WorldWideScience

Sample records for active site residue

  1. Crystallographic B factor of critical residues at enzyme active site

    张海龙; 宋时英; 林政炯

    1999-01-01

    Thirty-seven sets of crystallographic enzyme data were selected from Protein Data Bank (PDB, 1995). The average temperature factors (B) of the critical residues at the active site and the whole molecule of those enzymes were calculated respectively. The statistical results showed that the critical residues at the active site of most of the enzymes had lower B factors than did the whole molecules, indicating that in the crystalline state the critical residues at the active site of the natural enzymes possess more stable conformation than do the whole molecules. The flexibility of the active site during the unfolding by denaturing was also discussed.

  2. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  3. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    Qi Jian-Xun; Jiang Fan

    2011-01-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  4. SITE-DIRECTED MUTAGENESIS OF PROPOSED ACTIVE-SITE RESIDUES OF PENICILLIN-BINDING PROTEIN-5 FROM ESCHERICHIA-COLI

    VANDERLINDEN, MPG; DEHAAN, L; DIDEBERG, O; KECK, W

    1994-01-01

    Alignment of the amino acid sequence of penicillin-binding protein 5 (PBP5) with the sequences of other members of the family of active-site-serine penicillin-interacting enzymes predicted the residues playing a role in the catalytic mechanism of PBP5. Apart from the active-site (Ser(44)), Lys(47),

  5. Active sites residues of beef liver carnitine octanoyltransferase (COT) and carnitine palmitoyltransferase (CPT-II).

    Nic a'Bháird, N; Yankovskaya, V; Ramsay, R R

    1998-01-01

    The carnitine acyltransferases which catalyse the reversible transfer of fatty acyl groups between carnitine and coenzyme A have been proposed to contain a catalytic histidine. Here, the chemical reactivity of active site groups has been used to demonstrate differences between the active sites of beef liver carnitine octanoyltransferase (COT) and carnitine palmitoyltransferase-II (CPT-II). Treatment of CPT-II with the histidine-selective reagent, diethyl pyrocarbonate (DEPC), resulted in simple linear pseudo-first-order kinetics. The reversal of the inhibition by hydroxylamine and the pKa (7.1) of the modified residue indicated that the residue was a histidine. The order of the inactivation kinetics showed that 1mol of histidine was modified per mol of CPT-II.When COT was treated with DEPC the kinetics of inhibition were biphasic with an initial rapid loss of activity followed by a slower loss of activity. The residue reacting in the faster phase of inhibition was not a histidine but possibly a serine. The modification of this residue did not lead to complete loss of activity suggesting that a direct role in catalysis is unlikely. It was deduced that the residue modified by DEPC in the slower phase was a lysine and indeed fluorodinitrobenzene (FDNB) inactivated COT with linear pseudo-first-order kinetics. The COT peptide containing the FDNB-labelled lysine was isolated and sequenced. Alignment of this sequence placed it 10 amino acids downstream of the putative active-site histidine. PMID:9480926

  6. Binding stability of peptides derived from 1ALA residue and 7GLY residues to sites near active center of fluctuating papain

    Nishiyama, Katsuhiko

    2012-05-01

    We investigated the binding stability of peptides derived from 1ALA residue and 7GLY residues to sites near active center of fluctuating papain via molecular dynamics and docking simulations. Replacing GLY residue in 8GLY with ALA residue had a positive effect on binding stability to the sites in some cases although the replacing had a negative effect on it in other cases. Furthermore the replacing had a negative effect on the chance of binding to the sites. Residue in peptide should be replaced on the basis of systematic exploration of its position.

  7. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  8. Role of a cysteine residue in the active site of ERK and the MAPKK family

    Kinases of mitogen-activated protein kinase (MAPK) cascades, including extracellular signal-regulated protein kinase (ERK), represent likely targets for pharmacological intervention in proliferative diseases. Here, we report that FR148083 inhibits ERK2 enzyme activity and TGFβ-induced AP-1-dependent luciferase expression with respective IC50 values of 0.08 and 0.05 μM. FR265083 (1'-2' dihydro form) and FR263574 (1'-2' and 7'-8' tetrahydro form) exhibited 5.5-fold less and no activity, respectively, indicating that both the α,β-unsaturated ketone and the conformation of the lactone ring contribute to this inhibitory activity. The X-ray crystal structure of the ERK2/FR148083 complex revealed that the compound binds to the ATP binding site of ERK2, involving a covalent bond to Sγ of ERK2 Cys166, hydrogen bonds with the backbone NH of Met108, Nζ of Lys114, backbone C=O of Ser153, Nδ2 of Asn154, and hydrophobic interactions with the side chains of Ile31, Val39, Ala52, and Leu156. The covalent bond motif in the ERK2/FR148083 complex assures that the inhibitor has high activity for ERK2 and no activity for other MAPKs such as JNK1 and p38MAPKα/β/γ/δ which have leucine residues at the site corresponding to Cys166 in ERK2. On the other hand, MEK1 and MKK7, kinases of the MAPKK family which also can be inhibited by FR148083, contain a cysteine residue corresponding to Cys166 of ERK2. The covalent binding to the common cysteine residue in the ATP-binding site is therefore likely to play a crucial role in the inhibitory activity for these MAP kinases. These findings on the molecular recognition mechanisms of FR148083 for kinases with Cys166 should provide a novel strategy for the pharmacological intervention of MAPK cascades

  9. The role of active site aromatic residues in substrate degradation by the human chitotriosidase.

    Eide, Kristine Bistrup; Stockinger, Linn Wilhelmsen; Lewin, Anna Sofia; Tøndervik, Anne; Eijsink, Vincent G H; Sørlie, Morten

    2016-02-01

    Human chitotriosidase (HCHT) is a glycoside hydrolase family 18 chitinase synthesized and secreted in human macrophages thought be an innate part of the human immune system. It consists of a catalytic domain with the (β/α)8 TIM barrel fold having a large area of solvent-exposed aromatic amino acids in the active site and an additional family 14 carbohydrate-binding module. To gain further insight into enzyme functionality, especially the effect of the active site aromatic residues, we expressed two variants with mutations in subsites on either side of the catalytic acid, subsite -3 (W31A) and +2 (W218A), and compared their catalytic properties on chitin and high molecular weight chitosans. Exchange of Trp to Ala in subsite -3 resulted in a 12-fold reduction in extent of degradation and a 20-fold reduction in kcat(app) on chitin, while the values are 5-fold and 10-fold for subsite +2. Moreover, aromatic residue mutation resulted in a decrease of the rate of chitosan degradation contrasting previous observations for bacterial family 18 chitinases. Interestingly, the presence of product polymers of 40 sugar moieties and higher starts to disappear already at 8% degradation for HCHT50-W31A. Such behavior contrast that of the wild type and HCHT-W218A and resembles the action of endo-nonprocessive chitinases. PMID:26621384

  10. Site-directed mutagenesis reveals the importance of conserved charged residues for the transport activity of the PheP permease of Escherichia coli.

    Pi, J; Wookey, P J; Pittard, A. J.

    1993-01-01

    Site-directed mutagenesis has been used to identify a number of charged residues essential for the transport activity of the PheP protein. These residues are highly conserved in the cluster of amino acid transporters. However, some other conserved residues and a number of aromatic residues have been shown not to be essential for transport activity.

  11. Insight into the mechanism of phosphoenolpyruvate mutase catalysis derived from site-directed mutagenesis studies of active site residues.

    Jia, Y; Lu, Z; Huang, K; Herzberg, O; Dunaway-Mariano, D

    1999-10-26

    PEP mutase catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate in biosynthetic pathways leading to phosphonate secondary metabolites. A recent X-ray structure [Huang, K., Li, Z., Jia, Y., Dunaway-Mariano, D., and Herzberg, O. (1999) Structure (in press)] of the Mytilus edulis enzyme complexed with the Mg(II) cofactor and oxalate inhibitor reveals an alpha/beta-barrel backbone-fold housing an active site in which Mg(II) is bound by the two carboxylate groups of the oxalate ligand and the side chain of D85 and, via bridging water molecules, by the side chains of D58, D85, D87, and E114. The oxalate ligand, in turn, interacts with the side chains of R159, W44, and S46 and the backbone amide NHs of G47 and L48. Modeling studies identified two feasible PEP binding modes: model A in which PEP replaces oxalate with its carboxylate group interacting with R159 and its phosphoryl group positioned close to D58 and Mg(II) shifting slightly from its original position in the crystal structure, and model B in which PEP replaces oxalate with its phosphoryl group interacting with R159 and Mg(II) retaining its original position. Site-directed mutagenesis studies of the key mutase active site residues (R159, D58, D85, D87, and E114) were carried out in order to evaluate the catalytic roles predicted by the two models. The observed retention of low catalytic activity in the mutants R159A, D85A, D87A, and E114A, coupled with the absence of detectable catalytic activity in D58A, was interpreted as evidence for model A in which D58 functions in nucleophilic catalysis (phosphoryl transfer), R159 functions in PEP carboxylate group binding, and the carboxylates of D85, D87 and E114 function in Mg(II) binding. These results also provide evidence against model B in which R159 serves to mediate the phosphoryl transfer. A catalytic motif, which could serve both the phosphoryl transfer and the C-C cleavage enzymes of the PEP mutase superfamily, is proposed. PMID:10571990

  12. Mutagenesis of conserved active site residues of dihydrolipoamide succinyltransferase enhances the accumulation of α-ketoglutarate in Yarrowia lipolytica.

    Guo, Hongwei; Madzak, Catherine; Du, Guocheng; Zhou, Jingwen

    2016-01-01

    α-Ketoglutarate (α-KG) is an important intermediate in the tricarboxylic acid cycle and has broad applications. The mitochondrial ketoglutarate dehydrogenase (KGDH) complex catalyzes the oxidation of α-KG to succinyl-CoA. Disruption of KGDH, which may enhance the accumulation of α-KG theoretically, was found to be lethal to obligate aerobic cells. In this study, individual overexpression of dihydrolipoamide succinyltransferase (DLST), which serves as the inner core of KGDH, decreased overall activity of the enzyme complex. Furthermore, two conserved active site residues of DLST, His419, and Asp423 were identified. In order to determine whether these residues are engaged in enzyme reaction or not, these two conserved residues were individually mutated. Analysis of the kinetic parameters of the enzyme variants provided evidence that the catalytic reaction of DLST depended on residues His419 and Asp423. Overexpression of mutated DLST not only impaired balanced assembly of KGDH, but also disrupted the catalytic integrity of the enzyme complex. Replacement of the Asp423 residue by glutamate increased extracellular α-KG by 40 % to 50 g L(-1) in mutant strain. These observations uncovered catalytic roles of two conserved active site residues of DLST and provided clues for effective metabolic strategies for rational carbon flux control for the enhanced production of α-KG and related bioproducts. PMID:26428234

  13. Targeted reengineering of protein geranylgeranyltransferase type I selectivity functionally implicates active-site residues in protein-substrate recognition.

    Gangopadhyay, Soumyashree A; Losito, Erica L; Hougland, James L

    2014-01-21

    Posttranslational modifications are vital for the function of many proteins. Prenylation is one such modification, wherein protein geranylgeranyltransferase type I (GGTase-I) or protein farnesyltransferase (FTase) modify proteins by attaching a 20- or 15-carbon isoprenoid group, respectively, to a cysteine residue near the C-terminus of a target protein. These enzymes require a C-terminal Ca1a2X sequence on their substrates, with the a1, a2, and X residues serving as substrate-recognition elements for FTase and/or GGTase-I. While crystallographic structures of rat GGTase-I show a tightly packed and hydrophobic a2 residue binding pocket, consistent with a preference for moderately sized a2 residues in GGTase-I substrates, the functional impact of enzyme-substrate contacts within this active site remains to be determined. Using site-directed mutagenesis and peptide substrate structure-activity studies, we have identified specific active-site residues within rat GGTase-I involved in substrate recognition and developed novel GGTase-I variants with expanded/altered substrate selectivity. The ability to drastically alter GGTase-I selectivity mirrors similar behavior observed in FTase but employs mutation of a distinct set of structurally homologous active-site residues. Our work demonstrates that tunable selectivity may be a general phenomenon among multispecific enzymes involved in posttranslational modification and raises the possibility of variable substrate selectivity among GGTase-I orthologues from different organisms. Furthermore, the GGTase-I variants developed herein can serve as tools for studying GGTase-I substrate selectivity and the effects of prenylation pathway modifications on specific proteins. PMID:24344934

  14. Biochemical characterization of mutants in the active site residues of the β-galactosidase enzyme of Bacillus circulans ATCC 31382

    Bultema, Jelle B; Bas J.H. Kuipers; Lubbert Dijkhuizen

    2014-01-01

    The Bacillus circulans ATCC 31382 β-galactosidase (BgaD) is a retaining-type glycosidase of glycoside hydrolase family 2 (GH2). Its commercial enzyme preparation, Biolacta N5, is used for commercial-scale production of galacto-oligosaccharides (GOS). The BgaD active site and catalytic amino acid residues have not been studied. Using bioinformatic routines we identified two putative catalytic glutamates and two highly conserved active site histidines. The site-directed mutants E447N, E532Q, an...

  15. Identification of residues involved in nucleotidyltransferase activity of JHP933 from helicobacter pyloriby site-directed mutagenesis

    Ye Xianren

    2016-01-01

    Full Text Available Helicobacter pylori is a well-known bacterial pathogen involved in the development of peptic ulcer, gastric adenocarcinoma and other forms of gastric cancer. Evidence has suggested that certain strain-specific genes in the plasticity region may play key roles in the pathogenesis of H. pylori-associated gastroduodenal diseases. Therefore there is considerable interest in the strain-specific genes located in the plasticity regions of H. pylori. JHP933 is encoded by the gene in the plasticity region of H. pylori strain J99. Recently, the crystal structure of JHP933 has confirmed it as a nucleotidyltransferase (NTase superfamily protein and a putative active site has been proposed. However, no evidence from direct functional assay has been presented to confirm the active site and little is known about the functional mechanism of JHP933. Here, through superimposition with Cid1/NTP complex structures, we modelled the complex structures of JHP933 with different NTPs. Based on the models and using rational site-directed mutagenesis combined with enzymatic activity assays, we confirm the active site and identify several residues important for the nucleotidyl transferring function of JHP933. Furthermore, mutations of these active site residues result in the abolishment of the nucleotidyltransferase activity of JHP933. This work provides preliminary insight into the molecular mechanism underlying the pathophysiological role in H. pylori infection of JHP933 as a novel NTase superfamily protein.

  16. Analysis and radiological assessment of residues containing NORM materials resulting from earlier activities including modelling of typical industrial residues. Pt. 1. Historical investigation of the radiological relevance of NORM residues and concepts for site identification

    Natural radionuclides are part of the human environment and of the raw materials used. Technical processes may cause their accumulation in residues, and the result will be so-called NORM materials (Naturally occurring radioactive material). The amended Radiation Protection Ordinance (StrlSchV 2001) specifies how the public should be protected, but there are also residues dating back before the issuing of the StrlSchV 2001, the so-called NORM residues. The project intended to assess the risks resulting from these residues. It comprises four parts. Part 1 was for clarification of the radiological relevance of NORM residues and for the development of concepts to detect them. The criterion for their radiological relevance was their activity per mass unit and the material volume accumulated through the centuries. The former was calculated from a wide bibliographic search in the relevant literature on radiation protection, while the mass volume was obtained by a detailed historical search of the consumption of materials that may leave NORM residues. These are, in particular, residues from coal and ore mining and processing. To identify concrete sites, relevant data sources were identified, and a concept for identification of concrete NORM residues was developed on this basis. (orig.)

  17. A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.

    Agata Jacewicz

    Full Text Available Non-conserved amino acids that are far removed from the active site can sometimes have an unexpected effect on enzyme catalysis. We have investigated the effects of alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase, and identified a substitution in a weakly conserved palm residue (D714A, that renders the enzyme incapable of sustaining phage replication in vivo. D714, located several angstroms away from the active site, does not contact the DNA or the incoming dNTP, and our apoenzyme and ternary crystal structures of the Pol(D714A mutant demonstrate that D714A does not affect the overall structure of the protein. The structures reveal a conformational change of several amino acid side chains, which cascade out from the site of the substitution towards the catalytic center, substantially perturbing the geometry of the active site. Consistent with these structural observations, the mutant has a significantly reduced k pol for correct incorporation. We propose that the observed structural changes underlie the severe polymerization defect and thus D714 is a remote, non-catalytic residue that is nevertheless critical for maintaining an optimal active site conformation. This represents a striking example of an action-at-a-distance interaction.

  18. Mass spectrometry and site-directed mutagenesis identify several autophosphorylated residues required for the activity of PrkC, a Ser/Thr kinase from Bacillus subtilis

    Madec, Edwige; Stensballe, Allan; Kjellström, Sven; Cladière, Lionel; Obuchowski, Michal; Jensen, Ole Nørregaard; Séror, Simone J

    2003-01-01

    high mass accuracy electrospray tandem mass spectrometry (LC-MS/MS) and nanoelectrospray tandem mass spectrometry, we identified seven phosphorylated threonine and one serine residue in PrkCc. All the corresponding residues were replaced by systematic site-directed mutagenesis and the purified mutant...... proteins were tested for in vitro kinase activity. Single and multiple replacement of four threonine residues, clustered between residues 162 and 167 in a putative activation loop, substantially reduced kinase activity and the effect was clearly additive. Replacement of the other three threonine residues......, clustered between residues 290 and 320, had relatively little effect on activity. In contrast, substitution of Ser214, which is conserved in closely related receptor kinase-like bacterial proteins, independently affected activity and may represent a novel regulatory mechanism. When projected onto a 3D...

  19. Divergent Contributions of Conserved Active Site Residues to Transcription by Eukaryotic RNA Polymerases I and II

    Olga V. Viktorovskaya

    2013-09-01

    Full Text Available Multisubunit RNA polymerases (msRNAPs exhibit high sequence and structural homology, especially within their active sites, which is generally thought to result in msRNAP functional conservation. However, we show that mutations in the trigger loop (TL in the largest subunit of RNA polymerase I (Pol I yield phenotypes unexpected from studies of Pol II. For example, a well-characterized gain-of-function mutation in Pol II results in loss of function in Pol I (Pol II: rpb1- E1103G; Pol I: rpa190-E1224G. Studies of chimeric Pol II enzymes hosting Pol I or Pol III TLs suggest that consequences of mutations that alter TL dynamics are dictated by the greater enzymatic context and not solely the TL sequence. Although the rpa190-E1224G mutation diminishes polymerase activity, when combined with mutations that perturb Pol I catalysis, it enhances polymerase function, similar to the analogous Pol II mutation. These results suggest that Pol I and Pol II have different rate-limiting steps.

  20. Bromopyruvate, an active site-directed inactivator of E. coli 2-keto-4-hydroxyglutarate(KHG) aldolase, modifies glutamic acid residue-45

    Vlahos, C.J.; Dekker, E.E.

    1987-05-01

    E. coli KHG-aldolase (2-keto-4-hydroxyglutarate in equilibrium pyruvate + glyoxylate), a novel trimeric Class I aldolase, requires one active-site lysine residue (Lys 133)/subunit for Schiff-base formation as well as one arginine residue (Arg 49)/subunit for catalytic activity. The substrate analog, 3-bromopyruvate (BRPY), causes a time- and concentration-dependent loss of KHG-aldolase activity. This inactivation is regarded as active site-directed since: (a) BRPY modification results in complete loss of enzymatic activity; (b) saturation kinetics are exhibited, suggesting that a reversible complex is formed between the aldolase and BRPY prior to the rate-limiting inactivation step; (c) over 90% of the initial aldolase activity is protected by either substrate, pyruvate or KHG; (d) 1.1 mol of /sup 14/C-BRPY is bound/enzyme subunit. Peptide isolation and sequencing show that the incorporated radioactivity is associated with residue Glu-45. Denaturation of the enzyme with guanidine x HCl following treatment with excess /sup 14/C-BRPY allows for the incorporation of carbon-14 at Cys-159 and Cys-180 as well. The presence of pyruvate protects Glu-45 from being esterified but does not prevent the alkylation of the two cysteine residues. These results suggest that Glu-45 is essential for the catalytic activity of E. coli KHG-aldolase, most likely functioning as the active-site amphoteric proton donor/acceptor moiety that is involved in the overall mechanism of the reaction catalyzed by this enzyme.

  1. Bromopyruvate, an active site-directed inactivator of E. coli 2-keto-4-hydroxyglutarate(KHG) aldolase, modifies glutamic acid residue-45

    E. coli KHG-aldolase (2-keto-4-hydroxyglutarate ↔ pyruvate + glyoxylate), a novel trimeric Class I aldolase, requires one active-site lysine residue (Lys 133)/subunit for Schiff-base formation as well as one arginine residue (Arg 49)/subunit for catalytic activity. The substrate analog, 3-bromopyruvate (BRPY), causes a time- and concentration-dependent loss of KHG-aldolase activity. This inactivation is regarded as active site-directed since: (a) BRPY modification results in complete loss of enzymatic activity; (b) saturation kinetics are exhibited, suggesting that a reversible complex is formed between the aldolase and BRPY prior to the rate-limiting inactivation step; (c) over 90% of the initial aldolase activity is protected by either substrate, pyruvate or KHG; (d) 1.1 mol of 14C-BRPY is bound/enzyme subunit. Peptide isolation and sequencing show that the incorporated radioactivity is associated with residue Glu-45. Denaturation of the enzyme with guanidine x HCl following treatment with excess 14C-BRPY allows for the incorporation of carbon-14 at Cys-159 and Cys-180 as well. The presence of pyruvate protects Glu-45 from being esterified but does not prevent the alkylation of the two cysteine residues. These results suggest that Glu-45 is essential for the catalytic activity of E. coli KHG-aldolase, most likely functioning as the active-site amphoteric proton donor/acceptor moiety that is involved in the overall mechanism of the reaction catalyzed by this enzyme

  2. Residual activity criteria for decommissioning

    The U.S. Nuclear Regulatory Commission development of criteria for release of facilities and sites for unrestricted use following decommissioning is described. Residual activity limits for both materials and soil are covered. The objectives are: small risk of exposure, consistency with relevant existing standards, and feasibility of demonstration of compliance by measurement. Specific aspects discussed related to establishment of limits are: appropriate risk and dose limits, identification of radionuclides to be considered, dose assessment methodology, and confirmatory measurements

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

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

    2000-01-01

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

  4. Identification and clarification of the role of key active site residues in bacterial glutathione S-transferase zeta/maleylpyruvate isomerase

    Highlights: → Application of site-directed mutagenesis to probe the active site residues of glutathione-dependent maleylpyruvate isomerase. → Two conserved residues, Arg8 and Arg176, in zeta class glutathione S-transferases are critical for maleylpyruvate orientation and enolization. → Arg109, found exclusively in NagL, participates in kcat regulation. → The T11A mutant exhibited a significantly decreased Km value for glutathione with little impact on maleylpyruvate kinetics. → The Thr11 residue appears to have significance in the evolution of glutathione S-transferase classes. -- Abstract: The maleylpyruvate isomerase NagL from Ralstonia sp. strain U2, which has been structurally characterized previously, catalyzes the isomerization of maleylpyruvate to fumarylpyruvate. It belongs to the class zeta glutathione S-transferases (GSTZs), part of the cytosolic GST family (cGSTs). In this study, site-directed mutagenesis was conducted to probe the functions of 13 putative active site residues. Steady-state kinetic information for mutants in the reduced glutathione (GSH) binding site, suggested that (a) Gln64 and Asp102 interact directly with the glutamyl moiety of glutathione, (b) Gln49 and Gln64 are involved in a potential electron-sharing network that influences the ionization of the GSH thiol. The information also suggests that (c) His38, Asn108 and Arg109 interact with the GSH glycine moiety, (d) His104 has a role in the ionization of the GSH sulfur and the stabilization of the maleyl terminal carboxyl group in the reaction intermediate and (e) Arg110 influences the electron distribution in the active site and therefore the ionization of the GSH thiolate. Kinetic data for mutants altered in the substrate-binding site imply that (a) Arg8 and Arg176 are critical for maleylpyruvate orientation and enolization, and (b) Arg109 (exclusive to NagL) participates in kcat regulation. Surprisingly, the T11A mutant had a decreased GSH Km value, whereas little impact

  5. Structure-guided mutagenesis of active site residues in the dengue virus two-component protease NS2B-NS3

    Salaemae Wanisa

    2010-08-01

    Full Text Available Abstract Background The dengue virus two-component protease NS2B/NS3 mediates processing of the viral polyprotein precursor and is therefore an important determinant of virus replication. The enzyme is now intensively studied with a view to the structure-based development of antiviral inhibitors. Although 3-dimensional structures have now been elucidated for a number of flaviviral proteases, enzyme-substrate interactions are characterized only to a limited extend. The high selectivity of the dengue virus protease for the polyprotein precursor offers the distinct advantage of designing inhibitors with exquisite specificity for the viral enzyme. To identify important determinants of substrate binding and catalysis in the active site of the dengue virus NS3 protease, nine residues, L115, D129, G133, T134, Y150, G151, N152, S163 and I165, located within the S1 and S2 pockets of the enzyme were targeted by alanine substitution mutagenesis and effects on enzyme activity were fluorometrically assayed. Methods Alanine substitutions were introduced by site-directed mutagenesis at residues L115, D129, G133, T134, Y150, G151, N152, S163 and I165 and recombinant proteins were purified from overexpressing E. coli. Effects of these substitutions on enzymatic activity of the NS3 protease were assayed by fluorescence release from the synthetic model substrate GRR-amc and kinetic parameters Km, kcat and kcat/Km were determined. Results Kinetic data for mutant derivatives in the active site of the dengue virus NS3 protease were essentially in agreement with a functional role of the selected residues for substrate binding and/or catalysis. Only the L115A mutant displayed activity comparable to the wild-type enzyme, whereas mutation of residues Y150 and G151 to alanine completely abrogated enzyme activity. A G133A mutant had an approximately 10-fold reduced catalytic efficiency thus suggesting a critical role for this residue seemingly as part of the oxyanion

  6. Inhibition of Alkaline Phosphatase from Pearl Oyster Pinctada fucata by o-Phthalaldehyde: Involvement of Lysine and Histidine Residues at the Active Site

    CHEN Hongtao; XIE Liping; YU Zhenyan; ZHANG Rongqing

    2005-01-01

    Alkaline phosphatase from Pinctada fucata was inactivated by o-phthalaldehyde (OPA). The inactivation followed pseudo first-order kinetics with a second rate constant of 0.167 (mmol/L)-1·min-1 at pH 7.5 and 25°C. A Tsou's plot analysis showed that inactivation occurred upon formation of one isoindole group. The OPA-modified enzyme lost the ability to bind with the specific affinity column and the presence of substrates or competitive inhibitors protected the enzyme from inactivation. The results revealed that the OPA-reaction site was at the enzyme substrate binding site. Prior modification of the enzyme by lysine or histidine specific reagent abolished formation of the isoindole derivatives, suggesting that lysine and histidine residues were involved in the OPA-induced inactivation. Taken together, OPA inactivated the alkaline phosphatase from Pinctada fucata by cross-linking lysine and histidine residues at the active site and formed an isoindole group at the substrate binding site of the enzyme.

  7. HEU Measurements of Holdup and Recovered Residue in the Deactivation and Decommission Activities of the 321-M Reactor Fuel Fabrication Facility at the Savannah River Site

    This paper contains a summary of the holdup and material control and accountability assays conducted for the determination of highly enriched uranium in the deactivation and decommissioning of Building 321 -M at the Savannah River Site. The facility was the Reactor Fuel Fabrication Facility at SRS and assemblies and miscellaneous components for the SRS production reactors. The facility operated for 25 years. During this time thousands of uranium-aluminum-alloy production reactor fuel tubes were produced. After the facility ceased operations in 1995, all of the easily accessible U-Al was removed from the building, and only residual amounts remained. The D and D project is likely to represent an important example for D and D activities across SRS and across the Department of Energy weapons complex

  8. HEU Measurements of Holdup and Recovered Residue in the Deactivation and Decommissioning Activities of the 321-M Reactor Fuel Fabrication Facility at the Savannah River Site

    DEWBERRY, RAYMOND; SALAYMEH, SALEEM R.; CASELLA, VITO R.; MOORE, FRANK S.

    2005-03-11

    This paper contains a summary of the holdup and material control and accountability (MC&A) assays conducted for the determination of highly enriched uranium (HEU) in the deactivation and decommissioning (D&D) of Building 321-M at the Savannah River Site (SRS). The 321-M facility was the Reactor Fuel Fabrication Facility at SRS and was used to fabricate HEU fuel assemblies, lithium-aluminum target tubes, neptunium assemblies, and miscellaneous components for the SRS production reactors. The facility operated for more than 35 years. During this time thousands of uranium-aluminum-alloy (U-Al) production reactor fuel tubes were produced. After the facility ceased operations in 1995, all of the easily accessible U-Al was removed from the building, and only residual amounts remained. The bulk of this residue was located in the equipment that generated and handled small U-Al particles and in the exhaust systems for this equipment (e.g., Chip compactor, casting furnaces, log saw, lathes A & B, cyclone separator, Freon{trademark} cart, riser crusher, ...etc). The D&D project is likely to represent an important example for D&D activities across SRS and across the Department of Energy weapons complex. The Savannah River National Laboratory was tasked to conduct holdup assays to quantify the amount of HEU on all components removed from the facility prior to placing in solid waste containers. The U-235 holdup in any single component of process equipment must not exceed 50 g in order to meet the container limit. This limit was imposed to meet criticality requirements of the low level solid waste storage vaults. Thus the holdup measurements were used as guidance to determine if further decontamination of equipment was needed to ensure that the quantity of U-235 did not exceed the 50 g limit and to ensure that the waste met the Waste Acceptance Criteria (WAC) of the solid waste storage vaults. Since HEU is an accountable nuclear material, the holdup assays and assays of recovered

  9. HEU measurements of holdup and recovered residue in the deactivation and decommission activities of the 321-M Reactor Fuel Fabrication Facility at the Savannah River Site

    This paper contains a summary of the holdup and material control and accountability (MC and A) assays conducted for the determination of highly enriched uranium (HEU) in the deactivation and decommissioning (D and D) of the Reactor Fuel Fabrication Facility at the Savannah River Site (SRS). The facility was used to fabricate HEU fuel assemblies, lithium-aluminum target tubes, neptunium assemblies, and miscellaneous components for the SRS production reactors. The facility operated for more than 35 years. During this time thousands of uranium-aluminum alloy (U-Al) production reactor fuel tubes were produced. After the facility ceased operations in 1995, all of the easily accessible U-Al was removed from the building, and only residual amounts remained. The bulk of this residue was located in the equipment that generated and handled small U-Al particles and in the exhaust systems for this equipment (e.g., chip compactor, casting furnaces, log saw, lathes A and B, cyclone separator, FreonTM cart, riser crusher, ..., etc). The D and D project is likely to represent an important example for D and D activities across SRS and across the Department of Energy weapons complex. The Savannah River National Laboratory was tasked to conduct holdup assays to quantify the amount of HEU on all components removed from the facility prior to placing in solid waste containers. The 235U holdup in any single component of process equipment must not exceed 50 g in order to meet the container limit. This limit was imposed to meet criticality requirements of the low level solid waste storage vaults. Thus, the holdup measurements were used as guidance to determine if further decontamination of equipment was needed to ensure that the quantity of 235U did not exceed the 50 g limit and to ensure that the waste met the Waste Acceptance Criteria (WAC) of the solid waste storage vaults. Since HEU is an accountable nuclear material, the holdupassays and assays of recovered residue were also important

  10. Combining specificity determining and conserved residues improves functional site prediction

    Gelfand Mikhail S

    2009-06-01

    Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

  11. Residues from nuclear testing at the test site Azgir

    The Azgir test site is situated in the western part of the Republic of Kazakhstan, about 180 km north of the Caspian Sea. The Azgir test site was used for conducting peaceful nuclear explosions from 1966 to 1979. 17 underground tests were carried out in 10 wells which created 9 special cavities in the salt with depths from 160 to 1500 m. The total volume of these cavities is about 1,000,000 cubic meter. Resulting from this activity, there is an environmental contamination that may have affected population living in the adjacent areas. The results of investigations of radiological conditions that were performed after the closing of the Azgir test site, and current activities of international and Kazakhstan's institutions for studying residues from nuclear tests are also discussed in this report. (author)

  12. Identification of essential residues for binding and activation in the human 5-HT7(a receptor by molecular modeling and site-directed mutagenesis

    Agata Antonina Rita Impellizzeri

    2015-05-01

    We examined molecular determinants of ligand binding and G protein activation by the human 5-HT7(a receptor. The role of several key residues in the 7th transmembrane domain and helix 8 were elucidated combining in silico and experimental mutagenesis. Several single and two double point mutations of the 5-HT7(a wild type receptor were made (W7.33V, E7.35T, E7.35R, E7.35D, E7.35A, R7.36V, Y7.43A, Y7.43F, Y7.43T, R8.52D, D8.53K; E7.35T-R7.36V, R8.52D-D8.53K, and their effects upon ligand binding were assessed by radioligand binding using a potent agonist (5-CT and a potent antagonist (SB269970. In addition, the ability of the mutated 5-HT7(a receptors to activate G protein after 5-HT-stimulation was determined through activation of adenylyl cyclase. In silico investigation on mutated receptors substantiated the predicted importance of TM7 and showed critical roles of residues E7.35, W7.33, R7.36 and Y7.43 in agonist and antagonist binding and conformational changes of receptor structure affecting adenylyl cyclase activation. Experimental data showed that mutants E7.35T and E7.35R were incapable of ligand binding and adenylyl cyclase activation, consistent with a requirement for a negatively charged residue at this position. The mutant R8.52D was unable to activate adenylyl cyclase, despite unaffected ligand binding, consistent with the R8.52 residue playing an important role in the receptor-G protein interface. The mutants Y7.43A and Y7.43T displayed reduced agonist binding and AC agonist potency, not seen in Y7.43F, consistent with a requirement for an aromatic residue at this position. Knowledge of the molecular interactions important in h5-HT7 receptor ligand binding and G protein activation will aid the design of selective h5-HT7 receptor ligands for potential pharmacological use.

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

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

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

    Xu, K.Y.

    1988-01-01

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

  15. Identification of essential residues in 2',3'-cyclic nucleotide 3'-phosphodiesterase. Chemical modification and site-directed mutagenesis to investigate the role of cysteine and histidine residues in enzymatic activity.

    Lee, J; Gravel, M; Gao, E; O'Neill, R C; Braun, P E

    2001-05-01

    2',3'-Cyclic nucleotide 3'-phosphodiesterase (CNP; EC ) catalyzes in vitro hydrolysis of 3'-phosphodiester bonds in 2',3'-cyclic nucleotides to produce 2'-nucleotides exclusively. N-terminal deletion mapping of the C-terminal two-thirds of recombinant rat CNP1 identified a region that possesses the catalytic domain, with further truncations abolishing activity. Proteolysis and kinetic analysis indicated that this domain forms a compact globular structure and contains all of the catalytically essential features. Subsequently, this catalytic fragment of CNP1 (CNP-CF) was used for chemical modification studies to identify amino acid residues essential for activity. 5,5'-Dithiobis-(2-nitrobenzoic acid) modification studies and kinetic analysis of cysteine CNP-CF mutants revealed the nonessential role of cysteines for enzymatic activity. On the other hand, modification studies with diethyl pyrocarbonate indicated that two histidines are essential for CNPase activity. Consequently, the only two conserved histidines, His-230 and His-309, were mutated to phenylalanine and leucine. All four histidine mutants had k(cat) values 1000-fold lower than wild-type CNP-CF, but K(m) values were similar. Circular dichroism studies demonstrated that the low catalytic activities of the histidine mutants were not due to gross changes in secondary structure. Taken together, these results demonstrate that both histidines assume critical roles for catalysis. PMID:11278504

  16. Single Residue Mutation in Active Site of Serine Acetyltransferase Isoform 3 from Entamoeba histolytica Assists in Partial Regaining of Feedback Inhibition by Cysteine

    Kumar, Sudhir; Mazumder, Mohit; Dharavath, Sudhaker; Gourinath, S.

