzymes, glyoxalase I (Glo-I and glyoxalase II, plays an important role in a ubiquitous metabolic pathway involved in cellular detoxification of cytotoxic 2-oxoaldehydes. Tumor cells have high glycolytic activity, leading to increased cellular levels of these toxic metabolites. The increased activity of the detoxification system in cancerous cells makes this pathway a viable target for developing novel anticancer agents. In this study, we examined the potential utility of non-glutathione-based inhibitors of the Glo-I enzyme as novel anticancer drugs.Methods: Computer-aided drug design techniques, such as customized pharmacophoric features, virtual screening, and flexible docking, were used to achieve the project goals. Retrieved hits were extensively filtered and subsequently docked into the active site of the enzyme. The biological activities of retrieved hits were assessed using an in vitro assay against Glo-I.Results: Since Glo-I is a zinc metalloenzyme, a customized Zn-binding pharmacophoric feature was used to search for selective inhibitors via virtual screening of a small-molecule database. Seven hits were selected, purchased, and biologically evaluated. Three of the seven hits inhibited Glo-I activity, the most effective of which exerted 76.4% inhibition at a concentration of 25 µM.Conclusion: We successfully identified a potential Glo-I inhibitor that can serve as a lead compound for further optimization. Moreover, our in silico and experimental results were highly correlated. Hence, the docking protocol adopted in this study may

  17. Laser forming of structures of zinc oxide on a surface of products from copper alloys

    Science.gov (United States)

    Abramov, D. V.; Gorudko, T. N.; Koblov, A. N.; Nogtev, D. S.; Novikova, O. A.

    Laser formation of a protective zinc oxide layer on a surface of products from copper alloys is present. This layer is formed with using of carbon nanotubes. Destructions of the basic material are avoided or minimized at laser nanostructuring of product surfaces. Such laser processing can be made repeatedly. Offered covering have self-clearing and water-repellent properties.

  18. Mode of bindings of zinc oxide nanoparticles to myoglobin and horseradish peroxidase: A spectroscopic investigations

    Science.gov (United States)

    Mandal, Gopa; Bhattacharya, Sudeshna; Ganguly, Tapan

    2011-07-01

    The interactions between two heme proteins myoglobin (HMb) and horseradish peroxidase (HRP) with zinc oxide (ZnO) nanoparticles are investigated by using UV-vis absorption, steady state fluorescence, synchronous fluorescence, time-resolved fluorescence, FT-IR, atomic force microscopy (AFM) and circular dichroism (CD) techniques under physiological condition of pH˜7.4. The presence of mainly static mode in fluorescence quenching mechanism of HMb and HRP by ZnO nanoparticle indicates the possibility of formation of ground state complex. The processes of bindings of ZnO nanoparticles with the two proteins are spontaneous molecular interaction procedures. In both cases hydrogen bonding plays a major role. The circular dichroism (CD) spectra reveal that a helicity of the proteins is reduced by increasing ZnO nanoparticle concentration although the α-helical structures of HMb and HRP retain their identity. On binding to the ZnO nanoparticles the secondary structure of HRP molecules (or HMb molecules) remains unchanged while there is a substantial change in the environment of the tyrosin active site in case of HRP molecules and tryptophan active site in case of HMb molecules. Tapping mode atomic force microscopy (AFM) was applied for the investigation the structure of HRP adsorbed in the environment of nanoparticles on the silicon and on the bare silicon. HRP molecules adsorb and aggregate on the mica with ZnO nanoparticle. The aggregation indicates an attractive interaction among the adsorbed molecules. The molecules are randomly distributed on the bare silicon wafer. The adsorption of HRP in the environment of ZnO nanoparticle changes drastically the domains due to a strong interaction between HRP and ZnO nanoparticles. Similar situation is observed in case of HMb molecules. These findings demonstrate the efficacy of biomedical applications of ZnO nanoparticles as well as in elucidating their mechanisms of action as drugs in both human and plant systems.

  19. Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins.

    Science.gov (United States)

    Segal, David J; Beerli, Roger R; Blancafort, Pilar; Dreier, Birgit; Effertz, Karin; Huber, Adrian; Koksch, Beate; Lund, Caren V; Magnenat, Laurent; Valente, David; Barbas, Carlos F

    2003-02-25

    In previous studies, we have developed a technology for the rapid construction of novel DNA-binding proteins with the potential to recognize any unique site in a given genome. This technology relies on the modular assembly of modified zinc finger DNA-binding domains, each of which recognizes a three bp subsite of DNA. A complete set of 64 domains would provide comprehensive recognition of any desired DNA sequence, and new proteins could be assembled by any laboratory in a matter of hours. However, a critical parameter for this approach is the extent to which each domain functions as an independent, modular unit, without influence or dependence on its neighboring domains. We therefore examined the detailed binding behavior of several modularly assembled polydactyl zinc finger proteins. We first demonstrated that 80 modularly assembled 3-finger proteins can recognize their DNA target with very high specificity using a multitarget ELISA-based specificity assay. A more detailed analysis of DNA binding specificity for eight 3-finger proteins and two 6-finger proteins was performed using a target site selection assay. Results showed that the specificity of these proteins was as good or better than that of zinc finger proteins constructed using methods that allow for interdependency. In some cases, near perfect specificity was achieved. Complications due to target site overlap were found to be restricted to only one particular amino acid interaction (involving an aspartate in position 2 of the alpha-helix) that occurs in a minority of cases. As this is the first report of target site selection for designed, well characterized 6-finger proteins, unique insights are discussed concerning the relationship of protein length and specificity. These results have important implications for the design of proteins that can recognize extended DNA sequences, as well as provide insights into the general rules of recognition for naturally occurring zinc finger proteins.

  20. Vimentin filament organization and stress sensing depend on its single cysteine residue and zinc binding.

    Science.gov (United States)

    Pérez-Sala, Dolores; Oeste, Clara L; Martínez, Alma E; Carrasco, M Jesús; Garzón, Beatriz; Cañada, F Javier

    2015-06-02

    The vimentin filament network plays a key role in cell architecture and signalling, as well as in epithelial-mesenchymal transition. Vimentin C328 is targeted by various oxidative modifications, but its role in vimentin organization is not known. Here we show that C328 is essential for vimentin network reorganization in response to oxidants and electrophiles, and is required for optimal vimentin performance in network expansion, lysosomal distribution and aggresome formation. C328 may fulfil these roles through interaction with zinc. In vitro, micromolar zinc protects vimentin from iodoacetamide modification and elicits vimentin polymerization into optically detectable structures; in cells, zinc closely associates with vimentin and its depletion causes reversible filament disassembly. Finally, zinc transport-deficient human fibroblasts show increased vimentin solubility and susceptibility to disruption, which are restored by zinc supplementation. These results unveil a critical role of C328 in vimentin organization and open new perspectives for the regulation of intermediate filaments by zinc.

  1. AES and LEED study of the zinc blende SiC(100) surface

    Science.gov (United States)

    Dayan, M.

    1985-01-01

    Auger and LEED measurements have been carried out on the (100) surface of zinc blende SiC. Two different phases of the clean surface, in addition to two kinds of oxygen-covered surfaces, have been obtained, identified, and discussed. In the oxygen-covered surface, the oxygen is bonded to the Si. The carbon-rich phase is reconstructed (2 x 1), similar to the (100) clean surfaces of Si, Ge, and diamond. The Si-topped surface is reconstructed. A model of alternating Si dimers is suggested for this surface.

  2. Studies on the Interactions of Copper and Zinc Ions with β-Amyloid Peptides by a Surface Plasmon Resonance Biosensor

    Directory of Open Access Journals (Sweden)

    He Tian

    2012-09-01

    Full Text Available The aggregation of β-amyloid peptide (Aβ into fibrils plays an important role in the pathogenesis of Alzheimer’s disease (AD. Metal ions including copper and zinc are closely connected to the precipitation and toxicity of Aβ. In this study, a surface plasmon resonance (SPR biosensor was constructed to investigate the interactions between Aβ and metal ions. Aβ peptide was immobilized on the SPR chip surface through a preformed alkanethiol self-assembled monolayer (SAM. Our observations indicate that the immobilized Aβ undergoes a conformational change upon exposure to the metal ions. A difference in metal binding affinity between Aβ1–28 and Aβ1–42 was also detected. The results suggest that SPR is an effective method to characterize the interactions between Aβ and metal ions.

  3. Studies on the interactions of copper and zinc ions with β-amyloid peptides by a surface plasmon resonance biosensor.

    Science.gov (United States)

    Yao, Fujun; Zhang, Ruiping; Tian, He; Li, Xiangjun

    2012-01-01

    The aggregation of β-amyloid peptide (Aβ) into fibrils plays an important role in the pathogenesis of Alzheimer's disease (AD). Metal ions including copper and zinc are closely connected to the precipitation and toxicity of Aβ. In this study, a surface plasmon resonance (SPR) biosensor was constructed to investigate the interactions between Aβ and metal ions. Aβ peptide was immobilized on the SPR chip surface through a preformed alkanethiol self-assembled monolayer (SAM). Our observations indicate that the immobilized Aβ undergoes a conformational change upon exposure to the metal ions. A difference in metal binding affinity between Aβ(1-28) and Aβ(1-42) was also detected. The results suggest that SPR is an effective method to characterize the interactions between Aβ and metal ions.

  4. Surface and capillary forces encountered by zinc sulfide microspheres in aqueous electrolyte.

    Science.gov (United States)

    Gillies, Graeme; Kappl, Michael; Butt, Hans-Jürgen

    2005-06-21

    The colloid probe technique was used to investigate the interactions between individual zinc sulfide (ZnS) microspheres and an air bubble in electrolyte solution. Incorporation of zinc ions into the electrolyte solution overcomes the disproportionate zinc ion dissolution and mimics high-volume-fraction conditions common in flotation. Determined interaction forces revealed a distinct lack of long-ranged hydrophobic forces, indicated by the presence of a DLVO repulsion prior to particle engulfment. Single microsphere contact angles were determined from particle-bubble interactions. Contact angles increased with decreasing radii and with surface oxidation. Surface modification by the absorption of copper and subsequently potassium O-ethyldithiocarbonate (KED) reduced repulsive forces and strongly increased contact angles.

  5. The binding of zinc ions to Emericella nidulans endo-β-1,4-galactanase is essential for crystal formation

    DEFF Research Database (Denmark)

    Otten, Harm; Michalak, Malwina; Mikkelsen, Jørn Dalgaard

    2013-01-01

    A novel Emericella nidulans endo-β-1,4-galactanase (EnGAL) demonstrates a strong capacity to generate high levels of very potent prebiotic oligosaccharides from potato pulp, a by-product of the agricultural potato-starch industry. EnGAL belongs to glycoside hydrolase family 53 and shows high (72...... belonging to GH53. It also revealed 15 zinc ions bound to the protein, one of which is located in the active site, where it is coordinated by residues Glu136 and Glu246 which comprise the catalytic machinery. The majority of the zinc ions are located on the surface of the enzyme, in some cases with side...

  6. Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain

    DEFF Research Database (Denmark)

    Jensen, R B; Lykke-Andersen, K; Frandsen, G I

    2000-01-01

    containing the ZAC-C2 domain bind anionic phospholipids non-specifically, with some variance in Ca2+ and salt dependence. Similar assays demonstrated specific affinity of the ZAC N-terminal region (residues 1-174) for phosphatidylinositol 3-monophosphate (PI-3-P). Binding was dependent in part on an intact...... zinc finger motif, but proteins containing only the zinc finger domain (residues 1-105) did not bind PI-3-P. Recombinant ZAC possessed GTPase-activating activity on Arabidopsis ARF proteins. These data identify a novel PI-3-P-binding protein region and thereby provide evidence...

  7. Generation of metal-binding staphylococci through surface display of combinatorially engineered cellulose-binding domains.

    Science.gov (United States)

    Wernérus, H; Lehtiö, J; Teeri, T; Nygren, P A; Ståhl, S

    2001-10-01

    Ni(2+)-binding staphylococci were generated through surface display of combinatorially engineered variants of a fungal cellulose-binding domain (CBD) from Trichoderma reesei cellulase Cel7A. Novel CBD variants were generated by combinatorial protein engineering through the randomization of 11 amino acid positions, and eight potentially Ni(2+)-binding CBDs were selected by phage display technology. These new variants were subsequently genetically introduced into chimeric surface proteins for surface display on Staphylococcus carnosus cells. The expressed chimeric proteins were shown to be properly targeted to the cell wall of S. carnosus cells, since full-length proteins could be extracted and affinity purified. Surface accessibility for the chimeric proteins was demonstrated, and furthermore, the engineered CBDs, now devoid of cellulose-binding capacity, were shown to be functional with regard to metal binding, since the recombinant staphylococci had gained Ni(2+)-binding capacity. Potential environmental applications for such tailor-made metal-binding bacteria as bioadsorbents in biofilters or biosensors are discussed.

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

    Science.gov (United States)

    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...

  9. Prostasomes of canine seminal plasma - zinc-binding ability and effects on motility characteristics and plasma membrane integrity of spermatozoa.

    Science.gov (United States)

    Mogielnicka-Brzozowska, M; Strzeżek, R; Wasilewska, K; Kordan, W

    2015-06-01

    Prostasomes are small lipid membrane-confined vesicles that are involved in various fertilization-related processes. The aim of this study was to demonstrate canine seminal plasma prostasomes' ability to bind zinc ions, as well as examining their effects on sperm motility characteristics and plasma membrane integrity during cold storage. Ejaculates, collected from five cross-bred dogs (n = 50), were subjected to ultracentrifugation followed by gel filtration (GF) on a Superose 6 column. Prostasomes appeared as a single fraction in the elution profile. Transmission electron microscopy (TEM) analysis of canine prostasomes revealed the presence of membrane vesicles with diameters ranging from 20.3 to 301 nm. The zinc-affinity chromatography on a Chelating Sepharose Fast Flow - Zn(2 +) showed that from 93 to 100% of the prostasome proteins bind zinc ions (P(+) Zn). SDS-PAGE revealed that canine P(+) Zn comprised four protein bands, with low molecular weights (10.2-12 kDa). We have also shown a positive effect of prostasomes (p spermatozoa with intact plasma membrane (SYBR/PI dual staining) and intact acrosome (Giemsa stained), after 2 h storage at 5°C, was showed, in variant A (1.5% of total seminal plasma protein) and B, when compared with Control and variant C (2.5% of total seminal plasma protein). The prostasomes' effect on motility and plasma membrane integrity of canine cold-stored spermatozoa may be related to their ability to bind zinc ions and regulate their availability to the sperm.

  10. High surface area carbon for bifunctional air electrodes applied in zinc-air batteries

    Energy Technology Data Exchange (ETDEWEB)

    Arai, H. [on leave from NTT Laboratories (Japan); Mueller, S.; Haas, O. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    Bifunctional air electrodes with high surface area carbon substrates showed low reduction overpotential, thus are promising for enhancing the energy efficiency and power capability of zinc-air batteries. The improved performance is attributed to lower overpotential due to diffusion of the reaction intermediate, namely the peroxide ion. (author) 1 fig., 2 refs.

  11. Water soluble peripheral and non-peripheral tetrasubstituted zinc phthalocyanines: Synthesis, photochemistry and bovine serum albumin binding behavior

    Energy Technology Data Exchange (ETDEWEB)

    Çakır, Volkan; Çakır, Dilek [Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon (Turkey); Pişkin, Mehmet [Department of Food Technology, Çanakkale Vocational School of Technical Sciences, Çanakkale Onsekiz Mart University, 17100 Çanakkale (Turkey); Durmuş, Mahmut [Gebze Institute of Technology, Department of Chemistry, PO Box 141, Gebze 41400, Kocaeli (Turkey); Bıyıklıoğlu, Zekeriya, E-mail: zekeriya_61@yahoo.com [Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon (Turkey)

    2014-10-15

    The new peripherally and non-peripherally tetra-1,3-bis[3-(diethylamino)phenoxy]propan-2-ol substituted zinc(II) phthalocyanine complexes (2a and 3a) and their quaternized amphiphilic derivatives (2b and 3b) have been synthesized and characterized using UV–vis, FT-IR, {sup 1}H-NMR, {sup 13}C-NMR, MS spectroscopic data and elemental analysis for the first time. The quaternized complexes (2b and 3b) show excellent solubility in water and DMSO which makes them potential photosensitizers for use in photodynamic therapy (PDT) of cancer. The photochemical (singlet oxygen generation and photodegradation under light irradiation) properties of these novel phthalocyanines are investigated in dimethylsulfoxide (DMSO) for non-quaternized complexes and in DMSO, phosphate buffered solution (PBS) or PBS+triton X-100 (TX) solution for quaternized complexes. In this study, the effects of the aggregation of the molecules, quaternization, position of the substituents (peripherally or non-peripherally) and nature of the solvents (DMSO, PBS or PBS+triton X-100) on the photochemical parameters of the zinc (II) phthalocyanines are also reported. In addition, a spectroscopic investigation of the binding behavior of the quaternized zinc(II) phthalocyanine complexes to bovine serum albumin (BSA) is also presented in this work. - Highlights: • Synthesis of zinc phthalocyanines is performed. • Photophysical and photochemical properties of phthalocyanines are studied. • Photodynamic therapy studies are performed.

  12. Novel glyoxalase-I inhibitors possessing a “zinc-binding feature” as potential anticancer agents

    Science.gov (United States)

    Al-Balas, Qosay A; Hassan, Mohammad A; Al-Shar’i, Nizar A; Mhaidat, Nizar M; Almaaytah, Ammar M; Al-Mahasneh, Fatima M; Isawi, Israa H

    2016-01-01

    Background The glyoxalase system including two thiol-dependent enzymes, glyoxalase I (Glo-I) and glyoxalase II, plays an important role in a ubiquitous metabolic pathway involved in cellular detoxification of cytotoxic 2-oxoaldehydes. Tumor cells have high glycolytic activity, leading to increased cellular levels of these toxic metabolites. The increased activity of the detoxification system in cancerous cells makes this pathway a viable target for developing novel anticancer agents. In this study, we examined the potential utility of non-glutathione-based inhibitors of the Glo-I enzyme as novel anticancer drugs. Methods Computer-aided drug design techniques, such as customized pharmacophoric features, virtual screening, and flexible docking, were used to achieve the project goals. Retrieved hits were extensively filtered and subsequently docked into the active site of the enzyme. The biological activities of retrieved hits were assessed using an in vitro assay against Glo-I. Results Since Glo-I is a zinc metalloenzyme, a customized Zn-binding pharmacophoric feature was used to search for selective inhibitors via virtual screening of a small-molecule database. Seven hits were selected, purchased, and biologically evaluated. Three of the seven hits inhibited Glo-I activity, the most effective of which exerted 76.4% inhibition at a concentration of 25 µM. Conclusion We successfully identified a potential Glo-I inhibitor that can serve as a lead compound for further optimization. Moreover, our in silico and experimental results were highly correlated. Hence, the docking protocol adopted in this study may be efficiently employed in future optimization steps. PMID:27574401

  13. Chronic zinc exposure decreases the surface expression of NR2A-containing NMDA receptors in cultured hippocampal neurons.

    Directory of Open Access Journals (Sweden)

    Jia Zhu

    Full Text Available BACKGROUND: Zinc distributes widely in the central nervous system, especially in the hippocampus, amygdala and cortex. The dynamic balance of zinc is critical for neuronal functions. Zinc modulates the activity of N-methyl-D-aspartate receptors (NMDARs through the direct inhibition and various intracellular signaling pathways. Abnormal NMDAR activities have been implicated in the aetiology of many brain diseases. Sustained zinc accumulation in the extracellular fluid is known to link to pathological conditions. However, the mechanism linking this chronic zinc exposure and NMDAR dysfunction is poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We reported that chronic zinc exposure reduced the numbers of NR1 and NR2A clusters in cultured hippocampal pyramidal neurons. Whole-cell and synaptic NR2A-mediated currents also decreased. By contrast, zinc did not affect NR2B, suggesting that chronic zinc exposure specifically influences NR2A-containg NMDARs. Surface biotinylation indicated that zinc exposure attenuated the membrane expression of NR1 and NR2A, which might arise from to the dissociation of the NR2A-PSD-95-Src complex. CONCLUSIONS: Chronic zinc exposure perturbs the interaction of NR2A to PSD-95 and causes the disorder of NMDARs in hippocampal neurons, suggesting a novel action of zinc distinct from its acute effects on NMDAR activity.

  14. Coupling of Insulin Secretion and Display of a Granule-resident Zinc Transporter ZnT8 on the Surface of Pancreatic Beta Cells.

    Science.gov (United States)

    Huang, Qiong; Merriman, Chengfeng; Zhang, Hao; Fu, Dax

    2017-03-10

    The islet-specific zinc transporter ZnT8 mediates zinc enrichment in the insulin secretory granules of the pancreatic beta cell. This granular zinc transporter is also a major self-antigen found in type 1 diabetes patients. It is not clear whether ZnT8 can be displayed on the cell surface and how insulin secretion may regulate the level of ZnT8 exposure to extracellular immune surveillance. Here we report specific antibody binding to the extracellular surface of rat insulinoma INS-1E cells that stably expressed a tagged human zinc transporter ZnT8. Flow cytometry analysis after fluorescent antibody labeling revealed strong correlations among the levels of ZnT8 expression, its display on the cell surface, and glucose-stimulated insulin secretion (GSIS). Glucose stimulation increased the surface display of endogenous ZnT8 from a basal level to 32.5% of the housekeeping Na(+)/K(+) ATPase on the cell surface, thereby providing direct evidence for a GSIS-dependent surface exposure of the ZnT8 self-antigen. Moreover, the variation in tagged-ZnT8 expression and surface labeling enabled sorting of heterogeneous beta cells to subpopulations that exhibited marked differences in GSIS with parallel changes in endogenous ZnT8 expression. The abundant surface display of endogenous ZnT8 and its coupling to GSIS demonstrated the potential of ZnT8 as a surface biomarker for tracking and isolating functional beta cells in mixed cell populations.

  15. Screening of matrix metalloproteinases available from the protein data bank: insights into biological functions, domain organization, and zinc binding groups.

    Science.gov (United States)

    Nicolotti, Orazio; Miscioscia, Teresa Fabiola; Leonetti, Francesco; Muncipinto, Giovanni; Carotti, Angelo

    2007-01-01

    A total of 142 matrix metalloproteinase (MMP) X-ray crystallographic structures were retrieved from the Protein Data Bank (PDB) and analyzed by an automated and efficient routine, developed in-house, with a series of bioinformatic tools. Highly informative heat maps and hierarchical clusterograms provided a reliable and comprehensive representation of the relationships existing among MMPs, enlarging and complementing the current knowledge in the field. Multiple sequence and structural alignments permitted better location and display of key MMP motifs and quantification of the residue consensus at each amino acid position in the most critical binding subsites of MMPs. The MMP active site consensus sequences, the C-alpha root-mean-square deviation (RMSd) analysis of diverse enzymatic subsites, and the examination of the chemical nature, binding topologies, and zinc binding groups (ZBGs) of ligands extracted from crystallographic complexes provided useful insights on the structural arrangements of the most potent MMP inhibitors.

  16. Protein function annotation by local binding site surface similarity.

    Science.gov (United States)

    Spitzer, Russell; Cleves, Ann E; Varela, Rocco; Jain, Ajay N

    2014-04-01

    Hundreds of protein crystal structures exist for proteins whose function cannot be confidently determined from sequence similarity. Surflex-PSIM, a previously reported surface-based protein similarity algorithm, provides an alternative method for hypothesizing function for such proteins. The method now supports fully automatic binding site detection and is fast enough to screen comprehensive databases of protein binding sites. The binding site detection methodology was validated on apo/holo cognate protein pairs, correctly identifying 91% of ligand binding sites in holo structures and 88% in apo structures where corresponding sites existed. For correctly detected apo binding sites, the cognate holo site was the most similar binding site 87% of the time. PSIM was used to screen a set of proteins that had poorly characterized functions at the time of crystallization, but were later biochemically annotated. Using a fully automated protocol, this set of 8 proteins was screened against ∼60,000 ligand binding sites from the PDB. PSIM correctly identified functional matches that predated query protein biochemical annotation for five out of the eight query proteins. A panel of 12 currently unannotated proteins was also screened, resulting in a large number of statistically significant binding site matches, some of which suggest likely functions for the poorly characterized proteins.

  17. Superhydrophobic surfaces using selected zinc oxide microrod growth on ink-jetted patterns.

    Science.gov (United States)

    Myint, Myo Tay Zar; Kitsomboonloha, Rungrot; Baruah, Sunandan; Dutta, Joydeep

    2011-02-15

    The synthesis and properties of superhydrophobic surfaces based on binary surface topography made of zinc oxide (ZnO) microrod-decorated micropatterns are reported. ZnO is intrinsically hydrophilic but can be utilized to create hydrophobic surfaces by creating artificial roughness via microstructuring. Micron scale patterns consisting of nanocrystalline ZnO seed particles were applied to glass substrates with a modified ink-jet printer. Microrods were then grown on the patterns by a hydrothermal process without any further chemical modification. Water contact angle (WCA)(1) up to 153° was achieved. Different micro array patterned surfaces with varying response of static contact angle or sessile droplet analysis are reported.

  18. Crystal Structure of the Botulinum Neurotoxin Type G Binding Domain: Insight into Cell Surface Binding

    Energy Technology Data Exchange (ETDEWEB)

    Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R.; Stevens, Raymond C. (Scripps); (UW)

    2011-11-02

    Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-{angstrom} X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent.

  19. Zinc-dependent mechanical properties of Staphylococcus aureus biofilm-forming surface protein SasG.

    Science.gov (United States)

    Formosa-Dague, Cécile; Speziale, Pietro; Foster, Timothy J; Geoghegan, Joan A; Dufrêne, Yves F

    2016-01-12

    Staphylococcus aureus surface protein SasG promotes cell-cell adhesion during the accumulation phase of biofilm formation, but the molecular basis of this interaction remains poorly understood. Here, we unravel the mechanical properties of SasG on the surface of living bacteria, that is, in its native cellular environment. Nanoscale multiparametric imaging of living bacteria reveals that Zn(2+) strongly increases cell wall rigidity and activates the adhesive function of SasG. Single-cell force measurements show that SasG mediates cell-cell adhesion via specific Zn(2+)-dependent homophilic bonds between β-sheet-rich G5-E domains on neighboring cells. The force required to unfold individual domains is remarkably strong, up to ∼500 pN, thus explaining how SasG can withstand physiological shear forces. We also observe that SasG forms homophilic bonds with the structurally related accumulation-associated protein of Staphylococcus epidermidis, suggesting the possibility of multispecies biofilms during host colonization and infection. Collectively, our findings support a model in which zinc plays a dual role in activating cell-cell adhesion: adsorption of zinc ions to the bacterial cell surface increases cell wall cohesion and favors the projection of elongated SasG proteins away from the cell surface, thereby enabling zinc-dependent homophilic bonds between opposing cells. This work demonstrates an unexpected relationship between mechanics and adhesion in a staphylococcal surface protein, which may represent a general mechanism among bacterial pathogens for activating cell association.

  20. Expression and RNA-binding of human zinc-finger antiviral protein

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Mi Suk; Kim, Eun Jung [Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735 (Korea, Republic of); Jang, Se Bok, E-mail: sbjang@pusan.ac.kr [Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735 (Korea, Republic of)

    2010-06-04

    Zinc-finger antiviral protein (ZAP) is a recently isolated host antiviral factor that inhibits the replication of many viruses such as Moloney murine leukemia virus (MLV) and Sindbis virus (SIN) by preventing the accumulation of viral mRNA in the cytoplasm. ZAP comprises four CCCH zinc-finger motifs, the second and fourth of which are responsible for protein activity based on their integrity. Thus far, there have been no reports on whether or not ZAP expressed in Escherichia coli is soluble. Therefore, we expressed N-terminal ZAP (NZAP, 254 amino acids) in E. coli as a fusion protein with several different cleavage sites and protein tags. Cleaved ZAP in soluble form strongly bound to RNA through its four CCCH zinc-finger motifs. Here, we provide evidence indicating that ZAP directly interacted with viral RNA. Each conserved zinc-finger motif of ZAP coordinates a zinc ion using three cysteines and one histidine. These findings suggest that ZAP recruits the cellular RNA degradation machinery for the degradation of viral RNA.

  1. The binding of in vitro synthesized adenovirus DNA binding protein to single-stranded DNA is stimulated by zinc ions

    NARCIS (Netherlands)

    Vos, H.L.; Lee, F.M. van der; Sussenbach, J.S.

    1988-01-01

    We have synthesized wild type DNA binding protein (DBP) of adenovirus type 5 (Ad5) and several truncated forms of this protein by a combination of in vitro transcription and translation. The proteins obtained were tested for binding to a single-stranded DNA-cellulose column. It could be shown that f

  2. Purification and characterization of a native zinc-binding high molecular weight multiprotein complex from human seminal plasma.

    Science.gov (United States)

    Yadav, Vikash Kumar; Kumar, Vijay; Chhikara, Nirmal; Kumar, Sanjay; Manral, Pallavi; Kashav, Tara; Saini, Savita; Srinivasan, A; Singh, Sarman; Singh, Tej P; Yadav, Savita

    2011-05-01

    The seminal plasma comprises secretions from various accessory sex glands. During fertilization spermatozoa undergo complex sequences of precisely timed events that are regulated by the activation of different intracellular signaling pathways. The precision and efficacy of these pathways are often influenced by the assembly and interactions of multiprotein complexes, thereby directing the flow of regulatory information. Our knowledge about these protein complexes present in human seminal plasma (HuSP) is limited. Here we report the identification and characterization of a native high molecular weight zinc-binding multiprotein complex from HuSP by utilizing 2-DE followed by MS. Twenty-six proteins representing isoforms and/or fragments of 11 different proteins were found to be assembled in this complex. Prostate-specific antigen, zinc α2-glycoprotein, prostatic acid phosphatase, and prolactin inducible protein were the major proteins of this complex. Dynamic light scattering experiments revealed changes in aggregation pattern accompanied with deviation from physiological pH and in presence of SDS. However, no significant changes were observed in the presence of physiological ligands such as zinc and fructose. The present study will be useful and contribute to guide the future studies performed for elucidation of biological significance of this native complex in HuSP.

  3. The study of molten zinc interaction on the surface of refractories in the production of zinc oxide

    Directory of Open Access Journals (Sweden)

    Natália Luptáková

    2013-02-01

    Full Text Available This paper is closely connected with the complete process of indirect production of ZnO as well as with the problems which occur during the metallurgical process. Purity of raw materials has an important influence on the final quality of ZnO and the occurrence of slag that remains stuck on the walls of furnace linings. ZnO is generally produced in the melting furnaces with different types of ceramic linings. Input materials have to be analyzed and investigated in the order to the predict behaviour from the aspect of the complex production process. Moreover, analysis of occurrence of undesirable phases in the batch, the output materials, character of furnace linings and waste material have to be evaluated and observed. Mutual interaction of all components will have a significant impact on the final quality of the ZnO. The result of the investigation of interaction occurring in the components will be used for the proposal of the suitable surface for furnace lining while the mentioned result is mainly obtained on the principle of chemical reactions and bonds. This surface for lining should have a minimum adhesion of the zinc and its alloys relating to production of ZnO.

  4. THE STUDY OF MOLTEN ZINC INTERACTION ON THE SURFACE OF REFRACTORIES IN THE PRODUCTION OF ZINC OXIDE

    Directory of Open Access Journals (Sweden)

    Natália Luptáková

    2013-04-01

    Full Text Available This paper is closely connected with the complete process of indirect production of ZnO as well as with the problems which occur during the metallurgical process. Purity of raw materials has an important influence on the final quality of ZnO and the occurrence of slag that remains stuck on the walls of furnace linings. ZnO is generally produced in the melting furnaces with different types of ceramic linings. Input materials have to be analyzed and investigated in the order to the predict behavior from the aspect of the complex production process. Moreover, analysis of occurrence of undesirable phases in the batch, the output materials, character of furnace linings and waste material have to be evaluated and observed. Mutual interaction of all components will have a significant impact on the final quality of the ZnO. The result of the investigation of interaction occurring in the components will be used for the proposal of the suitable surface for furnace lining while the mentioned result is mainly obtained on the principle of chemical reactions and bonds. This surface for lining should have a minimum adhesion of the zinc and its alloys relating to production of ZnO.

  5. Relationship between seminal plasma zinc concentration and spermatozoa-zona pellucida binding and the ZP-induced acrosome reaction in subfertile men.

    Science.gov (United States)

    Liu, De-Yi; Sie, Boon-Shih; Liu, Ming-Li; Agresta, Franca; Baker, H W Gordon

    2009-07-01

    The aim of this study was to determine the relationship between seminal zinc concentration and spermatozoa-zona pellucida (ZP) binding and the ZP-induced acrosome reaction (ZPIAR) in subfertile men. Semen analyses and seminal zinc concentration assessments were carried out according to the World Health Organization manual for 458 subfertile men. A spermatozoa-ZP interaction test was carried out by incubating 2 x 10(6) motile spermatozoa with a group of four unfertilized oocytes obtained from a clinical in vitro fertilization programme. After 2 h of incubation, the number of spermatozoa bound per ZP and the ZPIAR of ZP-bound spermatozoa were examined. The effect of adding 0.5 mmol L(-1) zinc to the media on the ZPIAR of spermatozoa from normozoospermic men was also tested in vitro. Seminal zinc concentration positively correlated with sperm count and duration of abstinence, but negatively correlated with semen volume. On analysis of data from all participants, both spermatozoa-ZP binding and the ZPIAR were significantly correlated with sperm motility and normal morphology, but not with seminal zinc concentration. However, in men with normozoospermic semen, the seminal zinc concentration was significantly higher in men with defective ZPIAR (or= 16%) (P zinc to the culture media had no effect on spermatozoa-ZP binding, but significantly reduced the ZPIAR in vitro (P zinc concentration is correlated with sperm count and the duration of abstinence in subfertile men. In men with normozoospermic semen, high seminal zinc concentration may have an adverse effect on the ZPIAR.

  6. Relationship between seminal plasma zinc concentration and spermatozoa–zona pellucida binding and the ZP-induced acrosome reaction in subfertile men

    OpenAIRE

    Liu, De-Yi; Sie, Boon-Shih; Liu, Ming-Li; Agresta,Franca; Baker, HW Gordon

    2009-01-01

    The aim of this study was to determine the relationship between seminal zinc concentration and spermatozoa–zona pellucida (ZP) binding and the ZP-induced acrosome reaction (ZPIAR) in subfertile men. Semen analyses and seminal zinc concentration assessments were carried out according to the World Health Organization manual for 458 subfertile men. A spermatozoa–ZP interaction test was carried out by incubating 2 × 106 motile spermatozoa with a group of four unfertilized oocytes obtained from a ...

  7. An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins.

    Directory of Open Access Journals (Sweden)

    Cheng Zheng

    Full Text Available Zinc-binding proteins are the most abundant metalloproteins in the Protein Data Bank where the zinc ions usually have catalytic, regulatory or structural roles critical for the function of the protein. Accurate prediction of zinc-binding sites is not only useful for the inference of protein function but also important for the prediction of 3D structure. Here, we present a new integrative framework that combines multiple sequence and structural properties and graph-theoretic network features, followed by an efficient feature selection to improve prediction of zinc-binding sites. We investigate what information can be retrieved from the sequence, structure and network levels that is relevant to zinc-binding site prediction. We perform a two-step feature selection using random forest to remove redundant features and quantify the relative importance of the retrieved features. Benchmarking on a high-quality structural dataset containing 1,103 protein chains and 484 zinc-binding residues, our method achieved >80% recall at a precision of 75% for the zinc-binding residues Cys, His, Glu and Asp on 5-fold cross-validation tests, which is a 10%-28% higher recall at the 75% equal precision compared to SitePredict and zincfinder at residue level using the same dataset. The independent test also indicates that our method has achieved recall of 0.790 and 0.759 at residue and protein levels, respectively, which is a performance better than the other two methods. Moreover, AUC (the Area Under the Curve and AURPC (the Area Under the Recall-Precision Curve by our method are also respectively better than those of the other two methods. Our method can not only be applied to large-scale identification of zinc-binding sites when structural information of the target is available, but also give valuable insights into important features arising from different levels that collectively characterize the zinc-binding sites. The scripts and datasets are available at http://protein.cau.edu.cn/zincidentifier/.

  8. Fabrication of a super-hydrophobic nanofibrous zinc oxide film surface by electrospinning

    Energy Technology Data Exchange (ETDEWEB)

    Ding Bin [Faculty of Science and Technology, Keio University, Yokohama 223-8522 (Japan); Fiber and Polymer Science, University of California, Davis, CA 95616 (United States)], E-mail: bding@ucdavis.edu; Ogawa, Tasuku [Faculty of Science and Technology, Keio University, Yokohama 223-8522 (Japan); Kim, Jinho [Faculty of Science and Technology, Keio University, Yokohama 223-8522 (Japan); SNT Ltd, Kawasaki 212-0054 (Japan); Fujimoto, Kouji [Faculty of Science and Technology, Keio University, Yokohama 223-8522 (Japan); Shiratori, Seimei [Faculty of Science and Technology, Keio University, Yokohama 223-8522 (Japan); SNT Ltd, Kawasaki 212-0054 (Japan)], E-mail: shiratori@appi.keio.ac.jp

    2008-03-03

    We report a new approach for fabricating a super-hydrophobic nanofibrous zinc oxide (ZnO) film surface. The pure poly(vinyl alcohol) (PVA) and composite PVA/ZnO nanofibrous films can be obtained by electrospinning the PVA and PVA/zinc acetate solutions, respectively. After the calcination of composite fibrous films, the inorganic fibrous ZnO films with a reduced fiber diameter were fabricated. The wettability of three kinds of fibrous film surfaces were modified with a simple coating of fluoroalkylsilane (FAS) in hexane. The resultant samples were characterized by field emission scanning electron microscopy (FE-SEM), water contact angle (WCA), X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). It was found that the pure PVA fibrous films maintained the super-hydrophilic surface property even after the FAS modification. Additionally, the WCA of composite fibrous films was increased from 105 to 132 deg. with the coating of FAS. Furthermore, the surface property of inorganic ZnO fibrous films was converted from super-hydrophilic (WCA of 0 deg.) to super-hydrophobic (WCA of 165{sup o}) after the surface modification with FAS. Observed from XPS data, the hydrophobicity of FAS coated various film surfaces were found to be strongly affected by the ratio of fluoro:oxygen on the film surfaces.

  9. Bovine serum albumin surface imprinted polymer fabricated by surface grafting copolymerization on zinc oxide rods and its application for protein recognition.

    Science.gov (United States)

    Li, Xiangjie; Zhou, Jingjing; Tian, Lei; Li, Wei; Zhang, Baoliang; Zhang, Hepeng; Zhang, Qiuyu

    2015-10-01

    A novel bovine serum albumin (BSA) surface imprinted polymer based on ZnO rods was synthesized by surface grafting copolymerization. It exhibited an excellent recognition performance to bovine serum albumin. The adsorption capacity and imprinting factor of bovine serum albumin could reach 89.27 mg/g and 2.35, respectively. Furthermore, the fluorescence property of ZnO was used for tracing the process of protein imprinting and it implied the excellent optical sensing property of this material. More importantly, the hypothesis that the surface charge of carrier could affect the imprinting process was confirmed. That is, ZnO with positive surface charge could not only improve the recognition specificity of binding sites to template proteins (pI 7). It was also important that the reusability of ZnO@BSA molecularly imprinted polymers was satisfactory. This implied that the poor mechanical/chemical stability of traditional zinc oxide sensors could be solved by the introduction of surface grafting copolymerization. These results revealed that the ZnO@BSA molecularly imprinted polymers are a promising optical/electrochemical sensor element.

  10. Surfactant assisted surface studies of zinc sulfide nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Shahi, Ashutosh K., E-mail: akshahi.au@gmail.com [Laser Spectroscopy and Nanomaterials Lab, Department of Physics (UGC-CAS), University of Allahabad, Allahabad, 211002 (India); Pandey, B.K.; Swarnkar, R.K.; Gopal, R. [Laser Spectroscopy and Nanomaterials Lab, Department of Physics (UGC-CAS), University of Allahabad, Allahabad, 211002 (India)

    2011-09-15

    We report a simple soft chemical method for the synthesis of ZnS nanoparticles using varying concentration of cationic surfactant CTAB and examine its surface properties. Powder X-ray diffraction, UV-vis spectroscopy, photoluminescence spectroscopy, selective area electron diffraction, and transmission electron microscopy are used to characterize the as prepared ZnS nanoparticles. XRD and TEM measurements show the size of polydispersed ZnS nanoparticles is in the range of 2-5 nm with cubic phase structure. The photoluminescence spectrum of ZnS nanoparticles exhibits four fluorescence emission peaks centered at 387 nm, 412 nm, 489 nm and 528 nm showing the application potential for the optical devices. In Raman spectra of ZnS nanoparticles, the modes around 320, 615 and 700 cm{sup -1} are observed.

  11. Surfactant assisted surface studies of zinc sulfide nanoparticles

    Science.gov (United States)

    Shahi, Ashutosh K.; Pandey, B. K.; Swarnkar, R. K.; Gopal, R.

    2011-09-01

    We report a simple soft chemical method for the synthesis of ZnS nanoparticles using varying concentration of cationic surfactant CTAB and examine its surface properties. Powder X-ray diffraction, UV-vis spectroscopy, photoluminescence spectroscopy, selective area electron diffraction, and transmission electron microscopy are used to characterize the as prepared ZnS nanoparticles. XRD and TEM measurements show the size of polydispersed ZnS nanoparticles is in the range of 2-5 nm with cubic phase structure. The photoluminescence spectrum of ZnS nanoparticles exhibits four fluorescence emission peaks centered at 387 nm, 412 nm, 489 nm and 528 nm showing the application potential for the optical devices. In Raman spectra of ZnS nanoparticles, the modes around 320, 615 and 700 cm-1 are observed.

  12. In vitro DNA binding studies of the sweetening agent saccharin and its copper(II) and zinc(II) complexes.

    Science.gov (United States)

    Icsel, Ceyda; Yilmaz, Veysel T

    2014-01-05

    The interactions of fish sperm DNA (FS-DNA) with the sodium salt of sweetener saccharin (sacH) and its copper and zinc complexes, namely [M(sac)2(H2O)4]·2H2O (M=Cu(II) or Zn(II)) were studied by using UV-Vis titration, fluorometric competition, thermal denaturation, viscosity and gel electrophoresis measurements. The intrinsic binding constants (Kb) obtained from absorption titrations were estimated to be 2.86 (±0.06)×10(4)M(-1) for Na(sac), 6.67 (±0.12)×10(4)M(-1) for Cu-sac and 4.01 (±0.08)×10(4)M(-1) for Zn-sac. The Cu-sac complex binds to FS-DNA via intercalation with a KA value of 50.12 (±0.22)×10(4)M(-1) as evidenced by competitive binding studies with ethidium bromide. Moreover, competition experiments with Hoechst 33258 are indicative of a groove binding mode of Na(sac) and Zn-sac with binding constants of 3.13 (±0.16)×10(4)M(-1) and 5.25 (±0.22)×10(4)M(-1), respectively. The spectroscopic measurements indicate a moderate DNA binding affinity of Na(sac) and its metal complexes. The suggested binding modes are further confirmed by the thermal denaturation and viscosity measurements. In addition, Cu-sac and Zn-sac show weak ability to damage to pBR322 supercoiled plasmid DNA.

  13. The N-terminal zinc finger of the erythroid transcription factor GATA-1 binds GATC motifs in DNA.

    Science.gov (United States)

    Newton, A; Mackay, J; Crossley, M

    2001-09-21

    The mammalian transcription factor GATA-1 is required for normal erythroid and megakaryocytic development. GATA-1 contains two zinc fingers, the C-terminal finger, which is known to bind (A/T)GATA(A/G) motifs in DNA and the N-finger, which is important for interacting with co-regulatory proteins such as Friend of GATA (FOG). We now show that, like the C-finger, the N-finger of GATA-1 is also capable of binding DNA but recognizes distinct sequences with the core GATC. We demonstrate that the GATA-1 N-finger can bind these sequences in vitro and that in cellular assays, GATA-1 can activate promoters containing GATC motifs. Experiments with mutant GATA-1 proteins confirm the importance of the N-finger, as the C-finger is not required for transactivation from GATC sites. Recently four naturally occurring mutations in GATA-1 have been shown to be associated with familial blood disorders. These mutations all map to the N-finger domain. We have investigated the effect of these mutations on the recognition of GATC sites by the N-finger and show that one mutation R216Q abolishes DNA binding, whereas the others have only minor effects.

  14. Influence of surface roughness on performance of zinc-rich paint coatings

    Institute of Scientific and Technical Information of China (English)

    谢德明; 王建明; 胡吉明; 张鉴清

    2002-01-01

    The influence of surface roughness on the performance of zinc-rich paint(ZRP) coatings was studied. Electrochemical impedance spectroscopy(EIS) measurements were used to assess the corrosion prevention performance of the ZRP coatings. Furthermore, the EIS data of the steel-ZRP-sea water system were interpreted according to equivalent circuit models and the corresponding parameters were derived to assess the coating deterioration with time. The results show that the rougher surface favors better protection effect of the ZRP coatings. The protection potential of ZRP coatings for the standards and codes of practice is -0.78V(vs SCE).

  15. An investigation of the electrochemical action of the epoxy zinc-rich coatings containing surface modified aluminum nanoparticle

    Science.gov (United States)

    Jalili, M.; Rostami, M.; Ramezanzadeh, B.

    2015-02-01

    Aluminum nanoparticle was modified with amino trimethylene phosphonic acid (ATMP). The surface characterization of the nanoparticles was done by X-ray photo electron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR) and thermal gravimetric analysis. The influence of the replacement of 2 wt% of zinc dust in the standard zinc-rich epoxy coating by nanoparticles on the electrochemical action of the coating was studied by electrochemical impedance spectroscopy (EIS) and salt spray tests. The morphology and phase composition of the zinc rich paints were evaluated by X-ray diffraction (XRD) and filed-emission scanning electron microscopy (FE-SEM). Results showed that the ATMP molecules successfully adsorbed on the surface of Al nanoparticles. Results obtained from salt spray and electrochemical measurements revealed that the addition of surface modified nanoparticles to the zinc rich coating enhanced its galvanic action and corrosion protection properties.

  16. Adsorption of poly(vinyl formamide-co-vinyl amine) (PVFA-co-PVAm) polymers on zinc, zinc oxide, iron, and iron oxide surfaces.

    Science.gov (United States)

    Seifert, Susan; Simon, Frank; Baumann, Giesela; Hietschold, Michael; Seifert, Andreas; Spange, Stefan

    2011-12-06

    The adsorption of poly(vinyl formamide) (PVFA) and the statistic copolymers poly(vinyl formamide-co-vinyl amine) (PVFA-co-PVAm) onto zinc and iron metal particles as well as their oxides was investigated. The adsorbates were characterized by means of XPS, DRIFT spectroscopy, wet chemical analysis, and solvatochromic probes. Dicyano-bis-(1,10-phenanthroline)-iron(II) (1), 3-(4-amino-3-methylphenyl)-7-phenyl-benzo-[1,2-b:4,5-b']difuran-2,6-dione (2), and 4-tert-butyl-2-(dicyano-methylene)-5-[4-(diethylamino)-benzylidene]-Δ(3)-thiazoline (3) as solvatochromic probes were coadsorbed onto zinc oxide to measure various effects of surface polarity. The experimental findings showed that the adsorption mechanism of PVFA and PVFA-co-PVAm strongly depends on the degree of hydrolysis of PVFA and pH values and also on the kind of metal or metal oxide surfaces that were employed as adsorbents. The adsorption mechanism of PVFA/PVFA-co-PVAm onto zinc oxide and iron oxide surfaces is mainly affected by electrostatic interactions. Particularly in the region of pH 5, the adsorption of PVFA/PVFA-co-PVAm onto zinc and iron metal particles is additionally influenced by redox processes, dissolution, and complexation reactions.

  17. Improved discharge capacity and suppressed surface passivation of zinc anode in dilute alkaline solution using surfactant additives

    Science.gov (United States)

    Yang, Hanxi; Cao, Yuliang; Ai, Xinping; Xiao, Lifen

    The capacity utilization of zinc anode is usually very low in dilute alkaline solution or at high rate discharge because of the passivation of zinc surface. This problem can be considerably overcome by use of surfactant additive in electrolyte. In this work, it is found that with addition of 2% sodium dodecyl benzene sulfonate (SDBS) in 20% KOH solution, the discharge capacity of zinc anode increases from 360 to 490 mAh/g at moderate discharge rate of 40 mA/g, corresponding to a 35% increase in the capacity utilization. Based on the electrochemical and morphological observation of the anodic passivation behaviors of zinc electrode, this effect is revealed that due to the SDBS adsorption, the passive layer formed on the zinc surface has a loose and porous structure rather than a dense and compact film. This type of surface layer facilitates the diffusive exchange of the solution reactant and discharged product through the surface deposit layer and therefore effectively suppresses the surface passivation of zinc anode.

  18. Relativistic tight-binding model: Application to Pt surfaces

    Science.gov (United States)

    Tchernatinsky, A.; Halley, J. W.

    2011-05-01

    We report a parametrization of a previous self-consistent tight-binding model, suitable for metals with a high atomic number in which nonscalar-relativistic effects are significant in the electron physics of condensed phases. The method is applied to platinum. The model is fitted to density functional theory band structures and cohesive energies and spectroscopic data on platinum atoms in five oxidation states, and is then shown without further parametrization to correctly reproduce several low index surface structures. We also predict reconstructions of some vicinal surfaces.

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

    Energy Technology Data Exchange (ETDEWEB)

    Xu Juan, E-mail: doctorxue@126.com [Implant Center, School of Stomatology Jilin University, Changchun, Jilin (China) and Stomatological Hospital, Urumqi, Xinjiang (China); Ding Gang [Department of Stomatology, Yidu Central Hospital, Weifang, Shandong (China); Capital Medical University School of Stomatology, Beijing (China); Li Jinlu; Yang Shenhui; Fang Bisong [Capital Medical University School of Stomatology, Beijing (China); Sun Hongchen, E-mail: hcsun@jlu.edu.cn [Implant Center, School of Stomatology Jilin University, Changchun, Jilin (China); Zhou Yanmin, E-mail: zhouym62@126.com [Implant Center, School of Stomatology Jilin University, Changchun, Jilin (China)

    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.

  20. Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif

    Energy Technology Data Exchange (ETDEWEB)

    Maruyama, Yukie; Ochiai, Akihito [Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Mikami, Bunzo [Laboratory of Applied Structural Biology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Hashimoto, Wataru [Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Murata, Kousaku, E-mail: kmurata@kais.kyoto-u.ac.jp [Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2011-02-18

    Research highlights: {yields} Bacterial alginate-binding Algp7 is similar to component EfeO of Fe{sup 2+} transporter. {yields} We determined the crystal structure of Algp7 with a metal-binding motif. {yields} Algp7 consists of two helical bundles formed through duplication of a single bundle. {yields} A deep cleft involved in alginate binding locates around the metal-binding site. {yields} Algp7 may function as a Fe{sup 2+}-chelated alginate-binding protein. -- Abstract: A gram-negative Sphingomonas sp. A1 directly incorporates alginate polysaccharide into the cytoplasm via the cell-surface pit and ABC transporter. A cell-surface alginate-binding protein, Algp7, functions as a concentrator of the polysaccharide in the pit. Based on the primary structure and genetic organization in the bacterial genome, Algp7 was found to be homologous to an M75 peptidase motif-containing EfeO, a component of a ferrous ion transporter. Despite the presence of an M75 peptidase motif with high similarity, the Algp7 protein purified from recombinant Escherichia coli cells was inert on insulin B chain and N-benzoyl-Phe-Val-Arg-p-nitroanilide, both of which are substrates for a typical M75 peptidase, imelysin, from Pseudomonas aeruginosa. The X-ray crystallographic structure of Algp7 was determined at 2.10 A resolution by single-wavelength anomalous diffraction. Although a metal-binding motif, HxxE, conserved in zinc ion-dependent M75 peptidases is also found in Algp7, the crystal structure of Algp7 contains no metal even at the motif. The protein consists of two structurally similar up-and-down helical bundles as the basic scaffold. A deep cleft between the bundles is sufficiently large to accommodate macromolecules such as alginate polysaccharide. This is the first structural report on a bacterial cell-surface alginate-binding protein with an M75 peptidase motif.

  1. Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module on Cellulose

    Energy Technology Data Exchange (ETDEWEB)

    Nimlos, M. R.; Beckham, G. T.; Matthews, J. F.; Bu, L.; Himmel, M. E.; Crowley, M. F.

    2012-06-08

    Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 {mu}s of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.

  2. Work function shifts of a zinc oxide surface upon deposition of self-assembled monolayers: a theoretical insight.

    Science.gov (United States)

    Cornil, D; Van Regemorter, T; Beljonne, D; Cornil, J

    2014-10-14

    We have investigated at the theoretical Density Functional Theory level the way the work function of zinc oxide layers is affected upon deposition of self-assembled monolayers (SAMs). 4-tert-Butylpyridine (4TBP) and various benzoic acids (BA) were adsorbed on the apolar (101[combining macron]0) ZnO and used as probe systems to assess the influence of several molecular parameters. For the benzoid acids, we have investigated the impact of changing the nature of the terminal group (H, CN, OCH3) and the binding mode of the carboxylic acid (monodentate versus bidentate) on the apolar (101[combining macron]0) surface. For each system, we have quantified the contribution from the molecular core and the anchoring group as well as of the degree of surface reconstruction on the work function shift. For the benzoic acids, the structural reorganization of the surface induces a negative shift of the work function by about 0.3 ± 0.15 eV depending on the nature of the binding mode, irrespective of the nature of the terminal function. The bond-dipole potential strongly contributes to the modification of the work function, with values in the range +1.2 to +2.0 eV. In the case of 4TBP, we further characterized the influence of the degree of coverage and of co-adsorbed species (H, OH, and water molecules) on the ZnO/SAM electronic properties as well as the influence of the ZnO surface polarity by considering several models of the polar (0001) ZnO surface. The introduction of water molecules in the (un)dissociated form at full coverage on the non-polar surface only reduces the work function by 0.3-0.4 eV compared to a reference system without co-adsorbed species. Regarding the polar surface, the work function is also significantly reduced upon deposition of a single 4BTP molecule (from -1.44 eV to -1.73 eV for our model structures), with a shift similar in direction and magnitude compared to the non-polar surfaces.

  3. Surface plasmon resonance characterization of calspermin-calmodulin binding kinetics.

    Science.gov (United States)

    Murphy, Andrew J; Kemp, Fred; Love, John

    2008-05-01

    We cloned, expressed, and purified a chimeric fusion between a soluble green fluorescent protein (smGFP) and the calmodulin binding protein calspermin. We have shown that the fusion protein, labeled smGN, has a K(i) in the calmodulin-dependent cyclic nucleotide phosphodiesterase activity assay of 1.97 nM, i.e., 3800 times smaller than that of the commonly used calmodulin inhibitor W7. Association and dissociation rate constants (k(a) and k(d)) and the dissociation equilibrium constant (K(D)) of smGN for calmodulin were determined using surface plasmon resonance (SPR). The k(a)=1.24 x 10(6)M(-1)s(-1), the k(d)=5.49 x 10(-3)s(-1), and the K(D)=4.42 x 10(-9)M. We also found that the GFP moiety was important for successfully binding calspermin to the surface of the CM5 flow cell at a sufficiently high concentration for SPR, and that this procedure may be used for SPR analysis of other acidic polypeptides, whose pIliquid chromatography-tandem mass spectrometry, indicating a high level of specificity. We conclude that the high affinity and specific binding between smGN and calmodulin make it an easily localized recombinant alternative to chemical calmodulin inhibitors.

  4. Modulation of microtubule assembly by the HIV-1 Tat protein is strongly dependent on zinc binding to Tat

    Directory of Open Access Journals (Sweden)

    Muller Sylviane

    2008-07-01

    Full Text Available Abstract Background During HIV-1 infection, the Tat protein plays a key role by transactivating the transcription of the HIV-1 proviral DNA. In addition, Tat induces apoptosis of non-infected T lymphocytes, leading to a massive loss of immune competence. This apoptosis is notably mediated by the interaction of Tat with microtubules, which are dynamic components essential for cell structure and division. Tat binds two Zn2+ ions through its conserved cysteine-rich region in vitro, but the role of zinc in the structure and properties of Tat is still controversial. Results To investigate the role of zinc, we first characterized Tat apo- and holo-forms by fluorescence correlation spectroscopy and time-resolved fluorescence spectroscopy. Both of the Tat forms are monomeric and poorly folded but differ by local conformational changes in the vicinity of the cysteine-rich region. The interaction of the two Tat forms with tubulin dimers and microtubules was monitored by analytical ultracentrifugation, turbidity measurements and electron microscopy. At 20°C, both of the Tat forms bind tubulin dimers, but only the holo-Tat was found to form discrete complexes. At 37°C, both forms promoted the nucleation and increased the elongation rates of tubulin assembly. However, only the holo-Tat increased the amount of microtubules, decreased the tubulin critical concentration, and stabilized the microtubules. In contrast, apo-Tat induced a large amount of tubulin aggregates. Conclusion Our data suggest that holo-Tat corresponds to the active form, responsible for the Tat-mediated apoptosis.

  5. Nuclear import of cutaneous beta genus HPV8 E7 oncoprotein is mediated by hydrophobic interactions between its zinc-binding domain and FG nucleoporins

    Energy Technology Data Exchange (ETDEWEB)

    Onder, Zeynep; Moroianu, Junona, E-mail: moroianu@bc.edu

    2014-01-20

    We have previously discovered and characterized the nuclear import pathways for the E7 oncoproteins of mucosal alpha genus HPVs, type 16 and 11. Here we investigated the nuclear import of cutaneous beta genus HPV8 E7 protein using confocal microscopy after transfections of HeLa cells with EGFP-8E7 and mutant plasmids and nuclear import assays in digitonin-permeabilized HeLa cells. We determined that HPV8 E7 contains a nuclear localization signal (NLS) within its zinc-binding domain that mediates its nuclear import. Furthermore, we discovered that a mostly hydrophobic patch {sub 65}LRLFV{sub 69} within the zinc-binding domain is essential for the nuclear import and localization of HPV8 E7 via hydrophobic interactions with the FG nucleoporins Nup62 and Nup153. Substitution of the hydrophobic residues within the {sub 65}LRLFV{sub 69} patch to alanines, and not R66A mutation, disrupt the interactions between the 8E7 zinc-binding domain and Nup62 and Nup153 and consequently inhibit nuclear import of HPV8 E7. - Highlights: • HPV8 E7 has a cNLS within its zinc-binding domain that mediates its nuclear import. • Discovery of a hydrophobic patch that is critical for the nuclear import of HPV8 E7. • HPV8 E7 nuclear import is mediated by hydrophobic interactions with FG-Nups, Nup62 and Nup153.

  6. Detecting Latent Prints on Stone and Other Difficult Porous Surfaces via Indanedione/Zinc Chloride and Laser

    Directory of Open Access Journals (Sweden)

    Shiquan LIU

    2016-01-01

    Full Text Available Lasers and alternate light sources have been recognized as effective tools for latent print detection for over three decades. Luminescence often increases friction ridge contrast to reveal impressions otherwise undetectable. Indanedione/zinc chloride excited by a forensic light source is widely recognized as an effective process for developing latent prints on porous surfaces. This study was designed to evaluate the use of a combination of luminescence excitation and indanedione with zinc chloride to detect latent prints on stones, bricks, and similar difficult porous surfaces. The wavelengths evaluated included 400 nm (violet, 447 nm (blue, 532 nm (green, and 645 nm (red. Latent prints were deposited on a variety of porous surfaces including bricks, cement stones, wood, and cotton fabric, all commonly encountered at crime scenes in China. The surfaces were examined using white light (light-emitting diode flashlight and laser light sources separately, both before and after treatment with indanedione/zinc chloride. The goal of this study was to evaluate various light sources for their effectiveness in detecting impressions developed by indanedione/zinc chloride on difficult porous surfaces. Results indicated that latent prints on some brick and cement stone surfaces may be effectively detected using 532 nm laser excitation after indanedione/zinc chloride processing.

  7. Mutation of a zinc-binding residue in the glycine receptor α1 subunit changes ethanol sensitivity in vitro and alcohol consumption in vivo.

    Science.gov (United States)

    McCracken, Lindsay M; Blednov, Yuri A; Trudell, James R; Benavidez, Jillian M; Betz, Heinrich; Harris, R Adron

    2013-02-01

    Ethanol is a widely used drug, yet an understanding of its sites and mechanisms of action remains incomplete. Among the protein targets of ethanol are glycine receptors (GlyRs), which are potentiated by millimolar concentrations of ethanol. In addition, zinc ions also modulate GlyR function, and recent evidence suggests that physiologic concentrations of zinc enhance ethanol potentiation of GlyRs. Here, we first built a homology model of a zinc-bound GlyR using the D80 position as a coordination site for a zinc ion. Next, we investigated in vitro the effects of zinc on ethanol action at recombinant wild-type (WT) and mutant α1 GlyRs containing the D80A substitution, which eliminates zinc potentiation. At D80A GlyRs, the effects of 50 and 200 mM ethanol were reduced as compared with WT receptors. Also, in contrast to what was seen with WT GlyRs, neither adding nor chelating zinc changed the magnitude of ethanol enhancement of mutant D80A receptors. Next, we evaluated the in vivo effects of the D80A substitution by using heterozygous Glra1(D80A) knock-in (KI) mice. The KI mice showed decreased ethanol consumption and preference, and they displayed increased startle responses compared with their WT littermates. Other behavioral tests, including ethanol-induced motor incoordination and strychnine-induced convulsions, revealed no differences between the KI and WT mice. Together, our findings indicate that zinc is critical in determining the effects of ethanol at GlyRs and suggest that zinc binding at the D80 position may be important for mediating some of the behavioral effects of ethanol action at GlyRs.

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

    Science.gov (United States)

    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 S. mutans, a common bacterium in the oral environment.

  9. Surface half-metallicity and stability of zinc-blende sodium monoselenide

    Science.gov (United States)

    Tabatabaeifar, A.; Davatolhagh, S.; Moradi, M.

    2017-02-01

    The electronic structure and magnetic properties of relaxed (001) surfaces of the sp-electron half-metallic ferromagnet NaSe in the zinc-blende phase, are calculated on the basis of first principle density functional theory within the framework of self-consistent field plane wave pseudo-potential method, using the generalized gradient approximation for the exchange-correlation functional. The results of this study reveal that both Na- and Se-terminated surfaces retain the robust bulk half-metallic property. The negative value found for the bulk formation energy indicates that this material is stable against phase separation. We also obtain the surface energies and discuss their stability via the calculated bulk formation energy. The Curie temperature is estimated to be 920 K within mean field approximation, which is well above the room temperature. In the light of the above, zinc-blende NaSe appears to be a good candidate for spintronic applications as spin injection material.

  10. Structural Signatures of Enzyme Binding Pockets from Order-Independent Surface Alignment: A Study of Metalloendopeptidase and NAD Binding Proteins

    Science.gov (United States)

    Dundas, Joe; Adamian, Larisa; Liang, Jie

    2011-01-01

    Detecting similarities between local binding surfaces can facilitate identification of enzyme binding sites, prediction of enzyme functions, as well as aid in our understanding of enzyme mechanisms. A challenging task is to construct a template of local surface characteristics for a specific enzyme function or binding activity, as the size and shape of binding surfaces of a biochemical function often varies. Here we introduce the concept of signature binding pockets, which captures information about preserved and varied atomic positions at multi-resolution levels. For proteins with complex enzyme binding and activity, multiple signatures arise naturally in our model, which form a signature basis set that characterize this class of proteins. Both signatures and signature basis set can be automatically constructed by a method called Solar (Signature Of Local Active Regions). This method is based on a sequence order independent alignment of computed binding surface pockets. Solar also provides a structure based multiple sequence fragment alignment (MSFA) to facilitate interpretation of computed signatures. For studying a family of evolutionary related proteins, we show that for metzincin metalloendopeptidase, which has a broad spectrum of substrate binding, signature and basis set pockets can be used to discriminate metzincins from other enzymes, to predict the subclass of enzyme functions, and to identify the specific binding surfaces. For studying unrelated proteins which have evolved to bind to the same NAD co-factor, signatures of NAD binding pockets can be constructed and can be used to predict NAD binding proteins and to locate NAD binding pockets. By measuring preservation ratio and location variation, our method can identify residues and atoms important for binding affinity and specificity. In both cases, we show that signatures and signature basis set reveal significant biological insight. PMID:21145898

  11. Structure and Metal Binding Properties of ZnuA, a Periplasmic Zinc Transporter from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Yatsunyk,L.; Easton, J.; Kim, L.; Sugarbaker, S.; Bennett, B.; Breece, R.; Vorontsov, I.; Tierney, D.; Crowder, M.; Rosenzweig, A.

    2008-01-01

    ZnuA is the periplasmic Zn(2+)-binding protein associated with the high-affinity ATP-binding cassette ZnuABC transporter from Escherichia coli. Although several structures of ZnuA and its homologs have been determined, details regarding metal ion stoichiometry, affinity, and specificity as well as the mechanism of metal uptake and transfer remain unclear. The crystal structures of E. coli ZnuA (Eco-ZnuA) in the apo, Zn(2+)-bound, and Co(2+)-bound forms have been determined. ZnZnuA binds at least two metal ions. The first, observed previously in other structures, is coordinated tetrahedrally by Glu59, His60, His143, and His207. Replacement of Zn(2+) with Co(2+) results in almost identical coordination geometry at this site. The second metal binding site involves His224 and several yet to be identified residues from the His-rich loop that is unique to Zn(2+) periplasmic metal binding receptors. Electron paramagnetic resonance and X-ray absorption spectroscopic data on CoZnuA provide additional insight into possible residues involved in this second site. The second site is also detected by metal analysis and circular dichroism (CD) titrations. Eco-ZnuA binds Zn(2+) (estimated K (d) < 20 nM), Co(2+), Ni(2+), Cu(2+), Cu(+), and Cd(2+), but not Mn(2+). Finally, conformational changes upon metal binding observed in the crystal structures together with fluorescence and CD data indicate that only Zn(2+) substantially stabilizes ZnuA and might facilitate recognition of ZnuB and subsequent metal transfer.

  12. Substitution of Ala564 in the first zinc cluster of the deoxyribonucleic acid (DNA)-binding domain of the androgen receptor by Asp, Asn, or Leu exerts differential effects on DNA binding

    NARCIS (Netherlands)

    H.T. Brüggenwirth (Hennie); A.L.M. Boehmer (Annemie); J.M. Lobaccaro; L. Chiche; C. Sultan; J. Trapman (Jan); A.O. Brinkmann (Albert)

    1998-01-01

    textabstractIn the androgen receptor of a patient with androgen insensitivity, the alanine residue at position 564 in the first zinc cluster of the DNA-binding domain was substituted by aspartic acid. In other members of the steroid receptor family, either valine or ala

  13. Functionalised zinc oxide nanowire gas sensors: Enhanced NO2 gas sensor response by chemical modification of nanowire surfaces

    Directory of Open Access Journals (Sweden)

    Eric R. Waclawik

    2012-05-01

    Full Text Available Surface coating with an organic self-assembled monolayer (SAM can enhance surface reactions or the absorption of specific gases and hence improve the response of a metal oxide (MOx sensor toward particular target gases in the environment. In this study the effect of an adsorbed organic layer on the dynamic response of zinc oxide nanowire gas sensors was investigated. The effect of ZnO surface functionalisation by two different organic molecules, tris(hydroxymethylaminomethane (THMA and dodecanethiol (DT, was studied. The response towards ammonia, nitrous oxide and nitrogen dioxide was investigated for three sensor configurations, namely pure ZnO nanowires, organic-coated ZnO nanowires and ZnO nanowires covered with a sparse layer of organic-coated ZnO nanoparticles. Exposure of the nanowire sensors to the oxidising gas NO2 produced a significant and reproducible response. ZnO and THMA-coated ZnO nanowire sensors both readily detected NO2 down to a concentration in the very low ppm range. Notably, the THMA-coated nanowires consistently displayed a small, enhanced response to NO2 compared to uncoated ZnO nanowire sensors. At the lower concentration levels tested, ZnO nanowire sensors that were coated with THMA-capped ZnO nanoparticles were found to exhibit the greatest enhanced response. ΔR/R was two times greater than that for the as-prepared ZnO nanowire sensors. It is proposed that the ΔR/R enhancement in this case originates from the changes induced in the depletion-layer width of the ZnO nanoparticles that bridge ZnO nanowires resulting from THMA ligand binding to the surface of the particle coating. The heightened response and selectivity to the NO2 target are positive results arising from the coating of these ZnO nanowire sensors with organic-SAM-functionalised ZnO nanoparticles.

  14. Self-assembling of zinc phthalocyanines on ZnO (1010) surface through multiple time scales.

    Science.gov (United States)

    Melis, Claudio; Raiteri, Paolo; Colombo, Luciano; Mattoni, Alessandro

    2011-12-27

    We adopt a hierarchic combination of theoretical methods to study the assembling of zinc phthalocyanines (ZnPcs) on a ZnO (1010) surface through multiple time scales. Atomistic simulations, such as model potential molecular dynamics and metadynamics, are used to study the energetics and short time evolution (up to ∼100 ns) of small ZnPc aggregates. The stability and the lifetime of large clusters is then studied by means of an atomistically informed coarse-grained model using classical molecular dynamics. Finally, the macroscopic time scale clustering phenomenon is studied by Metropolis Monte Carlo algorithms as a function of temperature and surface coverage. We provide evidence that at room temperature the aggregation is likely to occur at sufficiently high coverage, and we characterize the nature, morphology, and lifetime of ZnPc's clusters. We identify the molecular stripes oriented along [010] crystallographic directions as the most energetically stable aggregates.

  15. Isothermal titration calorimetry and surface plasmon resonance allow quantifying substrate binding to different binding sites of Bacillus subtilis xylanase

    DEFF Research Database (Denmark)

    Cuyvers, Sven; Dornez, Emmie; Abou Hachem, Maher

    2012-01-01

    Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first was a cat......Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first...

  16. Surface functionalization of carbon nanofibers by sol-gel coating of zinc oxide

    Energy Technology Data Exchange (ETDEWEB)

    Shao Dongfeng [Key Laboratory of Eco-textiles, Ministry of Education, Jiangnan University, Wuxi 214122 (China); Changzhou Textile Garment Institute, Changzhou 213164 (China); Wei Qufu [Key Laboratory of Eco-textiles, Ministry of Education, Jiangnan University, Wuxi 214122 (China)], E-mail: qfwei@jiangnan.edu.cn; Zhang Liwei; Cai Yibing; Jiang Shudong [Key Laboratory of Eco-textiles, Ministry of Education, Jiangnan University, Wuxi 214122 (China)

    2008-08-15

    In this paper the functional carbon nanofibers were prepared by the carbonization of ZnO coated PAN nanofibers to expand the potential applications of carbon nanofibers. Polyacrylonitrile (PAN) nanofibers were obtained by electrospinning. The electrospun PAN nanofibers were then used as substrates for depositing the functional layer of zinc oxide (ZnO) on the PAN nanofiber surfaces by sol-gel technique. The effects of coating, pre-oxidation and carbonization on the surface morphology and structures of the nanofibers were characterized by X-ray diffraction (XRD), Fourier transform infrared (FTIR) and Scanning electron microscopy (SEM), respectively. The results of SEM showed a significant increase of the size of ZnO nanograins on the surface of nanofibers after the treatments of coating, pre-oxidation and carbonization. The observations by SEM also revealed that ZnO nanoclusters were firmly and clearly distributed on the surface of the carbon nanofibers. FTIR examination also confirmed the deposition of ZnO on the surface of carbon nanofibers. The XRD analysis indicated that the crystal structure of ZnO nanograins on the surface of carbon nanofibers.

  17. An electrochemical study of the formation of Benzotriazole surface films on Copper, Zinc and a Copper-Zinc alloy

    OpenAIRE

    Fenelon, Anna M.; Breslin, Carmel B.

    2001-01-01

    The electrochemical behaviour of Cu, Cu–37Zn and Zn in benzotriazole (BTA) containing chloride solutions was studied and compared using potentiodynamic, cyclic voltammetry and electrochemical impedance spectroscopy. The presence of BTA in the chloride-containing solutions gave rise to higher breakdown potentials, significantly higher polarisation resistances and inhibited the formation of CuCl2 and zinc-containing corrosion products. These effects were observed for pure Cu, Cu–Zn and to a som...

  18. Aggrecanase-2 inhibitors based on the acylthiosemicarbazide zinc-binding group.

    Science.gov (United States)

    Maingot, Lucie; Elbakali, Jamal; Dumont, Julie; Bosc, Damien; Cousaert, Nicolas; Urban, Agathe; Deglane, Gaelle; Villoutreix, Bruno; Nagase, Hideaki; Sperandio, Olivier; Leroux, Florence; Deprez, Benoit; Deprez-Poulain, Rebecca

    2013-11-01

    Osteoarthritis is a disabling disease characterized by the articular cartilage breakdown. Aggrecanases are potential therapeutic targets for the treatment of this pathology. At the starting point of this project, an acylthiosemicarbazide was discovered to inhibit aggrecanase-2. The acylthiosemicarbazide Zn binding group is also a convenient linker for library synthesis. A focused library of 920 analogs was thus prepared and screened to establish structure-activity relationships. The modification of the acylthiosemicarbazide was also explored. This strategy combining library design and discrete compounds synthesis yielded inhibitor 35, that is highly selective for aggrecanases over a panel of metalloproteases and inhibits the degradation of native fully glycosylated aggrecan. A docking study generated binding conformations explaining the structure-activity relationships.

  19. A New Metal Binding Domain Involved in Cadmium, Cobalt and Zinc Transport

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Aaron T. [Northwestern Univ., Evanston, IL (United States); Barupala, Dulmini [Wayne State Univ., Detroit, MI (United States); Stemmler, Timothy L. [Wayne State Univ., Detroit, MI (United States); Rosenzweig, Amy C. [Northwestern Univ., Evanston, IL (United States)

    2015-07-20

    In the P1B-ATPases, which couple cation transport across membranes to ATP hydrolysis, are central to metal homeostasis in all organisms. An important feature of P1B-ATPases is the presence of soluble metal binding domains (MBDs) that regulate transport activity. Only one type of MBD has been characterized extensively, but bioinformatics analyses indicate that a diversity of MBDs may exist in nature. Here we report the biochemical, structural and functional characterization of a new MBD from the Cupriavidus metallidurans P1B-4-ATPase CzcP (CzcP MBD). The CzcP MBD binds two Cd2+, Co2+ or Zn2+ ions in distinct and unique sites and adopts an unexpected fold consisting of two fused ferredoxin-like domains. Both in vitro and in vivo activity assays using full-length CzcP, truncated CzcP and several variants indicate a regulatory role for the MBD and distinct functions for the two metal binding sites. Moreover, these findings elucidate a previously unknown MBD and suggest new regulatory mechanisms for metal transport by P1B-ATPases.

  20. The eukaryotic translation initiation factor 5, eIF-5, a protein from Zea mays, containing a zinc-finger structure, binds nucleic acids in a zinc-dependent manner.

    Science.gov (United States)

    López Ribera, I; Ruiz-Avila, L; Puigdomènech, P

    1997-07-18

    A maize cDNA encoding the eukaryotic translation initiation factor 5 (eIF-5) has been isolated from an 8-day-old seedling cDNA library. The 1975 bp cDNA encodes a protein of 451 amino acids, with a predicted molecular weight of 49.04 kDa, and hybridizes to a single sequence in the maize genome. The deduced sequence contains motifs characteristic of proteins belonging to the GPTase superfamily, a zinc finger well conserved in all the protein sequences for eIF-5 reported so far, and a fragment also present in prokaryotic and chloroplast L11 ribosomal protein. Polymer-binding assays have been used to assess the predicted RNA binding property of the protein and to characterize its function. It is shown that the eIF-5-encoded protein binds to single-stranded DNA and to polyuridylic acid and that the binding is dependent on the presence of Zn2+ ions. These results suggest that the zinc-finger structure is involved in the binding of the eIF-5 protein to RNA.

  1. Surface cellulose modification with 2-aminomethylpyridine for copper, cobalt, nickel and zinc removal from aqueous solution

    Directory of Open Access Journals (Sweden)

    Edson Cavalcanti Silva Filho

    2013-02-01

    Full Text Available Cellulose was first modified with thionyl chloride, followed by reaction with 2-aminomethylpyridine to yield 6-(2'-aminomethylpyridine-6-deoxycellulose. The resulting chemically-immobilized surface was characterized by elemental analysis, FTIR, 13C NMR and thermogravimetry. From 0.28% of nitrogen incorporated in the polysaccharide backbone, the amount of 0.10 ± 0.01 mmol of the proposed molecule was anchored per gram of the chemically modified cellulose. The available basic nitrogen centers attached to the covalent pendant chain bonded to the biopolymer skeleton were investigated for copper, cobalt, nickel and zinc adsorption from aqueous solution at room temperature. The newly synthesized biopolymer gave maximum sorption capacities of 0.100 ± 0.012, 0.093 ± 0.021, 0.074 ± 0.011 and 0.071 ± 0.019 mmol.g-1 for copper, cobalt, nickel and zinc cations, respectively, using the batchwise method, whose data was fitted to different sorption models, the best fit being obtained with the Langmuir model. The results suggested the use of this anchored biopolymer for cation removal from the environment.

  2. First-principles study on half-metallic zinc-blende CrS and its (001) surface

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Bin, E-mail: hnsqxb@163.com [Department of Mathematics and Information Sciences, North China university of Water Resources and Electric Power, Zhengzhou 450011 (China); Chen, Leiming [Zhengzhou Institute of Aeronautical Industry Management, Zhengzhou, 450015 (China)

    2016-11-01

    Half-metallic magnets with complete (100%) spin polarization have attracted growing interest due to the potential in spintronic applications. In this paper, we use the first-principles calculations to explain the seeming contradiction between the recent experimental ferromagnetism (Demper et al., 2012 [22]) and the previous theoretical antiferromagnetic ground state for half-metallic zinc-blende CrS, and the experimental ferromagnetism of zinc-blende CrS arises from the substrate effect. We also show that both Cr- and S-terminated (001) surfaces of CrS preserve the bulk half-metallicity. The calculated surface energy indicates that the S-terminated (001) surface is more stable than the Cr-terminated (001) surface within the whole effective Cr chemical potentials, and thus the S-terminated (001) surface is more likely than the Cr-terminated (001) surface when the CrS thin films are grown on ZnSe substrate.

  3. Growth, intermixing, and surface phase formation for zinc tin oxide nanolaminates produced by atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Hägglund, Carl, E-mail: carl.hagglund@angstrom.uu.se [Department of Chemical Engineering, Stanford University, Stanford, California 94305 and Department of Engineering Sciences, Division of Solid State Electronics, Uppsala University, 75121 Uppsala (Sweden); Grehl, Thomas; Brongersma, Hidde H. [ION-TOF GmbH, Heisenbergstraße 15, 48149 Münster (Germany); Tanskanen, Jukka T.; Mullings, Marja N.; Mackus, Adriaan J. M.; MacIsaac, Callisto; Bent, Stacey Francine, E-mail: sbent@stanford.edu [Department of Chemical Engineering, Stanford University, Stanford, California 94305 (United States); Yee, Ye Sheng [Department of Electrical Engineering, Stanford University, Stanford, California 94305 (United States); Clemens, Bruce M. [Department of Material Science and Engineering, Stanford University, Stanford, California 94305 (United States)

    2016-03-15

    A broad and expanding range of materials can be produced by atomic layer deposition at relatively low temperatures, including both oxides and metals. For many applications of interest, however, it is desirable to grow more tailored and complex materials such as semiconductors with a certain doping, mixed oxides, and metallic alloys. How well such mixed materials can be accomplished with atomic layer deposition requires knowledge of the conditions under which the resulting films will be mixed, solid solutions, or laminated. The growth and lamination of zinc oxide and tin oxide is studied here by means of the extremely surface sensitive technique of low energy ion scattering, combined with bulk composition and thickness determination, and x-ray diffraction. At the low temperatures used for deposition (150 °C), there is little evidence for atomic scale mixing even with the smallest possible bilayer period, and instead a morphology with small ZnO inclusions in a SnO{sub x} matrix is deduced. Postannealing of such laminates above 400 °C however produces a stable surface phase with a 30% increased density. From the surface stoichiometry, this is likely the inverted spinel of zinc stannate, Zn{sub 2}SnO{sub 4}. Annealing to 800 °C results in films containing crystalline Zn{sub 2}SnO{sub 4}, or multilayered films of crystalline ZnO, Zn{sub 2}SnO{sub 4}, and SnO{sub 2} phases, depending on the bilayer period.

  4. Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T/V mutations within the MID1 zinc-binding Bbox1 domain.

    Directory of Open Access Journals (Sweden)

    Yunjie Zhao

    Full Text Available The zinc-binding Bbox1 domain in protein MID1, a member of the TRIM family of proteins, facilitates the ubiquitination of the catalytic subunit of protein phosphatase 2A and alpha4, a protein regulator of PP2A. The natural mutation of residue A130 to a valine or threonine disrupts substrate recognition and catalysis. While NMR data revealed the A130T mutant Bbox1 domain failed to coordinate both structurally essential zinc ions and resulted in an unfolded structure, the unfolding mechanism is unknown. Principle component analysis revealed that residue A130 served as a hinge point between the structured β-strand-turn-β-strand (β-turn-β and the lasso-like loop sub-structures that constitute loop1 of the ββα-RING fold that the Bbox1 domain adopts. Backbone RMSD data indicate significant flexibility and departure from the native structure within the first 5 ns of the molecular dynamics (MD simulation for the A130V mutant (>6 Å and after 30 ns for A130T mutant (>6 Å. Overall RMSF values were higher for the mutant structures and showed increased flexibility around residues 125 and 155, regions with zinc-coordinating residues. Simulated pKa values of the sulfhydryl group of C142 located near A130 suggested an increased in value to ~9.0, paralleling the increase in the apparent dielectric constants for the small cavity near residue A130. Protonation of the sulfhydryl group would disrupt zinc-coordination, directly contributing to unfolding of the Bbox1. Together, the increased motion of residues of loop 1, which contains four of the six zinc-binding cysteine residues, and the increased pKa of C142 could destabilize the structure of the zinc-coordinating residues and contribute to the unfolding.

  5. Characterization of zinc-binding sites in human stromelysin-1: stoichiometry of the catalytic domain and identification of a cysteine ligand in the proenzyme.

    Science.gov (United States)

    Salowe, S P; Marcy, A I; Cuca, G C; Smith, C K; Kopka, I E; Hagmann, W K; Hermes, J D

    1992-05-19

    A determination of the zinc stoichiometry of the catalytic domain of the human matrix metalloproteinase stromelysin-1 has been carried out using enzyme purified from recombinant Escherichia coli that express C-terminally truncated protein. Atomic absorption spectrometry revealed that both the proenzyme (prostrom255) and the mature active form (strom255) contained nearly 2 mol of Zn/mol of protein. Full-length prostromelysin purified from a mammalian cell culture line also contained zinc in excess of 1 equiv. While zinc in prostrom255 could not be removed by dialysis against o-phenanthroline, similar treatment of mature strom255 resulted in the loss of one-half of the original zinc content. The peptidase activity of the zinc-depleted protein was reduced by greater than 85% but could be restored upon addition of Zn2+ or Co2+. Addition of a thiol-containing inhibitor to a CoZn hybrid enzyme resulted in marked spectral changes in both the visible and ultraviolet regions characteristic of sulfur ligation to Co2+. This direct evidence for an integral role in catalysis and inhibitor binding confirms the location of the exchangeable metal at the active site. To examine the environment of zinc in the proenzyme, a fully cobalt-substituted proenzyme was prepared by in vivo metal replacement. The absorbance features of dicobalt prostrom255 were consistent with metal coordination by the single cysteine present in the propeptide, although the data do not allow assignment to a particular zinc site.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Zinc (hydr)oxide/graphite oxide/AuNPs composites: role of surface features in H₂S reactive adsorption.

    Science.gov (United States)

    Giannakoudakis, Dimitrios A; Bandosz, Teresa J

    2014-12-15

    Zinc hydroxide/graphite oxide/AuNPs composites with various levels of complexity were synthesized using an in situ precipitation method. Then they were used as H2S adsorbents in visible light. The materials' surfaces were characterized before and after H2S adsorption by various physical and chemical methods (XRD, FTIR, thermal analysis, potentiometric titration, adsorption of nitrogen and SEM/EDX). Significant differences in surface features and synergistic effects were found depending on the materials' composition. Addition of graphite oxide and the deposition of gold nanoparticles resulted in a marked increase in the adsorption capacity in comparison with that on the zinc hydroxide and zinc hydroxide/AuNP. Addition of AuNPs to zinc hydroxide led to a crystalline ZnO/AuNP composite while the zinc hydroxide/graphite oxide/AuNP composite was amorphous. The ZnOH/GO/AuNPs composite exhibited the greatest H2S adsorption capacity due to the increased number of OH terminal groups and the conductive properties of GO that facilitated the electron transfer and consequently the formation of superoxide ions promoting oxidation of hydrogen sulfide. AuNPs present in the composite increased the conductivity, helped with electron transfer to oxygen, and prevented the fast recombination of the electrons and holes. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Barley metallothioneins: MT3 and MT4 are localized in the grain aleurone layer and show differential zinc binding.

    Science.gov (United States)

    Hegelund, Josefine Nymark; Schiller, Michaela; Kichey, Thomas; Hansen, Thomas Hesselhøj; Pedas, Pai; Husted, Søren; Schjoerring, Jan Kofod

    2012-07-01

    Metallothioneins (MTs) are low-molecular-weight, cysteine-rich proteins believed to play a role in cytosolic zinc (Zn) and copper (Cu) homeostasis. However, evidence for the functional properties of MTs has been hampered by methodological problems in the isolation and characterization of the proteins. Here, we document that barley (Hordeum vulgare) MT3 and MT4 proteins exist in planta and that they differ in tissue localization as well as in metal coordination chemistry. Combined transcriptional and histological analyses showed temporal and spatial correlations between transcript levels and protein abundance during grain development. MT3 was present in tissues of both maternal and filial origin throughout grain filling. In contrast, MT4 was confined to the embryo and aleurone layer, where it appeared during tissue specialization and remained until maturity. Using state-of-the-art speciation analysis by size-exclusion chromatography inductively coupled plasma mass spectrometry and electrospray ionization time-of-flight mass spectrometry on recombinant MT3 and MT4, their specificity and capacity for metal ion binding were quantified, showing a strong preferential Zn binding relative to Cu and cadmium (Cd) in MT4, which was not the case for MT3. When complementary DNAs from barley MTs were expressed in Cu- or Cd-sensitive yeast mutants, MT3 provided a much stronger complementation than did MT4. We conclude that MT3 may play a housekeeping role in metal homeostasis, while MT4 may function in Zn storage in developing and mature grains. The localization of MT4 and its discrimination against Cd make it an ideal candidate for future biofortification strategies directed toward increasing food and feed Zn concentrations.

  8. Surface analysis of films formed on a zinc anode in a Zn Ni electroplating bath

    Science.gov (United States)

    Velichenko, A. B.; Portillo, J.; Sarret, M.; Muller, C.

    1999-06-01

    The films obtained on a zinc anode in a zinc-nickel electrolyte under open circuit conditions were characterized by XRD, SEM and XPS. The film consisted of metallic zinc and nickel and zinc dissolution products, showing a three-layers structure. In the first layer (the film|electrolyte interface) zinc was always present as Zn(OH) 2 with some adsorbed water. The second layer was a transition region where the content of metallic zinc increased and that of oxygen decreased until a constant composition was reached. The third layer was located in the bulk film and it was mainly composed of α-phase Zn-Ni alloy doped with zinc hydroxide or simonkolleite, depending on the time.

  9. Oxime amides as a novel zinc binding group in histone deacetylase inhibitors: synthesis, biological activity, and computational evaluation.

    Science.gov (United States)

    Botta, Cinzia B; Cabri, Walter; Cini, Elena; De Cesare, Lucia; Fattorusso, Caterina; Giannini, Giuseppe; Persico, Marco; Petrella, Antonello; Rondinelli, Francesca; Rodriquez, Manuela; Russo, Adele; Taddei, Maurizio

    2011-04-14

    Several oxime containing molecules, characterized by a SAHA-like structure, were explored to select a potentially new biasing binding element for the zinc in HDAC catalytic site. All compounds were evaluated for their in vitro inhibitory activity against the 11 human HDACs isoforms. After identification of a "hit" molecule, a programmed variation at the cap group and at the linker was carried out in order to increase HDAC inhibition and/or paralogue selectivity. Some of the new derivatives showed increased activity against a number of HDAC isoforms, even if their overall activity range is still far from the inhibition values reported for SAHA. Moreover, different from what was reported for their hydroxamic acid analogues the new α-oxime amide derivatives do not select between class I and class II HDACs; rather they target specific isoforms in each class. These somehow contradictory results were finally rationalized by a computational assisted SAR, which gave us the chance to understand how the oxime derivatives interact with the catalytic site and justify the observed activity profile.

  10. Human HDAC7 Harbors a Class IIa Histone Deacetylase-specific Zinc Binding Motif and Cryptic Deacetylase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Schuetz, Anja; Min, Jinrong; Allali-Hassani, Abdellah; Schapira, Matthieu; Shuen, Michael; Loppnau, Peter; Mazitschek, Ralph; Kwiatkowski, Nick P.; Lewis, Timothy A.; Maglathin, Rebecca L.; McLean, Thomas H.; Bochkarev, Alexey; Plotnikov, Alexander N.; Vedadi, Masoud; Arrowsmith, Cheryl H. (MIT); (Toronto)

    2010-10-18

    Histone deacetylases (HDACs) are protein deacetylases that play a role in repression of gene transcription and are emerging targets in cancer therapy. Here, we characterize the structure and enzymatic activity of the catalytic domain of human HDAC7 (cdHDAC7). Although HDAC7 normally exists as part of a multiprotein complex, we show that cdHDAC7 has a low level of deacetylase activity which can be inhibited by known HDAC inhibitors. The crystal structures of human cdHDAC7 and its complexes with two hydroxamate inhibitors are the first structures of the catalytic domain of class IIa HDACs and demonstrate significant differences with previously reported class I and class IIb-like HDAC structures. We show that cdHDAC7 has an additional class IIa HDAC-specific zinc binding motif adjacent to the active site which is likely to participate in substrate recognition and protein-protein interaction and may provide a site for modulation of activity. Furthermore, a different active site topology results in modified catalytic properties and in an enlarged active site pocket. Our studies provide mechanistic insights into class IIa HDACs and facilitate the design of specific modulators.

  11. Novel Catalytically-Inactive PII Metalloproteinases from a Viperid Snake Venom with Substitutions in the Canonical Zinc-Binding Motif

    Science.gov (United States)

    Camacho, Erika; Sanz, Libia; Escalante, Teresa; Pérez, Alicia; Villalta, Fabián; Lomonte, Bruno; Neves-Ferreira, Ana Gisele C.; Feoli, Andrés; Calvete, Juan J.; Gutiérrez, José María; Rucavado, Alexandra

    2016-01-01

    Snake venom metalloproteinases (SVMPs) play key biological roles in prey immobilization and digestion. The majority of these activities depend on the hydrolysis of relevant protein substrates in the tissues. Hereby, we describe several isoforms and a cDNA clone sequence, corresponding to PII SVMP homologues from the venom of the Central American pit viper Bothriechis lateralis, which have modifications in the residues of the canonical sequence of the zinc-binding motif HEXXHXXGXXH. As a consequence, the proteolytic activity of the isolated proteins was undetectable when tested on azocasein and gelatin. These PII isoforms comprise metalloproteinase and disintegrin domains in the mature protein, thus belonging to the subclass PIIb of SVMPs. PII SVMP homologues were devoid of hemorrhagic and in vitro coagulant activities, effects attributed to the enzymatic activity of SVMPs, but induced a mild edema. One of the isoforms presents the characteristic RGD sequence in the disintegrin domain and inhibits ADP- and collagen-induced platelet aggregation. Catalytically-inactive SVMP homologues may have been hitherto missed in the characterization of snake venoms. The presence of such enzymatically-inactive homologues in snake venoms and their possible toxic and adaptive roles deserve further investigation. PMID:27754342

  12. Effect of surface modification and UVA photoactivation on antibacterial bioactivity of zinc oxide powder

    Science.gov (United States)

    Ann, Ling Chuo; Mahmud, Shahrom; Bakhori, Siti Khadijah Mohd; Sirelkhatim, Amna; Mohamad, Dasmawati; Hasan, Habsah; Seeni, Azman; Rahman, Rosliza Abdul

    2014-02-01

    The effects of surface modification of zinc oxide (ZnO) powder and UVA illumination on the powder towards Escherichia coli and Staphylococcus aureus were investigated. FESEM-EDS results showed that oxygen annealing increased the O:Zn ratio on the surface of ZnO-rod and ZnO-plate samples. Surface conductances of ZnO-rod and ZnO-plate pellets were reduced from 1.05 nS to 0.15 nS and 1.34 nS to 0.23 nS, respectively. Meanwhile, UVA illumination on the surface of the ZnO-rod and ZnO-plate samples was found to improve surface conductance to 7.08 nS and 6.51 nS, respectively, due to the release of charge carrier. Photoluminescence results revealed that oxygen annealing halved the UV emission intensity and green emission intensity, presumably caused by oxygen absorption in the ZnO lattice. The antibacterial results showed that oxygen-treated ZnO exhibited slightly higher growth inhibition on E. coli and S. aureus compared with unannealed ZnO. UVA illumination on ZnO causes the greatest inhibition toward E. coli and S. aureus. Under the UVA excitation, the inhibition of E. coli increased by 18% (ZnO-rod) and 13% (ZnO-plate) while the inhibition of S. aureus increased by 22% (ZnO-rod) and 21% (ZnO-plate). Release of reactive oxygen species were proposed in antibacterial mechanisms, which were aided by surface modification and UVA photoactivation. The reactive oxygen species disrupted the DNA and protein synthesis of the bacterial cell, causing bacteriostatic effects toward E. coli and S. aureus.

  13. Surface precipitation of highly porous hydrotalcite-like film on Al from a zinc aqueous solution.

    Science.gov (United States)

    Gao, Y F; Nagai, M; Masuda, Y; Sato, F; Seo, W S; Koumoto, K

    2006-04-11

    A hydrotalcite-like film has been successfully deposited on an Al-bearing glass substrate based on an interface reaction between an Al layer and a zinc aqueous solution. The film selectively grew on the Al surface but not on the glass surface. The film on Al was composed of layered nanosheets of a hydrotalcite-like compound containing Al and Zn. Comparably, deposits on the plastic surface and precipitates in solution were wurzite-type ZnO with various morphologies depending upon the preparation conditions. At low supersaturation degrees, single crystals and superstructures of Zn-Al hydrotalcite were also obtained. This porous hydrotalcite film has a potential application as catalyst supports, environmental materials, or matrixes for hydrotalcite-based nanocomposite films. Using Al as a reaction interface makes it easy to coat porous hydrotalcites on a series of matrix materials varying in shapes and properties, which is important for achieving practical applications. In addition, the method developed should be widely applicable to other systems for the preparation of porous or oriented hydrotalcite-like thin films by an appropriate combination of divalent/trivalent solution-substrate systems.

  14. Effects of zinc-substituted nano-hydroxyapatite coatings on bone integration with implant surfaces

    Institute of Scientific and Technical Information of China (English)

    Shi-fang ZHAO; Wen-jing DONG; Qiao-hong JIANG; Fu-ming HE; Xiao-xiang WANG; Guo-li YANG

    2013-01-01

    Objective:The purpose of this study was to investigate the effects of a zinc-substituted nano-hydroxyapatite (Zn-HA) coating,applied by an electrochemical process,on implant osseointegraton in a rabbit model.Methods:A Zn-HA coating or an HA coating was deposited using an electrochemical process.Surface morphology was examined using field-emission scanning electron microscopy.The crystal structure and chemical composition of the coatings were examined using an X-ray diffractometer (XRD) and Fourier transform infrared spectroscopy (FTIR).A total of 78 implants were inserted into femurs and tibias of rabbits.After two,four,and eight weeks,femurs and tibias were retrieved and prepared for histomorphometric evaluation and removal torque (RTQ) tests.Results:Rod-like HA crystals appeared on both implant surfaces.The dimensions of the Zn-HA crystals seemed to be smaller than those of HA.XRD patterns showed that the peaks of both coatings matched well with standard HA patterns.FTIR spectra showed that both coatings consisted of HA crystals.The Zn-HA coating significantly improved the bone area within all threads after four and eight weeks (P<0.05),the bone to implant contact (BIC) at four weeks (P<0.05),and RTQ values after four and eight weeks (P<0.05).Conclusions:The study showed that an electrochemically deposited Zn-HA coating has potential for improving bone integration with an implant surface.

  15. Zinc-induced dimerization of the amyloid-β metal-binding domain 1-16 is mediated by residues 11-14.

    Science.gov (United States)

    Kozin, Sergey A; Mezentsev, Yuri V; Kulikova, Alexandra A; Indeykina, Maria I; Golovin, Andrey V; Ivanov, Alexis S; Tsvetkov, Philipp O; Makarov, Alexander A

    2011-04-01

    Analysis of complex formation between amyloid-β fragments using surface plasmon resonance biosensing and electrospray mass spectrometry reveals that region 11-14 mediates zinc-induced dimerization of amyloid-β and may serve as a potential drug target for preventing development and progression of Alzheimer's disease.

  16. Binding of Cationic Bis-porphyrins Linked with p- or m-Xylylenediamine and Their Zinc(II Complexes to Duplex DNA

    Directory of Open Access Journals (Sweden)

    Tadayuki Uno

    2008-12-01

    Full Text Available Spectroscopic, viscometric, and molecular docking analysis of binding of cationic bis-porphyrins linked with p- or m-xylylenediamine (H2pXy and H2mXy and their zinc(II complexes (ZnpXy and ZnmXy to duplex DNA are described. H2pXy and H2mXy bound to calf thymus DNA (CTDNA stronger than unichromophoric H2TMPyP, and showed exciton-type induced circular dichroism spectra of their Soret bands. The H2TMPyP-like units of the metal-free bis-porphyrins did not intercalate into CTDNA, and thus the binding mode is outside binding with intramolecular stacking. ZnpXy showed favorable binding to A·T over G·C region, and should lie in the major groove of A·T region.

  17. Differential Binding of Monomethylarsonous Acid Compared to Arsenite and Arsenic Trioxide with Zinc Finger Peptides and Proteins

    Science.gov (United States)

    2015-01-01

    Arsenic is an environmental toxin that enhances the carcinogenic effect of DNA-damaging agents, such as ultraviolet radiation and benzo[a]pyrene. Interaction with zinc finger proteins has been shown to be an important molecular mechanism for arsenic toxicity and cocarcinogenesis. Arsenicals such as arsenite, arsenic trioxide (ATO), and monomethylarsonous acid (MMA(III)) have been reported to interact with cysteine residues of zinc finger domains, but little is known about potential differences in their selectivity of interaction. Herein we analyzed the interaction of arsenite, MMA(III), and ATO with C2H2, C3H1, and C4 configurations of zinc fingers using UV–vis, cobalt, fluorescence, and mass spectrometry. We observed that arsenite and ATO both selectively bound to C3H1 and C4 zinc fingers, while MMA(III) interacted with all three configurations of zinc finger peptides. Structurally and functionally, arsenite and ATO caused conformational changes and zinc loss on C3H1 and C4 zinc finger peptide and protein, respectively, whereas MMA(III) changed conformation and displaced zinc on all three types of zinc fingers. The differential selectivity was also demonstrated in zinc finger proteins isolated from cells treated with these arsenicals. Our results show that trivalent inorganic arsenic compounds, arsenite and ATO, have the same selectivity and behavior when interacting with zinc finger proteins, while methylation removes the selectivity. These findings provide insights on the molecular mechanisms underlying the differential effects of inorganic versus methylated arsenicals, as well as the role of in vivo arsenic methylation in arsenic toxicity and carcinogenesis. PMID:24611629

  18. Differential binding of monomethylarsonous acid compared to arsenite and arsenic trioxide with zinc finger peptides and proteins.

    Science.gov (United States)

    Zhou, Xixi; Sun, Xi; Mobarak, Charlotte; Gandolfi, A Jay; Burchiel, Scott W; Hudson, Laurie G; Liu, Ke Jian

    2014-04-21

    Arsenic is an environmental toxin that enhances the carcinogenic effect of DNA-damaging agents, such as ultraviolet radiation and benzo[a]pyrene. Interaction with zinc finger proteins has been shown to be an important molecular mechanism for arsenic toxicity and cocarcinogenesis. Arsenicals such as arsenite, arsenic trioxide (ATO), and monomethylarsonous acid (MMA(III)) have been reported to interact with cysteine residues of zinc finger domains, but little is known about potential differences in their selectivity of interaction. Herein we analyzed the interaction of arsenite, MMA(III), and ATO with C2H2, C3H1, and C4 configurations of zinc fingers using UV-vis, cobalt, fluorescence, and mass spectrometry. We observed that arsenite and ATO both selectively bound to C3H1 and C4 zinc fingers, while MMA(III) interacted with all three configurations of zinc finger peptides. Structurally and functionally, arsenite and ATO caused conformational changes and zinc loss on C3H1 and C4 zinc finger peptide and protein, respectively, whereas MMA(III) changed conformation and displaced zinc on all three types of zinc fingers. The differential selectivity was also demonstrated in zinc finger proteins isolated from cells treated with these arsenicals. Our results show that trivalent inorganic arsenic compounds, arsenite and ATO, have the same selectivity and behavior when interacting with zinc finger proteins, while methylation removes the selectivity. These findings provide insights on the molecular mechanisms underlying the differential effects of inorganic versus methylated arsenicals, as well as the role of in vivo arsenic methylation in arsenic toxicity and carcinogenesis.

  19. Desiccation and zinc binding induce transition of tomato abscisic acid stress ripening 1, a water stress- and salt stress-regulated plant-specific protein, from unfolded to folded state.

    Science.gov (United States)

    Goldgur, Yehuda; Rom, Slava; Ghirlando, Rodolfo; Shkolnik, Doron; Shadrin, Natalia; Konrad, Zvia; Bar-Zvi, Dudy

    2007-02-01

    Abscisic acid stress ripening 1 (ASR1) is a low molecular weight plant-specific protein encoded by an abiotic stress-regulated gene. Overexpression of ASR1 in transgenic plants increases their salt tolerance. The ASR1 protein possesses a zinc-dependent DNA-binding activity. The DNA-binding site was mapped to the central part of the polypeptide using truncated forms of the protein. Two additional zinc-binding sites were shown to be localized at the amino terminus of the polypeptide. ASR1 protein is presumed to be an intrinsically unstructured protein using a number of prediction algorithms. The degree of order of ASR1 was determined experimentally using nontagged recombinant protein expressed in Escherichia coli and purified to homogeneity. Purified ASR1 was shown to be unfolded using dynamic light scattering, gel filtration, microcalorimetry, circular dichroism, and Fourier transform infrared spectrometry. The protein was shown to be monomeric by analytical ultracentrifugation. Addition of zinc ions resulted in a global change in ASR1 structure from monomer to homodimer. Upon binding of zinc ions, the protein becomes ordered as shown by Fourier transform infrared spectrometry and microcalorimetry, concomitant with dimerization. Tomato (Solanum lycopersicum) leaf soluble ASR1 is unstructured in the absence of added zinc and gains structure upon binding of the metal ion. The effect of zinc binding on ASR1 folding and dimerization is discussed.

  20. Copper and zinc binding properties of the N-terminal histidine-rich sequence of Haemophilus ducreyi Cu,Zn superoxide dismutase.

    Science.gov (United States)

    Paksi, Zoltán; Jancsó, Attila; Pacello, Francesca; Nagy, Nóra; Battistoni, Andrea; Gajda, Tamás

    2008-09-01

    The Cu,Zn superoxide dismutase (Cu,ZnSOD) isolated from Haemophilus ducreyi possesses a His-rich N-terminal metal binding domain, which has been previously proposed to play a copper(II) chaperoning role. To analyze the metal binding ability and selectivity of the histidine-rich domain we have carried out thermodynamic and solution structural analysis of the copper(II) and zinc(II) complexes of a peptide corresponding to the first 11 amino acids of the enzyme (H(2)N-HGDHMHNHDTK-OH, L). This peptide has highly versatile metal binding ability and provides one and three high affinity binding sites for zinc(II) and copper(II), respectively. In equimolar solutions the MHL complexes are dominant in the neutral pH-range with protonated lysine epsilon-amino group. As a consequence of its multidentate nature, L binds zinc and copper with extraordinary high affinity (K(D,Zn)=1.6x10(-9)M and K(D,Cu)=5.0x10(-12)M at pH 7.4) and appears as the strongest zinc(II) and copper(II) chelator between the His-rich peptides so far investigated. These K(D) values support the already proposed role of the N-terminal His-rich region of H. ducreyi Cu,ZnSOD in copper recruitment under metal starvation, and indicate a similar function in the zinc(II) uptake, too. The kinetics of copper(II) transfer from L to the active site of Cu-free N-deleted H. ducreyi Cu,ZnSOD showed significant pH and copper-to-peptide ratio dependence, indicating specific structural requirements during the metal ion transfer to the active site. Interestingly, the complex CuHL has significant superoxide dismutase like activity, which may suggest multifunctional role of the copper(II)-bound N-terminal His-rich domain of H. ducreyi Cu,ZnSOD.

  1. Improvement in micro-structural and mechanical properties of zinc film by surface treatment with low temperature argon plasma

    Energy Technology Data Exchange (ETDEWEB)

    Behera, Debadhyan, E-mail: debadhyan_25@yahoo.co.in [Institute of Minerals and Materials Technology, Council of Scientific and Industrial Research, Bhubaneswar 751013 (India); Mishra, Dilip K; Pradhan, Siddhartha K; Sakthivel, Ramasamy; Mohanty, Swagatika [Institute of Minerals and Materials Technology, Council of Scientific and Industrial Research, Bhubaneswar 751013 (India)

    2011-11-15

    Nanocrystalline zinc films were deposited on gold coated borosilicate glass substrates by thermal evaporation method using zinc powders as the source material and then treated with argon plasma at various temperatures. From X-ray diffraction study, the as-deposited films are found to be metallic Zn and polycrystalline in nature. The crystalline nature improves with the increase of temperature up to 200 Degree-Sign C and decreases with the further increase of temperature to 300 Degree-Sign C. The binding energy observed for Zn 2p{sub 3/2}, and the binding energy separation between Zn 2p{sub 3/2} and Zn 2p{sub 1/2} in the X-ray photoelectron spectrum indicate that the films are metallic zinc films. Transmission electron microscopic study shows hexagonal shaped grains having size {approx}58 nm upon treatment with Ar plasma. It is clearly shown the grain growth and distinct grain boundary with the increase in temperature. The average Young's modulus (E) and hardness (H) are measured to be 84 GPa and 4.0 GPa for as-deposited film, whereas 98 GPa and 5.8 GPa for plasma treated film at 200 Degree-Sign C. The enhancement in mechanical properties is attributed to improvement in crystalline nature of the film and better interlinking between grains and boundaries.

  2. Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design.

    Science.gov (United States)

    Wisz, M S; Garrett, C Z; Hellinga, H W

    1998-06-01

    A semi-automated, rational design strategy has been used to introduce a family of seven single, mononuclear Cys2His2 zinc sites at various locations in the hydrophobic core of Escherichia colithioredoxin, a protein that is normally devoid of metal centers. The electronic absorption spectra of the CoII complexes show that five of these designed proteins bind metal with the intended tetrahedral geometry. The designed sites differ in their metal-binding constants and effects on protein stability. Since these designs are constructed within the same host protein framework, comparison of their behavior allows a qualitative evaluation of dominant factors that contribute to metal-binding and metal-mediated protein stabilization. Metal-binding constants are dominated by steric interactions between the buried, designed coordination sphere and the surrounding protein matrix. Metal-mediated stability is the consequence of differential binding to the native and unfolded states. Increased interactions with the unfolded state decrease the stabilizing effect of metal binding. The affinity for the unfolded state is dependent on the placement of the primary coordination sphere residues within the linear protein sequence. These results indicate that a protein fold can have a remarkably broad potential for accommodating metal-mediated cross-links and suggest strategies for engineering protein stability by constructing metal sites that maximize metal binding to the native state and minimize binding to the unfolded state.

  3. Design and development of anisotropic inorganic/polystyrene nanocomposites by surface modification of zinc oxide nanoparticles.

    Science.gov (United States)

    Han, Xiao; Huang, Shiming; Wang, Yilong; Shi, Donglu

    2016-07-01

    Anisotropic yolk/shell or Janus inorganic/polystyrene nanocomposites were prepared by combining miniemulsion polymerization and sol-gel reaction. The morphologies of the anisotropic composites were found to be greatly influenced by surface modification of zinc oxide (ZnO) nanoparticle seeds. Two different types of the oleic acid modified ZnO nanoparticles (OA-ZnO) were prepared by post-treatment of commercial ZnO powder and homemade OA-ZnO nanoparticles. The morphologies and properties of the nanocomposites were investigated by transmission electron microscope (TEM), thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering (DLS), and energy dispersive X-ray spectroscopy (EDX). It was found that both post-treated OA-ZnO and in-situ prepared OA-ZnO nanoparticles resulted in the yolk-shell and Janus structure nanocomposites, but with varied size and morphology. These nanocomposites showed stable and strong fluorescence by introducing quantum dots as the co-seeds. The fluorescent anisotropic nanocomposites were decorated separately with surface carboxyl and hydroxyl groups. These composites with unique anisotropic properties will have high potential in biomedical applications, particularly in bio-detection.

  4. Preparation and rapid analysis of antibacterial silver, copper and zinc doped sol-gel surfaces.

    Science.gov (United States)

    Jaiswal, Swarna; McHale, Patrick; Duffy, Brendan

    2012-06-01

    The colonisation of clinical and industrial surfaces with microorganisms, including antibiotic-resistant strains, has promoted increased research into the development of effective antibacterial and antifouling coatings. This study describes the preparation of metal nitrate (Ag, Cu, Zn) doped methyltriethoxysilane (MTEOS) coatings and the rapid assessment of their antibacterial activity using polyproylene microtitre plates. Microtitre plate wells were coated with different volumes of liquid sol-gel and cured under various conditions. Curing parameters were analysed by thermogravimetric analysis (TGA) and visual examination. The optimum curing conditions were determined to be 50-70°C using a volume of 200 μl. The coated wells were challenged with Gram-positive and Gram-negative bacterial cultures, including biofilm-forming and antibiotic-resistant strains. The antibacterial activities of the metal doped sol-gel, at equivalent concentrations, were found to have the following order: silver>zinc>copper. The order is due to several factors, including the increased presence of silver nanoparticles at the sol-gel coating surface, as determined by X-ray photoelectron spectroscopy, leading to higher elution rates as measured by inductively coupled plasma atomic emission spectroscopy (ICP-AES). The use of microtitre plates enabled a variety of sol-gel coatings to be screened for their antibacterial activity against a wide range of bacteria in a relatively short time. The broad-spectrum antibacterial activity of the silver doped sol-gel showed its potential for use as a coating for biomaterials.

  5. Staphylococcus aureus immunodominant surface antigen B is a cell-surface associated nucleic acid binding protein

    Directory of Open Access Journals (Sweden)

    Cerca Nuno

    2009-03-01

    Full Text Available Abstract Background Staphylococcus aureus immunodominant surface antigen B (IsaB elicits an immune response during septicemia and is generally classified as a virulence factor, but its biological function remains completely undefined. In an attempt to identify staphylococcal RNA-binding proteins, we designed an RNA Affinity Chromatography assay and subsequently isolated IsaB. Results Western analysis indicated that IsaB was both secreted and cell-surface associated. Gel Shift analysis confirmed the RNA binding activity but revealed that IsaB bound to any nucleic acid without sequence specificity. IsaB exhibited the highest affinity for double-stranded DNA followed by single-stranded DNA and RNA. Because extracellular DNA has been shown to play a role in biofilm formation, we investigated the biofilm-forming capacity of an isogenic isaB deletion mutant but we found that IsaB did not contribute to biofilm formation under any conditions tested. Conclusion IsaB is an extracellular nucleic acid binding protein, with little to no sequence specificity, but its role in virulence remains unclear.