    2013-01-01

    The cysteine biosynthetic pathway is essential for survival of the protist pathogen Entamoeba histolytica, and functions by producing cysteine for countering oxidative attack during infection in human hosts. Serine acetyltransferase (SAT) and O-acetylserine sulfhydrylase (OASS) are involved in cysteine biosynthesis and are present in three isoforms each. While EhSAT1 and EhSAT2 are feedback inhibited by end product cysteine, EhSAT3 is nearly insensitive to such inhibition. The active site res...

  17. Investigation of the Role of Cytochrome P450 2B4 Active Site Residues in Substrate Metabolism Based on Crystal Structures of the Ligand-bound Enzyme

    Hernandez, Cynthia E.; Kumar, Santosh; Liu, Hong; Halpert, James R.

    2006-01-01

    Based on the x-ray crystal structures of 4-(4-chlorophenyl)imidazole (4-CPI)- and bifonazole (BIF)-bound P450 2B4, eight active site mutants at six positions were created in an N-terminal modified construct termed 2B4dH and characterized for enzyme inhibition and catalysis. I363A showed a > 4-fold decrease in differential inhibition by BIF and 4-CPI (IC50,BIF/IC50,4-CPI). F296A, T302A, I363A, V367A, and V477A showed a ≥ 2-fold decreased kcat for 7-ethoxy-4-trifluoromethylcoumarin O-deethylati...

  18. Contaminated Sites by Residues from Romanian Industry

    Full text: In Romania, the mining industries of ferrous ore, non-ferrous ore, bauxite, coal, chemical fertilisers, the extraction of natural gas and oil, etc. have a considerable weight in economy. The study lets us know that in these industries, in different by-products and waste from the process, some radionuclides come out. The preliminary data, which are determined in these industries, are compared with those data, which are published by the countries from EU. There were determined uranium, radium and thorium from ore and sterile (ferrous, non-ferrous, bauxite, talc, clay, asbestos, barytine, salt, coal and bituminous schist). Also, there have been determined the radium and the uranium content of waters from non-uraniferous mining sites. The level of radioactive noxa has been informative determined in each mine. The level of the concentrations requires a systematic research and an assessment of the risk and the impact against the environment, the workers, and the public. (author)

  19. Site-specific mutagenesis of histidine residues in the lac permease of Escherichia coli.

    Padan, E; Sarkar, H K; Viitanen, P V; Poonian, M S; Kaback, H R

    1985-01-01

    The lacY gene of Escherichia coli, which encodes the lac permease, has been modified by oligonucleotide-directed, site-specific mutagenesis such that each of the four histidine residues in the molecule is replaced with an arginine residue. Replacement of histidine-35 and histidine-39 with arginine has no apparent effect on permease activity. In contrast, replacement of either histidine-205 or histidine-322 by arginine causes a dramatic loss of transport activity, although the cells contain a ...

  20. Inventory of sites used to develop residual radioactivity criteria

    The US Environmental Protection Agency (EPA), in conjunction with the National Conference of Radiation Control Program Directors (CRCPD), has compiled an inventory of never licensed or otherwise poorly documented sites that may be contaminated with radioactive materials. This effort is in support of the EPA's development of radiation protection criteria for residual radioactivity at decommissioned sites. The inventory will help to establish the range of circumstances for which criteria are needed, as well as the suitability of candidate criteria for actual situations. The information will also be used to develop model sites and facilities for analyzing technical and economic feasibility of residual radioactivity criteria and to assess costs and benefits of alternate criteria. Relevant information about each site, such as radionuclides, waste forms, and quantities present will be included in the inventory when such information is available. The CRCPD has requested that each State radiation control agency furnish the information for the inventory. The inventory supplements the relatively extensive documentation of sites regulated by Federal or State agencies with information on old or unlicensed sites, such as old waste storage sites or radium ore processing facilities

  1. Combined Use of Residual Dipolar Couplings and Solution X-ray Scattering To Rapidly Probe Rigid-Body Conformational Transitions in a Non-phosphorylatable Active-Site Mutant of the 128 kDa Enzyme I Dimer

    Takayama, Yuki; Schwieters, Charles D.; Grishaev, Alexander; Ghirlando, Rodolfo; Clore, G. Marius (NIH)

    2012-10-23

    The first component of the bacterial phosphotransferase system, enzyme I (EI), is a multidomain 128 kDa dimer that undergoes large rigid-body conformational transitions during the course of its catalytic cycle. Here we investigate the solution structure of a non-phosphorylatable active-site mutant in which the active-site histidine is substituted by glutamine. We show that perturbations in the relative orientations and positions of the domains and subdomains can be rapidly and reliably determined by conjoined rigid-body/torsion angle/Cartesian simulated annealing calculations driven by orientational restraints from residual dipolar couplings and shape and translation information afforded by small- and wide-angle X-ray scattering. Although histidine and glutamine are isosteric, the conformational space available to a Gln side chain is larger than that for the imidazole ring of His. An additional hydrogen bond between the side chain of Gln189 located on the EIN{sup {alpha}/{beta}} subdomain and an aspartate (Asp129) on the EIN{sup {alpha}} subdomain results in a small ({approx}9{sup o}) reorientation of the EIN{sup {alpha}} and EIN{sup {alpha}/{beta}} subdomains that is in turn propagated to a larger reorientation ({approx}26{sup o}) of the EIN domain relative to the EIC dimerization domain, illustrating the positional sensitivity of the EIN domain and its constituent subdomains to small structural perturbations.

  2. Evidence for Participation of Remote Residues in the Catalytic Activity of Co-type Nitrile Hydratase from Pseudomonas putida†

    Brodkin, Heather R.; Novak, Walter R. P.; Milne, Amy C.; D’Aquino, J. Alejandro; Karabacak, N. M.; Agar, Jeffrey N.; Payne, Mark S.; Petsko, Gregory A; Ondrechen, Mary Jo; Ringe, Dagmar

    2011-01-01

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell, and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic prope...

  3. Residual Environmental Contamination at a Former Ferroniobium Production Site in Belgium

    From an aerial gamma survey, a site with residues from a former ferroniobium production facility was identified. In close collaboration with the current site operator, an inventory of the mineral residue piled on the ground was made and the material was characterized in terms of its radionuclide content (<1–12 and <1–60 Bq/g for radionuclides of the uranium and thorium decay series, respectively). The possibilities for total or partial use of this kind of heterogeneous material were evaluated and were mostly hindered by its chemical composition. Since it was documented that the residues had been used in the past for the levelling and filling of the site, a systematic gamma screening survey of the whole site was performed at ground level. Gamma dose rates of up to 6 μSv/h were detected at certain locations. Residues with elevated radionuclide concentrations were found to have been buried to depths of up to 1.5 m. In two measurement campaigns, the shallow and deep groundwater was screened for gross alpha and beta activity and for its chemical composition. Gross alpha and beta activity concentrations of up to 1000 and 6000 mBq/L, respectively, were found. At some locations, the pH reached a value of 12.9, as a result of past contamination by a certain calcium product. Short term and long term strategies for the cleanup process are currently under discussion. (author)

  4. Study on indium leaching from mechanically activated hard zinc residue

    Yao J.H.; Li X.H.; Li Y.W.

    2011-01-01

    In this study, changes in physicochemical properties and leachability of indium from mechanically activated hard zinc residue by planetary mill were investigated. The results showed that mechanical activation increased specific surface area, reaction activity of hard zinc residue, and decreased its particle size, which had a positive effect on indium extraction from hard zinc residue in hydrochloric acid solution. Kinetics of indium leaching from unmilled and activated hard zinc residue...

  5. Rehabilitation of storage sites for low radioactive uranium ore treatment residues. The example of the Ecarpiere Cogema's site (Loire-Atlantique, France)

    The rehabilitation of storage sites for residues of ore treatment represents the ultimate phase of this industrial activity and belongs to the ore processing cycle. In order to respect the enforced regulation, the objectives consist in ensuring the durable stability of the site and keeping all the residual environmental impacts as low as reasonably achievable. This paper presents the example of the rehabilitation of the Ecarpiere Cogema's site (Loire-Atlantique, France) where 7500000 t of uranium ore residues are stored. The preliminary studies (petrography and mineralogy of residues, hydrogeology, geotechnical study, cover definition, embankments stability), the works (plant dismantling, basins filling, embankments re-profiling, draining and revegetation), and the site surveillance (geotechnical and radiometric) are described. (J.S.)

  6. DOE site performance assessment activities

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

  7. Derivation of uranium residual radioactive material guidelines for the Shpack site

    Residual radioactive material guidelines for uranium were derived for the Shpack site in Norton, Massachusetts. This site has been identified for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy (DOE). The uranium guidelines were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the Shpack site should not exceed a dose of 100 mrem/yr following decontamination. The DOE residual radioactive material guideline computer code, RESRAD, which implements the methodology described in the DOE manual for implementing residual radioactive material guidelines, was used in this evaluation. Three potential scenarios were considered for the site; the scenarios vary with regard to time spent at the site, sources of water used, and sources of food consumed. The results of the evaluation indicate that the basic dose limit of 100 mrem/yr will not be exceeded for uranium (including uranium-234, uranium-235, and uranium-238) within 1000 years, provided that the soil concentration of combined uranium (uranium-234 and uranium-238) at the Shpack site does not exceed the following levels: 2500 pCi/g for Scenario A (recreationist: the expected scenario); 1100 pCi/g for Scenario B (industrial worker: a plausible scenario); and 53 pCi/g for Scenario C (resident farmer using a well water as the only water source: a possible but unlikely scenario). The uranium guidelines derived in this report apply to the combined activity concentration of uranium-234 and uranium-238 and were calculated on the basis of a dose of 100 mrem/yr. In setting the actual uranium guidelines for the Shpack site, DOE will apply the as low as reasonably achievable (ALARA) policy to the decision-making process, along with other factors, such as whether a particular scenario is reasonable and appropriate. 8 refs., 2 figs., 8 tabs

  8. Derivation of uranium residual radioactive material guidelines for the Aliquippa Forge site

    Residual radioactive material guidelines for uranium were derived for the Aliquippa Forge site in Aliquippa, Pennsylvania. This site has been identified for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy (DOE). The uranium guidelines were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the Aliquippa Forge site should not exceed a dose of 100 mrem/yr following decontamination. The DOE residual radioactive material guideline computer code, RESRAD, which implements the methodology described in the DOE manual for implementing residual radioactive material guidelines, was used in this evaluation. Four potential scenarios were considered for the site; the scenarios vary with regard to time spent at the site, sources of water used, and sources of food consumed. The results of the evaluation indicate that the basic dose limit of 100 mrem/yr will not be exceeded for uranium within 1,000 years, provided that the soil concentration of combined uranium (uranium-234, uranium-235, and uranium-238) at the Aliquippa Forge site does not exceed the following levels: 1,700 pCi/g for Scenario A (industrial worker: the expected scenario); 3,900 pCi/g for Scenario B (recreationist: a plausible scenario); 20 pCi/g for Scenario C (resident farmer using well water as the only water source: a possible but unlikely scenario), and 530 pCi/g for Scenario D (resident farmer using a distant water source not affected by site conditions as the only water source: a possible but unlikely scenario). The uranium guidelines derived in this report apply to the combined activity concentration of uranium-234, uranium-235, and uranium-238 and were calculated on the basis of a dose of 100 mrem/yr

  9. A radiographic study on the prevalence of knife-edge residual alveolar ridge at proposed dental implant sites

    Dental implants are widely used in restoration of completely or partially edentulous dental arches. Before placement of endosseous implants in the jaws, both the quantity and quality of the residual ridge must be assessed radiographically. Remodeling activity after tooth extraction is localized primarily at the crestal area of the residual ridges, resulting in reduction of the height of bone and creation of various three-dimensional shapes of the residual ridges. When bone resorption at the lingual and buccal aspects is greater than that at the crestal area, a knife-edge type of residual ridge develops. The aim of this study was to evaluate the prevalence of the knife-edge morphology of the residual alveolar bone at proposed implant sites in partially or completely edentulous patients. Computed tomography (CT) cross-sectional images of the upper and lower jaws were assessed at the proposed sites before implant placement. Images of 258 proposed implant sites belonging to 30 patients were assessed radiographically. In 120 proposed implant sites out of 258 (46.5%), the residual alveolar ridge had a knife-edge configuration, the majority belonging to completely edentulous patients who lost their teeth more than ten years previously. High prevalence of knife-edge ridge was found, therefore, replacement of missing teeth by immediate implant is recommended to prevent atrophy or knife-edge morphology of the residual ridge. (author)

  10. Site-directed Mutagenesis of Cysteine Residues in Phi-class Glutathione S-transferase F3 from Oryza sativa

    To elucidate the roles of cysteine residues in rice Phi-class GST F3, in this study, all three cysteine residues were replaced with alanine by site-directed mutagenesis in order to obtain mutants C22A, C73A and C77A. Three mutant enzymes were expressed in Escherichia coli and purified to electrophoretic homogeneity by affinity chromatography on immobilized GSH. The substitutions of Cys73 and Cys77 residues in OsGSTF3 with alanine did not affect the glutathione conjugation activities, showing non-essentiality of these residues. On the other hand, the substitution of Cys22 residue with alanine resulted in approximately a 60% loss of specific activity toward ethacrynic acid. Moreover, the KmCDNB value of the mutant C22A was approximately 2.2 fold larger than that of the wild type. From these results, the evolutionally conserved cysteine 22 residue seems to participate rather in the structural stability of the active site in OsGSTF3 by stabilizing the electrophilic substrates-binding site's conformation than in the substrate binding directly

  11. A coevolutionary residue network at the site of a functionally important conformational change in a phosphohexomutase enzyme family.

    Yingying Lee

    Full Text Available Coevolution analyses identify residues that co-vary with each other during evolution, revealing sequence relationships unobservable from traditional multiple sequence alignments. Here we describe a coevolutionary analysis of phosphomannomutase/phosphoglucomutase (PMM/PGM, a widespread and diverse enzyme family involved in carbohydrate biosynthesis. Mutual information and graph theory were utilized to identify a network of highly connected residues with high significance. An examination of the most tightly connected regions of the coevolutionary network reveals that most of the involved residues are localized near an interdomain interface of this enzyme, known to be the site of a functionally important conformational change. The roles of four interface residues found in this network were examined via site-directed mutagenesis and kinetic characterization. For three of these residues, mutation to alanine reduces enzyme specificity to ~10% or less of wild-type, while the other has ~45% activity of wild-type enzyme. An additional mutant of an interface residue that is not densely connected in the coevolutionary network was also characterized, and shows no change in activity relative to wild-type enzyme. The results of these studies are interpreted in the context of structural and functional data on PMM/PGM. Together, they demonstrate that a network of coevolving residues links the highly conserved active site with the interdomain conformational change necessary for the multi-step catalytic reaction. This work adds to our understanding of the functional roles of coevolving residue networks, and has implications for the definition of catalytically important residues.

  12. Proposed plan for remedial action at the quarry residuals operable unit of the Weldon Spring Site

    This proposed plan addresses the management of contamination present in various components of the quarry residuals operable unit (QROU) of the Weldon Spring site, which is located in St. Charles County, Missouri. The QROU consists of (1) residual waste at the quarry proper; (2) the Femme Osage Slough, Little Femme Osage Creek, and Femme Osage Creek; and (3) quarry groundwater located primarily north of the slough. Potential impacts to the St. Charles County well field downgradient of the quarry area are also being addressed as part of the evaluations for this operable unit. Remedial activities for the QROU will be conducted by the US Department of Energy (DOE) in accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended. As part of the remedial investigation/feasibility study (RI/FS) process required for the QROU under CERCLA, three major evaluation documents have been prepared to support cleanup decisions for this operable unit. decisions for this operable unit

  13. Derivation of uranium residual radioactive material guidelines for the Elza Gate Site

    Residual radioactive material guidelines for uranium were derived for a large, homogeneously contaminated area at the Elza Gate Site in Oak Ridge, Tennessee. The derivation of the single-nuclide and total uranium guidelines was based on the requirement that the 50-year committed effective dose equivalent to hypothetical individual who lives or works in the immediate vicinity of the Elza Gate Site should not exceed a dose of 100 mrem/yr following decontamination. The DOE residual radioactive guideline computer code RESRAD was used in this evaluation. Four potential scenarios were considered for the site; the scenarios vary with regard to time spent at the site, sources of water used, and sources of food consumed. The results of the evaluation indicate that the basic dose limit of 100 mrem/yr will not be exceeded for uranium within 1000 years, provided that the soil concentration of uranium at the Elza Gate Site does not exceed the following levels: 1800 pCi/g for Scenario A (industrial worker: the expected scenario); 4000 pCi/g for Scenario B (recreationist: a plausible scenario); 470 pCi/g for Scenario C (resident farmer using pond water as the only water source: a possible but unlikely scenario); and 120 pCi/g for Scenario D (resident farmer using well water as the only water source: a possible but unlikely scenario). The uranium guideline applies to the total activity concentration of uranium isotopes in their natural activity concentration ratio of 1:1: 0.046. These guidelines are calculated on the basis of a dose of 100 mrem/yr. In setting the actual uranium guideline for the Elza Gate Site, the DOE will apply the as low as reasonably achievable (ALARA) policy to the decision-making process, along with other factors, such as determining whether a particular scenario is reasonable and appropriate. 10 refs., 3 figs., 7 tabs

  14. Residual Chromium in Leather by Instrumental Neutron Activation Analysis

    S. Okoh

    2012-01-01

    Full Text Available Problem statement: Most tanning processes employ the use of chromium sulphate. For chromium tanned leather, finished products may contain high amount of residual chromium. This may pose some health hazards, since chromium is known to be toxic at elevated concentration. This justifies the need for the study. Approach: Various samples of leather were collected from a tannery, a leather crafts market, a leather dump site and from local tanners all in Kano, Nigeria in 2009. The samples were irradiated for 6 h in the inner site of the Nigerian Research Reactor (NIRR-1 at a flux of 5×1011 ncm-2 sec-1. Results: After evaluating the spectrum, the mean results for chromium in the samples were determined as 2.33±0.3, 2.23±0.3 and 2.93±0.4% for samples from the tannery, leather crafts market and leather dump sites respectively. Chromium concentration in samples collected from local tanners who use tannins from Acacia nilotica as tanning agent was below the detection limit of Instrumental Neutron Activation Analysis (INAA technique used in the study. Conclusion: Although, the concentrations of chromium in the analysed samples were not much higher than what were obtained in literature, they may be enough to sensitize the population that is allergic to chromium.

  15. Derivation of guidelines for uranium residual radioactive material in soil at the Colonie Site, Colonie, New York

    Residual radioactive material guidelines for uranium in soil were derived for the Colonie site located in Colonie, New York. This site has been designated for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the U.S. Department of Energy (DOE). The site became contaminated with radioactive material as a result of operations conducted by National Lead (NL) Industries from 1958 to 1984; these activities included brass foundry operations, electroplating of metal products, machining of various components using depleted uranium, and limited work with small amounts of enriched uranium and thorium. The Colonie site comprises the former NL Industries property, now designated the Colonie Interim Storage Site (CISS), and 56 vicinity properties contaminated by fallout from airborne emissions; 53 of the vicinity properties were previously remediated between 1984 and 1988. In 1984, DOE accepted ownership of the CISS property from NL Industries. Residual radioactive material guidelines for individual radionuclides and total uranium were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the site should not exceed a dose of 30 mrem/yr following remedial action for the current use and likely future use scenarios or a dose of 100 mrem/yr for less likely future use scenarios. The DOE residual radioactive material guideline computer code, RESRAD, was used in this evaluation; RESRAD implements the methodology described in the DOE manual for establishing residual radioactive material guidelines

  16. Fluorescence energy transfer studies on the active site of papain

    Henes, Jill B.; Briggs, Martha S.; Sligar, Stephen G.; Fruton, Joseph S.

    1980-01-01

    Measurements have been performed of the excited-state lifetimes and fluorescence yields of papain tryptophan units when acyl derivatives of Phe-glycinal are bound at the active site of the enzyme. The enhancement of tryptophan fluorescence in complexes of papain with the acetyl or benzyloxycarbonyl derivatives is not stereospecific with respect to the configuration of the phenylalanyl residue, and the L and D isomers are equally effective as active-site-directed inhibitors of papain action. E...

  17. Study on indium leaching from mechanically activated hard zinc residue

    Yao J.H.

    2011-01-01

    Full Text Available In this study, changes in physicochemical properties and leachability of indium from mechanically activated hard zinc residue by planetary mill were investigated. The results showed that mechanical activation increased specific surface area, reaction activity of hard zinc residue, and decreased its particle size, which had a positive effect on indium extraction from hard zinc residue in hydrochloric acid solution. Kinetics of indium leaching from unmilled and activated hard zinc residue were also investigated, respectively. It was found that temperature had an obvious effect on indium leaching rate. Two different kinetic models corresponding to reactions which are diffusion controlled, [1-(1- x1/3]2=kt and (1-2x/3-(1-x2/3=kt were used to describe the kinetics of indium leaching from unmilled sample and activated sample, respectively. Their activation energies were determined to be 17.89 kJ/mol (umilled and 11.65 kJ/mol (activated within the temperature range of 30°C to 90°C, which is characteristic for a diffusion controlled process. The values of activation energy demonstrated that the leaching reaction of indium became less sensitive to temperature after hard zinc residue mechanically activated by planetary mill.

  18. Derivation of residual radioactive material guidelines for uranium in soil at the Middlesex Sampling Plant Site, Middlesex, New Jersey

    Residual radioactive material guidelines for uranium in soil were derived for the Middlesex Sampling Plant (MSP) site in Middlesex, New Jersey. This site has been designated for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy. The site became contaminated from operations conducted in support of the Manhattan Engineer District (MED) and the Atomic Energy Commission (AEC) between 1943 and 1967. Activities conducted at the site included sampling, storage, and shipment of uranium, thorium, and beryllium ores and residues. Uranium guidelines for single radioisotopes and total uranium were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual living or working in the immediate vicinity of the MSP site should not exceed a dose of 30 mrem/yr following remedial action for the current-use and likely future-use scenarios or a dose of 100 mrem/yr for less likely future-use scenarios. The RESRAD computer code, which implements the methodology described in the DOE manual for establishing residual radioactive material guidelines, was used in this evaluation. Four scenarios were considered for the site. These scenarios vary regarding future land use at the site, sources of water used, and sources of food consumed

  19. Identification of critical residues of the mycobacterial dephosphocoenzyme a kinase by site-directed mutagenesis.

    Guneet Walia

    Full Text Available Dephosphocoenzyme A kinase performs the transfer of the γ-phosphate of ATP to dephosphocoenzyme A, catalyzing the last step of coenzyme A biosynthesis. This enzyme belongs to the P-loop-containing NTP hydrolase superfamily, all members of which posses a three domain topology consisting of a CoA domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. Differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have pointed out the tubercular CoaE as a high confidence drug target (HAMAP database. Unfortunately the absence of a three-dimensional crystal structure of the enzyme, either alone or complexed with either of its substrates/regulators, leaves both the reaction mechanism unidentified and the chief players involved in substrate binding, stabilization and catalysis unknown. Based on homology modeling and sequence analysis, we chose residues in the three functional domains of the enzyme to assess their contributions to ligand binding and catalysis using site-directed mutagenesis. Systematically mutating the residues from the P-loop and the nucleotide-binding site identified Lys14 and Arg140 in ATP binding and the stabilization of the phosphoryl intermediate during the phosphotransfer reaction. Mutagenesis of Asp32 and Arg140 showed catalytic efficiencies less than 5-10% of the wild type, indicating the pivotal roles played by these residues in catalysis. Non-conservative substitution of the Leu114 residue identifies this leucine as the critical residue from the hydrophobic cleft involved in leading substrate, DCoA binding. We show that the mycobacterial enzyme requires the Mg(2+ for its catalytic activity. The binding energetics of the interactions of the mutant enzymes with the substrates were characterized in terms of their enthalpic and entropic contributions by ITC, providing a complete picture of the effects of the mutations on activity. The properties of

  20. On-site treatment and landfilling of MSWI air pollution control residues

    Lundtorp, Kasper; Jensen, Dorthe Lærke; Sørensen, Mette Abildgaard;

    2003-01-01

    Air pollution control (APC) residues from municipal solid waste incineration (MSWI) are difficult to landfill due to substantial leaching of trace metals. An on-site pretreatment prior to landfilling of APC-residues was investigated in terms of bench-scale experiments with a semidry APC-residue and...... a fly ash. The treatment involved mixing of the residues with a ferrous sulphate solution and subsequent oxidation of the suspension. Afterwards, the suspension was spread on a dedicated landfill section and allowed to drain by gravity through the drainage system of the landfill. The wastewater from...

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

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

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

  2. Active Site Engineering in Electrocatalysis

    Verdaguer Casadevall, Arnau; Stephens, Ifan; Chorkendorff, Ib

    The overall goal of this thesis has been to design better catalysts for electrochemical reactions through a fundamental understanding of the materials at atomic scale. This has been achieved by combining electrochemical measurements with a variety of characterization techniques, often in ultra high...... under reaction conditions, which is ultimately controlled by the crystal structure of the underlying alloy.• Oxygen reduction to hydrogen peroxide has been investigated on single site catalysts, mainly alloys of noble metals with Hg. This resulted in a very special structure with isolated atoms of Pt or......, inexistent in other forms of Cu. The presence of strong CO binding sites correlates well with electrochemical activity, which paves the way for the rational development of even better electrocatalysts....

  3. Neuritogenic and neuroprotective activities of fruit residues.

    Tadtong, Sarin; Kanlayavattanakul, Mayuree; Lourith, Nattaya

    2013-11-01

    Neuritogenic and neuroprotective activities of litchi (Litchi chinensis Sonn., Sapindaceae) and salacca (Salacca edulis Reinw., Arecaceae) pericarp, and sapodilla (Achras sapota L., Sapotaceae) and tamarind Srichompu cultivar (Tamarindus indica L., Caesalpiniaceae) seed coat extracts were evaluated on cultured cholinergic P19-derived neurons. All the extracts, at a very low concentration (1 ng/mL of litchi and salacca pericarp extracts, 10 ng/mL of sapodilla and 100 ng/mL of tamarind seed coat extracts), enhanced the survival of cultured neurons (% viability more than 100%) by XTT reduction assay. The extracts were further evaluated for their neuritogenicity by observing cell morphology by phase-contrast microscopy and neuroprotective activity in serum deprivation and pre- and co-administration of hydrogen peroxide models. The phase-contrast micrographs displayed that all of the extracts possessed neurogenic activity by promoting the neurite outgrowth of the cultured neurons. Moreover, these extracts can protect neurons from oxidative stress-caused cell death in a serum deprivation model, and prevent and protect neuron cells from the toxicity of hydrogen peroxide. In this study we assured that the neuritogenic and neuroprotective activities of these extracts derived from the phenolic components and flavonoids contained in the extracts by acting as signaling molecules to enhance neuron survival and promote neurite outgrowth. These results suggest that all of the extracts are potentially sources of neuritogenic and neuroprotective components which might be used either as pharmaceutical products or dietary supplements for neurodegenerative disorder patients, for example, those suffering from Alzheimer's disease. PMID:24427947

  4. Derivation of uranium residual radioactive material guidelines for the 4400 Piehl Road Site, Ottawa Lake, Michigan

    Residual radioactive material guidelines for uranium were derived for the 4400 Piehl Road site in Ottawa Lake, Michigan. This site has been designated for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy (DOE). Single nuclide and total uranium guidelines were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the 4400 Piehl Road site should not exceed 30 mrem/yr following remedial action for the current use and plausible future use scenarios. The DOE residual radioactive material guideline computer code, RESRAD, which applies the methodology described in the DOE manual for implementing residual radioactive material guidelines, was used in this evaluation

  5. Derivation of uranium residual radioactive material guidelines for the Ventron site

    Residual radioactive material guidelines for uranium were derived for the Ventron site in Beverly, Massachusetts. This site has been identified for remedial action under the Formerly Utilized Sites Remedial Action Program of the US Department of Energy (DOE). The derivations for the single radionuclides and the total uranium guidelines were based on the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the Ventron site should not exceed a dose of 100 mrem/yr following remedial action. The DOE residual radioactive material guideline computer code, RESRAD, which implements the methodology described in the DOE manual for implementing residual radioactive material guidelines, was used in this evaluation

  6. Derivation of uranium residual radioactive material guidelines for the former Alba Craft Laboratory site, Oxford, Ohio

    Residual radioactive material guidelines for uranium were derived for the former Alba Craft Laboratory site in Oxford, Ohio. This site has been identified for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy (DOE). Single nuclide and total uranium guidelines were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the former Alba Craft Laboratory site should not exceed a dose of 30 mrem/yr following remedial action for the current use and likely future use scenarios or a dose of 100 mrem/yr for less likely future use scenarios (Yu et al. 1993). The DOE residual radioactive material guideline computer code, RESRAD, which implements the methodology described in the DOE manual for implementing residual radioactive material guidelines, was used in this evaluation

  7. 4-Oxalocrotonate tautomerase, a 41-kDa homohexamer: backbone and side-chain resonance assignments, solution secondary structure, and location of active site residues by heteronuclear NMR spectroscopy.

    Stivers, J T; Abeygunawardana, C; Whitman, C. P.; Mildvan, A. S.

    1996-01-01

    4-Oxalocrotonate tautomerase (4-OT), a homohexamer consisting of 62 residues per subunit, catalyzes the isomerization of unsaturated alpha-keto acids using Pro-1 as a general base (Stivers et al., 1996a, 1996b). We report the backbone and side-chain 1H, 15N, and 13C NMR assignments and the solution secondary structure for 4-OT using 2D and 3D homonuclear and heteronuclear NMR methods. The subunit secondary structure consists of an alpha-helix (residues 13-30), two beta-strands (beta 1, residu...

  8. Residual activity induced by ion bombardment on insulating samples

    In this work we investigate some properties of the residual activity induced by protons impinging on quartz, mylar and other insulating materials. In particular, we discuss the time constant related to the decay of the emitted radiation after the primary ion beam is turned off. This radiation includes a continuum of bremsstrahlung and, in some cases, characteristic X-rays induced in the process as well. In general, the results indicate the presence of two time constants in the decaying process. Moreover, it appears that the residual activity has a strong dependence on the material specifications and on the conditions of the surface under bombardment. A simple mechanism for this process is suggested

  9. Depleted uranium residual radiological risk assessment for Kosovo sites

    During the recent conflict in Yugoslavia, depleted uranium rounds were employed and were left in the battlefield. Health concern is related to the risk arising from contamination of areas in Kosovo with depleted uranium penetrators and dust. Although chemical toxicity is the most significant health risk related to uranium, radiation exposure has been allegedly related to cancers among veterans of the Balkan conflict. Uranium munitions are considered to be a source of radiological contamination of the environment. Based on measurements and estimates from the recent Balkan Task Force UNEP mission in Kosovo, we have estimated effective doses to resident populations using a well-established food-web mathematical model (RESRAD code). The UNEP mission did not find any evidence of widespread contamination in Kosovo. Rather than the actual measurements, we elected to use a desk assessment scenario (Reference Case) proposed by the UNEP group as the source term for computer simulations. Specific applications to two Kosovo sites (Planeja village and Vranovac hill) are described. Results of the simulations suggest that radiation doses from water-independent pathways are negligible (annual doses below 30 μSv). A small radiological risk is expected from contamination of the groundwater in conditions of effective leaching and low distribution coefficient of uranium metal. Under the assumptions of the Reference Case, significant radiological doses (>1 mSv/year) might be achieved after many years from the conflict through water-dependent pathways. Even in this worst-case scenario, DU radiological risk would be far overshadowed by its chemical toxicity

  10. Depleted uranium residual radiological risk assessment for Kosovo sites

    Durante, Marco E-mail: durante@na.infn.it; Pugliese, Mariagabriella

    2003-07-01

    During the recent conflict in Yugoslavia, depleted uranium rounds were employed and were left in the battlefield. Health concern is related to the risk arising from contamination of areas in Kosovo with depleted uranium penetrators and dust. Although chemical toxicity is the most significant health risk related to uranium, radiation exposure has been allegedly related to cancers among veterans of the Balkan conflict. Uranium munitions are considered to be a source of radiological contamination of the environment. Based on measurements and estimates from the recent Balkan Task Force UNEP mission in Kosovo, we have estimated effective doses to resident populations using a well-established food-web mathematical model (RESRAD code). The UNEP mission did not find any evidence of widespread contamination in Kosovo. Rather than the actual measurements, we elected to use a desk assessment scenario (Reference Case) proposed by the UNEP group as the source term for computer simulations. Specific applications to two Kosovo sites (Planeja village and Vranovac hill) are described. Results of the simulations suggest that radiation doses from water-independent pathways are negligible (annual doses below 30 {mu}Sv). A small radiological risk is expected from contamination of the groundwater in conditions of effective leaching and low distribution coefficient of uranium metal. Under the assumptions of the Reference Case, significant radiological doses (>1 mSv/year) might be achieved after many years from the conflict through water-dependent pathways. Even in this worst-case scenario, DU radiological risk would be far overshadowed by its chemical toxicity.

  11. Engineering assessment of radioactive sands and residues, Lowman Site, Lowman, Idaho

    1981-09-01

    Ford, Bacon and Davis Utah Inc. has reevaluated the Lowman site in order to revise the December 1977 engineering assessment of the problems resulting from the existence of radioactive sands and residues at Lowman, Idaho. This engineering assessment has included the preparation of topographic maps, the performance of core drillings and radiometric measurements sufficient to determine areas and volumes of radioactive sands and residues and radiation exposure of individuals and nearby populations, and investigations of site hydrology and meteorology, and the evaluation and costing of alternative corrective actions. Radon gas released from the 191,000 tons of radioactive sands, residues, and contaminated soils at the Lowman site constitutes the most significant environmental impact, although windblown radioactive sands and external gamma radiation also are factors.