  6. The zinc finger E-box-binding homeobox 1 (Zeb1) promotes the conversion of mouse fibroblasts into functional neurons.

    Science.gov (United States)

    Yan, Long; Li, Yue; Shi, Zixiao; Lu, Xiaoyin; Ma, Jiao; Hu, Baoyang; Jiao, Jianwei; Wang, Hongmei

    2017-08-04

    The zinc finger E-box-binding transcription factor Zeb1 plays a pivotal role in the epithelial-mesenchymal transition. Numerous studies have focused on the molecular mechanisms by which Zeb1 contributes to this process. However, the functions of Zeb1 beyond the epithelial-mesenchymal transition remain largely elusive. Using a transdifferentiation system to convert mouse embryonic fibroblasts (MEFs) into functional neurons via the neuronal transcription factors achaete-scute family bHLH (basic helix-loop-helix) transcription factor1 (Ascl1), POU class 3 homeobox 2 (POU3F2/Brn2), and neurogenin 2 (Neurog2, Ngn2) (ABN), we found that Zeb1 was up-regulated during the early stages of transdifferentiation. Knocking down Zeb1 dramatically attenuated the transdifferentiation efficiency, whereas Zeb1 overexpression obviously increased the efficiency of transdifferentiation from MEFs to neurons. Interestingly, Zeb1 improved the transdifferentiation efficiency induced by even a single transcription factor (e.g. Asc1 or Ngn2). Zeb1 also rapidly promoted the maturation of induced neuron cells to functional neurons and improved the formation of neuronal patterns and electrophysiological characteristics. Induced neuron cells could form functional synapse in vivo after transplantation. Genome-wide RNA arrays showed that Zeb1 overexpression up-regulated the expression of neuron-specific genes and down-regulated the expression of epithelial-specific genes during conversion. Taken together, our results reveal a new role for Zeb1 in the transdifferentiation of MEFs into neurons. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. In vitro bone formation by human marrow cell culture on the surface of zinc-releasing calcium phosphate ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Ikeuchi, M.; Noshi, T.; Horiuchi, K.; Yamamoto, K.; Sugimura, M. [Nara Medical Univ., Kashihara (Japan). Dept. of Oral and Maxillofacial Surgery; Dohi, Y. [Nara Medical Univ., Kashihara (Japan). Dept. of Public Health; Ohgushi, H. [Nara Medical Univ., Kashihara (Japan). Dept. of Orthopedics; Ito, A. [National Inst. for Advanced Interdisciplinary Research, MITI, Ibaraki (Japan)

    2001-07-01

    We examined the effect of zinc on the osteogenic differentiation of cultured human marrow cells on the surface of zinc-releasing TCP/HAP (Zn-TCP/HAP) ceramics in the shape of a disk. Three ml of human bone marrow harvested from the ilium was cultured in a medium containing 15% fetal bovine serum to reach confluent. After trypsinization, the cells were seeded at 20 x 10{sup 3} cells/16 mm {phi} on Falcon tissue wells with the ceramic disks (TCP/HAP containing 0, 0.32, 0.42, 0.63, 0.88 and 1.26 wt% Zn). After 2 weeks of subculture in the presence of {beta}-glycerophosphate, vitamin C phosphate, and dexamethasone (Dex), the cells were stained for alkaline phosphatase (ALP). The ALP stain was strengthened as zinc content of the disk increased. The data demonstrated that Zn-TCP/HAP influenced cell differentiation in human marrow cell culture and resulted in high osteoblastic activity. Furthermore, ALP activities of the cell layer significantly increased depending on zinc content of the disk in the presence of Dex. These results indicate that the surface of Zn-TCP/HAP stimulates osteogenic differentiation in human cultured marrow cells as well as in rat ones. Thus, Zn-TCP/HAP ceramics are expected to be useful materials for bone reconstructive surgery. (orig.)

  8. Zinc Composite Layers, Incorporating Polymeric Nano-aggregates: Surface Analysis and Electrochemical Behavior

    NARCIS (Netherlands)

    Koleva, D.A.; Zhang, X.; Petrov, P.; Boshkov, N.; Van Breugel, K.; De Wit, J.H.W.; Mol, J.M.C.; Tsvetkova, N.

    2008-01-01

    This study reports on a comparative investigation of the corrosion behavior of zinc (Zn) and nano-composite zinc (ZnC) galvanic layers in 5% NaCl solution. The metallic matrix of the ZnC layers incorporates nano-sized, stabilized polymeric aggregates, formed from the amphiphilic tri-block co-polymer

  9. Nickel, Lead and Zinc Contamination in the Surface Sediments of Agh Gel Wetland, Iran

    Directory of Open Access Journals (Sweden)

    Soheil Sobhan Ardakani

    2016-07-01

    Full Text Available Background & Aims of the Study: Due to the increased human activities around the Agh Gel wetland, this study aimed to measured accumulations of heavy metals (Ni, Pb and Zn in the surface sediment samples taken from this wetland. Materials & Methods: Samples were taken from 10 stations and exposed to bulk digestion and chemical partitioning. Finally, Ni, Pb and Zn concentrations were monitored with ICP-OES in the sediments. Also, geo-accumulation index, contamination factor and pollution load index were used to evaluate the magnitude of contaminants in the sediment profile. Results: The results showed, the average of metal concentration in samples (mg kg-1 wet weight were 34.20±3.58 for Ni, 25.37±2.52 for Pb and 127.20±15.21 for Zn, respectively. Therefore, the pattern of metal concentrations in sediment was determined as Zinc>Nickel >Lead. According to the mean I-geo values, sediments' qualities are classified as unpolluted category for Ni and Pb. Also, sediment's quality is classified as unpolluted to moderately polluted for Zn. The CF values for all elements are classified as moderate contamination. The PLI values indicated that metal pollution exists for all sampling stations. Conclusions: The obtained results indicated that the Agh Gel wetland has a potential to threaten by chemical pollutants such as agricultural effluent. So, in order to preserve the environment of the Agh Gel wetland from deterioration, monitoring of water and sediment qualities is recommended periodically.

  10. Electronic Structure of the Perylene / Zinc Oxide Interface: A Computational Study of Photoinduced Electron Transfer and Impact of Surface Defects

    KAUST Repository

    Li, Jingrui

    2015-07-29

    The electronic properties of dye-sensitized semiconductor surfaces consisting of pery- lene chromophores chemisorbed on zinc oxide via different spacer-anchor groups, have been studied at the density-functional-theory level. The energy distributions of the donor states and the rates of photoinduced electron transfer from dye to surface are predicted. We evaluate in particular the impact of saturated versus unsaturated aliphatic spacer groups inserted between the perylene chromophore and the semiconductor as well as the influence of surface defects on the electron-injection rates.

  11. Effect of carbamide peroxide and hydrogen peroxide on the surface morphology and zinc oxide levels of IRM fillings.

    Science.gov (United States)

    Rostein, I; Cohenca, N; Mor, C; Moshonov, J; Stabholz, A

    1995-12-01

    The effect of 10% carbamide peroxide or 10% hydrogen peroxide on the surface morphology and zinc oxide levels of IRM fillings was tested. Ninety IRM samples were treated with either 10% carbamide peroxide, 10% hydrogen peroxide or phosphate buffer which served as control. Treatment consisted of placing the samples in a dry incubator at 37 degrees C for 1, 3 or 7 days. At each time point, the samples were removed from the test solutions, dried and prepared for surface scanning electron microscopy and energy dispersive spectrometric analysis. After 3 days, 10% carbamide peroxide significantly reduced the zinc oxide levels as compared to the 10% hydrogen peroxide group (IRM fillings, but their modes of action differed.

  12. Zinc-finger domains of the transcriptional repressor KLF15 bind multiple sites in rhodopsin and IRBP promoters including the CRS-1 and G-rich repressor elements

    Directory of Open Access Journals (Sweden)

    Lai Hong

    2005-06-01

    Full Text Available Abstract Background In the retina, many of the genes that encode components of the visual transduction cascade and retinoid recycling are exclusively expressed in photoreceptor cells and show highly stereotyped temporal and spatial expression patterns. Multiple transcriptional activators of photoreceptor-specific genes have been identified, but little is known about negative regulation of gene expression in the retina. We recently identified KLF15, a member of the Sp/Krüppel-like Factor family of zinc-finger containing transcription factors, as an in vitro repressor of the promoters of the photoreceptor-specific genes rhodopsin and IRBP/Rbp3. To gain further insight into the mechanism of KLF15-mediated regulation of gene expression, we have characterized the binding characteristics and specificity of KLF15's DNA binding domains and defined the KLF15 binding sites in the rhodopsin and IRBP promoters. Results In EMSA and DNAseI footprinting assays, a KLF15-GST fusion protein containing the C-terminal zinc-finger domains (123 amino acids showed zinc-dependent and sequence-specific binding to a 9 bp consensus sequence containing a core CG/TCCCC. Both the bovine rhodopsin and IRBP promoters contained multiple KLF15 binding sites that included the previously identified CRS-1 and G-rich repressor elements. KLF15 binding sites were highly conserved between the bovine, human, chimp and dog rhodopsin promoters, but less conserved in rodents. KLF15 reduced luciferase expression by bRho130-luc (containing 4 KLF15 sites and repressed promoter activation by CRX (cone rod homeobox and/or NRL (neural retina leucine zipper, although the magnitude of the reduction was smaller than previously reported for a longer bRho225-luc (containing 6 KFL15 sites. Conclusion KLF15 binds to multiple 9 bp consensus sites in the Rhodospin and IRBP promoters including the CRS-1 and G-rich repressor elements. Based on the known expression pattern of KLF15 in non

  13. THE METHOD OF ROLL SURFACE QUALITY MEASUREMENT FOR CONTINUOUS HOT DIP ZINC COATED STEEL SHEET PRODUCTION LINE

    Directory of Open Access Journals (Sweden)

    Ki Yong Choi

    2015-01-01

    Full Text Available The present paper describes a developed analyzing system of roll surface during the process of continuous hot dip zinc coated steel sheet production line, in particular, adhering problem by transferred inclusions from roll to steel sheet surface during annealing process so called the pickup. The simulated test machine for coated roll surface in processing line has been designed and performed. The system makes it possible to analyze roll surface condition according to pickup phenomena from various roll coatings concerning operating conditions of hearth rolls in annealing furnace. The algorithm of fast pickup detection on surface is developed on the base of processing of several optical images of surface. The parameters for quality estimation of surface with pickups were developed. The optical system for images registration and image processing electronics may be used in real time and embed in processing line.

  14. Electronic structure and binding geometry of tetraphenylporphyrin-derived molecules adsorbed on metal and metal oxide surfaces

    Science.gov (United States)

    Coh, Senia

    Tetraphenylporphyrin (TPP)-derived molecules have been studied extensively as efficient photosensitizers when chemisorbed on the metal oxide substrates in dye-sensitized solar cells. Still, many fundamental electronic properties of the dye/oxide interface are not understood and need careful consideration. In this thesis we present a comprehensive study of the electronic structure, energy level alignment and the adsorption geometry of the TPP-derived dye molecules adsorbed on TiO2(110), ZnO(1120) and Ag(100) single crystal surfaces using ultra-high vacuum (UHV) based surface sensitive techniques. The alignment of the molecular energy levels with respect to the TiO 2 and ZnO band edges for all TPP-derived molecules we studied was found to be insensitive to either the nature of the functional groups located on the phenyl rings, presence of zinc as a central metal ion and different binding geometry of the molecules. Binding geometry, molecule-molecule interaction and the aggregation effects in the adsorbed layer, that were observed in the UV-visible spectra of the molecules adsorbed on ZnO substrate were not observed in the ultraviolet photoemission (UPS) and inverse photoemission (IPS) spectra of the occupied and unoccupied molecular states. Using near edge X-ray absorption fine structure (NEXAFS) and scanning tunneling microscopy (STM), binding geometry of the two representative TPP-derivatives was directly determined to be upright, with the porphyrin ring under large angle with respect to the surface for the p-ZnTCPP molecules and with the porphyrin ring parallel to the surface for the m-ZnTCPP molecules. We observe that the energies and the energy level alignment of the ZnTPP molecular levels measured in UPS and IPS depend on the substrate on which the molecules are adsorbed (Ag(100) or TiO2(110) single crystal surfaces). The differences are attributed to different charge screening properties of these two materials. Image charges created in the substrates during

  15. Cadmium and zinc relationships

    Energy Technology Data Exchange (ETDEWEB)

    Elinder, C.; Piscator, M.

    1978-08-01

    Higher mammals, such as homo sapiens, accumulate zinc in kidney cortex almost equimolarly with cadmium. A different pattern seems to be present in liverthere is a limited increase of zinc in two species of large farm animals compared with a marked increase in the laboratory. In large farm animals, an equimolar increase of zinc with cadmium in renal cortex seems to indicate that the form of metallothionein that binds equal amounts of cadmium and zinc in present. Differences in cadmium and zinc relationships in large animals and humans compared with laboratory animals must be carefully considered. (4 graphs, 26 references)

  16. Synthesis and characterization of a new zinc(II) complex with tetradentate azo-thioether ligand: X-ray structure, DNA binding study and DFT calculation

    Science.gov (United States)

    Mondal, Apurba Sau; Pramanik, Ajoy Kumar; Patra, Lakshman; Manna, Chandan Kumar; Mondal, Tapan Kumar

    2017-10-01

    A new zinc(II) complex, [Zn(L)(H2O)](ClO4) (1) with azo-thioether containing NSNO donor ligand, 3-(2-(2-((pyridin-2-ylmethyl)thio)phenyl)hydrazono)pentane-2,4-dione (HL) is synthesized and characterized by several spectroscopic techniques. The distorted square based pyramidal (DSBP) geometry is confirmed by single crystal X-ray structure. The ability of the complex to bind with CT DNA is investigated by UV-vis method and the binding constant is found to be 4.16 × 104 M-1. Competitive binding study with ethidium bromide (EB) by fluorescence method suggests that the zinc(II) complex efficiently displaces EB from EB-DNA. The Stern-Volmer dynamic quenching constant, Ksv is found to be 1.2 × 104 M-1. Theoretical calculations by DFT and TDDFT/CPCM methods are used to interpret the electronic structure and UV-vis spectrum of the complex.

  17. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines

    Directory of Open Access Journals (Sweden)

    Tatjana P Kristensen

    2014-03-01

    Full Text Available The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural

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

    Science.gov (United States)

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

    2004-02-01

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

  19. Atomic force microscopy study of cellulose surface interaction controlled by cellulose binding domains

    OpenAIRE

    Nigmatullin, R.; Lovitt, R.; Wright, C; Linder, M.; Nakari-Setälä, T; Gama, F. M.

    2004-01-01

    Colloidal probe microscopy has been used to study the interaction between model cellulose surfaces and the role of cellulose binding domain (CBD), peptides specifically binding to cellulose, in interfacial interaction of cellulose surfaces modified with CBDs. The interaction between pure cellulose surfaces in aqueous electrolyte solution is dominated by double layer repulsive forces with the range and magnitude of the net force dependent on electrolyte concentration. AFM imaging reve...

  20. Adherence of platelets to in situ albumin-binding surfaces under flow conditions: role of surface-adsorbed albumin.

    Science.gov (United States)

    Guha Thakurta, Sanjukta; Miller, Robert; Subramanian, Anuradha

    2012-08-01

    Surfaces that preferentially bind human serum albumin (HSA) were generated by grafting albumin-binding linear peptide (LP1) onto silicon surfaces. The research aim was to evaluate the adsorption pattern of proteins and the adhesion of platelets from platelet-poor plasma and platelet-rich plasma, respectively, by albumin-binding surfaces under physiological shear rate (96 and 319 s(-1)) conditions. Bound proteins were quantified using enzyme-linked immunosorbent assays (ELISAs) and two-dimensional gel electrophoresis. A ratio of ∼1000:100:1 of adsorbed HSA, human immunoglobulin (HIgG) and human fibrinogen (HFib) was noted, respectively, on LP1-functionalized surfaces, and a ratio of ∼5:2:1 of the same was noted on control surfaces, as confirmed by ELISAs. The surface-adsorbed von Willebrand factor was undetectable by sensitive ELISAs. The amount of adhered platelets correlated with the ratio of adsorbed HSA/HFib. Platelet morphology was more rounded on LP1-functionalized surfaces when compared to control surfaces. The platelet adhesion response on albumin-binding surfaces can be explained by the reduction in the co-adsorption of other plasma proteins in a surface environment where there is an excess of albumin molecules, coupled with restrictions in the conformational transitions of other surface-adsorbed proteins into hemostatically active forms.

  1. XPS investigation of DNA binding to zirconium-phosphonate surfaces.

    Science.gov (United States)

    Lane, Sarah M; Monot, Julien; Petit, Marc; Bujoli, Bruno; Talham, Daniel R

    2007-07-01

    The surface coverage of phosphorylated oligonucleotides immobilized on a zirconium-phosphonate surface was analyzed using X-ray photoelectron spectroscopy (XPS). By quantifying the intensity of the N 1s signal originating from the oligonucleotide and the Zr 3d peak from the metal-phosphonate surface, the surface coverage of the oligonucleotide could be calculated with a modified substrate-overlayer model. We found relatively low surface coverages indicating that once covalently bound via the terminal phosphate the polymer chain further physisorbs to the surface limiting the adsorption of additional molecules.

  2. Utilization of zinc chloride for surface modification of activated carbon derived from Jatropha curcas L. for absorbent material.

    Science.gov (United States)

    Pratumpong, P; Toommee, S

    2016-12-01

    The objective of this research is to produce the low-cost activated carbon from Jatropha curcas L. by chemical activation using zinc chloride ZnCl2. The effects of the impregnation ratio on the surface and chemical properties of activated carbon were investigated. The impregnation ratio was selected at the range of 1:1-10:1 for investigation. The optimum conditions resulted in an activated carbon with a carbon content of 80% wt, while the specific surface area evaluated using nitrogen adsorption isotherm corresponds to 600 m(2)/g.

  3. Surface investigation and tribological mechanism of a sulfate-based lubricant deposited on zinc-coated steel sheets

    Science.gov (United States)

    Timma, Christian; Lostak, Thomas; Janssen, Stella; Flock, Jörg; Mayer, Christian

    2016-12-01

    Phosphatation is a well-known technique to improve friction and wear behaviour of zinc coated steel, but has a variety of economic and ecologic limitations. In this study an alternative coating based on ammonium sulfate ((NH4)2SO4) is applied on skin-passed hot-dip galvanized steel sheets in order to investigate its surface chemical and tribological behaviour in a Pin-on-Disk Tribometer. Raman- and X-ray photoelectron spectroscopic results revealed a formation of ammonium zinc sulfate ((NH4)2Zn(SO4)2 * xH2O) on the surface, which is primarily located in the skin-passed areas of the steel material. Sulfate coated samples exhibited a superior friction behaviour in Pin-on-Disk Tests using squalane as a model substance for oil-like lubricated conditions and a formation of a thin lubrication film is obtained in the wear track. Squalane acts as a carrier substance for ammonium zinc sulfate, leading to an effective lubrication film in the wear track.

  4. Zinc-Induced Polymerization of Killer-Cell Ig-like Receptor into Filaments Promotes Its Inhibitory Function at Cytotoxic Immunological Synapses.

    Science.gov (United States)

    Kumar, Santosh; Rajagopalan, Sumati; Sarkar, Pabak; Dorward, David W; Peterson, Mary E; Liao, Hsien-Shun; Guillermier, Christelle; Steinhauser, Matthew L; Vogel, Steven S; Long, Eric O

    2016-04-07

    The inhibitory function of killer cell immunoglobulin-like receptors (KIR) that bind HLA-C and block activation of human natural killer (NK) cells is dependent on zinc. We report that zinc induced the assembly of soluble KIR into filamentous polymers, as detected by electron microscopy, which depolymerized after zinc chelation. Similar KIR filaments were isolated from lysates of cells treated with zinc, and membrane protrusions enriched in zinc were detected on whole cells by scanning electron microscopy and imaging mass spectrometry. Two independent mutations in the extracellular domain of KIR, away from the HLA-C binding site, impaired zinc-driven polymerization and inhibitory function. KIR filaments formed spontaneously, without the addition of zinc, at functional inhibitory immunological synapses of NK cells with HLA-C(+) cells. Adding to the recent paradigm of signal transduction through higher order molecular assemblies, zinc-induced polymerization of inhibitory KIR represents an unusual mode of signaling by a receptor at the cell surface.

  5. Zinc isotope investigation of surface and pore waters in a mountain watershed impacted by acid rock drainage

    Energy Technology Data Exchange (ETDEWEB)

    Aranda, Suzan [Department of Geological Sciences, University of Texas at El Paso, El Paso, TX 79968 (United States); Borrok, David M., E-mail: dborrok@utep.edu [Department of Geological Sciences, University of Texas at El Paso, El Paso, TX 79968 (United States); Wanty, Richard B. [US Geological Survey, MS 964d, Denver Federal Center, Denver, CO 80225 (United States); Balistrieri, Laurie S. [U.S. Geological Survey, University of Washington, School of Oceanography, Seattle, WA 98195 (United States)

    2012-03-15

    The pollution of natural waters with metals derived from the oxidation of sulfide minerals like pyrite is a global environmental problem. However, the metal loading pathways and transport mechanisms associated with acid rock drainage reactions are often difficult to characterize using bulk chemical data alone. In this study, we evaluated the use of zinc (Zn) isotopes to complement traditional geochemical tools in the investigation of contaminated waters at the former Waldorf mining site in the Rocky Mountains, Colorado, U.S.A. Geochemical signatures and statistical analysis helped in identifying two primary metal loading pathways at the Waldorf site. The first was characterized by a circumneutral pH, high alkalinity, and high Zn/Cd ratios. The second was characterized by acidic pHs and low Zn/Cd ratios. Zinc isotope signatures in surface water samples collected across the site were remarkably similar (the {delta}{sup 66}Zn, relative to JMC 3-0749-L, for most samples ranged from 0.20 to 0.30 Per-Mille-Sign {+-} 0.09 Per-Mille-Sign 2{sigma}). This probably suggests that the ultimate source of Zn is consistent across the Waldorf site, regardless of the metal loading pathway. The {delta}{sup 66}Zn of pore water samples collected within a nearby metal-impacted wetland area, however, were more variable, ranging from 0.20 to 0.80 Per-Mille-Sign {+-} 0.09 Per-Mille-Sign 2{sigma}. Here the Zn isotopes seemed to reflect differences in groundwater flow pathways. However, a host of secondary processes might also have impacted Zn isotopes, including adsorption of Zn onto soil components, complexation of Zn with dissolved organic matter, uptake of Zn into plants, and the precipitation of Zn during the formation of reduced sulfur species. Zinc isotope analysis proved useful in this study; however, the utility of this isotopic tool would improve considerably with the addition of a comprehensive experimental foundation for interpreting the complex isotopic relationships found in

  6. Regions outside the DNA-binding domain are critical for proper in vivo specificity of an archetypal zinc finger transcription factor.

    Science.gov (United States)

    Burdach, Jon; Funnell, Alister P W; Mak, Ka Sin; Artuz, Crisbel M; Wienert, Beeke; Lim, Wooi F; Tan, Lit Yeen; Pearson, Richard C M; Crossley, Merlin

    2014-01-01

    Transcription factors (TFs) are often regarded as being composed of a DNA-binding domain (DBD) and a functional domain. The two domains are considered separable and autonomous, with the DBD directing the factor to its target genes and the functional domain imparting transcriptional regulation. We examined an archetypal zinc finger (ZF) TF, Krüppel-like factor 3 with an N-terminal domain that binds the corepressor CtBP and a DBD composed of three ZFs at its C-terminus. We established a system to compare the genomic occupancy profile of wild-type Krüppel-like factor 3 with two mutants affecting the N-terminal functional domain: a mutant unable to contact the cofactor CtBP and a mutant lacking the entire N-terminal domain, but retaining the ZFs intact. Chromatin immunoprecipitation followed by sequencing was used to assess binding across the genome in murine embryonic fibroblasts. Unexpectedly, we observe that mutations in the N-terminal domain generally reduced binding, but there were also instances where binding was retained or even increased. These results provide a clear demonstration that the correct localization of TFs to their target genes is not solely dependent on their DNA-contact domains. This informs our understanding of how TFs operate and is of relevance to the design of artificial ZF proteins.

  7. Enhanced lubrication on tissue and biomaterial surfaces through peptide-mediated binding of hyaluronic acid.

    Science.gov (United States)

    Singh, Anirudha; Corvelli, Michael; Unterman, Shimon A; Wepasnick, Kevin A; McDonnell, Peter; Elisseeff, Jennifer H

    2014-10-01

    Lubrication is key for the efficient function of devices and tissues with moving surfaces, such as articulating joints, ocular surfaces and the lungs. Indeed, lubrication dysfunction leads to increased friction and degeneration of these systems. Here, we present a polymer-peptide surface coating platform to non-covalently bind hyaluronic acid (HA), a natural lubricant in the body. Tissue surfaces treated with the HA-binding system exhibited higher lubricity values, and in vivo were able to retain HA in the articular joint and to bind ocular tissue surfaces. Biomaterials-mediated strategies that locally bind and concentrate HA could provide physical and biological benefits when used to treat tissue-lubricating dysfunction and to coat medical devices.

  8. Enhanced lubrication on tissue and biomaterial surfaces through peptide-mediated binding of hyaluronic acid

    Science.gov (United States)

    Singh, Anirudha; Corvelli, Michael; Unterman, Shimon A.; Wepasnick, Kevin A.; McDonnell, Peter; Elisseeff, Jennifer H.

    2014-10-01

    Lubrication is key for the efficient function of devices and tissues with moving surfaces, such as articulating joints, ocular surfaces and the lungs. Indeed, lubrication dysfunction leads to increased friction and degeneration of these systems. Here, we present a polymer-peptide surface coating platform to non-covalently bind hyaluronic acid (HA), a natural lubricant in the body. Tissue surfaces treated with the HA-binding system exhibited higher lubricity values, and in vivo were able to retain HA in the articular joint and to bind ocular tissue surfaces. Biomaterials-mediated strategies that locally bind and concentrate HA could provide physical and biological benefits when used to treat tissue-lubricating dysfunction and to coat medical devices.

  9. Surface selective binding of nanoclay particles to polyampholyte protein chains

    Science.gov (United States)

    Pawar, Nisha; Bohidar, H. B.

    2009-07-01

    Binding of nanoclay (Laponite) to gelatin-A and gelatin-B (both polyampholytes) molecules was investigated at room temperature (25 °C) both experimentally and theoretically. The stoichiometric binding ratio between gelatin and Laponite was found to be strongly dependent on the solution ionic strength. Large soluble complexes were formed at higher ionic strengths of the solution, a result supported by data obtained from light scattering, viscosity, and zeta potential measurements. The binding problem was theoretically modeled by choosing a suitable two-body screened Coulomb potential, U(R+)=(q-/2ɛ)[(Q-/R-)e-kR--(Q+/R+)e-kR+], where the protein dipole has charges Q+ and Q_ that are located at distances R+ and R_ from the point Laponite charge q- and the dispersion liquid has dielectric constant (ɛ). U(R+) accounted for electrostatic interactions between a dipole (protein molecule) and an effective charge (Laponite particle) located at an angular position θ. Gelatin-A and Laponite association was facilitated by a strong attractive interaction potential that led to preferential binding of the biopolymer chains to negatively charged face of Laponite particles. In the case of gelatin-B selective surf ace patch binding dominated the process where the positively charged rim and negatively charged face of the particles were selectively bound to the oppositely charged segments of the biopolymer. The equilibrium separation (Re) between the protein and nanoclay particle revealed monovalent salt concentration dependence given by Re˜[NaCl]α where α =0.6±0.2 for gelatin-A and α =0.4±0.2 for gelatin-B systems. The equilibrium separations were ≈30% less compared to the gelatin-A system implying preferential short-range ordering of the gelatin-B-nanoclay pair in the solvent.

  10. Surface-binding through polyfunction groups of Rhodamine B on composite surface and its high performance photodegradation

    Science.gov (United States)

    Wan, Yiqun; Wang, Xiaofen; Gu, Yun; Guo, Lan; Xu, Zhaodi

    2016-03-01

    A kind of novel composite ZnS/In(OH)3/In2S3 is synthesized using zinc oxide nanoplates as zinc raw material during hydrothermal process. Although the obtained samples are composited of ZnS and In(OH)3 and In2S3 phase, the samples possess different structure, morphology and optical absorption property depending on molar ratio of raw materials. Zeta potential analysis indicates different surface electrical property since various content and particle size of the phases. The equilibrium adsorption study confirms the composite ZnS/In(OH)3/In2S3 with surface negative charge is good adsorbent for Rhodamine B (Rh B) dye. In addition, the degradation of Rh B over the samples with surface negative charge under visible light (λ ≥ 420 nm) is more effective than the samples with surface positive charge. The samples before and after adsorbing Rh B molecule are examined by FTIR spectra and Zetasizer. It is found that the three function groups of Rh B molecule, especially carboxyl group anchors to surface of the sample through electrostatic adsorption, coordination and hydrogen-bond. It contributes to rapid transformation of photogenerated electron to conduction band of In(OH)3 and suppresses the recombination of photogenerated carrier. The possible adsorption modes of Rh B are discussed on the basis of the experiment results.

  11. Pulmonary toxicity of inhaled nanoscale and fine zinc oxide particles: mass and surface area as an exposure metric.

    Science.gov (United States)

    Ho, Meng; Wu, Kuen-Yuh; Chein, Hung-Min; Chen, Lung-Chi; Cheng, Tsun-Jen

    2011-12-01

    The total surface area is known to be an effective exposure metric for predicting the lung toxicity of low solubility nanoparticles (NPs). However, if NPs are dissolved quickly enough in the lungs, the mass may be correlated with the toxicity. Recent studies have found that the toxicity of zinc oxide (ZnO) NPs was caused by the release of zinc ions. Thus, we hypothesized that mass could be used as an exposure metric for the toxicity of ZnO NPs. Healthy Sprague-Dawley rats were exposed to a low, moderate, or high dose of 35 and 250 nm ZnO particles or filtered air. Bronchoalveolar lavage fluid was collected to determine lung inflammation, injury and oxidative stress. The lung inflammation induced by ZnO particles according to different concentration metrics, including number, mass and surface area, was compared. The mass concentration was significantly correlated with the percentage of neutrophils (R(2) = 0.84), number of neutrophils (R(2) = 0.84) and total cells (R(2) = 0.73). Similarly, surface area concentration was significantly correlated with the percentage of neutrophils (R(2) = 0.94), number of neutrophils (R(2) = 0.81) and total cells (R(2) = 0.76). There was no correlation between the number and lung inflammation. We found that both mass and surface area were effective as metrics for the toxicity of ZnO NPs, although only surface area was previously indicated to be an effective metric. Our results are also consistent with recent study results that ZnO NPs and released zinc ions may play a role mediating the toxicity of NPs.

  12. Adsorption of DNA binding proteins to functionalized carbon nanotube surfaces with and without DNA wrapping.

    Science.gov (United States)

    Ishibashi, Yu; Oura, Shusuke; Umemura, Kazuo

    2017-09-01

    We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH2 groups (CONH2-SWNT) exhibited very strong interactions between the CONH2-SWNT and DNA binding proteins. Instead, when these SWNT surfaces were wrapped with DNA molecules (thymine 30-mers), protein binding was a little decreased. Our results revealed that DNA wrapped PEG-SWNT was one of the most promising candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces. In addition, the DNA binding protein RecA was more adhesive than single-stranded DNA binding proteins to the functionalized SWNT surfaces.

  13. Zinc-binding proteins from boar seminal plasma -- isolation, biochemical characteristics and influence on spermatozoa stored at 4°C.

    Science.gov (United States)

    Mogielnicka-Brzozowska, Marzena; Wysocki, Paweł; Strzeżek, Jerzy; Kordan, Władysław

    2011-01-01

    Affinity chromatography on Chelating Sepharose Fast Flow Gel-Zn(2+) was used for fractionation of boar seminal plasma proteins. Approximately 30% of total boar seminal plasma proteins showed affinity for zinc ions (ZnBP fraction). Native electrophoresis (PAGE) of ZnBP revealed six protein fractions which separated into 27 bands under denaturing conditions (SDS/PAGE). Two-dimensional electrophoresis (2D PAGE) showed 148 polypeptides with isoelectric points mostly in the basic and neutral pH range. The zinc-binding proteins comprise mainly 10-20 kDa polypeptides which are probably members of the spermadhesin family. ZnBP present in the incubation mixture of spermatozoa stored for 1 or 24 h at 4 °C allowed preservation of a higher percentage of cells exhibiting linear motility in comparison to a control sample stored in PBS. Presented results indicate that proteins binding Zn(2+) ions have a shielding effect on the sperm plasma membrane and acrosome of spermatozoa, protecting these structures against consequences of cold shock.

  14. A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD

    Directory of Open Access Journals (Sweden)

    Yu Wei-Hsuan

    2012-05-01

    Full Text Available Abstract Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C. The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6

  15. Divacancy binding energy, formation energy and surface energy of BCC transition metals using MEAM potentials

    Science.gov (United States)

    Uniyal, Shweta; Chand, Manesh; Joshi, Subodh; Semalty, P. D.

    2016-05-01

    The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.

  16. Probing and mapping the binding sites on streptavidin imprinted polymer surface

    Energy Technology Data Exchange (ETDEWEB)

    Duman, Memed, E-mail: memi@hacettepe.edu.tr

    2014-10-01

    Molecular imprinting is an effective technique for preparing recognition sites which act as synthetic receptors on polymeric surfaces. Herein, we synthesized MIP surfaces with specific binding sites for streptavidin and characterized them at nanoscale by using two different atomic force microscopy (AFM) techniques. While the single molecule force spectroscopy (SMFS) reveals the unbinding kinetics between streptavidin molecule and binding sites, simultaneous topography and recognition imaging (TREC) was employed, for the first time, to directly map the binding sites on streptavidin imprinted polymers. Streptavidin modified AFM cantilever showed specific unbinding events with an unbinding force around 300 pN and the binding probability was calculated as 35.2% at a given loading rate. In order to prove the specificity of the interaction, free streptavidin molecules were added to AFM liquid cell and the binding probability was significantly decreased to 7.6%. Moreover, the recognition maps show that the smallest recognition site with a diameter of around ∼ 21 nm which corresponds to a single streptavidin molecule binding site. We believe that the potential of combining SMFS and TREC opens new possibilities for the characterization of MIP surfaces with single molecule resolution under physiological conditions. - Graphical abstract: Simultaneous Topography and RECognition (TREC) imaging is a novel characterization technique to reveal binding sites on molecularly imprinted polymer surfaces with single molecule resolution under physiological conditions. - Highlights: • Highly specific streptavidin printed polymer surfaces were synthesized. • Unbinding kinetic rate of single streptavidin molecule was studied by SMFS. • The distribution of binding pockets was revealed for the first time by TREC imaging. • TREC showed that the binding pockets formed nano-domains on MIP surface. • SMFS and TREC are powerful AFM techniques for characterization of MIP surfaces.

  17. Effects of size and surface of zinc oxide and aluminum-doped zinc oxide nanoparticles on cell viability inferred by proteomic analyses

    Directory of Open Access Journals (Sweden)

    Pan CH

    2014-08-01

    Full Text Available Chih-Hong Pan,1,2,* Wen-Te Liu,3,4,* Mauo-Ying Bien,4,5 I-Chan Lin,6 Ta-Chih Hsiao,7 Chih-Ming Ma,8 Ching-Huang Lai,2 Mei-Chieh Chen,9 Kai-Jen Chuang,10,11 Hsiao-Chi Chuang3,4 On behalf of the Taiwan CardioPulmonary Research (T-CPR Group 1Institute of Labor, Occupational Safety and Health, Ministry of Labor, 2School of Public Health, National Defense Medical Center, 3Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, 4School of Respiratory Therapy, College of Medicine, 5Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, 6Department of Ophthalmology, Shuang Ho Hospital, Taipei Medical University, Taipei, 7Graduate Institute of Environmental Engineering, National Central University, Taoyuan, 8Department of Cosmetic Application and Management, St Mary’s Junior College of Medicine, Nursing and Management, Sanxing, 9Department of Microbiology and Immunology, College of Medicine, 10Department of Public Health, School of Medicine, College of Medicine, 11School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan *These authors contributed equally to this work Abstract: Although the health effects of zinc oxide nanoparticles (ZnONPs on the ­respiratory system have been reported, the fate, potential toxicity, and mechanisms in biological cells of these particles, as related to particle size and surface characteristics, have not been well elucidated. To determine the physicochemical properties of ZnONPs that govern cytotoxicity, we investigated the effects of size, electronic properties, zinc concentration, and pH on cell viability using human alveolar-basal epithelial A549 cells as a model. We observed that a 2-hour or longer exposure to ZnONPs induced changes in cell viability. The alteration in cell viability was associated with the zeta potentials and pH values of the ZnONPs. Proteomic profiling of A549 exposed to Zn

  18. Surface Plasmon Resonance Analysis of Antifungal Azoles Binding to CYP3A4 with Kinetic Resolution of Multiple Binding Orientations†

    Science.gov (United States)

    Pearson, Josh T.; Hill, John J.; Swank, Jennifer; Isoherranen, Nina; Kunze, Kent L.; Atkins, William M.

    2008-01-01

    The heme-containing Cytochrome P450s (CYPs) are a major enzymatic determinant of drug clearance and drug-drug interactions. The CYP3A4 isoform is inhibited by antifungal imidazoles or triazoles, which form low spin heme iron complexes via formation of a nitrogen-ferric iron coordinate bond. However, CYP3A4 also slowly oxidizes the antifungal itraconazole (ITZ) at a site that is ∼ 25 Å from the triazole nitrogens, suggesting that large antifungal azoles can adopt multiple orientations within the CYP3A4 active site. Here, we report a surface plasmon resonance (SPR) analysis with kinetic resolution of two binding modes of ITZ, and the related drug ketoconazole (KTZ). SPR reveals a very slow off-rate for one binding orientation. Multiphasic binding kinetics are observed and one of the two binding components resolved by curve-fitting exhibits ‘equilibrium overshoot’. Pre-loading of CYP3A4 with the heme ligand imidazole abolishes this component of the antifungal azole binding trajectories, and it eliminates the conspicuously slow off-rate. The fractional populations of CYP3A4 complexes corresponding to different drug orientations can be manipulated by altering the duration of the pulse of drug exposure. UV-vis difference absorbance titrations yield low spin spectra and KD values that are consistent with the high affinity complex resolved by SPR. These results demonstrate that ITZ and KTZ bind in multiple orientations, including a catalytically productive mode and a slowly-dissociating inhibitory mode. Most importantly, they provide the first example of an SPR-based method for the kinetic characterization of drug binding to any human CYP, including mechanistic insight not available from other methods. PMID:16700545

  19. Co-adsorption of phosphate and zinc(II) on the surface of ferrihydrite.

    Science.gov (United States)

    Liu, Jing; Zhu, Runliang; Xu, Tianyuan; Xu, Yin; Ge, Fei; Xi, Yunfei; Zhu, Jianxi; He, Hongping

    2016-02-01

    Ferrihydrite (Fh) is of great importance in affecting the migration and transformation of heavy-metal cations and oxyanions. To advance the understanding of co-adsorption reactions on Fh surface, the co-adsorption of phosphate and Zn(II) from aqueous solution to a synthesized Fh was determined. The batch experiments demonstrated a synergistic adsorption of phosphate and Zn(II) on Fh. In the pH range of 3.5-6, the adsorption of the two contaminants showed strong pH dependence in the single solute adsorption systems, but the dependence alleviated in the simultaneous adsorption system. X-ray photoelectron spectroscopy (XPS) revealed that the chemical shifts of Zn 2p1/2 and Zn 2p3/2 binding energies were more significant than that of P 2p in the single and simultaneous adsorption systems. On the other side, in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) observed increased formation of outer- and inner-sphere complexes of phosphate in the simultaneous system. Thus, the synergistic adsorption of the two contaminants could be attributed to the formation of ternary complexes as well as electrostatic interactions, while surface precipitation could not be completely ruled out. On the basis of the results from both the batch adsorption experiments and structural characterization, these two contaminants were likely to form phosphate-bridged ternary complexes (≡Fe-P-Zn) in the simultaneous adsorption system.

  20. Binding of Solvent Molecules to a Protein Surface in Binary Mixtures Follows a Competitive Langmuir Model.

    Science.gov (United States)

    Kulschewski, Tobias; Pleiss, Jürgen

    2016-09-06

    The binding of solvent molecules to a protein surface was modeled by molecular dynamics simulations of of Candida antarctica (C. antarctica) lipase B in binary mixtures of water, methanol, and toluene. Two models were analyzed: a competitive Langmuir model which assumes identical solvent binding sites with a different affinity toward water (KWat), methanol (KMet), and toluene (KTol) and a competitive Langmuir model with an additional interaction between free water and already bound water (KWatWat). The numbers of protein-bound molecules of both components of a binary mixture were determined for different compositions as a function of their thermodynamic activities in the bulk phase, and the binding constants were simultaneously fitted to the six binding curves (two components of three different mixtures). For both Langmuir models, the values of KWat, KMet, and KTol were highly correlated. The highest binding affinity was found for methanol, which was almost 4-fold higher than the binding affinities of water and toluene (KMet ≫ KWat ≈ KTol). Binding of water was dominated by the water-water interaction (KWatWat). Even for the three protein surface patches of highest water affinity, the binding affinity of methanol was 2-fold higher than water and 8-fold higher than toluene (KMet > KWat > KTol). The Langmuir model provides insights into the protein destabilizing mechanism of methanol which has a high binding affinity toward the protein surface. Thus, destabilizing solvents compete with intraprotein interactions and disrupt the tertiary structure. In contrast, benign solvents such as water or toluene have a low affinity toward the protein surface. Water is a special solvent: only few water molecules bind directly to the protein; most water molecules bind to already bound water molecules thus forming water patches. A quantitative mechanistic model of protein-solvent interactions that includes competition and miscibility of the components contributes a robust basis

  1. A general scheme for the estimation of oxygen binding energies on binary transition metal surface alloys

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

    A simple scheme for the estimation of oxygen binding energies on transition metal surface alloys is presented. It is shown that a d-band center model of the alloy surfaces is a convenient and appropriate basis for this scheme; variations in chemical composition, strain effects, and ligand effects...... for the estimation of oxygen binding energies on a wide variety of transition metal alloys. (c) 2005 Elsevier B.V. All rights reserved....

  2. Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation

    DEFF Research Database (Denmark)

    Cockburn, Darrell; Nielsen, Morten M.; Christiansen, Camilla

    2015-01-01

    Carbohydrate converting enzymes often possess extra substrate binding regions that enhance their activity. These can be found either on separate domains termed carbohydrate binding modules or as so-called surface binding sites (SBSs) situated on the catalytic domain. SBSs are common in starch...... to soluble polysaccharides and oligosaccharides with α-1,6 linkages, suggesting that branch points are key structural elements in recognition by SBS2. Mutation at both SBS1 and SBS2 eliminated binding to all starch granule types tested. Taken together, the findings indicate that the two SBSs act in concert...

  3. Brominated lipids identify lipid binding sites on the surface of the reaction center from Rhodobacter sphaeroides.

    Science.gov (United States)

    Roszak, Aleksander W; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J

    2007-03-20

    This study describes the use of brominated phospholipids to distinguish between lipid and detergent binding sites on the surface of a typical alpha-helical membrane protein. Reaction centers isolated from Rhodobacter sphaeroides were cocrystallized with added brominated phospholipids. X-ray structural analysis of these crystals has revealed the presence of two lipid binding sites from the characteristic strong X-ray scattering from the bromine atoms. These results demonstrate the usefulness of this approach to mapping lipid binding sites at the surface of membrane proteins.

  4. Roles of multiple surface sites, long substrate binding clefts, and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates

    DEFF Research Database (Denmark)

    Nielsen, Morten Munch; Seo, E.S.; Dilokpimol, Adiphol

    2008-01-01

    with a characteristic subsite binding energy profile around the catalytic site. Furthermore, several amylolytic enzymes that facilitate attack on the natural substrate, i.e. the endosperm starch granules, have secondary sugar binding sites either situated on the surface of the protein domain or structural unit...... that contains the catalytic site or belonging to a separate starch binding domain. The role of surface sites in the function of barley alpha-amylase 1 has been investigated by using mutational analysis in conjunction with carbohydrate binding analyses and crystallography. The ability to bind starch depends...

  5. 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.

    Science.gov (United States)

    Fischer, Thomas; Riedl, Rainer

    2016-03-01

    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).

  6. The Mesenchymal Precursor Cell Marker Antibody STRO-1 Binds to Cell Surface Heat Shock Cognate 70.

    Science.gov (United States)

    Fitter, Stephen; Gronthos, Stan; Ooi, Soo Siang; Zannettino, Andrew C W

    2016-12-27

    Since its discovery more than 25 years ago, the STRO-1 antibody has played a fundamental role in defining the hierarchical nature of mesenchymal precursor cells (MPC) and their progeny. STRO-1 antibody binding remains a hallmark of immature pluripotent MPC. Despite the significance of STRO-1 in the MPC field, the identity of the antigen has remained elusive. Using a combination of two-dimensional gel electrophoresis, coupled with Western blotting and Tandem mass spectroscopy, we have identified the STRO-1 antigen as heat shock cognate 70 (HSC70;HSPA8). STRO-1 binds to immune-precipitated HSC70 and siRNA-mediated knock down of HSPA8 reduced STRO-1 binding. STRO-1 surface binding does not correlate with HSC70 expression and sequestration of cholesterol reduces STRO-1 surface binding, suggesting that the plasma membrane lipid composition may be an important determinant in the presentation of HSC70 on the cell surface. HSC70 is present on the surface of STRO-1(+) but not STRO-1(-) cell lines as assessed by cell surface biotinylation and recombinant HSC70 blocks STRO-1 binding to the cell surface. The STRO-1 epitope on HSC70 was mapped to the ATPase domain using a series of deletion mutants in combination with peptide arrays. Deletion of the first four amino acids of the consensus epitope negated STRO-1 binding. Notably, in addition to HSC70, STRO-1 cross-reacts with heat shock protein 70 (HSP70), however all the clonogenic cell activity is restricted to the STRO-1(BRIGHT) /HSP70(-) fraction. These results provide important insight into the properties that define multipotent MPC and provide the impetus to explore the role of cell surface HSC70 in MPC biology. Stem Cells 2016.

  7. SIgA binding to mucosal surfaces is mediated by mucin-mucin interactions.

    Directory of Open Access Journals (Sweden)

    Hannah L Gibbins

    Full Text Available The oral mucosal pellicle is a layer of absorbed salivary proteins, including secretory IgA (SIgA, bound onto the surface of oral epithelial cells and is a useful model for all mucosal surfaces. The mechanism by which SIgA concentrates on mucosal surfaces is examined here using a tissue culture model with real saliva. Salivary mucins may initiate the formation of the mucosal pellicle through interactions with membrane-bound mucins on cells. Further protein interactions with mucins may then trigger binding of other pellicle proteins. HT29 colon cell lines, which when treated with methotrexate (HT29-MTX produce a gel-forming mucin, were used to determine the importance of these mucin-mucin interactions. Binding of SIgA to cells was then compared using whole mouth saliva, parotid (mucin-free saliva and a source of purified SIgA. Greatest SIgA binding occurred when WMS was incubated with HT29-MTX expressing mucus. Since salivary MUC5B was only able to bind to cells which produced mucus and purified SIgA showed little binding to the same cells we conclude that most SIgA binding to mucosal cells occurs because SIgA forms complexes with salivary mucins which then bind to cells expressing membrane-bound mucins. This work highlights the importance of mucin interactions in the development of the mucosal pellicle.

  8. Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation.

    Science.gov (United States)

    Cockburn, Darrell; Nielsen, Morten M; Christiansen, Camilla; Andersen, Joakim M; Rannes, Julie B; Blennow, Andreas; Svensson, Birte

    2015-04-01

    Carbohydrate converting enzymes often possess extra substrate binding regions that enhance their activity. These can be found either on separate domains termed carbohydrate binding modules or as so-called surface binding sites (SBSs) situated on the catalytic domain. SBSs are common in starch degrading enzymes and critically important for their function. The affinity towards a variety of starch granules as well as soluble poly- and oligosaccharides of barley α-amylase 1 (AMY1) wild-type and mutants of two SBSs (SBS1 and SBS2) was investigated using Langmuir binding analysis, confocal laser scanning microscopy, affinity gel electrophoresis and surface plasmon resonance to unravel functional roles of the SBSs. SBS1 was critical for binding to different starch types as Kd increased by 7-62-fold or was not measurable upon mutation. By contrast SBS2 was particularly important for binding to soluble polysaccharides and oligosaccharides with α-1,6 linkages, suggesting that branch points are key structural elements in recognition by SBS2. Mutation at both SBS1 and SBS2 eliminated binding to all starch granule types tested. Taken together, the findings indicate that the two SBSs act in concert to localize AMY1 to the starch granule surface and that SBS2 works synergistically with the active site in the degradation of amylopectin.

  9. Nanopatterned submicron pores as a shield for nonspecific binding in surface plasmon resonance-based sensing

    NARCIS (Netherlands)

    Raz, Sabina Rebe; Marchesini, Gerardo R.; Bremer, Maria G. E. G.; Colpo, Pascal; Garcia, Cesar Pascual; Guidetti, Guido; Norde, Willem; Rossi, Francois

    2012-01-01

    We present a novel approach to tackle the most common drawback of using surface plasmon resonance for analyte screening in complex biological matrices - the nonspecific binding to the sensor chip surface. By using a perforated membrane supported by a polymeric gel structure at the evanescent wave pe

  10. Mapping the interfacial binding surface of human secretory group IIa phospholipase A2.

    Science.gov (United States)

    Snitko, Y; Koduri, R S; Han, S K; Othman, R; Baker, S F; Molini, B J; Wilton, D C; Gelb, M H; Cho, W

    1997-11-25

    Human secretory group IIa phospholipase A2 (hIIa-PLA2) contains a large number of prominent cationic patches on its molecular surface and has exceptionally high affinity for anionic surfaces, including anionic membranes. To identify the cationic amino acid residues that support binding of hIIa-PLA2 to anionic membranes, we have performed extensive site-directed mutagenesis of this protein and measured vesicle binding and interfacial kinetic properties of the mutants using polymerized liposomes and nonpolymerized anionic vesicles. Unlike other secretory PLA2s, which have a few cationic residues that support binding of enzyme to anionic membranes, interfacial binding of hIIa-PLA2 is driven in part by electrostatic interactions involving a number of cationic residues forming patches on the putative interfacial binding surface. Among these residues, the amino-terminal patch composed of Arg-7, Lys-10, and Lys-16 makes the most significant contribution to interfacial adsorption, and this is supplemented by contributions from other patches, most notably Lys-74/Lys-87/Arg-92 and Lys-124/Arg-127. For these mutants, complete vesicle binding occurs in the presence of high vesicle concentrations, and under these conditions the mutants display specific activities comparable to that of wild-type enzyme. These studies indicate that electrostatic interactions between surface lysine and arginine residues and the interface contribute to interfacial binding of hIIa-PLA2 to anionic vesicles and that cationic residues closest to the opening of the active-site slot make the most important interactions with the membrane. However, because the wild type binds extremely tightly to anionic vesicles, it was not possible to exactly determine what fraction of the total interfacial binding energy is due to electrostatics.

  11. Inhibitors incorporating zinc-binding groups target the GlcNAc-PI de-N-acetylase in Trypanosoma brucei, the causative agent of African sleeping sickness.

    Science.gov (United States)

    Abdelwahab, Nuha Z; Crossman, Arthur T; Sullivan, Lauren; Ferguson, Michael A J; Urbaniak, Michael D

    2012-03-01

    Disruption of glycosylphosphatidylinositol biosynthesis is genetically and chemically validated as a drug target against the protozoan parasite Trypanosoma brucei, the causative agent of African sleeping sickness. The N-acetylglucosamine-phosphatidylinositol de-N-acetylase (deNAc) is a zinc metalloenzyme responsible for the second step of glycosylphosphatidylinositol biosynthesis. We recently reported the synthesis of eight deoxy-2-C-branched monosaccharides containing carboxylic acid, hydroxamic acid, or N-hydroxyurea substituents at the C2 position that may act as zinc-binding groups. Here, we describe the synthesis of a glucocyclitol-phospholipid incorporating a hydroxamic acid moiety and report the biochemical evaluation of the monosaccharides and the glucocyclitol-phospholipid as inhibitors of the trypanosome deNAc in the cell-free system and against recombinant enzyme. Monosaccharides with carboxylic acid or hydroxamic acid substituents were found to be the inhibitors of the trypanosome deNAc with IC(50) values 0.1-1.5mM and the glucocyclitol-phospholipid was found to be a dual inhibitor of the deNAc and the α1-4-mannose transferase with an apparent IC(50)= 19±0.5μm. © 2011 John Wiley & Sons A/S.

  12. Evaluation of the Significance of Starch Surface Binding Sites on Human Pancreatic α-Amylase.

    Science.gov (United States)

    Zhang, Xiaohua; Caner, Sami; Kwan, Emily; Li, Chunmin; Brayer, Gary D; Withers, Stephen G

    2016-11-01

    Starch provides the major source of caloric intake in many diets. Cleavage of starch into malto-oligosaccharides in the gut is catalyzed by pancreatic α-amylase. These oligosaccharides are then further cleaved by gut wall α-glucosidases to release glucose, which is absorbed into the bloodstream. Potential surface binding sites for starch on the pancreatic amylase, distinct from the active site of the amylase, have been identified through X-ray crystallographic analyses. The role of these sites in the degradation of both starch granules and soluble starch was probed by the generation of a series of surface variants modified at each site to disrupt binding. Kinetic analysis of the binding and/or cleavage of substrates ranging from simple maltotriosides to soluble starch and insoluble starch granules has allowed evaluation of the potential role of each such surface site. In this way, two key surface binding sites, on the same face as the active site, are identified. One site, containing a pair of aromatic residues, is responsible for attachment to starch granules, while a second site featuring a tryptophan residue around which a malto-oligosaccharide wraps is shown to heavily influence soluble starch binding and hydrolysis. These studies provide insights into the mechanisms by which enzymes tackle the degradation of largely insoluble polymers and also present some new approaches to the interrogation of the binding sites involved.

  13. Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

    Science.gov (United States)

    Sael, Lee; Kihara, Daisuke

    2012-04-01

    Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations.

  14. Synthesis of zinc aluminate with high surface area by microwave hydrothermal method applied in the transesterification of soybean oil (biodiesel)

    Energy Technology Data Exchange (ETDEWEB)

    Quirino, M.R. [Chemistry Laboratory of Federal University of Paraiba (LABQUIM), Campus III, 58200-000 Bananeiras, PB (Brazil); Oliveira, M.J.C. [Academic Unit of Materials Engineering, UFCG, Campina Grande Campus I, 58429-900 Campina Grande, PB (Brazil); Keyson, D. [Laboratory of study in Science, DME, Federal University of Paraíba, Campus I, 58051-900 João Pessoa, PB (Brazil); Lucena, G.L., E-mail: guilherme_leo1@yahoo.com.br [Chemistry Laboratory of Federal University of Paraiba (LABQUIM), Campus III, 58200-000 Bananeiras, PB (Brazil); Oliveira, J.B.L. [Federal University of Rio Grande do Norte, UFRN, Campus I, 59078-970 Natal, RN (Brazil); Gama, L. [Academic Unit of Materials Engineering, UFCG, Campina Grande Campus I, 58429-900 Campina Grande, PB (Brazil)

    2016-02-15

    Highlights: • ZnAl{sub 2}O{sub 4} spinel was synthesized by the microwave hydrothermal method in only 15 or 30 min. • The powders show high specific surface area. • ZAT{sub b}15 showed activity of 52.22% for the conversion of soybean oil into biodiesel. - Abstract: Zinc aluminate is a material with high thermal stability and high mechanical strength that, owing to these properties, is used as a catalyst or support. In this work, zinc aluminate spinel was synthesized by the microwave hydrothermal method in only 15 or 30 min at a low temperature (150 °C) without templates, using only Al(NO{sub 3}){sub 3}·9H{sub 2}O, Zn(NO{sub 3}){sub 2}·6H{sub 2}O, and urea as precursors and applied in the transesterification of soybean oil. X-ray diffraction analysis showed that ZnAl{sub 2}O{sub 4} had a cubic structure without secondary phases. The nitrogen adsorption measurements (BET) revealed a high surface area (266.57 m{sup 2} g{sup −1}) for the nanopowder synthesized in 15 min. This powder showed activity of 52.22% for the catalytic conversion of soybean oil into biodiesel by transesterification.

  15. Improved Sensitization of Zinc Oxide Nanorods by Cadmium Telluride Quantum Dots through Charge Induced Hydrophilic Surface Generation

    Directory of Open Access Journals (Sweden)

    Karthik Laxman

    2014-01-01

    Full Text Available This paper reports on UV-mediated enhancement in the sensitization of semiconductor quantum dots (QDs on zinc oxide (ZnO nanorods, improving the charge transfer efficiency across the QD-ZnO interface. The improvement was primarily due to the reduction in the interfacial resistance achieved via the incorporation of UV light induced surface defects on zinc oxide nanorods. The photoinduced defects were characterized by XPS, FTIR, and water contact angle measurements, which demonstrated an increase in the surface defects (oxygen vacancies in the ZnO crystal, leading to an increase in the active sites available for the QD attachment. As a proof of concept, a model cadmium telluride (CdTe QD solar cell was fabricated using the defect engineered ZnO photoelectrodes, which showed ∼10% increase in photovoltage and ∼66% improvement in the photocurrent compared to the defect-free photoelectrodes. The improvement in the photocurrent was mainly attributed to the enhancement in the charge transfer efficiency across the defect rich QD-ZnO interface, which was indicated by the higher quenching of the CdTe QD photoluminescence upon sensitization.

  16. Hydroxyethyl cellulose as efficient organic inhibitor of zinc-carbon battery corrosion in ammonium chloride solution: Electrochemical and surface morphology studies

    Science.gov (United States)

    Deyab, M. A.

    2015-04-01

    Hydroxyethyl cellulose (HEC) has been investigated as corrosion inhibitor for zinc-carbon battery by polarization and electrochemical impedance spectroscopy (EIS) measurements. The obtained results show that the maximum inhibition efficiency by HEC in 26% NH4Cl solution at 300 ppm and 298 K is 92.07%. Tafel polarization studies reveal that HEC acts as an efficient mixed inhibitor. The corrosion rate is suppressed by the adsorption of HEC on the zinc surface. HEC adsorption obeys the Langmuir isotherm and the thermodynamic parameters Kads and Δ Gadso have been also calculated and discussed. Both physisorption and chemisorption may occur on the zinc surface. Surface characterization investigation using Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) is used to ascertain the nature of the protective film.

  17. Toward a Code for the Interactions of Zinc Fingers with DNA: Selection of Randomized Fingers Displayed on Phage

    Science.gov (United States)

    Choo, Yen; Klug, Aaron

    1994-11-01

    We have used two selection techniques to study sequence-specific DNA recognition by the zinc finger, a small, modular DNA-binding minidomain. We have chosen zinc fingers because they bind as independent modules and so can be linked together in a peptide designed to bind a predetermined DNA site. In this paper, we describe how a library of zinc fingers displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets. The amino acid sequences of selected fingers which bind the same triplet are compared to examine how sequence-specific DNA recognition occurs. Our results can be rationalized in terms of coded interactions between zinc fingers and DNA, involving base contacts from a few α-helical positions. In the paper following this one, we describe a complementary technique which confirms the identity of amino acids capable of DNA sequence discrimination from these positions.

  18. Specific bindings of glycine peptides of distinctly different chain length on dynamic papain surfaces

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2011-06-01

    We investigated the specific bindings of peptides of 1-10 glycine residues (1-10GLY) on dynamic papain surfaces via molecular dynamics and docking simulations. Although the binding specificities of 1-5GLY on papain fluctuated little with time, the binding specificities of 6-10GLY on papain considerably fluctuated with time. Some residues had a significant impact on bindings of 6-10GLY to sites near active center of papain, and some of their residues were specific for each 6GLY, 8GLY, and 10GLY. Modification of these specific residues should allow for control of binding specificity of 6GLY, 8GLY, and 10GLY to the active center.

  19. Influence of Zinc on the Surface Tension, Density and Molar Volume of (Ag-Sneut +Zn Liquid Alloys

    Directory of Open Access Journals (Sweden)

    Gąsior W.

    2016-03-01

    Full Text Available The dilatometric and maximum bubble pressure methods were applied for the measurements of the density and surface tension of liquid (Ag-Sneut +Zn lead-free solders. The experiments were carried out in the temperature range from 515 to 1223 K for the alloys of the zinc concentration equaling 0.01, 0.02, 0.04, 0.05, 0.1 and 0.2 of the mole fraction. It was found that the temperature dependence of both the density and the surface tension could be thought as linear, so they were interpreted by straight line equations. The experimental data of the molar volume of the investigated alloys were described by the polynomial dependent on the composition and temperature.

  20. Surface magnetic contribution in zinc ferrite thin films studied by element- and site-specific XMCD hysteresis-loops

    Science.gov (United States)

    Mendoza Zélis, P.; Pasquevich, G. A.; Salcedo Rodríguez, K. L.; Sánchez, F. H.; Rodríguez Torres, C. E.

    2016-12-01

    Element- and site-specific magnetic hysteresis-loops measurements on a zinc ferrite (ZnFe2O4) thin film were performed by X-ray magnetic circular dichroism. Results show that iron in octahedral and tetrahedral sites of spinel structure are coupled antiferromagnetically between them, and when magnetic field is applied the magnetic moment of the ion located at octahedral sites aligns along the field direction. The magnetic measurements reveal a distinctive response of the surface with in-plane anisotropy and an effective anisotropy constant value of 12.6 kJ/m3. This effective anisotropy is due to the combining effects of demagnetizing field and, volume and surface magnetic anisotropies KV =3.1 kJ/m3 and KS =16 μJ/m2.

  1. Guanine Nucleotides Modulate Cell Surface cAMP-Binding Sites in Membranes from Dictyostelium discoideum

    NARCIS (Netherlands)

    Haastert, Peter J.M. van

    1984-01-01

    D. discoideum contains kinetically distinguishable cell surface cAMP binding sites. One class, S, is slowly dissociating and has high affinity for cAMP (Kd = 15 nM, t½ = 15 s). A second class is fast dissociating (t½ about 1 s) and is composed of high affinity binding sites H (Kd ≈ 60 nM), and low a

  2. Role of surface modification in zinc oxide nanoparticles and its toxicity assessment toward human dermal fibroblast cells

    Directory of Open Access Journals (Sweden)

    Ramasamy M

    2014-08-01

    Full Text Available Mohankandhasamy Ramasamy,1 Minakshi Das,1 Seong Soo A An,1 Dong Kee Yi2 1Division of Bionanotechnology, Gachon University, Seongnam, 2Department of Chemistry, Myongji University, Yongin, South Korea Abstract: The wide-scale applications of zinc oxide (ZnO nanoparticles (NPs in ­photocatalysts, gas sensors, and cosmetics may cause toxicity to humans and environments. Therefore, the aim of the present study was to reduce the toxicity of ZnO NPs by coating them with a silica (SiO2 layer, which could be used in human applications, such as cosmetic preparations. The sol–gel method was used to synthesize core ZnO with SiO2-shelled NPs (SiO2/ZnO NPs with varying degrees of coating. Diverse studies were performed to analyze the toxicity of NPs against cells in a dose- and time-dependent manner. To ensure the decreased toxicity of the produced SiO2/ZnO NPs, cytotoxicity in membrane damage and/or intracellular reactive oxygen species (ROS were assessed by employing 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide, lactate dehydrogenase, 2',7'-dichlorofluorescin, and lipid peroxide estimations. The cores of ZnO NPs exhibited cytotoxicity over time, regardless of shell thickness. Nevertheless, the thicker SiO2/ZnO NPs revealed reduced enzyme leakage, decreased peroxide production, and less oxidative stress than their bare ZnO NPs or thinner SiO2/ZnO NPs. Therefore, thicker SiO2/ZnO NPs moderated the toxicity of ZnO NPs by restricting free radical formation and the release of zinc ions, and decreasing surface contact with cells. Keywords: zinc oxide, silica coating, photostability, human dermal fibroblast, membrane damage, oxidative stress

  3. Zinc isotope investigation of surface and pore waters in a mountain watershed impacted by acid rock drainage.

    Science.gov (United States)

    Aranda, Suzan; Borrok, David M; Wanty, Richard B; Balistrieri, Laurie S

    2012-03-15

    The pollution of natural waters with metals derived from the oxidation of sulfide minerals like pyrite is a global environmental problem. However, the metal loading pathways and transport mechanisms associated with acid rock drainage reactions are often difficult to characterize using bulk chemical data alone. In this study, we evaluated the use of zinc (Zn) isotopes to complement traditional geochemical tools in the investigation of contaminated waters at the former Waldorf mining site in the Rocky Mountains, Colorado, U.S.A. Geochemical signatures and statistical analysis helped in identifying two primary metal loading pathways at the Waldorf site. The first was characterized by a circumneutral pH, high alkalinity, and high Zn/Cd ratios. The second was characterized by acidic pHs and low Zn/Cd ratios. Zinc isotope signatures in surface water samples collected across the site were remarkably similar (the δ(66)Zn, relative to JMC 3-0749-L, for most samples ranged from 0.20 to 0.30‰±0.09‰ 2σ). This probably suggests that the ultimate source of Zn is consistent across the Waldorf site, regardless of the metal loading pathway. The δ(66)Zn of pore water samples collected within a nearby metal-impacted wetland area, however, were more variable, ranging from 0.20 to 0.80‰±0.09‰ 2σ. Here the Zn isotopes seemed to reflect differences in groundwater flow pathways. However, a host of secondary processes might also have impacted Zn isotopes, including adsorption of Zn onto soil components, complexation of Zn with dissolved organic matter, uptake of Zn into plants, and the precipitation of Zn during the formation of reduced sulfur species. Zinc isotope analysis proved useful in this study; however, the utility of this isotopic tool would improve considerably with the addition of a comprehensive experimental foundation for interpreting the complex isotopic relationships found in soil pore waters.

  4. Identification of pneumococcal surface protein A as a lactoferrin-binding protein of Streptococcus pneumoniae.

    Science.gov (United States)

    Hammerschmidt, S; Bethe, G; Remane, P H; Chhatwal, G S

    1999-04-01

    Lactoferrin (Lf), an iron-sequestering glycoprotein, predominates in mucosal secretions, where the level of free extracellular iron (10(-18) M) is not sufficient for bacterial growth. This represents a mechanism of resistance to bacterial infections by prevention of colonization of the host by pathogens. In this study we were able to show that Streptococcus pneumoniae specifically recognizes and binds the iron carrier protein human Lf (hLf). Pretreatment of pneumococci with proteases reduced hLf binding significantly, indicating that the hLf receptor is proteinaceous. Binding assays performed with 63 clinical isolates belonging to different serotypes showed that 88% of the tested isolates interacted with hLf. Scatchard analysis showed the existence of two hLf-binding proteins with dissociation constants of 5.7 x 10(-8) and 2.74 x 10(-7) M. The receptors were purified by affinity chromatography, and internal sequence analysis revealed that one of the S. pneumoniae proteins was homologous to pneumococcal surface protein A (PspA). The function of PspA as an hLf-binding protein was confirmed by the ability of purified PspA to bind hLf and to competitively inhibit hLf binding to pneumococci. S. pneumoniae may use the hLf-PspA interaction to overcome the iron limitation at mucosal surfaces, and this might represent a potential virulence mechanism.

  5. Transformation of zinc-concentrate in surface and subsurface environments: Implications for assessing zinc mobility/toxicity and choosing an optimal remediation strategy.

    Science.gov (United States)

    Kwon, Man Jae; Boyanov, Maxim I; Yang, Jung-Seok; Lee, Seunghak; Hwang, Yun Ho; Lee, Ju Yeon; Mishra, Bhoopesh; Kemner, Kenneth M

    2017-07-01

    Zinc contamination in near- and sub-surface environments is a serious threat to many ecosystems and to public health. Sufficient understanding of Zn speciation and transport mechanisms is therefore critical to evaluating its risk to the environment and to developing remediation strategies. The geochemical and mineralogical characteristics of contaminated soils in the vicinity of a Zn ore transportation route were thoroughly investigated using a variety of analytical techniques (sequential extraction, XRF, XRD, SEM, and XAFS). Imported Zn-concentrate (ZnS) was deposited in a receiving facility and dispersed over time to the surrounding roadside areas and rice-paddy soils. Subsequent physical and chemical weathering resulted in dispersal into the subsurface. The species identified in the contaminated areas included Zn-sulfide, Zn-carbonate, other O-coordinated Zn-minerals, and Zn species bound to Fe/Mn oxides or clays, as confirmed by XAFS spectroscopy and sequential extraction. The observed transformation from S-coordinated Zn to O-coordinated Zn associated with minerals suggests that this contaminant can change into more soluble and labile forms as a result of weathering. For the purpose of developing a soil washing remediation process, the contaminated samples were extracted with dilute acids. The extraction efficiency increased with the increase of O-coordinated Zn relative to S-coordinated Zn in the sediment. This study demonstrates that improved understanding of Zn speciation in contaminated soils is essential for well-informed decision making regarding metal mobility and toxicity, as well as for choosing an appropriate remediation strategy using soil washing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Antibacterial surfaces by adsorptive binding of polyvinyl-sulphonate-stabilized silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Vasilev, Krasimir; Sah, Vasu R; Goreham, Renee V; Short, Robert D [Mawson Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, Adelaide, SA 5095 (Australia); Ndi, Chi; Griesser, Hans J, E-mail: Krasimir.vasilev@unisa.edu.au [Ian Wark Research Institute, University of South Australia, Mawson Lakes, Adelaide, SA 5095 (Australia)

    2010-05-28

    This paper presents a novel and facile method for the generation of efficient antibacterial coatings which can be applied to practically any type of substrate. Silver nanoparticles were stabilized with an adsorbed surface layer of polyvinyl sulphonate (PVS). This steric layer provided excellent colloidal stability, preventing aggregation over periods of months. PVS-coated silver nanoparticles were bound onto amine-containing surfaces, here produced by deposition of an allylamine plasma polymer thin film onto various substrates. SEM imaging showed no aggregation upon surface binding of the nanoparticles; they were well dispersed on amine surfaces. Such nanoparticle-coated surfaces were found to be effective in preventing attachment of Staphylococcus epidermidis bacteria and also in preventing biofilm formation. Combined with the ability of plasma polymerization to apply the thin polymeric binding layer onto a wide range of materials, this method appears promising for the fabrication of a wide range of infection-resistant biomedical devices.

  7. Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.

    Directory of Open Access Journals (Sweden)

    Cristiano De Michele

    2016-03-01

    Full Text Available In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, we work out a theoretical model that allows to explain all the features observed in the simulations. Our combined computational and theoretical framework is in excellent agreement with surface-plasmon resonance data and allows us to establish a number of important results. (i Internal flexibility is key to maximize bivalent binding, flexible IgGs being able to explore the surface with their second arm in search for an available hapten. This is made clear by the strongly reduced ability to bind with both arms displayed by artificial IgGs designed to rigidly keep a prescribed shape. (ii The large size of IgGs is instrumental to keep neighboring molecules at a certain distance (surface repulsion, which essentially makes antigens within reach of the second Fab always unoccupied on average. (iii One needs to account independently for the thermodynamic and geometric factors that regulate the binding equilibrium. The key geometrical parameters, besides excluded-volume repulsion, describe the screening of free haptens by neighboring bound antibodies. We prove that the thermodynamic parameters govern the low-antigen-concentration regime, while the surface screening and repulsion only affect the binding at high hapten densities. Importantly, we prove that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies. Overall, our model provides a valuable, accurate theoretical paradigm beyond existing frameworks to interpret experimental profiles of antibodies binding to multi-valent surfaces of different sorts in many contexts.

  8. Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

    Science.gov (United States)

    De Michele, Cristiano; De Los Rios, Paolo; Foffi, Giuseppe; Piazza, Francesco

    2016-01-01

    In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, we work out a theoretical model that allows to explain all the features observed in the simulations. Our combined computational and theoretical framework is in excellent agreement with surface-plasmon resonance data and allows us to establish a number of important results. (i) Internal flexibility is key to maximize bivalent binding, flexible IgGs being able to explore the surface with their second arm in search for an available hapten. This is made clear by the strongly reduced ability to bind with both arms displayed by artificial IgGs designed to rigidly keep a prescribed shape. (ii) The large size of IgGs is instrumental to keep neighboring molecules at a certain distance (surface repulsion), which essentially makes antigens within reach of the second Fab always unoccupied on average. (iii) One needs to account independently for the thermodynamic and geometric factors that regulate the binding equilibrium. The key geometrical parameters, besides excluded-volume repulsion, describe the screening of free haptens by neighboring bound antibodies. We prove that the thermodynamic parameters govern the low-antigen-concentration regime, while the surface screening and repulsion only affect the binding at high hapten densities. Importantly, we prove that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies. Overall, our model provides a valuable, accurate theoretical paradigm beyond existing frameworks to interpret experimental profiles of antibodies binding to multi-valent surfaces of different sorts in many contexts. PMID:26967624

  9. Spatially selective surface platforms for binding fibrinogen prepared by particle lithography with organosilanes.

    Science.gov (United States)

    Englade-Franklin, Lauren E; Saner, Chamarra K; Garno, Jayne C

    2013-06-06

    We introduce an approach based on particle lithography to prepare spatially selective surface platforms of organosilanes that are suitable for nanoscale studies of protein binding. Particle lithography was applied for patterning fibrinogen, a plasma protein that has a major role in the clotting cascade for blood coagulation and wound healing. Surface nanopatterns of mercaptosilanes were designed as sites for the attachment of fibrinogen within a protein-resistant matrix of 2-[methoxy(polyethyleneoxy)propyl] trichlorosilane (PEG-silane). Preparing site-selective surfaces was problematic in our studies, because of the self-reactive properties of PEG-organosilanes. Certain organosilanes presenting hydroxyl head groups will cross react to form mixed surface multi-layers. We developed a clever strategy with particle lithography using masks of silica mesospheres to protect small, discrete regions of the surface from cross reactions. Images acquired with atomic force microscopy (AFM) disclose that fibrinogen attached primarily to the surface areas presenting thiol head groups, which were surrounded by PEG-silane. The activity for binding anti-fibrinogen was further evaluated using ex situ AFM studies, confirming that after immobilization the fibrinogen nanopatterns retained capacity for binding immunoglobulin G. Studies with AFM provide advantages of achieving nanoscale resolution for detecting surface changes during steps of biochemical surface reactions, without requiring chemical modification of proteins or fluorescent labels.

  10. Nano silver and nano zinc-oxide in surface waters - exposure estimation for Europe at high spatial and temporal resolution.

    Science.gov (United States)

    Dumont, Egon; Johnson, Andrew C; Keller, Virginie D J; Williams, Richard J

    2015-01-01

    Nano silver and nano zinc-oxide monthly concentrations in surface waters across Europe were modeled at ~6 x 9 km spatial resolution. Nano-particle loadings from households to rivers were simulated considering household connectivity to sewerage, sewage treatment efficiency, the spatial distribution of sewage treatment plants, and their associated populations. These loadings were used to model temporally varying nano-particle concentrations in rivers, lakes and wetlands by considering dilution, downstream transport, water evaporation, water abstraction, and nano-particle sedimentation. Temporal variability in concentrations caused by weather variation was simulated using monthly weather data for a representative 31-year period. Modeled concentrations represent current levels of nano-particle production.Two scenarios were modeled. In the most likely scenario, half the river stretches had long-term average concentrations exceeding 0.002 ng L(-1) nano silver and 1.5 ng L(-1) nano zinc oxide. In 10% of the river stretches, these concentrations exceeded 0.18 ng L(-1) and 150 ng L(-1), respectively. Predicted concentrations were usually highest in July.

  11. The binding of phosphonic acids at aluminium oxide surfaces and correlation with passivation of aluminium flake.

    Science.gov (United States)

    Cooper, Rachel J; Camp, Philip J; Henderson, David K; Lovatt, Paul A; Nation, David A; Richards, Stuart; Tasker, Peter A

    2007-04-07

    Measurements of adsorption isotherms of a series of thirteen mono- and di-phosphonic acids have shown that these bind strongly to the surface of high surface area aluminium trihydroxide. The incorporation of such phosphonates into a suspension of aluminium flake in an aqueous medium, modelling the continuous phase of a water-based paint, greatly suppresses the evolution of hydrogen. Whilst strong binding of the phosphonate to aluminium oxides is an essential criterion for good passivation, other factors such as the hydrophobicity of the ligand are also important in suppressing hydrogen-evolution.

  12. Surface magnetic contribution in zinc ferrite thin films studied by element- and site-specific XMCD hysteresis-loops

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza Zélis, P.; Pasquevich, G.A. [IFLP-CCT-La Plata-CONICET and Departamento de Física, Facultad de Ciencias Exactas, C. C. 67, Universidad Nacional de La Plata, 1900 La Plata (Argentina); Departamento de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de La Plata, 1900 La Plata (Argentina); Salcedo Rodríguez, K.L.; Sánchez, F.H. [IFLP-CCT-La Plata-CONICET and Departamento de Física, Facultad de Ciencias Exactas, C. C. 67, Universidad Nacional de La Plata, 1900 La Plata (Argentina); Rodríguez Torres, C.E., E-mail: torres@fisica.unlp.edu.ar [IFLP-CCT-La Plata-CONICET and Departamento de Física, Facultad de Ciencias Exactas, C. C. 67, Universidad Nacional de La Plata, 1900 La Plata (Argentina)

    2016-12-01

    Element- and site-specific magnetic hysteresis-loops measurements on a zinc ferrite (ZnFe{sub 2}O{sub 4}) thin film were performed by X-ray magnetic circular dichroism. Results show that iron in octahedral and tetrahedral sites of spinel structure are coupled antiferromagnetically between them, and when magnetic field is applied the magnetic moment of the ion located at octahedral sites aligns along the field direction. The magnetic measurements reveal a distinctive response of the surface with in-plane anisotropy and an effective anisotropy constant value of 12.6 kJ/m{sup 3}. This effective anisotropy is due to the combining effects of demagnetizing field and, volume and surface magnetic anisotropies K{sub V} =3.1 kJ/m{sup 3} and K{sub S} =16 μJ/m{sup 2}. - Highlights: • Surface magnetic response in ZnFe{sub 2}O{sub 4} film (thickness t ∼57 nm) by XMCD is studied. • Measurements of magnetic moment vs. applied field cycles via XMCD are presented. • Fe{sup 3+} at A- and B-sites are coupled antiferromagnetically between them. • A distinctive response of the surface with in-plane magnetic anisotropy is determined. • Volume and surface magnetic anisotropy are determined: 3.1 kJ/m{sup 3} and 16 μJ/m{sup 2}.

  13. Flow cytometric analysis of lectin binding to in vitro-cultured Perkinsus marinus surface carbohydrates

    Science.gov (United States)

    Gauthier, J.D.; Jenkins, J.A.; La Peyre, Jerome F.

    2004-01-01

    Parasite surface glycoconjugates are frequently involved in cellular recognition and colonization of the host. This study reports on the identification of Perkinsus marinus surface carbohydrates by flow cytometric analyses of fluorescein isothiocyanate-conjugated lectin binding. Lectin-binding specificity was confirmed by sugar inhibition and Kolmogorov-Smirnov statistics. Clear, measurable fluorescence peaks were discriminated, and no parasite autofluorescence was observed. Parasites (GTLA-5 and Perkinsus-1 strains) harvested during log and stationary phases of growth in a protein-free medium reacted strongly with concanavalin A and wheat germ agglutinin, which bind to glucose-mannose and N-acetyl-D-glucosamine (GlcNAc) moieties, respectively. Both P. marinus strains bound with lower intensity to Maclura pomifera agglutinin, Bauhinia purpurea agglutinin, soybean agglutinin (N-acetyl-D-galactosamine-specific lectins), peanut agglutinin (PNA) (terminal galactose specific), and Griffonia simplicifolia II (GlcNAc specific). Only background fluorescence levels were detected with Ulex europaeus agglutinin I (L-fucose specific) and Limulus polyphemus agglutinin (sialic acid specific). The lectin-binding profiles were similar for the 2 strains except for a greater relative binding intensity of PNA for Perkinsus-1 and an overall greater lectin-binding capacity of Perkinsus-1 compared with GTLA-5. Growth stage comparisons revealed increased lectin-binding intensities during stationary phase compared with log phase of growth. This is the first report of the identification of surface glycoconjugates on a Perkinsus spp. by flow cytometry and the first to demonstrate that differential surface sugar expression is growth phase and strain dependent. ?? American Society of Parasitologists 2004.

  14. Surface Morphology and Microstructure of Zinc Deposit From Imidazole with Zinc Chloride Low Temperature Molten Salt Electrolyte in The Presence of Aluminium Chloride

    Directory of Open Access Journals (Sweden)

    Shanmugasigamani Srinivasan, M. Selvam

    2013-07-01

    Full Text Available Low temperature molten salts have variety of applications in organic synthesis, catalytic processing, batteries and electrode position due to their air and water stability. They have wide potential window for their applications in voltage and temperature and hence there is a possibility to deposit metals which could not be deposited from aqueous electrolytes. Our aim and scope of our research was to deposit zinc from low temperature molten salt electrolyte (LTMS containing zinc salt in the presence of aluminium chloride at different current densities and to qualify the nature of deposits. We could identify the effect of current density on the deposit at low temperature molten salt electrolyte by analysing the nature of deposits using different instrumental techniques. Compact, adherent, dense fine grained deposits of zinc with average grain size of 40-150 nm could be obtained from low temperature molten salt electrolyte. (LTMS

  15. Zinc fixation preserves flow cytometry scatter and fluorescence parameters and allows simultaneous analysis of DNA content and synthesis, and intracellular and surface epitopes

    DEFF Research Database (Denmark)

    Jensen, Uffe Birk; Owens, David; Pedersen, Søren

    2010-01-01

    Zinc salt-based fixation (ZBF) has proved advantageous in histochemical analyses conducted on intact tissues but has not been exploited in flow cytometry procedures that focus on quantitative analysis of individual cells. Here, we show that ZBF performs equally well to paraformaldehyde in the pre......Zinc salt-based fixation (ZBF) has proved advantageous in histochemical analyses conducted on intact tissues but has not been exploited in flow cytometry procedures that focus on quantitative analysis of individual cells. Here, we show that ZBF performs equally well to paraformaldehyde...... allowing subsequent quantitative PCR analysis or labeling for incorporation of the thymidine analog EdU following surface and intracellular epitope staining. Finally, ZBF treatment allows for long-term storage of labeled cells with little change in these parameters. Thus, we present a protocol for zinc...... salt fixation of cells that allows for the simultaneous analysis of DNA and intracellular and cell surface proteins by flow cytometry....

  16. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, A.

    1997-10-08

    The author`s group has previously shown that isocyanides are readily adsorbed from solutions to Au powder and bind to the Au surface in an end-on fashion through the terminal carbon. Later work demonstrated that the equilibrium constants for the reversible adsorption of electronically inequivalent isocyanides could be obtained using the Langmuir isotherm technique. This dissertation describes two projects completed which complement the initial findings of this group. Initially, several alkylisocyanides were synthesized to examine the effect of tail length on Au powder adsorption. It was observed that the length of the alkyl chain affected not only the Au surface binding affinity, but also the rate of surface saturation and saturation coverage values. Direct competition studies were also studied using a {sup 13}C-labeled isocyanide. These studies demonstrated the stabilization afforded by substrate-substrate packing forces in SAM`s formed by the longer chain isocyanides. In a second study, di and triisocyanides were synthesized to determine the effect that the length of the connecting link and the number of isocyanide groups (as points of attachment) have on Au adsorption stability. The work in this area describes the binding modes, relative binding affinities and surface coverage values for a series of flexible alkyl and xylyldiisocyanides on Au powder surfaces. This report contains only the introductory material, and general summary. Two chapters have been processed separately. 56 refs.

  17. Quantifying cell binding kinetics mediated by surface-bound blood type B antigen to immobilized antibodies

    Institute of Scientific and Technical Information of China (English)

    LI BaoXia; CHEN Juan; LONG Mian

    2008-01-01

    Cell adhesion is crucial to many biological processes, such as inflammatory responses, tumor metastasis and thrombosis formation. Recently a commercial surface plasmon resonance (SPR)-based BIAcore biosensor has been extended to determine cell binding mediated by surface-bound biomolecular interactions. How such cell binding is quantitatively governed by kinetic rates and regulating factors, however, has been poorly understood. Here we developed a novel assay to determine the binding kinetics of surface-bound biomolecular interactions using a commercial BIAcore 3000 biosensor. Human red blood cells (RBCs) presenting blood group B antigen and CM5 chip bearing immobilized anti-B monoclonal antibody (mAb) were used to obtain the time courses of response unit, or sensorgrams, when flowing RBCs over the chip surface. A cellular kinetic model was proposed to correlate the sensorgrams with kinetic rates. Impacts of regulating factors, such as cell concentration,flow duration and rate, antibody-presenting level, as well as Ph value and osmotic pressure of suspending medium were tested systematically, which imparted the confidence that the approach can be applied to kinetic measurements of cell adhesion mediated by surface-bound biomolecular interactions.These results provided a new insight into quantifying cell binding using a commercial SPR-based BIAcore biosensor.

  18. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, Alyn [Iowa State Univ., Ames, IA (United States)

    1997-10-08

    The author`s group has previously shown that isocyanides are readily adsorbed from solutions to Au powder and bind to the Au surface in an end-on fashion through the terminal carbon. Later work demonstrated that the equilibrium constants for the reversible adsorption of electronically inequivalent isocyanides could be obtained using the Langmuir isotherm technique. This dissertation describes two projects completed which complement the initial findings of this group. Initially, several alkylisocyanides were synthesized to examine the effect of tail length on Au powder adsorption. It was observed that the length of the alkyl chain affected not only the Au surface binding affinity, but also the rate of surface saturation and saturation coverage values. Direct competition studies were also studied using a 13C-labeled isocyanide. These studies demonstrated the stabilization afforded by substrate-substrate packing forces in SAM`s formed by the longer chain isocyanides. In a second study, di and triisocyanides were synthesized to determine the effect that the length of the connecting link and the number of isocyanide groups (as points of attachment) have on Au adsorption stability. The work in this area describes the binding modes, relative binding affinities and surface coverage values for a series of flexible alkyl and xylyldiisocyanides on Au powder surfaces. This report contains only the introductory material, and general summary. Two chapters have been processed separately. 56 refs.

  19. Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer

    Directory of Open Access Journals (Sweden)

    Brett Adina

    2008-07-01

    Full Text Available Abstract Background Gene expression analyses have led to a better understanding of growth control of prostate cancer cells. We and others have identified the presence of several zinc finger transcription factors in the neoplastic prostate, suggesting a potential role for these genes in the regulation of the prostate cancer transcriptome. One of the transcription factors (TFs identified in the prostate cancer epithelial cells was the Wilms tumor gene (WT1. To rapidly identify coordinately expressed prostate cancer growth control genes that may be regulated by WT1, we used an in silico approach. Results Evolutionary conserved transcription factor binding sites (TFBS recognized by WT1, EGR1, SP1, SP2, AP2 and GATA1 were identified in the promoters of 24 differentially expressed prostate cancer genes from eight mammalian species. To test the relationship between sequence conservation and function, chromatin of LNCaP prostate cancer and kidney 293 cells were tested for TF binding using chromatin immunoprecipitation (ChIP. Multiple putative TFBS in gene promoters of placental mammals were found to be shared with those in human gene promoters and some were conserved between genomes that diverged about 170 million years ago (i.e., primates and marsupials, therefore implicating these sites as candidate binding sites. Among those genes coordinately expressed with WT1 was the kallikrein-related peptidase 3 (KLK3 gene commonly known as the prostate specific antigen (PSA gene. This analysis located several potential WT1 TFBS in the PSA gene promoter and led to the rapid identification of a novel putative binding site confirmed in vivo by ChIP. Conversely for two prostate growth control genes, androgen receptor (AR and vascular endothelial growth factor (VEGF, known to be transcriptionally regulated by WT1, regulatory sequence conservation was observed and TF binding in vivo was confirmed by ChIP. Conclusion Overall, this targeted approach rapidly identified

  20. Structural insights into alginate binding by bacterial cell-surface protein.

    Science.gov (United States)

    Temtrirath, Kanate; Murata, Kousaku; Hashimoto, Wataru

    2015-03-02

    A gram-negative Sphingomonas sp. strain A1 inducibly forms a mouth-like pit on the cell surface in the presence of alginate and directly incorporates polymers into the cytoplasm via the pit and ABC transporter. Among the bacterial proteins involved in import of alginate, a cell-surface EfeO-like Algp7 shows an ability to bind alginate, suggesting its contribution to accumulate alginate in the pit. Here, we show identification of its positively charged cluster involved in alginate binding using X-ray crystallography, docking simulation, and site-directed mutagenesis. The tertiary structure of Algp7 was determined at a high resolution (1.99Å) by molecular replacement, although no alginates were included in the structure. Thus, an in silico model of Algp7/oligoalginate was constructed by docking simulation using atomic coordinates of Algp7 and alginate oligosaccharides, where some charged residues were found to be potential candidates for alginate binding. Site-directed mutagenesis was conducted and five purified mutants K68A, K69A, E194A, N221A, and K68A/K69A were subjected to a binding assay. UV absorption difference spectroscopy along with differential scanning fluorimetry analysis indicated that K68A/K69A exhibited a significant reduction in binding affinity with alginate than wild-type Algp7. Based on these data, Lys68/Lys69 residues of Algp7 probably play an important role in binding alginate.

  1. Differential carbohydrate binding and cell surface glycosylation of human cancer cell lines.

    Science.gov (United States)

    Arndt, Nadia X; Tiralongo, Joe; Madge, Paul D; von Itzstein, Mark; Day, Christopher J

    2011-09-01

    Currently there is only a modest level knowledge of the glycosylation status of immortalised cell lines that are commonly used in cancer biology as well as their binding affinities to different glycan structures. Through use of glycan and lectin microarray technology, this study has endeavoured to define the different bindings of cell surface carbohydrate structures to glycan-binding lectins. The screening of breast cancer MDA-MB435 cells, cervical cancer HeLa cells and colon cancer Caco-2, HCT116 and HCT116-FM6 cells was conducted to determine their differential bindings to a variety of glycan and lectin structures printed on the array slides. An inverse relationship between the number of glycan structures recognised and the variety of cell surface glycosylation was observed. Of the cell lines tested, it was found that four bound to sialylated structures in initial screening. Secondary screening in the presence of a neuraminidase inhibitor (4-deoxy-4-guanidino-Neu5Ac2en) significantly reduced sialic acid binding. The array technology has proven to be useful in determining the glycosylation signatures of various cell-lines as well as their glycan binding preferences. The findings of this study provide the groundwork for further investigation into the numerous glycan-lectin interactions that are exhibited by immortalised cell lines.

  2. Use of surface plasmon resonance in the binding study of vitamin D, metabolites and analogues with vitamin D binding protein.

    Science.gov (United States)

    Canoa, Pilar; Rivadulla, Marcos L; Popplewell, Jonathan; van Oosten, René; Gómez, Generosa; Fall, Yagamare

    2017-04-01

    Vitamin D3 and its metabolites are lipophilic molecules with low aqueous solubility and must be transported bound to plasma carrier proteins, primarily to vitamin D binding protein (DBP). The biological functions of vitamin D3 metabolites are intimately dependent on the protein, hence the importance of determining their affinity for DBP. In this study, we developed a novel procedure for measuring the kinetic and equilibrium constants of human-DBP with vitamin D3 and three metabolites: 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], 25-hydroxyvitamin D3 (25OHD3) and 24,25-dihydroxyvitamin D3 [24,25(OH)2D3] by surface plasmon resonance (SPR). At the same time, five different analogues, synthetized in our laboratory, were evaluated in order to compare the affinity values with the metabolites. Real-time SPR measurements showed that 25OHD3 and 24,25(OH)2D3 had higher affinity (0.3 μM) than 1,25(OH)2D3 (5 μM), with the higher affinity of 25OHD3 and 24,25(OH)2D3 due to dissociation constants 1 order of magnitude slower. In the case of the analogues, the affinity values were lower, with 1-hydroxy-25-nitro-vitamin D3 (NO2-446), structurally closer to 1,25(OH)2D3, showing the highest value with a K D of 50 μM. (24R)-1,25-dihydroxyvitamin-24-buthyl-28-norvitamin D2 (Bu-471) and (24R)-1,25-dihydroxyvitamin-24-phenyl-28-norvitamin D2 (Ph-491), structurally similar, had affinities of 180 and 170 μM, respectively. (22R,23E)-1-hydroxy-22-ethenyl-25-methoxy-23-dehydrovitamin D3 (MeO-455) and 1-hydroxy-20(R)-[5(S)-(2,2-dimethyltetrahydropyran-5-yl)]-22,23-dinor vitamin D3 (Oxan-429) had affinities of 310 and 100 μM, respectively. The binding of the metabolites and analogues was reversible allowing the rapid capture of data for replicates. The kinetic and equilibrium data for both the metabolites and the analogues fitted to the Langmuir model describing a 1:1 interaction. Graphical Abstract Label-free, real time binding study between vitamin D binding protein immmobilized on the

  3. Zinc electrode and rechargeable zinc-air battery

    Science.gov (United States)

    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. Ligand-receptor binding kinetics in surface plasmon resonance cells: A Monte Carlo analysis

    CERN Document Server

    Carroll, Jacob; Forsten-Williams, Kimberly; Täuber, Uwe C

    2016-01-01

    Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities. We report detailed Monte Carlo simulations of ligand binding kinetics in an SPR cell subject to laminar flow. We extract the binding and dissociation rates by means of the techniques frequently employed in experimental analysis that are motivated by the mean-field approximation. We find major discrepancies in a wide parameter regime between the thus extracted rates and the known input simulation values. These results underscore the crucial quantitative importance of s...

  5. Effects of sodium on cell surface and intracellular TH-naloxone binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Pollack, A.E.; Wooten, G.F.

    1987-07-27

    The binding of the opiate antagonist TH-naloxone was examined in rat whole brain homogenates and in crude subcellular fractions of these homogenates (nuclear, synaptosomal, and mitochondrial fractions) using buffers that approximated intra- (low sodium concentration) and extracellular (high sodium concentration) fluids. Saturation studies showed a two-fold decrease in the dissociation constant (Kd) in all subcellular fractions examined in extracellular buffer compared to intracellular buffer. In contrast, there was no significant effect of the buffers on the Bmax. Thus, TH-naloxone did not distinguish between binding sites present on cell surface and intracellular tissues in these two buffers. These results show that the sodium effect of opiate antagonist binding is probably not a function of altered selection of intra- and extracellular binding sites. 17 references, 2 tables.

  6. Nonlinear Interactions of Zinc Phthalocyanine-Graphene Quantum Dots Nanocomposites: Investigation of Effects of Surface Functionalization with Heteroatoms.

    Science.gov (United States)

    Bankole, Owolabi M; Achadu, Ojodomo J; Nyokong, Tebello

    2017-03-01

    This study reports the development of functional optical limiting materials composed of pristine graphene (GQDs), nitrogen-doped (NGQDs) and sulfur-nitrogen co-doped (SNGQDs) graphene quantum dots covalently linked to mono-amino substituted zinc phthalocyanine (Pc). Open aperture Z-scan technique was employed to monitor the behaviour of the conjugates under tightly focussed Gaussian laser beam using a mode-locked Nd:YAG laser delivering 10 nanosecond (FWHM) pulses at 532 nm wavelength. Nonlinear effect due to reverse saturable absorption was the predominant mechanism; and was attributed to the moderately enhanced triplet population. The major factor(s) responsible for the enhanced nonlinearities in the Pc-NGQDs and Pc-SNGQDs was fully described and attributed to the surface defects caused by the presence of heteroatoms of N and S.

  7. ATRX binds to atypical chromatin domains at the 3' exons of zinc finger genes to preserve H3K9me3 enrichment.

    Science.gov (United States)

    Valle-García, David; Qadeer, Zulekha A; McHugh, Domhnall S; Ghiraldini, Flávia G; Chowdhury, Asif H; Hasson, Dan; Dyer, Michael A; Recillas-Targa, Félix; Bernstein, Emily

    2016-06-02

    ATRX is a SWI/SNF chromatin remodeler proposed to govern genomic stability through the regulation of repetitive sequences, such as rDNA, retrotransposons, and pericentromeric and telomeric repeats. However, few direct ATRX target genes have been identified and high-throughput genomic approaches are currently lacking for ATRX. Here we present a comprehensive ChIP-sequencing study of ATRX in multiple human cell lines, in which we identify the 3' exons of zinc finger genes (ZNFs) as a new class of ATRX targets. These 3' exonic regions encode the zinc finger motifs, which can range from 1-40 copies per ZNF gene and share large stretches of sequence similarity. These regions often contain an atypical chromatin signature: they are transcriptionally active, contain high levels of H3K36me3, and are paradoxically enriched in H3K9me3. We find that these ZNF 3' exons are co-occupied by SETDB1, TRIM28, and ZNF274, which form a complex with ATRX. CRISPR/Cas9-mediated loss-of-function studies demonstrate (i) a reduction of H3K9me3 at the ZNF 3' exons in the absence of ATRX and ZNF274 and, (ii) H3K9me3 levels at atypical chromatin regions are particularly sensitive to ATRX loss compared to other H3K9me3-occupied regions. As a consequence of ATRX or ZNF274 depletion, cells with reduced levels of H3K9me3 show increased levels of DNA damage, suggesting that ATRX binds to the 3' exons of ZNFs to maintain their genomic stability through preservation of H3K9me3.

  8. Study of MMLV RT- Binding with DNA using Surface Plasmon Resonance Biosensor

    Institute of Scientific and Technical Information of China (English)

    Lei WU; Ming-Hui HUANG; Jian-Long ZHAO; Meng-Su YANG

    2005-01-01

    Surface plasmon resonance biosensor technique was used to study the binding of Moloney murine leukemia virus reverse transcriptase without RNase H domain (MMLV RT-) with DNA in the absence and in the presence of inhibitors. Different DNA substrates, including single-stranded DNA (ssDNA),DNA template-primer (T-P) duplex and gapped DNA, were immobilized on the biosensor chip surface using streptavidin-biotin, and MMLV RT--DNA binding kinetics were analyzed by different models. MMLV RT-could bind with ssDNA and the binding was involved in conformation change. MMLV RT- binding DNA T-P duplex and gapped DNA could be analyzed using the simple 1:1 Langmuir model. The lack of RNase H domain reduced the affinity between MMLV RT- and T-P duplex. The effects of RT inhibitors, including efavirenz, nevirapine and quercetin, on the interaction between MMLV RT- and gapped DNA were analyzed according to recovered kinetics parameters. Efavirenz slightly interfered with the binding between RT and DNA and the affinity constant in the presence of the inhibitor (KA=1.21× 106 M-1) was lower than in the absence of the inhibitor (KA=4.61× 106 M-1). Nevirapine induced relatively tight binding between RT and DNA and the affinity constant in the presence of the inhibsitor (KA=l.47×107 M-1) was approximately three folds higher than without nevirapine, mainly due to rapid association and slow dissociation. Quercetin, a flavonoid originating from plant which has previously shown strong inhibition of the activity of RT, was found to have minimal effect on the RT-DNA binding.

  9. Spatially selective surface platforms for binding fibrinogen prepared by particle lithography with organosilanes

    OpenAIRE

    Englade-Franklin, Lauren E.; Saner, ChaMarra K.; Garno, Jayne C.

    2013-01-01

    We introduce an approach based on particle lithography to prepare spatially selective surface platforms of organosilanes that are suitable for nanoscale studies of protein binding. Particle lithography was applied for patterning fibrinogen, a plasma protein that has a major role in the clotting cascade for blood coagulation and wound healing. Surface nanopatterns of mercaptosilanes were designed as sites for the attachment of fibrinogen within a protein-resistant matrix of 2-[methoxy(polyethy...

  10. The zinc binuclear cluster activator AlcR is able to bind to single sites but requires multiple repeated sites for synergistic activation of the alcA gene in Aspergillus nidulans.

    Science.gov (United States)

    Panozzo, C; Capuano, V; Fillinger, S; Felenbok, B

    1997-09-01

    The alcA gene which is part of the recently identified ethanol regulon, is one of the most strongly inducible genes in Aspergillus nidulans. Its transcriptional activation is mediated by the AlcR transactivator which contains a DNA-binding domain belonging to the C6 zinc binuclear cluster family. AlcR differs from the other members of this family by several features, the most striking characteristic being its binding to both symmetric and asymmetric DNA sites with the same apparent affinity. However, AlcR is also able to bind to a single site with high affinity, suggesting that unlike the other C6 proteins, AlcR binds as a monomer. In this report, we show that AlcR targets, to be functional in vivo, have to be organized as inverted or direct repeats. In addition, we show a strong synergistic activation of alcA transcription in which the number and the position of the AlcR-binding sites are crucial. The fact that the AlcR unit for in vitro binding is a single site whereas the in vivo functional unit is a repeat opens the question of the mechanism of the strong alcA transactivation. These results show that AlcR displays both in vitro and in vivo a new range of binding specificity and provides a novel example in the C6 zinc cluster protein family.

  11. The ligand-binding domain of the cell surface receptor for urokinase-type plasminogen activator

    DEFF Research Database (Denmark)

    Behrendt, N; Ploug, M; Patthy, L;

    1991-01-01

    part of the intact receptor, probably including the whole sequence 1-87, and contained N-linked carbohydrate. After detergent phase separation in the Triton X-114 system, the fragment was present in the water phase where its binding activity could be demonstrated in the absence of the rest...... applications in interfering with cell-surface plasmin-mediated proteolysis....

  12. Selectivity of the surface binding site (SBS) on barley starch synthase I

    DEFF Research Database (Denmark)

    Wilkens, Casper; Cuesta-Seijo, Jose A.; Palcic, Monica

    2014-01-01

    Starch synthase I (SSI) from various sources has been shown to preferentially elongate branch chains of degree of polymerisation (DP) from 6–7 to produce chains of DP 8–12. In the recently determined crystal structure of barley starch synthase I (HvSSI) a so-called surface binding site (SBS) was ...

  13. Potential ecological risk assessment and predicting zinc accumulation in soils.

    Science.gov (United States)

    Baran, Agnieszka; Wieczorek, Jerzy; Mazurek, Ryszard; Urbański, Krzysztof; Klimkowicz-Pawlas, Agnieszka

    2017-02-22

    The aims of this study were to investigate zinc content in the studied soils; evaluate the efficiency of geostatistics in presenting spatial variability of zinc in the soils; assess bioavailable forms of zinc in the soils and to assess soil-zinc binding ability; and to estimate the potential ecological risk of zinc in soils. The study was conducted in southern Poland, in the Malopolska Province. This area is characterized by a great diversity of geological structures and types of land use and intensity of industrial development. The zinc content was affected by soil factors, and the type of land use (arable lands, grasslands, forests, wastelands). A total of 320 soil samples were characterized in terms of physicochemical properties (texture, pH, organic C content, total and available Zn content). Based on the obtained data, assessment of the ecological risk of zinc was conducted using two methods: potential ecological risk index and hazard quotient. Total Zn content in the soils ranged from 8.27 to 7221 mg kg(-1) d.m. Based on the surface semivariograms, the highest variability of zinc in the soils was observed from northwest to southeast. The point sources of Zn contamination were located in the northwestern part of the area, near the mining-metallurgical activity involving processing of zinc and lead ores. These findings were confirmed by the arrangement of semivariogram surfaces and bivariate Moran's correlation coefficients. The content of bioavailable forms of zinc was between 0.05 and 46.19 mg kg(-1) d.m. (0.01 mol dm(-3) CaCl2), and between 0.03 and 71.54 mg kg(-1) d.m. (1 mol dm(-3) NH4NO3). Forest soils had the highest zinc solubility, followed by arable land, grassland and wasteland. PCA showed that organic C was the key factor to control bioavailability of zinc in the soils. The extreme, very high and medium zinc accumulation was found in 69% of studied soils. There is no ecological risk of zinc to living organisms in the study area, and in 90

  14. Surface free energy of copper-zinc alloy for energy-saving of boiler

    Institute of Scientific and Technical Information of China (English)

    WANG Man; LIANG Jinsheng; TANG Qingguo; MING Xing; MENG Junping; DING Yan

    2006-01-01

    Cu-Zn, Cu-Zn-Sn, Cu-Zn-Ni alloys were melted by vacuum smelter. The effect factors to the surface free energy of the alloys such as chemical composition, crystal structure and surface crystal lattice distortion etc. were investigated by OCA30 automatic contact angle test instrument, metallography microscope and XRD instrument etc. Results suggests: adding alloy element to Cu may increase its surface free energy, and the more kinds of alloy elements are added, the more surface free energy increases; the alloy element Sn an increase the surface free energy of Cu-Zn alloy; Cu-Zn alloy with fir-tree crystal structure, great phase discrepancy and obvious composition aliquation has greater surface free energy; Cu-Zn alloy with compounds and serious surface crystal lattice distortion has greater surface free energy.

  15. Construction of a high affinity zinc binding site in the metabotropic glutamate receptor mGluR1

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Sheppard, P O; Jensen, L B

    2001-01-01

    and the loops connecting these. The findings offer valuable insight into the mechanism of ATD closure and family C receptor activation. Furthermore, the findings demonstrate that ATD regions other than those participating in agonist binding could be potential targets for new generations of ligands......The metabotropic glutamate receptors (mGluRs) belong to family C of the G-protein-coupled receptor (GPCR) superfamily. The receptors are characterized by having unusually long amino-terminal domains (ATDs), to which agonist binding has been shown to take place. Previously, we have constructed...... of a "closed" conformation, and thus stabilizing a more or less inactive "open" form of the ATD. This study presents the first metal ion site constructed in a family C GPCR. Furthermore, it is the first time a metal ion site has been created in a region outside of the seven transmembrane regions of a GPCR...

  16. Histatins: salivary peptides with copper(II)- and zinc(II)-binding motifs: perspectives for biomedical applications.

    Science.gov (United States)

    Melino, Sonia; Santone, Celeste; Di Nardo, Paolo; Sarkar, Bibudhendra

    2014-02-01

    Natural antimicrobial peptides represent a primordial mechanism of immunity in both vertebrate and nonvertebrate organisms. Among them, histatins belong to a family of human salivary metal-binding peptides displaying potent antibacterial, antifungal and wound-healing activities. These properties, along with the ability of histatins to inhibit collagenases and cysteine proteases, have attracted much attention for their potential use in the treatment of several oral diseases. This review critically assesses the studies carried out to date in order to provide a comprehensive and systematic vision of the information accumulated so far. In particular, the relationship between metal-binding and peptide activity is extensively analysed. The review provides important clues for developing possible therapeutic applications of histatins and their synthetic peptide analogues by creating a set of necessary resource materials to support investigators and industries interested in exploiting their unique properties.

  17. Compartmentation of metals in foliage of Populus tremula grown on soils with mixed contamination. II. Zinc binding inside leaf cell organelles

    Energy Technology Data Exchange (ETDEWEB)

    Vollenweider, Pierre, E-mail: pierre.vollenweider@wsl.c [Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zuercherstrasse 111, 8903 Birmensdorf (Switzerland); Bernasconi, Petra [Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zuercherstrasse 111, 8903 Birmensdorf (Switzerland); Environmental Protection Office (AfU), Aabachstrasse 5, 6300 Zug (Switzerland); Gautschi, Hans-Peter [Centre for Microscopy and Image Analysis (CMI), University of Zurich, Gloriastrasse 30, 8006 Zuerich (Switzerland); Menard, Terry; Frey, Beat; Guenthardt-Goerg, Madeleine S. [Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zuercherstrasse 111, 8903 Birmensdorf (Switzerland)

    2011-01-15

    The phytoextraction potential of plants for removing heavy metals from polluted soils is determined by their capacity to store contaminants in aboveground organs and complex them safely. In this study, the metal compartmentation, elemental composition of zinc deposits and zinc complexation within leaves from poplars grown on soil with mixed metal contamination was analysed combining several histochemical and microanalytical approaches. Zinc was the only heavy metal detected and was stored in several organelles in the form of globoid deposits showing {beta}-metachromasy. It was associated to oxygen anions and different cations, noteworthy phosphorous. The deposit structure, elemental composition and element ratios indicated that zinc was chelated by phytic acid ligands. Maturation processes in vacuolar vs. cytoplasmic deposits were suggested by differences in size and amounts of complexed zinc. Hence, zinc complexation by phytate contributed to metal detoxification and accumulation in foliage but could not prevent toxicity reactions therein. - Zinc contaminants translocated to symplast of aged leaves were detoxified by phytic acid ligands.

  18. Sensitivity Analysis of Grain Surface Chemistry to Binding Energies of Ice Species

    Science.gov (United States)

    Penteado, E. M.; Walsh, C.; Cuppen, H. M.

    2017-07-01

    Advanced telescopes, such as ALMA and the James Webb Space Telescope, are likely to show that the chemical universe may be even more complex than currently observed, requiring astrochemical modelers to improve their models to account for the impact of new data. However, essential input information for gas-grain models, such as binding energies of molecules to the surface, have been derived experimentally only for a handful of species, leaving hundreds of species with highly uncertain estimates. We present in this paper a systematic study of the effect of uncertainties in the binding energies on an astrochemical two-phase model of a dark molecular cloud, using the rate equations approach. A list of recommended binding energy values based on a literature search of published data is presented. Thousands of simulations of dark cloud models were run, and in each simulation a value for the binding energy of hundreds of species was randomly chosen from a normal distribution. Our results show that the binding energy of H2 is critical for the surface chemistry. For high binding energies, H2 freezes out on the grain forming an H2 ice. This is not physically realistic, and we suggest a change in the rate equations. The abundance ranges found are in reasonable agreement with astronomical ice observations. Pearson correlation coefficients revealed that the binding energy of HCO, HNO, CH2, and C correlate most strongly with the abundance of dominant ice species. Finally, the formation route of complex organic molecules was found to be sensitive to the branching ratios of H2CO hydrogenation.

  19. Spectroscopic study of binding of chlorogenic acid with the surface of ZnO nanoparticles

    Science.gov (United States)

    Belay, Abebe; Kim, Hyung Kook; Hwang, Yoon-Hwae

    2017-09-01

    Understanding the interaction properties of biological materials with ZnO NPs is fundamental interest in the field of biotechnological applications as well as in the formation of optoelectronic devices. In this research, the binding of ZnO NPs and chlorogenic acid (CGA) were investigated using fluorescence quenching, UV-Vis absorption spectroscopy, Fourier transform infrared (FTIR), Raman spectroscopy, scanning electron microscopy (TEM), and dynamic light scattering (DLS) techniques. The study results indicated the fluorescence quenching between ZnO NPs and CGA rationalized in terms of static quenching mechanism or the formation of nonfluorescent CGA-ZnO. From fluorescence quenching spectral analysis the binding constant ( K a ), number of binding sites ( n), and thermodynamic properties, were determined. The quenching constants ( K sv) and binding constant ( K a ), decrease with increasing the temperature and their binding sites n are 2. The thermodynamic parameters determined using Van't Hoff equation indicated binding occurs spontaneously involving the hydrogen bond and van der Walls forces played the major role in the reaction of ZnO NPs with CGA. The Raman, SEM, DLS, and Zeta potential measurements were also indicated the differences in the structure, morphology and sizes of CGA, ZnO NPs, and their corresponding CGA-ZnO due to adsorption of CGA on the surface of ZnO NPs

  20. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition.

    Science.gov (United States)

    Wienk, Hans; Slootweg, Jack C; Speerstra, Sietske; Kaptein, Robert; Boelens, Rolf; Folkers, Gert E

    2013-07-01

    To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.

  1. First-principles calculation of core-level binding energy shift in surface chemical processes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.

  2. Modelling of binding free energy of targeted nanocarriers to cell surface

    Science.gov (United States)

    Liu, Jin; Ayyaswamy, Portonovo S.; Eckmann, David M.; Radhakrishnan, Ravi

    2014-03-01

    We have developed a numerical model based on Metropolis Monte Carlo and the weighted histogram analysis method that enables the calculation of the absolute binding free energy between functionalized nanocarriers (NC) and endothelial cell (EC) surfaces. The binding affinities are calculated according to the free energy landscapes. The model predictions quantitatively agree with the analogous measurements of specific antibody coated NCs (100 nm in diameter) to intracellular adhesion molecule-1 (ICAM-1) expressing EC surface in in vitro cell culture experiments. The model also enables an investigation of the effects of a broad range of parameters that include antibody surface coverage of NC, glycocalyx in both in vivo and in vitro conditions, shear flow and NC size. Using our model we explore the effects of shear flow and reproduce the shear-enhanced binding observed in equilibrium measurements in collagen-coated tube. Furthermore, our results indicate that the bond stiffness, representing the specific antibody-antigen interaction, significantly impacts the binding affinities. The predictive success of our computational protocol represents a sound quantitative approach for model driven design and optimization of functionalized NC in targeted vascular drug delivery.