  12. Engineering assessment of radioactive sands and residues, Lowman Site, Lowman, Idaho

    Ford, Bacon and Davis Utah Inc. has reevaluated the Lowman site in order to revise the December 1977 engineering assessment of the problems resulting from the existence of radioactive sands and residues at Lowman, Idaho. This engineering assessment has included the preparation of topographic maps, the performance of core drillings and radiometric measurements sufficient to determine areas and volumes of radioactive sands and residues and radiation exposure of individuals and nearby populations, and investigations of site hydrology and meteorology, and the evaluation and costing of alternative corrective actions. Radon gas released from the 191,000 tons of radioactive sands, residues, and contaminated soils at the Lowman site constitutes the most significant environmental impact, although windblown radioactive sands and external gamma radiation also are factors

  13. Summary of the engineering assessment of radioactive sands and residues, Lowman Site, Lowman, Idaho

    Ford, Bacon and Davis Utah Inc. has reevaluated the Lowman site in order to revise the December 1977 engineering assessment of the problems resulting from the existence of radioactive sands and residues at Lowman, Idaho. This engineering assessment has included the preparation of topographic maps, the performance of core drillings and radiometric measurements sufficient to determine areas and volumes of radioactive sands and residues and radiation exposures of individuals and nearby populations, the investigations of site hydrology and meteorology, and the evaluation and costing of alternative corrective actions. Radon gas released from the 191,000 tons of radioactive sands, residues, and contaminated soils at the Lowman site constitutes the most significant environmental impact, although windblown radioactive sands and external gamma radiation also are factors

  14. Derivation of residual radioactive material guidelines for the Laboratory for Energy-Related Health Research site

    Residual radioactive material guidelines were derived for the Laboratory for Energy-Related Health Research (LEHR) Environmental Restoration (ER) site in Davis, California. The guideline derivation was based on a dose limit of 100 mrem/yr. The US Department of Energy (DOE) residual radioactive material guideline computer code was used in this evaluation. This code implements the methodology described in the DOE manual for implementing residual radioactive material guidelines. Three potential site utilization scenarios were considered with the assumption that following ER action, the site will be used without radiological restrictions. The defined scenarios vary with regard to use of the site, time spent at the site, and sources of food consumed. The results of the evaluation indicate that the basic dose limit of 100 mrem/yr will not be exceeded, provided that the soil concentrations of these radionuclides at the LEHR site do not exceed the scenario-specific values calculated by this study. Except for the extent of the contaminated zone (which is very conservative), assumptions used are as site-specific as possible, given available information. The derived guidelines are single- radionuclide guidelines and are linearly proportional to the dose limit used in the calculations. In setting the actual residual soil contamination guides for the LEHR site, DOE will apply the as low as reasonably achievable policy to the decision-making process, along with other factors such as whether a particular scenario is reasonable and appropriate, as well as using site-specific inputs to computer models based on data not yet fully determined

  15. Identification of protein-RNA interaction sites using the information of spatial adjacent residues

    Cheng Yong-Mei

    2011-10-01

    Full Text Available Abstract Background Protein-RNA interactions play an important role in numbers of fundamental cellular processes such as RNA splicing, transport and translation, protein synthesis and certain RNA-mediated enzymatic processes. The more knowledge of Protein-RNA recognition can not only help to understand the regulatory mechanism, the site-directed mutagenesis and regulation of RNA–protein complexes in biological systems, but also have a vitally effecting for rational drug design. Results Based on the information of spatial adjacent residues, novel feature extraction methods were proposed to predict protein-RNA interaction sites with SVM-KNN classifier. The total accuracies of spatial adjacent residue profile feature and spatial adjacent residues weighted accessibility solvent area feature are 78%, 67.07% respectively in 5-fold cross-validation test, which are 1.4%, 3.79% higher than that of sequence neighbour residue profile feature and sequence neighbour residue accessibility solvent area feature. Conclusions The results indicate that the performance of feature extraction method using the spatial adjacent information is superior to the sequence neighbour information approach. The performance of SVM-KNN classifier is little better than that of SVM. The feature extraction method of spatial adjacent information with SVM-KNN is very effective for identifying protein-RNA interaction sites and may at least play a complimentary role to the existing methods.

  16. Partial enterectomy decreases somatostatin-binding sites in residual intestine of rabbits

    Colás Escudero, Begoña; Bodega Magro, Guillermo; Sanz, M.; Prieto Villapún, Juan Carlos; Arilla Ferreiro, Eduardo

    1988-01-01

    Three weeks after partial enterectomy in the rabbit there was an increased somatostatin concentration and a decreased number of somatostatin-binding sites (without changes in the corresponding affinity values) in the cytosol of the residual intestinal tissue, except in the terminal ileum and the colon. Five weeks after surgery both the somatostatin concentration and the number of somatostatin-binding sites returned towards control values. These results suggest that an increase in bowel ...

  17. Site energy distribution analysis of Cu (Ⅱ) adsorption on sediments and residues by sequential extraction method.

    Jin, Qiang; Yang, Yan; Dong, Xianbin; Fang, Jimin

    2016-01-01

    Many models (e.g., Langmuir model, Freundlich model and surface complexation model) have been successfully used to explain the mechanism of metal ion adsorption on the pure mineral materials. These materials usually have a homogeneous surface where all sites have the same adsorption energies. However, it's hardly appropriate for such models to describe the adsorption on heterogeneous surfaces (e.g., sediment surface), site energy distribution analysis can be to. In the present study, the site energy distribution analysis was used to describe the surface properties and adsorption behavior of the non-residual and residual components extracted from the natural aquatic sediment samples. The residues were prepared "in-situ" by using the sequential extraction procedure. The present study is intended to investigate the roles of different components and the change of site energy distribution at different temperatures of the sediment samples in controlling Cu (Ⅱ) adsorption. The results of the site energy distribution analysis indicated firstly, that the sorption sites of iron/manganese hydrous oxides (IMHO) and organic matter (OM) have higher energy. Secondly, light fraction (LF) and carbonates have little influence on site energy distribution. Finally, there was increase in site energies with the increase of temperature. Specially, low temperature (5 °C) significantly influenced the site energies of IMHO and OM, and also had obvious effect on the energy distribution of the sediments after removing target components. The site energy distribution analysis proved to be a useful method for us to further understand the energetic characteristics of sediment in comparison with those previously obtained. PMID:26552542

  18. Status policy and criteria for the remediation of sites with radioactive residues in China

    This paper introduces the status policy and criteria for remediation of sites with radioactive residues in China. We deal with the sites in difference patterns according to their circumstances. For the sites related with the decommissioning of the nuclear fuel cycle facilities, the programs for environmental restoration must be reviewed and approved by the State Environmental Protection Administration (SEPA). And the radioactive waste resulting from these facilities should be collected and eventually disposed of at the regional disposal repositories built by the country. For the sites related with use of radionuclides in medicine, research and industry, as well as the small scale extraction and processing of materials containing natural radionuclides, the provincial environmental authority is responsible for approving the restoration projects. These radioactive wastes should finally be sent to the special radioactive waste repositories built by the provincial environmental authorities. So far 21 waste repositories have been built in some provinces. More then 10 sites with radioactive residues have been restored. The standards for general public dose limit and soil residual radionuclides content have been established. (author)

  19. Identification of key residues involved in the activation and signaling properties of dopamine D3 receptor.

    Kota, Kokila; Kuzhikandathil, Eldo V; Afrasiabi, Milad; Lacy, Brett; Kontoyianni, Maria; Crider, A Michael; Song, Daniel

    2015-09-01

    The dopamine D3 receptor exhibits agonist-dependent tolerance and slow response termination (SRT) signaling properties that distinguish it from the closely-related D2 receptors. While amino acid residues important for D3 receptor ligand binding have been identified, the residues involved in activation of D3 receptor signaling and induction of signaling properties have not been determined. In this paper, we used cis and trans isomers of a novel D3 receptor agonist, 8-OH-PBZI, and site-directed mutagenesis to identify key residues involved in D3 receptor signaling function. Our results show that trans-8-OH-PBZI, but not cis-8-OH-PBZI, elicit the D3 receptor tolerance and SRT properties. We show that while both agonists require a subset of residues in the orthosteric binding site of D3 receptors for activation of the receptor, the ability of the two isomers to differentially induce tolerance and SRT is mediated by interactions with specific residues in the sixth transmembrane helix and third extracellular loop of the D3 receptor. We also show that unlike cis-8-OH-PBZI, which is a partial agonist at the dopamine D2S receptor and full agonist at dopamine D2L receptor, trans-8-OH-PBZI is a full agonist at both D2S and D2L receptors. The different effect of the two isomers on D3 receptor signaling properties and D2S receptor activation correlated with differential effects of the isomers on agonist-induced mouse locomotor activity. The two isomers of 8-OH-PBZI represent novel pharmacological tools for in silico D3 and D2 receptor homology modeling and for determining the role of D3 receptor tolerance and SRT properties in signaling and behavior. PMID:26116441

  20. Derivation of cesium-137 residual radioactive material guidelines for the Peek Street site, Schenectady, New York

    Residual radioactive material guidelines for cesium-137 were derived for the Peek rk. The derivation was based on the requirement that the Street site in Schenectady, New York. The derivation was based on the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the Peek Street site should not exceed a dose of 100 mrem/yr following remedial action. The US Department of Energy (DOE) residual radioactive material guideline computer code, RESRAD was used in this evaluation. Three potential scenarios were considered for the site on the assumption that for a period of 1,000 years following remedial action, the site wig be utilized without radiological restrictions. The scenarios vary with regard to use of the site, time spent at the site, and sources of food consumed. Results indicate that the basic dose limit of 100 mrem/yr will not be exceeded for cesium-137 within 1,000 years, provided that the soil concentration of cesium-137 at the Peek Street site does not exceed the following levels: 98 pCi/g for Scenario A (industrial worker: the expected scenario), 240 pCi/g for Scenario B (recreationist: a plausible scenario), and 34 pCi/g for Scenario C (resident farmer ingesting food produced in the decontaminated area: a plausible scenario)

  1. Water quality changes at three reclaimed mine sites related to the injection of coal combustion residues

    Surface and groundwater pollution is a common problem associated with post-surface mining operations. The US Bureau of Mines (BOM) participated in the testing of subsurface injections of coal combustion residues (CCR) at three reclaimed surface mine sites. The addition of alkaline CCR to the subsurface environment can raise the pH, limit propagation of pyrite oxidizing bacteria and reduce the rate of acid generation. Many CCR's can also form cement-like grout, which when injected into buried spoil may decrease its permeability and porosity, diverting water away from the pyritic material. The objective of this work was to develop an effective, economical and permanent method to abate or reduce post-mining water pollution. The effectiveness of CCR injection as an acid mine drainage abatement technique was evaluated by the BOM by monitoring water quality at three sites in: Upshur County, WV, Clinton County, PA and Greene County, PA. Geophysical techniques were used at all sites to locate monitoring and injection wells that were subsequently drilled into the spoil. Grout injection work was completed between 1990 and 1994 at the three sites. Baseline water quality data were collected at all three sites for a minimum of one year. Post-grouting water quality at the discharge of the three sites showed a slight, long-term improvement and no apparent degradation in water quality resulting from the injection of the coal combustion residues. Notable and long-term improvements in water quality at various monitoring wells (on all sites) were also observed

  2. Regulatory Closure Options for the Residue in the Hanford Site Single-Shell Tanks

    Cochran, J.R. Shyr, L.J.

    1998-10-05

    Liquid, mixed, high-level radioactive waste (HLW) has been stored in 149 single-shell tanks (SSTS) located in tank farms on the U.S. Department of Energy's (DOE's) Hanford Site. The DOE is developing technologies to retrieve as much remaining HLW as technically possible prior to physically closing the tank farms. In support of the Hanford Tanks Initiative, Sandia National Laboratories has addressed the requirements for the regulatory closure of the radioactive component of any SST residue that may remain after physical closure. There is significant uncertainty about the end state of each of the 149 SSTS; that is, the nature and amount of wastes remaining in the SSTS after retrieval is uncertain. As a means of proceeding in the face of these uncertainties, this report links possible end-states with associated closure options. Requirements for disposal of HLW and low-level radioactive waste (LLW) are reviewed in detail. Incidental waste, which is radioactive waste produced incidental to the further processing of HLW, is then discussed. If the low activity waste (LAW) fraction from the further processing of HLW is determined to be incidental waste, then DOE can dispose of that incidental waste onsite without a license from the U.S. Nuclear Regulatory Commissions (NRC). The NRC has proposed three Incidental Waste Criteria for determining if a LAW fraction is incidental waste. One of the three Criteria is that the LAW fraction should not exceed the NRC's Class C limits.

  3. Regulatory Closure Options for the Residue in the Hanford Site Single-Shell Tanks

    Liquid, mixed, high-level radioactive waste (HLW) has been stored in 149 single-shell tanks (SSTS) located in tank farms on the U.S. Department of Energy's (DOE's) Hanford Site. The DOE is developing technologies to retrieve as much remaining HLW as technically possible prior to physically closing the tank farms. In support of the Hanford Tanks Initiative, Sandia National Laboratories has addressed the requirements for the regulatory closure of the radioactive component of any SST residue that may remain after physical closure. There is significant uncertainty about the end state of each of the 149 SSTS; that is, the nature and amount of wastes remaining in the SSTS after retrieval is uncertain. As a means of proceeding in the face of these uncertainties, this report links possible end-states with associated closure options. Requirements for disposal of HLW and low-level radioactive waste (LLW) are reviewed in detail. Incidental waste, which is radioactive waste produced incidental to the further processing of HLW, is then discussed. If the low activity waste (LAW) fraction from the further processing of HLW is determined to be incidental waste, then DOE can dispose of that incidental waste onsite without a license from the U.S. Nuclear Regulatory Commissions (NRC). The NRC has proposed three Incidental Waste Criteria for determining if a LAW fraction is incidental waste. One of the three Criteria is that the LAW fraction should not exceed the NRC's Class C limits

  4. Engineering evaluation of alternatives for the disposition of Niagara Falls Storage Site, its residues and wastes

    The final disposition scenarios selected by DOE for assessment in this document are consistent with those stated in the Notice of Intent to prepare an Environmental Impact Statement (EIS) for the Niagara Falls Storage Site (NFSS) (DOE, 1983d) and the modifications to the alternatives resulting from the public scoping process. The scenarios are: take no action beyond interim remedial measures other than maintenance and surveillance of the NFSS; retain and manage the NFSS as a long-term waste management facility for the wastes and residues on the site; decontaminate, certify, and release the NFSS for other use, with long-term management of the wastes and residues at other DOE sites; and partially decontaminate the NFSS by removal and transport off site of only the more radioactive residues, and upgrade containment of the remaining wastes and residues on site. The objective of this document is to present to DOE the conceptual engineering, occupational radiation exposure, construction schedule, maintenance and surveillance requirements, and cost information relevant to design and implementation of each of the four scenarios. The specific alternatives within each scenario used as the basis for discussion in this document were evaluated on the bases of engineering considerations, technical feasibility, and regulatory requirements. Selected alternatives determined to be acceptable for each of the four final disposition scenarios for the NFSS were approved by DOE to be assessed and costed in this document. These alternatives are also the subject of the EIS for the NFSS currently being prepared by Argonne National Laboratory (ANL). 40 figures, 38 tables

  5. 10 CFR 40.27 - General license for custody and long-term care of residual radioactive material disposal sites.

    2010-01-01

    ... lease any subsurface mineral rights associated with land on which residual radioactive materials are... radioactive material disposal sites. 40.27 Section 40.27 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC... residual radioactive material disposal sites. (a) A general license is issued for the custody of and...

  6. Binding site residues control inhibitor selectivity in the human norepinephrine transporter but not in the human dopamine transporter

    Andersen, Jacob; Ringsted, Kristoffer B; Bang-Andersen, Benny; Strømgaard, Kristian; Kristensen, Anders S

    2015-01-01

    in the central site of DAT to the corresponding residues in NET had modest effects on the same inhibitors, suggesting that non-conserved binding site residues in DAT play a minor role for selective inhibitor recognition. Our data points towards distinct structural determinants governing inhibitor...

  7. Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins

    Jiang, Yang; Li, Bi-Qing; Zhang, Yuchao; Feng, Yuan-Ming; Gao, Yu-Fei; Zhang, Ning; Cai, Yu-Dong

    2013-01-01

    Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-cons...

  8. On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases

    Reggy Ekkebus; van Kasteren, Sander I.; Yogesh Kulathu; Arjen Scholten; Ilana Berlin; Geurink, Paul P; Annemieke de Jong; Soenita Goerdayal; Jacques Neefjes; Heck, Albert J.R.; David Komander; Huib Ovaa

    2013-01-01

    Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality, a selective reaction with the active-site cysteine residue of de-ubiquitinating enzymes was observed. The resulting product was shown to be a quaternary vinyl thioether, as determined by X-ray crystallography. Proteomic analysis of proteins boun...

  9. Epimerase and Reductase Activities of Polyketide Synthase Ketoreductase Domains Utilize the Same Conserved Tyrosine and Serine Residues.

    Xie, Xinqiang; Garg, Ashish; Keatinge-Clay, Adrian T; Khosla, Chaitan; Cane, David E

    2016-03-01

    The role of the conserved active site tyrosine and serine residues in epimerization catalyzed by polyketide synthase ketoreductase (PKS KR) domains has been investigated. Both mutant and wild-type forms of epimerase-active KR domains, including the intrinsically redox-inactive EryKR3° and PicKR3° as well as redox-inactive mutants of EryKR1, were incubated with [2-(2)H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP ([2-(2)H]-2) and 0.05 equiv of NADP(+) in the presence of the redox-active, epimerase-inactive EryKR6 domain. The residual epimerase activity of each mutant was determined by tandem equilibrium isotope exchange, in which the first-order, time-dependent washout of isotope from 2 was monitored by liquid chromatography-tandem mass spectrometry with quantitation of the deuterium content of the diagnostic pantetheinate ejection fragment (4). Replacement of the active site Tyr or Ser residues, alone or together, significantly reduced the observed epimerase activity of each KR domain with minimal effect on substrate binding. Our results demonstrate that the epimerase and reductase activities of PKS KR domains share a common active site, with both reactions utilizing the same pair of Tyr and Ser residues. PMID:26863427

  10. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    Selvaraj S; Jayaram B; Saranya N; Gromiha M; Fukui Kazuhiko

    2011-01-01

    Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such...

  11. Prediction of residual metabolic activity after treatment in NSCLC patients

    Rios Velazquez, Emmanuel; Aerts, Hugo J.W.L.; Oberije, Cary; Ruysscher, Dirk De; Lambin, Philippe (Dept. of Radiation Oncology, School for Oncology and Developmental Biology, Maastricht Univ. Medical Center, Maastricht (Netherlands)), E-mail: emmanuel.rios@maastro.nl

    2010-10-15

    Purpose. Metabolic response assessment is often used as a surrogate of local failure and survival. Early identification of patients with residual metabolic activity is essential as this enables selection of patients who could potentially benefit from additional therapy. We report on the development of a pre-treatment prediction model for metabolic response using patient, tumor and treatment factors. Methods. One hundred and one patients with inoperable NSCLC (stage I-IV), treated with 3D conformal radical (chemo)-radiotherapy were retrospectively included in this study. All patients received a pre and post-radiotherapy fluorodeoxyglucose positron emission tomography-computed tomography FDG-PET-CT scan. The electronic medical record system and the medical patient charts were reviewed to obtain demographic, clinical, tumor and treatment data. Primary outcome measure was examined using a metabolic response assessment on a post-radiotherapy FDG-PET-CT scan. Radiotherapy was delivered in fractions of 1.8 Gy, twice a day, with a median prescribed dose of 60 Gy. Results. Overall survival was worse in patients with residual metabolic active areas compared with the patients with a complete metabolic response (p=0.0001). In univariate analysis, three variables were significantly associated with residual disease: larger primary gross tumor volume (GTVprimary, p=0.002), higher pre-treatment maximum standardized uptake value (SUV{sub max}, p=0.0005) in the primary tumor and shorter overall treatment time (OTT, p=0.046). A multivariate model including GTVprimary, SUV{sub max}, equivalent radiation dose at 2 Gy corrected for time (EQD2, T) and OTT yielded an area under the curve assessed by the leave-one-out cross validation of 0.71 (95% CI, 0.65-0.76). Conclusion. Our results confirmed the validity of metabolic response assessment as a surrogate of survival. We developed a multivariate model that is able to identify patients at risk of residual disease. These patients may

  12. Evidence for the existence of a tyrosyl residue in the nicotinamide adenine dinucleotide binding site of chicken liver xanthine dehydrogenase

    Xanthine-NAD and NADH-methylene blue oxidoreductase activities of chicken liver xanthine dehydrogenase were inactivated by incubation with 5'-[p-(fluorosulfonyl)benzoyl]adenosine (5'-FSBA), an active site directed reagent for nucleotide binding sites. The inactivation reaction displayed pseudo-first-order kinetics. A double-reciprocal plot of inactivation velocity vs. 5'-FSBA concentration showed that 5'-FSBA and enzyme formed a complex prior to inactivation. NAD protected the enzyme from inactivation by 5'-FSBA in a competitive fashion. The modified enzyme had the same xanthine-dichlorophenolindophenol and xanthine-O2 oxidoreductase activities as the native enzyme, and on addition of xanthine to the modified enzyme, bleaching of the spectrum occurred in the visible region. The amount of radioactivity incorporated into the enzyme by incubation with [14C]-5'-FSBA was parallel to the loss of xanthine-NAD oxidoreductase activity, and the stoichiometry was 1 mol/mol of enzyme-bound FAD for complete inactivation. These results indicated that 5'-FSBA modified specifically the binding site for NAD of chicken liver xanthine dehydrogenase. The incorporated radioactivity was released slowly from 14C-labeled enzyme by incubation with dithiothreitol with concomitant restoration of catalytic activity. The modified residue responsible for inactivation was identified as a tyrosine

  13. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    Selvaraj S

    2011-10-01

    Full Text Available Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching. Results We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix. Conclusions The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

  14. Application of RESRAD family of computer codes to sites contaminated with radioactive residues

    The RESRAD family of computer codes was developed to provide a scientifically defensible answer to the question 'How clean is clean?' and to provide useful tools for evaluating human health risk at sites contaminated with radioactive residues. The RESRAD codes include (1) RESRAD for soil contaminated with radionuclides; (2) RESRAD-BUILD for buildings contaminated with radionuclides; (3) RESRAD-CHEM for soil contaminated with hazardous chemicals; (4) RESRAD-BASELINE for baseline risk assessment with measured media concentrations of both radionuclides and chemicals; (5) RESRAD-ECORISK for ecological risk assessment; (6) RESRAD-RECYCLE for recycle and reuse of radiologically contaminated metals and equipment; and (7) RESRAD-OFFSITE for off-site receptor radiological dose assessment. Four of these seven codes (RESRAD, RESRAD-BUILD, RESRAD-RECYCLE, and RESRAD-OFFSITE) also have uncertainty analysis capabilities that allow the user to input distributions of parameters. RESRAD has been widely used in the United States and abroad and approved by many federal and state agencies. Experience has shown that the RESRAD codes are useful tools for evaluating sites contaminated with radioactive residues. The use of RESRAD codes has resulted in significant savings in cleanup cost. Analysis of 19 site-specific uranium guidelines is discussed in the paper. (author)

  15. Contaminant Release from Residual Waste in Single Shell Tanks at the Hanford Site, Washington, USA - 9276

    Determinations of elemental and solid-phase compositions, and contaminant release studies have been applied in an ongoing study of residual tank wastes (i.e., waste remaining after final retrieval operations) from five of 149 underground single-shell storage tanks (241-C-103, 241-C-106, 241-C-202, 241-C-203, and 241-S-112) at the U.S. Department of Energy's Hanford Site in Washington State. This work is being conducted to support performance assessments that will be required to evaluate long-term health and safety risks associated with tank site closure. The results of studies completed to date show significant variability in the compositions, solid phase properties, and contaminant release characteristics from these residual tank wastes. This variability is the result of differences in waste chemistry/composition of wastes produced from several different spent fuel reprocessing schemes, subsequent waste reprocessing to remove certain target constituents, tank farm operations that concentrated wastes and mixed wastes between tanks, and differences in retrieval processes used to remove the wastes from the tanks. Release models were developed based upon results of chemical characterization of the bulk residual waste, solid-phase characterization (see companion paper 9277 by Krupka et al.), leaching and extraction experiments, and geochemical modeling. In most cases empirical release models were required to describe contaminant release from these wastes. Release of contaminants from residual waste was frequently found to be controlled by the solubility of phases that could not be identified and/or for which thermodynamic data and/or dissolution rates have not been measured. For example, significant fractions of Tc-99, I-129, and Cr appear to be coprecipitated at trace concentrations in metal oxide phases that could not be identified unambiguously. In the case of U release from tank 241-C-103 residual waste, geochemical calculations indicated that leachate

  16. Recombinant expression, antimicrobial activity and mechanism of action of tritrpticin analogs containing fluoro-tryptophan residues.

    Arias, Mauricio; Hoffarth, Elesha R; Ishida, Hiroaki; Aramini, James M; Vogel, Hans J

    2016-05-01

    The increase in antibiotic-resistant bacterial infections has prompted significant academic research into new therapeutic agents targeted against these pathogens. Antimicrobial peptides (AMPs) appear as promising candidates, due their potent antimicrobial activity and their ubiquitous presence in almost all organisms. Tritrpticin is a member of this family of peptides and has been shown to exert a strong antimicrobial activity against several bacterial strains. Tritrpticin's main structural characteristic is the presence of three consecutive Trp residues at the center of the peptide. These residues play an important role in the activity of tritrpticin against Escherichia coli. In this work, a recombinant version of tritrpticin was produced in E. coli using calmodulin as a fusion protein expression tag to overcome the toxicity of the peptide. When used in combination with glyphosate, an inhibitor of the endogenous synthesis of aromatic amino acids, this expression system allowed for the incorporation of fluorinated Trp analogs at very high levels (>90%). The antimicrobial activity of the 4-, 5- and 6-fluoro-Trp-containing tritrpticins against E. coli was as strong as the activity of the native peptide. Similarly, the tritrpticin analogs exhibited comparable abilities to perturb and permeabilize synthetic lipid bilayers as well as the outer and inner membrane of E. coli. Furthermore, the use of 19F NMR spectroscopy established that each individual fluoro-Trp residue interacts differently with SDS micelles, supporting the idea that each Trp in the original tritrpticin plays a different role in the perturbing/permeabilizing activity of the peptide. Moreover, our work demonstrates that the use of fluoro-Trp in solvent perturbation 19F NMR experiments provides detailed site-specific information on the insertion of the Trp residues in biological membrane mimetics. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai

  17. Characterization of Reuse Activities at Contaminated Sites

    Angela Vitulli; Charlotte Dougherty; Kimberly Bosworth

    2004-01-01

    Given the increased focus on reuse activity within EPA and state site cleanup programs, policy makers would benefit from looking across programs to better understand the extent and nature of reuse; examine site characteristics that influence reuse; leverage lessons learned; and coordinate reuse activities, data collection, and information management. This research paper begins to examine these issues. It reports the results of a preliminary review and analysis of available EPA and state progr...

  18. Fingerprinting differential active site constraints of ATPases

    Hacker, Stephan M.; Hardt, Norman; Buntru, Alexander; Pagliarini, Dana; Möckel, Martin; Mayer, Thomas U; Scheffner, Martin; Hauck, Christof R.; Marx, Andreas

    2013-01-01

    The free energy provided by adenosine triphosphate (ATP) hydrolysis is central to many cellular processes and, therefore, the number of enzymes utilizing ATP as a substrate is almost innumerable. Modified analogues of ATP are a valuable means to understand the biological function of ATPases. Although these enzymes have evolved towards binding to ATP, large differences in active site architectures were found. In order to systematically access the specific active site constraints of different A...

  19. Mapping the active site of vaccinia virus RNA triphosphatase

    The RNA triphosphatase component of vaccinia virus mRNA capping enzyme (the product of the viral D1 gene) belongs to a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi, protozoa, Chlorella virus, and baculoviruses. The family is defined by two glutamate-containing motifs (A and C) that form the metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight-stranded β barrel (the so-called ''triphosphate tunnel''). Here we queried whether vaccinia virus capping enzyme is a member of the tunnel subfamily, via mutational mapping of amino acids required for vaccinia triphosphatase activity. We identified four new essential side chains in vaccinia D1 via alanine scanning and illuminated structure-activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight a constellation of six acidic and three basic amino acids that likely compose the vaccinia triphosphatase active site (Glu37, Glu39, Arg77, Lys107, Glu126, Asp159, Lys161, Glu192, and Glu194). These nine essential residues are conserved in all vertebrate and invertebrate poxvirus RNA capping enzymes. We discerned no pattern of clustering of the catalytic residues of the poxvirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). We infer that the poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Their unique active site, which is completely different from that of the host cell's capping enzyme, recommends the poxvirus RNA triphosphatase as a molecular target for antipoxviral drug discovery

  20. Feasibility study for remedial action for the Quarry Residuals Operable Unit at the Weldon Spring Site, Weldon Spring, Missouri

    NONE

    1998-03-01

    The U.S. Department of Energy (DOE) is conducting cleanup activities at the Weldon Spring site, which is located in St. Charles County, Missouri, about 48 km (30 mi) west of St. Louis (Figure 1.1). Cleanup of the Weldon Spring site consists of several integrated components. The quarry residuals operable unit (QROU) is one of four operable units being evaluated. In accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended, a remedial investigation/feasibility study (RI/FS) is being conducted to evaluate conditions and potential responses for the following areas and/or media that constitute the QROU: (1) the residual material (soil and sediment) remaining at the Weldon Spring quarry after removal of the bulk waste (about 11 million L [3 million gal] of uranium-contaminated ponded water was also addressed previous to bulk waste removal); (2) other media located in the surrounding vicinity of the quarry, including adjacent soil, surface water, and sediment in Femme Osage Slough and several creeks; and (3) quarry groundwater located primarily north of Femme Osage Slough. Potential impacts to the St. Charles County well field downgradient of the quarry area are also being addressed as part of QROU RI/FS evaluations. For remedial action sites, it is DOE policy to integrate values associated with the National Environmental Policy Act (NEPA) into the CERCLA decision-making process. The analyses contained herein address NEPA values as appropriate to the actions being considered for the QROU. A work plan summarizing initial site conditions and providing conceptual site hydrogeological and exposure models was published in January 1994. The RI and baseline risk assessment (BRA) reports have been completed. The RI discusses in detail the nature and extent and the fate and transport of contamination at the quarry area.

  1. Feasibility study for remedial action for the Quarry Residuals Operable Unit at the Weldon Spring Site, Weldon Spring, Missouri

    The U.S. Department of Energy (DOE) is conducting cleanup activities at the Weldon Spring site, which is located in St. Charles County, Missouri, about 48 km (30 mi) west of St. Louis (Figure 1.1). Cleanup of the Weldon Spring site consists of several integrated components. The quarry residuals operable unit (QROU) is one of four operable units being evaluated. In accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended, a remedial investigation/feasibility study (RI/FS) is being conducted to evaluate conditions and potential responses for the following areas and/or media that constitute the QROU: (1) the residual material (soil and sediment) remaining at the Weldon Spring quarry after removal of the bulk waste (about 11 million L [3 million gal] of uranium-contaminated ponded water was also addressed previous to bulk waste removal); (2) other media located in the surrounding vicinity of the quarry, including adjacent soil, surface water, and sediment in Femme Osage Slough and several creeks; and (3) quarry groundwater located primarily north of Femme Osage Slough. Potential impacts to the St. Charles County well field downgradient of the quarry area are also being addressed as part of QROU RI/FS evaluations. For remedial action sites, it is DOE policy to integrate values associated with the National Environmental Policy Act (NEPA) into the CERCLA decision-making process. The analyses contained herein address NEPA values as appropriate to the actions being considered for the QROU. A work plan summarizing initial site conditions and providing conceptual site hydrogeological and exposure models was published in January 1994. The RI and baseline risk assessment (BRA) reports have been completed. The RI discusses in detail the nature and extent and the fate and transport of contamination at the quarry area

  2. Site-directed mutagenesis of boar proacrosin reveals residues involved in binding of zona pellucida glycoproteins.

    Jansen, S; Jones, R; Jenneckens, I; Marschall, B; Kriegesmann, B; Coadwell, J; Brenig, B

    1998-10-01

    Proacrosin, the zymogen form of the serine protease beta-acrosin, is thought to function as a secondary binding molecule between mammalian gametes during fertilization (Jansen et al., 1995: Int J Dev Biol 39, 501-510). The interaction involves strong ionic bonds between positively charged amino acids on proacrosin and negatively charged polysulphate groups on zona pellucida glycoproteins. In this investigation, we identified the basic residues on proacrosin that are important for this binding. Site-directed mutagenesis shows that two groups of amino acids comprising His47, Arg50, and Arg51 together with Arg250, Lys252, and Arg253 are crucial because their deletion or replacement severely reduces affinity for zona glycoproteins. Molecular models of proacrosin reveal that these residues are located along one face of the protein on two exposed surface loops that project over and around the catalytic site. These findings support the hypothesis that polysulphate binding sites on proacrosin are formed by a restricted number of basic amino acids on the surface of the protein, presenting a specific orientation that is complementary to negatively charged sulphate groups on zona glycoproteins. Identification and elucidation of the stereochemistry of these charged moieties will aid design of new kinds of nonsteroidal antifertility agents. PMID:9740326

  3. Rebaselining of the plutonium residue elimination project at Rocky Flats Environmental Technology Site

    Systems Engineering and Value Engineering principles were put into practice in rebaselining the Pu Residue Stabilization and Elimination Project at the Rocky Flats Environmental Technology Site. Tradeoff studies were conducted as to how to best rebaseline the system under the new Safeguards Termination Limits (STSs) issued by the Department of Energy. Through the use of a computerized database, the means by which Stakeholder values and other high-level requirements have been included in the tradeoff studies were documented. 13 refs., 2 figs., 1 tab

  4. A C. elegans-based foam for rapid on-site detection of residual live virus.

    Negrete, Oscar A.; Branda, Catherine; Hardesty, Jasper O. E. (Sandia National Laboratories, Albuquerque, NM); Tucker, Mark David (Sandia National Laboratories, Albuquerque, NM); Kaiser, Julia N. (Global Product Management, Hilden, Germany); Kozina, Carol L.; Chirica, Gabriela S.

    2012-02-01

    In the response to and recovery from a critical homeland security event involving deliberate or accidental release of biological agents, initial decontamination efforts are necessarily followed by tests for the presence of residual live virus or bacteria. Such 'clearance sampling' should be rapid and accurate, to inform decision makers as they take appropriate action to ensure the safety of the public and of operational personnel. However, the current protocol for clearance sampling is extremely time-intensive and costly, and requires significant amounts of laboratory space and capacity. Detection of residual live virus is particularly problematic and time-consuming, as it requires evaluation of replication potential within a eukaryotic host such as chicken embryos. The intention of this project was to develop a new method for clearance sampling, by leveraging Sandia's expertise in the biological and material sciences in order to create a C. elegans-based foam that could be applied directly to the entire contaminated area for quick and accurate detection of any and all residual live virus by means of a fluorescent signal. Such a novel technology for rapid, on-site detection of live virus would greatly interest the DHS, DoD, and EPA, and hold broad commercial potential, especially with regard to the transportation industry.

  5. Full scale amendment of a contaminated wood impregnation site with iron water treatment residues

    Nielsen, Sanne Skov; Kjeldsen, Peter; Jakobsen, Rasmus

    2016-01-01

    by 95% in the upper samplers. Dosage and mixing of Fe-WTR in the soil proved to be difficult in the deeper part of the field, and pore water concentrations of arsenic was generally higher. Despite water logged conditions no increase in dissolved iron or arsenic was observed in the amended soil. Our......Iron water treatment residues (Fe-WTR) are a free by-product of the treatment of drinking water with high concentration of iron oxides and potential for arsenic sorption. This paper aims at applying Fe-WTR to a contaminated site, measuring the reduction in contaminant leaching, and discussing...... the design of delivery and mixing strategy for soil stabilization at field scale and present a cost-effective method of soil mixing by common contractor machinery. Soil contaminated by As, Cr, and Cu at an abandoned wood impregnation site was amended with 0.22% (dw) Fe-WTR. To evaluate the full scale...

  6. Stringency of the 2-His-1-Asp active-site motif in prolyl 4-hydroxylase.

    Kelly L Gorres

    Full Text Available The non-heme iron(II dioxygenase family of enzymes contain a common 2-His-1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C-H bonds. Prolyl 4-hydroxylase (P4H is an alpha-ketoglutarate-dependent iron(II dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His-1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change.