  3. Hydration behavior at the ice-binding surface of the Tenebrio molitor antifreeze protein.

    Science.gov (United States)

    Midya, Uday Sankar; Bandyopadhyay, Sanjoy

    2014-05-08

    Molecular dynamics (MD) simulations have been carried out at two different temperatures (300 and 220 K) to study the conformational rigidity of the hyperactive Tenebrio molitor antifreeze protein (TmAFP) in aqueous medium and the structural arrangements of water molecules hydrating its surface. It is found that irrespective of the temperature the ice-binding surface (IBS) of the protein is relatively more rigid than its nonice-binding surface (NIBS). The presence of a set of regularly arranged internally bound water molecules is found to play an important role in maintaining the flat rigid nature of the IBS. Importantly, the calculations reveal that the strategically located hydroxyl oxygens of the threonine (Thr) residues in the IBS influence the arrangements of five sets of ordered waters around it on two parallel planes that closely resemble the basal plane of ice. As a result, these waters can register well with the ice basal plane, thereby allowing the IBS to preferentially bind at the ice interface and inhibit its growth. This provides a possible molecular reason behind the ice-binding activity of TmAFP at the basal plane of ice.

  4. Diagnostic study of the roughness surface effect of zirconium on the third-order nonlinear-optical properties of thin films based on zinc oxide nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Bahedi, K., E-mail: bahedikhadija@yahoo.com [Laboratoire Optoelectronique et Physico-chimie des Materiaux Universite Ibn Tofail, Faculte des Sciences BP 133 Kenitra 14000, Maroc (Morocco); Addou, M.; El Jouad, M.; Sofiani, Z.; Alaoui Lamrani, M.; El Habbani, T.; Fellahi, N.; Bayoud, S.; Dghoughi, L. [Laboratoire Optoelectronique et Physico-chimie des Materiaux Universite Ibn Tofail, Faculte des Sciences BP 133 Kenitra 14000, Maroc (Morocco); Sahraoui, B.; Essaidi, Z. [Laboratoire POMA, UMR CNRS 6136, Universite d' Angers 2, Bd Lavoisier, 49045 France (France)

    2009-02-01

    Zinc oxide (ZnO) and zirconium doped zinc oxide (ZnO:Zr) thin films were deposited by reactive chemical pulverization spray pyrolysis technique on heated glass substrates at 500 deg. C using zinc and zirconium chlorides as precursors. Effects of zirconium doping agent and surface roughness on the nonlinear optical properties were investigated in detail using atomic force microscopy (AFM) and third harmonic generation (THG) technique. The best value of nonlinear optical susceptibility {chi}{sup (3)} was obtained from the doped films with less roughness. A strong third order nonlinear optical susceptibility {chi}{sup (3)} = 20.12 x 10{sup -12} (esu) of the studied films was found for the 3% doped sample.

  5. Nucleus Accumbens 1, a Pox virus and Zinc finger/Bric-a-brac Tramtrack Broad protein binds to TAR DNA-binding protein 43 and has a potential role in Amyotrophic Lateral Sclerosis.

    Science.gov (United States)

    Scofield, M D; Korutla, L; Jackson, T G; Kalivas, P W; Mackler, S A

    2012-12-27

    Protein degradation is a critical component of cellular maintenance. The intracellular translocation and targeting of the Ubiquitin Proteasome System (UPS) differentially coordinates a protein's half-life and thereby its function. Nucleus Accumbens 1 (NAC1), a member of the Pox virus and Zinc finger/Bric-a-brac Tramtrack Broad complex (POZ/BTB) family of proteins, participates in the coordinated proteolysis of synaptic proteins by mediating recruitment of the UPS to dendritic spines. Here we report a novel interaction between NAC1 and TAR DNA-binding protein 43 (TDP-43), a protein identified as the primary component of ubiquitinated protein aggregates found in patients with Amyotrophic Lateral Sclerosis (ALS). In vitro translated full-length TDP-43 associated with both the POZ/BTB domain and the non-POZ/BTB domain of NAC1 in GST pulldown assays. Other POZ/BTB proteins (including zinc finger POZ/BTB proteins and atypical POZ/BTB proteins) showed weak interactions with TDP-43. In addition, NAC1 and TDP-43 were present in the same immunocomplexes in different regions of mouse brain and spinal cord. In primary spinal cord cultures, TDP-43 expression was mainly nuclear, whereas NAC1 was both nuclear and cytoplasmic. In order to mimic ALS-like toxicity in the spinal cord culture system, we elevated extracellular glutamate levels resulting in the selective loss of motor neurons. Using this model, it was found that glutamate toxicity elicited a dose-dependent translocation of TDP-43 out of the nucleus of cholinergic neurons and increased the co-localization of NAC1 and TDP-43. These findings suggest that NAC1 may function to link TDP-43 to the proteasome; thereby, facilitating the post-translational modifications of TDP-43 that lead to the development of ALS.

  6. Controlled FCC/on-top binding of H/Pt(111) using surface stress

    Science.gov (United States)

    Shuttleworth, I. G.

    2016-08-01

    The preferred binding site of H/Pt(111) has been shown to be change from the on-top to FCC as the Pt(111) surface goes approximately from a state of compressive to tensile strain. A chemical analysis of the system has shown that for both FCC and on-top bound cases the H ssbnd Pt s and H ssbnd Pt d interactions have a similar importance in determining the preferred binding position. It has been seen that FCC-bound H forms a distinct state below the Pt d-band, whereas the on-top bound H does not.

  7. Both host and parasite MIF molecules bind to chicken macrophages via CD74 surface receptor.

    Science.gov (United States)

    Kim, Sungwon; Cox, Chasity M; Jenkins, Mark C; Fetterer, Ray H; Miska, Katarzyna B; Dalloul, Rami A

    2014-12-01

    Macrophage migration inhibitory factor (MIF) is recognized as a soluble protein that inhibits the random migration of macrophages and plays a pivotal immunoregulatory function in innate and adaptive immunity. Our group has identified both chicken and Eimeria MIFs, and characterized their function in enhancing innate immune responses during inflammation. In this study, we report that chicken CD74 (ChCD74), a type II transmembrane protein, functions as a macrophage surface receptor that binds to MIF molecules. First, to examine the binding of MIF to chicken monocytes/macrophages, fresh isolated chicken peripheral blood mononuclear cells (PBMCs) were stimulated with rChIFN-γ and then incubated with recombinant chicken MIF (rChMIF). Immunofluorescence staining with anti-ChMIF followed by flow cytometry revealed the binding of MIF to stimulated PBMCs. To verify that ChCD74 acts as a surface receptor for MIF molecules, full-length ChCD74p41 was cloned, expressed and its recombinant protein (rChCD74p41) transiently over-expressed with green fluorescent protein in chicken fibroblast DF-1 cells. Fluorescence analysis revealed a higher population of cells double positive for CD74p41 and rChMIF, indicating the binding of rChMIF to DF-1 cells via rChCD74p41. Using a similar approach, it was found that Eimeria MIF (EMIF), which is secreted by Eimeria sp. during infection, bound to chicken macrophages via ChCD74p41 as a surface receptor. Together, this study provides conclusive evidence that both host and parasite MIF molecules bind to chicken macrophages via the surface receptor ChCD74.

  8. Surface tension method for determining binding constants for cyclodextrin inclusion complexes of ionic surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Dharmawardana, U.R.; Christian, S.D.; Tucker, E.E.; Taylor, R.W.; Scamehorn, J.F. (Univ. of Oklahoma, Norman, OK (United States))

    1993-09-01

    A new method has been developed for determining binding constants of complexes of cyclodextrins with surface-active compounds, including water-soluble ionic surfactants. The technique requires measuring the change in surface tension caused by addition of a cyclodextrin (CD) to aqueous solutions of the surfactant; the experimental results lead directly to inferred values of the thermodynamic activity of the surfactant. Surface tension results are reported for three different surfactants sodium dodecyl sulfate (SDS), cetylpyridinium chloride (CPC), and cetyltrimethylammonium bromide (CTAB) in the presence and in the absence of added [beta]-CD. Data for CPC have been obtained at surfactant concentrations below and above the critical micelle concentration. Correlations between surface tension and surfactant activity are expressed by the Szyszkowski equation, which subsumes the Langmuir adsorption model and the Gibbs equation. It is observed that the surface tension increases monotonically as [beta]-cyclodextrin is added to ionic surfactant solutions. At concentrations of CD well in excess of the surfactant concentration, the surface tension approaches that of pure water, indicating that neither the surfactant-CD complexes nor CD itself are surface active. Binding constants are inferred from a model that incorporates the parameters of the Szyszkowski equation and mass action constants relating to the formation of micelles from monomers of the surfactant and the counterion. Evidence is given that two molecules of CD can complex the C-16 hydrocarbon chain of the cetyl surfactants. 30 refs., 5 figs., 1 tab.

  9. Characterization of metal contacts on and surfaces of cadmium zinc telluride

    CERN Document Server

    Bürger, A; Chattopadhyay, K; Shi, D; Morgan, S H; Collins, W E; James, R B

    1999-01-01

    In the past several years significant progress has been made in building a database of physical properties for detector quality Cd sub x Zn sub 1 sub - sub x Te (CZT) (x=0.1-0.2) crystal material. CZT's high efficiency combined with its room temperature operation make the material an excellent choice for imaging and spectroscopy in the 10-200 keV energy range. For detector grade material, superior crystallinity and high bulk resistivity are required. The surface preparation during the detector fabrication plays a vital role in determining the contact characteristics and the surface leakage current, which are often the dominant factors influencing its performance. This paper presents a surface and contact characterization study aimed at establishing the effects of the surface preparation steps prior to contacting (polishing and chemical etching), the choice of the metal and contact deposition technique, and the surface oxidation process. A photoconductivity mapping technique is used for studying the effects of...

  10. Theranostic multimodular potential of zinc-doped ferrite-saturated metal-binding protein-loaded novel nanocapsules in cancers

    Directory of Open Access Journals (Sweden)

    Kamalapuram SK

    2016-04-01

    Full Text Available Sishir K Kamalapuram,1 Rupinder K Kanwar,1 Kislay Roy,1 Rajneesh Chaudhary,1 Rakesh Sehgal,2 Jagat R Kanwar1 1Nanomedicine Laboratory of Immunology and Molecular Biomedical Research, School of Medicine, Centre for Molecular and Medical Research, Faculty of Health, Deakin University, Geelong, VIC, Australia; 2Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India Abstract: The present study successfully developed orally deliverable multimodular zinc (Zn iron oxide (Fe3O4-saturated bovine lactoferrin (bLf-loaded polymeric nanocapsules (NCs, and evaluated their theranostic potential (antitumor efficacy, magnetophotothermal efficacy and imaging capability in an in vivo human xenograft CpG-island methylator phenotype (CIMP-1+/CIMP2−/chromosome instability-positive colonic adenocarcinoma (Caco2 and claudin-low, triple-negative (ER−/PR−/HER2−; MDA-MB-231 breast cancer model. Mice fed orally on the Zn-Fe-bLf NC diet showed downregulation in tumor volume and complete regression in tumor volume after 45 days of feeding. In human xenograft colon cancer, vehicle-control NC diet-group (n=5 mice showed a tumor volume of 52.28±11.55 mm3, and Zn-Fe-bLf NC diet (n=5-treated mice had a tumor-volume of 0.10±0.073 mm3. In the human xenograft breast cancer model, Zn-Fe-bLf NC diet (n=5-treated mice showed a tumor volume of 0.051±0.062 mm3 within 40 days of feeding. Live mouse imaging conducted by near-infrared fluorescence imaging of Zn-Fe-bLf NCs showed tumor site-specific localization and regression of colon and breast tumor volume. Ex vivo fluorescence-imaging analysis of the vital organs of mice exhibited sparse localization patterns of Zn-Fe-bLf NCs and also confirmed tumor-specific selective localization patterns of Zn-Fe-bLf NCs. Dual imaging using magnetic resonance imaging and computerized tomography scans revealed an unprecedented theranostic ability of the Zn-Fe-bLf NCs. These

  11. Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains

    Directory of Open Access Journals (Sweden)

    Mir A Hossain

    2016-01-01

    Full Text Available Reactivation of γ-globin expression has been shown to ameliorate disease phenotypes associated with mutations in the adult β-globin gene, including sickle cell disease. Specific mutations in the promoter of the γ-globin genes are known to prevent repression of the genes in the adult and thus lead to hereditary persistence of fetal hemoglobin. One such hereditary persistence of fetal hemoglobin is associated with a sequence located 567 bp upstream of the Gγ-globin gene which assembles a GATA-containing repressor complex. We generated two synthetic zinc-finger DNA-binding domains (ZF-DBDs targeting this sequence. The -567Gγ ZF-DBDs associated with high affinity and specificity with the target site in the γ-globin gene promoter. We delivered the -567Gγ ZF-DBDs directly to primary erythroid cells. Exposure of these cells to the recombinant -567Gγ ZF-DBDs led to increased expression of the γ-globin gene. Direct protein delivery of ZF-DBDs that compete with transcription regulatory proteins will have broad implications for modulating gene expression in analytical or therapeutic settings.

  12. Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Foster, Mark P.; Wuttke, Deborah S.; Clemens, Karen R.; Jahnke, Wolfgang; Radhakrishnan, Ishwar; Tennant, Linda; Reymond, Martine; Chung, John; Wright, Peter E. [Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology (United States)

    1998-07-15

    We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone{sup 1} H{sup N}, {sup 15}N,{sup 13} C{sup {alpha}} and{sup 13} C{sup {beta}} and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.

  13. Binding and activation of host plasminogen on the surface of Francisella tularensis

    Directory of Open Access Journals (Sweden)

    Whitt Michael A

    2010-03-01

    Full Text Available Abstract Background Francisella tularensis (FT is a gram-negative facultative intracellular coccobacillus and is the causal agent of a life-threatening zoonotic disease known as tularemia. Although FT preferentially infects phagocytic cells of the host, recent evidence suggests that a significant number of bacteria can be found extracellularly in the plasma fraction of the blood during active infection. This observation suggests that the interaction between FT and host plasma components may play an important role in survival and dissemination of the bacterium during the course of infection. Plasminogen (PLG is a protein zymogen that is found in abundance in the blood of mammalian hosts. A number of both gram-positive and gram-negative bacterial pathogens have the ability to bind to PLG, giving them a survival advantage by increasing their ability to penetrate extracellular matrices and cross tissue barriers. Results We show that PLG binds to the surface of FT and that surface-bound PLG can be activated to plasmin in the presence of tissue PLG activator in vitro. In addition, using Far-Western blotting assays coupled with proteomic analyses of FT outer membrane preparations, we have identified several putative PLG-binding proteins of FT. Conclusions The ability of FT to acquire surface bound PLG that can be activated on its surface may be an important virulence mechanism that results in an increase in initial infectivity, survival, and/or dissemination of this bacterium in vivo.

  14. Short term memory for single surface features and bindings in ageing: A replication study.

    Science.gov (United States)

    Isella, Valeria; Molteni, Federica; Mapelli, Cristina; Ferrarese, Carlo

    2015-06-01

    In the present study we replicated a previous experiment investigating visuo-spatial short term memory binding in young and older healthy individuals, in the attempt to verify the pattern of impairment that can be observed in normal elderly for short term memory for single items vs short term memory for bindings. Assessing a larger sample size (25 young and 25 older subjects), using a more appropriate measure of accuracy for a change detection task (A'), and adding the evaluation of speed of performance, we confirmed that old normals show a decline in short term memory for bindings of shape and colour that is of comparable extent, and not major, to the decline in memory for single shapes and single colours. The absence of a specific deficit of short term memory for conjunctions of surface features seems to distinguish cognitive ageing from Alzheimer's Disease. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Binding of Streptavidin to Surface-attached Biotin with Different Spacer Thicknesses

    Institute of Scientific and Technical Information of China (English)

    LI Yifei; ZHANG Haining

    2015-01-01

    The specific binding of receptor to ligand covalently attached to surface with different surface densities was studied using streptavidin-biotin model pair. Biotinylated substrates with different spacer thicknesses as formed through a simple reaction between amine immobilized surfaces and N-hydroxysucciimide groups at the end of biotin modiifed PEG in anhydrous organic solutions (“grafting to”technique). The amount of the speciifcally adsorbed protein was measured as a function of spacer thickness between hard surface and biotin moieties. It has been shown that the amount of specifically adsorbed streptavidin decreases with the increase spacer thickness and the protein adsorbs onto the functionalized surfaces in a single molecular manner. It provides an interesting model system for studying single molecular interactions.

  16. Surface water characterization of three rivers in the lead/zinc mining region of northeastern Macedonia.

    Science.gov (United States)

    Ramani, Sheriban; Dragun, Zrinka; Kapetanović, Damir; Kostov, Vasil; Jordanova, Maja; Erk, Marijana; Hajrulai-Musliu, Zehra

    2014-05-01

    Mine waste is recognized as being one of the most serious threats for freshwater ecosystems, and it still represents one of the greatest environmental concerns in Macedonia. The aim of our investigation was to obtain an in-depth understanding of mining influence on freshwater systems from water contamination to effects on aquatic organisms. In this study, we assessed the impact of active lead (Pb)/zinc (Zn) mines Zletovo and Toranica on the water quality of three rivers in northeastern Macedonia (Bregalnica, Zletovska, and Kriva rivers) based on data collected in spring and autumn of 2012. The Bregalnica River, near Shtip, was characterized mainly by weak contamination with arsenic, barium, iron, molybdenum, titanium, uranium, vanadium, nitrate, and phosphate, as well as critical faecal pollution, which alltogether could be connected to agricultural activities; however, an impact of the mines was not observed. Contrary, both the Zletovska and Kriva rivers showed a clear impact of Pb/Zn mines on water quality. In the Zletovska River, increased concentrations of cadmium (Cd), cobalt, cesium, copper, lithium, manganese (Mn), nickel, rubidium, tin, strontium, thallium, Zn, sulphates, and chlorides were found, especially in autumn (e.g., Cd 2.0 μg L(-1); Mn 2.5 mg L(-1); Zn 1.5 mg L(-1)). In the Kriva River, increased Cd (0.270 μg L(-1)) and Pb (1.85 μg L(-1)) concentrations were found only in spring, possibly due to sediment resuspension during greater water discharge. The selected sampling sites on the Bregalnica, Zletovska, and Kriva rivers were confirmed as being appropriate locations for further studies of mining waste's impact on freshwater ecosystems, the first one as a nonimpacted site and the other two as possible areas of increased exposure of aquatic organisms to metals.

  17. Surface textured molybdenum doped zinc oxide thin films prepared for thin film solar cells using pulsed direct current magnetron sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Y.C., E-mail: ielinyc@cc.ncue.edu.tw; Wang, B.L.; Yen, W.T.; Shen, C.H.

    2011-06-01

    In this study, we examined the effect of etching on the electrical properties, transmittance, and scattering of visible light in molybdenum doped zinc oxide, ZnO:Mo (MZO) thin films prepared by pulsed direct current magnetron sputtering. We used two different etching solutions - KOH and HCl - to alter the surface texture of the MZO thin film so that it could trap light. The experimental results showed that an MZO film with a minimum resistivity of about 8.9 x 10{sup -4} {Omega} cm and visible light transitivity of greater than 80% can be obtained without heating at a Mo content of 1.77 wt.%, sputtering power of 100 W, working pressure of 0.4 Pa, pulsed frequency of 10 kHz, and film thickness of 500 nm. To consider the effect of resistivity and optical diffuse transmittance, we performed etching of an 800 nm thick MZO thin film with 0.5 wt.% HCl for 3-6 s at 300 K. Consequently, we obtained a resistivity of 1.74-2.75 x 10{sup -3} {Omega} cm, total transmittance at visible light of 67%-73%, diffuse transmittance at visible light of 25.1%-28.4%, haze value of 0.34-0.42, and thin film surface crater diameters of 220-350 nm.

  18. Laser-induced periodic surface structures on zinc oxide crystals upon two-colour femtosecond double-pulse irradiation

    Science.gov (United States)

    Höhm, S.; Rosenfeld, A.; Krüger, J.; Bonse, J.

    2017-03-01

    In order to study the temporally distributed energy deposition in the formation of laser-induced periodic surface structures (LIPSS) on single-crystalline zinc oxide (ZnO), two-colour double-fs-pulse experiments were performed. Parallel or cross-polarised double-pulse sequences at 400 and 800 nm wavelength were generated by a Mach–Zehnder interferometer, exhibiting inter-pulse delays up to a few picoseconds between the sub-ablation 50-fs-pulses. Twenty two-colour double-pulse sequences were collinearly focused by a spherical mirror to the sample surface. The resulting LIPSS periods and areas were analysed by scanning electron microscopy. The delay-dependence of these LIPSS characteristics shows a dissimilar behaviour when compared to the semiconductor silicon, the dielectric fused silica, or the metal titanium. A wavelength-dependent plasmonic mechanism is proposed to explain the delay-dependence of the LIPSS on ZnO when considering multi-photon excitation processes. Our results support the involvement of nonlinear processes for temporally overlapping pulses. These experiments extend previous two-colour studies on the indirect semiconductor silicon towards the direct wide band-gap semiconductor ZnO and further manifest the relevance of the ultrafast energy deposition for LIPSS formation.

  19. Transcriptional activation is a conserved feature of the early embryonic factor Zelda that requires a cluster of four zinc fingers for DNA binding and a low-complexity activation domain.

    Science.gov (United States)

    Hamm, Danielle C; Bondra, Eliana R; Harrison, Melissa M

    2015-02-01

    Delayed transcriptional activation of the zygotic genome is a nearly universal phenomenon in metazoans. Immediately following fertilization, development is controlled by maternally deposited products, and it is not until later stages that widespread activation of the zygotic genome occurs. Although the mechanisms driving this genome activation are currently unknown, the transcriptional activator Zelda (ZLD) has been shown to be instrumental in driving this process in Drosophila melanogaster. Here we define functional domains of ZLD required for both DNA binding and transcriptional activation. We show that the C-terminal cluster of four zinc fingers mediates binding to TAGteam DNA elements in the promoters of early expressed genes. All four zinc fingers are required for this activity, and splice isoforms lacking three of the four zinc fingers fail to activate transcription. These truncated splice isoforms dominantly suppress activation by the full-length, embryonically expressed isoform. We map the transcriptional activation domain of ZLD to a central region characterized by low complexity. Despite relatively little sequence conservation within this domain, ZLD orthologs from Drosophila virilis, Anopheles gambiae, and Nasonia vitripennis activate transcription in D. melanogaster cells. Transcriptional activation by these ZLD orthologs suggests that ZLD functions through conserved interactions with a protein cofactor(s). We have identified distinct DNA-binding and activation domains within the critical transcription factor ZLD that controls the initial activation of the zygotic genome.

  20. A20 zinc finger protein inhibits TNF-induced apoptosis and stress response early in the signaling cascades and independently of binding to TRAF2 or 14-3-3 proteins.

    Science.gov (United States)

    Lademann, U; Kallunki, T; Jäättelä, M

    2001-03-01

    A20 zinc finger protein is a negative regulator of tumor necrosis factor (TNF)-induced signaling pathways leading to apoptosis, stress response and inflammation. A20 has been shown to bind to TNF-receptor-associated factor 2 (TRAF2) and 14-3-3 chaperone proteins. Our data indicate that the zinc finger domain of A20 is sufficient and that neither TRAF2 nor 14-3-3 binding is necessary for the inhibitory effects of A20. Mutations in the 14-3-3 binding site of A20 did, however, result in a partial cleavage of A20 protein suggesting that 14-3-3 chaperone proteins may stabilize A20. Furthermore, we show that A20 acts early in TNF-induced signaling cascades blocking both TNF-induced rapid activation of c-Jun N-terminal kinase and processing of the receptor-associated caspase-8. Taken together our data indicate that the zinc finger domain of A20 contains all necessary functional domains required for the inhibition of TNF signaling and that A20 may function at the level of the receptor signaling complex.

  1. Influence of stripping and cooling atmospheres on surface properties and corrosion of zinc galvanizing coatings

    Science.gov (United States)

    Yasakau, K. A.; Giner, I.; Vree, C.; Ozcan, O.; Grothe, R.; Oliveira, A.; Grundmeier, G.; Ferreira, M. G. S.; Zheludkevich, M. L.

    2016-12-01

    In this work the influence of stripping/cooling atmospheres used after withdrawal of steel sheet from Zn or Zn-alloy melt on surface properties of Zn (Z) and Zn-Al-Mg (ZM) hot-dip galvanizing coatings has been studied. The aim was to understand how the atmosphere (composed by nitrogen (N2) or air) affects adhesion strength to model adhesive and corrosive behaviour of the galvanized substrates. It was shown that the surface chemical composition and Volta potential of the galvanizing coatings prepared under the air or nitrogen atmosphere are strongly influenced by the atmosphere. The surface chemistry Z and ZM surfaces prepared under N2 contained a higher content of metal atoms and a richer hydroxide density than the specimens prepared under air atmosphere as assessed by X-ray photoelectron spectroscopy (XPS). The induced differences on the microstructure of the galvanized coatings played a key role on the local corrosion induced defects as observed by means of in situ Atomic force microscopy (AFM). Peel force tests performed on the substrates coated by model adhesive films indicate a higher adhesive strength to the surfaces prepared under nitrogen atmosphere. The obtained results have been discussed in terms of the microstructure and surface chemical composition of the galvanizing coatings.

  2. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer.

    Science.gov (United States)

    Wu, Tsai-Chin; Vasudev, Milana; Dutta, Mitra; Stroscio, Michael A

    2013-06-01

    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.

  3. Nickel(II), copper(II) and zinc(II) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation.

    Science.gov (United States)

    Lauria, Antonino; Bonsignore, Riccardo; Terenzi, Alessio; Spinello, Angelo; Giannici, Francesco; Longo, Alessandro; Almerico, Anna Maria; Barone, Giampaolo

    2014-04-28

    We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-dC)]2 and [poly(dA-dT)]2. Structural details of the intercalation site of the three metal complexes within [dodeca(dA-dT)]2 were obtained by molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations. The calculations revealed that three major intermolecular interactions contribute to the strong affinity between DNA and the three metal complexes: (1) the electrostatic attraction between the two positively charged triethylammoniummethyl groups of the metal complexes and the negatively charged phosphate groups of the DNA backbone; (2) the intercalation of the naphthalene moiety within the four nitrogen bases of the intercalation site; (3) the metal coordination by exocyclic donor atoms of the bases, specifically the carbonyl oxygen and amine nitrogen atoms. Remarkably, the Gibbs formation free energy calculated for the intercalation complexes of 1, 2 and 3 with [dodeca(dA-dT)]2 in the implicit water solution is in agreement with the experimental Gibbs free energy values obtained from the DNA-binding constants as ΔG° = -RT ln(K(b)). In particular, the DNA-binding affinity trend, 1 > 2 > 3, is reproduced. Finally, the first shell coordination distances calculated for the intercalation complex 3/[dodeca(dA-dT)]2 are in

  4. Genome-wide analysis of the DNA-binding with one zinc finger (Dof) transcription factor family in bananas.

    Science.gov (United States)

    Dong, Chen; Hu, Huigang; Xie, Jianghui

    2016-12-01

    DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences. Based on the genome-wide analysis, we identified 74 full-length protein-coding MaDof genes unevenly distributed on 11 chromosomes. Phylogenetic analysis with Dof members from diverse plant species showed that MaDof genes can be classified into four subgroups (StDof I, II, III, and IV). The detailed genomic information of the MaDof gene homologs in the present study provides opportunities for functional analyses to unravel the exact role of the genes in plant growth and development.

  5. Tight attachment of chitin-binding-domain-tagged proteins to surfaces coated with acetylated chitosan.

    Science.gov (United States)

    Bernard, Michael P; Cao, Donghui; Myers, Rebecca V; Moyle, William R

    2004-04-15

    Several excellent procedures for trapping tagged proteins have been devised, but many of these are expensive, cannot be used outside a limited pH range, fail to work in the presence of chaotropic agents, or are difficult to use. The chitin binding domain (CBD) of Bacillus circulans chitinase, which binds to chitin matrices prepared from inexpensive reagents isolated from crab shells, is an alternative tag that can be used under a variety of pH and denaturing conditions. Kits based on the interaction between the CBD and the chitin beads are available commercially. Here, we show that simultaneous treatment of microtiter plates with chitosan, a deacetylated form of chitin, and acetic anhydride produces a surface-bound film of chitin that also interacts tightly with the CBD. Chitin-coated microtiter well plates captured a CBD-tagged heterodimeric human glycoprotein hormone analog directly from mammalian cell culture media, even when present in trace amounts. Binding to the surface was stable in sodium dodecylsulfate and reversed only partially at low pH or in 8M urea at 37 degrees C. This technique appears well suited to surface attachment and permits biochemical or other analyses of molecules that can be tagged with a CBD.

  6. Characterization of homing endonuclease binding and cleavage specificities using yeast surface display SELEX (YSD-SELEX).

    Science.gov (United States)

    Jacoby, Kyle; Lambert, Abigail R; Scharenberg, Andrew M

    2017-02-17

    LAGLIDADG homing endonucleases (LHEs) are a class of rare-cleaving nucleases that possess several unique attributes for genome engineering applications. An important approach for advancing LHE technology is the generation of a library of design ‘starting points’ through the discovery and characterization of natural LHEs with diverse specificities. However, while identification of natural LHE proteins by sequence homology from genomic and metagenomic sequence databases is straightforward, prediction of corresponding target sequences from genomic data remains challenging. Here, we describe a general approach that we developed to circumvent this issue that combines two technologies: yeast surface display (YSD) of LHEs and systematic evolution of ligands via exponential enrichment (SELEX). Using LHEs expressed on the surface of yeast, we show that SELEX can yield binding specificity motifs and identify cleavable LHE targets using a combination of bioinformatics and biochemical cleavage assays. This approach, which we term YSD-SELEX, represents a simple and rapid first principles approach to determining the binding and cleavage specificity of novel LHEs that should also be generally applicable to any type of yeast surface expressible DNA-binding protein. In this marriage, SELEX adds DNA specificity determination to the YSD platform, and YSD brings diagnostics and inexpensive, facile protein-matrix generation to SELEX.

  7. Intracellular zinc distribution in mitochondria, ER and the Golgi apparatus.

    Science.gov (United States)

    Lu, Qiping; Haragopal, Hariprakash; Slepchenko, Kira G; Stork, Christian; Li, Yang V

    2016-01-01

    Zinc (Zn(2+)) is required for numerous cellular functions. As such, the homeostasis and distribution of intracellular zinc can influence cellular metabolism and signaling. However, the exact distribution of free zinc within live cells remains elusive. Previously we showed the release of zinc from thapsigargin/IP3-sensitive endoplasmic reticulum (ER) storage in cortical neurons. In the present study, we investigated if other cellular organelles also contain free chelatable zinc and function as organelle storage for zinc. To identify free zinc within the organelles, live cells were co-stained with Zinpyr-1, a zinc fluorescent dye, and organelle-specific fluorescent dyes (MitoFluor Red 589: mitochondria; ER Tracker Red: endoplasmic reticulum; BODIPY TR ceramide: Golgi apparatus; Syto Red 64: nucleus). We examined organelles that represent potential storing sites for intracellular zinc. We showed that zinc fluorescence staining was co-localized with MitoFluor Red 589, ER Tracker Red, and BODIPY TR ceramide respectively, suggesting the presence of free zinc in mitochondria, endoplasmic reticulum, and the Golgi apparatus. On the other hand, cytosol and nucleus had nearly no detectable zinc fluorescence. It is known that nucleus contains high amount of zinc binding proteins that have high zinc binding affinity. The absence of zinc fluorescence suggests that there is little free zinc in these two regions. It also indicates that the zinc fluorescence detected in mitochondria, ER and Golgi apparatus represents free chelatable zinc. Taken together, our results support that these organelles are potential zinc storing organelles during cellular zinc homeostasis.

  8. Surface Binding and Organization of Sensitizing Dyes on Metal Oxide Single Crystal Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Parkinson, Bruce

    2010-06-04

    Even though investigations of dye-sensitized nanocrystalline semiconductors in solar cells has dominated research on dye-sensitized semiconductors over the past two decades. Single crystal electrodes represent far simpler model systems for studying the sensitization process with a continuing train of studies dating back more than forty years. Even today single crystal surfaces prove to be more controlled experimental models for the study of dye-sensitized semiconductors than the nanocrystalline substrates. We analyzed the scientific advances in the model sensitized single crystal systems that preceded the introduction of nanocrystalline semiconductor electrodes. It then follows the single crystal research to the present, illustrating both their striking simplicity of use and clarity of interpretation relative to nanocrystalline electrodes. Researchers have employed many electrochemical, photochemical and scanning probe techniques for studying monolayer quantities of sensitizing dyes at specific crystallographic faces of different semiconductors. These methods include photochronocoulometry, electronic spectroscopy and flash photolysis of dyes at potential-controlled semiconductor electrodes and the use of total internal reflection methods. In addition, we describe the preparation of surfaces of single crystal SnS2 and TiO2 electrodes to serve as reproducible model systems for charge separation at dye sensitized solar cells. This process involves cleaving the SnS2 electrodes and a photoelectrochemical surface treatment for TiO2 that produces clean surfaces for sensitization (as verified by AFM) resulting in near unity yields for electron transfer from the molecular excited dyes into the conduction band.

  9. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

    Directory of Open Access Journals (Sweden)

    Schroeder Michael

    2006-09-01

    Full Text Available Abstract Background Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed. Results We present LIGSITEcsc, an extension and implementation of the LIGSITE algorithm. LIGSITEcsc is based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcsc performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. Conclusion The use of the Connolly surface leads to slight improvements, the prediction re-ranking by conservation to significant improvements of the binding site predictions. A web server for LIGSITEcsc and its source code is available at scoppi.biotec.tu-dresden.de/pocket.

  10. Requirement of aggregation propensity of Alzheimer amyloid peptides for neuronal cell surface binding

    Directory of Open Access Journals (Sweden)

    McLaurin JoAnne

    2007-05-01

    Full Text Available Abstract Background Aggregation of the amyloid peptides, Aβ40 and Aβ42, is known to be involved in the pathology of Alzheimer's disease (AD. Here we investigate the relationship between peptide aggregation and cell surface binding of three forms of Aβ (Aβ40, Aβ42, and an Aβ mutant. Results Using confocal microscopy and flow cytometry with fluorescently labelled Aβ, we demonstrate a correlation between the aggregation propensity of the Alzheimer amyloid peptides and their neuronal cell surface association. We find that the highly aggregation prone Aβ42 associates with the surface of neuronal cells within one hour, while the less aggregation prone Aβ40 associates over 24 hours. We show that a double mutation in Aβ42 that reduces its aggregation propensity also reduces its association with the cell surface. Furthermore, we find that a cell line that is resistant to Aβ cytotoxicity, the non-neuronal human lymphoma cell line U937, does not bind either Aβ40 or Aβ42. Conclusion Taken together, our findings reveal that amyloid peptide aggregation propensity is an essential determinant of neuronal cell surface association. We anticipate that our approach, involving Aβ imaging in live cells, will be highly useful for evaluating the efficacy of therapeutic drugs that prevent toxic Aβ association with neuronal cells.

  11. Second Harmonic Correlation Spectroscopy: Theory and Principles for Determining Surface Binding Kinetics.

    Science.gov (United States)

    Sly, Krystal L; Conboy, John C

    2017-06-01

    A novel application of second harmonic correlation spectroscopy (SHCS) for the direct determination of molecular adsorption and desorption kinetics to a surface is discussed in detail. The surface-specific nature of second harmonic generation (SHG) provides an efficient means to determine the kinetic rates of adsorption and desorption of molecular species to an interface without interference from bulk diffusion, which is a significant limitation of fluorescence correlation spectroscopy (FCS). The underlying principles of SHCS for the determination of surface binding kinetics are presented, including the role of optical coherence and optical heterodyne mixing. These properties of SHCS are extremely advantageous and lead to an increase in the signal-to-noise (S/N) of the correlation data, increasing the sensitivity of the technique. The influence of experimental parameters, including the uniformity of the TEM00 laser beam, the overall photon flux, and collection time are also discussed, and are shown to significantly affect the S/N of the correlation data. Second harmonic correlation spectroscopy is a powerful, surface-specific, and label-free alternative to other correlation spectroscopic methods for examining surface binding kinetics.

  12. Elucidating the domain architecture and functions of non-core RAG1: The capacity of a non-core zinc-binding domain to function in nuclear import and nucleic acid binding

    Directory of Open Access Journals (Sweden)

    Zhao Shuying

    2011-05-01

    Full Text Available Abstract Background The repertoire of the antigen-binding receptors originates from the rearrangement of immunoglobulin and T-cell receptor genetic loci in a process known as V(DJ recombination. The initial site-specific DNA cleavage steps of this process are catalyzed by the lymphoid specific proteins RAG1 and RAG2. The majority of studies on RAG1 and RAG2 have focused on the minimal, core regions required for catalytic activity. Though not absolutely required, non-core regions of RAG1 and RAG2 have been shown to influence the efficiency and fidelity of the recombination reaction. Results Using a partial proteolysis approach in combination with bioinformatics analyses, we identified the domain boundaries of a structural domain that is present in the 380-residue N-terminal non-core region of RAG1. We term this domain the Central Non-core Domain (CND; residues 87-217. Conclusions We show how the CND alone, and in combination with other regions of non-core RAG1, functions in nuclear localization, zinc coordination, and interactions with nucleic acid. Together, these results demonstrate the multiple roles that the non-core region can play in the function of the full length protein.

  13. Bulk growth and surface characterization of epitaxy ready cadmium zinc telluride substrates for use in IR imaging applications

    Science.gov (United States)

    Flint, J. P.; Martinez, B.; Betz, T. E. M.; MacKenzie, J.; Kumar, F. J.; Bindley, G.

    2016-05-01

    Cadmium Zinc Telluride (CZT) is an important compound semiconductor material upon which Mercury Cadmium Telluride (MCT) layers are deposited epitaxially to form structures that are used in high performance detectors covering a wide infrared (IR) spectral band. The epitaxial growth of high quality MCT layers presents many technical challenges and a critical determinant of material performance is the quality of the underlying bulk CZT substrate. CZT itself is a difficult material to manufacture where traditional methods of bulk growth are complex and low yielding, which constrains the supply of commercially available substrates. In this work we report on the epitaxy-ready finishing of Travelling Heather Method (THM) grown Cd0.96Zn0.04Te substrates. The THM method is well established for the growth of high quality CZT crystals used in nuclear, X-ray and spectroscopic imaging applications and in this work we demonstrate the application of this technique to the growth of IR specification CZT substrates with areas of up to 5 cm x 5 cm square. We will discuss the advantages of the THM method over alternative methods of bulk CZT growth where the high yield and material uniformity advantages of this technique will be demonstrated. Chemo-mechanical polishing (CMP) of 4 cm x 4 cm CZT substrates reveals that III-V (InSb/GaSb) like levels of epitaxy-ready surface finishing may be obtained with modified process chemistries. Surface quality assessments will be made by various surface analytical and microscopy techniques from which the suitability of the material for subsequent assessment of quality by epitaxial growth will be ascertained.

  14. DNA- and BSA-binding studies and anticancer activity against human breast cancer cells (MCF-7) of the zinc(II) complex coordinated by 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine

    Science.gov (United States)

    Anjomshoa, Marzieh; Fatemi, Seyed Jamilaldin; Torkzadeh-Mahani, Masoud; Hadadzadeh, Hassan

    2014-06-01

    Binding studies of a mononuclear zinc(II) complex, [Zn(dppt)2Cl2] (dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), with DNA and bovine serum albumin (BSA) have been investigated under physiological conditions. The binding properties of the complex with fish sperm DNA (FS-DNA) have been investigated by UV-Vis absorption, thermal denaturation, competitive DNA-binding studies with ethidium bromide (EB) by fluorescence, and gel electrophoresis techniques. The competitive study with (EB) shows that the complex can displace EB from the DNA-EB system and compete for the DNA-binding sites with EB, which is usually characteristic of the intercalative interaction of compounds with DNA. The value of the fluorescence quenching constant (Ksv) was obtained as 3.1 × 104 M-1, indicating that this complex shows a high quenching efficiency and a significant degree of binding to DNA. Moreover, the intercalative binding mode has also been verified by the results of UV-Vis absorption, thermal denaturation and gel electrophoresis. The value of Kb at room temperature was calculated to be 1.97 × 105 M-1, indicating that the complex possesses strong tendency to bind with DNA. This value is very greater than to the values obtained for other zinc(II) complexes. The interaction of the complex with BSA has been studied by UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopic techniques. The results indicate that the complex has a quite strong ability to quench the fluorescence of BSA and the binding reaction is mainly a static quenching process. The quenching constants (KSV), the binding constants (Kb), the number of binding sites at different temperatures, the binding distance between BSA and the complex (r), and the thermodynamic parameters (ΔHo, ΔSo and ΔGo) between BSA and the complex were calculated. The complex exhibits good binding propensity to BSA showing relatively high binding constant values. The positive ΔHo and ΔSo values indicate that the

  15. DNA- and BSA-binding studies and anticancer activity against human breast cancer cells (MCF-7) of the zinc(II) complex coordinated by 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine.

    Science.gov (United States)

    Anjomshoa, Marzieh; Fatemi, Seyed Jamilaldin; Torkzadeh-Mahani, Masoud; Hadadzadeh, Hassan

    2014-06-01

    Binding studies of a mononuclear zinc(II) complex, [Zn(dppt)2Cl2] (dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), with DNA and bovine serum albumin (BSA) have been investigated under physiological conditions. The binding properties of the complex with fish sperm DNA (FS-DNA) have been investigated by UV-Vis absorption, thermal denaturation, competitive DNA-binding studies with ethidium bromide (EB) by fluorescence, and gel electrophoresis techniques. The competitive study with (EB) shows that the complex can displace EB from the DNA-EB system and compete for the DNA-binding sites with EB, which is usually characteristic of the intercalative interaction of compounds with DNA. The value of the fluorescence quenching constant (Ksv) was obtained as 3.1×10(4)M(-1), indicating that this complex shows a high quenching efficiency and a significant degree of binding to DNA. Moreover, the intercalative binding mode has also been verified by the results of UV-Vis absorption, thermal denaturation and gel electrophoresis. The value of Kb at room temperature was calculated to be 1.97×10(5)M(-1), indicating that the complex possesses strong tendency to bind with DNA. This value is very greater than to the values obtained for other zinc(II) complexes. The interaction of the complex with BSA has been studied by UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopic techniques. The results indicate that the complex has a quite strong ability to quench the fluorescence of BSA and the binding reaction is mainly a static quenching process. The quenching constants (KSV), the binding constants (Kb), the number of binding sites at different temperatures, the binding distance between BSA and the complex (r), and the thermodynamic parameters (ΔH(o), ΔS(o) and ΔG(o)) between BSA and the complex were calculated. The complex exhibits good binding propensity to BSA showing relatively high binding constant values. The positive ΔH(o) and ΔS(o) values indicate that

  16. Zinc-blende MnN bilayer formation on the GaN(111) surface

    Science.gov (United States)

    Gutierrez-Ojeda, S. J.; Guerrero-Sánchez, J.; Garcia-Diaz, R.; Ramirez-Torres, A.; Takeuchi, Noboru; Cocoletzi, Gregorio H.

    2017-07-01

    Atomic layers of manganese nitride, deposited on the cubic gallium nitride (111) surface, are investigated using spin polarized periodic density functional theory calculations. The adsorption of a manganese atom has been evaluated at different high symmetry sites. Incorporation into the GaN substrate by replacing gallium atoms drives the formation of a site in which the displaced Ga atom forms bonds with Ga atoms at the surface. This energetically favorable configuration shows a ferromagnetic alignment. Surface formation energy calculations demonstrate that when a full Mn ML is incorporated into the GaN structure, a Ga ML on top of a MnN bilayer may be formed for very Ga-rich conditions. On the other hand, when a full Mn ML is deposited on top of the nitrogen terminated surface, an epitaxial MnN bilayer is formed with antiferromagnetic characteristics. Density of states and partial density of states are reported to show the antiferromagnetic alignment in both structures. This behavior is mainly induced by the Mn-d orbitals.

  17. Insights into molecular plasticity of choline binding proteins (pneumococcal surface proteins) by SAXS.

    Science.gov (United States)

    Buey, Rubén M; Monterroso, Begoña; Menéndez, Margarita; Diakun, Greg; Chacón, Pablo; Hermoso, Juan Antonio; Díaz, J Fernando

    2007-01-12

    Phosphocholine moieties decorating the pneumococcal surface are used as a docking station for a family of modular proteins, the so-called choline binding proteins or CBPs. Choline recognition is essential for CBPs function and may also be a determinant for their quaternary structure. There is little knowledge about modular arrangement or oligomeric structures in this family. Therefore, we have used the small angle X-ray scattering (SAXS) technique combined with analytical ultracentrifugation in order to model the three-dimensional envelope of two highly different CBPs: the phage encoded Cpl-1 lysozyme and the pneumococcal phosphorylcholine esterase Pce. Both enzymes have an N-terminal catalytic module and a C-terminal choline-binding module (CBM) that attaches them to the bacterial surface and comprises six and ten sequence repeats in Cpl-1 and Pce, respectively. SAXS experiments have shown an inherent conformational plasticity in Cpl-1 that accounts for the different relative position of these regions in the solution and crystal structures. Dimerization of Cpl-1 upon choline binding has been also visualised for the first time, and monomer-monomer interactions take place through the first CBR where a non-canonical choline binding site has now been identified. This mode of association seems to be independent of the absence or presence of the Cpl-1 catalytic module and reveals that the arrangement of the monomers differs from that previously found in the isolated CBM dimer of pneumococcal LytA amidase. In contrast, Pce displays the same modular disposition in the solution and crystal structures, and remains almost invariant upon choline binding. The present results suggest that protein dimerization and duplication of CBRs may be alternative but not equivalent ways of improving cell wall recognition by CBPs, since they provide different interaction geometries for choline residues present in (lipo)teichoic acids.

  18. Sensing (un)binding events via surface plasmons: effects of resonator geometry

    Science.gov (United States)

    Antosiewicz, Tomasz J.; Claudio, Virginia; Käll, Mikael

    2016-04-01

    The resonance conditions of localized surface plasmon resonances (LSPRs) can be perturbed in any number ways making plasmon nanoresonators viable tools in detection of e.g. phase changes, pH, gasses, and single molecules. Precise measurement via LSPR of molecular concentrations hinge on the ability to confidently count the number of molecules attached to a metal resonator and ideally to track binding and unbinding events in real-time. These two requirements make it necessary to rigorously quantify relations between the number of bound molecules and response of plasmonic sensors. This endeavor is hindered on the one hand by a spatially varying response of a given plasmonic nanosensor. On the other hand movement of molecules is determined by stochastic effects (Brownian motion) as well as deterministic flow, if present, in microfluidic channels. The combination of molecular dynamics and the electromagnetic response of the LSPR yield an uncertainty which is little understood and whose effect is often disregarded in quantitative sensing experiments. Using a combination of electromagnetic finite-difference time-domain (FDTD) calculations of the plasmon resonance peak shift of various metal nanosensors (disk, cone, rod, dimer) and stochastic diffusion-reaction simulations of biomolecular interactions on a sensor surface we clarify the interplay between position dependent binding probability and inhomogeneous sensitivity distribution. We show, how the statistical characteristics of the total signal upon molecular binding are determined. The proposed methodology is, in general, applicable to any sensor and any transduction mechanism, although the specifics of implementation will vary depending on circumstances. In this work we focus on elucidating how the interplay between electromagnetic and stochastic effects impacts the feasibility of employing particular shapes of plasmonic sensors for real-time monitoring of individual binding reactions or sensing low concentrations

  19. Studies on nanocrystalline zinc coating

    Indian Academy of Sciences (India)

    H B Muralidhara; Y Arthoba Naik

    2008-08-01

    Nano zinc coatings were deposited on mild steel by electrodeposition. The effect of additive on the morphology of crystal size on zinc deposit surface and corrosion properties were investigated. Corrosion tests were performed for dull zinc deposits and bright zinc deposits in aqueous NaCl solution (3.5 wt.%) using electrochemical measurements. The results showed that addition of additive in the deposition process of zinc significantly increased the corrosion resistance. The surface morphology of the zinc deposits was studied by scanning electron microscopy (SEM). The preferred orientation and average size of the zinc electrodeposited particles were obtained by X-ray diffraction analysis. The particles size was also characterized by TEM analysis.

  20. Glyceraldehyde-3-phosphate dehydrogenase is a surface-associated, fibronectin-binding protein of Trichomonas vaginalis.

    Science.gov (United States)

    Lama, A; Kucknoor, A; Mundodi, V; Alderete, J F

    2009-07-01

    Trichomonas vaginalis colonizes the urogenital tract of humans and causes trichomonosis, the most prevalent nonviral sexually transmitted disease. We have shown an association of T. vaginalis with basement membrane extracellular matrix components, a property which we hypothesize is important for colonization and persistence. In this study, we identify a fibronectin (FN)-binding protein of T. vaginalis. A monoclonal antibody (MAb) from a library of hybridomas that inhibited the binding of T. vaginalis organisms to immobilized FN was identified. The MAb (called ws1) recognized a 39-kDa protein and was used to screen a cDNA expression library of T. vaginalis. A 1,086-bp reactive cDNA clone that encoded a protein of 362 amino acids with identity to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was obtained. The gapdh gene was cloned, and recombinant GAPDH (rGAPDH) was expressed in Escherichia coli cells. Natural GAPDH and rGAPDH bound to immobilized FN and to plasminogen and collagen but not to laminin. MAb ws1 inhibited binding to FN. GAPDH was detected on the surface of trichomonads and was upregulated in synthesis and surface expression by iron. Higher levels of binding to FN were seen for organisms grown in iron-replete medium than for organisms grown in iron-depleted medium. In addition, decreased synthesis of GAPDH by antisense transfection of T. vaginalis gave lower levels of organisms bound to FN and had no adverse effect on growth kinetics. Finally, GAPDH did not associate with immortalized vaginal epithelial cells (VECs), and neither GAPDH nor MAb ws1 inhibited the adherence of trichomonads to VECs. These results indicate that GAPDH is a surface-associated protein of T. vaginalis with alternative functions.

  1. Perylene Bisimide as a Promising Zinc Oxide Surface Modifier: Enhanced Interfacial Combination for Highly Efficient Inverted Polymer Solar Cells.

    Science.gov (United States)

    Nian, Li; Zhang, Wenqiang; Wu, Siping; Qin, Leiqiang; Liu, Linlin; Xie, Zengqi; Wu, Hongbin; Ma, Yuguang

    2015-11-25

    We report the application of a perylene bisimide (PBI-H) as zinc oxide (ZnO) surface modifier to afford an organic-inorganic co-interlayer for highly efficient inverted organic photovoltaics (i-OPV). By thermal annealing, a N-Zn chemical bond formed between PBI-H and ZnO, inducing close organic-inorganic combination. In addition, this co-interlayer shows decreased work function and increased electron transportation and conductivity, which are benefits for the cathode to enhance charge extraction efficiency and decrease recombination losses. As a result a highly efficient i-OPV was achieved with a power conversion efficiency (PCE) of 9.43% based on this co-interlayer with PTB7:PC71BM as the active layer, which shows over 35% enhancement compared to that of the device without the PBI-H layer. Moreover, this co-interlayer was widely applicable for i-OPVs based on various material systems, such as P3HT:PC61BM and PTB7-Th:PC71BM, resulting in PCE as high as 4.78% and 10.31%, respectively.

  2. Bioremediation of surface water co-contaminated with zinc (II) and linear alkylbenzene sulfonates by Spirulina platensis

    Science.gov (United States)

    Meng, Huijuan; Xia, Yunfeng; Chen, Hong

    Potential remediation of surface water contaminated with linear alkylbenzene sulfonates (LAS) and zinc (Zn (II)) by sorption on Spirulina platensis was studied using batch techniques. Results show that LAS can be biodegraded by Spirulina platensis, and its biodegradation rate after 5 days was 87%, 80%, and 70.5% when its initial concentration was 0.5, 1, and 2 mg/L, respectively. The maximum Zn (II) uptake capacity of Spirulina platensis was found to be 30.96 mg/g. LAS may enhance the maximum Zn (II) uptake capacity of Spirulina platensis, which can be attributed to an increase in bioavailability due to the presence of LAS. The biodegradation rates of LAS by Spirulina platensis increased with Zn (II) and reached the maximum when Zn (II) was 4 mg/L. The joint toxicity test showed that the combined effect of LAS and Zn (II) was Synergistic. LAS can enhance the biosorption of Zn (II), and reciprocally, Zn (II) can enhance LAS biodegradation.

  3. Surface structure and field emission properties of cost effectively synthesized zinc oxide nanowire/multiwalled carbon nanotube heterojunction arrays

    Science.gov (United States)

    Dehghan Nayeri, F.; Darbari, S.; Soleimani, E. A.; Mohajerzadeh, S.

    2012-07-01

    A cost-effective and efficient approach for the synthesis of single-crystalline zinc oxide nanowires on vertically aligned multiwalled carbon nanotube (CNT) array is presented. ZnO nanowires are grown on the base of individual CNT through the low-temperature wet-chemical batch deposition technique, while the size and interspacing of the nanowires can be controlled by precursor concentration, growth temperature and time duration. The scanning electron microscopy image showed that the ZnO nanostructures are successfully grown on the CNT's surface uniformly. The produced nanostructures are characterized by x-ray diffraction, x-ray photoelectron spectroscopy and Raman spectroscopy. Also, field emission characteristics of the fabricated double-stage ZnO nanowire/CNT array are investigated and compared with the emission behaviour of CNT and ZnO nanowire arrays. The ZnO nanowire/CNT heterojunction array resulted in a low turn-on field of 1.5 V µm-1 and a threshold field of 4.5 V µm-1, which were lower than both the vertical CNT and ZnO arrays. The field emission properties and stability of the fabricated nanostructures also demonstrated great potential for field emission applications.

  4. Acetone gas sensing mechanism on zinc oxide surfaces: A first principles calculation

    Science.gov (United States)

    Sadeghian Lemraski, M.; Nadimi, E.

    2017-03-01

    Semiconducting metal oxide gas sensors have attracted growing interest as a result of their outstanding performance in the bio and industrial applications. Nevertheless, the sensing mechanism is yet not totally understood. In this study, we extensively investigate the adsorption mechanism of acetone molecule on ZnO-based thin film sensors by performing ab initio density functional theory calculations and employing quantum molecular dynamic simulations. Since the sensitivity of a metal oxide sensor is exceedingly depends on molecular oxygen exposure and operating temperature, we explore the competitive adsorption of acetone and oxygen molecule on the most stable orientation of ZnO surface (10 1 ̅ 0) at different temperatures. Results indicate that at elevated temperatures acetone gains required thermal energy to remove preadsorbed oxygen molecule from the surface in a competitive process. We will show that this competition is responsible for the resistive switching behavior in the ZnO-based gas sensors.

  5. Preparation and Rapid Analysis of Antibacterial Silver, Copper and Zinc Doped Sol–gel Surfaces

    OpenAIRE

    Jaiswal, Swarna; Duffy, Brendan; McHale, Patrick

    2012-01-01

    The colonisation of clinical and industrial surfaces with microorganisms, including antibiotic-resistant strains, has promoted increased research into the development of effective antibacterial and antifouling coatings. This study describes the preparation of metal nitrate (Ag, Cu, Zn) doped methyltriethoxysilane (MTEOS) coatings and the rapid assessment of their antibacterial activity using polyproylene microtitre plates. Microtitre plate wells were coated with different volumes of liquid so...