  7. Baseline risk assessment for the quarry residuals operable unit of the Weldon Spring Site, Weldon Spring, Missouri

    The U.S. Department of Energy (DOE) is conducting cleanup activities at the Weldon Spring site, located in St. Charles County, Missouri, about 48 km (30 mi) west of St. Louis. Cleanup of the site consists of several integrated components. The quarry residuals operable unit (QROU), consisting of the Weldon Spring quarry and its surrounding area, is one of four operable units being evaluated. In accordance with requirements of the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended, DOE is conducting a remedial investigation/feasibility study (RI/FS) to determine the proper response to address various contaminated media that constitute the QROU. Specifically, the operable unit consists of the following areas and media: the residual material remaining at the Weldon Spring quarry after removal of the pond water and the bulk waste; groundwater underlying the quarry and surrounding area; and other media located in the surrounding vicinity of the quarry, including surface water and sediment at Femme Osage Slough, Little Femme Osage Creek, and Femme Osage Creek. An initial evaluation of conditions at the quarry area identified remaining data requirements needed to support the conceptual site exposure and hydrogeological models. These data requirements are discussed in the RI/FS work plan issued in January 1994. Soil contamination located at a property adjacent to the quarry, referred to as Vicinity Property 9 (VP9), was originally part of the scope of the QROU, as discussed in the work plan. However, a decision was subsequently made to remediate this vicinity property as part of cleanup activities for the chemical plant operable unit, as provided for in the Record of Decision (ROD). Remediation of VP9 was completed in early 1996. Hence, this baseline risk assessment (BRA) does not address VP9

  8. Baseline risk assessment for the quarry residuals operable unit of the Weldon Spring Site, Weldon Spring, Missouri

    NONE

    1998-02-01

    The U.S. Department of Energy (DOE) is conducting cleanup activities at the Weldon Spring site, located in St. Charles County, Missouri, about 48 km (30 mi) west of St. Louis. Cleanup of the site consists of several integrated components. The quarry residuals operable unit (QROU), consisting of the Weldon Spring quarry and its surrounding area, is one of four operable units being evaluated. In accordance with requirements of the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended, DOE is conducting a remedial investigation/feasibility study (RI/FS) to determine the proper response to address various contaminated media that constitute the QROU. Specifically, the operable unit consists of the following areas and media: the residual material remaining at the Weldon Spring quarry after removal of the pond water and the bulk waste; groundwater underlying the quarry and surrounding area; and other media located in the surrounding vicinity of the quarry, including surface water and sediment at Femme Osage Slough, Little Femme Osage Creek, and Femme Osage Creek. An initial evaluation of conditions at the quarry area identified remaining data requirements needed to support the conceptual site exposure and hydrogeological models. These data requirements are discussed in the RI/FS work plan issued in January 1994. Soil contamination located at a property adjacent to the quarry, referred to as Vicinity Property 9 (VP9), was originally part of the scope of the QROU, as discussed in the work plan. However, a decision was subsequently made to remediate this vicinity property as part of cleanup activities for the chemical plant operable unit, as provided for in the Record of Decision (ROD). Remediation of VP9 was completed in early 1996. Hence, this baseline risk assessment (BRA) does not address VP9.

  9. Testing in support of on-site storage of residues in the Pipe Overpack Container

    The disposition of the large back-log of plutonium residues at the Rocky Flats Environmental Technology Site (Rocky Flats) will require interim storage and subsequent shipment to a waste repository. Current plans call for disposal at the Waste Isolation Pilot Plant (WIPP) and the transportation to WIPP in the TRUPACT-II. The transportation phase will require the residues to be packaged in a container that is more robust than a standard 55-gallon waste drum. Rocky Flats has designed the Pipe Overpack Container to meet this need. It is desirable to use this same waste packaging for interim on-site storage in non-hardened buildings. To meet the safety concerns for this storage the Pipe Overpack Container has been subjected to a series of tests at Sandia National Laboratories in Albuquerque, New Mexico. In addition to the tests required to qualify the Pipe Overpack Container as a waste container for shipment in the TRUPACT-II several tests were performed solely for the purpose of qualifying the container for interim storage. This report will describe these tests and the packages response to the tests. 12 figs., 3 tabs

  10. Substitution of Val72 residue alters the enantioselectivity and activity of Penicillium expansum lipase.

    Tang, Lianghua; Su, Min; Zhu, Ling; Chi, Liying; Zhang, Junling; Zhou, Qiong

    2013-01-01

    Error-prone PCR was used to create more active or enantioselective variants of Penicillium expansum lipase (PEL). A variant with a valine to glycine substitution at residue 72 in the lid structure exhibited higher activity and enantioselectivity than those of wild-type PEL. Site-directed saturation mutagenesis was used to explore the sequence-function relationship and the substitution of Val72 of P. expansum lipase changed both catalytic activity and enantioselectivity greatly. The variant V72A, displayed a highest enantioselectivity enhanced to about twofold for the resolution of (R, S)-naproxen (E value increased from 104 to 200.7 for wild-type PEL and V72A variant, respectively). In comparison to PEL, the variant V72A showed a remarkable increase in specific activity towards p-nitrophenyl palmitate (11- and 4-fold increase at 25 and 35 °C, respectively) whereas it had a decreased thermostability. The results suggest that the enantioselective variant V72A could be used for the production of pharmaceutical drugs such as enantiomerically pure (S)-naproxen and the residue Val 72 of P. expansum lipase plays a significant role in the enantioselectivity and activity of this enantioselective lipase. PMID:22972595

  11. Bound residues of lindane: Magnitude, microbial release, plant uptake and effects on microbial activities

    Bound residues were detected in unflooded and flooded soils, even one year after the application of 14C-lindane, the higher occurrence being in unflooded soils. Considerably less bound residues were formed in flooded soils which had been amended with green manure. Bound residue formation was higher in neutral and alkaline soils and appeared to be related to the organic matter content of these soils. The bound residues were associated with the fulvic acid and humic acid fractions. When unflooded and flooded soils containing bound residues were incubated under moist conditions, more extractable residues were found in unflooded soils than in flooded soils. The uptake of 14C-residues from soils containing bound 14C-residues by barley plants was observed. The bound residues appeared to have no effect on general soil microbial activities. (author)

  12. Active site and laminarin binding in glycoside hydrolase family 55.

    Bianchetti, Christopher M; Takasuka, Taichi E; Deutsch, Sam; Udell, Hannah S; Yik, Eric J; Bergeman, Lai F; Fox, Brian G

    2015-05-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  13. Site-directed mutagenesis of the heterotrimeric killer toxin zymocin identifies residues required for early steps in toxin action.

    Wemhoff, Sabrina; Klassen, Roland; Meinhardt, Friedhelm

    2014-10-01

    Zymocin is a Kluyveromyces lactis protein toxin composed of αβγ subunits encoded by the cytoplasmic virus-like element k1 and functions by αβ-assisted delivery of the anticodon nuclease (ACNase) γ into target cells. The toxin binds to cells' chitin and exhibits chitinase activity in vitro that might be important during γ import. Saccharomyces cerevisiae strains carrying k1-derived hybrid elements deficient in either αβ (k1ORF2) or γ (k1ORF4) were generated. Loss of either gene abrogates toxicity, and unexpectedly, Orf2 secretion depends on Orf4 cosecretion. Functional zymocin assembly can be restored by nuclear expression of k1ORF2 or k1ORF4, providing an opportunity to conduct site-directed mutagenesis of holozymocin. Complementation required active site residues of α's chitinase domain and the sole cysteine residue of β (Cys250). Since βγ are reportedly disulfide linked, the requirement for the conserved γ C231 was probed. Toxicity of intracellularly expressed γ C231A indicated no major defect in ACNase activity, while complementation of k1ΔORF4 by γ C231A was lost, consistent with a role of β C250 and γ C231 in zymocin assembly. To test the capability of αβ to carry alternative cargos, the heterologous ACNase from Pichia acaciae (P. acaciae Orf2 [PaOrf2]) was expressed, along with its immunity gene, in k1ΔORF4. While efficient secretion of PaOrf2 was detected, suppression of the k1ΔORF4-derived k1Orf2 secretion defect was not observed. Thus, the dependency of k1Orf2 on k1Orf4 cosecretion needs to be overcome prior to studying αβ's capability to deliver other cargo proteins into target cells. PMID:25128337

  14. FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions.

    Daniel B Roche

    Full Text Available The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP experiment, utilizing the Matthews Correlation Coefficient (MCC and Binding-site Distance Test (BDT metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall's τ, Spearman's ρ and Pearson's r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC when Receiver Operator Characteristic (ROC analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%, and one of the top manual groups (FN293 tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site

  15. Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation

    Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole;

    2006-01-01

    to form high affinity metal ion sites in both the bidentate and potential tridentate settings. This indicates that the residues involved in the main ligand-binding pocket will have to move closer to each other during receptor activation. On the basis of the distance constraints from these activating metal...

  16. Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics.

    Shirke, Abhijit N; Basore, Danielle; Holton, Samantha; Su, An; Baugh, Evan; Butterfoss, Glenn L; Makhatadze, George; Bystroff, Christopher; Gross, Richard A

    2016-05-01

    Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding. PMID:26758295

  17. Managing Siting Activities for Nuclear Power Plants

    One of the IAEA's statutory objectives is to ''seek to accelerate and enlarge the contribution of atomic energy to peace, health and prosperity throughout the world''. One way this objective is achieved is through the publication of a range of technical series. Two of these are the IAEA Nuclear Energy Series and the IAEA Safety Standards Series. According to Article III.A.6 of the IAEA Statute, the safety standards establish 'standards of safety for protection of health and minimization of danger to life and property.' The safety standards include the Safety Fundamentals, Safety Requirements and Safety Guides. These standards are written primarily in a regulatory style, and are binding on the IAEA for its own programmes. The principal users are the regulatory bodies in Member States and other national authorities. The IAEA Nuclear Energy Series comprises reports designed to encourage and assist R and D on, and application of, nuclear energy for peaceful uses. This includes practical examples to be used by owners and operators of utilities in Member States, implementing organizations, academia, and government officials, among others. This information is presented in guides, reports on technology status and advances, and best practices for peaceful uses of nuclear energy based on inputs from international experts. The IAEA Nuclear Energy Series complements the IAEA Safety Standards Series. The introduction of nuclear power brings new challenges to States - one of them being the selection of appropriates sites. It is a project that needs to begin early, be well managed, and deploy good communications with all stakeholders; including regulators. This is important, not just for those States introducing nuclear power for the first time, but for any State looking to build a new nuclear power plant. The purpose of the siting activities goes beyond choosing a suitable site and acquiring a licence. A large part of the project is about producing and maintaining a validated

  18. Derivation of guidelines for uranium residual radioactive material in soil at the New Brunswick Site, Middlesex County, New Jersey

    Residual radioactive material guidelines for uranium in soil were derived for the New Brunswick Site, located in Middlesex County, New Jersey. This site has been designated for remedial action under the Formerly Utilized Sites Remedial Action Program of the US Department of Energy (DOE). Residual radioactive material guidelines for individual radionuclides of concern and total uranium were derived on the basis of the requirement that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works in the immediate vicinity of the New Brunswick Site should not exceed a dose of 30 mrem/yr following remedial action for the current-use and likely future-use scenarios or a dose of 100 mrem/yr for less likely future-use scenarios. The DOE residual radioactive material guideline computer code, RESRAD, was used in this evaluation; RESRAD implements the methodology described in the DOE manual for establishing residual radioactive material guidelines. The guidelines derived in this report are intended to apply to the remediation of these remaining residual radioactive materials at the site. The primary radionuclides of concern in these remaining materials are expected to be radium-226 and, to a lesser extent, natural uranium and thorium. The DOE has established generic cleanup guidelines for radium and thorium in soil; however, cleanup guidelines for other radionuclides must be derived on a site-specific basis

  19. Efficient oxygen electrocatalysis on special active sites

    Halck, Niels Bendtsen

    cobalt incorporated in ruthenium dioxide at high overpotentials during the oxygen reduction reaction (ORR). Density functional theory calculations were used to explain this phenomenon. The special active sites concepts are used to propose a general unified approach to increase the efficiency for oxygen...

  20. SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

    Jessen, Leon Ivar; Hoof, Ilka; Lund, Ole; Nielsen, Morten

    Site does not require any pre-definition of subgroups or binary classification. Input is a set of protein sequences where each sequence has an associated real number, quantifying a given phenotype. SigniSite will then identify which amino acid residues are significantly associated with the data set...

  1. A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome

    Relly Brandman; Yigal Brandman; Pande, Vijay S.

    2012-01-01

    The ribosome is a large macromolecular machine, and correlated motion between residues is necessary for coordinating function across multiple protein and RNA chains. We ran two all-atom, explicit solvent molecular dynamics simulations of the bacterial ribosome and calculated correlated motion between residue pairs by using mutual information. Because of the short timescales of our simulation (ns), we expect that dynamics are largely local fluctuations around the crystal structure. We hypothes...

  2. Measurement of residual CO2 saturation at a geological storage site using hydraulic tests

    Rötting, T. S.; Martinez-Landa, L.; Carrera, J.; Russian, A.; Dentz, M.; Cubillo, B.

    2012-12-01

    Estimating long term capillary trapping of CO2 in aquifers remains a key challenge for CO2 storage. Zhang et al. (2011) proposed a combination of thermal, tracer, and hydraulic experiments to estimate the amount of CO2 trapped in the formation after a CO2 push and pull test. Of these three types of experiments, hydraulic tests are the simplest to perform and possibly the most informative. However, their potential has not yet been fully exploited. Here, a methodology is presented to interpret these tests and analyze which parameters can be estimated. Numerical and analytical solutions are used to simulate a continuous injection in a porous medium where residual CO2 has caused a reduction in hydraulic conductivity and an increase in storativity over a finite thickness (a few meters) skin around the injection well. The model results are interpreted using conventional pressure build-up and diagnostic plots (a plot of the drawdown s and the logarithmic derivative d s / d ln t of the drawdown as a function of time). The methodology is applied using the hydraulic parameters estimated for the Hontomin site (Northern Spain) where a Technology Demonstration Plant (TDP) for geological CO2 storage is planned to be set up. The reduction of hydraulic conductivity causes an increase in observed drawdowns, the increased storativity in the CO2 zone causes a delay in the drawdown curve with respect to the reference curve measured before CO2 injection. The duration (characteristic time) of these effects can be used to estimate the radius of the CO2 zone. The effects of reduced permeability and increased storativity are well separated from wellbore storage and natural formation responses, even if the CO2-brine interface is inclined (i.e. the CO2 forms a cone around the well). We find that both skin hydraulic conductivity and storativity (and thus residual CO2 saturation) can be obtained from the water injection test provided that water flow rate is carefully controlled and head build

  3. Role of cysteine-58 and cysteine-95 residues in the thiol di-sulfide oxidoreductase activity of Macrophage Migration Inhibitory Factor-2 of Wuchereria bancrofti.

    Chauhan, Nikhil; Hoti, S L

    2016-01-01

    Macrophage Migration Inhibitory Factor (MIF) is the first human cytokine reported and was thought to have a central role in the regulation of inflammatory responses. Homologs of this molecule have been reported in bacteria, invertebrates and plants. Apart from cytokine activity, it also has two catalytic activities viz., tautomerase and di-sulfide oxidoreductase, which appear to be involved in immunological functions. The CXXC catalytic site is responsible for di-sulfide oxidoreductase activity of MIF. We have recently reported thiol-disulfide oxidoreductase activity of Macrophage Migration Inhibitory Factor-2 of Wuchereria bancrofti (Wba-MIF-2), although it lacks the CXXC motif. We hypothesized that three conserved cysteine residues might be involved in the formation of di-sulfide oxidoreductase catalytic site. Homology modeling of Wba-MIF-2 showed that among the three cysteine residues, Cys58 and Cys95 residues came in close proximity (3.23Å) in the tertiary structure with pKa value 9, indicating that these residues might play a role in the di-sulfide oxidoreductase catalytic activity. We carried out site directed mutagenesis of these residues (Cys58Ser & Cys95Ser) and expressed mutant proteins in Escherichia coli. The mutant proteins did not show any oxidoreductase activity in the insulin reduction assay, thus indicating that these two cysteine residues are vital for the catalytic activity of Wba-MIF-2. PMID:26432350

  4. Addendum to the East Tennessee Technology Park Site-Wide Residual Contamination Remedial Investigation Work Plan Oak Ridge, Tennessee

    SAIC

    2011-04-01

    The East Tennessee Technology Park Site-Wide Residual Contamination Remedial Investigation Work Plan (DOE 2004) describes the planned fieldwork to support the remedial investigation (RI) for residual contamination at the East Tennessee Technology Park (ETTP) not addressed in previous Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) decisions. This Addendum describes activities that will be conducted to gather additional information in Zone 1 of the ETTP for groundwater, surface water, and sediments. This Addendum has been developed from agreements reached in meetings held on June 23, 2010, August 25, 2010, October 13, 2010, November 13, 2010, December 1, 2010, and January 13, 2011, with representatives of the U. S. Department of Energy (DOE), U. S. Environmental Protection Agency (EPA), and Tennessee Department of Environment and Conservation (TDEC). Based on historical to recent groundwater data for ETTP and the previously completed Sitewide Remedial Investigation for the ETTP (DOE 2007a), the following six areas of concern have been identified that exhibit groundwater contamination downgradient of these areas above state of Tennessee and EPA drinking water maximum contaminant levels (MCLs): (1) K-720 Fly Ash Pile, (2) K-770 Scrap Yard, (3) Duct Island, (4) K-1085 Firehouse Burn/J.A. Jones Maintenance Area, (5) Contractor's Spoil Area (CSA), and (6) Former K-1070-A Burial Ground. The paper presents a brief summary of the history of the areas, the general conceptual models for the observed groundwater contamination, and the data gaps identified.

  5. Efficient oxygen electrocatalysis on special active sites

    Halck, Niels Bendtsen

    Oxygen electrocatalysis will be pivotal in future independent of fossil fuels. Renewable energy production will rely heavily on oxygen electrocatalysis as a method for storing energy from intermittent energy sources such as the wind and sun in the form of chemical bonds and to release the energy ...... electrocatalysis (ORR and OER) using organic functional groups on another class of catalysts. These consist of graphene sheets modified to have a local porphyrine site with different transition metals ions as model systems....... stored in these bonds in an eco-friendly fashion in fuel cells. This thesis explores catalysts for oxygen electrocatalysis and how carefully designed local structures on catalysts surfaces termed special active sites can influence the activity. Density functional theory has been used as a method...... throughout this thesis to understand these local structure effects and their influence on surface reactions. The concept of these special active sites is used to explain how oxygen evolution reaction (OER) catalysts can have activities beyond the limits of what was previously thought possible. The concept is...

  6. Radioactive residues at nuclear sites in the United States of America

    The United States of America has a large number of sites where radioactive materials have been mined, processed, produced, or used. Upon completion of activities at these sites, some will be cleaned up completely and released for unrestricted future use. However, at other sites, contamination will remain on the site following cleanup, requiring long term institutional controls. Depending on the purpose or the activity conducted at a specific site, these locations are generally under the jurisdiction of a federal agency: the United States Department of Energy, the United States Nuclear Regulatory Commission, the United States Environmental Protection Agency, or the United States Department of Defense. However, under certain conditions, the Nuclear Regulatory Commission relinquishes regulatory authority to individual states to regulate the commercial uses of radioactive materials (except for nuclear reactors), so some locations with radioactive materials are under the jurisdiction of individual states. Other sites with naturally occurring radioactive contamination may also be controlled by individual states. One or two sites under the jurisdiction of each agency are discussed where radioactive materials either existed in the past or exist today, and the source of contamination, the anticipated end state, and the process by which the responsible agency did or will conduct cleanup and site closure are described. Several issues are reviewed that must be addressed in order to design and implement remediations that will ensure long term protection for the environment and future inhabitants. The role of citizens in environmental cleanups is examined, and how institutional controls may be applied to ensure long term protection of remediations that leave some contaminants in place. (author)

  7. Effect of soil-bound residues of malathion on microbial activities

    The effect of soil-bound residues of malathion on CO/sub 2/ evolution, dehydrogenase activity and some nitrogen transformations in a loam soil was investigated under laboratory conditions. The soil samples containing bound residues arising from 10 mg g-1 of the applied malathion were mixed in equal quantity with fresh soil and compared with solvent extracted control soil without bound residues (extracted in the same way as soil containing bound residues). Another control comprising un extracted fresh soil without bound residues was also kept to study the effect of solvent extraction on the biological activity. Rate of Carbon mineralization (CO/sub 2/ evolution) was decreased in the presence of soil-bound residues of malathion. Bound residues also affected dehydrogenase activity of soil. Over 40% inhibition of dehydrogenase activity was observed after 4 days and the inhibition persisted at least for 12 days. Nitrogen mineralization was stimulated in soil containing bound residues of malathion and this stimulatory effect increased with time of incubation. Nitrification was partially inhibited in the presence of soil-bound residues of malathion. The inhibitory effect of the soil-bound residues on nitrification did not show much variation with time. The soil-bound residues did not affect denitrification rate (N/sub 2/O evolution). Nitrogen fixation (acetylene reduction) was partially inhibited in soil amended with bound residues of malathion and the inhibitory effect persisted for at least one week. In general, soil bound residues of malathion inhibited CO/sub 2/ evolution, dehydrogenase activity, nitrification and nitrogen fixation while mineralization of nitrogen was stimulated. Denitrification was not affected by the applied insecticide. (author)

  8. Decommissioning and decontamination activity, Gnome Site, Eddy County, New Mexico

    The purpose of this assessment is to present a brief description of the proposed activity and its potential impacts on the environment. This assessment will constitute an evaluation as to whether or not a formal Environmental Statement need be prepared. As background to the proposed activity, Project Gnome was an underground nuclear test conducted in December 1961 as part of the PLOWSHARE Program. The project site is located about 25 miles southeast of Carlsbad, New Mexico. By means of an excavated shaft and tunnel, a 3-kiloton nuclear explosive was emplaced and detonated in a salt bed about 1200 feet below the surface. The uncontaminated rock and salt muck from the original excavation and subsequent contaminated muck and minor construction debris from reentry activities into the nuclear cavity is commingled and stored in a pile near the Gnome/Coach Shaft. Other areas on the site are known to have been contaminated. In 1969, a program was conducted to cleanup and dispose of all surface contamination to whatever depth it occurred in excess of 0.1 mR/hr. Contaminated materials and soil were collected and disposed into the Gnome shaft, which was filled and sealed. Since then, NV has proposed to DOE/HQ much lower criteria for residual radioactive contamination for the Gnome Site. These proposed criteria were to collect and dispose of surficial materials which contain more than 2 x 10-5 microcuries per gram of soil for beta/gamma emitters and 3 x 10-2 microcuries per milliliter of tritium in soil moisture. According to the latest reconnaissance in 1972, low concentrations of Cs-137, Sr-90 and tritium were present at various locations on the site in excess of these proposed guidelines. Other operational areas within the site are suspected of containing radioactive contamination in much lesser volume, which are to be determined by careful probing and monitoring, as described in the next section

  9. Environmental evaluation of the feasibility of disposal and utilization of coal combustion residues in abandoned mine sites

    The combustion of fossil fuels to generate electricity produces large volumes of solid wastes containing chemicals particularly trace elements. About one fourth of these 80 million tons of coal combustion residues are currently utilized and the remaining accumulate in on site piles and ponds, or are carried away to landfills for disposal. The US Environmental Protection Agency has promulgated regulations governing the disposal of such solid wastes in an environmentally acceptable manner. The major impetus behind these regulations is protection of ground water. Since landfill sites are becoming more scarce, it is highly desirable to find large volume beneficial uses for these combustion residues provided the environmental impacts are minimal and socially acceptable. This study determines the possibility of returning these residues to abounded mine sites for reclamation with subsequent evaluation of environmental implications on groundwater quality. 12 refs., 1 fig., 3 tabs

  10. Allowable Residual Contamination Levels in soil for decommissioning the Shippingport Atomic Power Station site

    As part of decommissioning the Shippingport Atomic Power Station, a fundamental concern is the determination of Allowable Residual Contamination Levels (ARCL) for radionuclides in the soil at the site. The ARCL method described in this report is based on a scenario/exposure-pathway analysis and compliance with an annual dose limit for unrestricted use of the land after decommissioning. In addition to naturally occurring radionuclides and fallout from weapons testing, soil contamination could potentially come from five other sources. These include operation of the Shippingport Station as a pressurized water reactor, operations of the Shippingport Station as a light-water breeder, operation of the nearby Beaver Valley reactors, releases during decommissioning, and operation of other nearby industries, including the Bruce-Mansfield coal-fired power plants. ARCL values are presented for 29 individual radionculides and a worksheet is provided so that ARCL values can be determined for any mixture of the individual radionuclides for any annual dose limit selected. In addition, a worksheet is provided for calculating present time soil concentration value that will decay to the ARCL values after any selected period of time, such as would occur during a period of restricted access. The ARCL results are presented for both unconfined (surface) and confined (subsurface) soil contamination. The ARCL method and results described in this report provide a flexible means of determining unrestricted-use site release conditions after decommissioning the Shippingport Atomic Power Station

  11. Residual radioactivity in the vicinity of formerly utilized MED/AEC sites

    As demand for uranium and thorium was accelerated during the 1940's, services of chemical and metallurgical firms and major research facilities were contracted as needed by the Manhattan Engineer District (MED). A lack of documentation of the radiological status at the time contracts were terminated at these facilities led the Department of Energy (DOE), and its predecessor the Energy Research and Development Administration (ERDA), to develop a major radiological resurvey program to fill this information void. A combination of aerial and ground-level radiological monitoring teams were utilized to identify and assess off-site radioactivity. Results from comprehensive aerial surveys provide the approximate areal extent of elevated radiation levels on the ground. These aerial survey results led to two types of ground-level surveys: (1) gamma-ray scanning on foot or from a motorized vehicle (mobile lab based system) to pinpoint the location of residual radioactivity; and (2) compehensive radiological surveys to determine the amount and type of materials present on specific parcels of private and public property identified during the scanning. This type of investigation was initiated in 1978 and has been successful in identifying and assessing the potential radiation hazard from property on which materials bearing natural radioactivity have been found. This paper contains a description of the techniques used to find and evaluate radioactive material displaced outside the boundaries of a formerly utilized site

  12. ANALYTICAL DETERMINATION OF RESIDUAL STRENGTH AND LINKUP STRENGTH FOR CURVED PANELS, WITH MULTIPLE SITE DAMAGE

    Elangovan.R ,

    2011-05-01

    Full Text Available Airplane fuselage has a large number of riveted joints and is subjected to a major loading of differential internal pressure at cruise altitude and zero pressure on the ground. This constitutes one of the major load cycle on the fuselage often referred to as ground air ground (G-A-G cycle. Due to presence of large number of rivet holes, the fuselage skins have a large number of high stress locations and these are locations of potential crack initiation. Thus at the skin joints of the fuselage shell one can have a number of cracks as it ages (i.e used over a period of time. The practice in earlier time was to consider the largest sized crack and considerits acceptance or otherwise. But in fuselage panels one may have one dominate crack and number of smaller secondary cracks. The understanding the safety of a panel with multi site damages is of concern to airline operations. The present paper deals with the estimation of the strength of a flat panel with multi site damage andlead on to estimation of residual life, using fracture mechanics based approach.

  13. Residual radioactivity guidelines for the heavy water components test reactor at the Savannah River Site

    Guidelines were developed for acceptable levels of residual radioactivity in the Heavy Water Components Test Reactor (HWCTR) facility at the conclusion of its decommissioning. Using source terms developed from data generated in a detailed characterization study, the RESRAD and RASRAD-BUILD computer codes were used to calculate derived concentration guideline levels (DCGLs) for the radionuclides that will remain in the facility. The calculated DCGLs, when compared to existing concentrations of radionuclides measured during a 1996 characterization program, indicate that no decontamination of concrete surfaces will be necessary. Also, based on the results of the calculations, activated concrete in the reactor biological shield does not have to be removed, and imbedded radioactive piping in the facility can remain in place. Viewed in another way, the results of the calculations showed that the present inventory of residual radioactivity in the facility (not including that associated with the reactor vessel and steam generators) would produce less than one millirem per year above background to a hypothetical individual on the property. The residual radioactivity is estimated to be approximately 0.04 percent of the total inventory in the facility as of March, 1997. According to the results, the only radionuclides that would produce greater than 0.0.1-millirem per year are Am-241 (0.013 mrem/yr at 300 years), C-14 (0.022 mrem/yr at 1000 years) and U-238 (0.034 mrem/yr at 6000 years). Human exposure would occur only through the groundwater pathways, that is, from water drawn from, a well on the property. The maximum exposure would be approximately one percent of the 4 millirem per year ground water exposure limit established by the U.S. Environmental Protection Agency. 11 refs., 13 figs., 15 tabs

  14. Residual radioactivity guidelines for the heavy water components test reactor at the Savannah River Site

    Owen, M.B. Smith, R.; McNeil, J.

    1997-04-01

    Guidelines were developed for acceptable levels of residual radioactivity in the Heavy Water Components Test Reactor (HWCTR) facility at the conclusion of its decommissioning. Using source terms developed from data generated in a detailed characterization study, the RESRAD and RASRAD-BUILD computer codes were used to calculate derived concentration guideline levels (DCGLs) for the radionuclides that will remain in the facility. The calculated DCGLs, when compared to existing concentrations of radionuclides measured during a 1996 characterization program, indicate that no decontamination of concrete surfaces will be necessary. Also, based on the results of the calculations, activated concrete in the reactor biological shield does not have to be removed, and imbedded radioactive piping in the facility can remain in place. Viewed in another way, the results of the calculations showed that the present inventory of residual radioactivity in the facility (not including that associated with the reactor vessel and steam generators) would produce less than one millirem per year above background to a hypothetical individual on the property. The residual radioactivity is estimated to be approximately 0.04 percent of the total inventory in the facility as of March, 1997. According to the results, the only radionuclides that would produce greater than 0.0.1-millirem per year are Am-241 (0.013 mrem/yr at 300 years), C-14 (0.022 mrem/yr at 1000 years) and U-238 (0.034 mrem/yr at 6000 years). Human exposure would occur only through the groundwater pathways, that is, from water drawn from, a well on the property. The maximum exposure would be approximately one percent of the 4 millirem per year ground water exposure limit established by the U.S. Environmental Protection Agency. 11 refs., 13 figs., 15 tabs.

  15. SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.

    Jessen, Leon Eyrich; Hoof, Ilka; Lund, Ole; Nielsen, Morten

    2013-07-01

    Identifying which mutation(s) within a given genotype is responsible for an observable phenotype is important in many aspects of molecular biology. Here, we present SigniSite, an online application for subgroup-free residue-level genotype-phenotype correlation. In contrast to similar methods, SigniSite does not require any pre-definition of subgroups or binary classification. Input is a set of protein sequences where each sequence has an associated real number, quantifying a given phenotype. SigniSite will then identify which amino acid residues are significantly associated with the data set phenotype. As output, SigniSite displays a sequence logo, depicting the strength of the phenotype association of each residue and a heat-map identifying 'hot' or 'cold' regions. SigniSite was benchmarked against SPEER, a state-of-the-art method for the prediction of specificity determining positions (SDP) using a set of human immunodeficiency virus protease-inhibitor genotype-phenotype data and corresponding resistance mutation scores from the Stanford University HIV Drug Resistance Database, and a data set of protein families with experimentally annotated SDPs. For both data sets, SigniSite was found to outperform SPEER. SigniSite is available at: http://www.cbs.dtu.dk/services/SigniSite/. PMID:23761454

  16. Development of an on-site measurement method for residual stress in primary system piping of nuclear power plants

    In residual stress measurement for large-scale pipes and vessels in high radiation areas and highly contaminated areas of nuclear plants, it is difficult to bring the radioactivated pipes and vessels out of the areas as they are. If they can brought out, it is very burdensome to handle them for the measurement. Development of an on-site measurement method of residual stress which can be quickly applied and has sufficient measurement accuracy is desirable. In this study, a new method combining an electric discharge skim-cut method with a microscopic strain measurement method using markers was proposed to realize the on-site residual stress measurement on pipes in high radiation areas and highly contaminated areas. In the electric discharge skim-cut method, a boat-type sample is skimmed out of a pipe outer/inner surface using electric discharge machining and released residual stress is measured. The on-site measurement of residual stress by the method can be done using a small, portable electric discharge machine. In the microscopic strain measurement method using markers, the residual stress is estimated by microscopic measurement of the distance between markers after the stress release. The combination of both methods can evaluate the residual stress with the same accuracy as conventional methods offer and it can achieve reduction of radiation exposure in the measurement because the work is done simply and rapidly. In this study, the applicability of the electric discharge skim-cut method was investigated because the applicability of the microscopic strain measurement method using markers was confirmed previously. The experimental examination clarified the applicable conditions for the residual stress measurement with the same accuracy as the conventional methods. Furthermore, the electric discharge machining conditions using pure water as the machining liquid was found to eliminate the amount of liquid radioactive waste completely. (author)

  17. Synthesis and evaluation of radioactive and fluorescent residualizing labels for identifying sites of plasma protein catabolism

    Inulin and lactose were each coupled to tyramine by reductive amination with NaBH3CN and the tyramine then labeled with 125I. Dilactitol-125I-tyramine (DLT) and inulin-125I-tyramine (InTn) were coupled by reductive amination and cyanuric chloride, respectively, to asialofetuin (ASF), fetuin and rat serum albumin (RSA). Attachment of either label had no effect on the circulating half-lives of the proteins. Radioactivity from labeled ASF was recovered in rat liver (> 90%) by 1 h post-injection and remained in liver with half-lives of 2 and 6 days, respectively, for the DLT and InTn labels. Whole body recoveries of radioactivity from DLT- and InTn labels. Whole body recoveries of radioactivity from DLT- and InTn-labeled RSA were 5 and 6.5 days, respectively, again indicating that the larger glycoconjugate label residualized more efficiently in cells following protein degradation. (Lactitol)2-N-CH2-CH2-NH-fluroescein (DLF) was also coupled to ASF by reductive amination and recovered quantitatively in liver at 1 h post-injection. Native ASF was an effective competitor for clearance of DLF-ASF from the circulation. Fluorescent degradation products were retained in liver with a half-life of 1.2 days. Residualizing fluorescent labels should be useful for identification and sorting of cells active in the degradation of plasma proteins

  18. Identification of critical residues in loop E in the 5-HT3ASR binding site

    Muthalagi Mani

    2002-06-01

    Full Text Available Abstract Background The serotonin type 3 receptor (5-HT3R is a member of a superfamily of ligand gated ion channels. All members of this family share a large degree of sequence homology and presumably significant structural similarity. A large number of studies have explored the structure-function relationships of members of this family, particularly the nicotinic and GABA receptors. This information can be utilized to gain additional insights into specific structural and functional features of other receptors in this family. Results Thirteen amino acids in the mouse 5-HT3ASR that correspond to the putative E binding loop of the nicotinic α7 receptor were chosen for mutagenesis. Due to the presence of a highly conserved glycine in this region, it has been suggested that this binding loop is comprised of a hairpin turn and may form a portion of the ligand-binding site in this ion channel family. Mutation of the conserved glycine (G147 to alanine eliminated binding of the 5-HT3R antagonist [3H]granisetron. Three tyrosine residues (Y140, Y142 and Y152 also significantly altered the binding of 5-HT3R ligands. Mutations in neighboring residues had little or no effect on binding of these ligands to the 5-HT3ASR. Conclusion Our data supports a role for the putative E-loop region of the 5-HT3R in the binding of 5-HT, mCPBG, d-tc and lerisetron. 5-HT and mCPBG interact with Y142, d-tc with Y140 and lerisetron with both Y142 and Y152. Our data also provides support for the hypothesis that this region of the receptor is present in a loop structure.