  6. Analysis of novel iron-regulated, surface-anchored hemin-binding proteins in Corynebacterium diphtheriae.

    Science.gov (United States)

    Allen, Courtni E; Burgos, Jonathan M; Schmitt, Michael P

    2013-06-01

    Corynebacterium diphtheriae utilizes hemin and hemoglobin (Hb) as iron sources during growth in iron-depleted environments, and recent studies have shown that the surface-exposed HtaA protein binds both hemin and Hb and also contributes to the utilization of hemin iron. Conserved (CR) domains within HtaA and in the associated hemin-binding protein, HtaB, are required for the ability to bind hemin and Hb. In this study, we identified and characterized two novel genetic loci in C. diphtheriae that encode factors that bind hemin and Hb. Both genetic systems contain two-gene operons that are transcriptionally regulated by DtxR and iron. The gene products of these operons are ChtA-ChtB and ChtC-CirA (previously DIP0522-DIP0523). The chtA and chtB genes are carried on a putative composite transposon associated with C. diphtheriae isolates that dominated the diphtheria outbreak in the former Soviet Union in the 1990s. ChtA and ChtC each contain a single N-terminal CR domain and exhibit significant sequence similarity to each other but only limited similarity with HtaA. The chtB and htaB gene products exhibited a high level of sequence similarity throughout their sequences, and both proteins contain a single CR domain. Whole-cell binding studies as well as protease analysis indicated that all four of the proteins encoded by these two operons are surface exposed, which is consistent with the presence of a transmembrane segment in their C-terminal regions. ChtA, ChtB, and ChtC are able to bind hemin and Hb, with ChtA showing the highest affinity. Site-directed mutagenesis showed that specific tyrosine residues within the ChtA CR domain were critical for hemin and Hb binding. Hemin iron utilization assays using various C. diphtheriae mutants indicate that deletion of the chtA-chtB region and the chtC gene has no affect on the ability of C. diphtheriae to use hemin or Hb as iron sources; however, a chtB htaB double mutant exhibits a significant decrease in hemin iron use

  7. Sources of strong copper-binding ligands in Antarctic Peninsula surface waters

    Science.gov (United States)

    Bundy, Randelle M.; Barbeau, Katherine A.; Buck, Kristen N.

    2013-06-01

    Copper-binding organic ligands were measured during austral winter in surface waters around the Antarctic Peninsula using competitive ligand exchange-adsorptive cathodic stripping voltammetry with multiple analytical windows. Samples were collected from four distinct water masses including the Antarctic Circumpolar Current, Southern Antarctic Circumpolar Current Front, Bransfield Strait, and the shelf region of the Antarctic Peninsula. Strong copper-binding organic ligands were detected in each water mass. The strongest copper-binding ligands were detected at the highest competition strength in the Antarctic Circumpolar Current, with an average conditional stability constant of logKCuL,Cucond=16.00±0.82. The weakest ligands were found at the lowest competition strength in the shelf region with logKCuL,Cucond=12.68±0.48. No ligands with stability constants less than logKCuL,Cucond=13.5 were detected in the Antarctic Circumpolar Current at any competition strength, suggesting a shelf source of weaker copper-binding ligands. Free, hydrated copper ion concentrations, the biologically available form of dissolved copper, were less than 10-14 M in all samples, approaching levels that may be limiting for some types of inducible iron acquisition.

  8. Zinc tolerance and zinc removal ability of living and dried biomass of Desmodesmus communis.

    Science.gov (United States)

    Novák, Zoltán; Jánószky, Mihály; B-Béres, Viktória; Nagy, Sándor Alex; Bácsi, István

    2014-12-01

    Effects of zinc on growth, cell morphology, oxidative stress, and zinc removal ability of the common phytoplankton species Desmodesmus communis were investigated at a concentration range of 0.25-160 mg L(-1) zinc. Cell densities and chlorophyll content decreased in treated cultures, changes in coenobia morphology and elevated lipid peroxidation levels appeared above 2.5 mg L(-1) zinc. The most effective zinc removal was observed at 5 mg L(-1) zinc concentration, while maximal amount of removed zinc appeared in 15 mg L(-1) zinc treated culture. Removed zinc is mainly bound on the cell surface. Dead biomass adsorbed more zinc than living biomass relative to unit of dry mass, but living biomass was more effective, relative to initial zinc content. This study comprehensively examines the zinc tolerance and removal ability of D. communis and demonstrates, in comparison with published literature, that these characteristics of different isolates of the same species can vary within a wide range.

  9. Three zinc-finger RNA-binding proteins in cabbage (Brassica rapa) play diverse roles in seed germination and plant growth under normal and abiotic stress conditions.

    Science.gov (United States)

    Park, Ye Rin; Choi, Min Ji; Park, Su Jung; Kang, Hunseung

    2017-01-01

    Despite the increasing understanding of the stress-responsive roles of zinc-finger RNA-binding proteins (RZs) in several plant species, such as Arabidopsis thaliana, wheat (Triticum aestivum) and rice (Oryza sativa), the functions of RZs in cabbage (Brassica rapa) have not yet been elucidated. In this study, the functional roles of the three RZ family members present in the cabbage genome, designated as BrRZ1, BrRZ2 and BrRZ3, were investigated in transgenic Arabidopsis under normal and environmental stress conditions. Subcellular localization analysis revealed that all BrRZ proteins were exclusively localized in the nucleus. The expression levels of each BrRZ were markedly increased by cold, drought or salt stress and by abscisic acid (ABA) treatment. Expression of BrRZ3 in Arabidopsis retarded seed germination and stem growth and reduced seed yield of Arabidopsis plants under normal growth conditions. Germination of BrRZ2- or BrRZ3-expressing Arabidopsis seeds was delayed compared with that of wild-type seeds under dehydration or salt stress conditions and cold stress conditions, respectively. Seedling growth of BrRZ3-expressing transgenic Arabidopsis plants was significantly inhibited under salt, dehydration or cold stress conditions. Notably, seedling growth of all three BrRZ-expressing transgenic Arabidopsis plants was inhibited upon ABA treatment. Importantly, all BrRZs possessed RNA chaperone activity. Taken together, these results indicate that the three cabbage BrRZs harboring RNA chaperone activity play diverse roles in seed germination and seedling growth of plants under abiotic stress conditions as well as in the presence of ABA. © 2016 Scandinavian Plant Physiology Society.

  10. Design of cyclic peptides that bind protein surfaces with antibody-like affinity.

    Science.gov (United States)

    Millward, Steven W; Fiacco, Stephen; Austin, Ryan J; Roberts, Richard W

    2007-09-21

    There is a pressing need for new molecular tools to target protein surfaces with high affinity and specificity. Here, we describe cyclic messenger RNA display with a trillion-member covalent peptide macrocycle library. Using this library, we have designed a number of high-affinity, redox-insensitive, cyclic peptides that target the signaling protein G alpha i1. In addition to cyclization, our library construction took advantage of an expanded genetic code, utilizing nonsense suppression to insert N-methylphenylalanine as a 21st amino acid. The designed macrocycles exhibit several intriguing features. First, the core motif seen in all of the selected variants is the same and shares an identical context with respect to the macrocyclic scaffold, consistent with the idea that selection simultaneously optimizes both the cyclization chemistry and the structural placement of the binding epitope. Second, detailed characterization of one molecule, cyclic G alpha i binding peptide (cycGiBP), demonstrates substantially enhanced proteolytic stability relative to that of the parent linear molecule. Third and perhaps most important, the cycGiBP peptide binds the target with very high affinity ( K i approximately 2.1 nM), similar to those of many of the best monoclonal antibodies and higher than that of the betagamma heterodimer, an endogenous G alpha i1 ligand. Overall the work provides a general route to design novel, low-molecular-weight, high-affinity ligands that target protein surfaces.

  11. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    Science.gov (United States)

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  12. Adeno-associated virus type 2 binding study on model heparan sulfate surface

    Science.gov (United States)

    Negishi, Atsuko; Liu, Jian; McCarty, Douglas; Samulski, Jude; Superfine, Richard

    2003-11-01

    Understanding the mechanisms involved in virus infections is useful in its application in areas such as gene therapy, drug development and delivery, and biosensors. In collaboration with UNC Gene Therapy Center and School of Pharmacy, we are specifically looking at the interaction between human parvovirus adeno-associated virus type 2 (AAV2), a potential viral vector, and heparan sulfate proteoglycan (HSPG), a known cell surface receptor for AAV2. Recent development in glycobiology has shown that some protein-polysaccharide binding is sugar sequence dependent. Heparan sulfate (HS) is a polysaccharide chain of sulfated iduronic/glucuronic and sulfate glucosamine residues and can be differentiated into sequence specific structures by enzymes. These enzymatic modifications, known as heparan sulfate sulfotransferase modified modifications, have been shown to change the biological nature of heparan sulfate such as specific binding to proteins and viruses. For understanding HS-assisted viral infection mechanisms, we are interested in investigating the binding affinity and stability of AAV to different HS structures. We have developed a model heparan sulfate surface in which AAV adsorption studies are done and analyzed using the atomic force microscope (AFM). In addition, a miniArray assay has been created to facilitate to this study. Adsorption studies are done in 4 white LED wells with approximately 3 mm2 reaction areas which minimize sample use and waste.

  13. Surface-effects-dominated thermal and mechanical responses of zinc oxide nanobelts

    Institute of Scientific and Technical Information of China (English)

    A.J.Kulkarni; M.Zhou

    2006-01-01

    Molecular dynamics(MD)simulations are carried out to characterize the mechanical and thermal responses of [ol(l)o]-oriented ZnO nanobelts with lateral dimensions of 21.22(A)×18.95(A),31.02(A)×29.42(A) and 40.81(A)×39.89(A) over the temperature range of 300-1000 K. The Young's modulus and thermal conductivity of the nanobelts are evaluated. Significant surface effects on properties due to the highsurface-to-volume ratios of the nanobelts are observed. For the mechanical response, surface-stress-induced internal stress plays an important role. For the thermal response, surface scattering of phonons dominates. Calculations show that the Young's modulus is higher than the corresponding value for bulk ZnO and decreases by~33%as the lateral dimensions increase from 21.22(A)×18.95(A) to 40.8l(A)×39.89(A).The thermal conductivity is one order of magnitude lower than the corresponding value for bulk ZnO single crystal and decreases with wire size. Specifically, the conductivity of the 21.22(A)×18.95(A) beltis approximately(31-18)% lower than that of the 40.81(A)×39.89(A) belt over the temperature range analyzed. A significant dependence of properties on temperature is also observed. with the Young's modulus decreasing on average by 12% and the conductivity decreasing by 50% as temperature increases from 300 K to 1000 K.

  14. Differential affinity of FLIP and procaspase 8 for FADD's DED binding surfaces regulates DISC assembly.

    Science.gov (United States)

    Majkut, J; Sgobba, M; Holohan, C; Crawford, N; Logan, A E; Kerr, E; Higgins, C A; Redmond, K L; Riley, J S; Stasik, I; Fennell, D A; Van Schaeybroeck, S; Haider, S; Johnston, P G; Haigh, D; Longley, D B

    2014-02-28

    Death receptor activation triggers recruitment of FADD, which via its death effector domain (DED) engages the DEDs of procaspase 8 and its inhibitor FLIP to form death-inducing signalling complexes (DISCs). The DEDs of FADD, FLIP and procaspase 8 interact with one another using two binding surfaces defined by α1/α4 and α2/α5 helices, respectively. Here we report that FLIP has preferential affinity for the α1/α4 surface of FADD, whereas procaspase 8 has preferential affinity for FADD's α2/α5 surface. These relative affinities contribute to FLIP being recruited to the DISC at comparable levels to procaspase 8 despite lower cellular expression. Additional studies, including assessment of DISC stoichiometry and functional assays, suggest that following death receptor recruitment, the FADD DED preferentially engages FLIP using its α1/α4 surface and procaspase 8 using its α2/α5 surface; these tripartite intermediates then interact via the α1/α4 surface of FLIP DED1 and the α2/α5 surface of procaspase 8 DED2.

  15. Early stages of the oxidation of metal surfaces. [photoelectron spectroscopy of zinc oxide

    Science.gov (United States)

    Gatos, H. C.; Johnson, K. H.

    1978-01-01

    Photoemission cross sections were calculated for the ZnO4(-6) cluster using the self consistent-chi alpha- scattered wave theory to display the main features of the ultraviolet and X-ray photoemission data from ZnO. A solid model is suggested for an absolute photoemission intensity comparison resulting in chi alpha intensities which are roughly 70% of the experimental values. Together with the experimental data, the calculations allow a complete determination of the electronic structure of a ZnO surface.

  16. Aflatoxin Toxicity Reduction in Feed by Enhanced Binding to Surface-Modified Clay Additives

    Directory of Open Access Journals (Sweden)

    Richard E. Zartman

    2011-06-01

    Full Text Available Animal feeding studies have demonstrated that clay additives, such as bentonites, can bind aflatoxins in ingested feed and reduce or eliminate the toxicity. Bentonite deposits are found throughout the world and mostly consist of expandable smectite minerals, such as montmorillonite. The surfaces of smectite minerals can be treated with organic compounds to create surface-modified clays that more readily bind some contaminants than the untreated clay. Montmorillonites treated with organic cations, such as hexadecyltrimethylammonium (HDTMA and phenyltrimethylammonium (PTMA, more effectively remove organic contaminants, such as benzene and toluene, from water than untreated clay. Similarly, montmorillonite treated with PTMA (Kd = 24,100 retained more aflatoxin B1 (AfB1 from aqueous corn flour than untreated montmorillonite (Kd = 944. Feed additives that reduced aflatoxin toxicity in animal feeding studies adsorbed more AfB1 from aqueous corn flour than feed additives that were less effective. The organic cations HDTMA and PTMA are considered toxic and would not be suitable for clay additives used in feed or food, but other non-toxic or nutrient compounds can be used to prepare surface-modified clays. Montmorillonite (SWy treated with choline (Kd = 13,800 and carnitine (Kd = 3960 adsorbed much more AfB1 from aqueous corn flour than the untreated clay (Kd = 944. A choline-treated clay prepared from a reduced-charge, high-charge montmorillonite (Kd = 20,100 adsorbed more AfB1 than the choline-treated high-charge montmorillonite (Kd = 1340 or the untreated montmorillonite (Kd = 293. Surface-modified clay additives prepared using low-charge smectites and nutrient or non-toxic organic compounds might be used to more effectively bind aflatoxins in contaminated feed or food and prevent toxicity.

  17. Detection of vitamin D binding protein on the surface of cytotrophoblasts isolated from human placentae

    Energy Technology Data Exchange (ETDEWEB)

    Nestler, J.E.; McLeod, J.F.; Kowalski, M.A.; Strauss, J.F. 3d.; Haddad, J.G. Jr.

    1987-05-01

    Vitamin D binding protein (DBP), a Mr 56,000-58,000 alpha 2-glycoprotein, is the major serum protein involved in the transport of vitamin D sterols. Recently it has been suggested that DBP may also be involved in immunoglobulin G binding to cells. Because the trophoblast is involved in the transport of molecules such as vitamin D and immunoglobulin G to the fetus, we asked whether DBP could be detected on the surface of human placental trophoblast cells. Cytotrophoblasts purified from human term placentae were fixed and made permeant with Triton X-100 and examined by indirect immunofluorescence after incubation with a monoclonal antibody to DBP. Greater than 90% of these cells stained positively, whereas no staining was observed with nonimmune antiserum. The presence of DBP on/in the surface of cytotrophoblasts could also be demonstrated by fluorescent cytometry. When cell surface-associated proteins of cytotrophoblasts were radioiodinated, a Mr 57,000 radiolabeled protein could be immunoisolated from the cell lysate with a purified monospecific polyclonal antibody to DBP. Immunoisolation of this radiolabeled protein was prevented by the addition of excess unlabeled human DBP to the cell lysate before incubation with antibody. This Mr 57,000 radiolabeled protein could also be isolated by affinity chromatography selecting for proteins that bind to globular actin. When cytotrophoblasts were incubated with (/sup 35/S)methionine for 3 or 18 h, active synthesis of DBP could not be demonstrated by immunoisolation techniques. These studies demonstrate the presence of DBP on the surface of well washed, human cytotrophoblasts. This DBP may be maternally derived, since active synthesis of DBP could not be demonstrated.

  18. INVESTIGATION OF BLACK TARNISHED FILM ON ZINC PLATED SURFACE%电镀锌层表面黑变膜的研究*

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The composition and structure of black tamished film on zinc plated surface were investigated by means of SEM, EDX, XRD and XPS. It was found that black tamished film is a corrosion products formed on zinc plated surface, and impurity Pb accelerates electrochemical corrosion process of zinc by depolarization.This film possibly composed of and trace PbO. The results of XPS analyses showed that Zn exists as stoichimetric compound ZnO in the surface layer of the film, while as non-stoichimetric compound in the inner layer of the film. It was also found that the color of black tarnished film was induced by light interference effect to the film.%用SEM、EDX、XRD、XPS等技术分析了电镀锌层表面黑变膜的组成和结构.结果表明,黑变膜是锌的腐蚀作用及杂质Pb去极化作用的共同产物.它由及微量PbO组成,膜表层Zn是以ZnO形态存在,而膜内层则以非化学计量化合物形态存在.并发现黑变膜是一种锌受腐蚀所形成的表面膜上产生的光干涉现象.

  19. Self-consistent tight-binding study of low-index titanium surfaces

    Science.gov (United States)

    Erdin, Serkan; Lin, You; Halley, J. Woods

    2005-07-01

    We report development of a self-consistent tight-binding (SCTB) model for metallic titanium and its use to simulate relaxed, self-consistent low-index surfaces of hcp titanium. We find oscillations in atomic plane separation and electronic density as a function of depth below the surface that do not stabilize until the supercell slab used in the calculation is more than ten layers deep. The SCTB model can only give stable, structures and reasonable surface structures and energies if multipole (particularly dipole) moments are allowed to be induced at the atomic sites and if the first-principles data base includes calculations on short wave length (“frozen phonon”) distortions of the bulk unit cell.

  20. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    Science.gov (United States)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-01

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  1. Surface binding sites (SBSs), mechanism and regulation of enzymes degrading amylopectin and α-limit dextrins

    DEFF Research Database (Denmark)

    Møller, Marie Sofie; Cockburn, Darrell; Nielsen, Jonas W.;

    2013-01-01

    Certain enzymes interact with polysaccharides at surface binding sites (SBSs) situated outside of their active sites. SBSs are not easily identified and their function has been discerned in relatively few cases. Starch degradation is a concerted action involving GH13 hydrolases. New insight...... into barley seed α-amylase 1 (AMY1) and limit dextrinase (LD) includes i. kinetics of bi-exponential amylopectin hydrolysis by AMY1, one reaction having low Km (8 μg/mL) and high kcat (57 s-1) and the other high Km (97 μg/mL) and low kcat (23 s-1). β-Cyclodextrin (β-CD) inhibits the first reaction by binding...

  2. Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins

    Energy Technology Data Exchange (ETDEWEB)

    Lok, Shee-Mei; Kostyuchenko, Victor; Nybakken, Grant E.; Holdaway, Heather A.; Battisti, Anthony J.; Sukupolvi-Petty, Soila; Sedlak, Dagmar; Fremont, Daved H.; Chipman, Paul R.; Roehrig, John T.; Diamond, Michael S.; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (WU-MED); (CDC)

    2008-04-02

    The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization of the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells.

  3. Surface displaced alfa-enolase of Lactobacillus plantarum is a fibronectin binding protein

    Science.gov (United States)

    Castaldo, Cristiana; Vastano, Valeria; Siciliano, Rosa Anna; Candela, Marco; Vici, Manuela; Muscariello, Lidia; Marasco, Rosangela; Sacco, Margherita

    2009-01-01

    Background Lactic acid bacteria of the genus Lactobacillus and Bifidobacterium are one of the most important health promoting groups of the human intestinal microbiota. Their protective role within the gut consists in out competing invading pathogens for ecological niches and metabolic substrates. Among the features necessary to provide health benefits, commensal microorganisms must have the ability to adhere to human intestinal cells and consequently to colonize the gut. Studies on mechanisms mediating adhesion of lactobacilli to human intestinal cells showed that factors involved in the interaction vary mostly among different species and strains, mainly regarding interaction between bacterial adhesins and extracellular matrix or mucus proteins. We have investigated the adhesive properties of Lactobacillus plantarum, a member of the human microbiota of healthy individuals. Results We show the identification of a Lactobacillus plantarum LM3 cell surface protein (48 kDa), which specifically binds to human fibronectin (Fn), an extracellular matrix protein. By means of mass spectrometric analysis this protein was identified as the product of the L. plantarum enoA1 gene, coding the EnoA1 alfa-enolase. Surface localization of EnoA1 was proved by immune electron microscopy. In the mutant strain LM3-CC1, carrying the enoA1 null mutation, the 48 kDa adhesin was not anymore detectable neither by anti-enolase Western blot nor by Fn-overlay immunoblotting assay. Moreover, by an adhesion assay we show that LM3-CC1 cells bind to fibronectin-coated surfaces less efficiently than wild type cells, thus demonstrating the significance of the surface displaced EnoA1 protein for the L. plantarum LM3 adhesion to fibronectin. Conclusion Adhesion to host tissues represents a crucial early step in the colonization process of either pathogens or commensal bacteria. We demonstrated the involvement of the L. plantarum Eno A1 alfa-enolase in Fn-binding, by studying LM3 and LM3-CC1 surface

  4. Optimized preparation of zinc-inorganic antibacterial material containing samariumusing response surface methodology

    Institute of Scientific and Technical Information of China (English)

    毛翠萍; 张彬; 唐晓宁; 李欢; 何素琼

    2014-01-01

    A Box-Behnken design (BBD) of response surface methodology (RSM) was used to optimize the preparation of the Zn-Sm antibacterial white carbon black by the sol-gel method. The statistical analysis of the results showed that the particle size of the Zn-Sm antibacterial white carbon black was significantly affected by the reaction time, reaction temperature and the stirring speed. According to analysis of variance (ANOVA), the values of the determination coefficient (R2=0.9821) and the "Pred R-Squared" of 0.8227 were in reasonable agreement with the "Adj R-Squared" of 0.9591. It was indicated that this model could be used to navigate the design space. The optimized reaction time, temperature and the stirring speed were 0.88 h, 87.83 ºC, and 473.45 r/min, respec-tively. In addition, the bacteriostasis rate of the product was about 97.92%.

  5. Measuring binding kinetics of aromatic thiolated molecules with nanoparticles via surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Devetter, Brent M.; Mukherjee, Prabuddha; Murphy, Catherine J.; Bhargava, Rohit

    2015-05-01

    Colloidal plasmonic nanomaterials, consisting of metals such as gold and silver, are excellent candidates for advanced optical probes and devices, but precise control over surface chemistry is essential for realizing their full potential. Coupling thiolated (R-SH) molecules to nanoprobe surfaces is a convenient and established route to tailor surface properties. The ability to dynamically probe and monitor the surface chemistry of nanoparticles in solution is essential for rapidly manufacturing spectroscopically tunable nanoparticles. In this study, we report the development of surface-enhanced Raman spectroscopy (SERS) as a method to monitor the kinetics of gold-thiolate bond formation on colloidal gold nanoparticles. A theoretical model combining SERS enhancement with the Beer-Lambert law is proposed to explain ensemble scattering and absorption effects in colloids during chemisorption. In order to maximize biological relevance and signal reproducibility, experiments used to validate the model focused on maintaining nanoparticle stability after the addition of water-soluble aromatic thiolated molecules. Our results indicate that ligand exchange on gold nanoparticles follow a first-order Langmuir adsorption model with rate constants on the order of 0.01 min-1. This study demonstrates an experimental spectroscopic method and theoretical model for monitoring binding kinetics that may prove useful for designing novel probes.Colloidal plasmonic nanomaterials, consisting of metals such as gold and silver, are excellent candidates for advanced optical probes and devices, but precise control over surface chemistry is essential for realizing their full potential. Coupling thiolated (R-SH) molecules to nanoprobe surfaces is a convenient and established route to tailor surface properties. The ability to dynamically probe and monitor the surface chemistry of nanoparticles in solution is essential for rapidly manufacturing spectroscopically tunable nanoparticles. In this

  6. Selective Binding, Self-Assembly and Nanopatterning of the Creutz-Taube Ion on Surfaces

    Directory of Open Access Journals (Sweden)

    Qingling Hang

    2009-02-01

    Full Text Available The surface attachment properties of the Creutz-Taube ion, i.e., [(NH35Ru(pyrazineRu(NH35]5+, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS. The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO2 and –OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as –CH3 terminated organic SAMs and poly(methylmethacrylate (PMMA thin films covered gold or SiO2 substrates was observed. Further ellipsometric, atomic force microscopy (AFM and time-dependent XPS studies suggested that the attached cations could form an inorganic analog of the self-assembled monolayer on SiO2 substrate with a “lying-down” orientation. The strong electrostatic interaction between the highly charged cations and the anionic SiO2 surface was believed to account for these observations. Based on its selective binding property, patterning of wide (~200 nm and narrow (~35 nm lines of the Creutz-Taube ions on SiO2 surface were demonstrated through PMMA electron resist masks written by electron beam lithography (EBL.

  7. Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates

    Directory of Open Access Journals (Sweden)

    Mariya Tarazanova

    2017-09-01

    Full Text Available Surface properties of bacteria are determined by the molecular composition of the cell wall and they are important for interactions of cells with their environment. Well-known examples of bacterial interactions with surfaces are biofilm formation and the fermentation of solid materials like food and feed. Lactococcus lactis is broadly used for the fermentation of cheese and buttermilk and it is primarily isolated from either plant material or the dairy environment. In this study, we characterized surface hydrophobicity, charge, emulsification properties, and the attachment to milk proteins of 55 L. lactis strains in stationary and exponential growth phases. The attachment to milk protein was assessed through a newly developed flow cytometry-based protocol. Besides finding a high degree of biodiversity, phenotype-genotype matching allowed the identification of candidate genes involved in the modification of the cell surface. Overexpression and gene deletion analysis allowed to verify the predictions for three identified proteins that altered surface hydrophobicity and attachment of milk proteins. The data also showed that lactococci isolated from a dairy environment bind higher amounts of milk proteins when compared to plant isolates. It remains to be determined whether the alteration of surface properties also has potential to alter starter culture functionalities.

  8. Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates.

    Science.gov (United States)

    Tarazanova, Mariya; Huppertz, Thom; Beerthuyzen, Marke; van Schalkwijk, Saskia; Janssen, Patrick; Wels, Michiel; Kok, Jan; Bachmann, Herwig

    2017-01-01

    Surface properties of bacteria are determined by the molecular composition of the cell wall and they are important for interactions of cells with their environment. Well-known examples of bacterial interactions with surfaces are biofilm formation and the fermentation of solid materials like food and feed. Lactococcus lactis is broadly used for the fermentation of cheese and buttermilk and it is primarily isolated from either plant material or the dairy environment. In this study, we characterized surface hydrophobicity, charge, emulsification properties, and the attachment to milk proteins of 55 L. lactis strains in stationary and exponential growth phases. The attachment to milk protein was assessed through a newly developed flow cytometry-based protocol. Besides finding a high degree of biodiversity, phenotype-genotype matching allowed the identification of candidate genes involved in the modification of the cell surface. Overexpression and gene deletion analysis allowed to verify the predictions for three identified proteins that altered surface hydrophobicity and attachment of milk proteins. The data also showed that lactococci isolated from a dairy environment bind higher amounts of milk proteins when compared to plant isolates. It remains to be determined whether the alteration of surface properties also has potential to alter starter culture functionalities.

  9. Detection of Biomolecular Binding Through Enhancement of Localized Surface Plasmon Resonance (LSPR by Gold Nanoparticles

    Directory of Open Access Journals (Sweden)

    Min-Gon Kim

    2009-03-01

    Full Text Available To amplify the difference in localized surface plasmon resonance (LSPR spectra of gold nano-islands due to intermolecular binding events, gold nanoparticles were used. LSPR-based optical biosensors consisting of gold nano-islands were readily made on glass substrates using evaporation and heat treatment. Streptavidin (STA and biotinylated bovine serum albumin (Bio-BSA were chosen as the model receptor and the model analyte, respectively, to demonstrate the effectiveness of this detection method. Using this model system, we were able to enhance the sensitivity in monitoring the binding of Bio-BSA to gold nano-island surfaces functionalized with STA through the addition of gold nanoparticle-STA conjugates. In addition, SU-8 well chips with gold nano-island surfaces were fabricated through a conventional UV patterning method and were then utilized for image detection using the attenuated total reflection mode. These results suggest that the gold nano-island well chip may have the potential to be used for multiple and simultaneous detection of various bio-substances.

  10. Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide.

    Science.gov (United States)

    Wright, Louise B; Walsh, Tiffany R

    2013-04-07

    Harnessing the properties of biomolecules, such as peptides, adsorbed on inorganic surfaces is of interest to many cross-disciplinary areas of science, ranging from biomineralisation to nanomedicine. Key to advancing research in this area is determination of the peptide conformation(s) in its adsorbed state, at the aqueous interface. Molecular simulation is one such approach for accomplishing this goal. In this respect, use of temperature-based replica-exchange molecular dynamics (T-REMD) can yield enhanced sampling of the interfacial conformations, but does so at great computational expense, chiefly because of the need to include an explicit representation of water at the interface. Here, we investigate a number of more economical variations on REMD, chiefly those based on Replica Exchange with Solvent Tempering (REST), using the aqueous quartz-binding peptide S1-(100) α-quartz interfacial system as a benchmark. We also incorporate additional implementation details specifically targeted at improving sampling of biomolecules at interfaces. We find the REST-based variants yield configurational sampling of the peptide-surface system comparable with T-REMD, at a fraction of the computational time and resource. Our findings also deliver novel insights into the binding behaviour of the S1 peptide at the quartz (100) surface that are consistent with available experimental data.

  11. Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77

    DEFF Research Database (Denmark)

    Cockburn, Darrell; Wilkens, Casper; Ruzanski, Christian

    2014-01-01

    Surface binding sites (SBSs) interact with carbohydrates outside of the enzyme active site. They are frequently situated on catalytic domains and are distinct from carbohydrate binding modules (CBMs). SBSs are found in a variety of enzymes and often seen in crystal structures. Notably about half ...

  12. Specific binding of avidin to biotin containing lipid lamella surfaces studied with monolayers and liposomes.

    Science.gov (United States)

    Liu, Z; Qin, H; Xiao, C; Wen, C; Wang, S; Sui, S F

    1995-01-01

    The interaction of avidin (from egg white) with phospholipid (monolayer and bilayer) model membranes containing biotin-conjugated phospholipids has been studied. In the first part, using surface sensitive techniques (ellipsometry and surface plasmon resonance) we demonstrated that the nonspecific adsorption of avidin to phospholipid lamella could be abolished by adding an amount of Ca2+, Mg2+ or Ba2+ that led to an electrostatic interaction. The specific binding of avidin to lipid mixtures containing biotin-conjugated phospholipids was obviously composition dependent. The ratio 1:12 of a B-DPPE/DPPE mixture was found to be the optimum molar ratio. When we compared the results from the surface sensitive techniques with those from the electron micrographs of a two dimensional crystal of avidin (obtained in our laboratory), the optimum ratio was found to be determined by the effect of lateral steric hindrance. In the second part, we observed the pattern of the layers of fluorescently labeled phospholipid and adsorbed proteins with a home-made micro fluorescence film balance. The fluorescence images showed that avidin was preferentially bound to the receptors that were in the fluid domains. Further, with a sensitive fluorescence assay method, the effect of the phase behavior of liposomes on the specific binding of avidin was measured. This showed that avidin interacted with biotinlipid more weakly in the gel state liposome than in the liquid state liposome. The major conclusion was that the binding of avidin to a membrane bound model receptor was significantly restricted by two factors: one was the lateral steric hindrance and the other was the fluidity of the model membrane.

  13. Weakly Hydrated Surfaces and the Binding Interactions of Small Biological Solutes

    Energy Technology Data Exchange (ETDEWEB)

    Brady, J. W.; Tavagnacco, L.; Ehrlich, L.; Chen, M.; Schnupf, U.; Himmel, M. E.; Saboungi, M. L.; Cesaro, A.

    2012-04-01

    Extended planar hydrophobic surfaces, such as are found in the side chains of the amino acids histidine, phenylalanine, tyrosine, and tryptophan, exhibit an affinity for the weakly hydrated faces of glucopyranose. In addition, molecular species such as these, including indole, caffeine, and imidazole, exhibit a weak tendency to pair together by hydrophobic stacking in aqueous solution. These interactions can be partially understood in terms of recent models for the hydration of extended hydrophobic faces and should provide insight into the architecture of sugar-binding sites in proteins.

  14. Vibrations of small cobalt clusters on low-index surfaces of copper: Tight-binding simulations

    Science.gov (United States)

    Borisova, S. D.; Eremeev, S. V.; Rusina, G. G.; Stepanyuk, V. S.; Bruno, P.; Chulkov, E. V.

    2008-08-01

    Vibrational properties (frequencies, polarizations, and lifetimes) of a single adatom, dimer, and trimer of Co on low-index Cu surfaces, Cu(111), Cu(001), and Cu(110) are studied by using tight-binding second moment approximation interatomic interaction potentials. We show that structural and vibrational properties of the Co clusters strongly depend on the substrate orientation. The longest lifetimes of 1-2.5 ps have been found for high-frequency z -polarized vibrations in all the Co clusters considered. The shortest lifetimes of 0.1-0.8 ps have been obtained for low-frequency horizontal (frustrated translation) vibrational modes.

  15. Binding of dengue virus particles and dengue proteins onto solid surfaces.

    Science.gov (United States)

    Pereira, Edla M A; Dario, Aline F; França, Rafael F O; Fonseca, Benedito A L; Petri, Denise F S

    2010-09-01

    The interaction between dengue virus particles (DENV), sedimentation hemagglutinin particles (SHA), dengue virus envelope protein (Eprot), and solid surfaces was investigated by means of ellipsometry and atomic force microscopy (AFM). The surfaces chosen are bare Si/SiO2 wafers and Si/SiO2 wafers covered with concanavalin A (ConA), jacalin (Jac), polystyrene (PS), or poly(styrene sulfonate) (PSS) films. Adsorption experiments at pH 7.2 and pH 3 onto all surfaces revealed that (i) adsorption of DENV particles took place only onto ConA under pH 7.2, because of specific recognition between glycans on DENV surface and ConA binding site; (ii) DENV particles did not attach to any of the surfaces at pH 3, suggesting the presence of positive charges on DENV surface at this pH, which repel the positively charged lectin surfaces; (iii) SHA particles are positively charged at pH 7.2 and pH 3 because they adhered to negatively charged surfaces at pH 7.2 and repelled positively charged layers at pH 3; and (iv) SHA particles carry polar groups on the surface because they attached to silanol surfaces at pH 3 and avoided hydrophobic PS films at pH 3 and pH 7.2. The adsorption behavior of Eprot at pH 7.2 revealed affinity for ConA>Jac>PSS>PS≈bare Si/SiO2 layers. These findings indicate that selectivity of the Eprot adsorption is higher when it is part of virus structure than when it is free in solution. The correlation between surface energy values determined by means of contact angle measurements and DENV, SHA, or Eprot adsorption behavior was used to understand the intermolecular forces at the interfaces. A direct correlation was not found because the contributions from surface energy were probably surpassed by specific contributions.

  16. Decorin core protein (decoron shape complements collagen fibril surface structure and mediates its binding.

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    Joseph P R O Orgel

    Full Text Available Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM. With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein and binding sites in the d and e(1 bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e(1 bands. This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.

  17. Cargo binding promotes KDEL receptor clustering at the mammalian cell surface.

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    Becker, Björn; Shaebani, M Reza; Rammo, Domenik; Bubel, Tobias; Santen, Ludger; Schmitt, Manfred J

    2016-06-29

    Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand (eGFP-RTA(H/KDEL)), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface.

  18. Exhaustive comparison and classification of ligand-binding surfaces in proteins

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    Murakami, Yoichi; Kinoshita, Kengo; Kinjo, Akira R; Nakamura, Haruki

    2013-01-01

    Many proteins function by interacting with other small molecules (ligands). Identification of ligand-binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand-binding protein sequences and functions. Consequently, we classified the patches into ∼2000 well-characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross-fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes. PMID:23934772

  19. Targeting of cytosolic mRNA to mitochondria: naked RNA can bind to the mitochondrial surface.

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    Michaud, Morgane; Maréchal-Drouard, Laurence; Duchêne, Anne-Marie

    2014-05-01

    Mitochondria contain hundreds of proteins but only a few are encoded by the mitochondrial genome. The other proteins are nuclear-encoded and imported into mitochondria. These proteins can be translated on free cytosolic polysomes, then targeted and imported into mitochondria. Nonetheless, numerous cytosolic mRNAs encoding mitochondrial proteins are detected at the surface of mitochondria in yeast, plants and animals. The localization of mRNAs to the vicinity of mitochondria would be a way for mitochondrial protein sorting. The mechanisms responsible for mRNA targeting to mitochondria are not clearly identified. Sequences within the mRNA molecules (cis-elements), as well as a few trans-acting factors, have been shown to be essential for targeting of some mRNAs. In order to identify receptors involved in mRNA docking to the mitochondrial surface, we have developed an in vitro mRNA binding assay with isolated plant mitochondria. We show that naked mRNAs are able to bind to isolated mitochondria, and our results strongly suggest that mRNA docking to the plant mitochondrial outer membrane requires at least one component of TOM complex.

  20. Brownian nanoimaging of interface dynamics and ligand-receptor binding at cell surfaces in 3-D.

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    Kuznetsov, Igor R; Evans, Evan A

    2013-04-01

    We describe a method for nanoimaging interfacial dynamics and ligand-receptor binding at surfaces of live cells in 3-D. The imaging probe is a 1-μm diameter glass bead confined by a soft laser trap to create a "cloud" of fluctuating states. Using a facile on-line method of video image analysis, the probe displacements are reported at ~10 ms intervals with bare precisions (±SD) of 4-6 nm along the optical axis (elevation) and 2 nm in the transverse directions. We demonstrate how the Brownian distributions are analyzed to characterize the free energy potential of each small probe in 3-D taking into account the blur effect of its motions during CCD image capture. Then, using the approach to image interactions of a labeled probe with lamellae of leukocytic cells spreading on cover-glass substrates, we show that deformations of the soft distribution in probe elevations provide both a sensitive long-range sensor for defining the steric topography of a cell lamella and a fast telemetry for reporting rare events of probe binding with its surface receptors. Invoking established principles of Brownian physics and statistical thermodynamics, we describe an off-line method of super resolution that improves precision of probe separations from a non-reactive steric boundary to ~1 nm.

  1. Antibody binding site mapping of SARS-CoV spike protein receptor-binding domain by a combination of yeast surface display and phage peptide library screening.

    Science.gov (United States)

    Zhang, Xiaoping; Wang, Jingxue; Wen, Kun; Mou, Zhirong; Zou, Liyun; Che, Xiaoyan; Ni, Bing; Wu, Yuzhang

    2009-12-01

    The receptor-binding domain (RBD) of severe acute respiratory syndrome coronavirus (SARS-CoV) spike (S) protein plays an important role in viral infection, and is a potential major neutralizing determinant. In this study, three hybridoma cell lines secreting specific monoclonal antibodies against the RBD of the S protein were generated and their exact binding sites were identified. Using yeast surface display, the binding sites of these antibodies were defined to two linear regions on the RBD: S(337-360) and S(380-399). Using these monoclonal antibodies in phage peptide library screening identified 10 distinct mimotopes 12 amino acids in length. Sequence comparison between native epitopes and these mimotopes further confirmed the binding sites, and revealed key amino acid residues involved in antibody binding. None of these antibodies could neutralize the murine leukemia virus pseudotyped expressing the SARS-CoV spike protein (MLV/SARS-CoV). However, these mAbs could be useful in the diagnosis of SARS-CoV due to their exclusive reactivity with SARS-CoV. Furthermore, this study established a feasible platform for epitope mapping. Yeast surface display combined with phage peptide library screening provides a convenient strategy for the identification of epitope peptides from certain antigenic proteins.

  2. Prostate cancer stem cell-targeted efficacy of a new-generation taxoid, SBT-1214 and novel polyenolic zinc-binding curcuminoid, CMC2.24.

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    Galina I Botchkina

    Full Text Available BACKGROUND: Prostate cancer is the second leading cause of cancer death among men. Multiple evidence suggests that a population of tumor-initiating, or cancer stem cells (CSCs is responsible for cancer development and exceptional drug resistance, representing a highly important therapeutic target. The present study evaluated CSC-specific alterations induced by new-generation taxoid SBT-1214 and a novel polyenolic zinc-binding curcuminoid, CMC2.24, in prostate CSCs. PRINCIPAL FINDINGS: The CD133(high/CD44(high phenotype was isolated from spontaneously immortalized patient-derived PPT2 cells and highly metastatic PC3MM2 cells. Weekly treatment of the NOD/SCID mice bearing PPT2- and PC3MM3-induced tumors with the SBT-1214 led to dramatic suppression of tumor growth. Four of six PPT2 and 3 of 6 PC3MM2 tumors have shown the absence of viable cells in residual tumors. In vitro, SBT-1214 (100 nM-1 µM; for 72 hr induced about 60% cell death in CD133(high/CD44(+/high cells cultured on collagen I in stem cell medium (in contrast, the same doses of paclitaxel increased proliferation of these cells. The cytotoxic effects were increased when SBT-1214 was combined with the CMC2.24. A stem cell-specific PCR array assay revealed that this drug combination mediated massive inhibition of multiple constitutively up-regulated stem cell-related genes, including key pluripotency transcription factors. Importantly, this drug combination induced expression of p21 and p53, which were absent in CD133(high/CD44(high cells. Viable cells that survived this treatment regimen were no longer able to induce secondary spheroids, exhibited significant morphological abnormalities and died in 2-5 days. CONCLUSIONS: We report here that the SBT-1214 alone, or in combination with CMC2.24, possesses significant activity against prostate CD133(high/CD44(+/high tumor-initiating cells. This drug combination efficiently inhibits expression of the majority of stem cell-related genes and

  3. MiRNA-205 modulates cellular invasion and migration via regulating zinc finger E-box binding homeobox 2 expression in esophageal squamous cell carcinoma cells

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    Yamashita Shunichi

    2011-03-01

    Full Text Available Abstract Background Esophageal squamous cell carcinoma (ESCC is often diagnosed at later stages until they are incurable. MicroRNA (miR is a small, non-coding RNA that negatively regulates gene expression mainly via translational repression. Accumulating evidence indicates that deregulation of miR is associated with human malignancies including ESCC. The aim of this study was to identify miR that could be specifically expressed and exert distinct biological actions in ESCC. Methods Total RNA was extracted from ESCC cell lines, OE21 and TE10, and a non-malignant human esophageal squamous cell line, Het-1A, and subjected to microarray analysis. Expression levels of miR that showed significant differences between the 2 ESCC and Het-1A cells based on the comprehensive analysis were analyzed by the quantitative reverse transcriptase (RT-PCR method. Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. Using ESCC tumor samples and paired surrounding non-cancerous tissue obtained endoscopically, the association with histopathological differentiation was examined with quantitative RT-PCR. Results Based on the miR microarray analysis, there were 14 miRs that showed significant differences (more than 2-fold in expression between the 2 ESCC cells and non-malignant Het-1A. Among the significantly altered miRs, miR-205 expression levels were exclusively higher in 5 ESCC cell lines examined than any other types of malignant cell lines and Het-1A. Thus, miR-205 could be a specific miR in ESCC. Modulation of miR-205 expression by transfection with its precursor or anti-miR-205 inhibitor did not affect ESCC cell proliferation and apoptosis, but miR-205 was found to be involved in cell invasion and migration. Western blot revealed that knockdown of miR-205 expression in ESCC cells substantially enhanced expression of zinc finger E-box binding homeobox 2

  4. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d

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    Moffatt Barbara A

    2010-08-01

    Full Text Available Abstract Background Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB for coplanar aromatic motifs similar to those found in known glycan-binding proteins. Results The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192 in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Conclusions Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

  5. Cadmium down-regulation of kidney Sp1 binding to mouse SGLT1 and SGLT2 gene promoters: possible reaction of cadmium with the zinc finger domain of Sp1.

    Science.gov (United States)

    Kothinti, Rajendra K; Blodgett, Amy B; Petering, David H; Tabatabai, Niloofar M

    2010-05-01

    Cadmium (Cd) exposure causes glucosuria (glucose in the urine). Previously, it was shown that Cd exposure of primary cultures of mouse kidney cells (PMKC) decreased mRNA levels of the glucose transporters, SGLT1 and SGLT2 and that Sp1 from Cd-exposed cells displayed reduced binding to the GC boxes of the mouse SGLT1 promoter in vitro. Here, we identified a GC box upstream of mouse SGLT2 gene. ChIP assays on PMKC revealed that exposure to 5 microM Cd abolished Sp1 binding to SGLT1 GC box while it decreased Sp1 binding to SGLT2 GC sequence by 30% in vivo. The in vitro DNA binding assay, EMSA, demonstrated that binding of Sp1 from Cd (7.5 microM)-treated PMKC to the SGLT2 GC probe was 86% lower than in untreated cells. Sp1 is a zinc finger protein. Compared to PMKC exposed to 5 microM Cd alone, inclusion of 5 microM Zn restored SGLT1 and 2 mRNA levels by 15% and 30%, respectively. Cd (10 microM) decreased the binding of recombinant Sp1 (rhSp1) to SGLT1 and SGLT2 GC probes to 12% and 8% of untreated controls. Cd exerted no effect on GC-bound rhSp1. Co-treatment with Cd and Zn showed that added Zn significantly restored rhSp1 binding to the SGLT1 and SGLT2. Addition of Zn post Cd treatment was not stimulatory. We conclude that Cd can replace Zn in Sp1 DNA binding domain to reduce its binding to GC sites in mouse SGLT1 and SGLT2 promoters. Copyright 2010 Elsevier Inc. All rights reserved.

  6. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area.

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    Chen, Jieming; Sawyer, Nicholas; Regan, Lynne

    2013-04-01

    Protein-protein interactions play key roles in many cellular processes and their affinities and specificities are finely tuned to the functions they perform. Here, we present a study on the relationship between binding affinity and the size and chemical nature of protein-protein interfaces. Our analysis focuses on heterodimers and includes curated structural and thermodynamic data for 113 complexes. We observe a direct correlation between binding affinity and the amount of surface area buried at the interface. For a given amount of surface area buried, the binding affinity spans four orders of magnitude in terms of the dissociation constant (Kd ). Across the entire dataset, we observe no obvious relationship between binding affinity and the chemical composition of the interface. We also calculate the free energy per unit surface area buried, or "surface energy density," of each heterodimer. For interfacial surface areas between 500 and 2000 Å(2) , the surface energy density decreases as the buried surface area increases. As the buried surface area increases beyond about 2000 Å(2) , the surface energy density levels off to a constant value. We believe that these analyses and data will be useful for researchers with an interest in understanding, designing or inhibiting protein-protein interfaces.

  7. The Porphyromonas gingivalis HmuY haemophore binds gallium(iii), zinc(ii), cobalt(iii), manganese(iii), nickel(ii), and copper(ii) protoporphyrin IX but in a manner different to iron(iii) protoporphyrin IX.

    Science.gov (United States)

    Wójtowicz, Halina; Bielecki, Marcin; Wojaczyński, Jacek; Olczak, Mariusz; Smalley, John W; Olczak, Teresa

    2013-04-01

    Porphyromonas gingivalis, a major etiological agent of chronic periodontitis, acquires haem from host haemoproteins through a haem transporter HmuR and a haemophore HmuY. The aim of this study was to analyse the binding specificity of HmuY towards non-iron metalloporphyrins which may be employed as antimicrobials to treat periodontitis. HmuY binds gallium(iii), zinc(ii), cobalt(iii), manganese(iii), nickel(ii), and copper(ii) protoporphyrin IX but in a manner different to iron(iii) protoporphyrin IX which uses His(134) and His(166) as axial ligands. The metal ions in Ga(iii)PPIX and Zn(ii)PPIX can accept only His(166) as an axial ligand, whereas nickel(ii) and copper(ii) interact exclusively with His(134). Two forms of pentacoordinate manganese(iii) are present in the Mn(iii)PPIX-HmuY complex since the metal accepts either His(134) or His(166) as a single axial ligand. The cobalt ion is hexacoordinate in the Co(iii)PPIX-HmuY complex and binds His(134) and His(166) as axial ligands; however, some differences in their environments exist. Despite different coordination modes of the central metal ion, gallium(iii), zinc(ii), cobalt(iii), and manganese(iii) protoporphyrin IX bound to the HmuY haemophore cannot be displaced by excess haem. All of the metalloporphyrins examined bind to a P. gingivalis wild-type strain with higher ability compared to a mutant strain lacking a functional hmuY gene, thus corroborating binding of non-iron metalloporphyrins to purified HmuY protein. Our results further clarify the basis of metalloporphyrin acquisition by P. gingivalis and add to understanding of the interactions with porphyrin derivatives which exhibit antimicrobial activity against P. gingivalis.

  8. Motility assays using myosin attached to surfaces through specific binding to monoclonal antibodies.

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    Winkelmann, D A; Bourdieu, L; Kinose, F; Libchaber, A

    1995-04-01

    We have analyzed the dependence of actin filament movement on the mode of myosin attachment to surfaces. Monoclonal antibodies that bind to three distinct sites were used to tether myosin to nitrocellulose-coated glass. One antibody reacts with an epitope on the regulatory light chain located at the head-rod junction. The other two react with sites in the rod domain, one in the S2 region near the S2-LMM hinge, and the other at the C terminus of the myosin rod. These monoclonal antibodies were used to provide increasing flexibility in the mode of attachment. Fast skeletal muscle myosin monomers were bound to the surfaces through the specific interaction with these monoclonal antibodies and the sliding movement of fluorescently labeled actin filaments analyzed by video microscopy. Each of these antibodies produced stable, myosin-coated surfaces that supported uniform movement of actin over the course of several hours. Attachment of myosin through the anti-S2 and anti-LMM monoclonal antibodies yielded a maximum velocity of 10 microns/s at 30 degrees C, whereas attachment through anti-LC2 produced a lower velocity of 4-5 microns/s. Each antibody showed a characteristic minimum myosin density below which sliding movement was no longer supported and an exponential dependence of actin filament velocity on myosin surface density below Vmax. Maximum sliding velocity was achieved over a range of myosin surface densities. Thus, the specific mode of attachment can influence the characteristic velocity of actin filament movement and the surface density needed to support movement. These data are being used to analyze the dynamics of sliding filament assays and evaluate estimates of the average number of motor molecules per unit length of actin required to support movement.

  9. Comparative study of binding constants from Love wave surface acoustic wave and surface plasmon resonance biosensors using kinetic analysis.

    Science.gov (United States)

    Lee, Sangdae; Kim, Yong-Il; Kim, Ki-Bok

    2013-11-01

    Biosensors are used in a variety of fields for early diagnosis of diseases, measurement of toxic contaminants, quick detection of pathogens, and separation of specific proteins or DNA. In this study, we fabricated and evaluated the capability of a high sensitivity Love wave surface acoustic wave (SAW) biosensor. The experimental setup was composed of the fabricated 155-MHz Love wave SAW biosensor, a signal measurement system, a liquid flow system, and a temperature-control system. Subsequently, we measured the lower limit of detection (LOD) of the 155-MHz Love wave SAW biosensor, and calculated the association and dissociation constants between protein G and anti-mouse IgG using kinetic analysis. We compared these results with those obtained using a commercial surface plasmon resonance (SPR) biosensor. We found that the LOD of the SAW biosensor for anti-mouse IgG and mouse IgG was 0.5 and 1 microg/ml, respectively, and the resultant equilibrium association and dissociation constants were similar to the corresponding values obtaining using the commercial SPR biosensor. Thus, we conclude that the fabricated 155-MHz Love wave SAW biosensor exhibited the high sensitivity of the commercial SPR biosensor and was able to analyze the binding properties of the ligand and receptor by kinetic analysis similarly to the commercial SPR biosensor.

  10. Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

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    Ashford Paul

    2012-03-01

    Full Text Available Abstract Background Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins' dynamic behaviour. In particular, ligand-binding conformations can be observed as transiently populated states of the apo protein, so it is possible to gain insight into ligand-bound forms by considering conformational variation in apo proteins. This variation can be explored by considering sets of related structures: computationally generated conformers, solution NMR ensembles, multiple crystal structures, homologues or homology models. It is non-trivial to compare pockets, either from different programs or across sets of structures. For a single structure, difficulties arise in defining particular pocket's boundaries. For a set of conformationally distinct structures the challenge is how to make reasonable comparisons between them given that a perfect structural alignment is not possible. Results We have developed a computational method, Provar, that provides a consistent representation of predicted binding pockets across sets of related protein structures. The outputs are probabilities that each atom or residue of the protein borders a predicted pocket. These probabilities can be readily visualised on a protein using existing molecular graphics software. We show how Provar simplifies comparison of the outputs of different pocket prediction algorithms, of pockets across multiple simulated conformations and between homologous structures. We demonstrate the benefits of use of multiple structures for protein-ligand and protein-protein interface analysis on a set of complexes and consider three case studies in detail: i analysis of a kinase superfamily highlights the

  11. Design and development of in situ albumin binding surfaces: Evaluation in the paradigm of blood-biomaterial compatibility

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    Guha Thakurta, Sanjukta

    Biocompatibility of natural and synthetic implant materials as blood contacting devices is crucial to host response. Implantation often raises complications from thrombotic and thromboembolic events. The aspect of hemocompatibility concentrates on minimizing thrombotic and thromboembolic response of foreign materials in contact with blood. The initial layer of surface adsorbed proteins plays a pivotal role in the adhesion and subsequent aggregation of platelets and in the activation of the coagulation cascade. Therefore, an improved surface architecture is required to gain control over the initial protein adsorption events, thereby extending the sustainability of an implantable device. In general, surfaces with an ability to bind endogenous albumin has been known to minimize platelet adhesion and activation. While the scope of applicability is broad, in this study silicon-based surfaces were selected as model surfaces. A densely packed uniformly distributed silane monolayer was achieved on silicon based surfaces with -- NH2 functionality, upon a careful optimization of hydroxylation and the subsequent silanization with 2 vol% of 3-Aminopropyltriethoxy Silane (APTES). Two linear peptides with affinity for albumin over other serum proteins were selected to create affinity surfaces. Silanized surfaces covalently immobilized with albumin binding peptides were evaluated in the paradigm of blood-biomaterial compatibility. When compared to control surfaces, albumin binding surfaces prepared in this study: (a) possessed 2.0 to 3.0 mug/cm2 of surface bound albumin with minimal surface adsorbed fibrinogen, (b) depicted low levels of adhered platelets and supported a rounded platelet morphology, (c) displayed delayed clotting, (d) showed reduced platelet adhesion and activation under shearing, and (f) exhibited faster adsorption kinetics. Conclusively, in-situ albumin binding surfaces selectively and specifically interacted with albumin without being severely displaced by

  12. Characterization of the Trichomonas vaginalis surface-associated AP65 and binding domain interacting with trichomonads and host cells.

    Science.gov (United States)

    Garcia, Ana F; Alderete, Jf

    2007-12-25

    AP65 is a prominent adhesin of Trichomonas vaginalis that mediates binding of parasites to host vaginal epithelial cells (VECs). AP65 with no secretion signal sequence, membrane targeting peptide, and anchoring motif was recently found to be secreted. We first wanted to demonstrate surface association of AP65 to the parasite followed by the identification of the binding epitope interacting with both organisms and VECs. AP65 was found to bind to trichomonads, but not to trypsin-treated parasites, in an auto-ligand assay, suggesting the existence of a surface protein associating with AP65. Since rabbit antiserum IgG antibodies reactive with epitopes localized to the N-terminal region of AP65 inhibit the attachment of live parasites to VECs, we hypothesized that the binding domain was localized to this region. We subcloned five overlapping fragments of AP65 called c1 through c5, and expression of recombinant clones was confirmed with antibodies to AP65. Each purified recombinant protein was then tested for binding activity using an established ligand assay, and fragment c1 with the first twenty-five amino acids in the N-terminal domain was required for binding to VECs and, surprisingly, also to parasites. Importantly, c1 competed with the binding of AP65 to both cells types. T. vaginalis AP65 is a secreted, surface-associated protein and a model is proposed to explain how this secreted protein functions as an adhesin.

  13. Characterization of the Trichomonas vaginalis surface-associated AP65 and binding domain interacting with trichomonads and host cells

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    Alderete JF

    2007-12-01

    Full Text Available Abstract Background AP65 is a prominent adhesin of Trichomonas vaginalis that mediates binding of parasites to host vaginal epithelial cells (VECs. AP65 with no secretion signal sequence, membrane targeting peptide, and anchoring motif was recently found to be secreted. Results We first wanted to demonstrate surface association of AP65 to the parasite followed by the identification of the binding epitope interacting with both organisms and VECs. AP65 was found to bind to trichomonads, but not to trypsin-treated parasites, in an auto-ligand assay, suggesting the existence of a surface protein associating with AP65. Since rabbit antiserum IgG antibodies reactive with epitopes localized to the N-terminal region of AP65 inhibit the attachment of live parasites to VECs, we hypothesized that the binding domain was localized to this region. We subcloned five overlapping fragments of AP65 called c1 through c5, and expression of recombinant clones was confirmed with antibodies to AP65. Each purified recombinant protein was then tested for binding activity using an established ligand assay, and fragment c1 with the first twenty-five amino acids in the N-terminal domain was required for binding to VECs and, surprisingly, also to parasites. Importantly, c1 competed with the binding of AP65 to both cells types. Conclusion T. vaginalis AP65 is a secreted, surface-associated protein and a model is proposed to explain how this secreted protein functions as an adhesin.