  19. Site reactivity in the free radicals induced damage to leucine residues: a theoretical study.

    Medina, M E; Galano, A; Alvarez-Idaboy, J R

    2015-02-21

    Several recent computational studies have tried to explain the observed selectivity in radical damage to proteins. In this work we use Density Functional Theory and Transition State Theory including tunnelling corrections, reaction path degeneracy, the effect of diffusion, and the role of free radicals to get further insights into this important topic. The reaction between a leucine derivative and free radicals of biological significance, in aqueous and lipid media, has been investigated. Both thermochemical and kinetic analyses, in both hydrophilic and hydrophobic environments, have been carried out. DPPH, ˙OOH, ˙OOCH3, ˙OOCH2Cl, ˙OOCHCl2 and ˙OOCHCH2 radicals do not react with the target molecule. The reactions are proposed to be kinetically controlled. The leucine gamma site was the most reactive for the reactions with ˙N3, ˙OOCCl3, ˙OCH3, ˙OCH2Cl, and ˙OCHCl2 radicals, with rate constants equal to 1.97 × 10(5), 3.24 × 10(4), 6.68 × 10(5), 5.98 × 10(6) and 8.87 × 10(8) M(-1) s(-1), respectively, in aqueous solution. The ˙Cl, ˙OH and ˙OCCl3 radicals react with leucine at the beta, gamma, and delta positions at rates close to the diffusion limit with the alpha position which is the slowest path and the most thermodynamically favored. The presented results confirm that the Bell-Evans-Polanyi principle does not apply for the reactions between amino acid residues and free radicals. Regarding the influence of the environment on the reactivity of the studied series of free radicals towards leucine residues, it is concluded that hydrophilic media slightly lower the reactivity of the studied radicals, compared to hydrophobic ones, albeit the trends in reactivity are very similar. PMID:25592549

  20. An evaluation of remote sensing technologies for the detection of residual contamination at ready-for-anticipated use sites

    Slonecker, E. Terrence; Fisher, Gary B.

    2014-01-01

    Operational problems with site access and information, XRF instrument operation, and imagery collections hampered the effective data collection and analysis process. Of the 24 sites imaged and analyzed, 17 appeared to be relatively clean with no discernible metal contamination, hydrocarbons, or asbestos in the soil. None of the samples for the sites in Louisiana had any result exceeding the appropriate industrial or residential standard for arsenic or lead. One site in South Carolina (North Street Dump) had two samples that exceeded the residential standard for lead. One site in Texas (Cadiz Street), and four sites in Florida (210 North 12th Street, Encore Retail Site, Clearwater Auto, and 22nd Street Mixed Use) were found to have some level of residual metal contamination above the applicable residential or commercial Risk-Based Concentration (RBC) standard. Three of the Florida sites showing metal contamination also showed a pattern of vegetation stress based on standard vegetation analysis techniques.

  1. Chaperone-Like Activity of ß-Casein and Its Effect on Residual in Vitro Activity of Food Enzymes

    Sulewska, Anna Maria

    , tyrosinase from Agaricus bisporus and equine cytochrome c. Only for the first target β-casein was acting as a molecular chaperone i.e. its presence resulted in higher residual activity (higher degree of the function preservation). β-Casein did not have any influence on the residual activity of tyrosinase...

  2. Arylfluorosulfates Inactivate Intracellular Lipid Binding Protein(s) through Chemoselective SuFEx Reaction with a Binding Site Tyr Residue.

    Chen, Wentao; Dong, Jiajia; Plate, Lars; Mortenson, David E; Brighty, Gabriel J; Li, Suhua; Liu, Yu; Galmozzi, Andrea; Lee, Peter S; Hulce, Jonathan J; Cravatt, Benjamin F; Saez, Enrique; Powers, Evan T; Wilson, Ian A; Sharpless, K Barry; Kelly, Jeffery W

    2016-06-15

    Arylfluorosulfates have appeared only rarely in the literature and have not been explored as probes for covalent conjugation to proteins, possibly because they were assumed to possess high reactivity, as with other sulfur(VI) halides. However, we find that arylfluorosulfates become reactive only under certain circumstances, e.g., when fluoride displacement by a nucleophile is facilitated. Herein, we explore the reactivity of structurally simple arylfluorosulfates toward the proteome of human cells. We demonstrate that the protein reactivity of arylfluorosulfates is lower than that of the corresponding aryl sulfonyl fluorides, which are better characterized with regard to proteome reactivity. We discovered that simple hydrophobic arylfluorosulfates selectively react with a few members of the intracellular lipid binding protein (iLBP) family. A central function of iLBPs is to deliver small-molecule ligands to nuclear hormone receptors. Arylfluorosulfate probe 1 reacts with a conserved tyrosine residue in the ligand-binding site of a subset of iLBPs. Arylfluorosulfate probes 3 and 4, featuring a biphenyl core, very selectively and efficiently modify cellular retinoic acid binding protein 2 (CRABP2), both in vitro and in living cells. The X-ray crystal structure of the CRABP2-4 conjugate, when considered together with binding site mutagenesis experiments, provides insight into how CRABP2 might activate arylfluorosulfates toward site-specific reaction. Treatment of breast cancer cells with probe 4 attenuates nuclear hormone receptor activity mediated by retinoic acid, an endogenous client lipid of CRABP2. Our findings demonstrate that arylfluorosulfates can selectively target single iLBPs, making them useful for understanding iLBP function. PMID:27191344

  3. BET is active on Sellafield site

    Several companies, all part of BET Plant Services are carrying out work at the British Nuclear Fuels (BNFL) site at Sellafield, Cumbria, on one of the largest construction projects in Europe. The main development scheme is the THORP (Thermal Oxide Reprocessing Plant) buildings. One of the BET companies has the contract to paint the inside of the fuel storage ponds. It will also coat the surfaces of the MASWEP (Medium Active Solid Waste Encapsulation Plant) complex. Other work includes insulation and fire prevention installation. Scaffolding at the EARP (Enhanced Actinide Removal Plant) site is being provided on a common user basis so all the contractors can use the scaffolding and share the cost. Temporary office and living accommodation blocks have been provide by another BET company. (author)

  4. Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins.

    Yang Jiang

    Full Text Available Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-consuming. In this study, we initiated in an attempt for the computational predictions of such serine sites with Feature Selection based on a Random Forest. Since only a small number of experimentally verified pyruvoyl-modified proteins are collected in the protein database at its current version, we only used a small dataset in this study. After removing proteins with sequence identities >60%, a non-redundant dataset was generated and was used, which contained only 46 proteins, with one pyruvoyl serine site for each protein. Several types of features were considered in our method including PSSM conservation scores, disorders, secondary structures, solvent accessibilities, amino acid factors and amino acid occurrence frequencies. As a result, a pretty good performance was achieved in our dataset. The best 100.00% accuracy and 1.0000 MCC value were obtained from the training dataset, and 93.75% accuracy and 0.8441 MCC value from the testing dataset. The optimal feature set contained 9 features. Analysis of the optimal feature set indicated the important roles of some specific features in determining the pyruvoyl-group-serine sites, which were consistent with several results of earlier experimental studies. These selected features may shed some light on the in-depth understanding of the mechanism of the post-translational self-maturation process, providing guidelines for experimental validation. Future work should be made as more pyruvoyl-modified proteins are

  5. Residual matrix from different separation techniques impacts exosome biological activity

    Lucia Paolini; Andrea Zendrini; Giuseppe Di Noto; Sara Busatto; Elisabetta Lottini; Annalisa Radeghieri; Alessandra Dossi; Andrea Caneschi; Doris Ricotta; Paolo Bergese

    2016-01-01

    Exosomes are gaining a prominent role in research due to their intriguing biology and several therapeutic opportunities. However, their accurate purification from body fluids and detailed physicochemical characterization remain open issues. We isolated exosomes from serum of patients with Multiple Myeloma by four of the most popular purification methods and assessed the presence of residual contaminants in the preparations through an ad hoc combination of biochemical and biophysical technique...

  6. Strategy utilized for assessing baseline risks to human health from K-65 and metal oxide residues stored at the Fernald Site

    The U.S. Department of Energy (DOE) is responsible for cleanup activities at the Fernald Environmental Management Project (FEMP) site in southwestern Ohio. The 425-hectare site consists of a former 55-hectare Production Area, an adjacent Waste Storage Area and various support facilities. From 1952 until 1989, the FEMP processed uranium into metallic open-quotes feedclose quotes materials for other DOE facilities in the nation's defense program. In accordance with the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA), the FEMP site is currently listed on the National Priorities List (NPL). To facilitate an expeditious cleanup effort, environmental issues associated with site cleanup are being managed under five operable units. This paper summarizes the risk assessment strategy employed to determine baseline human health risks associated with K-65 and metal oxide residues currently stored in Operable Unit 4. The K-65 and metal oxide residues were generated during the 1950s as a result of the extraction of uranium from uranium-bearing ores and concentrates. These residues are currently stored within Operable Unit 4 in concrete silos. Silos I and 2 contain approximately 6,120 cubic meters [m3] (8,005 cubic yards [yd3]) of K-65 residues, while silos 3 contains approximately 3890 m3 (5,080 yd3) of cold metal oxides. These concrete silos are beyond their design life and require remedial action. The risk assessment conducted for Operable Unit 4 constitutes the first detailed human health risk assessment to be approved by the Environmental Protection Agency (EPA) for the CERCLA clean-up effort at the FEMP Site. This paper discusses the FEMP's use of a Risk Information Quality Objective process in concert with the traditional risk assessment approach to determine baseline risk to human health and the environment posed by Operable Unit 4. A summary of the baseline risks to human health is also presented

  7. Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

    Cristina Marino Buslje

    Full Text Available Identification of catalytic residues (CR is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI, and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls, combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.

  8. Radiological conditions at four selected sites in South Iraq with residues of depleted uranium

    During the Iraq war of 2003 several air attacks and tank battles were conducted, which utilized depleted uranium (DU) munitions. Consequently, the possible health effects on the Iraqi population of DU residues in the battlefields raised concerns within the Iraqi population, its authorities responsible for the environment, as well as the media in various parts of the world. In 2006 and 2007 technical staff from the Iraqi Radiation Protection Centre collected environmental samples at four selected sites in Southern Iraq, namely As Samawah, Al Nassiryah, Al Basrah and Al Zubayr. A total of 520 samples of soil, water, vegetation and smear tests, were taken. The samples were shipped from Iraq to the Spiez Laboratory in Switzerland, which, on behalf of UNEP, analyzed them using Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS). The radioanalytical results were then made available to the IAEA in order to make a prospective estimation of the radiation doses to the Iraqi population living in the above-mentioned four locations and the associated radiological risks. The annual radiation doses to the public that could arise from the various types of exposure scenarios were calculated. On the basis of the measurements carried out on the samples collected in this study the radiation doses from DU were found sufficiently low not pose a radiological hazard to the population living at the four studied locations. (author)

  9. Recognition of triplex forming oligodeoxynucleotides incorporating abasic sites by 5-arylcytosine residues in duplex DNAs.

    Mizuta, Masahiro; Banba, Jun-Ichi; Kanamori, Takashi; Ohkubo, Akihiro; Sekine, Mitsuo; Seio, Kohji

    2007-01-01

    In this paper, we reported our attempt to use a 5arylcytosine (dC(ar)) and the abasic site () as an artificial base pair for DNA triplex. The idea was confirmed by the molecular modeling studied in which the aromatic group of (ph) which protrudes in the major groove was buried into the cleft formed by the residue in the TFO. We synthesized three kinds of dC(ar) and the oligonucleotides incorporating them. Our UV-melting experiments revealed that the DNA triplex containing the dC(ph).phi was more stable than that containing dC.phi pair. Moreover, the dC.phi pair was more stable than any other dC.Y pairs such as dC(ph).G, dC(ph).C, dC(ph).T and dC(ph).A. These results indicated the possibility that the appropriate pair of dC(Ar) and could be the new sequence code of DNA triplex. We also carried out the Tm analyses of other TFOs incorporating dC(Ar) and , and clarified the stability of these triplexes. PMID:18029568

  10. Quantum delocalization of protons in the hydrogen bond network of an enzyme active site

    Wang, Lu; Boxer, Steven G; Markland, Thomas E

    2015-01-01

    Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

  11. Effect of different detoxification procedures on the residual pertussis toxin activities in vaccines.

    Yuen, Chun-Ting; Asokanathan, Catpagavalli; Cook, Sarah; Lin, Naomi; Xing, Dorothy

    2016-04-19

    Pertussis toxin (PTx) is a major virulence factor produced by Bordetella pertussis and its detoxified form is one of the major protective antigens in vaccines against whooping cough. Ideally, PTx in the vaccine should be completely detoxified while still preserving immunogenicity. However, this may not always be the case. Due to multilevel reaction mechanisms of chemical detoxification that act on different molecular sites and with different production processes, it is difficult to define a molecular characteristic of a pertussis toxoid. PTx has two functional distinctive domains: the ADP-ribosyltransferase enzymatic subunit S1 (A-protomer) and the host cell binding carbohydrate-binding subunits S2-5 (B-oligomer); and in this study, we investigated the effect of different detoxification processes on these two functional activities of the residual PTx in toxoids and vaccines currently marketed worldwide using a recently developed in vitro biochemical assay system. The patho-physiological activities in these samples were also estimated using the in vivo official histamine sensitisation tests. Different types of vaccines, detoxified by formaldehyde, glutaraldehyde or by both, have different residual functional and individual baseline activities. Of the vaccines tested, PT toxoid detoxified by formaldehyde had the lowest residual PTx ADP-ribosyltransferase activity. The carbohydrate binding results detected by anti-PTx polyclonal (pAb) and anti-PTx subunits monoclonal antibodies (mAb) showed specific binding profiles for toxoids and vaccines produced from different detoxification methods. In addition, we also demonstrated that using pAb or mAb S2/3 as detection antibodies would give a better differential difference between these vaccine lots than using mAbs S1 or S4. In summary, we showed for the first time that by measuring the activities of the two functional domains of PTx, we could characterise pertussis toxoids prepared from different chemical detoxification

  12. Identification of key residues that confer Rhodobacter sphaeroides LPS activity at horse TLR4/MD-2.

    Katherine L Irvine

    Full Text Available The molecular determinants underpinning how hexaacylated lipid A and tetraacylated precursor lipid IVa activate Toll-like receptor 4 (TLR4 are well understood, but how activation is induced by other lipid A species is less clear. Species specificity studies have clarified how TLR4/MD-2 recognises different lipid A structures, for example tetraacylated lipid IVa requires direct electrostatic interactions for agonism. In this study, we examine how pentaacylated lipopolysaccharide from Rhodobacter sphaeroides (RSLPS antagonises human TLR4/MD-2 and activates the horse receptor complex using a computational approach and cross-species mutagenesis. At a functional level, we show that RSLPS is a partial agonist at horse TLR4/MD-2 with greater efficacy than lipid IVa. These data suggest the importance of the additional acyl chain in RSLPS signalling. Based on docking analysis, we propose a model for positioning of the RSLPS lipid A moiety (RSLA within the MD-2 cavity at the TLR4 dimer interface, which allows activity at the horse receptor complex. As for lipid IVa, RSLPS agonism requires species-specific contacts with MD-2 and TLR4, but the R2 chain of RSLA protrudes from the MD-2 pocket to contact the TLR4 dimer in the vicinity of proline 442. Our model explains why RSLPS is only partially dependent on horse TLR4 residue R385, unlike lipid IVa. Mutagenesis of proline 442 into a serine residue, as found in human TLR4, uncovers the importance of this site in RSLPS signalling; horse TLR4 R385G/P442S double mutation completely abolishes RSLPS activity without its counterpart, human TLR4 G384R/S441P, being able to restore it. Our data highlight the importance of subtle changes in ligand positioning, and suggest that TLR4 and MD-2 residues that may not participate directly in ligand binding can determine the signalling outcome of a given ligand. This indicates a cooperative binding mechanism within the receptor complex, which is becoming increasingly

  13. Mutational analysis of GlnB residues critical for NifA activation in Azospirillum brasilense.

    Inaba, Juliana; Thornton, Jeremy; Huergo, Luciano Fernandes; Monteiro, Rose Adele; Klassen, Giseli; Pedrosa, Fábio de Oliveira; Merrick, Mike; de Souza, Emanuel Maltempi

    2015-02-01

    PII proteins are signal transduction that sense cellular nitrogen status and relay this signals to other targets. Azospirillum brasilense is a nitrogen fixing bacterium, which associates with grasses and cereals promoting beneficial effects on plant growth and crop yields. A. brasilense contains two PII encoding genes, named glnB and glnZ. In this paper, glnB was mutagenised in order to identify amino acid residues involved in GlnB signaling. Two variants were obtained by random mutagenesis, GlnBL13P and GlnBV100A and a site directed mutant, GlnBY51F, was obtained. Their ability to complement nitrogenase activity of glnB mutant strains of A. brasilense were determined. The variant proteins were also overexpressed in Escherichia coli, purified and characterized biochemically. None of the GlnB variant forms was able to restore nitrogenase activity in glnB mutant strains of A. brasilense LFH3 and 7628. The purified GlnBY51F and GlnBL13P proteins could not be uridylylated by GlnD, whereas GlnBV100A was uridylylated but at only 20% of the rate for wild type GlnB. Biochemical and computational analyses suggest that residue Leu13, located in the α helix 1 of GlnB, is important to maintain GlnB trimeric structure and function. The substitution V100A led to a lower affinity for ATP binding. Together the results suggest that NifA activation requires uridylylated GlnB bound to ATP. PMID:25644954

  14. Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase.

    Kiss, András L; Palló, Anna; Náray-Szabó, Gábor; Harmat, Veronika; Polgár, László

    2008-05-01

    It is widely accepted that the catalytic activity of serine proteases depends primarily on the Asp-His-Ser catalytic triad and other residues within the vicinity of this motif. Some of these residues form the oxyanion binding site that stabilizes the tetrahedral intermediate by hydrogen bonding to the negatively charged oxyanion. In acylaminoacyl peptidase from the thermophile Aeropyrum pernix, the main chain NH group of Gly369 is one of the hydrogen bond donors forming the oxyanion binding site. The side chain of His367, a conserved residue in acylaminoacyl peptidases across all species, fastens the loop holding Gly369. Determination of the crystal structure of the H367A mutant revealed that this loop, including Gly369, moves away considerably, accounting for the observed three orders of magnitude decrease in the specificity rate constant. For the wild-type enzyme ln(k(cat)/K(m)) vs. 1/T deviates from linearity indicating greater rate enhancement with increasing temperature for the dissociation of the enzyme-substrate complex compared with its decomposition to product. In contrast, the H367A variant provided a linear Arrhenius plot, and its reaction was associated with unfavourable entropy of activation. These results show that a residue relatively distant from the active site can significantly affect the catalytic activity of acylaminoacyl peptidase without changing the overall structure of the enzyme. PMID:18325786

  15. Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site

    Misquitta Stephanie A

    2004-02-01

    Full Text Available Abstract Background Glutaminyl cyclase (QC forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP and mutated the apparent active site residues to assess their role in QC catalysis. Results The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence of the disulfide. Mutagenesis of the six active site residues present in both 1AMP and QC reveal essential roles for the two histidines (140 and 330, QC numbering and the two glutamates (201 and 202, while the two aspartates (159 and 248 appear to play no catalytic role. ICP-MS analysis shows less than stoichiometric zinc (0.3:1 in the purified enzyme. Conclusions We conclude that human pituitary glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site residues. In contrast to the aminopeptidase, however, QC does not appear to require zinc for enzymatic activity.

  16. A method for the determination of residual beta activity in drinking water samples

    Idoeta, R. [Dpto. Ingenieria Nuclear y Mecanica de Fluidos, E. T. S. Ingenieria de Bilbao - Universidad del Pais Vasco (UPV/EHU), Alda. Urquijo s/n. 48013 Bilbao (Spain)], E-mail: raquel.idoeta@ehu.es; Herranz, M.; Abelairas, A.; Legarda, F. [Dpto. Ingenieria Nuclear y Mecanica de Fluidos, E. T. S. Ingenieria de Bilbao - Universidad del Pais Vasco (UPV/EHU), Alda. Urquijo s/n. 48013 Bilbao (Spain)

    2007-09-15

    The determination of residual beta activity in drinking water is usually needed in most monitoring programs. In this work a procedure for its determination is described and expressions for the calculations of detection limits and uncertainties are proposed.

  17. A method for the determination of residual beta activity in drinking water samples

    The determination of residual beta activity in drinking water is usually needed in most monitoring programs. In this work a procedure for its determination is described and expressions for the calculations of detection limits and uncertainties are proposed

  18. Residues accessible in the binding site crevice of transmembrane helix 6 of the CB2 cannabinoid receptor†

    Nebane, Ntsang M.; Hurst, Dow P.; Carrasquer, Carl A.; Qiao, Zhuanhong; Reggio, Patricia H.; Song, Zhao-Hui

    2008-01-01

    We have used the substituted-cysteine accessibility method (SCAM) to map the residues in the sixth membrane-spanning segment of the CB2 cannabinoid receptor that contribute to the surface of the water-accessible binding-site crevice. Using a background of the mutant C2.59S which is relatively insensitive to the methanethiosulfonate (MTS) reagents, we mutated to cysteine, one at a time, 34 consecutive residues in TMH6 of the CB2 receptor. These mutant receptors were then expressed in HEK293 ce...

  19. Pneumatic transport system development: residuals and releases program at Westinghouse Cheswick site

    Plutonium oxide and uranium oxide powders are processed within glove boxes or within confinement systems during the fabrication of mixed oxide (MOX) pellets for recycle fuel. The release of these powders to the glove box or to the confinement results in some airborne material that is deposited in the enclosure or is carried in the air streams to the effluent air filtration system. Release tests on simulated leaks in pneumatic transport equipment and release tests on simulated failures with powder blending equipment were conducted. A task to develop pneumatic transport for the movement of powders within an MOX fabrication plant has been underway at the Westinghouse Research Laboratories. While testing and evaluating selected pneumatic transport components on a full scale were in progress, it was deemed necessary that final verification of the technology would have to be performed with plutonium-bearing powders because of the marked differences in certain properties of plutonium from those of uranium oxides. A smaller was designed and constructed for the planned installation in glove boxes at the Westinghouse Plutonium Fuel Development Laboratory. However, prior to use with plutonium it was agreed that this system be set up and tested with uranium oxide powder. The test program conducted at the Westinghouse Cheswick site was divided into two major parts. The first of these examined the residuals left as a result of the pneumatic transport of nuclear fuel powders and verified the operability of this one-third scale system. The second part of the program studied the amount of powder released to the air when off-standard process procedures or maintenance operations were conducted on the pneumatic transport system. Air samplers located within the walk-in box housing the transport loop were used to measure the solids concentration in the air. From this information, the total amount of airborne powder was determined

  20. Allowable residual-contamination levels for decommissioning facilities in the 100 areas of the Hanford Site

    This report contains the results of a study sponsored by UNC Nuclear Industries to determine Allowable Residual Contamination Levels (ARCL) for five generic categories of facilities in the 100 Areas of the Hanford Site. The purpose of this study is to provide ARCL data useful to UNC engineers in conducting safety and cost comparisons for decommissioning alternatives. The ARCL results are based on a scenario/exposure-pathway analysis and compliance with an annual dose limit for three specific modes of future use of the land and facilities. These modes of use are restricted, controlled, and unrestricted. The information on ARCL values for restricted and controlled use provided by this report is intended to permit a full consideration of decommissioning alternatives. ARCL results are presented both for surface contamination remaining in facilities (in dpm/100 cm2), and for unconfined surface and confined subsurface soil conditions (in pCi/g). Two confined soil conditions are considered: contamination at depths between 1 and 4 m, and contamination at depths greater than or equal to 5 m. A set of worksheets are presented in an appendix for modifying the ARCL values to accommodate changes in the radionuclide mixture or concentrations, to consider the impacts of radioactive decay, and to predict instrument responses. Finally, a comparison is made between the unrestricted release ARCL values for the 100 Area facilities and existing decommissioning and land disposal regulations. For surface contamination, the comparison shows good agreement. For soil contamination, the comparison shows good agreement if reasonable modification factors are applied to account for the differences in modeling soil contamination and licensed low-level waste

  1. Identification of Functionally Relevant Lysine Residues That Modulate Human Farnesoid X Receptor Activation

    Sun, An-Qiang; Luo, Yuhuan; Backos, Donald S.; Xu, Shuhua; Balasubramaniyan, Natarajan; Reigan, Philip; Suchy, Frederick J.

    2013-01-01

    Base amino acid lysine residues play an important role in regulation of nuclear receptors [e.g., farnesyl X receptor (FXR)], leading to enhanced or suppressed biologic activity. To understand the molecular mechanisms and the subsequent effects in modulating FXR functions in diverse biologic processes, we individually replaced eight highly conserved lysine residues of human FXR (hFXR) with arginine. The effects of each mutated FXR on target gene activation, subcellular localization, protein-pr...

  2. Work plan for the remedial investigation/feasibility study-environmental assessment for the quarry residuals operable unit at the Weldon Spring Site

    The US Department of Energy (DOE) is conducting cleanup activities at the Weldon Spring site, which is located in St. Charles County, Missouri, about 48 km (30 mi) west of St. Louis. The Weldon Spring site consists of two noncontiguous areas -- the chemical plant area, which includes four raffinate pits, and the quarry. Cleanup activities at the Weldon Spring site are conducted in accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended, incorporating the values of the National Environmental Policy Act (NEPA). The contents of the documents prepared for the project are not intended to represent a statement regarding the legal applicability of NEPA to remedial actions conducted under CERCLA. In accordance with the integrated CERCLA/NEPA approach, a remedial investigation/feasibility study-environmental assessment (RI/FS-EA) is being conducted to evaluate conditions and potential responses for the quarry residuals operable unit (QROU). This operable unit consists of the following areas and/or media: the residual material remaining at the Weldon Spring quarry after removal of the pond water and bulk waste; underlying groundwater; and other media located in the surrounding vicinity of the quarry, including adjacent soil, surface water, and sediment in Femme Osage Slough. This work plan identifies the activities within the RI/FS-EA process that are being proposed to address contamination remaining at the quarry area

  3. Work plan for the remedial investigation/feasibility study-environmental assessment for the quarry residuals operable unit at the Weldon Spring Site

    1994-01-01

    The US Department of Energy (DOE) is conducting cleanup activities at the Weldon Spring site, which is located in St. Charles County, Missouri, about 48 km (30 mi) west of St. Louis. The Weldon Spring site consists of two noncontiguous areas -- the chemical plant area, which includes four raffinate pits, and the quarry. Cleanup activities at the Weldon Spring site are conducted in accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), as amended, incorporating the values of the National Environmental Policy Act (NEPA). The contents of the documents prepared for the project are not intended to represent a statement regarding the legal applicability of NEPA to remedial actions conducted under CERCLA. In accordance with the integrated CERCLA/NEPA approach, a remedial investigation/feasibility study-environmental assessment (RI/FS-EA) is being conducted to evaluate conditions and potential responses for the quarry residuals operable unit (QROU). This operable unit consists of the following areas and/or media: the residual material remaining at the Weldon Spring quarry after removal of the pond water and bulk waste; underlying groundwater; and other media located in the surrounding vicinity of the quarry, including adjacent soil, surface water, and sediment in Femme Osage Slough. This work plan identifies the activities within the RI/FS-EA process that are being proposed to address contamination remaining at the quarry area.

  4. Gamma exposure rate reduction and residual radium-226 concentrations resulting from decontamination activities conducted at the former uranium millsite in Shiprock, New Mexico

    Gamma radiation surveys and residual radium 226 soil samples were taken as part of the decontamination activities of the former Shiprock uranium mill site in New Mexico. In order to facilitate the decontamination activities, the mill site and its contaminated environs were divided into 6 major areas. Extensive data are presented in 2 appendices of the pre- and post-decontamination gamma ray exposure rates made on mill site, and of radium 226 concentrations in surface soil samples. A training program established on the mill site by the Navajo Engineering and Construction Authority is described

  5. Residual radioactivity in the terrestrial environment of the Mururoa and Fangataufa Atolls nuclear weapon test sites

    Activity concentration of alpha-emitting Pu isotopes, 241Pu, 241Am, the pure beta-emitting isotope 90Sr, and the gamma-emitting isotope 137Cs measured in geological and biological samples collected in the terrestrial environment of the former French nuclear test sites of Mururoa and Fangataufa is presented. The samples were collected during an international sampling campaign conducted by the IAEA staff and a team of international experts in summer 1996. The IAEA's Seibersdorf Laboratories and a network of test laboratories, selected on the basis of a proficiency test, carried out the analytical determination of the activity concentrations of the radionuclides. The results obtained were compared with the French data. The study concluded that the radioactivity levels are generally low and of no radiological significance. (author)

  6. European sites contaminated by residues from the ore extracting and processing industries

    Activities linked with the ore extraction and processing industries may lead to enhanced levels of naturally occurring radionuclides (NORs) in products, by-products and waste and at the installations and in the surroundings of the facility. In the framework of the EC-DGXI CARE project (Common Approach for REstoration of contaminated sites) nine important categories of industries were identified and discussions were summarized on the industrial processes and the levels of NORs in parent material, waste and by-products. The most contaminating industries are uranium mining and milling, metal mining and smelting and the phosphate industry. Radionuclide levels in products and/or waste products from the oil and gas extraction industry and of the rare earth, zirconium and ceramics industries may be particularly elevated, but waste streams are limited. The impact on the public from coal mining and power production from coal is commonly considered low. No typical values are available for contaminant levels in materials, buildings and surroundings of radium extraction and luminizing plants, nor for thorium extraction and processing plants. An attempt to give an overview of sites in Europe contaminated with NORs, with emphasis on past practices, was only partly successful since information was often limited or unavailable. The most prominent case of environmental contamination due to mining and processing activities (uranium, metal and coal mining) is in eastern Germany. (author)

  7. Active site studies of Escherichia coli 2-keto-4-hydroxyglutarate aldolase

    Vlahos, C.J.

    1987-01-01

    The data presented delineate the complete amino acid sequence of E. coli KHG aldolase and also identify Lys-133, Glu-45, and Arg-49 as aminoacyl residues required for catalytic activity. Incubation of E. coli KHG aldolase with (/sup 14/C)pyruvate in the presence of NaCNBH/sub 3/ results in the incorporation of one mol of /sup 14/C per mol of enzyme subunit. Digestion of this enzyme-adduct with trypsin, followed by purification of the peptides, allowed for the isolation of a unique radioactive peptide. Its amino acid sequence showed that the pyruvate-binding (i.e., Schiff-base forming) lysine residue is located at position 133 in the intact enzyme. E. coli KHG aldolase activity is lost when the enzyme is reacted with bromopyruvate; saturation kinetics are observed. The substrates, pyruvate and KHG, protect the enzyme from inactivation. Both facts suggest that the reagent is active-site specific. Incubation of the aldolase with (3-/sup 14/C)bromopyruvate is associated with a concomitant loss of enzymatic activity and esterification of Glu-45; if the enzyme is denatured in the presence of excess bromopyruvate, Cys-159 and Cys-180 are also alkylated. Blocking the active-site lysine residue with pyruvate prevents Glu-45 from being esterified but does not eliminate alkylation of these two cysteine residues. Woodward's Reagent K was also found to inactivate the aldolase under conditions that are usually specific for carboxyl group modification. This aldolase is also inactivated by 1,2-cyclohexanedione. Loss of enzymatic activity occurs concomitantly with modification of one arginine residue per enzyme subunit. Treatment of the aldolase with the arginine-specific reagent, 4-(oxyacetyl)phenoxyacetic acid, followed by digestion with trypsin allowed for the isolation of a unique peptide and the identification of Arg-49 as the specific residue involved.

  8. Isolation of active site and antibody-binding fragments of human erythrocyte transglutaminase

    Catalytically active human erythrocyte transglutaminase (TGase) was purified using an immunoaffinity column prepared from a monoclonal antibody to guinea pig liver TGase. The enzyme activity was completely inhibited by incorporation of iodo[14C]acetamide to the level of 1 mole per 1 mole of TGase. The 14C-labeled TGase was digested with cyanogen bromide, subjected to HPLC, and four pure peptides were isolated with molecular weights ranging from 3-22 KDa. Only one of the peptides was radiolabeled and characterized as an active site peptide of 10 KDa. Another peptide of 18 KDa was identified as a monoclonal antibody-binding domain of TGase. Although the active site and the antibody-binding domain were present on different cyanogen bromide fragments, the mouse anti-TGase inhibited 100% of TGase activity. The results suggest that the antibody-binding site is not located on the enzyme active site sequence, but that the three dimensional space configuration of the antigen-antibody complex hinders substrate binding to the active site. The radiolabeled active site cysteine residue was not found in the N-terminal 21 amino acids of the 10 KDa peptide. Additional fragments of the active site peptide are currently being analyzed

  9. Two histidine residues are essential for ribonuclease T1 activity as is the case for ribonuclease

    Ribonuclease T1 (RNase T1, EC 3.1.27.3) is a guanosine-specific ribonuclease that cleaves the 3',5'-phosphodiester linkage of single-stranded RNA. It is assumed that the reaction is generated by concerted acid-base catalysis between residues Glu-58 and His-92 or His-40. From the results of chemical modification and NMR studies, it appeared that the residue Glu-58 was indispensable for nucleolytic activity. However, the authors have recently demonstrated that Glu-58 is an important but not an essential residue for catalytic activity, using the methods of genetic engineering to change Glu-58 to Gln-58 etc. In the present paper, the authors report that mutants of RNase T1 with residue Ala-40 or Ala-92 have almost no activity, while mutants that contain Ala-58 retain considerable activity. These results show that the two histidine residues, His-40 and His-92, but not Glu-58, are indispensable for the catalytic activity of the enzyme. They propose a revised reaction mechanism in which two histidine residues play a major role, as they do in the case of RNase A

  10. Serine substitution for cysteine residues in levansucrase selectively abolishes levan forming activity.

    Senthilkumar, Velusamy; Busby, Stephen J W; Gunasekaran, Paramasamy; Senthikumar, Velusamy; Bushby, Stephen J W

    2003-10-01

    Levansucrase is responsible for levan formation during sucrose fermentation of Zymomonas mobilis, and this decreases the efficiency of ethanol production. As thiol modifying agents decrease levan formation, a role for cysteine residues in levansucrase activity has been examined using derivatives of Z. mobilis levansucrase that carry serine substitutions of cysteine at positions 121, 151 or 244. These substitutions abolished the levan forming activity of levansucrase whilst only halving its activity in sucrose hydrolysis. Thus, polymerase and hydrolase activities of Z. mobilis levansucrase are separate and have different requirements for the enzyme's cysteine residues. PMID:14584923

  11. Identification of the active site histidine in Staphylococcus hyicus lipase using chemical modification and mass spectrometry.

    Boots, J W; van Dongen, W D; Verheij, H M; de Haas, G H; Haverkamp, J; Slotboom, A J

    1995-04-01

    Staphylococcus hyicus lipase is a serine hydrolase. In order to identify the active site histidine of S. hyicus lipase we have chemically modified S. hyicus lipase with 1-bromo-octan-2-one. The enzyme is rapidly inactivated by this inhibitor with a half-time of 578 s at pH 6.5 and 30 degrees C. Addition of the enzyme's cofactor calcium increases the inactivation rate approx. 2-fold. When n-hexadecylphosphocholine, a non-hydrolysable substrate analogue, is added the inactivation rate decreases about 3-fold, suggesting that a residue in the active site of S. hyicus lipase is involved in the inactivation reaction. Inactivation of S. hyicus lipase with 14C-labelled 1-bromo-octan-2-one shows that 1.4 moles of inhibitor per mole of lipase are incorporated. The results of an electrospray mass spectrometric study of the inactivated enzyme are consistent with this finding. In order to identify the modified residue, both the inactivated and the unmodified lipase were digested with cyanogen bromide followed by trypsin. The resulting peptides were analysed using HPLC and fast atom bombardment mass spectrometry. The results allow the modified residue to be assigned to the peptide Gly597-Lys612. Collision induced dissociation mass spectrometry allowed the modified residue to be identified as His-600. From these results we conclude that this residue forms part of the catalytic triad of S. hyicus lipase. PMID:7711054

  12. Prediction of residual stress due to early age behaviour of massive concrete structures: on site experiments and macroscopic modelling

    Zreiki, Jihad; Lamour, Vincent; Chaouche, Mohend; Moranville, Micheline

    2008-01-01

    Early age behaviour of concrete is based on complex multi-physical and multiscale phenomena. The predication of both cracking risk and residual stresses in hardened concrete structures is still a challenging task. We propose in this paper a practical method to characterize in the construction site the material parameters and to identify a macroscopic model from simple tests. We propose for instance to use a restrained shrinkage ring test to identify a basic early age creep model based on a si...

  13. Opposing influences by subsite -1 and subsite +1 residues on relative xylopyranosidase/arabinofuranosidase activities of bifunctional beta-D-xylosidase/alpha-L-arabinofuranosidase

    Conformational inversion occurs 7-8 kcal/mol more readily in furanoses than pyranoses. This difference is exploited here to disclose active-site residues involved in distorting substrate towards reactivity. Spontaneous glycoside hydrolysis rates are ordered 4-nitrophenyl-alpha-L-arabinofuranoside (4...

  14. A Single Residue Change in Vibrio harveyi Hemolysin Results in the Loss of Phospholipase and Hemolytic Activities and Pathogenicity for Turbot (Scophthalmus maximus)▿

    Sun, Boguang; Zhang, Xiao-Hua; Tang, Xuexi; Wang, Shushan; Zhong, Yingbin; Chen, Jixiang; Austin, Brian

    2007-01-01

    Vibrio harveyi hemolysin, an important virulence determinant in fish pathogenesis, was further characterized, and the enzyme was identified as a phospholipase B by gas chromatography. Site-directed mutagenesis revealed that a specific residue, Ser153, was critical for its enzymatic activity and for its virulence in fish. PMID:17220231

  15. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

    Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

    2012-05-01

    Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds. PMID:21877154

  16. How do activities walking, standing, and resting influence trans-tibial amputee residual limb fluid volume?

    Sanders, Joan; Cagle, John; Allyn, Katheryn; Harrison, Daniel; Ciol, Marcia

    2014-01-01

    The purpose of this research was to determine how fluid volume changes in the residual limbs of people with trans-tibial amputation were affected by activity during test sessions with equal durations of resting, standing, and walking. Residual limb extracellular fluid volume was measured using biompedance analysis on 24 participants. Results showed that all subjects lost fluid volume during standing with equal weight-bearing, averaging a loss rate of 0.4%/min, and a mean loss over the 25 min ...

  17. Physical Properties and Microbial Activity in Forest Residual Substrate

    Many growers in the horticulture industry have expressed concern that switching from a pine bark-based substrate to one with a significant wood content will increase microbial activity, resulting in nitrogen (N) immobilization. This study evaluated four growth substrates (pine bark, peat moss and tw...

  18. Thermodynamic Model for Uranium Release from Hanford Site Tank Residual Waste

    A thermodynamic model of U phase solubility and paragenesis was developed for Hanford tank residual waste that will remain after tank closure. The model was developed using a combination of waste composition data, waste leach test data, and thermodynamic modeling of the leach test data. The testing and analyses were conducted using actual Hanford tank residual waste. Positive identification of the U phases by X-ray diffraction (XRD) was generally not possible because solids in the waste were amorphous, or below the detection limit of XRD for both as-received residual waste and leached residual waste. Three leachant solutions were used in the studies, dionized water, CaCO3 saturated solution, and Ca(OH)2 saturated solution. Thermodynamic modeling verified that equilibrium between U phases in the initial residual waste samples and the leachants was attained in less than a month. The paragenetic sequence of secondary phases that occur as waste leaching progresses for two closure scenarios was identified. These results have significant implications for tank closure design.

  19. Effects of plastic film residues on occurrence of phthalates and microbial activity in soils.

    Wang, Jun; Lv, Shenghong; Zhang, Manyun; Chen, Gangcai; Zhu, Tongbin; Zhang, Shen; Teng, Ying; Christie, Peter; Luo, Yongming

    2016-05-01

    Plastic film mulching has played an important role in Chinese agriculture, especially in vegetable production, but large amounts of film residues can accumulate in the soil. The present study investigated the effects of plastic film residues on the occurrence of soil PAEs and microbial activities using a batch pot experiment. PAE concentrations increased with increasing plastic film residues but the soil microbial carbon and nitrogen, enzyme activities and microbial diversity decreased significantly. At the end of the experiment the PAE concentrations were 0-2.02 mg kg(-1) in the different treatments. Soil microbial C and N, enzyme activities, AWCD value, and Shannon-Weaver and Simpson indices declined by about 28.9-76.2%, 14.9-59.0%, 4.9-22.7%, 23.0-42.0% and 1.8-18.7%, respectively. Soil microbial activity was positively correlated with soil PAE concentration, and soil PAE concentrations were impacted by plastic color and residue volume. Correlations among, and molecular mechanisms of, plastic film residues, PAE occurrence and microbial activity require further study. PMID:26938679

  20. Hanford Site Tank 241-C-108 Residual Waste Contaminant Release Models and Supporting Data

    This report presents the results of laboratory characterization, testing, and analysis for a composite sample (designated 20578) of residual waste collected from single-shell tank C-108 during the waste retrieval process after modified sluicing. These studies were completed to characterize concentration and form of contaminant of interest in the residual waste; assess the leachability of contaminants from the solids; and develop release models for contaminants of interest. Because modified sluicing did not achieve 99% removal of the waste, it is expected that additional retrieval processing will take place. As a result, the sample analyzed here is not expected to represent final retrieval sample.

  1. Hanford Site Tank 241-C-108 Residual Waste Contaminant Release Models and Supporting Data

    Cantrell, Kirk J.; Krupka, Kenneth M.; Geiszler, Keith N.; Arey, Bruce W.; Schaef, Herbert T.

    2010-06-18

    This report presents the results of laboratory characterization, testing, and analysis for a composite sample (designated 20578) of residual waste collected from single-shell tank C-108 during the waste retrieval process after modified sluicing. These studies were completed to characterize concentration and form of contaminant of interest in the residual waste; assess the leachability of contaminants from the solids; and develop release models for contaminants of interest. Because modified sluicing did not achieve 99% removal of the waste, it is expected that additional retrieval processing will take place. As a result, the sample analyzed here is not expected to represent final retrieval sample.

  2. Promoter proximal polyadenylation sites reduce transcription activity

    Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

  3. Comparison of long-term stability of containment systems for residues and wastes contaminated with naturally occurring radionuclides at an arid site and two humid sites

    The long-term stability of near-surface containment systems designed for the management of radioactive wastes and residues contaminated with naturally occurring radionuclides are compared at the three different sites. The containment designs are: (1) a diked 8.9-m high mound, including a 3.2-m layered cap at a site (humid) near Lewiston, New York, (2) a 6.8-m-high mound, including a similar 3.2-m cap at a site (humid) near Oak Ridge, Tennessee, and (3) 4.8-m deep trenches with 3.0-m backfilled caps at a site (arid) near Hanford, Washington. Geological, hydrological, and biological factors affecting the long-term (1000-year) integrity of the containment systems at each site are examined, including: erosion, flooding, drought, wildfire, slope and cover failure, plant root penetration, burrowing animals, other soil-forming processes, and land-use changes. For the containment designs evaluated, releases of radon-222 at the arid site are predicted to be several orders of magnitude higher than at the two humid sites-upon initial burial and at 1000 years (after severe erosion). Transfer of wastes containing naturally occurring radionuclides from a humid to an arid environment offers little or no advantage relative to long-term stability of the containment system and has a definite disadvantage in terms of gaseous radioactive releases. 26 references, 2 figures, 4 tables

  4. Comparison of long-term stability of containment systems for residues and wastes contaminated with naturally occurring radionuclides at an arid site and two humid sites

    The long-term stability of near-surface containment systems designed for the management of radioactive wastes and residues contaminated with naturally occurring radionuclides are compared at the three different sites. The containment designs are: (1) a diked 8.9-m high mound, including a 3.2-m layered cap at a site (humid) near Lewiston, New York, (2) a 6.8-m-high mound, including a similar 3.2-m cap at a site (humid) near Oak Ridge, Tennessee, and (3) 4.8-m deep trenches with 3.0-m backfilled caps at a site (arid) near Hanford, Washington. Geological, hydrological, and biological factors affecting the long-term (1000-year) integrity of the containment systems at each site are examined, including: erosion, flooding, drought, wildfire, slope and cover failure, plant root penetration, burrowing animals, other soil-forming processes, and land-use changes. For the containment designs evaluated, releases of radon-222 at the arid site are predicted to be several orders of magnitude higher than at the two humid sites - upon initial burial and at 1000 years (after severe erosion). Transfer of wastes containing naturally occurring radionuclides from a humid to an arid environment offers little or no advantage relative to long-term stability of the containment system and has a definite disadvantage in terms of gaseous radioactive releases. 26 references, 3 figures, 4 tables

  5. Persistence and residue activity of deltamethrin on indoor residual spraying surfaces against malaria vectors in southeastern Iran

    Abtahi Mohammad; Shayeghi Mansoreh; Khoobdel Mehdi; Vatandoost Hasan; Abaei Mohammad Reza; Akbarzadeh Kamran

    2011-01-01

    Objective:To evaluate the efficacy of deltamethrin and find a relation between persistence and residue of this insecticide on the prevalent surfaces against malaria vectors in southeastern Iran. Methods:After indoor residual spraying on prevalent surfaces in studied areas (plaster and mud as absorbent surfaces, wood as non absorbent surface and filter paper as control) for malaria control, conical tests as a bioassay method and chromatographic method as an analytical method were used for evolution of persistence and residue of deltamethrin insecticide. Results were investigated statistically by ANOVA and Tukey-HSD tests for determining relations or differences between residue and persistence of deltamethrin. Results:According to the results, there was no significant difference between mortality rates from bioassay tests on different surfaces, and deltamethrin kept its utility to malaria vector control until 120 days after indoor residual spraying on these surfaces. In the case of residue, there was no significant relation between residue amounts and mortality rates on different surfaces, whereas this relation existed between residual amounts on filter papers and mortality rates from bioassay tests. Conclusions: This study shows that measurement of residue in filter papers is a suitable tool for evolution and dictum of efficiency of deltamethrin insecticide in indoor residual spraying for malaria control.

  6. Mechanical Activation-Assisted Reductive Leaching of Cadmium from Zinc Neutral Leaching Residue Using Sulfur Dioxide

    Zhang, Chun; Min, Xiaobo; Chai, Liyuan; Zhang, Jianqiang; Wang, Mi

    2015-12-01

    In this work, zinc neutral leaching residue was mechanically activated by ball-milling. The subsequent leaching behavior and kinetics of cadmium extraction in a mixed SO2-H2SO4 system were studied. Changes in the crystalline phase, lattice distortion, particle size and morphology, which were induced by mechanical activation, were also investigated. The activated samples showed different physicochemical characteristics, and cadmium extraction was found to be easier than for the un-activated samples. Under the same conditions, mechanical activation contributed to higher cadmium leaching. The cadmium extraction kinetics at 75-95°C was found to fit the shrinking core model. The raw neutral leaching residue, and the samples activated for 60 min and 120 min had a calculated activation energy of 65.02 kJ/mol, 59.45 kJ/mol and 53.46 kJ/mol, respectively. The leaching residue was characterized by ICP, XRD and SEM analysis. According to XRD analysis, the main phases in the residue were lead sulfate (PbSO4), zinc sulfide (ZnS) and cadmium sulfide (CdS).

  7. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment

    Astani, Elahe; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L.; Shekarsaraei, Setareh

    2016-04-01

    A theoretical study was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond (HB), in the active site of enzyme human dehydroepiandrosterone sulphotransferase (SULT2A1/DHEA) using the local (M06-L) and hybrid (M06, M06-2X) meta-GGA functionals of density functional theory (DFT). Results revealed that DHEA is able to form HBs with residues His99, Tyr231, Met137 and Met16 in the active site of the SULT2A1/DHEA. It was found that DHEA interacts with the other residues through electrostatic and Van der Waals interactions.

  8. Residual nutational activity of the sunflower hypocotyl in simulated weightlessness

    Chapman, D. K.; Brown, A. H.

    1979-01-01

    The gravity dependence of circumnutational activity in the sunflower hypocotyl is investigated under conditions of simulated weightlessness. Seedling cultures of the sunflower Helianthus annuus were placed four days after planting in clinostats rotating at a rate of 1.0 rpm in the horizontal or somersaulting configurations, and plant movements around their growth axes were recorded in infrared light by a time-lapse closed-circuit video system. The amplitudes and mean cycle durations of the plant nutations in the horizontal and tumbling clinostats are observed to be 20% and 72%, and 32% and 74%, respectively, of the values observed in stationary plants; extrapolations to a state of zero g by the imposition of small centripetal forces on horizontally clinostated plants also indicate some nutational motion in the absence of gravity. It is concluded that the results are incompatible with the model of Israelsson and Johnsson (1967) of geotropic response with overshoot for sunflower circumnutation; however, results of the Spacelab 1 mission experiment are needed to unambiguously define the role of gravitation.

  9. Effect of Amino Acid Residue and Oligosaccharide Chain Chemical Modifications on Spectral and Hemagglutinating Activity of Millettia dielsiana Harms. ex Diels. Lectin

    Shun GAO; Jie AN; Chuan-Fang WU; Ying GU; Fang CHEN; Yuan YU; Qia-Qing WU; Jin-Ku BAO

    2005-01-01

    The effects of modifying the carbohydrate chain and amino acids on the conformation and activity of Millettia dielsiana Harms. ex Diels. lectin (MDL) were studied by hemagglutination, fluorescence and circular dichroism analysis. The modification of tryptophan residues led to a compete loss of hemagglutinating activity; however, the addition of mannose was able to prevent this loss of activity. The results indicate that two tryptophan residues are involved in the carbohydrate-binding site. Modifications of the carboxyl group residues produced an 80% loss of activity, but the presence of mannose protected against the modification. The results suggest that the carboxyl groups of aspartic and glutamic acids are involved in the carbohydrate-binding site of the lectin. However, oxidation of the carbohydrate chain and modification of the histidine and arginine residues did not affect the hemagglutinating activity of MDL. Fluorescence studies of MDL indicate that tryptophan residues are present in a relatively hydrophobic region, and the binding of mannose to MDL could quench tryptophan fluorescence without any change in λmax. The circular dichroism spectrum showed that all of these modifications affected the conformation of the MDL molecule to different extents, except the modification of arginine residues. Fluorescence quenching showed that acrylamide and iodoacetic acids are able to quench 77% and 98% of the fluorescence of tryptophan in MDL, respectively.However, KI produced a barely perceptible effect on the fluorescence of MDL, even when the concentration of I- was 0.15 M. This demonstrates that most of tryptophan residues are located in relatively hydrophobic or negatively charged areas near the surface of the MDL molecule.

  10. A tiered analytical protocol for the characterization of heavy oil residues at petroleum-contaminated hazardous waste sites

    The analysis of hydrocarbon-contaminated soils from abandoned refinery sites in Alberta, Canada is used to illustrate a tiered analytical approach to the characterization of complex hydrocarbon wastes. Soil extracts isolated from heavy oil- and creosote-contaminated sites were characterized by thin layer chromatography with flame ionization detection (TLC-FID), ultraviolet fluorescence, simulated distillation (GC-SIMDIS) and chemical ionization GC-MS analysis. The combined screening and detailed analytical methods provided information essential to remedial technology selection including the extent of contamination, the class composition of soil extracts, the distillation profile of component classes and the distribution of individual class components within various waste fractions. Residual contamination was characteristic of heavy, degraded oils, consistent with documented site operations and length of hydrocarbon exposure at the soil surface

  11. Activities on the site during construction phase

    A survey is given of the work done on the site from site-opening till turn over of the plant to the client. After a short introduction to time schedules, manpower on site, site facilities and civil work and constructions, the commissioning and trial operation phase is discussed in detail. This phase begins with finishing the assembly of individual systems and components and ends with the trial operation and the acceptance measurement. During this period the subsystems are started-up in a useful sequence, first from cold, then from hot conditions and are finally operated as a total with nuclear energy. The single steps are: a) commissioning of indivudal systems; b) hot functional test 1 (without fuels) c) baseline inspection at the reactor pressure vessel; d) hot functional test 2 (with fuels); e) preparation for first criticality; f) postcriticality test program; g) trial operation: h) acceptance measurement. (HP)

  12. Key amino acid residues for the endo-processive activity of GH74 xyloglucanase.

    Matsuzawa, Tomohiko; Saito, Yuji; Yaoi, Katsuro

    2014-05-01

    Unlike endo-dissociative-xyloglucanases, Paenibacillus XEG74 is an endo-processive xyloglucanase that contains four unique tryptophan residues in the negative subsites (W61 and W64) and the positive subsites (W318 and W319), as indicated by three-dimensional homology modelling. Selective replacement of the positive subsite residues with alanine mutations reduced the degree of processive activity and resulted in the more endo-dissociative-activity. The results showed that W318 and W319, which are found in the positive subsites, are essential for processive degradation and are responsible for maintaining binding interactions with xyloglucan polysaccharide through a stacking effect. PMID:24657616

  13. Engineering feasibility analysis for in-situ stabilization of Burrell Township site residues

    The Burrell Township site, located in western Pennsylvania, received approximately 11,600 tons of radioactively-contaminated material in late 1956 and early 1957 from the Vitro Manufacturing Company's operations in Canonsburg, Pennsylvania. WESTON was requested to conduct an engineering study to determine the feasibility of stabilizing the site in accordance with the US Environmental Protection Agency's (EPA) interim and proposed standards (45 FR 27366--27368, April 22, 1980, and 46 FR 2556--2563, January 9, 1981). The scope of this study is limited to those alternatives that can be implemented on the site and will not require removal and offsite disposal of radioactively-contaminated material. Four alternatives for control of the radioactive material at the Burrell site were considered and evaluated, as follows: 1. Site stabilization and closure. 2. Site control and containment. 3. Waste excavation and encapsulation. 4. Waste excavation, incineration, and encapsulation. 2 refs., 32 figs., 12 tabs

  14. Engineering feasibility analysis for in-situ stabilization of Burrell Township site residues. [UMTRA

    1982-11-01

    The Burrell Township site, located in western Pennsylvania, received approximately 11,600 tons of radioactively-contaminated material in late 1956 and early 1957 from the Vitro Manufacturing Company's operations in Canonsburg, Pennsylvania. WESTON was requested to conduct an engineering study to determine the feasibility of stabilizing the site in accordance with the US Environmental Protection Agency's (EPA) interim and proposed standards (45 FR 27366--27368, April 22, 1980, and 46 FR 2556--2563, January 9, 1981). The scope of this study is limited to those alternatives that can be implemented on the site and will not require removal and offsite disposal of radioactively-contaminated material. Four alternatives for control of the radioactive material at the Burrell site were considered and evaluated, as follows: 1. Site stabilization and closure. 2. Site control and containment. 3. Waste excavation and encapsulation. 4. Waste excavation, incineration, and encapsulation. 2 refs., 32 figs., 12 tabs.

  15. Antibacterial and leishmanicidal activities of temporin-SHd, a 17-residue long membrane-damaging peptide.

    Abbassi, Feten; Raja, Zahid; Oury, Bruno; Gazanion, Elodie; Piesse, Christophe; Sereno, Denis; Nicolas, Pierre; Foulon, Thierry; Ladram, Ali

    2013-02-01

    Temporins are a family of short antimicrobial peptides (8-17 residues) that mostly show potent activity against Gram-positive bacteria. Herein, we demonstrate that temporin-SHd, a 17-residue peptide with a net charge of +2 (FLPAALAGIGGILGKLF(amide)), expressed a broad spectrum of antimicrobial activity. This peptide displayed potent antibacterial activities against Gram-negative and Gram-positive bacteria, including multi-drug resistant Staphylococcus aureus strains, as well as antiparasitic activity against promastigote and the intracellular stage (amastigote) of Leishmania infantum, at concentration not toxic for the macrophages. Temporin-SHd that is structured in a non-amphipathic α-helix in anionic membrane-mimetic environments, strongly and selectively perturbs anionic bilayer membranes by interacting with the polar head groups and acyl region of the phospholipids, with formation of regions of two coexisting phases: one phase rich in peptide and the other lipid-rich. The disruption of lipid packing within the bilayer may lead to the formation of transient pores and membrane permeation/disruption once a threshold peptide accumulation is reached. To our knowledge, Temporin-SHd represents the first known 17-residue long temporin expressing such broad spectrum of antimicrobial activity including members of the trypanosomatidae family. Additionally, since only a few shorter members (13 residues) of the temporin family are known to display antileishmanial activity (temporins-TA, -TB and -SHa), SHd is an interesting tool to analyze the antiparasitic mechanism of action of temporins. PMID:23116712

  16. Residues accessible in the binding-site crevice of transmembrane helix 6 of the CB2 cannabinoid receptor.

    Nebane, Ntsang M; Hurst, Dow P; Carrasquer, Carl A; Qiao, Zhuanhong; Reggio, Patricia H; Song, Zhao-Hui

    2008-12-30

    We have used the substituted-cysteine accessibility method (SCAM) to map the residues in the sixth membrane-spanning segment of the CB2 cannabinoid receptor that contribute to the surface of the water-accessible binding-site crevice. Using a background of the mutant C2.59S which is relatively insensitive to the methanethiosulfonate (MTS) reagents, we mutated to cysteine, one at a time, 34 consecutive residues in TMH6 of the CB2 receptor. These mutant receptors were then expressed in HEK293 cells. By incubating HEK293 cells stably transfected with CB2 receptors with the small, charged, hydrophilic, thiol-specific reagent methanethiosulfonate ethylammonium (MTSEA), [(3)H]CP55940 binding was significantly inhibited for six mutant receptors. All six of the mutants that reacted with MTSEA were protected from the reaction when pretreated with the cannabinoid agonist WIN55212-2, suggesting that MTSEA modification occurred within the binding crevice. Therefore, the side chains of the residues at these reactive loci (V6.51, L6.52, L6.54, M6.55, L6.59, and T6.62) are on the water-accessible surface of the binding-site crevice. These residues are extracellular to the TMH6 CWXP hinge motif. The pattern of accessibility is consistent with a alpha-helical conformation for this segment of TMH6. Molecular modeling studies performed in the context of the CB2 model show that V6.51, L6.52, L6.54, M6.55, L6.59, and T6.62 face into the CB2 binding pocket, further confirming our SCAM results. These results are similar to the accessibility patterns determined by SCAM studies of TMH6 in the opioid and dopamine D2 receptors. PMID:19053233

  17. Decomposition of biogas residues in soil and their effects on microbial growth kinetics and enzyme activities

    The rapid development of biogas production will result in increased use of biogas residues as organic fertilizers. However, control of microbial activity by organic fertilizers remains a challenge for modern land use, especially with respect to mitigating greenhouse effects and increasing C sequestration in soil. To address this issue, we compared CO2 emissions, microbial growth and extracellular enzyme activities in agricultural soil amended with biogas residues (BGR) versus maize straw (MST). Over a 21 day incubation period, 6.4% of organic C added was mineralised and evolved as CO2 with BGR and 30% with MST. As shown by the substrate-induced growth respiration approach, BGR and MST significantly decreased the specific microbial growth rate (μ) and increased the microbial biomass C in the soil, indicating a clear shift in the microbial community to slower-growing microorganisms. Because of the reduced availability of C associated with the less labile C and more lignin in biogas residues, observed μ values and microbial biomass C were lower after BGR application than after MST application. After 21 days incubation, BGR had no effect on the activity of three extracellular enzymes: β-glucosidase and cellobiohydrolase, both of which are involved in cellulose decomposition; and xylanase, which is involved in hemicellulose decomposition. In contrast, MST significantly increased the activity of these three enzymes. The application of biogas residues in short-term experiment leads to a 34% increase in soil C content and slower C turnover as compared to common maize residues. -- Highlights: ► Biogas residues (BGR) applied to soil as organic fertilizers were decomposed 2.5 times slower as compared to maize straw. ► BGR application stimulated mainly slow-growing soil microorganisms. ► In contrast to maize straw the BGR did not increase the activity of cellulose-degrading soil enzymes. ► BGR leads to slower C turnover and a 34% increase in C sequestration versus

  18. Mining the waste: prospecting valuable residues optimising processes with modern technology sustainably remediating legacy sites

    Lemière, Bruno

    2012-01-01

    Prospecting valuable residuesAbandoned waste from closed mines or past operations may contain profitably recoverable commodities:-when the market price of the commodity increased significantly since mine closure,-when processing technology improved significantly since mine closure,-when another commodity present in the ore was not recovered and thus sent to waste, because it was not of commercial value at the time. This is especially relevant for some high-tech elements.Abandoned waste rock h...

  19. Criteria and measurement techniques applicable to residual radioactivity on a decommissioned reactor site

    This document summarises the radiological criteria which might be developed to cover the release of a partly decommissioned nuclear reactor site, then looks at the techniques available by which the site could be monitored to assure compliance with these criteria. In particular, the implications of existing levels of radioactive contamination resulting from airburst nuclear weapons tests and the Chernobyl accident are discussed. (author)

  20. Relevance of Co, Ag-ferrierite catalysts acidity and cation siting to CH4-NOx-SCR activity

    The influence of acidity on Ag.Co exchanged ferrierite obtained from different parent forms was tested in CH4-DeNOx reaction. Ag and Co cation siting distribution and residual zeolite acidity were evaluated by means of a quantitative evaluation of catalyst acidity through NH3-TPD experiments and a detailed structural catalyst characterization by Rietveld refinement. A new nomenclature for the cation sites in hydrated and dehydrated cation exchange ferrierites was introduced for sake of clarity. The sites relative populations obtained by the UV-Vis spectra did not agree with the values given by the Rietveld refinement and the SCR. activity scale since the high abundance of Co cations in the retained most active position. Co2a, was shown by the less active catalyst obtained from the Na,K form. It was concluded that SCR activity does not only depend on Co and Ag siting within the zeolite framework but also by the presence of residual acidity evidenced on the most active catalysts. CH4 combustion tests showed that the presence of residual acidity appears relevant to SCR catalytic performances, likely related to its ability in methane activation. The importance of the coexistence of Co and zeolitic, acid sites for the HC-SCR suggested that SCR reaction could proceed on a dual site.

  1. Acidic Residues C-Terminal to the A2 Domain Facilitate Thrombin-Catalyzed Activation of Factor VIII

    Newell, Jennifer L.; Fay, Philip J.

    2008-01-01

    Factor VIII is activated by thrombin through proteolysis at Arg740, Arg372, and Arg1689. One region implicated in this exosite-dependent interaction is the factor VIII a2 segment (residues 711-740) separating the A2 and B domains. Residues 717-725 (DYYEDSYED) within this region consist of five acidic residues and three sulfo-Tyr residues, thus representing a high density of negative charge potential. The contributions of these residues to thrombin-catalyzed activation of factor VIII were asse...

  2. Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

    Buslje, Cristina Marino; Teppa, Elin; Di Doménico, Tomas;

    2010-01-01

    to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed...... hypothesis. A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity...

  3. Identification of residues essential for catalysis and binding of calmodulin in Bordetella pertussis adenylate cyclase by site-directed mutagenesis.

    Glaser, P; Elmaoglou-Lazaridou, A; Krin, E.; Ladant, D.; Bârzu, O; Danchin, A

    1989-01-01

    In order to identify molecular features of the calmodulin (CaM) activated adenylate cyclase of Bordetella pertussis, a truncated cya gene was fused after the 459th codon in frame with the alpha-lacZ' gene fragment and expressed in Escherichia coli. The recombinant, 604 residue long protein was purified to homogeneity by ion-exchange and affinity chromatography. The kinetic parameters of the recombinant protein are very similar to that of adenylate cyclase purified from B.pertussis culture sup...

  4. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  5. Use of activated carbons to remove undesirable residual amylase from factory and refinery streams

    In recent years, there has been increased world-wide concern over residual (carry-over) activity of mostly high temperature (HT) and very high temperature (VHT) stable amylases in white, refined sugars from refineries to various food and end-user industries. HT and VHT stable amylases were develope...

  6. Biotransformation of fluoroquinolone antibiotics by ligninolytic fungi - Metabolites, enzymes and residual antibacterial activity

    Čvančarová, Monika; Moeder, M.; Filipová, Alena; Cajthaml, Tomáš

    2015-01-01

    Roč. 136, OCT 2015 (2015), s. 311-320. ISSN 0045-6535 R&D Projects: GA TA ČR TE01020218; GA ČR GA13-28283S Institutional support: RVO:61388971 Keywords : Fluoroquinolone antibiotics * White rot fungi * Residual antibacterial activity Subject RIV: EE - Microbiology, Virology Impact factor: 3.340, year: 2014

  7. Procedure of Active Residual Heat Removal after Emergency Shutdown of High-Temperature-Gas-Cooled Reactor

    Xingtuan Yang; Yanfei Sun; Huaiming Ju; Shengyao Jiang

    2014-01-01

    After emergency shutdown of high-temperature-gas-cooled reactor, the residual heat of the reactor core should be removed. As the natural circulation process spends too long period of time to be utilized, an active residual heat removal procedure is needed, which makes use of steam generator and start-up loop. During this procedure, the structure of steam generator may suffer cold/heat shock because of the sudden load of coolant or hot helium at the first few minutes. Transient analysis was ca...

  8. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

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

  9. Savannah River Site prioritization of transition activities

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

  10. Savannah River Site prioritization of transition activities

    Finley, R.H.

    1993-11-01

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

  11. An Acidic Thermostable Recombinant Aspergillus nidulans Endoglucanase Is Active towards Distinct Agriculture Residues

    Marcio Jose Poças-Fonseca; Ildinete Silva-Pereira; Cynthia Maria Kyaw; Edivaldo Ximenes Ferreira Filho; Fabrícia Paula de Faria; Gilvan Caetano Duarte; Marciano Regis Rubini; Thiago Machado Mello-de-Sousa; Eveline Queiroz de Pinho Tavares

    2013-01-01

    Aspergillus nidulans is poorly exploited as a source of enzymes for lignocellulosic residues degradation for biotechnological purposes. This work describes the A. nidulans Endoglucanase A heterologous expression in Pichia pastoris, the purification and biochemical characterization of the recombinant enzyme. Active recombinant endoglucanase A (rEG A) was efficiently secreted as a 35 kDa protein which was purified through a two-step chromatography procedure. The highest enzyme activity was dete...

  12. Bats at risk? Bat activity and insecticide residue analysis of food items in an apple orchard.

    Stahlschmidt, Peter; Brühl, Carsten A

    2012-07-01

    Although bats are reported as being threatened by pesticides, they are currently not considered in European Union pesticide risk assessments. The reason for that contradiction is probably related to the scarcity of information on bat activity in pesticide-treated fields and the pesticide residues on their food items. The authors recorded bat activity and measured pesticide residues on bat-specific food items following applications of two insecticides in an apple orchard. High activity levels of the common pipistrelle bat, a foraging habitat generalist, were detected. Airborne foragers and bats that take part of their food by gleaning arthropods from the vegetation were recorded frequently. The initial value and the decline of pesticide residues were found to depend on the arthropod type, their surface to volume ratio, their mobility, and the mode of action of the applied pesticide. The highest initial residue values were measured on foliage-dwelling arthropods. By following the toxicity-exposure ratio approaches of the current pesticide risk assessment, no acute dietary risk was found for all recorded bat species. However, a potential reproductive risk for bat species that include foliage-dwelling arthropods in their diet was indicated. The results emphasize the importance of adequately evaluating the risks of pesticides to bats, which, compared to other mammals, are potentially more sensitive due to their ecological traits. PMID:22505289

  13. Transport and Application of Heat-Activated Persulfate for In-situ Chemical Oxidation of Residual Trichloroethylene

    Quig, L.; Johnson, G. R.

    2015-12-01

    Persulfate ISCO has been shown to treat a wide range of contaminants. While persulfate ISCO can be tailored to site and pollutant specific characteristics (e.g., activation via energy or catalysis), thermal activation of persulfate is particularly promising as it can be easily controlled and requires no additional reagents. A mechanistic study of the physical and chemical processes controlling the effectiveness of this remedial approach is not well documented in the literature with much therein focused on reactions in batch systems. The purpose of this research was twofold. Initial studies characterized the overall transport behavior of unactivated and thermally-activated persulfate (20, 60, and 90°C) in one-dimensional soil column systems. Finally, experiments were conducted to investigate persulfate ISCO as a remedial approach for residual-phase trichloroethylene (TCE). At all activation temperatures investigated, persulfate exhibited ideal transport behavior in miscible displacement experiments. Moment analysis of persulfate ion breakthrough curves indicated negligible interaction of persulfate with the natural sandy material. Persulfate ISCO for residual-phase TCE was characterized at two flow rates, 0.2 mL/min and 0.5 mL/min, resulting in two degrees of persulfate activation, 39.5% and 24.6%, respectively. Both ISCO soil column systems showed an initial, long-term plateau in effluent TCE concentrations indicating steady-state dissolution of pure phase TCE. Observed effluent concentrations decreased after 75 and 100 pore volumes (normalized for the measured residual NAPL fraction) compared to 110 pore volumes in the control study. Pseudo first-order reaction rate constants for the decreasing TCE concentrations equaled 0.063/hr and 0.083/hr, respectively, compared to 0.041/hr for the control. Moment analysis of the complete dissolution of TCE in the persulfate/activated persulfate remediation systems indicated approximately 33% oxidation of TCE mass present. By

  14. Inulin-125I-tyramine, an improved residualizing label for studies on sites of catabolism of circulating proteins

    Residualizing labels for protein, such as dilactitol-125I-tyramine (125I-DLT) and cellobiitol-125I-tyramine, have been used to identify the tissue and cellular sites of catabolism of long-lived plasma proteins, such as albumin, immunoglobulins, and lipoproteins. The radioactive degradation products formed from labeled proteins are relatively large, hydrophilic, resistant to lysosomal hydrolases, and accumulate in lysosomes in the cells involved in degradation of the carrier protein. However, the gradual loss of the catabolites from cells (t1/2 approximately 2 days) has limited the usefulness of residualizing labels in studies on longer lived proteins. We describe here a higher molecular weight (Mr approximately 5000), more efficient residualizing glycoconjugate label, inulin-125I-tyramine (125I-InTn). Attachment of 125I-InTn had no effect on the plasma half-life or tissue sites of catabolism of asialofetuin, fetuin, or rat serum albumin in the rat. The half-life for hepatic retention of degradation products from 125I-InTn-labeled asialofetuin was 5 days, compared to 2.3 days for 125I-DLT-labeled asialofetuin. The whole body half-lives for radioactivity from 125I-InTn-, 125I-DLT-, and 125I-labeled rat serum albumin were 7.5, 4.3, and 2.2 days, respectively. The tissue distribution of degradation products from 125I-InTn-labeled proteins agreed with results of previous studies using 125I-DLT, except that a greater fraction of total degradation products was recovered in tissues. Kinetic analyses indicated that the average half-life for retention of 125I-InTn degradation products in tissues is approximately 5 days and suggested that in vivo there are both slow and rapid routes for release of degradation products from cells

  15. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115.