  14. Chloroquine is a zinc ionophore.

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    Jing Xue

    Full Text Available Chloroquine is an established antimalarial agent that has been recently tested in clinical trials for its anticancer activity. The favorable effect of chloroquine appears to be due to its ability to sensitize cancerous cells to chemotherapy, radiation therapy, and induce apoptosis. The present study investigated the interaction of zinc ions with chloroquine in a human ovarian cancer cell line (A2780. Chloroquine enhanced zinc uptake by A2780 cells in a concentration-dependent manner, as assayed using a fluorescent zinc probe. This enhancement was attenuated by TPEN, a high affinity metal-binding compound, indicating the specificity of the zinc uptake. Furthermore, addition of copper or iron ions had no effect on chloroquine-induced zinc uptake. Fluorescent microscopic examination of intracellular zinc distribution demonstrated that free zinc ions are more concentrated in the lysosomes after addition of chloroquine, which is consistent with previous reports showing that chloroquine inhibits lysosome function. The combination of chloroquine with zinc enhanced chloroquine's cytotoxicity and induced apoptosis in A2780 cells. Thus chloroquine is a zinc ionophore, a property that may contribute to chloroquine's anticancer activity.

  15. Binding characteristics of thrombin-activatable fibrinolysis inhibitor to streptococcal surface collagen-like proteins A and B

    NARCIS (Netherlands)

    Seron, Mercedes Valls; Plug, Tom; Marquart, J. Arnoud; Marx, Pauline F.; Herwald, Heiko; de Groot, Philip G.; Meijers, Joost C. M.

    2011-01-01

    Streptococcus pyogenes is the causative agent in a wide range of diseases in humans. Thrombin-activatable fibrinolysis inhibitor (TAFI) binds to collagen-like proteins ScIA and ScIB at the surface of S. pyogenes. Activation of TAFI at this surface redirects inflammation from a transient to chronic s

  16. ZIP8 is an iron and zinc transporter whose cell-surface expression is up-regulated by cellular iron loading.

    Science.gov (United States)

    Wang, Chia-Yu; Jenkitkasemwong, Supak; Duarte, Stephanie; Sparkman, Brian K; Shawki, Ali; Mackenzie, Bryan; Knutson, Mitchell D

    2012-10-05

    ZIP8 (SLC39A8) belongs to the ZIP family of metal-ion transporters. Among the ZIP proteins, ZIP8 is most closely related to ZIP14, which can transport iron, zinc, manganese, and cadmium. Here we investigated the iron transport ability of ZIP8, its subcellular localization, pH dependence, and regulation by iron. Transfection of HEK 293T cells with ZIP8 cDNA enhanced the uptake of (59)Fe and (65)Zn by 200 and 40%, respectively, compared with controls. Excess iron inhibited the uptake of zinc and vice versa. In RNA-injected Xenopus oocytes, ZIP8-mediated (55)Fe(2+) transport was saturable (K(0.5) of ∼0.7 μm) and inhibited by zinc. ZIP8 also mediated the uptake of (109)Cd(2+), (57)Co(2+), (65)Zn(2+) > (54)Mn(2+), but not (64)Cu (I or II). By using immunofluorescence analysis, we found that ZIP8 expressed in HEK 293T cells localized to the plasma membrane and partially in early endosomes. Iron loading increased total and cell-surface levels of ZIP8 in H4IIE rat hepatoma cells. We also determined by using site-directed mutagenesis that asparagine residues 40, 88, and 96 of rat ZIP8 are glycosylated and that N-glycosylation is not required for iron or zinc transport. Analysis of 20 different human tissues revealed abundant ZIP8 expression in lung and placenta and showed that its expression profile differs markedly from ZIP14, suggesting nonredundant functions. Suppression of endogenous ZIP8 expression in BeWo cells, a placental cell line, reduced iron uptake by ∼40%, suggesting that ZIP8 participates in placental iron transport. Collectively, these data identify ZIP8 as an iron transport protein that may function in iron metabolism.

  17. Surface-associated plasminogen binding of Cryptococcus neoformans promotes extracellular matrix invasion.

    Directory of Open Access Journals (Sweden)

    Jamal Stie

    Full Text Available BACKGROUND: The fungal pathogen Cryptococcus neoformans is a leading cause of illness and death in persons with predisposing factors, including: malignancies, solid organ transplants, and corticosteroid use. C. neoformans is ubiquitous in the environment and enters into the lungs via inhalation, where it can disseminate through the bloodstream and penetrate the central nervous system (CNS, resulting in a difficult to treat and often-fatal infection of the brain, called meningoencephalitis. Plasminogen is a highly abundant protein found in the plasma component of blood and is necessary for the degradation of fibrin, collagen, and other structural components of tissues. This fibrinolytic system is utilized by cancer cells during metastasis and several pathogenic species of bacteria have been found to manipulate the host plasminogen system to facilitate invasion of tissues during infection by modifying the activation of this process through the binding of plasminogen at their surface. METHODOLOGY: The invasion of the brain and the central nervous system by penetration of the protective blood-brain barrier is a prerequisite to the establishment of meningoencephalitis by the opportunistic fungal pathogen C. neoformans. In this study, we examined the ability of C. neoformans to subvert the host plasminogen system to facilitate tissue barrier invasion. Through a combination of biochemical, cell biology, and proteomic approaches, we have shown that C. neoformans utilizes the host plasminogen system to cross tissue barriers, providing support for the hypothesis that plasminogen-binding may contribute to the invasion of the blood-brain barrier by penetration of the brain endothelial cells and underlying matrix. In addition, we have identified the cell wall-associated proteins that serve as plasminogen receptors and characterized both the plasminogen-binding and plasmin-activation potential for this significant human pathogen. CONCLUSIONS: The results of

  18. Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

    Energy Technology Data Exchange (ETDEWEB)

    Buhrman, Greg; O; #8242; Connor, Casey; Zerbe, Brandon; Kearney, Bradley M.; Napoleon, Raeanne; Kovrigina, Elizaveta A.; Vajda, Sandor; Kozakov, Dima; Kovrigin, Evgenii L.; Mattos, Carla (NCSU); (MCW); (BU)

    2012-09-17

    We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the 'off' and 'on' allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the active site. Comparison of FTMaps for the H and K isoforms reveals essentially identical hot spots. Furthermore, using NMR measurements of spin relaxation, we determined that K-Ras exhibits global conformational dynamics very similar to those we previously reported for H-Ras. We thus hypothesize that the global conformational rearrangement serves as a mechanism for allosteric coupling between the effector interface and remote hot spots in all Ras isoforms. At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well. Ras has so far been elusive as a target for drug design. The present work identifies various unexplored hot spots throughout the entire surface of Ras, extending the focus from the disordered active site to well-ordered locations that should be easier to target.

  19. Chelation gradients for investigation of metal ion binding at silica surfaces.

    Science.gov (United States)

    Kannan, Balamurali; Higgins, Daniel A; Collinson, Maryanne M

    2014-08-26

    Centimeter-long surface gradients in bi- and tridentate chelating agents have been formed via controlled rate infusion, and the coordination of Cu(2+) and Zn(2+) to these surfaces has been examined as a function of distance by X-ray photoelectron spectroscopy (XPS). 3-(Trimethoxysilylpropyl)ethylenediamine and 3-(trimethoxysilylpropyl)diethylenetriamine were used as precursor silanes to form the chelation gradients. When the gradients were exposed to a metal ion solution, a series of coordination complexes formed along the length of the substrate. For both chelating agents at the three different concentrations studied, the amine content gradually increased from top to bottom as expected for a surface chemical gradient. While the Cu 2p peak area had nearly the same profile as nitrogen, the Zn 2p peak area did not and exhibited a plateau along much of the gradient. The normalized nitrogen-to-metal peak area ratio (N/M) was found to be highly dependent on the type of ligand, its surface concentration, and the type of metal ion. For Cu(2+), the N/M ratio ranged from 8 to 11 on the diamine gradient and was ∼4 on the triamine gradient, while for Zn(2+), the N/M ratio was 4-8 on diamine and 5-7 on triamine gradients. The extent of protonation of amine groups was higher for the diamine gradients, which could lead to an increased N/M ratio. Both 1:1 and 1:2 ligand/metal complexes along with dinuclear complexes are proposed to form, with their relative amounts dependent on the ligand, ligand density, and metal ion. Collectively, the methods and results described herein represent a new approach to study metal ion binding and coordination on surfaces, which is especially important to the extraction, preconcentration, and separation of metal ions.

  20. Tailoring odorant-binding protein coatings characteristics for surface acoustic wave biosensor development

    Science.gov (United States)

    Di Pietrantonio, F.; Benetti, M.; Dinca, V.; Cannatà, D.; Verona, E.; D'Auria, S.; Dinescu, M.

    2014-05-01

    In this study, wild type bovine odorant-binding proteins (wtbOBPs) were deposited by matrix-assisted pulsed laser evaporation (MAPLE) and utilized as active material on surface acoustic wave (SAW) biosensors. Fourier transform infrared spectroscopy (FTIR), and atomic force microscopy (AFM) were used to determine the chemical, morphological characteristics of the protein thin films. The FTIR data demonstrates that the functional groups of wtbOBPs do not suffer significant changes in the MAPLE-deposited films when compared to the reference one. The topographical studies show that the homogeneity, density and the roughness of the coatings are related mainly to the laser parameters (fluence and number of pulses). SAW biosensor responses to different concentrations of R-(-)-1-octen-3-ol (octenol) and R-(-)-carvone (carvone) were evaluated. The obtained sensitivities, achieved through the optimization of deposition parameters, demonstrated that MAPLE is a promising deposition technique for SAW biosensor implementation.

  1. An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces

    Directory of Open Access Journals (Sweden)

    Ovidiu Ivanciuc

    2010-10-01

    Full Text Available Recent progress in the biochemical classification and structural determination of allergens and allergen–antibody complexes has enhanced our understanding of the molecular determinants of allergenicity. Databases of allergens and their epitopes have facilitated the clustering of allergens according to their sequences and, more recently, their structures. Groups of similar sequences are identified for allergenic proteins from diverse sources, and all allergens are classified into a limited number of protein structural families. A gallery of experimental structures selected from the protein classes with the largest number of allergens demonstrate the structural diversity of the allergen universe. Further comparison of these structures and identification of areas that are different from innocuous proteins within the same protein family can be used to identify features specific to known allergens. Experimental and computational results related to the determination of IgE binding surfaces and methods to define allergen-specific motifs are highlighted.

  2. Tailoring odorant-binding protein coatings characteristics for surface acoustic wave biosensor development

    Energy Technology Data Exchange (ETDEWEB)

    Di Pietrantonio, F., E-mail: fabio.dp@idasc.cnr.it [Institute of Acoustics and Sensors “O. M. Corbino”, National Research Council of Italy, Via del Fosso del Cavaliere 100, 00133 Rome (Italy); Benetti, M. [Institute of Acoustics and Sensors “O. M. Corbino”, National Research Council of Italy, Via del Fosso del Cavaliere 100, 00133 Rome (Italy); Dinca, V. [National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor Street, PO Box MG-16, 077125 Magurele (Romania); Cannatà, D. [Institute of Acoustics and Sensors “O. M. Corbino”, National Research Council of Italy, Via del Fosso del Cavaliere 100, 00133 Rome (Italy); Verona, E. [Institute for Photonics and Nanotechnologies, National Research Council of Italy, Via del Cineto Romano 42, 00156 Rome (Italy); D’Auria, S. [Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples (Italy); Dinescu, M. [National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor Street, PO Box MG-16, 077125 Magurele (Romania)

    2014-05-01

    In this study, wild type bovine odorant-binding proteins (wtbOBPs) were deposited by matrix-assisted pulsed laser evaporation (MAPLE) and utilized as active material on surface acoustic wave (SAW) biosensors. Fourier transform infrared spectroscopy (FTIR), and atomic force microscopy (AFM) were used to determine the chemical, morphological characteristics of the protein thin films. The FTIR data demonstrates that the functional groups of wtbOBPs do not suffer significant changes in the MAPLE-deposited films when compared to the reference one. The topographical studies show that the homogeneity, density and the roughness of the coatings are related mainly to the laser parameters (fluence and number of pulses). SAW biosensor responses to different concentrations of R-(–)-1-octen-3-ol (octenol) and R-(–)-carvone (carvone) were evaluated. The obtained sensitivities, achieved through the optimization of deposition parameters, demonstrated that MAPLE is a promising deposition technique for SAW biosensor implementation.

  3. Fractal binding and dissociation kinetics of lecithin cholesterol acyl transferase (LCAT), a heart-related compound, on biosensor surfaces

    Science.gov (United States)

    Doke, Atul M.; Sadana, Ajit

    2006-05-01

    A fractal analysis is presented for the binding and dissociation of different heart-related compounds in solution to receptors immobilized on biosensor surfaces. The data analyzed include LCAT (lecithin cholesterol acyl transferase) concentrations in solution to egg-white apoA-I rHDL immobilized on a biosensor chip surface.1 Single- and dual- fractal models were employed to fit the data. Values of the binding and the dissociation rate coefficient(s), affinity values, and the fractal dimensions were obtained from the regression analysis provided by Corel Quattro Pro 8.0 (Corel Corporation Limited).2 The binding rate coefficients are quite sensitive to the degree of heterogeneity on the sensor chip surface. Predictive equations are developed for the binding rate coefficient as a function of the degree of heterogeneity present on the sensor chip surface and on the LCAT concentration in solution, and for the affinity as a function of the ratio of fractal dimensions present in the binding and the dissociation phases. The analysis presented provided physical insights into these analyte-receptor reactions occurring on different biosensor surfaces.

  4. Depleted zinc: Properties, application, production.

    Science.gov (United States)

    Borisevich, V D; Pavlov, A V; Okhotina, I A

    2009-01-01

    The addition of ZnO, depleted in the Zn-64 isotope, to the water of boiling water nuclear reactors lessens the accumulation of Co-60 on the reactor interior surfaces, reduces radioactive wastes and increases the reactor service-life because of the inhibitory action of zinc on inter-granular stress corrosion cracking. To the same effect depleted zinc in the form of acetate dihydrate is used in pressurized water reactors. Gas centrifuge isotope separation method is applied for production of depleted zinc on the industrial scale. More than 20 years of depleted zinc application history demonstrates its benefits for reduction of NPP personnel radiation exposure and combating construction materials corrosion.

  5. [Role of zinc in type 2 diabetes].

    Science.gov (United States)

    Tamaki, Motoyuki; Fujitani, Yoshio

    2014-01-01

    Pancreatic β cells contain the highest amount of zinc among cells within the human body, and hence, the relationship between zinc and diabetes has been of great interest. To date, many studies of zinc and diabetes have been reported, including studies demonstrating that diabetic patients and mice have a decreased amount of zinc in the pancreas. Zinc may counteract the deleterious effects of oxidative stress, which contributes to reduced insulin resistance, and may also protect pancreatic β cells from glucolipotoxicity. Recently, we have shown that SLC30A8/zinc transporter 8, which is a transporter expressed on the surface of insulin granules, plays a key role in zinc transport into insulin granules and in the regulation of hepatic insulin clearance. Here, we review the role of zinc in whole-body maintenance and the latest information on the relationship between zinc and diabetes.

  6. Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates.

    Science.gov (United States)

    Xue, Liang; Xi, Hongjuan; Kumar, Sunil; Gray, David; Davis, Erik; Hamilton, Paris; Skriba, Michael; Arya, Dev P

    2010-07-06

    Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA).2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1-4) stabilized poly(dA).2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (T(m3-->2)) at which poly(dA).2poly(dT) dissociated into poly(dA).poly(dT) and poly(dT) increased dramatically (>12 degrees C) in the presence of intercalator-neomycin conjugates (1-4) even at a very low concentration (2 muM). In contrast to intercalator-neomycin conjugates, the increment of T(m3-->2) of poly(dA).2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA).2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1-4 had slightly larger binding site size ( approximately 7-7.5) with poly(dA).2poly(dT) as compared to neomycin ( approximately 6.5). The thermodynamic parameters of these intercalator-neomycin conjugates with poly(dA).2poly(dT) were derived from an integrated van't Hoff equation using the T(m3-->2) values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA).2poly(dT) increased in the following order: neomycin intercalator-neomycin conjugates for poly(dA).2poly(dT) increases as a function of

  7. Use of silane coupling agent for surface modification of zinc oxide as inorganic filler and preparation of poly(amide–imide)/zinc oxide nanocomposite containing phenylalanine moieties

    Indian Academy of Sciences (India)

    Shadpour Mallakpour; Maryam Madani

    2012-06-01

    A series of novel poly(amide–imide)/ZnO nanocomposites with modified ZnO nanoparticles contents was prepared by ultrasonic irradiation. For this purpose, surface of ZnO nanoparticle was modified with -aminopropyltriethoxysilane as a coupling agent. Then the effect of surface modification on dispersion of nanoparticles, thermal stability and UV absorption property of the obtained nanocomposites were investigated. The resulting novel nanocomposites were characterized by several techniques. Field emission scanning electron microscopy and transmission electron microscopy analyses of the nanocomposites were performed in order to study the dispersion of nanofillers in the polymer matrix. According to thermogravimetry analysis results, the addition of ZnO nanoparticles improved thermal stability of the obtained nanocomposites. Since the resulting nanocomposites contain phenylalanine amino acid and ZnO, they are expected to be biocompatible as well as biodegradable.

  8. Binding of chloroquine to ionic micelles: Effect of pH and micellar surface charge

    Energy Technology Data Exchange (ETDEWEB)

    Souza Santos, Marcela de, E-mail: marcelafarmausp77@gmail.com [Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, Ribeirão Preto, São Paulo 14040-903 (Brazil); Perpétua Freire de Morais Del Lama, Maria, E-mail: mpemdel@fcfrp.usp.br [Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, Ribeirão Preto, São Paulo 14040-903 (Brazil); Instituto Nacional de Ciência e Tecnologia de Bioanalítica, Departamento de Química Analítica, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, s/n, Campinas, São Paulo 13083-970 (Brazil); Siuiti Ito, Amando, E-mail: amandosi@ffclrp.usp.br [Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, São Paulo 14040-901 (Brazil); and others

    2014-03-15

    The pharmacological action of chloroquine relies on its ability to cross biological membranes in order to accumulate inside lysosomes. The present work aimed at understanding the basis for the interaction between different chloroquine species and ionic micelles of opposite charges, the latter used as a simple membrane model. The sensitivity of absorbance and fluorescence of chloroquine to changes in its local environment was used to probe its interaction with cetyltrimethylammonium micelles presenting bromide (CTAB) and sulfate (CTAS) as counterions, in addition to dodecyl sulfate micelles bearing sodium (SDS) and tetramethylammonium (TMADS) counterions. Counterion exchange was shown to have little effect on drug–micelle interaction. Chloroquine first dissociation constant (pKa{sub 1}) shifted to opposite directions when anionic and cationic micelles were compared. Chloroquine binding constants (K{sub b}) revealed that electrostatic forces mediate charged drug–micelle association, whereas hydrophobic interactions allowed neutral chloroquine to associate with anionic and cationic micelles. Fluorescence quenching studies indicated that monoprotonated chloroquine is inserted deeper into the micelle surface of anionic micelles than its neutral form, the latter being less exposed to the aqueous phase when associated with cationic over anionic assemblies. The findings provide further evidence that chloroquine–micelle interaction is driven by a tight interplay between the drug form and the micellar surface charge, which can have a major effect on the drug biological activity. -- Highlights: • Chloroquine (CQ) pKa{sub 1} increased for SDS micelles and decreased for CTAB micelles. • CQ is solubilized to the surface of both CTAB and SDS micelles. • Monoprotonated CQ is buried deeper into SDS micelles than neutral CQ. • Neutral CQ is less exposed to aqueous phase in CTAB over SDS micelles. • Local pH and micellar surface charge mediate interaction of CQ with

  9. Cytisine binds with similar affinity to nicotinic alpha4beta2 receptors on the cell surface and in homogenates.

    Science.gov (United States)

    Zhang, Jessie; Steinbach, Joe Henry

    2003-01-03

    Cytisine and nicotine bound to specific sites in homogenates prepared from HEK 293 cells which stably express human neuronal nicotinic alpha4 and beta2 subunits. The number of sites was the same for both ligands and nicotine was a full competitive inhibitor of cytisine binding. However, when binding was done to intact cells the number of binding sites per cell for nicotine was approximately 4-fold the number of sites for cytisine. Nicotine fully blocked cytisine binding, but cytisine only partially blocked nicotine binding to intact cells. When cells were permeabilized with saponin, the number of sites for nicotine was unchanged, while the number of sites for cytisine was increased, and cytisine was able to fully block nicotine binding. These data indicate that cytisine binds only to surface receptors on intact cells. The apparent affinity of cytisine for surface receptors (K(d)=0.8 nM) was not significantly different from that for receptors in the cell homogenate (0.3 nM).

  10. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein: Protein Redesign to Lower Protein-lignin Binding

    Energy Technology Data Exchange (ETDEWEB)

    Haarmeyer, Carolyn N. [Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing Michigan 48824; Smith, Matthew D. [Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing Michigan 48824; Chundawat, Shishir P. S. [Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing Michigan; Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway New Jersey; Sammond, Deanne [Biosciences Center, National Renewable Energy Laboratory, Golden Colorado; Whitehead, Timothy A. [Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing Michigan 48824; Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing Michigan 48824

    2016-11-07

    Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue towards energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28 to 0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Overall, our study provides strategies to identify highly active

  11. Comparison of drug delivery potentials of surface functionalized cobalt and zinc ferrite nanohybrids for curcumin in to MCF-7 breast cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Sawant, V.J., E-mail: v11131@rediffmail.com [Department of Chemistry, Smt.K.W.College, Sangli, MS 416416 (India); Bamane, S.R. [Department of Chemistry, Raja Shripatrao Bhagwantrao College, Aundh, Satara, MS (India); Shejwal, R.V. [L.B.S. College, Satara, MS (India); Patil, S.B. [A.Birnale College of Pharmacy, Sangli, MS (India)

    2016-11-01

    The functionalization and surface engineering of CoFe{sub 2}O{sub 4} and ZnFe{sub 2}O{sub 4} nanoparticles were performed by coating with PEG and Chitosan respectively using simple wet co-precipitation. Then multiactive therapeutic drug curcumin was loaded to form drug delivery nanohybrids by precipitation. These nanohybrids were characterized separately using UV–vis, FTIR, PL spectroscopy, XRD, VSM, SEM and TEM analysis. The moderate antibacterial activities of the nanohybrids were elaborated by in vitro antibacterial screening on Escherichia coli and Staphylococcus aureus. The anticancer potentials, apoptotic effects and enhanced drug delivery properties of these nanohybrids were confirmed and compared on MCF-7 cells by in vitro MTT assay. The drug delivery activities for hydrophobic drug and anticancer effects of chitosan coated zinc ferrite functionalized nanoparticles were higher than PEG coated cobalt ferrite nanohybrids. - Highlights: • CoFe{sub 2}O{sub 4} and ZnFe{sub 2}O{sub 4} nanoparticles were surface functionalized with PEG and Chitosan respectively. • Hydrophobic multi therapeutic anticancer drug curcumin was loaded into these nanohybrids and their structure, morphologies were confirmed. • The effects of PEG and Chitosan coating over ferrites for curcumin release have been elaborated, and the Chitosan coated curcumin loaded Zinc ferrite nanohybrid exhibited higher drug delivery and anticancer effects.

  12. The Non-Specific Binding of Fluorescent-Labeled MiRNAs on Cell Surface by Hydrophobic Interaction.

    Directory of Open Access Journals (Sweden)

    Ting Lu

    Full Text Available MicroRNAs are small noncoding RNAs about 22 nt long that play key roles in almost all biological processes and diseases. The fluorescent labeling and lipofection are two common methods for changing the levels and locating the position of cellular miRNAs. Despite many studies about the mechanism of DNA/RNA lipofection, little is known about the characteristics, mechanisms and specificity of lipofection of fluorescent-labeled miRNAs.Therefore, miRNAs labeled with different fluorescent dyes were transfected into adherent and suspension cells using lipofection reagent. Then, the non-specific binding and its mechanism were investigated by flow cytometer and laser confocal microscopy. The results showed that miRNAs labeled with Cy5 (cyanine fluorescent dye could firmly bind to the surface of adherent cells (Hela and suspended cells (K562 even without lipofection reagent. The binding of miRNAs labeled with FAM (carboxyl fluorescein to K562 cells was obvious, but it was not significant in Hela cells. After lipofectamine reagent was added, most of the fluorescently labeled miRNAs binding to the surface of Hela cells were transfected into intra-cell because of the high transfection efficiency, however, most of them were still binding to the surface of K562 cells. Moreover, the high-salt buffer which could destroy the electrostatic interactions did not affect the above-mentioned non-specific binding, but the organic solvent which could destroy the hydrophobic interactions eliminated it.These results implied that the fluorescent-labeled miRNAs could non-specifically bind to the cell surface by hydrophobic interaction. It would lead to significant errors in the estimation of transfection efficiency only according to the cellular fluorescence intensity. Therefore, other methods to evaluate the transfection efficiency and more appropriate fluorescent dyes should be used according to the cell types for the accuracy of results.

  13. Binding of semenogelin I to intact human spermatozoa studied by flow cytometry and surface plasmon resonance.

    Science.gov (United States)

    Jonsson, Magnus; Frohm, Birgitta; Malm, Johan

    2010-01-01

    Approximately 1 in 10 couples is infertile. No definite cause can be found in about 25% of those cases. Studies have indicated that seminal vesicle secretion functions as an optimizer of fertilization. The Zn(2+) binding protein semenogelin I (SgI) represents a major fraction of the proteins present in seminal vesicle fluid, and it serves as a structural component of the coagulum that is formed after ejaculation. Cleavage of SgI by prostate-specific antigen results in liquefaction of the coagulum. Fragmented SgI has antibacterial effects and inhibits spermatozoa mobility. SgI has also been found complexed to eppin on spermatozoa, and this complex has been suggested to be of importance for fertility. Here, we used flow cytometry and surface plasmon resonance to study SgI regarding its association with spermatozoa and the interaction dependency on Zn(2+). The concentration of Zn(2+) in seminal plasma is approximately 100 times higher than in blood plasma, and the metal ion is known to change the structure of SgI. We found that SgI binds to spermatozoa in a concentration-dependent and saturable manner. In solution, SgI bound to spermatozoa in a non-Zn(2+)-dependent way, whereas immobilized SgI interacts with spermatozoa only in the presence of Zn(2+). It indicates that SgI must exhibit a specific structure or free flexibility to be able to interact with that ligand. Our results indicate that the association of SgI to spermatozoa is conformation dependent and specific. These findings could constitute a basis for the development of a male contraceptive.

  14. Anchorless surface associated glycolytic enzymes from Lactobacillus plantarum 299v bind to epithelial cells and extracellular matrix proteins.

    Science.gov (United States)

    Glenting, Jacob; Beck, Hans Christian; Vrang, Astrid; Riemann, Holger; Ravn, Peter; Hansen, Anne Maria; Antonsson, Martin; Ahrné, Siv; Israelsen, Hans; Madsen, Søren

    2013-06-12

    An important criterion for the selection of a probiotic bacterial strain is its ability to adhere to the mucosal surface. Adhesion is usually mediated by proteins or other components located on the outer cell surface of the bacterium. In the present study we characterized the adhesive properties of two classical intracellular enzymes glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and enolase (ENO) isolated from the outer cell surface of the probiotic bacterium Lactobacillus plantarum 299v. None of the genes encoded signal peptides or cell surface anchoring motifs that could explain their extracellular location on the bacterial surface. The presence of the glycolytic enzymes on the outer surface was verified by western blotting using polyclonal antibodies raised against the specific enzymes. GAPDH and ENO showed a highly specific binding to plasminogen and fibronectin whereas GAPDH but not ENO showed weak binding to mucin. Furthermore, a pH dependent and specific binding of GAPDH and ENO to intestinal epithelial Caco-2 cells at pH 5 but not at pH 7 was demonstrated. The results showed that these glycolytic enzymes could play a role in the adhesion of the probiotic bacterium L. plantarum 299v to the gastrointestinal tract of the host. Finally, a number of probiotic as well non-probiotic Lactobacillus strains were analyzed for the presence of GAPDH and ENO on the outer surface, but no correlation between the extracellular location of these enzymes and the probiotic status of the applied strains was demonstrated.

  15. Cell surface syndecan-1 contributes to binding and function of macrophage migration inhibitory factor (MIF) on epithelial tumor cells.

    Science.gov (United States)

    Pasqualon, Tobias; Lue, Hongqi; Groening, Sabine; Pruessmeyer, Jessica; Jahr, Holger; Denecke, Bernd; Bernhagen, Jürgen; Ludwig, Andreas

    2016-04-01

    Surface expressed proteoglycans mediate the binding of cytokines and chemokines to the cell surface and promote migration of various tumor cell types including epithelial tumor cells. We here demonstrate that binding of the chemokine-like inflammatory cytokine macrophage migration inhibitory factor (MIF) to epithelial lung and breast tumor cell lines A549 and MDA-MB231 is sensitive to enzymatic digestion of heparan sulphate chains and competitive inhibition with heparin. Moreover, MIF interaction with heparin was confirmed by chromatography and a structural comparison indicated a possible heparin binding site. These results suggested that proteoglycans carrying heparan sulphate chains are involved in MIF binding. Using shRNA-mediated gene silencing, we identified syndecan-1 as the predominant proteoglycan required for the interaction with MIF. MIF binding was decreased by induction of proteolytic shedding of syndecan-1, which could be prevented by inhibition of the metalloproteinases involved in this process. Finally, MIF induced the chemotactic migration of A549 cells, wound closure and invasion into matrigel without affecting cell proliferation. These MIF-induced responses were abrogated by heparin or by silencing of syndecan-1. Thus, our study indicates that syndecan-1 on epithelial tumor cells promotes MIF binding and MIF-mediated cell migration. This may represent a relevant mechanism through which MIF enhances tumor cell motility and metastasis.

  16. Effect of seminal plasma zinc–binding proteins on motility and membrane integrity of canine spermatozoa stored at 5°C

    OpenAIRE

    Mogielnicka-Brzozowska Marzena; Dziekońska Anna; Strzeżek Rafał; Załęcki Michał; Majewska Anna; Tołścik Karolina; Kordan Władysław

    2014-01-01

    Sperm surface binding sites for non-zinc-binding proteins (nZnBPs) and zinc-binding proteins (ZnBPs) were studied by the fluorescence technique with biotin-labelled proteins. The nZnBPs binding pattern was unspecific, no characteristic sites on plasmalemma were found. ZnBPs were attached mainly to the acrosomal region of sperm head and to the sperm flagellum. ZnBPs added to the incubation mixture of the canine spermatozoa allowed the preservation of higher values for total motility, progressi...

  17. Distinctive receptor binding properties of the surface glycoprotein of a natural Feline Leukemia Virus isolate with unusual disease spectrum

    Directory of Open Access Journals (Sweden)

    Albritton Lorraine M

    2011-05-01

    Full Text Available Abstract Background Feline leukemia virus (FeLV-945, a member of the FeLV-A subgroup, was previously isolated from a cohort of naturally infected cats. An unusual multicentric lymphoma of non-T-cell origin was observed in natural and experimental infection with FeLV-945. Previous studies implicated the FeLV-945 surface glycoprotein (SU as a determinant of disease outcome by an as yet unknown mechanism. The present studies demonstrate that FeLV-945 SU confers distinctive properties of binding to the cell surface receptor. Results Virions bearing the FeLV-945 Env protein were observed to bind the cell surface receptor with significantly increased efficiency, as was soluble FeLV-945 SU protein, as compared to the corresponding virions or soluble protein from a prototype FeLV-A isolate. SU proteins cloned from other cohort isolates exhibited increased binding efficiency comparable to or greater than FeLV-945 SU. Mutational analysis implicated a domain containing variable region B (VRB to be the major determinant of increased receptor binding, and identified a single residue, valine 186, to be responsible for the effect. Conclusions The FeLV-945 SU protein binds its cell surface receptor, feTHTR1, with significantly greater efficiency than does that of prototype FeLV-A (FeLV-A/61E when present on the surface of virus particles or in soluble form, demonstrating a 2-fold difference in the relative dissociation constant. The results implicate a single residue, valine 186, as the major determinant of increased binding affinity. Computational modeling suggests a molecular mechanism by which residue 186 interacts with the receptor-binding domain through residue glutamine 110 to effect increased binding affinity. Through its increased receptor binding affinity, FeLV-945 SU might function in pathogenesis by increasing the rate of virus entry and spread in vivo, or by facilitating entry into a novel target cell with a low receptor density.

  18. Meningococcal surface fibril (Msf) binds to activated vitronectin and inhibits the terminal complement pathway to increase serum resistance.

    Science.gov (United States)

    Griffiths, Natalie J; Hill, Darryl J; Borodina, Elena; Sessions, Richard B; Devos, Nathalie I; Feron, Christiane M; Poolman, Jan T; Virji, Mumtaz

    2011-12-01

    Complement evasion is an important survival strategy of Neisseria meningitidis (Nm) during colonization and infection. Previously, we have shown that Nm Opc binds to serum vitronectin to inhibit complement-mediated killing. In this study, we demonstrate meningococcal interactions with vitronectin via a novel adhesin, Msf (meningococcal surface fibril, previously NhhA or Hsf). As with Opc, Msf binds preferentially to activated vitronectin (aVn), engaging at its N-terminal region but the C-terminal heparin binding domain may also participate. However, unlike Opc, the latter binding is not heparin-mediated. By binding to aVn, Msf or Opc can impart serum resistance, which is further increased in coexpressers, a phenomenon dependent on serum aVn concentrations. The survival fitness of aVn-binding derivatives was evident from mixed population studies, in which msf/opc mutants were preferentially depleted. In addition, using vitronectin peptides to block Msf-aVn interactions, aVn-induced inhibition of lytic C5b-9 formation and of serum killing could be reversed. As Msf-encoding gene is ubiquitous in the meningococcal strains examined and is expressed in vivo, serum resistance via Msf may be of significance to meningococcal pathogenesis. The data imply that vitronectin binding may be an important strategy for the in vivo survival of Nm for which the bacterium has evolved redundant mechanisms.

  19. Isolation of a glycopeptide fraction from the surface of the sea urchin egg that inhibits sperm-egg binding and fertilization

    OpenAIRE

    1981-01-01

    The role of cell surface glycoproteins of the sea urchin egg in binding sperm has been examined by studying the biological activity of glycopeptides derived from these glycoproteins. Glycopeptides were produced from egg surface glycoproteins by Pronase digestion. After fractionation by gel filtration the glycopeptides were tested for their ability to inhibit the binding of sperm to eggs, presumably by competing with the egg surface glycoproteins for binding sites on the sperm. One glycopeptid...

  20. Direct biomolecule binding on nonfouling surfaces via newly discovered supramolecular self-assembly of lysozyme under physiological conditions.

    Science.gov (United States)

    Yang, Peng

    2012-08-01

    When lysozyme is dissolved in a neutral HEPES buffer solution (pH = 7.4) with 0.001-0.050 M TCEP added, a fast phase transition process occurs and the resulting novel fiber-like hierarchical supramolecular assemblies made by primary spherical-particle aggregation can function as a "superglue" that binds strongly and quickly onto non-fouling coatings. This binding is highly selective towards lysozyme, and excludes synthetic, chemical/physical activation/deactivation (blocking) steps. By using biotinylated lysozyme, such a phase transition quickly creates a perfect biotinylated surface on non-fouling surfaces for avidin binding, showing great potential for the development of low-cost and practical biochips.

  1. Protection of nonself surfaces from complement attack by factor H-binding peptides: implications for therapeutic medicine.

    Science.gov (United States)

    Wu, You-Qiang; Qu, Hongchang; Sfyroera, Georgia; Tzekou, Apostolia; Kay, Brian K; Nilsson, Bo; Nilsson Ekdahl, Kristina; Ricklin, Daniel; Lambris, John D

    2011-04-01

    Exposure of nonself surfaces such as those of biomaterials or transplanted cells and organs to host blood frequently triggers innate immune responses, thereby affecting both their functionality and tolerability. Activation of the alternative pathway of complement plays a decisive role in this unfavorable reaction. Whereas previous studies demonstrated that immobilization of physiological regulators of complement activation (RCA) can attenuate this foreign body-induced activation, simple and efficient approaches for coating artificial surfaces with intact RCA are still missing. The conjugation of small molecular entities that capture RCA with high affinity is an intriguing alternative, as this creates a surface with autoregulatory activity upon exposure to blood. We therefore screened two variable cysteine-constrained phage-displayed peptide libraries for factor H-binding peptides. We discovered three peptide classes that differed with respect to their main target binding areas. Peptides binding to the broad middle region of factor H (domains 5-18) were of particular interest, as they do not interfere with either regulatory or binding activities. One peptide in this group (5C6) was further characterized and showed high factor H-capturing activity while retaining its functional integrity. Most importantly, when 5C6 was coated to a model polystyrene surface and exposed to human lepirudin-anticoagulated plasma, the bound peptide captured factor H and substantially inhibited complement activation by the alternative pathway. Our study therefore provides a promising and novel approach to produce therapeutic materials with enhanced biocompatibility.

  2. The Role of OOH Binding Site and Pt Surface Structure on ORR Activities

    Science.gov (United States)

    Jia, Qingying; Caldwell, Keegan; Ziegelbauer, Joseph M.; Kongkanand, Anusorn; Wagner, Frederick T.; Mukerjee, Sanjeev; Ramaker, David E.

    2015-01-01

    We present experimentally observed molecular adsorbate coverages (e.g., O(H), OOH and HOOH) on real operating dealloyed bimetallic PtMx (M = Ni or Co) catalysts under oxygen reduction reaction (ORR) conditions obtained using X-ray absorption near edge spectroscopy (XANES). The results reveal a complex Sabatier catalysis behavior and indicate the active ORR mechanism changes with Pt–O bond weakening from the O2 dissociative mechanism, to the peroxyl mechanism, and finally to the hydrogen peroxide mechanism. An important rearrangement of the OOH binding site, an intermediate in the ORR, enables facile H addition to OOH and faster O–O bond breaking on 111 faces at optimal Pt–O bonding strength, such as that occurring in dealloyed PtM core-shell nanoparticles. This rearrangement is identified by previous DFT calculations and confirmed from in situ measured OOH adsorption coverages during the ORR. The importance of surface structural effects and 111 ordered faces is confirmed by the higher specific ORR rates on solid core vs porous multi-core nanoparticles. PMID:26190857

  3. Determination of specific binding interactions at L-cystine crystal surfaces with chemical force microscopy.

    Science.gov (United States)

    Mandal, Trinanjana; Ward, Michael D

    2013-04-17

    The pathogenesis of L-cystine kidney stones involves four critical steps: nucleation, crystal growth, crystal aggregation, and crystal adhesion to cells. Although inhibition of crystal growth by L-cystine "imposters" at L-cystine crystal surfaces has been suggested as a plausible route for the suppression of stones, understanding the factors that govern crystal-crystal aggregation and adhesion of crystals to epithelial cells also is essential for devising strategies to mitigate L-cystine stone formation. Chemical force microscopy performed with atomic force microscope tips decorated with functional groups commonly found in urinary constituents that likely mediate aggregation and attachment (e.g., COOH, NH2, SH, CH3, OH) revealed signatures that reflect differences in the chemical affinity of these groups for the (001) and {100} faces of the naturally occurring hexagonal form of L-cystine single crystals and the {110} faces of the non-native tetragonal form. These signatures can be explained by the different chemical compositions of the crystal faces, and they reveal a remarkable binding specificity of the thiol group for the sulfur-rich {100} and {110} faces of the hexagonal and tetragonal forms, respectively. Collectively, these observations suggest that alterations of the crystal habit and polymorph by crystal growth inhibitors may not affect crystal aggregation or adhesion to cells significantly.

  4. Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags.

    Science.gov (United States)

    Park, Dan M; Reed, David W; Yung, Mimi C; Eslamimanesh, Ali; Lencka, Malgorzata M; Anderko, Andrzej; Fujita, Yoshiko; Riman, Richard E; Navrotsky, Alexandra; Jiao, Yongqin

    2016-03-01

    With the increasing demand for rare earth elements (REEs) in many emerging clean energy technologies, there is an urgent need for the development of new approaches for efficient REE extraction and recovery. As a step toward this goal, we genetically engineered the aerobic bacterium Caulobacter crescentus for REE adsorption through high-density cell surface display of lanthanide binding tags (LBTs) on its S-layer. The LBT-displayed strains exhibited enhanced adsorption of REEs compared to cells lacking LBT, high specificity for REEs, and an adsorption preference for REEs with small atomic radii. Adsorbed Tb(3+) could be effectively recovered using citrate, consistent with thermodynamic speciation calculations that predicted strong complexation of Tb(3+) by citrate. No reduction in Tb(3+) adsorption capacity was observed following citrate elution, enabling consecutive adsorption/desorption cycles. The LBT-displayed strain was effective for extracting REEs from the acid leachate of core samples collected at a prospective rare earth mine. Our collective results demonstrate a rapid, efficient, and reversible process for REE adsorption with potential industrial application for REE enrichment and separation.

  5. Discovery and characterization of surface binding sites in polysaccharide converting enzymes

    DEFF Research Database (Denmark)

    Wilkens, Casper

    polysaccharide binding interactions to also occur at a distance from the active site. AnAbf62A-m2,3’s preferred substrate is wheat arabinoxylan having kcat and KM of 178 ± 26 s-1 and 4.90 ± 0.91 mg ml-1, respectively. While AnAbf62A-m2,3 from singly substituted xylose releases 1,2-linked at threefold higher rate...... than 1,3-linked arabinosyl residues, it has no activity towards doubly 1,2- and 1,3-arabinose substituted xylosyl residues. 1H NMR identified produced arabinose as the β-furanose form indicating AnAbf62A-m2,3 to have an inverting mechanism as also inferred from the similarity with GH43 that together...... almost 10 years ago that a SBS was present on AgaA. AgaA E147S was subjected to a surface plasmon resonance (SPR) analysis and KD values were determined for deca-agarose (92.5 ± 9.8 µM), octa-agarose (128.0 ± 0.5 µM) and hexa-agarose (266.4 ± 7.2 µM). The three-fold difference in affinity between deca...

  6. Physiological roles of semenogelin I and zinc in sperm motility and semen coagulation on ejaculation in humans.

    Science.gov (United States)

    Yoshida, Kaoru; Kawano, Natsuko; Yoshiike, Miki; Yoshida, Manabu; Iwamoto, Teruaki; Morisawa, Masaaki

    2008-03-01

    At ejaculation, human sperm are considered to be mechanically trapped and become immotile in the semen coagulum by binding to semenogelins (Sgs) from the seminal vesicle and zinc ions from the prostate. However, the physiological combined roles of the protein and heavy metal on sperm motility are unknown. Here, we have first demonstrated that Sg I alone, which does not form the semen coagulum without zinc, is an inhibitor of the motility of intact human sperm at physiological concentration. On the other hand, zinc ions alone had no effect on sperm motility, but confer recovery of sperm motility that has been inhibited by Sg I at a concentration equal to or less than 1 mg/ml. These observations suggest that the roles played by Sg I and zinc on sperm motility are not mechanical but physiological. Quartz crystal microbalance analysis suggests that the sperm extract first bind to Sg I and then zinc ions which subsequently increase the protein accumulation, suggesting that Sgs inhibit sperm motility by directly binding to the sperm surface. Further accumulation of Sg I mediated by zinc ions may entrap the quiescent sperm at semen ejaculation.

  7. MTF-1-mediated repression of the zinc transporter Zip10 is alleviated by zinc restriction.

    Directory of Open Access Journals (Sweden)

    Louis A Lichten

    Full Text Available The regulation of cellular zinc uptake is a key process in the overall mechanism governing mammalian zinc homeostasis and how zinc participates in cellular functions. We analyzed the zinc transporters of the Zip family in both the brain and liver of zinc-deficient animals and found a large, significant increase in Zip10 expression. Additionally, Zip10 expression decreased in response to zinc repletion. Moreover, isolated mouse hepatocytes, AML12 hepatocytes, and Neuro 2A cells also respond differentially to zinc availability in vitro. Measurement of Zip10 hnRNA and actinomycin D inhibition studies indicate that Zip10 was transcriptionally regulated by zinc deficiency. Through luciferase promoter constructs and ChIP analysis, binding of MTF-1 to a metal response element located 17 bp downstream of the transcription start site was shown to be necessary for zinc-induced repression of Zip10. Furthermore, zinc-activated MTF-1 causes down-regulation of Zip10 transcription by physically blocking Pol II movement through the gene. Lastly, ZIP10 is localized to the plasma membrane of hepatocytes and neuro 2A cells. Collectively, these results reveal a novel repressive role for MTF-1 in the regulation of the Zip10 zinc transporter expression by pausing Pol II transcription. ZIP10 may have roles in control of zinc homeostasis in specific sites particularly those of the brain and liver. Within that context ZIP10 may act as an important survival mechanism during periods of zinc inadequacy.

  8. Oxidising alternative species to chromium VI in zinc-galvanised steel surface treatment. Part 2. An electrochemical study

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, E. [Inst. Nacional de Engenharia e Tecnologia Industrial, Lisbon (Portugal); Fedrizzi, L. [Material Engineering Department, University of Trento, Trento (Italy); Diamantinio, T.C. [Inst. Nacional de Engenharia e Tecnologia Industrial, Lisbon (Portugal)]|[Instituto do Ambiente e Vida, Departamento de Zoologia, Universidade de Coimbra, Coimbra (Portugal)

    1998-06-05

    In the first part of this work, the authors present the main results and conclusions of a morphological and chemical study carried out on zinc conversion layers (ZCLs) obtained with oxidising alternative passivation baths, that includes molybdates, permanganates, vanadates and tungstates. A good chromate-based bath was used as reference. In this second part of the work, the authors present the main results obtained on selected zinc conversion layers (ZCLs), using a.c. electrochemical impedance spectroscopy (EIS). The results obtained were correlated with the morphological and chemical data obtained with the same ZCLs in the first part of this work. Finally, it is concluded that the alternative ZCLs studied, does not seem to be as efficient as that obtained with a chromate-based passivation bath used as reference. It is believed that a better understanding of the mechanisms involved in the ZCL`s formation, can be useful for studying, in the very near future, possible synergetic effects between molybdates and other chemical species. (orig.) 24 refs.

  9. Molecular Statics Calculations of Proton Binding to Goethite Surfaces: Thermodynamic Modeling of the Surface Charging and Protonation of Goethite in Aqueous Solution

    Science.gov (United States)

    Felmy, Andrew R.; Rustad, James R.

    1998-01-01

    Molecular statics calculations of proton binding at the hydroxylated faces of goethite are used to guide the development of a thermodynamic model which describes the surface charging properties of goethite in electrolyte solutions. The molecular statics calculations combined with a linear free energy relation between the energies of the hydroxylated surface and the aqueous solvated surface predict that the acidity constants for most singly (aqua or hydroxo), doubly (μ-hydroxo), and triply (μ 3-hydroxo or μ 3-oxo) coordinated surface sites all have similar values. This model which binds protons to the goethite 110 and 021 faces satisfactorily describes the surface charging behavior of goethite, if pair formation between bulk electrolyte species, i.e., Na +, Cl -, and NO 3-, is included in the model. Inclusion of minor species of quite different charging behavior (designed to describe the possible presence of defect species) did not improve our predictions of surface charge since the protonation of the major surface sites changed when these minor species were introduced into the calculations thereby negating the effect of small amounts of defect species on the overall charging behavior. The final thermodynamic model is shown to be consistent with the surface charging properties of goethite over a range of pH values, NaNO 3, and NaCl concentrations.

  10. Purification, crystallization and preliminary crystallographic analysis of AHP IX-bp, a zinc ion and pH-dependent coagulation factor IX binding protein from Agkistrodon halys Pallas venom.

    Science.gov (United States)

    Zang, Jianye; Teng, Maikun; Niu, Liwen

    2003-04-01

    A new coagulation factor IX binding protein, AHP IX-bp, has been purified from Agkistrodon halys Pallas venom and estimated to be an AB heterodimer of about 25 kDa consisting of two chains (an A chain of 15.5 kDa and a B chain of 15 kDa) linked by one or more disulfide bonds. The N-terminal sequence of AHP IX-bp has been determined and aligned with C-type lectin-like proteins. The protein has a high sequence similarity to some snake-venom C-type lectin-like proteins. AHP IX-bp binds to coagulation factor IX but not to coagulation factor X. Moreover, AHP IX-bp shows binding to coagulation factor IX in both zinc ion-dependent and pH-dependent manners. The affinity between AHP IX-bp and coagulation factor IX is higher under neutral or weakly alkaline conditions than under weakly acidic conditions. Single crystals of AHP IX-bp grown at pH 6.5 and 7.5 diffract X-rays to 2.0 and 1.8 A resolution, respectively. Both crystals are isomorphous and belong to the space group P1; only one AB heterodimer is present in the unit cell.

  11. Engineering a Highly Hydrophilic PVDF Membrane via Binding TiO₂Nanoparticles and a PVA Layer onto a Membrane Surface.

    Science.gov (United States)

    Qin, Aiwen; Li, Xiang; Zhao, Xinzhen; Liu, Dapeng; He, Chunju

    2015-04-29

    A highly hydrophilic PVDF membrane was fabricated through chemically binding TiO2 nanoparticles and a poly(vinyl alcohol) (PVA) layer onto a membrane surface simultaneously. The chemical composition of the modified membrane surface was determined by X-ray photoelectron spectroscopy, and the binding performance of TiO2 nanoparticles and the PVA layer was investigated by a rinsing test. The results indicated that the TiO2 nanoparticles were uniformly and strongly tailored onto the membrane surface, while the PVA layer was firmly attached onto the surface of TiO2 nanoparticles and the membrane by adsorption-cross-linking. The possible mechanisms during the modification process and filtration performance, i.e., water permeability and bovine serum albumin (BSA) rejection, were investigated as well. Furthermore, antifouling property was discussed through multicycles of BSA solution filtration tests, where the flux recovery ratio was significantly increased from 20.0% for pristine PVDF membrane to 80.5% for PVDF/TiO2/PVA-modified membrane. This remarkable promotion is mainly ascribed to the improvement of surface hydrophilicity, where the water contact angle of the membrane surface was decreased from 84° for pristine membrane to 24° for PVDF/TiO2/PVA membrane. This study presents a novel and varied strategy for immobilization of nanoparticles and PVA layer on substrate surface, which could be easily adapted for a variety of materials for surface modification.

  12. Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ

    Energy Technology Data Exchange (ETDEWEB)

    Alekozai, Emal M. [Univ. of Heidelberg (Germany); Univ. of Tennessee, Knoxville, TN (United States); GhattyVenkataKrishna, Pavan K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Uberbacher, Edward C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Crowley, Michael F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States); Smith, Jeremy C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Cheng, Xiaolin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)

    2013-08-22

    The Family 7 cellobiohydrolase (Cel7A) from Trichoderma reesei consists of a carbohydrate-binding module (CBM) joined by a linker to a catalytic domain. Cellulose hydrolysis is limited by the accessibility of Cel7A to crystalline substrates, which is perceived to be primarily mediated by the CBM. The binding of CBM to the cellulose I fiber is characterized by combined Brownian dynamics (BD) and molecular dynamics (MD) simulations. Our results confirm that CBM prefers to dock to the hydrophobic than to the hydrophilic fiber faces. Both electrostatic (ES) and van der Waals (VDW) interactions are required for achieving the observed binding preference. The VDW interactions play a more important role in stabilizing the CBM-fiber binding, whereas the ES interactions contribute through the formation of a number of hydrogen bonds between the CBM and the fiber. At long distances, an ES steering effect is also observed that tends to align the CBM in an antiparallel manner relative to the fiber axis. Moreover, the MD results reveal hindered diffusion of the CBM on all fiber surfaces. The binding of the CBM to the hydrophobic surfaces is found to involve partial dewetting at the CBM-fiber interface coupled with local structural arrangements of the protein. The present simulation results complement and rationalize a large body of previous work and provide detailed insights into the mechanism of the CBM-cellulose fiber interactions.

  13. First aminoacetone chelate: [Co(tren){NH2CH2C(O)CH3}]3+-a substrate binding and activation model for zinc(II)-dependent 5-aminolaevulinic acid dehydratase.

    Science.gov (United States)

    Gumm, Andreas; Hammershøi, Anders; Kofod-Hansen, Mikael; Mønsted, Ole; Osholm Sørensen, Henning

    2007-08-14

    The complex p-[Co(tren){NH(2)CH(2)C(O)CH(3)}](ClO(4))(3).H(2)O was produced stereoselectively from [Co(tren)(O(3)SCF(3))(2)]O(3)SCF(3) () and 2-(aminomethyl)-2-methyl-1,3-dioxolane. The structure of was determined by X-ray crystallography. The complex is the first aminoacetone chelate to be reported and the first structurally characterized example of a non-conjugated ketone moiety coordinated to cobalt(iii). The robust complex was stable to aquation in strong acid and behaved as an acid with pK(a) = 4.99(1) indicative of a strong activation of the aminoacetone ligand towards deprotonation. The complex constitutes a structural model for a proposed substrate binding mode relevant for substrate activation of the zinc(ii)-dependent enzyme 5-aminolaevulinic acid dehydratase.

  14. Metal binding is critical for the folding and function of laminin binding protein, Lmb of Streptococcus agalactiae.

    Directory of Open Access Journals (Sweden)

    Preethi Ragunathan

    Full Text Available Lmb is a 34 kDa laminin binding surface adhesin of Streptococcus agalactiae. The structure of Lmb reported by us recently has shown that it consists of a metal binding crevice, in which a zinc ion is coordinated to three highly conserved histidines. To elucidate the structural and functional significance of the metal ion in Lmb, these histidines have been mutated to alanine and single, double and triple mutants were generated. These mutations resulted in insolubility of the protein and revealed altered secondary and tertiary structures, as evidenced by circular dichroism and fluorescence spectroscopy studies. The mutations also significantly decreased the binding affinity of Lmb to laminin, implicating the role played by the metal binding residues in maintaining the correct conformation of the protein for its binding to laminin. A highly disordered loop, proposed to be crucial for metal acquisition in homologous structures, was deleted in Lmb by mutation (ΔLmb and its crystal structure was solved at 2.6 Å. The ΔLmb structure was identical to the native Lmb structure with a bound zinc ion and exhibited laminin binding activity similar to wild type protein, suggesting that the loop might not have an important role in metal acquisition or adhesion in Lmb. Targeted mutations of histidine residues confirmed the importance of the zinc binding crevice for the structure and function of the Lmb adhesin.

  15. Differential affinity of FLIP and procaspase 8 for FADD’s DED binding surfaces regulates DISC assembly

    OpenAIRE

    2014-01-01

    Death receptor activation triggers recruitment of FADD, which via its death effector domain (DED) engages DEDs in procaspase 8 and its inhibitor FLIP to form death-inducing signalling complexes (DISCs). The DEDs of FADD, FLIP and procaspase 8 interact with one another using two binding surfaces defined by α1/α4 and α2/α5 helices respectively. Here we report that FLIP has preferential affinity for the α1/α4 surface of FADD, whereas procaspase 8 has preferential affinity for FADD’s α2/α5 surfac...

  16. Scaling properties of the radius of gyration and surface area for EF-hand calcium binding proteins

    Energy Technology Data Exchange (ETDEWEB)

    Pitulice, L. [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania); Isvoran, A. [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)], E-mail: aisvoran@cbg.uvt.ro; Craescu, C.T. [INSERM U759/Institute Curie-Recherche, Centre Universitaire Paris-Sud, Batiment 112, 91405 Orsay (France); Chiriac, A. [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)

    2009-04-30

    In this paper, we analyze the scaling properties of both the radius of gyration and the surface area for EF-hand calcium binding proteins. These properties are different for two conformational subfamilies: proteins with extended and compact structures, respectively. The radius of gyration is a measure of the shape of protein, whereas its surface fractal dimension is a measure of its interatomic packing. Different scaling properties for the radius of gyration underline that these two subfamilies present different shapes whilst different scaling properties for the surface area reveal different strengths of their intermolecular forces. All these data suggest different mechanisms responsible for the global folding of proteins belonging to these two subfamilies.