    Nakamichi, Yusuke; Oiki, Sayoko; Mikami, Bunzo; Murata, Kousaku; Hashimoto, Wataru

    2016-08-01

    Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst. PMID:27402448

  16. Functional residues essential for the activation of the CB1 cannabinoid receptor.

    Shim, Joong-Youn; Padgett, Lea

    2013-01-01

    Recently developed X-ray crystal structures of active state G-protein-coupled receptors have opened the way for detailed examination of the movement of the transmembrane (TM) helices and the specific residues involved in the receptor activation upon ligand binding. Previous modeling studies have indicated that the brain cannabinoid (CB1) receptor binds with a ligand at least in part through a hydrophobic tail on the ligand. This interaction is believed to be similar to the rotameric toggle switch proposed for the β2 adrenergic receptor (β2AR). In the present study, an active state model for the CB1 receptor, guided by the X-ray structure of the active state for β2AR, was constructed with HU210 bound as a ligand. Molecular dynamics (MD) simulations were employed to provide a smooth progression between inactive and active states of the receptor. This model was compared with our previously published CB1 receptor model to identify the functional residues that play key roles in triggering receptor conformational changes upon agonist binding. Movements in TM helices and functional residues are discussed. W279(5.43), contributing to an inward movement of the fifth TM helix (TM5) to the helical core, could serve as another rotameric switch for receptor activation. V282(5.46), interacting with the ligand's hydrophobic C3 alkyl chain, appears to play a key role in TM5 inward movement centered at L286(5.50) and subsequent coupling to V204(3.40). V204(3.40), closely interacting with the TM5 and TM6 hydrophobic patch residues in the middle of the receptor, particularly I290(5.54) and L352(6.44), appears to facilitate helical rearrangements, leading to the breakage of the ionic lock and the rotameric change of Y397(7.53), which are key features of the active state. PMID:23332708

  17. Overall adsorption rate of metronidazole, dimetridazole and diatrizoate on activated carbons prepared from coffee residues and almond shells.

    Flores-Cano, J V; Sánchez-Polo, M; Messoud, J; Velo-Gala, I; Ocampo-Pérez, R; Rivera-Utrilla, J

    2016-03-15

    This study analyzed the overall adsorption rate of metronidazole, dimetridazole, and diatrizoate on activated carbons prepared from coffee residues and almond shells. It was also elucidated whether the overall adsorption rate was controlled by reaction on the adsorbent surface or by intraparticle diffusion. Experimental data of the pollutant concentration decay curves as a function of contact time were interpreted by kinetics (first- and second-order) and diffusion models, considering external mass transfer, surface and/or pore volume diffusion, and adsorption on an active site. The experimental data were better interpreted by a first-order than second-order kinetic model, and the first-order adsorption rate constant varied linearly with respect to the surface area and total pore volume of the adsorbents. According to the diffusion model, the overall adsorption rate is governed by intraparticle diffusion, and surface diffusion is the main mechanism controlling the intraparticle diffusion, representing >90% of total intraparticle diffusion. PMID:26731310

  18. Pathways analysis and radiation-dose estimates for radioactive residues at formerly utilized MED/AEC sites

    Methods of analysis are developed for estimating the largest individual radiation dose that could result from residual radioactivity at sites identified by the Formerly Utilized Sites Remedial Action Program (FUSRAP) of the US Department of Energy. Two unique aspects of the methods are (1) a systematic structuring of the radiation pathways analysis into source terms, source-to-exposure analysis, and exposure-to-dose analysis, and (2) the systematic use of data on the average concentrations of naturally occurring radionuclides in soil, food, and the human body in order to assess the validity of model calculations and obtain more realistic values. The methods are applied to a typical FUSRAP site in order to obtain generic source-to-dose (D/S) conversion factors for estimating the radiation dose to the maximally exposed individual from a known concentration of radionuclides in the soil. The D/S factors are used to derive soil guidelines, i.e., the limiting concentrations of radionuclides at a typical FUSRAP site that are unlikely to result in individual dose limits that exceed generally accepted radiation protection standards. The results lead to the conclusion that the soil guidelines should not exceed 17, 75, and 300 pCi/g for Ra-226, U-238, and Th-230, respectively

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

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang; (NU Sinapore); (Nankai); (Oxford); (Chinese Aca. Sci.); (Tsinghua)

    2009-11-10

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

  20. Probing the putative active site of YjdL

    Jensen, Johanne Mørch; Ismat, Fouzia; Szakonyi, Gerda;

    2012-01-01

    with Glu388, a preliminary orientation model of a dipeptide in the YjdL cavity is presented. Single site mutations of particularly Ala281 and Trp278 support the presented orientation. A dipeptide bound in the cavity of YjdL appears to be oriented such that the N-terminal side chain protrudes into a sub...... pocket that opens towards the extracellular space. The C-terminal side chain faces in the opposite direction into a sub pocket that faces the cytoplasm. These data indicated a stabilizing effect on a bulky N-terminal residue by an Ala281Phe variant and on the dipeptide backbone by Trp278. In the...... presented orientation model, Tyr25 and Tyr58 both appear to be in proximity of the dipeptide backbone while Lys117 appears to be in proximity of the peptide C-terminus. Mutational studies of these conserved residues highlight their functional importance....

  1. Key residues at the riboflavin kinase catalytic site of the bifunctional riboflavin kinase/FMN adenylyltransferase from Corynebacterium ammoniagenes.

    Serrano, Ana; Frago, Susana; Herguedas, Beatriz; Martínez-Júlvez, Marta; Velázquez-Campoy, Adrián; Medina, Milagros

    2013-01-01

    Many known prokaryotic organisms depend on a single bifunctional enzyme, encoded by the RibC of RibF gene and named FAD synthetase (FADS), to convert Riboflavin (RF), first into FMN and then into FAD. The reaction occurs through the sequential action of two activities present on a single polypeptide chain where the N-terminus is responsible for the ATP:FMN adenylyltransferase (FMNAT) activity and the C-terminus for the ATP: riboflavin kinase (RFK) activity. Sequence and structural analysis suggest that T208, N210 and E268 at the C-terminus RFK module of Corynebacterium ammoniagenes FADS (CaFADS) might be key during RF phosphorylation. The effect of site-directed mutagenesis on the RFK activity, as well as on substrates and products binding, indicates that T208 and N210 provide the RFK active-site geometry for binding and catalysis, while E268 might be involved in the catalytic step as catalytic base. These data additionally suggest concerted conformational changes at the RFK module of CaFADS during its activity. Mutations at the RFK site also modulate the binding parameters at the FMNAT active site of CaFADS, altering the catalytic efficiency in the transformation of FMN into FAD. This observation supports the hypothesis that the hexameric assembly previously revealed by the crystal structure of CaFADS might play a functional role during catalysis. PMID:22892871

  2. Enzymatic activity measured by microcalorimetry in soil amended with organic residues

    Karina Cenciani

    2011-08-01

    Full Text Available Enzymatic activity is an important property for soil quality evaluation. Two sequences of experiments were carried out in order to evaluate the enzymatic activity in a soil (Rhodic Eutrudox amended with cattle manure, earthworm casts, or sewage sludges from the municipalities of Barueri and Franca. The activity of commercial enzymes was measured by microcalorimetry in the same soil samples after sterilization. In the first experiment, the enzyme activities of cellulase, protease, and urease were determined in the soil samples during a three month period. In the second sequence of experiments, the thermal effect of the commercial enzymes cellulase, protease, and urease on sterilized soil samples under the same tretaments was monitored for a period of 46 days. The experimental design was randomized and arranged as factorial scheme in five treatments x seven samplings with five replications. The treatment effects were statistically evaluated by one-way analysis of variance. Tukey´s test was used to compare means at p < 0.05. The presence of different sources of organic residues increased the enzymatic activity in the sampling period. Cattle manure induced the highest enzymatic activity, followed by municipal sewage sludge, whereas earthworm casts induced the lowest activity, but differed from control treatment. The thermal effect on the enzyme activity of commercial cellulase, protease, and urease showed a variety of time peaks. These values probably oscillated due to soil physical-chemical factors affecting the enzyme activity on the residues.

  3. Three novel acetylation sites in the Foxp3 transcription factor regulate the suppressive activity of regulatory T cells

    Kwon, Hye-Sook; Lim, Hyung W; Wu, Jessica; Schnoelzer, Martina; Verdin, Eric; Ott, Melanie

    2012-01-01

    The Foxp3 transcription factor is the master regulator of regulatory T cell (Treg) differentiation and function. Its activity is regulated by reversible acetylation. Using mass spectrometry of immunoprecipitated proteins, we identify three novel acetylation sites in murine Foxp3 (K31, K262, and K267) and the corresponding sites in human FoxP3 proteins. Newly raised modification-specific antibodies against acetylated K31 and K267 confirm acetylation of these residues in murine Tregs. Mutant Fo...

  4. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    Soares Alexei S

    2007-11-01

    Full Text Available Abstract Background Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions. Results We found that the smallest ligand stabilizing an open conformer of the RTA active site pocket was an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also revealed a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and red-shift in tryptophan fluorescence upon ligand binding. Using the observed fluorescence signal, we determined the thermodynamic changes of adenine binding to the RTA active site, as well as the site-specific binding of urea. Urea binding had a favorable enthalpy change and unfavorable entropy change, with a ΔH of -13 ± 2 kJ/mol and a ΔS of -0.04 ± 0.01 kJ/(K*mol. The side-chain position of residue Tyr80 in a complex with adenine was found not to involve as large an overlap of rings with the purine as previously considered, suggesting a smaller role for aromatic stacking at the RTA active site. Conclusion We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the

  5. The Surface Groups and Active Site of Fibrous Mineral Materials

    DONG Fa-qin; WAN Pu; FENG Qi-ming; SONG Gong-bao; PENG Tong-jiang; LI Ping; LI Guo-wu

    2004-01-01

    The exposed and transformed groups of fibrous brucite,wollastonite,chrysotile asbestos,sepiolite,palygorskite,clinoptilolite,crocidolite and diatomaceous earth mineral materials are analyzed by IR spectra after acid and alikali etching,strong mechanical and polarity molecular interaction.The results show the active sites concentrate on the ends in stick mineral materials and on the defect or hole edge in pipe mineral materials.The inside active site of mineral materials plays a main role in small molecular substance.The shape of minerals influence their distribution and density of active site.The strong mechanical impulsion and weak chemical force change the active site feature of minerals,the powder process enables minerals exposed more surface group and more combined types.The surface processing with the small polarity molecular or the brand of middle molecular may produce ionation and new coordinate bond,and change the active properties and level of original mineral materials.

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

    The pyridoxal phosphate (PLP)-dependent 1-aminocyclopropane-1-carboxylic acid (ACC) synthase the key enzyme in ethylene biosynthesis, is inactivated by its substrate S-adenosylmethionine (AdoMet). Apple ACC synthase was purified with an immunoaffinity gel, and its active site was probed with NaB3H4 or Ado[14C]Met. Peptide sequencing of both 3H- and 14C-labeled peptides revealed a common dodecapeptide of Ser-Leu-Ser-Xaa-Asp-Leu-Gly-Leu-Pro-Gly-Phe-Arg, where Xaa was the modified, radioactive residue in each case. Acid hydrolysis of the 3H-labeled enzyme released radioactive N-pyridoxyllysine, indicating that the active-site peptide contained lysine at position 4. Mass spectrometry of the 14C-labeled peptide indicated a protonated molecular ion at m/z 1390.6, from which the mass of Xaa was calculated to be 229, a number that is equivalent to the mass of a lysine residue alkylated by the 2-aminobutyrate portion of AdoMet, as we previously proposed. These results indicate that the same active-site lysine binds the PLP and convalently links to the 2-aminobutyrate portion of AdoMet during inactivation. The active site of tomato ACC synthase was probed in the same manner with Ado [14C]Met. Sequencing of the tomato active-site peptide revealed two highly conserved dodecapeptides; the minor peptide possessed a sequence identical to that of the apple enzyme, whereas the major peptide differed from the minor peptide in that methionine replaced leucine at position 6

  7. The effect of administering long-acting oxytetracycline and tilmicosin either by dart gun or by hand on injection site lesions and drug residues in beef cattle.

    Van Donkersgoed, J; VanderKop, M; Salisbury, C.; L. Sears; Holowath, J

    1999-01-01

    Forty yearling cattle were injected intramuscularly with long-acting oxytetracycline and subcutaneously with tilmicosin by dart gun or by hand in a chute 28 days prior to slaughter. The drugs caused injection site lesions and antibiotic residues in the neck and thigh that varied by technique, dose, and site.

  8. Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK.

    Truongvan, Ngoc; Jang, Sei-Heon; Lee, ChangWoo

    2016-06-28

    Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes. PMID:27259687

  9. Assessment of alternatives for long-term management of uranium ore residues and contaminated soils located at DOE's Niagara Falls Storage Site

    Merry-Libby, P.

    1984-11-05

    About 11,000 m/sup 3/ of uranium ore residues and 180,000 m/sup 3/ of wastes (mostly slightly contaminated soils) are consolidated within a diked containment area at the Niagara Falls Storage Site (NFSS) located about 30 km north of Buffalo, NY. The residues account for less than 6% of the total volume of contaminated materials but almost 99% of the radioactivty. The average /sup 226/Ra concentration in the residues is 67,000 pCi/g. Several alternatives for long-term management of the wastes and residues are being considered, including: improvement of the containment at NFSS, modification of the form of the residues, management of the residues separately from the wastes, management of the wastes and residues at another humid site (Oak Ridge, TN) or arid site (Hanford, WA), and dispersal of the wastes in the ocean. Potential radiological risks are expected to be smaller than the nonradiological risks of occupational and transportation-related injuries and deaths. Dispersal of the slightly contaminated wastes in the ocean is not expected to result in any significant impacts on the ocean environment or pose any significant radiological risk to humans. It will be necessary to take perpetual care of the near-surface burial sites because the residues and wastes will remain hazardous for thousands of years. If controls cease, the radioactive materials will eventually be dispersed in the environment. Predicted loss of the earthen covers over the buried materials ranges from several hundred to more than two million years, depending primarily on the use of the land surface. Groundwater will eventually be contaminated in all alternatives; however, the groundwater pathway is relatively insignificant with respect to radiological risks to the general population. A person intruding into the residues would incur an extremely high radiation dose.

  10. Assessment of alternatives for long-term management of uranium ore residues and contaminated soils located at DOE's Niagara Falls Storage Site

    About 11,000 m3 of uranium ore residues and 180,000 m3 of wastes (mostly slightly contaminated soils) are consolidated within a diked containment area at the Niagara Falls Storage Site (NFSS) located about 30 km north of Buffalo, NY. The residues account for less than 6% of the total volume of contaminated materials but almost 99% of the radioactivty. The average 226Ra concentration in the residues is 67,000 pCi/g. Several alternatives for long-term management of the wastes and residues are being considered, including: improvement of the containment at NFSS, modification of the form of the residues, management of the residues separately from the wastes, management of the wastes and residues at another humid site (Oak Ridge, TN) or arid site (Hanford, WA), and dispersal of the wastes in the ocean. Potential radiological risks are expected to be smaller than the nonradiological risks of occupational and transportation-related injuries and deaths. Dispersal of the slightly contaminated wastes in the ocean is not expected to result in any significant impacts on the ocean environment or pose any significant radiological risk to humans. It will be necessary to take perpetual care of the near-surface burial sites because the residues and wastes will remain hazardous for thousands of years. If controls cease, the radioactive materials will eventually be dispersed in the environment. Predicted loss of the earthen covers over the buried materials ranges from several hundred to more than two million years, depending primarily on the use of the land surface. Groundwater will eventually be contaminated in all alternatives; however, the groundwater pathway is relatively insignificant with respect to radiological risks to the general population. A person intruding into the residues would incur an extremely high radiation dose

  11. Derivation of residual radioactive material guidelines for uranium in soil at the Former Associate Aircraft Tool and Manufacturing Company Site, Fairfield, Ohio

    Residual radioactive material guidelines for uranium in soil were derived for the former Associate Aircraft Tool and Manufacturing Company site in Fairfield, Ohio. This site has been identified for remedial action under the U.S. Department of Energy's (DOE's) Formerly Utilized Sites Remedial Action Program (FUSRAP). Single-nuclide and total-uranium guidelines were derived on the basis of the requirement that, after remedial action, the 50-year committed effective dose equivalent to a hypothetical individual living or working in the immediate vicinity of the site should not exceed (1) 30 mrem/yr for the current-use and likely future-use scenarios or (2) 100 mrem/yr for less likely future-use scenarios. The DOE residual radioactive material (RESRAD) computer code, which implements the methodology described in the DOE manual for establishing residual radioactive material guidelines, was used in this evaluation

  12. Limitations on the Activity Concentration of Mineral Processing Residues Used as Building Material

    The use of mineral processing residue as a building material accounts for a significant proportion of the various uses of such material. The activity concentrations of radionuclides of natural origin in the material can be significantly elevated, resulting in enhanced exposure of occupants of the buildings concerned unless some restriction is placed on the radioactivity content. Accordingly, in order to comply with the dose limitation requirements of the relevant laws and standards, the activity concentration in the material has to be restricted. The use of mineral processing residues in building material is controlled in three categories according to a parameter known as the equivalent concentration, which can guide the product specification of the building material and control the dose received by a building occupant. (author)

  13. Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

    Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

    2015-03-01

    Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed. PMID:25613522

  14. Chaperone-like activity of β-casein and its effect on residual in vitro activity of horseradish peroxidase

    Sulewska, Anna Maria; Olsen, Karsten; Sørensen, Jens Christian; Øgendal, Lars Holm

    2014-01-01

    In this study, the residual activity horseradish peroxidase was used as a novel marker of chaperone-like activity of β-casein under elevated temperature. It was shown that β-casein does affect residual activity of horseradish peroxidase (HRP) depending on the concentration and molar ratio between...

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

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

    2011-01-01

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

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

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

    2016-06-17

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

  17. Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA

    Price, Nathan E.; Catalano, Michael J.; Liu, Shuo; Wang, Yinsheng; Gates, Kent S.

    2015-01-01

    A new type of interstrand DNA–DNA cross-link between abasic (Ap) sites and 2′-deoxyadenosine (dA) residues was recently reported, but the chemical structure and properties of this lesion were not rigorously established. Here we characterized the nucleoside cross-link remnant released by enzymatic digestion of duplex DNA containing the dA-Ap cross-link. A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N6-amino group of dA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that the synthetic material 6 matched the authentic cross-link remnant released by enzymatic digestion of cross-linked DNA. These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA. Both the nucleoside cross-link remnant 6 and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes. PMID:25779045

  18. Prediction of residual stress due to early age behaviour of massive concrete structures: on site experiments and macroscopic modelling

    Zreiki, Jihad; Chaouche, Mohend; Moranville, Micheline

    2008-01-01

    Early age behaviour of concrete is based on complex multi-physical and multiscale phenomena. The predication of both cracking risk and residual stresses in hardened concrete structures is still a challenging task. We propose in this paper a practical method to characterize in the construction site the material parameters and to identify a macroscopic model from simple tests. We propose for instance to use a restrained shrinkage ring test to identify a basic early age creep model based on a simple ageing visco-elastic Kelvin model. The strain data obtained from this test can be treated through an early age finite element incremental procedure such that the fitting parameters of the creep law can be quickly identified. The others properties of concrete have been measured at different ages (elastic properties, hydration kinetics, and coefficient of thermal expansion). From the identified early age model, we computed the temperature rise and the stress development in a non reinforced concrete stress for nuclear w...

  19. Solid radioactive waste: evaluation of residual activity in nuclear medicine services

    An experimental programme to estimate, with a better degree of accuracy, the activity that remains adsorbed in flasks and syringes used in Nuclear Medicine Services for the administration of radionuclides to patients submitted to diagnostic or therapy is been conducted under the coordination of the Radioactive Waste Division of the Brazilian Nuclear Energy Commission, CNEN. The adopted recommendation in Brazil to allow an expedite solid waste management in nuclear medicine facilities, up to the present, is to consider that 2% of the initial activity remains adsorbed in the solid waste, which easily allows the calculation of the storage time to achieve regulatory clearance levels by decay. This research evaluates 17 different kinds of radiopharmaceuticals and three radioisotopes: 99mTc, 67Ga and 201Tl. Results obtained by means of a weighting method to estimate the residual mass in flasks show that the ratio of the mass of the liquid that remains in the solid waste to the mass of the empty flask is constant. This suggests that the residual activity depends on the initial activity concentration of radiopharmaceutical contained in each flask, as assumed by the regulatory body. Additionally, results obtained by determining the remaining activity in flasks, shortly after the injection of its radionuclide contents in patients, indicate that an average value for the residual activity of the order of 10% of the initial activity contained in the flasks or syringes should be adopted to determine the decay storage time before the release of solid waste in the urban conventional land fill disposal system. The 'rule of thumb' of 10 half-lives for storage before clearance is also discussed in the present work. (author)

  20. Reduction of urease activity by interaction with the flap covering the active site.

    Macomber, Lee; Minkara, Mona S; Hausinger, Robert P; Merz, Kenneth M

    2015-02-23

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes, and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  1. Preparation of mesoporous activated carbons from coal liquefaction residue for methane decomposition

    Jianbo Zhang; Lijun Jin; Shengwei Zhu; Haoquan Hu

    2012-01-01

    Mesoporous activated carbons were prepared from direct coal liquefaction residue (CLR) by KOH activation method,and the experiments were carried out to investigate the effects of KOH/CLR ratio,solvent for mixing the CLR and KOH,and carbonization procedure on the resultant carbon texture and catalytic activity for catalytic methane decomposition (CMD).The results showed that optimal KOH/CLR ratio of 2 ∶ 1;solvent with higher solubility to KOH or the CLR,and an appropriate carbonization procedure are conductive to improving the carbon pore structure and catalytic activity for CMD.The resultant mesoporous carbons show higher and more stable activity than microporous carbons.Additionally,the relationship between the carbon textural properties and the catalytic activity for CMD was also discussed.

  2. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200.

    Kovaleva, Elena G; Rogers, Melanie S; Lipscomb, John D

    2015-09-01

    Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady-state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures determined at 1.35-1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild-type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second-sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in the steric bulk and charge of the residue at position 200 appear to be capable of altering the rate-limiting step in catalysis and, perhaps, the nature of the reactive species. PMID:26267790

  3. Behavior of peptides combining 1 alanine residue and 8 glycine residues on papain associated with structural fluctuations

    Nishiyama, Katsuhiko

    2011-12-01

    I investigated the behavior of the peptides combining 1 ALA residue and 8 GLY residues on papain associated with structural fluctuations via molecular dynamics and docking simulations. Although the chance of binding to sites near the active center of papain was reduced by replacing the GLY residue in 9GLY with ALA residue, binding stability was improved by the replacement. Furthermore, both the chance and binding stability were greatly affected by positioning of ALA residue in the peptides. Residue in peptides should be replaced in view of the balance between chance of binding to sites near active center and binding stability.

  4. Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum

    Udatha, D.B.R.K. Gupta; Madsen, Karina Marie; Panagiotou, Gianni; Olsson, Lisbeth

    2015-01-01

    The catalytic residues in carbohydrate esterase enzyme families constitute a highly conserved triad: serine, histidine and aspartic acid. This catalytic triad is generally located in a very sharp turn of the protein backbone structure, called the nucleophilic elbow and identified by the consensus...... sequence GXSXG. An esterase from Sorangium cellulosum Soce56 that contains five nucleophilic elbows was cloned and expressed in Escherichia coli and the function of each nucleophilic elbowed site was characterized. In order to elucidate the function of each nucleophilic elbow, site directed mutagenesis was...... used to generate variants with deactivated nucleophilic elbows and the functional promiscuity was analyzed. In silico analysis together with enzymological characterization interestingly showed that each nucleophilic elbow formed a local active site with varied substrate specificities and affinities. To...

  5. Key messages from active CO2 storage sites

    Wildenborg, T.; Wollenweber, J. [TNO, Princetonlaan 6, 3584 CB Utrecht (Netherlands); Chadwick, A. [BGS, Environmental Science Centre, Keyworth, Nottingham, NG12 5GG (United Kingdom); Deflandre, J.P. [IFP Energies nouvelles, 1-4 avenue de Bois Preau, 92852 Rueil-Malmaison (France); Eiken, O. [Statoil Research Centre, Rotvoll, Arkitekt Ebbells vei 10, 7005 Trondheim (Norway); Mathieson, A. [BP, Alternative Energy, Chertsey Road, Sunbury on Thames (United Kingdom); Metcalfe, R. [QUINTESSA, The Hub, 14 Station Road, Henley-on-Thames, Oxfordshire (United Kingdom); Schmidt Hattenberger, C. [GFZ German Research Centre for Geosciences, Centre for CO2Storage, Potsdam (Germany)

    2013-07-01

    An extensive programme of modelling, monitoring and verification activities was deployed at a set of active storage sites worldwide including Sleipner, In Salah, Ketzin, Weyburn, K12-B and Snoehvit (EU CO2ReMoVe project). All investigated storage sites were well managed and did not have a negative impact on humans or the environment. Time-lapse seismic and pressure monitoring are key in verifying the deep subsurface performance of the storage sites. Evidence gathered during the site characterisation and operational phases is key to handover responsibility of the storage site to governmental authorities after injection has definitely ceased, which is the focus of the follow-up EU project CO2CARE.

  6. Klipperaas study site. Scope of activities and main results

    During the period from 1977 - 1986 SKB (Swedish Nuclear Fuel and Waste Management Co.) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection rpogramme will be to perform detailed characterisation, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if any of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favorable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concern the Klipperaas study site. The main topics are the scope of activities, geologic model, geohydrological model, groundwater chemistry, assessment of solute transport, and rock mechanics

  7. Sustainable Activated Carbons from Agricultural Residues Dedicated to Antibiotic Removal by Adsorption

    Jonatan Torres-Perez; Claire Gerente; Yves Andres

    2012-01-01

    The. objectives.of this study are to convert at laboratory s.cale agric.ultural residues into activated carbons (AC) with specific properties, to characterize them and to test them in adsorption reactor for tetracycline removal, a common antibiotic. Two new ACs were produced by direct activation with steam from beet pulp (BP-H2O) and peanut hu_lls (PH-H2O) in environmental friendly conditions BP-H2O and PH-H2Opresentcarbon content rangedcarbons with different intrinsic properties.

  8. Relative toxicity and residual activity of insecticides used in blueberry pest management: mortality of natural enemies.

    Roubos, Craig R; Rodriguez-Saona, Cesar; Holdcraft, Robert; Mason, Keith S; Isaacs, Rufus

    2014-02-01

    A series of bioassays were conducted to determine the relative toxicities and residual activities of insecticides labeled for use in blueberry (Vaccinium corymbosum L.) on natural enemies, to identify products with low toxicity or short duration effects on biological control agents. In total, 14 insecticides were evaluated using treated petri dishes and four commercially available natural enemies (Aphidius colemani Viereck, Orius insidiosus [Say], Chrysoperla rufilabris [Burmeister], and Hippodamia convergens [Guérin-Menéville]). Dishes were aged under greenhouse conditions for 0, 3, 7, or 14 d before introducing insects to test residual activity. Acute effects (combined mortality and knockdown) varied by insecticide, residue age, and natural enemy species. Broad-spectrum insecticides caused high mortality to all biocontrol agents, whereas products approved for use in organic agriculture had little effect. The reduced-risk insecticide acetamiprid consistently caused significant acute effects, even after aging for 14 d. Methoxyfenozide, novaluron, and chlorantraniliprole, which also are classified as reduced-risk insecticides, had low toxicity, and along with the organic products could be compatible with biological control. This study provides information to guide blueberry growers in their selection of insecticides. Further research will be needed to determine whether adoption of a pest management program based on the use of more selective insecticides will result in higher levels of biological control in blueberry. PMID:24665711

  9. Residual radioactive contamination of the test site at Emu from nuclear weapons tests conducted in 1953

    The detailed distributions and soil concentrations of long-lived radionuclides remaining from nuclear weapons trials conducted at Emu in October 1953, are presented. Significant radiation levels due to long-lived neutron activation products in soil, 60Co and 152Eu, occur only in the immediate vicinity of the ground zeros of TOTEM 1 and TOTEM 2. It is shown that the levels of contamination due to fallout products in the soil are well below those which would constitute a health hazard to occupants of the area

  10. Distribution patterns of firearm discharge residues as revealed by neutron activation analysis

    A systematic investigation using a variety of handguns has revealed the existence of distinguisable distribution patterns of firearm discharge residues on surfaces below the flight path of a bullet. The residues are identificable even at distances of 12 meters from the gun using nondestructive neutron activation analysis. The results of these investigations show that the distribution pattern for a gun is reproducible using similar ammunition and that there exist two distinct regions to the patterns developed between the firearm and the target-one with respect to the position of the gun and the other in the vicinity of the target. The judicious applications of these findings could be of significant value in criminal investigations. (T.G.)

  11. Review of the incineration of 500 tonnes of radio-active residues

    During its first five years operation, the incinerator at the Marcoule Centre has burnt almost 500 tonnes of radio-active residues. Improvements in some of the details of the process have been made during this period; they concern the nature of the materials involved. The technical and radiological results for the installation are very favorable, and have made it possible to maintain a high charge factor.Although the overall economic results are not advantageous in the case of ungraded solid residues this method represents nevertheless the best available for eliminating oils, solvents, wood and dead animals. It can also be of use furthermore each time that a dilution in the atmosphere can advantageously be used as a method of disposing of certain radio elements such as tritium or carbon 14 in the form of gases or vapours. (author)

  12. FEASIBILITY OF REMOVING FURFURALS FROM SUGAR SOLUTIONS USING ACTIVATED BIOCHARS MADE FROM AGRICULTURAL RESIDUES

    Isabel Lima

    2011-06-01

    Full Text Available Lignocellulosic feedstocks are often prepared for ethanol fermentation by treatment with a dilute mineral acid catalyst that hydrolyzes the hemicellulose and possibly cellulose into soluble carbohydrates. The acid-catalyzed reaction scheme is sequential, whereby the released monosaccharides are further degraded to furans and other chemicals that are inhibitory to the subsequent fermentation step. This work tests the use of agricultural residues (e.g., plant waste as starting materials for making activated biochars to adsorb these degradation products. Results show that both furfural and hydroxymethylfurfural (HMF are adsorbed by phosphoric acid-activated and steam-activated biochars prepared from residues collected from cotton and linen production. Best results were obtained with steam-activated biochars. The activated biochars adsorbed about 14% (by weight of the furfurals at an equilibrium concentration of 0.5 g/L, and by adding 2.5% of char to a sugar solution, with either furfural or HMF (at 1 g/L, 99% of the furans were removed.

  13. Water molecule network and active site flexibility of apo protein tyrosine phosphatase 1B

    Pedersen, A.K.; Peters, Günther H.J.; Møller, K.B.;

    2004-01-01

    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including...... the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 Angstrom apo PTP1B structure has been obtained, showing four highly coordinated water molecules...

  14. SARS-coronavirus spike S2 domain flanked by cysteine residues C822 and C833 is important for activation of membrane fusion

    The S2 domain of the coronavirus spike (S) protein is known to be responsible for mediating membrane fusion. In addition to a well-recognized cleavage site at the S1-S2 boundary, a second proteolytic cleavage site has been identified in the severe acute respiratory syndrome coronavirus (SARS-CoV) S2 domain (R797). C-terminal to this S2 cleavage site is a conserved region flanked by cysteine residues C822 and C833. Here, we investigated the importance of this well conserved region for SARS-CoV S-mediated fusion activation. We show that the residues between C822-C833 are well conserved across all coronaviruses. Mutagenic analysis of SARS-CoV S, combined with cell-cell fusion and pseudotyped virion infectivity assays, showed a critical role for the core-conserved residues C822, D830, L831, and C833. Based on available predictive models, we propose that the conserved domain flanked by cysteines 822 and 833 forms a loop structure that interacts with components of the SARS-CoV S trimer to control the activation of membrane fusion.

  15. Dashboard applications to monitor experiment activities at sites

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

    2010-04-01

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

  16. Dashboard applications to monitor experiment activities at sites

    Andreeva, J; Boehm, M; Casajus, A; Flix, J; Gaidioz, B; Grigoras, C; Kokoszkiewicz, L; Lanciotti, E; Rocha, R; Saiz, P; Santinelli, R; Sidorova, I; Sciabà, A; Tsaregorodtsev, A

    2010-01-01

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

  17. Dashboard applications to monitor experiment activities at sites

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

  18. Biosynthesis of selenosubtilisin: A novel way to target selenium into the active site of subtilisin

    LI Jing; LIU XiaoMan; JI YueTong; QI ZhenHui; GE Yan; XU JiaYun; LIU JunQiu; LUO GuiMin; SHEN JiaCong

    2008-01-01

    Glutathione peroxidase (GPx,EC1.11.1.9),an important anti-oxidative selenoenzyme,can catalyze the reduction of harmful hydroperoxides with concomitant glutathione,thereby protecting cells and other biological issues against oxidative damage.It captures considerable interest in redesign of its function for either the mechanism study or the pharmacological development as an antioxidant.In order to de-velop a general strategy for specifically targeting and operating selenium in active sites of enzymes,the catalytically essential residue selenocysteine (Sec) was first successfully bioincorporated into the catalytic center of subtilisin by using an auxotrophic expression system.The studies of the catalytic activity and the steady-state kinetics demonstrated that selenosubtilisin is an excellent GPx-like bio-catalyst.In comparison with the chemically modified method,biosynthesis exhibits obvious advan-tages:Sec could be site-directly incorporated into active sites of enzymes to overcome the non-speci-ficity generated by chemical modification.This study provides an important strategy for specifically targeting and operating selenium in the active site of an enzyme.

  19. Kinetic and conformational effects of lysine substitutions for arginines 35 and 87 in the active site of Staphylococcal nuclease

    The high-resolution X-ray crystal structure of staphylococcal nuclease (SNase) suggests that the guanidinium groups of Arg 35 and Arg 87 participate as electrophilic catalysts in the attack of water on the substrate phosphodiester. Both arginine residues have been replaced with conservative lysine residues so that both the importance of these residues in catalysis and the effect of changes in electrostatic interactions on active site conformation can be assessed. The catalytic efficiencies of R35K and R87K are decreased by factors of 104 and 105 relative to wild-type SNase, with R87K showing a very significant reduction in its affinity for both DNA substrate and the competitive inhibitor thymidine 3',5'-bisphosphate (pdTp). The thermal denaturation behavior of both mutant enzymes differs from that of wild type both in the absence and in the presence of the active site ligands Ca2+ and pdTp. Both the 1H NMR chemical shifts and interresidue nuclear Overhauser effects (NOEs) of residues previously assigned to be in the hydrophobic core of SNase are altered in R35K and R87K. These observations suggest that lysine substitutions are not conservative in SNase and disrupt the conformation of the active site. Thus, the kinetic properties of R35K and R87K cannot be used to describe the roles of Arg 35 and Arg 87 in catalysis by the wild-type enzyme. Furthermore, on the basis of the effects of these conservative substitutions for Arg 35 and Arg 87. The authors predict that other substitutions for these residues, including neutral substitutions, are also likely to cause conformational alterations in the active site

  20. The catalytic residues of Tn3 resolvase

    Olorunniji, F.J.; Stark, W M

    2009-01-01

    To characterize the residues that participate in the catalysis of DNA cleavage and rejoining by the site-specific recombinase Tn3 resolvase, we mutated conserved polar or charged residues in the catalytic domain of an activated resolvase variant. We analysed the effects of mutations at 14 residues on proficiency in binding to the recombination site ('site I'), formation of a synaptic complex between two site Is, DNA cleavage and recombination. Mutations of Y6, R8, S10, D36, R68 and R71 result...