  17. The salivary scavenger and agglutinin (SALSA binds MBL and regulates the lectin pathway of complement in solution and on surfaces

    Directory of Open Access Journals (Sweden)

    Martin eParnov Reichhardt

    2012-07-01

    Full Text Available The scavenger receptor cysteine-rich (SRCR protein SALSA, also known as gp340, salivary agglutinin (SAG and deleted in malignant brain tumor 1 (DMBT1, is a 340 kDa glycoprotein expressed on mucosal surfaces and secreted into several body fluids. SALSA binds to a broad variety of microbes and endogenous ligands, such as complement factor C1q, surfactant proteins D and A (SP-D and SP-A and IgA. Our search for novel ligands of SALSA by direct protein-interaction studies led to the identification of mannan binding lectin (MBL as a new binding partner. We observed that surface-associated SALSA activates complement via binding of MBL. On the other hand, soluble SALSA was found to inhibit C. albicans-induced complement activation. Thus, SALSA has a dual complement regulatory function. It activates the lectin pathway when bound to a surface and inhibits it when free in the fluid-phase. These activities are mediated via a direct interaction with MBL.

  18. Development of a Surface Plasmon Resonance Assay for the Characterization of Small-Molecule Binding Kinetics and Mechanism of Binding to Kynurenine 3-Monooxygenase.

    Science.gov (United States)

    Poda, Suresh B; Kobayashi, Masakazu; Nachane, Ruta; Menon, Veena; Gandhi, Adarsh S; Budac, David P; Li, Guiying; Campbell, Brian M; Tagmose, Lena

    2015-10-01

    Kynurenine 3-monooxygenase (KMO), a pivotal enzyme in the kynurenine pathway, was identified as a potential therapeutic target for treating neurodegenerative and psychiatric disorders. In this article, we describe a surface plasmon resonance (SPR) assay that delivers both kinetics and the mechanism of binding (MoB) data, enabling a detailed characterization of KMO inhibitors for the enzyme in real time. SPR assay development included optimization of the protein construct and the buffer conditions. The stability and inhibitor binding activity of the immobilized KMO were significantly improved when the experiments were performed at 10°C using a buffer containing 0.05% n-dodecyl-β-d-maltoside (DDM) as the detergent. The KD values of the known KMO inhibitors (UPF648 and RO61-8048) from the SPR assay were in good accordance with the biochemical LC/MS/MS assay. Also, the SPR assay was able to differentiate the binding kinetics (k(a) and k(d)) of the selected unknown KMO inhibitors. For example, the inhibitors that showed comparable IC50 values in the LC/MS/MS assay displayed differences in their residence time (τ = 1/k(d)) in the SPR assay. To better define the MoB of the inhibitors to KMO, an SPR-based competition assay was developed, which demonstrated that both UPF648 and RO61-8048 bound to the substrate-binding site. These results demonstrate the potential of the SPR assay for characterizing the affinity, the kinetics, and the MoB profiles of the KMO inhibitors.

  19. Molecular statics calculations of proton binding to goethite surfaces: A new approach to estimation of stability constants for multisite surface complexation models

    Science.gov (United States)

    Rustad, James R.; Felmy, Andrew R.; Hay, Benjamin P.

    1996-05-01

    A new approach to estimating stability constants for proton binding in multisite surface complexation models is presented. The method is based on molecular statics computation of energies for the formation of proton vacancies and interstitials in ideal periodic slabs representing the (100), (110), (010), (001), and (021) surfaces of goethite. Gas-phase energies of clusters representing the hydrolysis products of ferric iron are calculated using the same potential energy functions used for the surface. These energies are linearly related to the hydrolysis constants for ferric iron in aqueous solution. Stability constants for proton binding at goethite surfaces are estimated by assuming the same log K- Δ E relationship for goethite surface protonation reactions. These stability constants predict a pH of zero charge of 8.9, in adequate agreement with measurements on CO 2-free goethite. The estimated stability constants differ significantly from previous estimations based on Pauling bond strength. We find that nearly all the surface oxide ions are reactive; nineteen of the twenty-six surface sites investigated have log Kint between 7.7 and 9.4. This implies a site density between fifteen and sixteen reactive sites/nm for crystals dominated by (110) and (021) crystal faces.

  20. An immunogenic, surface-exposed domain of Haemophilus ducreyi outer membrane protein HgbA is involved in hemoglobin binding.

    Science.gov (United States)

    Nepluev, Igor; Afonina, Galyna; Fusco, William G; Leduc, Isabelle; Olsen, Bonnie; Temple, Brenda; Elkins, Christopher

    2009-07-01

    HgbA is the sole TonB-dependent receptor for hemoglobin (Hb) acquisition of Haemophilus ducreyi. Binding of Hb to HgbA is the initial step in heme acquisition from Hb. To better understand this step, we mutagenized hgbA by deletion of each of the 11 putative surface-exposed loops and expressed each of the mutant proteins in trans in host strain H. ducreyi FX547 hgbA. All mutant proteins were expressed, exported, and detected on the surface by anti-HgbA immunoglobulin G (IgG). Deletion of sequences in loops 5 and 7 of HgbA abolished Hb binding in two different formats. In contrast, HgbA proteins containing deletions in the other nine loops retained the ability to bind Hb. None of the clones expressing mutant proteins were able to grow on plates containing low concentrations of Hb. Previously we demonstrated in a swine model of chancroid infection that an HgbA vaccine conferred complete protection from a challenge infection. Using anti-HgbA IgG from this study and the above deletion mutants, we show that loops 4, 5, and 7 of HgbA were immunogenic and surface exposed and that IgG directed against loops 4 and 5 blocked Hb binding. Furthermore, loop 6 was cleaved by protease on intact H. ducreyi, suggesting surface exposure. These data implicate a central domain of HgbA (in respect to the primary amino acid sequence) as important in Hb binding and suggest that this region of the molecule might have potential as a subunit vaccine.

  1. High level theoretical study of binding and of the potential energy surface in benzene-hydride system

    Energy Technology Data Exchange (ETDEWEB)

    Coletti, Cecilia, E-mail: ccoletti@unich.it [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy); Re, Nazzareno [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy)

    2012-04-04

    Graphical abstract: In-plane minimum geometries for benzene-H{sup -} non-covalent adducts: linear adduct (left) with the hydride ion hydrogen bonded to one aromatic hydrogen; bifurcated adduct (right), with the hydride ion hydrogen bonded to two adjacent aromatic hydrogens. Highlights: Black-Right-Pointing-Pointer Theoretical study on covalent and non-covalent binding in benzene-hydride. Black-Right-Pointing-Pointer Two non-covalent stable adducts were characterized in the in-plane geometry. Black-Right-Pointing-Pointer Significant sections of the potential energy surface were determined. Black-Right-Pointing-Pointer Formation of a very stable C{sub 6}H{sub 7}{sup -} anion upon covalent binding to carbon. - Abstract: High level ab initio calculations were performed on the interaction of the hydride anion with benzene, a system of potential interest for modelling the interactions occurring in hydrogen rich planetary atmospheres. We investigated both non-covalent and covalent binding, exploring the complete basis set limit using highly correlated MP2 and CCSD(T) levels of theory. Two non-covalent minima on the potential energy surface have been characterized, and found to correspond to moderately strong hydrogen bonding interactions. To gain further insight on the nature of binding, the total interaction energy was decomposed into its physically meaningful components and selected sections of the potential energy surface were calculated. Moreover, we found that H{sup -} can easily covalently bind to one of the carbon atoms of benzene to form a stable C{sub 6}H{sub 7}{sup -} anion, a global minimum on the potential energy surface, characterized by a puckered geometry, with a carbon atom bending out of the benzene plane. A slightly less stable planar C{sub 6}H{sub 7}{sup -} structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

  2. Non-Chromate Passivation of Zinc

    DEFF Research Database (Denmark)

    Tang, Peter Torben; Bech-Nielsen, G.

    1993-01-01

    . There is no known environmental or health risk involved using the treatments mentioned above. All components used in the baths are non toxic compared to Cr(VI). Alloy coatings such as zinc/nickel, zinc/cobalt, zinc/tin and all types of pure zinc coating (from cyanide, acidic or alkaline baths) have been treated...... minutes, in any one of the baths, at 60¢XC. Some movement of the submerged samples, or stirring with air-bubbles, should be applied, just as a thorough rinse of the zinc surface immediately before the pas-sivation is extremely important....

  3. Zinc Is Involved in Depression by Modulating G Protein-Coupled Receptor Heterodimerization.

    Science.gov (United States)

    Tena-Campos, Mercè; Ramon, Eva; Lupala, Cecylia S; Pérez, Juan J; Koch, Karl-W; Garriga, Pere

    2016-04-01

    5-Hydroxytryptamine 1A receptor and galanin receptor 1 belong to the G protein-coupled receptors superfamily, and they have been described to heterodimerize triggering an anomalous physiological state that would underlie depression. Zinc supplementation has been widely reported to improve treatment against major depressive disorder. Our work has focused on the study and characterization of these receptors and its relationships with zinc both under purified conditions and in cell culture. To this aim, we have designed a strategy to purify the receptors in a conformationally active state. We have used receptors tagged with the monoclonal Rho-1D4 antibody and employed ligand-assisted purification in order to successfully purify both receptors in a properly folded and active state. The interaction between both purified receptors has been analyzed by surface plasmon resonance in order to determine the kinetics of dimerization. Zinc effect on heteromer has also been tested using the same methodology but exposing the 5-hydroxytryptamine 1A receptor to zinc before the binding experiment. These results, combined with Förster resonance energy transfer (FRET) measurements, in the absence and presence of zinc, suggest that this ion is capable of disrupting this interaction. Moreover, molecular modeling suggests that there is a coincidence between zinc-binding sites and heterodimerization interfaces for the serotonin receptor. Our results establish a rational explanation for the role of zinc in the molecular processes associated with receptor-receptor interactions and its relationship with depression, in agreement with previously reported evidence for the positive effects of zinc in depression treatment, and the involvement of our target dimer in the same disease.

  4. Cell-surface changes in cadmium-resistant Euglena: Studies using lectin-binding techniques and flow cytometry

    Energy Technology Data Exchange (ETDEWEB)

    Bonaly, J.; Brochiero, E. [Faculte de Pharmacie, Chatenay-Malabry (France)

    1994-01-01

    Most in vitro studies on contaminants focus on the short-term effects of pollutants on cells, without regard to long-term effects and the ability of cells or microorganisms to develop a specific resistance to a pollutant. Cadmium is ubiquitous environmental contaminant. This heavy metal enters the aquatic environment mainly through vapor emissions and fallout during smelting operations. Diverse mechanisms of algal resistance to toxic metals are known. Among these, the most general mechanism is the development of metal-binding proteins. In cadmium-resistant unicellular Euglena gracilis Z algae cells, the metal did not appear to be sequestered on soluble metal-binding ligands. Previous experiments have shown that resistance development is related to a diminution of cadmium penetration into cells, implicating cell surface or membrane alteration. This research investigates the mechanisms of development of cadmium resistance in Euglena cells at the cell-surface level. Sugar chains of glycoproteins and glycolipids are a predominant feature of the surface of cells. Moreover, the cell-response to environmental changes is often orchestrated through surface macromolecules such as glycoproteins. In this study, we applied this lectin method to investigate surface carbohydrate expression during and after resistance development. Our interest was twofold: (1) to learn more about the carbohydrate composition of the cell-surface of Euglena; and (2) to determine whether transition from wild cells to Cd-resistant cells changes the expression of cell-surface carbohydrates. 13 refs., 2 figs., 1 tab.

  5. Effective enhancement of hydrophilicity of solution indium zinc oxide-based thin-film transistors by oxygen plasma treatment of deposition layer surface

    Science.gov (United States)

    You, Hsin-Chiang; Wang, Yu-Chih

    2016-06-01

    In this paper, we describe the use of a simple and efficient sol-gel solution method for synthesizing indium zinc oxide (IZO) films for use as semiconductor channel layers in thin-film transistors (TFTs) on p-type silicon substrates. The performance of IZO-based TFTs was investigated, and the effect of oxygen plasma treatment on the surface of dielectric SiN x was observed. Oxygen plasma treatment effectively enhanced the electron mobility in IZO-based TFT devices from 0.005 to 1.56 cm2 V-1 s-1, an increase of more than 312 times, and effectively enhanced device performance. X-ray photoelectron spectroscopy analysis of the IZO film was performed to clarify element bonding.

  6. Electrochemical Deposition of Zinc Oxide on the Surface of Composite Membrane Polysulfone-Graphene-Polystyrene in the Presence of Water Soluble Polymers

    Directory of Open Access Journals (Sweden)

    Alexandra Mocanu

    2017-01-01

    Full Text Available The aim of this study consisted in the development of an alternative synthesis procedure for hybrid ultrafiltration membranes for water purification. The membranes were obtained by wet-phase inversion method based on aliquots of polysulfone (PSF and graphene nanoplatelets modified with poly(styrene (G-PST. The hybrid materials were modified by electrochemical deposition of zinc oxide (ZnO on one side of the membranes in the presence of water soluble polymers. Raman, XPS, and TGA analyses were used to characterize the chemical and thermal characteristics of the PST-G. SEM analysis showed the formation of asymmetric porous configuration in all cases and the generation of ZnO with different shapes/structures on the bottom surface of the membrane or inside the porous channels. EDS analysis confirmed the formation of ZnO.

  7. Comparison of drug delivery potentials of surface functionalized cobalt and zinc ferrite nanohybrids for curcumin in to MCF-7 breast cancer cells

    Science.gov (United States)

    Sawant, V. J.; Bamane, S. R.; Shejwal, R. V.; Patil, S. B.

    2016-11-01

    The functionalization and surface engineering of CoFe2O4 and ZnFe2O4 nanoparticles were performed by coating with PEG and Chitosan respectively using simple wet co-precipitation. Then multiactive therapeutic drug curcumin was loaded to form drug delivery nanohybrids by precipitation. These nanohybrids were characterized separately using UV-vis, FTIR, PL spectroscopy, XRD, VSM, SEM and TEM analysis. The moderate antibacterial activities of the nanohybrids were elaborated by in vitro antibacterial screening on Escherichia coli and Staphylococcus aureus. The anticancer potentials, apoptotic effects and enhanced drug delivery properties of these nanohybrids were confirmed and compared on MCF-7 cells by in vitro MTT assay. The drug delivery activities for hydrophobic drug and anticancer effects of chitosan coated zinc ferrite functionalized nanoparticles were higher than PEG coated cobalt ferrite nanohybrids.

  8. Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter.

    Science.gov (United States)

    Park, Hyeong Cheol; Kim, Man Lyang; Lee, Sang Min; Bahk, Jeong Dong; Yun, Dae-Jin; Lim, Chae Oh; Hong, Jong Chan; Lee, Sang Yeol; Cho, Moo Je; Chung, Woo Sik

    2007-01-01

    Calmodulin (CaM) is involved in defense responses in plants. In soybean (Glycine max), transcription of calmodulin isoform 4 (GmCaM4) is rapidly induced within 30 min after pathogen stimulation, but regulation of the GmCaM4 gene in response to pathogen is poorly understood. Here, we used the yeast one-hybrid system to isolate two cDNA clones encoding proteins that bind to a 30-nt A/T-rich sequence in the GmCaM4 promoter, a region that contains two repeats of a conserved homeodomain binding site, ATTA. The two proteins, GmZF-HD1 and GmZF-HD2, belong to the zinc finger homeodomain (ZF-HD) transcription factor family. Domain deletion analysis showed that a homeodomain motif can bind to the 30-nt GmCaM4 promoter sequence, whereas the two zinc finger domains cannot. Critically, the formation of super-shifted complexes by an anti-GmZF-HD1 antibody incubated with nuclear extracts from pathogen-treated cells suggests that the interaction between GmZF-HD1 and two homeodomain binding site repeats is regulated by pathogen stimulation. Finally, a transient expression assay with Arabidopsis protoplasts confirmed that GmZF-HD1 can activate the expression of GmCaM4 by specifically interacting with the two repeats. These results suggest that the GmZF-HD1 and -2 proteins function as ZF-HD transcription factors to activate GmCaM4 gene expression in response to pathogen.

  9. A new route for visible/near-infrared-light-driven H2 production over titania: Co-sensitization of surface charge transfer complex and zinc phthalocyanine

    Science.gov (United States)

    Zhang, Xiaohu; Peng, Bosi; Peng, Tianyou; Yu, Lijuan; Li, Renjie; Zhang, Jing

    2015-12-01

    This work introduces a new strategy for visible/near-infrared (NIR) light responsive H2 production over TiO2 nanoparticles co-sensitized with zinc phthalocyanine derivative (Zn-tri-PcNc) and surface ligand-to-metal charge transfer (LMCT) complex, which is in situ formed on the TiO2 nanoparticles' surfaces by using ascorbic acid (AA). The in situ formed surface LMCT complex (AA-TiO2) exhibits obvious visible-light-responsive photoactivity (126.2 μmol/h) for H2 production with a high apparent quantum yield (AQY) of 16.1% at 420 nm monochromatic light irradiation. Moreover, the co-sensitized TiO2 nanoparticles (Zn-tri-PcNc-TiO2-AA) shows a much higher photoactivity (162.2 μmol/h) for H2 production than the surface LMCT complex, and broader spectral responsive region (400-800 nm) with a relatively high AQY value (0.97%) at 700 nm monochromatic light irradiation. The present result reveals a possible substitute for the conventional Ru(II)-bipyridyl complexes or organic dyes as sensitizer of semiconductors in the field of solar fuel conversion.

  10. Use of zinc-rich primers co-pigmented with phosphates applied on rusty steel surfaces contaminated with soluble salts

    Directory of Open Access Journals (Sweden)

    de la Fuente, D.

    2003-12-01

    Full Text Available Zinc-rich primers (ZRP offer good anti-corrosive behaviour, and are an ecologically acceptable solution, when applied on carbon steel substrates that are rusted and contaminated with soluble salts (chlorides and sulphates, provided certain critical contamination thresholds are not exceeded. The use of phosphate-type co-pigments in ZRP formulations, could lead to an increase in tolerable critical levels for soluble salts. This work discusses the results of a comparative study carried out with ZRP and non-ZRP systems incorporating various types of co-pigments in several concentrations, applied on substrates contaminated with different chloride and sulphate levels. The study considers the results of atmospheric exposure test (24 months in Madrid atmosphere and of accelerated humidity condensation tests.

    Las imprimaciones ricas en zinc (IRZ ofrecen un buen comportamiento, además de ser una solución ecológicamente aceptable, cuando se aplican sobre substratos de acero al carbono herrumbrado y contaminado con sales solubles (cloruros y sulfatos, siempre que no se superen ciertos umbrales críticos de contaminación. El empleo en la formulación de las IRZ de copigmentos de tipo fosfato podría suponer un aumento en los niveles críticos tolerables de sales solubles. En el presente trabajo se discuten los resultados del estudio comparativo llevado a cabo con sistemas IRZ y no IRZ con diferentes tipos de estos copigmentos en varias proporciones, aplicados sobre substratos contaminados con distintos niveles de cloruros y sulfatos. El estudio incluye los resultados tanto del ensayo de exposición atmosférica (24 meses en la atmósfera de Madrid como el ensayo acelerado de condensación de humedad.

  11. Molecular binding mechanisms of aqueous cadmium and lead to siderophores, bacteria and mineral surfaces

    Science.gov (United States)

    Mishra, Bhoopesh

    Recent studies have shown that diverse groups of bacteria adsorb metals to similar extents and uptake can be modeled using a universal adsorption model. In this study, XAFS has been used to resolve whether binding sites determined for single species systems are responsible for adsorption in more complex natural bacterial assemblages. Results obtained from a series of XAFS experiments on pure Gram positive and Gram negative bacterial strains and consortia of bacteria as a function of pH and Cd loading suggests that every bacterial strain has a complex physiology and they are all slightly different from each other. Nevertheless from the metal adsorption chemistry point of view, the main difference between them lies in the site ratio of three fundamental sites only - carboxyl, phosphoryl and sulfide. Two completely different consortia of bacteria (obtained from natural river water, and soil system with severe organic contamination) were successfully modeled in the pH range 3.4--7.8 using the EXAFS models developed for single species systems. Results thus obtained can potentially have very high impact on the modeling of the complex bacterial systems in realistic geological settings, leading to further refinement and development of robust remediation strategies for metal contamination at macroscopic level. In another study, solution speciation of Pb and Cd with DFO-B has been examined using a combination of techniques (ICP, TOC, thermodynamic modeling and XAFS). Results indicate that Pb does not complex with DFO-B at all until about pH 3.5, but forms a totally caged structure at pH 7.5. At intermediate pH conditions, mixture of species (one and two hydroxamate groups complexed) is formed. Cd on the other hand, does not complex until pH 5, forms intermediate complexes at pH 8 and is totally chelated at pH 9. Further studies were conducted for Pb sorption to mineral surface kaolinite with and without DFO-B. In the absence of DFO-B, results suggest outer sphere and inner

  12. Binding of the Galanthus nivalis agglutinin to thymocytes reveals alterations in surface glycosylation during T-cell development.

    Science.gov (United States)

    Sinkora, J; Kolínská, J; Reháková, Z; Cerný, J; Doubravská, L

    2002-02-01

    Surface binding of the Galanthus nivalis agglutinin (GNA) to thymocyte subsets has been studied in pigs and rodents by multicolour flow cytometry. In all the species examined, analogous staining profiles have been recorded. Counter-staining with anti-CD3epsilon, anti-CD4 and anti-CD8 monoclonal antibodies (MoAb) revealed that a significant increase of the GNA targets on the cell surface occurred during early thymocyte differentiation and reached its maximum at the level of the CD3loCD4+CD8+ small cortical thymocyte. This was followed by a decrease in the GNA binding capacity upon terminal maturation to the single positive thymocytes. PAGE analysis has revealed a dominant GNA-binding glycoprotein (molar mass approx. 90 kDa) present on thymocyte plasma membranes and absent on the surface of splenic lymphocytes, although both the whole cell lysates from both organs contained GNA ligands of the same size. Our findings are in agreement with previous data showing that immature thymocytes differ from their mature counterparts and peripheral T lymphocytes in the surface glycosylation pattern, and support the hypothesis that lectin-glycoprotein interaction plays a significant role in the cell-to-cell crosstalk in the thymic cortex.

  13. Direct Biomolecules Binding on Nonfouling Surface via Newly Discovered Supramolecular Self-assembly of Lysozyme under Physiological Condition

    Science.gov (United States)

    Yang, Peng

    2013-01-01

    A major challenge in the development of low cost and practical strategies for biomolecules immobilization on solid supports is that the multi-step chemical/physical activating and following deactivating procedures on nonfouling substrates often increase the cost and complexity of surface functional group types as well as deteriorate the surface integrity. Herein, we show a novel phase transition of lysozyme could be used to constitute a major step to address the above problem. It is found that when lysozyme is dissolved in a neutral buffer solution of 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, pH 7.4) with 1–50 mM tris(2-carboxyethyl)phosphine (TCEP) added, a fast phase transition process occurs and the resulting novel fibra-like hierarchical supramolecular assemblies made by primary spherical particles aggregation would function as a “superglue” that strongly and quickly bind onto non-fouling coatings. This binding is highly selective towards lysozyme, and excludes completely tedious synthetical, chemical/physical activation/deactivation (blocking) steps. When biotin is conjugated with lysozyme, such phase transition quickly constructs a perfect biotinylated surface on nonfouling surface for avidin binding, showing great potential for the development of low-cost and practical biochips. PMID:22707360

  14. Targeting folded RNA: A branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA†

    Science.gov (United States)

    Zhang, Wenyu; Bryson, David I.; Crumpton, Jason B.; Wynn, Jessica; Santos, Webster L.

    2013-01-01

    On-bead high throughput screening of a medium sized (1000–2000 Da) branched peptide boronic acid (BPBA) library consisting of 46,656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a Kd of 1.4 µM with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure-activity studies suggest that the boronic acid moiety and “branching” in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB. PMID:23925474

  15. Cell surface binding and uptake of arginine- and lysine-rich penetratin peptides in absence and presence of proteoglycans

    KAUST Repository

    Åmand, Helene L.

    2012-11-01

    Cell surface proteoglycans (PGs) appear to promote uptake of arginine-rich cell-penetrating peptides (CPPs), but their exact functions are unclear. To address if there is specificity in the interactions of arginines and PGs leading to improved internalization, we used flow cytometry to examine uptake in relation to cell surface binding for penetratin and two arginine/lysine substituted variants (PenArg and PenLys) in wildtype CHO-K1 and PG-deficient A745 cells. All peptides were more efficiently internalized into CHO-K1 than into A745, but their cell surface binding was independent of cell type. Thus, PGs promote internalization of cationic peptides, irrespective of the chemical nature of their positive charges. Uptake of each peptide was linearly dependent on its cell surface binding, and affinity is thus important for efficiency. However, the gradients of these linear dependencies varied significantly. Thus each peptide\\'s ability to stimulate uptake once bound to the cell surface is reliant on formation of specific uptake-promoting interactions. Heparin affinity chromatography and clustering experiments showed that penetratin and PenArg binding to sulfated sugars is stabilized by hydrophobic interactions and result in clustering, whereas PenLys only interacts through electrostatic attraction. This may have implications for the molecular mechanisms behind arginine-specific uptake stimulation as penetratin and PenArg are more efficiently internalized than PenLys upon interaction with PGs. However, PenArg is also least affected by removal of PGs. This indicates that an increased arginine content not only improve PG-dependent uptake but also that PenArg is more adaptable as it can use several portals of entry into the cell. © 2012 Elsevier B.V.

  16. Binding of /sup 125/I-labeled reovirus to cell surface receptors

    Energy Technology Data Exchange (ETDEWEB)

    Epstein, R.L.; Powers, M.L.; Rogart, R.B.; Weiner, H.L.

    1984-02-01

    Quantitative studies of /sup 125/I-labeled reovirus binding at equilibrium to several cell types was studied, including (1) murine L cell fibroblasts; (2) murine splenic T lymphocytes; (3) YAC cells, a murine lymphoma cell line; and (4) R1.1 cells, a murine thymoma cell line. Competition and saturation studies demonstrated (1) specific, saturable, high-affinity binding of reovirus types 1 and 3 to nonidentical receptors on L cell fibroblasts; (2) high-affinity binding of type 3 reovirus to murine splenic lymphocytes and R1.1 cells; (3) low-affinity binding of reovirus type 1 to lymphocytes and R1.1 cells; and (4) no significant binding of either serotype to YAC cells. Differences in the binding characteristics of the two reovirus serotypes to L cell fibroblasts were found to be a property of the viral hemagglutinin, as demonstrated using a recombinant viral clone. The equilibrium dissociation constant (Kd) for viral binding was of extremely high affinity (Kd in the range of 0.5 nM), and was slowly reversible. Experiments demonstrated temperature and pH dependence of reovirus binding and receptor modification studies using pronase, neuraminidase, and various sugars confirmed previous studies that reovirus receptors are predominantly protein in structure. The reovirus receptor site density was in the range of 2-8 X 10(4) sites/cell. These studies demonstrate that the pseudo-first-order kinetic model for ligand-receptor interactions provides a useful model for studying interactions of viral particles with membrane viral receptors. They also suggest that one cell may have distinct receptor sites for two serotypes of the same virus, and that one viral serotype may bind with different kinetics depending on the cell type.

  17. Binding Studies of Cucurbit[7]uril with Gold Nanoparticles Bearing Different Surface Functionalities.

    Science.gov (United States)

    Tonga, Gulen Yesilbag; Mizuhara, Tsukasa; Saha, Krishnendu; Jiang, Ziwen; Hou, Singyuk; Das, Riddha; Rotello, Vincent M

    2015-06-03

    Host-guest interactions between a synthetic receptor, cucurbit[7]uril (CB[7]), and gold nanoparticles (AuNPs) have been quantified using isothermal titration calorimetry. AuNPs were functionalized with ligands containing tertiary or quaternary benzylamine derivatives, with electron donating or withdrawing groups at the para position of the benzene ring. Analysis of binding interactions reveals that functional groups at the para position have no significant effect on binding constant. However, headgroups bearing a permanent positive charge increased the binding of AuNPs to CB[7] ten-fold compared to monomethyl counterparts.

  18. Modeling the Interaction between Integrin-Binding Peptide (RGD) and Rutile Surface: The Effect of Cation Mediation on Asp Adsorption

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Chunya [Harbin Institute of Technology; Skelton, Adam [Vanderbilt University; Chen, Mingjun [Harbin Institute of Technology; Vlcek, Lukas [ORNL; Cummings, Peter T [ORNL

    2012-01-01

    The binding of a negatively charged residue, aspartic acid (Asp) in tripeptide arginine-glycine-aspartic acid, onto a negatively charged hydroxylated rutile (110) surface in aqueous solution, containing divalent (Mg{sup 2+}, Ca{sup 2+}, or Sr{sup 2+}) or monovalent (Na{sup +}, K{sup +}, or Rb{sup +}) cations, was studied by molecular dynamics (MD) simulations. The results indicate that ionic radii and charges will significantly affect the hydration, adsorption geometry, and distance of cations from the rutile surface, thereby regulating the Asp/rutile binding mode. The adsorption strength of monovalent cations on the rutile surface in the order Na{sup +} > K{sup +} > Rb{sup +} shows a 'reverse' lyotropic trend, while the divalent cations on the same surface exhibit a 'regular' lyotropic behavior with decreasing crystallographic radii (the adsorption strength of divalent cations: Sr{sup 2+} > Ca{sup 2+} > Mg{sup 2+}). The Asp side chain in NaCl, KCl, and RbCl solutions remains stably H-bonded to the surface hydroxyls and the inner-sphere adsorbed compensating monovalent cations act as a bridge between the COO{sup -} group and the rutile, helping to 'trap' the negatively charged Asp side chain on the negatively charged surface. In contrast, the mediating divalent cations actively participate in linking the COO{sup -} group to the rutile surface; thus the Asp side chain can remain stably on the rutile (110) surface, even if it is not involved in any hydrogen bonds with the surface hydroxyls. Inner- and outer-sphere geometries are all possible mediation modes for divalent cations in bridging the peptide to the rutile surface.

  19. Screening Mixtures of Small Molecules for Binding to Multiple Sites on the Surface Tetanus Toxin C Fragment by Bioaffinity NMR

    Energy Technology Data Exchange (ETDEWEB)

    Cosman, M; Zeller, L; Lightstone, F C; Krishnan, V V; Balhorn, R

    2002-01-01

    The clostridial neurotoxins include the closely related tetanus (TeNT) and botulinum (BoNT) toxins. Botulinum toxin is used to treat severe muscle disorders and as a cosmetic wrinkle reducer. Large quantities of botulinum toxin have also been produced by terrorists for use as a biological weapon. Because there are no known antidotes for these toxins, they thus pose a potential threat to human health whether by an accidental overdose or by a hostile deployment. Thus, the discovery of high specificity and affinity compounds that can inhibit their binding to neural cells can be used as antidotes or in the design of chemical detectors. Using the crystal structure of the C fragment of the tetanus toxin (TetC), which is the cell recognition and cell surface binding domain, and the computational program DOCK, sets of small molecules have been predicted to bind to two different sites located on the surface of this protein. While Site-1 is common to the TeNT and BoNTs, Site-2 is unique to TeNT. Pairs of these molecules from each site can then be linked together synthetically to thereby increase the specificity and affinity for this toxin. Electrospray ionization mass spectroscopy was used to experimentally screen each compound for binding. Mixtures containing binders were further screened for activity under biologically relevant conditions using nuclear magnetic resonance (NMR) methods. The screening of mixtures of compounds offers increased efficiency and throughput as compared to testing single compounds and can also evaluate how possible structural changes induced by the binding of one ligand can influence the binding of the second ligand. In addition, competitive binding experiments with mixtures containing ligands predicted to bind the same site could identify the best binder for that site. NMR transfer nuclear Overhauser effect (trNOE) confirm that TetC binds doxorubicin but that this molecule is displaced by N-acetylneuraminic acid (sialic acid) in a mixture that

  20. Rashba-Dirac cones at the tungsten surface: Insights from a tight-binding model and thin film subband structure

    Science.gov (United States)

    Kirczenow, George

    2016-11-01

    A tight-binding model of bcc tungsten that includes spin-orbit coupling is developed and applied to the surface states of (110) tungsten thin films. The model describes accurately the anisotropic Dirac conelike dispersion and Rashba-like spin polarization of the surface states, including the crucial effect of the relaxation of the surface atomic layer of the tungsten towards the bulk. It is shown that the surface relaxation affects the tungsten surface states because it results in increased overlaps between atomic orbitals of the surface atomic layer and nearby layers, whereas electric fields that are due to charge transfer between the tungsten and the vacuum near the surface or between the bulk and surface layers do not significantly affect the Rashba-Dirac surface states. It is found that hybridization with bulk modes has differing strengths for thin film surface states belonging to the upper and lower Rashba-Dirac cones and results in reversal of the directions of travel of spin ↑ and ↓ electrons in most of the upper Rashba-Dirac cone relative to those expected from phenomenology. It is also shown that intrasite (not intersite) matrix elements of the spin-orbit Hamiltonian are primarily responsible for the formation of the Rashba-Dirac cones and their spin polarization. This finding should be considered when modeling topological insulators, the spin Hall effect, and related phenomena.

  1. Effects of Multiwalled Carbon Nanotube Surface Modification and Purification on Bovine Serum Albumin Binding and Biological Responses

    Directory of Open Access Journals (Sweden)

    Wei Bai

    2016-01-01

    Full Text Available Carboxylation of multiwalled carbon nanotubes (MWCNTs has been used to improve solubility in aqueous systems and for further functionalization with biologically active moieties for biomedical uses. An important consideration is that oxidation debris is generated during the process of carboxylation, which can be removed by base washing. We hypothesized that surface modification as well as purification by debris removal may alter physicochemical properties of MWCNTs and their ability to bind proteins. We utilized pristine MWCNT, carboxylated MWCNTs (F-MWCNTs, and base-washed carboxylated MWCNTs (BW-F-MWCNTs to examine formation of a bovine serum albumin (BSA protein corona and impact on biological responses. We found that carboxylation increased the capability of F-MWCNTs to bind BSA, and base washing further increased this binding. Functionalization increased cellular uptake by rat aortic endothelial cells (RAEC and mouse macrophages (RAW264.7, while base washing showed results similar to the functionalized analog. Interestingly, BSA binding downregulated mRNA levels of interleukin-6 (IL-6 and heme oxygenase 1 (Hmox1 in RAEC cells but upregulated the expression of IL-6 and Hmox1 in RAW264.7 cells. Overall, our study demonstrated that surface modification as well as further purification impacted the interaction of MWCNTs with proteins and subsequent cellular responses.

  2. Novel zinc complexes of a non-steroidal anti-inflammatory drug, niflumic acid: Structural characterization, human-DNA and albumin binding properties.

    Science.gov (United States)

    Smolková, Romana; Zeleňák, Vladimír; Smolko, Lukáš; Kuchár, Juraj; Rabajdová, Miroslava; Ferenčáková, Michaela; Mareková, Mária

    2017-05-05

    Three novel Zn(II) complexes of NSAID niflumic acid (Hnif) were prepared and studied, namely; [Zn(MeOH)4(nif)2] (1), [Zn(cyclam)(nif)2] (2) and [Zn(nif)2(tmen)] (3), where nif is deprotonated niflumic acid, cyclam is 1,4,8,11-Tetraazacyclotetradecane and tmen is N,N,N',N'-Tetramethylethylenediamine. The complexes have been characterized by infrared spectroscopy, elemental and thermal analysis and single-crystal X-ray structure analysis. All three complexes contain two deprotonated niflumato anions monodentately coordinated via carboxylato groups. Furthermore, fluorescence binding studies of the prepared compounds with human genomic DNA-EB (ethidium bromide) were carried out, which suggest that all complexes are able to bind to DNA via intercalation. Moreover, from the obtained results it followed that complexes 2 and 3 bind to DNA from the tissue with aortic aneurysm (aDNA) and control (cDNA) with a different strength. Additionally, complexes 1-3 exhibit good binding affinity to human serum albumin with high binding constant. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. Binding Interactions Between α-glucans from Lactobacillus reuteri and Milk Proteins Characterised by Surface Plasmon Resonance

    DEFF Research Database (Denmark)

    Diemer, Silja Kej; Svensson, Birte; Babol, Linnéa N.

    2012-01-01

    Interactions between milk proteins and α-glucans at pH 4.0–5.5 were investigated by use of surface plasmon resonance. The α-glucans were synthesised with glucansucrase enzymes from Lactobacillus reuteri strains ATCC-55730, 180, ML1 and 121. Variations in the molecular characteristics of the α......-glucans, such as molecular weight, linkage type and degree of branching, influenced the interactions with native and denatured β-lactoglobulin and κ-casein. The highest overall binding levels were reached with α-(1,4) compared to α-(1,3) linked glucans. Glucans with many α-(1,6) linkages demonstrated the highest binding......-casein were not pH dependent, whereas binding to denatured β-lactoglobulin was highest at pH 4.0 and binding to native β-lactoglobulin was optimal at pH 4.5–5.0. This study shows that molecular weight, linkage type and degree of branching of α-glucans highly influence the binding interactions with milk...

  4. Characterization of heparin-binding site of tissue transglutaminase: its importance in cell surface targeting, matrix deposition, and cell signaling.

    Science.gov (United States)

    Wang, Zhuo; Collighan, Russell J; Pytel, Kamila; Rathbone, Daniel L; Li, Xiaoling; Griffin, Martin

    2012-04-13

    Tissue transglutaminase (TG2) is a multifunctional Ca(2+)-activated protein cross-linking enzyme secreted into the extracellular matrix (ECM), where it is involved in wound healing and scarring, tissue fibrosis, celiac disease, and metastatic cancer. Extracellular TG2 can also facilitate cell adhesion important in wound healing through a nontransamidating mechanism via its association with fibronectin, heparan sulfates (HS), and integrins. Regulating the mechanism how TG2 is translocated into the ECM therefore provides a strategy for modulating these physiological and pathological functions of the enzyme. Here, through molecular modeling and mutagenesis, we have identified the HS-binding site of TG2 (202)KFLKNAGRDCSRRSSPVYVGR(222). We demonstrate the requirement of this binding site for translocation of TG2 into the ECM through a mechanism involving cell surface shedding of HS. By synthesizing a peptide NPKFLKNAGRDCSRRSS corresponding to the HS-binding site within TG2, we also demonstrate how this mimicking peptide can in isolation compensate for the RGD-induced loss of cell adhesion on fibronectin via binding to syndecan-4, leading to activation of PKCα, pFAK-397, and ERK1/2 and the subsequent formation of focal adhesions and actin cytoskeleton organization. A novel regulatory mechanism for TG2 translocation into the extracellular compartment that depends upon TG2 conformation and the binding of HS is proposed.

  5. Tannic acid binding of cell surfaces in normal, premalignant, and malignant squamous epithelium of the human uterine cervix.

    Science.gov (United States)

    Davina, J H; Lamers, G E; van Haelst, U J; Kenemans, P; Stadhouders, A M

    1984-01-01

    Alterations in tannic acid (TA) binding capacity of cell surface carbohydrates in normal, premalignant, and malignant squamous epithelium of the human uterine cervix have been studied using electron microscopic visualization in combination with microdensitometric evaluation. While in normal epithelium there is distinct binding in four to five cell layers of the deep intermediate zone, cells of carcinoma in situ and invasive cancer lesions lack TA binding. In moderate dysplasia an intermediate reacting pattern is found. Deep intermediate cells in areas bordering the carcinoma in situ lesions do not show any binding, although their ultrastructure cannot be distinguished from similar cells in normal tissue. The TA deposition within the deep intermediate zone is probably related to the presence here of glycoprotein-containing membrane-coating granules. The finding that TA binding discriminates between cells in normal squamous epithelium and morphologically normal cells in juxtaposition with lesional areas in premalignant and malignant epithelium opens the possibility for a more reliable cytologic diagnosis of cervical epithelial neoplasia.

  6. Binding Studies of Cucurbit[7]uril with Gold Nanoparticles Bearing Different Surface Functionalities‡

    OpenAIRE

    Tonga, Gulen Yesilbag; Mizuhara, Tsukasa; Saha, Krishnendu; Jiang, Ziwen; Hou, Singyuk; Das, Riddha; Rotello, Vincent M.

    2015-01-01

    Host-guest interactions between a synthetic receptor, cucurbit[7]uril (CB[7]), and gold nanoparticles (AuNPs) have been quantified using isothermal titration calorimetry. AuNPs were functionalized with ligands containing tertiary or quaternary benzylamine derivatives, with electron donating or withdrawing groups at the para position of the benzene ring. Analysis of binding interactions reveals that functional groups at the para position have no significant effect on binding constant. However,...

  7. 响应面法优化蚕沙叶绿素锌钾盐的制备工艺%Optimization of Preparation Technology for Potassium Zinc Chlorophyllin by Response Surface Method from Silkworm Faeces

    Institute of Scientific and Technical Information of China (English)

    包立军; 胡必利; 彭云武

    2011-01-01

    Response surface method (RSM) was used for optimizing the preparation technology of potassium zinc chlorophyllin. Based on single-factor experiment, saponification time, temperature of zinc reaction and time of zinc reaction were selected as influencing factors during extraction. The experiment mathematical model was arranged according to Box-Behnken central composite experiment design. The results showed that the optimum preparation technology for potassium zinc chlorophyllin were saponification time 58 min, zinc reaction temperature 57 XI, zinc reaction time 83 min. The predicted productivity ratio of potassium zinc chlorophyllin was 8. 95%, and the verification productivity ratio was 9. 23%, with relative error of 3.13%.%在单因素试验基础上,选取皂化时间、锌代温度和锌代时间作为影响因子,应用Box-Behnken中心组合设计建立数学模型,以叶绿素锌钾盐产率为响应值,进行响应面分析(RSA).结果表明,叶绿素锌钾盐的最佳制备工艺为皂化时间58 min,锌代温度57℃,锌代时间83 min.响应面模型在此条件下预测的叶绿素锌钾盐产率为8.95%,验证值(9.23%)与预测值相对误差3.13%.

  8. Tight-binding calculation of the electronic states of bulk-terminated GaAs(311)A and B surfaces

    Institute of Scientific and Technical Information of China (English)

    贾瑜; 马丙现; 姚乾凯; 唐明生

    2002-01-01

    We have carried out theoretical investigations on the electronic structure of GaAs(311)A and GaAs(311)B sur-faces. The bulk electronic structure of GaAs has been described by the second-neighbour tight-binding formalism andthe surface electronic structure was evaluated via an analytic Green function method. First, we present the surfaceband structure together with the projected bulk band of both Ga-terminated and As-terminated for GaAs(311)A andGaAs(311)B surfaces, respectively. In each case, the number of surface states is determined, and the localized surfacefeatures and orbitproperties of these surface states along -Y-S-X- high symmetry lines of the surface Brillouinzone are discussed. For the Ga-terminated GaAs(311)A (1×1) surface, we have tested two possible structure models,i.e. "the bridge site" and "the hollow site" models. In comparison with the angle-resolved photoelectron spectroscopystudied recently, the results have shown that the surface electronic states of the hollow site model are in good agreementwith the experiments, whereas those of the bridge site model are not. So we have concluded that the hollow site modelis favourable for the Ga-terminated GaAs(311) (1× 1) surface and the bridge site model should be excluded.

  9. Morphology study of electrodeposited zinc from zinc sulfate solutions as anode for zinc-air and zinc-carbon batteries

    OpenAIRE

    Nurhaswani Alias; Ahmad Azmin Mohamad

    2015-01-01

    The morphology of Zinc (Zn) deposits was investigated as anode for aqueous batteries. The Zn was deposited from zinc sulfate solution in direct current conditions on a copper surface at different current densities. The morphology characterization of Zn deposits was performed via field emission scanning electron microscopy. The Zn deposits transformed from a dense and compact structure to dendritic form with increasing current density. The electrodeposition of Zn with a current density of 0.02...

  10. Iron Oxide Surface Chemistry: The Effect of Chemical Structure on Binding in Benzoic Acid and Catechol Derivatives.

    Science.gov (United States)

    Korpany, Katalin V; Majewski, Dorothy D; Chiu, Cindy T; Cross, Shoronia N; Blum, Amy Szuchmacher

    2017-02-18

    Excellent performance of functionalized iron oxide nanoparticles in nanomaterial and biomedical applications often relies on achieving attachment of ligands to the iron oxide surface both in sufficient number and with proper orientation. Towards this end, we determine relationships between ligand chemical structure and surface binding on magnetic iron oxide nanoparticles for a series of related benzoic acid and catechol derivatives. Ligand exchange was used to introduce the model ligands, and the resulting nanoparticles were characterized by FTIR-ATR, transmission electron microscopy (TEM), and nanoparticle solubility behavior. An in-depth analysis of ligand electronic effects and reaction conditions reveals that the nature of ligand binding does not solely depend on the presence of functional groups known to bind to iron oxide nanoparticles. The structure of the resulting ligand-surface complex was primarily influenced by the relative positioning of hydroxyl and carboxylic acid groups within the ligand as well as whether or not HCl(aq) was added to the ligand exchange reaction. Overall, this study will help guide future ligand design and ligand exchange strategies towards realizing truly custom-built iron oxide nanoparticles.

  11. The zinc electrode - Its behaviour in the nickel oxide-zinc accumulator

    Science.gov (United States)

    Certain aspects of zinc electrode reaction and behavior are investigated in view of their application to batteries. The properties of the zinc electrode in a battery system are discussed, emphasizing porous structure. Shape change is emphasized as the most important factor leading to limited battery cycle life. It is shown that two existing models of shape change based on electroosmosis and current distribution are unable to consistently describe observed phenomena. The first stages of electrocrystallization are studied and the surface reactions between the silver substrate and the deposited zinc layer are investigated. The reaction mechanism of zinc and amalgamated zinc in an alkaline electrolyte is addressed, and the batter system is studied to obtain information on cycling behavior and on the shape change phenomenon. The effect on cycle behavior of diferent amalgamation techniques of the zinc electrode and several additives is addressed. Impedance measurements on zinc electrodes are considered, and battery behavior is correlated with changes in the zinc electrode during cycling.

  12. Textured surface structures formed using new techniques on transparent conducting Al-doped zinc oxide films prepared by magnetron sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Minami, Tadatsugu [Optoelectronic Device System R& D Center, Kanazawa Institute of Technology, Nonoichi, Ishikawa 921-8501 (Japan); Miyata, Toshihiro, E-mail: tmiyata@neptune.kanazawa-it.ac.jp [Optoelectronic Device System R& D Center, Kanazawa Institute of Technology, Nonoichi, Ishikawa 921-8501 (Japan); Uozaki, Ryousuke [Optoelectronic Device System R& D Center, Kanazawa Institute of Technology, Nonoichi, Ishikawa 921-8501 (Japan); Sai, Hitoshi; Koida, Takashi [Research Center for Photovoltaics, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan)

    2016-09-01

    Surface-textured Al-doped ZnO (AZO) films formed using two new techniques based on magnetron sputtering deposition were developed by optimizing the light scattering properties to be suitable for transparent electrode applications in thin-film silicon solar cells. Scrambled egg-like surface-textured AZO films were prepared using a new texture formation technique that post-etched pyramidal surface-textured AZO films prepared under deposition conditions suppressing c-axis orientation. In addition, double surface-textured AZO films were prepared using another new texture formation technique that completely removed, by post-etching, the pyramidal surface-textured AZO films previously prepared onto the initially deposited low resistivity AZO films; simultaneously, the surface of the low resistivity films was slightly etched. However, the obtained very high haze value in the range from the near ultraviolet to visible light in the scrambled egg-like surface-textured AZO films did not contribute significantly to the obtainable photovoltaic properties in the solar cells fabricated using the films. Significant light scattering properties as well as a low sheet resistance could be achieved in the double surface-textured AZO films. In addition, a significant improvement of external quantum efficiency in the range from the near ultraviolet to visible light was achieved in superstrate-type n-i-p μc-Si:H solar cells fabricated using a double surface-textured AZO film prepared under optimized conditions as the transparent electrode. - Highlights: • Double surface-textured AZO films prepared using a new texture formation technique • Extensive light scattering properties with low sheet resistance achieved in the double surface-textured AZO films • Improved external quantum efficiency of μc-Si:H solar cells using a double surface-textured AZO film.

  13. Staphylococcus aureus surface protein SdrE binds complement regulator factor H as an immune evasion tactic.

    Directory of Open Access Journals (Sweden)

    Julia A Sharp

    Full Text Available Similar to other highly successful invasive bacterial pathogens, Staphylococcus aureus recruits the complement regulatory protein factor H (fH to its surface to inhibit the alternative pathway of complement. Here, we report the identification of the surface-associated protein SdrE as a fH-binding protein using purified fH overlay of S. aureus fractionated cell wall proteins and fH cross-linking to S. aureus followed by mass spectrometry. Studies using recombinant SdrE revealed that rSdrE bound significant fH whether from serum or as a purified form, in both a time- and dose-dependent manner. Furthermore, rSdrE-bound fH exhibited cofactor functionality for factor I (fI-mediated cleavage of C3b to iC3b which correlated positively with increasing amounts of fH. Expression of SdrE on the surface of the surrogate bacterium Lactococcus lactis enhanced recruitment of fH which resulted in increased iC3b generation. Moreover, surface expression of SdrE led to a reduction in C3-fragment deposition, less C5a generation, and reduced killing by polymorphonuclear cells. Thus, we report the first identification of a S. aureus protein associated with the staphylococcal surface that binds factor H as an immune evasion mechanism.

  14. Direct observation of the binding process between protein and quantum dots by in situ surface plasmon resonance measurements

    Energy Technology Data Exchange (ETDEWEB)

    Xiao Qi; Zhou Bo; Tian Fangfang; Ge Yushu; Liu Xiaorong; Liu Yi [State Key Laboratory of Virology, College of Chemistry and Molecular Science, Wuhan University, Wuhan 430072 (China); Huang Shan; Guan Hongliang; He Zhike, E-mail: prof.liuyi@263.ne [Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China)

    2009-08-12

    A layer-by-layer surface decoration technique has been developed to anchor quantum dots (QDs) onto a gold substrate and an in situ surface plasmon resonance technique has been used to study interactions between the QDs and different proteins. Direct observation of the binding of the protein onto the QDs and the kinetics of the adsorption and dissociation of different proteins on the QDs has been achieved. This would be helpful for the identification of particle-associated proteins and may offer a fundamental prerequisite for nanobiology, nanomedicine and nanotoxicology. The combination of the novel layer-by-layer surface modification method and in situ surface plasmon resonance would be powerful in studying biological systems such as DNA and cells.

  15. Selective binding of oligonucleotide on TiO{sub 2} surfaces modified by swift heavy ion beam lithography

    Energy Technology Data Exchange (ETDEWEB)

    Vicente Pérez-Girón, J. [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Emerging Viruses Department Heinrich Pette Institute, Hamburg 20251 (Germany); Hirtz, M. [Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology - KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); McAtamney, C.; Bell, A.P. [Advanced Microscopy Laboratory, CRANN, Trinity College Dublin, Dublin 2 (Ireland); Antonio Mas, J. [Laboratorio de Genómica del Centro de Apoyo Tecnológico, Universidad Rey Juan Carlos, Campus de Alcorcón 28922, Madrid (Spain); Jaafar, M. [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid (Spain); Luis, O. de [Nanoate, S.L. C/Poeta Rafael Morales 2, San Sebastian de los Reyes, 28702 Madrid (Spain); Departamento de Bioquímica, Fisiología y Genética Molecular, Facultad de Ciencias de la Salud, Universidad Rey Juan Carlos, Campus de Alcorcón, 28922 Madrid (Spain); Fuchs, H. [Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology - KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Physical Institute and Center for Nanotechnology (CeNTech), Wilhelm-Klemm-Straße 10, University of Münster (Germany); and others

    2014-11-15

    We have used swift heavy-ion beam based lithography to create patterned bio-functional surfaces on rutile TiO{sub 2} single crystals. The applied lithography method generates a permanent and well defined periodic structure of micrometre sized square holes having nanostructured TiO{sub 2} surfaces, presenting different physical and chemical properties compared to the surrounding rutile single crystal surface. On the patterned substrates selective binding of oligonucleotides molecules is possible at the surfaces of the holes. This immobilisation process is only being controlled by UV light exposure. The patterned transparent substrates are compatible with fluorescence detection techniques, are mechanically robust, have a high tolerance to extreme chemical and temperature environments, and apparently do not degrade after ten cycles of use. These qualities make the patterned TiO{sub 2} substrates useful for potential biosensor applications.

  16. Ecological risk assessment of heavy metals in surface seawater and sediment near the outlet of a zinc factory in Huludao City, Liaoning Province, China

    Science.gov (United States)

    Feng, Yongliang; Chen, Yanzhen; Wang, Jing; Gong, Yufeng; Liu, Xigang; Mu, Gang; Tian, Hua

    2016-11-01

    At present, the methods widely applied to assess ecological risk of heavy metals are essentially single-point estimates in which exposure and toxicity data cannot be fully used and probabilities of adverse biological eff ects cannot be achieved. In this study, based on investigation of concentrations of six heavy metals (As, Hg, Pb, Cd, Cu, and Zn) in the surface seawater and sediment near the outlet of a zinc factory, located in Huludao City, Liaoning Province, China, a tiered approach consisting of several probabilistic options was used to refine ecological risk assessment for the individuals. A mixture of various heavy metals was detected in the surface seawater, and potential ecological risk index (PERI) was adopted to assess the potential ecological risk of heavy metals in the surface sediment. The results from all levels of aquatic ecological risk assessment in the tiered framework, ranging from comparison of single eff ects and exposure values to the use of distribution-based Hazard Quotient obtained through Monte Carlo simulation, are consistent with each other. Briefly, aquatic Zn and Cu posed a clear ecological risk, while Cd, Pb, Hg, and As in the water column posed potential risk. As expected, combined ecological risk of heavy metal mixture in the surface seawater was proved significantly higher than the risk caused by any individual heavy metal, calculated using the concept of total equivalent concentration. According to PERI, the severity of pollution by the six heavy metals in the surface sediment decreased in the following sequence: Cd>Hg>As>Pb>Cu>Zn, and the total heavy metals in the sediment posed a very high risk to the marine environment. This study provides a useful mathematical framework for ecological risk assessment of heavy metals.

  17. The biological inorganic chemistry of zinc ions.

    Science.gov (United States)

    Krężel, Artur; Maret, Wolfgang

    2016-12-01

    The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the "mobile" zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn(2+) without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn(2+) differs from s-block cations such as Ca(2+) with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is

  18. Surface plasmon resonance and circular dichroism characterization of cucurbitacins binding to serum albumins for early pharmacokinetic profiling.

    Science.gov (United States)

    Fabini, Edoardo; Fiori, Giovana Maria Lanchoti; Tedesco, Daniele; Lopes, Norberto Peporine; Bertucci, Carlo

    2016-04-15

    Cucurbitacins are a group of tetracyclic triterpenoids, known for centuries for their anti-cancer and anti-inflammatory properties, which are being actively investigated over the past decades in order to elucidate their mechanism of action. In perspective of being used as therapeutic molecules, a pharmacokinetic characterization is crucial to assess the affinity toward blood carrier proteins and extrapolate distribution volumes. Usually, pharmacokinetic data are first collected on animal models and later translated to humans; therefore, an early characterization of the interaction with carrier proteins from different species is highly desirable. In the present study, the interactions of cucurbitacins E and I with human and rat serum albumins (HSA and RSA) were investigated by means of surface plasmon resonance (SPR)-based optical biosensing and circular dichroism (CD) spectroscopy. Active HSA and RSA sensor chip surfaces were prepared through an amine coupling reaction protocol, and the equilibrium dissociation constants (Kd) for the different cucurbitacins-serum albumins complexes were then determined by SPR analysis. Further information on the binding of cucurbitacins to serum albumins was obtained by CD competition experiments with biliverdin, a specific marker binding to subdomain IB of HSA. SPR data unveiled a previously unreported binding event between CucI and HSA; the determined binding affinities of both compounds were slightly higher for RSA with respect to HSA, even though all the compounds can be ranked as high-affinity binders for both carriers. CD analysis showed that the two cucurbitacins modify the binding of biliverdin to serum albumins through opposite allosteric modulation (positive for HSA, negative for RSA), confirming the need for caution in the translation of pharmacokinetic data across species. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Ionic Surfactant B