  1. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity.

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-12-15

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser(696) and Ser(698) in the JM (juxtamembrane) region and probably Ser(886) and/or Ser(893) in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser(717) in the JM, and at Ser(733), Thr(752), Ser(783), Ser(864), Ser(911), Ser(958) and Thr(998) in the kinase domain. The LC-ESI-MS/MS spectra provided support that up to three sites (Thr(890), Ser(893) and Thr(894)) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr(890), Ser(893), Thr(894) and Thr(899), differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response. PMID:26472115

  2. In silico Modeling of 1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist

    Ramchandran Vijayan

    2007-01-01

    Full Text Available Noradrenaline, like most other neurotransmitters, acts through various adrenoceptor subtypes. The structure and active site of adrenoceptors for the binding of noradrenaline were unknown, however, such information are crucial for understanding the molecular mechanism of action of neurotransmitters, including noradrenaline, in health and disease as well as for drug designing. In this in silico study, we modeled the α1A-adrenoceptor; a G protein coupled receptor and defined its active site. Further, molecular docking and interaction of noradrenaline and its agonist as well as antagonist with the so defined active site of the receptor was studied before and after in silico site directed mutation of several amino acid residues forming the active site. Our results indicate that the ARG166 is the most crucial residue for binding of noradrenaline and methoxamine to α1A-adrenoceptor and ILE178 is the most important residue for binding of prazosin to it. Thus, the observations provide new insights into the structure function relationship of α1A-adrenoceptor. A significant finding of this study is that the same residue of the active site may not be necessary for binding of a receptor with its natural ligand and its pharmacologically active known agonist and antagonist.

  3. Characterization of Solids in Residual Wastes from Underground Storage Tanks at the Hanford Site, Washington, U.S.A

    Solid phase physical and chemical characterization methods have been used in an ongoing study of residual wastes from several single-shell underground waste tanks at the U.S. Department of Energy's Hanford Site in southeastern Washington State. Because these wastes are highly-radioactive dispersible powders and are chemically-complex assemblages of crystalline and amorphous solids that contain contaminants as discrete phases and/or co-precipitated within oxide phases, their detailed characterization offers an extraordinary technical challenge. X-ray diffraction (XRD) and scanning electron microscopy/energy dispersive x-ray spectroscopy (SEM/EDS) are the two principal methods used to characterize solid phases and their contaminant associations in these wastes. Depending on the specific tank, numerous solids (such as eejkaite; Na2U2O7; clarkeite; gibbsite; boehmite; dawsonite; cancrinite; Fe oxides such as hematite, goethite, and maghemite; rhodochrosite; lindbergite; whewellite; nitratine; and several amorphous phases) have been identified in residual wastes studied to date. Because many contaminants of concern are heavy elements, SEM analysis using the backscattered electron (BSE) signal has proved invaluable in distinguishing phases containing elements, such as U and Hg, within the complex assemblage of particles that make up each waste. XRD, SEM/EDS, and synchrotron-based methods provide different, but complimentary characterization data about the morphologies, crystallinity, particle sizes, surface coatings, and compositions of phases in the wastes. The impact of these techniques is magnified when each is used in an iterative fashion to help interpret the results from the other analysis methods and identify additional, more focused analyses

  4. Contribution of tryptophan residues to the combining site of a monoclonal anti dinitrophenyl spin-label antibody

    Two Fab fragments of the monoclonal anti dinitrophenyl (DNP) spin-label antibody AN02 were prepared by recombination of specifically deuterated heavy and light chains. In the recombinant H(I)L(II) all the tyrosines and phenylalanines were perdeuterated as were the tryptophan residues of the heavy chain. In the recombinant H(II)L(I) all the tyrosines and phenylalanines were perdeuterated as were the tryptophan residues of the light chain. Saturation of three resonances of H(I)L(II), assigned to tryptophan protons of the light chain, resulted in magnetization transfer to the aromatic proton at position 6 of the DNP ring and to the CH2 protons of the glycines linked to the DNP in a diamagnetic hapten (DNP-DG). Saturation of three resonances of H(II)L(I) assigned to tryptophan protons of the heavy chain resulted in magnetization transfer to the CH2 protons of the glycines in DNP-DG. From the dependence of the magnetization transfer on the irradiation time, the cross relaxation rates between the involved protons were estimated. The inferred distances between these protons of the hapten and certain tryptophan protons are 3-4 A. It is concluded that in the combining site of AN02 there is one tryptophan from the light chain and one tryptophan from the heavy chain that are very near the hapten. When all tyrosines and phenylalanines were perdeuterated and all tryptophan aromatic protons were deuterated except for the protons at positions 2 and 5, titration of the Fab fragments with variable amounts of paramagnetic hapten showed that one proton from the light chain tryptophan is near (less than 7 A) the unpaired electron and that three other protons are significantly closer than 15 A

  5. Gideaa study site. Scope of activities and main results

    During the period from 1977-1986 SKB (Swedish Nuclear Fuel and Waste Management Co) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other site with geological and/or socio-economical characteristics judged more favourable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concerns the Gideaa study site. (au)

  6. Fjaellveden study site. Scope of activities and main results

    During the period from 1977-1986 SKB (Swedish Nuclear Fuel and Waste Management CO) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favourable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need for complementary investigations. This report concerns the Fjaellveden study site. (au)

  7. Kamlunge study site. Scope of activities and main results

    During the period from 1977-1986 SKB (Swedish nuclear Fuel and Waste Management Co.) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favourable may very well be selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concerns the Kamlunge study site. (79 refs.) (au)

  8. Minimizing high spatial frequency residual error in active space telescope mirrors

    Gray, Thomas L.; Smith, Matthew W.; Cohan, Lucy E.; Miller, David W.

    2009-08-01

    The trend in future space telescopes is towards larger apertures, which provide increased sensitivity and improved angular resolution. Lightweight, segmented, rib-stiffened, actively controlled primary mirrors are an enabling technology, permitting large aperture telescopes to meet the mass and volume restrictions imposed by launch vehicles. Such mirrors, however, are limited in the extent to which their discrete surface-parallel electrostrictive actuators can command global prescription changes. Inevitably some amount of high spatial frequency residual error is added to the wavefront due to the discrete nature of the actuators. A parameterized finite element mirror model is used to simulate this phenomenon and determine designs that mitigate high spatial frequency residual errors in the mirror surface figure. Two predominant residual components are considered: dimpling induced by embedded actuators and print-through induced by facesheet polishing. A gradient descent algorithm is combined with the parameterized mirror model to allow rapid trade space navigation and optimization of the mirror design, yielding advanced design heuristics formulated in terms of minimum machinable rib thickness. These relationships produce mirrors that satisfy manufacturing constraints and minimize uncorrectable high spatial frequency error.

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

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

    1991-10-01

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

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

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

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

  11. A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

    Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

    2007-10-01

    Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase. PMID:17850513

  12. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations.

    Haibo Yu

    2007-02-01

    Full Text Available Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP, the recovery stroke in the conventional myosin has been shown to be dependent on the hydrolysis of ATP. To obtain a clearer mechanistic picture for such "mechanochemical coupling" in myosin, equilibrium active-site simulations with explicit solvent have been carried out to probe the behavior of the motor domain as functions of the nucleotide chemical state and conformation of the converter/relay helix. In conjunction with previous studies of ATP hydrolysis with different active-site conformations and normal mode analysis of structural flexibility, the results help establish an energetics-based framework for understanding the mechanochemical coupling. It is proposed that the activation of hydrolysis does not require the rotation of the lever arm per se, but the two processes are tightly coordinated because both strongly couple to the open/close transition of the active site. The underlying picture involves shifts in the dominant population of different structural motifs as a consequence of changes elsewhere in the motor domain. The contribution of this work and the accompanying paper [] is to propose the actual mechanism behind these "population shifts" and residues that play important roles in the process. It is suggested that structural flexibilities at both the small and large scales inherent to the motor domain make it possible to implement tight couplings between different structural motifs while maintaining small free-energy drops for processes that occur in the detached states, which is likely a feature shared among many molecular motors. The significantly different flexibility of the active site in different X-ray structures with variable level arm orientations supports the notation that external force sensed by the lever arm may transmit into the active site and influence the chemical steps (nucleotide

  13. Residue 21 of human granulocyte-macrophage colony-stimulating factor is critical for biological activity and for high but not low affinity binding.

    Lopez, A F; Shannon, M F; Hercus, T; Nicola, N A; Cambareri, B; Dottore, M; Layton, M. J.; Eglinton, L; Vadas, M A

    1992-01-01

    The functional role of the predicted first alpha-helix of human granulocyte-macrophage colony-stimulating factor (GM-CSF) was analysed by site-directed mutagenesis and multiple biological and receptor binding assays. Initial deletion mutagenesis pointed to residues 20 and 21 being critical. Substitution mutagenesis showed that by altering Gln20 to Ala full GM-CSF activity was retained but that by altering Glu21 for Ala GM-CSF activity and high affinity receptor binding were decreased. Substit...

  14. Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity.

    Joel Raborn

    Full Text Available The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala(252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS of integrins α4β7 and αLβ2 increased the binding and adhesion abilities compared to the wild-type, while the same mutations in the α2β1, α5β1, αVβ3, and αIIbβ3 integrins demonstrated decreased ligand binding and adhesion. We introduced a mutation in the αIIbβ3 to convert this MIDAS associated Ala(252 to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding and adhesion. Then, we performed molecular dynamics simulations on the wild-type and mutant αIIbβ3 integrin β I domains, and investigated the dynamics of metal ion binding sites in different integrin-RGD complexes. We found that the tendency of calculated binding free energies was in excellent agreement with the experimental results, suggesting that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins. This study sheds more light on the role of the MIDAS associated residue pertaining to ligand binding and adhesion and suggests that this residue may play a pivotal role in integrin-mediated cell rolling and firm adhesion.

  15. Residual activity of cetrimide and chlorhexidine on Enterococcus faecalis-infected root canals

    Carmen Mara Ferrer-Luque; Mara Teresa Arias-Moliz; Matilde Ruz-Linares; Mara Elena Martnez Garca; Pilar Baca

    2014-01-01

    Effective final irrigation regimen is an important step in order to achieve better disinfection and ensure residual antimicrobial effects after root canal preparation. The aim of this study was to compare the residual antimicrobial activity of 0.2%cetrimide, and 0.2%and 2%chlorhexidine in root canals infected with Enterococcus faecalis. Biofilms of E. faecalis were grown on uniradicular roots for 4 weeks. After root canal preparation, root canals were irrigated with 17%ethylenediaminetetraacetic acid (EDTA) to remove the smear layer. The roots were randomly divided into three experimental groups (n526) according to the final irrigating solution:Group I, 5 mL 0.2%cetrimide;Group II, 5 mL 0.2%chlorhexidine;and Group III, 5 mL 2%chlorhexidine. Samples were collected for 50 days to denote the presence of bacterial growth. The proportion of ungrown specimens over 50 days was evaluated using the nonparametric Kaplan-Meier survival analysis. Differences among groups were tested using the log-rank test and the level of statistical significance was set at P,0.05. The highest survival value was found with 2%chlorhexidine, showing statistically significant differences from the other two groups. At 50 days, E. faecalis growth was detected in 69.23%specimens in Groups I and II, and in 34.61%specimens of Group III. There were no significant differences between 0.2%cetrimide and 0.2%chlorhexidine. Final irrigation with 2%chlorhexidine showed greater residual activity than 0.2%chlorhexidine and 0.2%cetrimide in root canals infected with E. faecalis.

  16. Anionic Sites, Fucose Residues and Class I Human Leukocyte Antigen Fate During Interaction of Toxoplasma gondii with Endothelial Cells

    Stumbo Ana Carolina

    2002-01-01

    Full Text Available Toxoplasma gondii invades and proliferates in human umbilical vein endothelial cells where it resides in a parasitophorous vacuole. In order to analyze which components of the endothelial cell plasma membrane are internalized and become part of the parasitophorous vacuole membrane, the culture of endothelial cells was labeled with cationized ferritin or UEA I lectin or anti Class I human leukocytte antigen (HLA before or after infection with T. gondii. The results showed no cationized ferritin and UEA I lectin in any parasitophorous vacuole membrane, however, the Class I HLA molecule labeling was observed in some endocytic vacuoles containing parasite until 1 h of interaction with T. gondii. After 24 h parasite-host cell interaction, the labeling was absent on the vacuolar membrane, but presents only in small vesicles near parasitophorous vacuole. These results suggest the anionic site and fucose residues are excluded at the time of parasitophorous vacuole formation while Class I HLA molecules are present only on a minority of Toxoplasma-containig vacuoles.

  17. Allowable residual contamination levels for decommissioning the 115-F and 117-F facilities at the Hanford Site

    This report contains the results of a study sponsored by UNC Nuclear Industries to determine Allowable Residual Contamination Levels (ARCL) for the 115-F and 117-F facilities at the Hanford Site. The purpose of this study is to provide data useful to UNC engineers in conducting safety and cost comparisons for decommissioning alternatives. The ARCL results are based on a scenario/exposure-pathway analysis and compliance with an annual dose limit for three specific modes of future use of the land and facilities. These modes of use are restricted, controlled, and unrestricted. Information on restricted and controlled use is provided to permit a full consideration of decommissioning alternatives. Procedures are presented for modifying the ARCL values to accommodate changes in the radionuclide mixture or concentrations and to determine instrument responses for various mixtures of radionuclides. Finally, a comparison is made between existing decommissioning guidance and the ARCL values calculated for unrestricted release of the 115-F and 117-F facilities. The comparison shows a good agreement

  18. Elaboration and characterization of a new activated carbon obtained from oregano residue: Application in environmental field

    Oumam N.

    2013-09-01

    Full Text Available This study focuses on the valorization of extraction residues of medicinal plants which represent approximately 80% of the gross weight of the plant. In this context we proceeded to the transformation of “marc oregano” to a material adsorbent type activated carbon. The oregano marc, obtained after extraction of essential oils and organic compounds, has undergone a chemical activation using the phosphoric acid 85% (H3PO4. It is well known as precursors of lignocellulosic activating agent, allows the development of a large porosity in the activated material. The activated product has subsequently underwent heat treatment in the temperature range from 200 to 350 °C. The optimum temperature for development was set at 300 °C. The results obtained showed that the adsorbent material O300 has developed the interesting textural properties. It is an adsorbent material like activated carbon, which presents, according to the BET method, a specific surface of 1200 m2·g−1 (specific surface area of commercial activated carbon is of about 905 m2·g−1. The application of adsorbent material developed O300 in microbial decontamination of urban waste water, has revealed its effectiveness and its important adsorptive properties against pathogens pollutants from wastewater.

  19. Radiological dose assessment for residual radioactive material in soil at the clean slate sites 1, 2, and 3, Tonopah Test Range

    A radiological dose assessment has been performed for Clean Slate Sites 1, 2, and 3 at the Tonopah Test Range, approximately 390 kilometers (240 miles) northwest of Las Vegas, Nevada. The assessment demonstrated that the calculated dose to hypothetical individuals who may reside or work on the Clean Slate sites, subsequent to remediation, does not exceed the limits established by the US Department of Energy for protection of members of the public and the environment. The sites became contaminated as a result of Project Roller Coaster experiments conducted in 1963 in support of the US Atomic Energy Commission (Shreve, 1964). Remediation of Clean Slate Sites 1, 2, and 3 is being performed to ensure that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works on a Clean Slate site should not exceed 100 millirems per year. The DOE residual radioactive material guideline (RESRAD) computer code was used to assess the dose. RESRAD implements the methodology described in the DOE manual for establishing residual radioactive material guidelines (Yu et al., 1993a). In May and June of 1963, experiments were conducted at Clean Slate Sites 1, 2, and 3 to study the effectiveness of earth-covered structures for reducing the dispersion of nuclear weapons material as a result of nonnuclear explosions. The experiments required the detonation of various simulated weapons using conventional chemical explosives (Shreve, 1964). The residual radioactive contamination in the surface soil consists of weapons grade plutonium, depleted uranium, and their radioactive decay products

  20. Radiological dose assessment for residual radioactive material in soil at the clean slate sites 1, 2, and 3, Tonopah Test Range

    NONE

    1997-06-01

    A radiological dose assessment has been performed for Clean Slate Sites 1, 2, and 3 at the Tonopah Test Range, approximately 390 kilometers (240 miles) northwest of Las Vegas, Nevada. The assessment demonstrated that the calculated dose to hypothetical individuals who may reside or work on the Clean Slate sites, subsequent to remediation, does not exceed the limits established by the US Department of Energy for protection of members of the public and the environment. The sites became contaminated as a result of Project Roller Coaster experiments conducted in 1963 in support of the US Atomic Energy Commission (Shreve, 1964). Remediation of Clean Slate Sites 1, 2, and 3 is being performed to ensure that the 50-year committed effective dose equivalent to a hypothetical individual who lives or works on a Clean Slate site should not exceed 100 millirems per year. The DOE residual radioactive material guideline (RESRAD) computer code was used to assess the dose. RESRAD implements the methodology described in the DOE manual for establishing residual radioactive material guidelines (Yu et al., 1993a). In May and June of 1963, experiments were conducted at Clean Slate Sites 1, 2, and 3 to study the effectiveness of earth-covered structures for reducing the dispersion of nuclear weapons material as a result of nonnuclear explosions. The experiments required the detonation of various simulated weapons using conventional chemical explosives (Shreve, 1964). The residual radioactive contamination in the surface soil consists of weapons grade plutonium, depleted uranium, and their radioactive decay products.

  1. The quorum sensing transcriptional regulator TraR has separate binding sites for DNA and the anti-activator

    Zheng, Zhida; Fuqua, Clay [Department of Molecular and Cellular Biochemistry, 212 S. Hawthorne Dr. Simon Hall 400A, Indiana University, Bloomington, IN 47405 (United States); Chen, Lingling, E-mail: linchen@indiana.edu [Department of Molecular and Cellular Biochemistry, 212 S. Hawthorne Dr. Simon Hall 400A, Indiana University, Bloomington, IN 47405 (United States)

    2012-02-10

    Highlights: Black-Right-Pointing-Pointer Quorum sensing transcription factor TraR is inhibited by forming TraR-TraM complex. Black-Right-Pointing-Pointer K213 is a key DNA binding residue, but not involved in interaction with TraM. Black-Right-Pointing-Pointer Mutations of TraM-interacting TraR residues did not affect DNA-binding of TraR. Black-Right-Pointing-Pointer Mutations of TraR residues reduced the TraR-TraM interaction more than those of TraM. Black-Right-Pointing-Pointer TraM inhibition on DNA-binding of TraR is driven by thermodynamics. -- Abstract: Quorum sensing represents a mechanism by which bacteria control their genetic behaviors via diffusible signals that reflect their population density. TraR, a quorum sensing transcriptional activator in the Rhizobiaceae family, is regulated negatively by the anti-activator TraM via formation of a TraR-TraM heterocomplex. Prior structural analysis suggests that TraM and DNA bind to TraR in distinct sites. Here we combined isothermal titration calorimetry (ITC) and electrophoretic mobility shift assays (EMSA) to investigate roles of TraR residues from Rhizobium sp. NGR234 in binding of both TraM and DNA. We found that K213A mutation of TraR{sub NGR} abolished DNA binding, however, did not alter TraM binding. Mutations of TraM-interfacing TraR{sub NGR} residues decreased the TraR-TraM interaction, but did not affect the DNA-binding activity of TraR{sub NGR}. Thus, our biochemical studies support the independent binding sites on TraR for TraM and DNA. We also found that point mutations in TraR{sub NGR} appeared to decrease the TraR-TraM interaction more effectively than those in TraM{sub NGR}, consistent with structural observations that individual TraR{sub NGR} residues contact with more TraM{sub NGR} residues than each TraM{sub NGR} residues with TraR{sub NGR} residues. Finally, we showed that TraM inhibition on DNA-binding of TraR was driven thermodynamically. We discussed subtle mechanistic differences in Tra

  2. Molybdenum cofactor properties and [Fe-S] cluster coordination in Escherichia coli nitrate reductase A: investigation by site-directed mutagenesis of the conserved his-50 residue in the NarG subunit.

    Magalon, A; Asso, M; Guigliarelli, B; Rothery, R A; Bertrand, P; Giordano, G; Blasco, F

    1998-05-19

    Most of the molybdoenzymes contain, in the amino-terminal region of their catalytic subunits, a conserved Cys group that in some cases binds an [Fe-S] cluster. In dissimilatory nitrate reductases, the first Cys residue of this motif is replaced by a conserved His residue. Site-directed mutagenesis of this residue (His-50) was performed on the NarG subunit from Escherichia coli nitrate reductase A. The results obtained by EPR spectroscopy enable us to exclude the implication of this residue in [Fe-S] binding. Additionally, we showed that the His-50 residue does not coordinate the molybdenum atom, but its substitution by Cys or Ser introduces a perturbation of the hydrogen bonding network around the molybdenum cofactor. From potentiometric studies, it is proposed that the high-pH and the low-pH forms of the Mo(V) are both involved during the redox turnover of the enzyme. Perturbation of the Mo(V) pKV value might be responsible for the low activity reported in the His-50-Cys mutant enzyme. A catalytic model is proposed in which the protonation/deprotonation of the Mo(V) species is an essential step. Thus, one of the two protons involved in the catalytic cycle could be the one coupled to the molybdenum atom in the dissimilatory nitrate reductase of E. coli. PMID:9585550

  3. Activity and residual effect of two formulations of lambdacyhalothrin sprayed on palm leaves to Rhodnius prolixus.

    Mazariego-Arana, Miguel Angel; Ramirez-San Juan, Eduardo; Alejandre-Aguilar, Ricardo; Nogueda-Torres, Benjamín

    2002-04-01

    The insecticidal activity and residual effect of two formulations of lambdacyhalothrin were evaluated with Rhodnius prolixus; laboratory and field tests were conducted in the State of Chiapas, Mexico. The results indicate that the lethal concentrations of the active ingredient of SC (LC50 = 2.37 and LC90 = 8.5 mg, a.i./m2) were 4-8 times than those with the insecticide WP applied on R. prolixus bugs in palm leaves, a common building material for thatched roofs. Other investigators in South America recommended applying 30 mg a.i./m2 in porous materials; we obtained that the products WP and SC were 3.5 and 16 times more effective on palm leaves. Regarding the evaluation of the residual effects in field spraying, there was up to 15 months persistence after the application of WP in two doses (8.6 mg a.i./m2 and 3.752 mg a.i./m2) with SC. We consider R. prolixus highly susceptible to the employed pyrethroids; they could be used to control this vector in the state of Chiapas, Mexico. PMID:12048565

  4. Effective diffusivity and activation energy in flours of residuals annatto grains

    Dyego da Costa Santos

    2014-03-01

    Full Text Available The residual annatto grains are the subproduct from the extraction process of bixin, dye used in food, cosmetic and pharmaceutical industries. The most of this waste has been discarded in the environment, what constitutes wasteful since, like other grains, is source of carbohydrates, protein and food fibers. One way to facilitate the use of these grains is suing them for making flour and incorporating them in commercial flour of other grains. This work aimed to determine the effective diffusivity and obtain the activation energy in the drying process of flours of residuals annatto grains, with and without the oil layer from the process of industrial extraction of bixin. The dryings was performed at 40, 50, 60 and 70 °C, and air velocity of about 1 m s-1. The calculated value of the effective diffusivity ranged from 0.23 × 10-11 to 2.24 × 10-11 m2 s-1 for the sample with oil, and 0.66 × 10- 11 to 4.89 × 10-11 m2 s-1 for the sample without oil. The activation energies were of 70.56 and 58.95 KJ mol-1 for the sample with oil and without oil, respectively, in which the samples without oil presented higher rates of drying.

  5. A negatively charged transmembrane aspartate residue controls activation of the relaxin-3 receptor RXFP3.

    Liu, Yu; Zhang, Lei; Shao, Xiao-Xia; Hu, Meng-Jun; Liu, Ya-Li; Xu, Zeng-Guang; Guo, Zhan-Yun

    2016-08-15

    Relaxin-3 is an insulin/relaxin superfamily neuropeptide involved in the regulation of food intake and stress response via activation of its cognate receptor RXFP3, an A-class G protein-coupled receptor (GPCR). In recent studies, a highly conserved ExxxD motif essential for binding of relaxin-3 has been identified at extracellular end of the second transmembrane domain (TMD2) of RXFP3. For most of the A-class GPCRs, a highly conserved negatively charged Asp residue (Asp(2.50) using Ballesteros-Weinstein numbering and Asp128 in human RXFP3) is present at the middle of TMD2. To elucidate function of the conserved transmembrane Asp128, in the present work we replaced it with other residues and the resultant RXFP3 mutants all retained quite high ligand-binding potency, but their activation and agonist-induced internalization were abolished or drastically decreased. Thus, the negatively charged transmembrane Asp128 controlled transduction of agonist-binding information from the extracellular region to the intracellular region through maintaining RXFP3 in a metastable state for efficient conformational change induced by binding of an agonist. PMID:27353281

  6. Activity and Residual Effect of Two Formulations of Lambdacyhalothrin Sprayed on Palm Leaves to Rhodnius prolixus

    Mazariego-Arana Miguel Angel

    2002-01-01

    Full Text Available The insecticidal activity and residual effect of two formulations of lambdacyhalothrin were evaluated with Rhodnius prolixus;laboratory and field tests were conducted in the State of Chiapas, Mexico. The results indicate that the lethal concentrations of the active ingredient of SC (LC50 = 2.37 and LC90 = 8.5 mg, a.i./m² were 4-8 times than those with the insecticide WP applied on R. prolixus bugs in palm leaves, a common building material for thatched roofs. Other investigators in South America recommended applying 30 mg a.i./m² in porous materials; we obtained that the products WP and SC were 3.5 and 16 times more effective on palm leaves. Regarding the evaluation of the residual effects in field spraying, there was up to 15 months persistence after the application of WP in two doses (8.6 mg a.i./m² and 3.752 mg a.i./m² with SC. We consider R. prolixus highly susceptible to the employed pyrethroids; they could be used to control this vector in the state of Chiapas, Mexico.

  7. Purification, characterization and antioxidant activity of polysaccharides from Flammulina velutipes residue.

    Liu, Ying; Zhang, Bin; Ibrahim, S A; Gao, Shuang-Shuang; Yang, Hong; Huang, Wen

    2016-07-10

    In this study, we isolated polysaccharides from Flammulina velutipes residue (FVRP) using microwave-assisted extraction and then purified the polysaccharides by column chromatography to yield FVRP-1, FVRP-2 and FVRP-3. The structural characteristics of FVRP-1, FVRP-2 and FVRP-3 were investigated, and their antioxidant activities against ABTS(+), DPPH and hydroxyl radicals were also analyzed in vitro. FVRP-1 was found to be neutral and rich in galactose. However, FVRP-2 and FVRP-3 were acidic polysaccharides and were rich in glucose. The average molecular weight of FVRP-1, FVRP-2 and FVRP-3 were 29,930, 62,290, and 36,310Da, respectively. The glycosyl residue of FVRP-1 was an α-type glycosidic linkage, whereas FVRP-2 and FVRP-3 were β-type glycosidic linkages. We found FVRP-1, FVRP-2 and FVRP-3 had strong potential antioxidant activities in the order of FVRP-1

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

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

    2016-03-01

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

  9. The arginine residue within the C-terminal active core of Bombyx mori pheromone biosynthesis-activating neuropeptide (PBAN is essential for receptor binding and activation

    Takeshi eKawai

    2012-03-01

    Full Text Available In most lepidopteran insects, the biosynthesis of sex pheromones is regulated by pheromone biosynthesis activating neuropeptide (PBAN. Bombyx mori PBAN (BomPBAN consists of 33 amino acid residues and contains a C-terminus FSPRLamide motif as the active core. Among neuropeptides containing the FXPRLamide motif, the arginine (Arg, R residue two positions from the C-terminus is highly conserved across several neuropeptides, which can be designated as RXamide peptides. The purpose of this study was to reveal the role of the Arg residue in the BomPBAN active core. We synthesized a ten-residue peptide corresponding to the C-terminal part of BomPBAN with a series of point mutants at the 2nd position (ie, Arg from the C-terminus, termed the C2 position, and measured their efficacy in stimulating Ca2+ influx in insect cells concomitantly expressing a fluorescent PBAN receptor chimera (PBANR-EGFP and loaded with the fluorescent Ca2+ indicator, Fura Red-AM. PBAN analogs with the C2 position replaced with alanine (Ala, A, aspartic acid (Asp, D, serine (Ser, S or L-2-aminooctanoic acid (Aoc decreased PBAN-like activity. RC2A (SKTRYFSPALamide and RC2D (SKTRYFSPDLamide had the lowest activity and could not inhibit the activity of PBAN C10 (SKTRYFSPRLamide. We also prepared Rhodamine Red-labeled PBAN analogs of the mutants and examined their ability to bind PBANR. In contrast to 100 nM Rhodamine Red-PBAN C10, none of the mutants at the same concentration exhibited PBANR binding. Taken together, our results demonstrate that the C2 Arg residue in BomPBAN is essential for PBANR binding and activation.

  10. Position-Dependent Influence of the Three Trp Residues on the Membrane Activity of the Antimicrobial Peptide, Tritrpticin

    Mauricio Arias

    2014-11-01

    Full Text Available Antimicrobial peptides (AMPs constitute promising candidates for the development of new antibiotics. Among the ever-expanding family of AMPs, tritrpticin has strong antimicrobial activity against a broad range of pathogens. This 13-residue peptide has an unusual amino acid sequence that is almost symmetrical and features three central Trp residues with two Arg residues near each end of the peptide. In this work, the role of the three sequential Trp residues in tritrpticin was studied in a systematic fashion by making a series of synthetic peptides with single-, double- and triple-Trp substitutions to Tyr or Ala. 1H NMR and fluorescence spectroscopy demonstrated the ability of all of the tritrpticin-analog peptides to interact with negatively-charged membranes. Consequently, most tritrpticin analogs exhibited the ability to permeabilize synthetic ePC:ePG (egg-yolk phosphatidylcholine (ePC, egg-yolk phosphatidylglycerol (ePG vesicles and live Escherichia coli bacteria. The membrane perturbation characteristics were highly dependent on the location of the Trp residue substitution, with Trp6 being the most important residue and Trp8 the least. The membrane permeabilization activity of the peptides in synthetic and biological membranes was directly correlated with the antimicrobial potency of the peptides against E. coli. These results contribute to the understanding of the role of each of the three Trp residues to the antimicrobial activity of tritrpticin.

  11. Using residual stacking to mitigate site-specific errors in order to improve the quality of GNSS-based coordinate time series of CORS

    Knöpfler, Andreas; Mayer, Michael; Heck, Bernhard

    2014-05-01

    Within the last decades, positioning using GNSS (Global Navigation Satellite Systems; e.g., GPS) has become a standard tool in many (geo-) sciences. The positioning methods Precise Point Positioning and differential point positioning based on carrier phase observations have been developed for a broad variety of applications with different demands for example on accuracy. In high precision applications, a lot of effort was invested to mitigate different error sources: the products for satellite orbits and satellite clocks were improved; the misbehaviour of satellite and receiver antennas compared to an ideal antenna is modelled by calibration values on absolute level, the modelling of the ionosphere and the troposphere is updated year by year. Therefore, within processing of data of CORS (continuously operating reference sites), equipped with geodetic hardware using a sophisticated strategy, the latest products and models nowadays enable positioning accuracies at low mm level. Despite the considerable improvements that have been achieved within GNSS data processing, a generally valid multipath model is still lacking. Therefore, site specific multipath still represents a major error source in precise GNSS positioning. Furthermore, the calibration information of receiving GNSS antennas, which is for instance derived by a robot or chamber calibration, is valid strictly speaking only for the location of the calibration. The calibrated antenna can show a slightly different behaviour at the CORS due to near field multipath effects. One very promising strategy to mitigate multipath effects as well as imperfectly calibrated receiver antennas is to stack observation residuals of several days, thereby, multipath-loaded observation residuals are analysed for example with respect to signal direction, to find and reduce systematic constituents. This presentation will give a short overview about existing stacking approaches. In addition, first results of the stacking approach

  12. Probing the active sites for CO dissociation on ruthenium nanoparticles

    Strebel, Christian Ejersbo; Murphy, Shane; Nielsen, Rasmus Munksgård;

    2012-01-01

    The active sites for CO dissociation were probed on mass-selected Ru nanoparticles on a HOPG support by temperature programmed desorption spectroscopy using isotopically labelled CO. Combined with transmission electron microscopy we gain insight on how the size and morphology of the nanoparticles...

  13. Active site modeling in copper azurin molecular dynamics simulations

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  14. Active Sites Environmental Monitoring Program: FY 1990 annual report

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

    1991-10-01

    Chapter 3 of US Department of Energy (DOE) Order 5820.2A (DOE 1988) sets forth requirements for environmental monitoring of active low-level waste (LLW) disposal sites. Active sites are defined as those LLW facilities that were in use on or after the date of the order (September 1988). The transuranic (TRU) waste storage areas in Solid Waste Storage Area (SWSA) 5 North are covered by Chap. 2 of the order. In both chapters, monitoring is required to provide for early warning of leaks before those leaks pose a threat to human health or the environment. Chapter 3 also requires that monitoring be conducted to evaluate the short- and long-term performance of LLW disposal facilities. In accordance with this order, the Solid Waste Operations Department at Oak Ridge National Laboratory (ORNL) has established an Active Sites Environmental Monitoring Program (ASEMP) that is implemented by staff of the Environmental Sciences Division (ESD) at ORNL. This report summarizes data from ASEMP monitoring activities for the final 6 months of FY 1990. A brief summary of the monitoring methodology for each site is presented also.

  15. The nature of the active site in heterogeneous metal catalysis

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk;

    2008-01-01

    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced, and...

  16. Active Sites Environmental Monitoring Program: FY 1990 annual report

    Chapter 3 of US Department of Energy (DOE) Order 5820.2A (DOE 1988) sets forth requirements for environmental monitoring of active low-level waste (LLW) disposal sites. Active sites are defined as those LLW facilities that were in use on or after the date of the order (September 1988). The transuranic (TRU) waste storage areas in Solid Waste Storage Area (SWSA) 5 North are covered by Chap. 2 of the order. In both chapters, monitoring is required to provide for early warning of leaks before those leaks pose a threat to human health or the environment. Chapter 3 also requires that monitoring be conducted to evaluate the short- and long-term performance of LLW disposal facilities. In accordance with this order, the Solid Waste Operations Department at Oak Ridge National Laboratory (ORNL) has established an Active Sites Environmental Monitoring Program (ASEMP) that is implemented by staff of the Environmental Sciences Division (ESD) at ORNL. This report summarizes data from ASEMP monitoring activities for the final 6 months of FY 1990. A brief summary of the monitoring methodology for each site is presented also

  17. Study of the residual activity in the syringe and the manifold of perfusion after injection of fluorodeoxyglucose-(18F)

    this study shows that the rinsing allow to mobilize the F.D.G. having stuck to the inner surfaces; The two realised rinsing of the syringe make negligible the residual activity of the syringe and the pipe.So, the activity measured during the conditioning of the syringe corresponds to the activity really injected to the patient. (N.C.)

  18. Inhibition of Mg2+ binding and DNA religation by bacterial topoisomerase I via introduction of an additional positive charge into the active site region

    Sorokin, Elena P.; Cheng, Bokun; Rathi, Siddarth; Aedo, Sandra J.; Abrenica, Maria V.; Tse-Dinh, Yuk-Ching

    2008-01-01

    Among bacterial topoisomerase I enzymes, a conserved methionine residue is found at the active site next to the nucleophilic tyrosine. Substitution of this methionine residue with arginine in recombinant Yersinia pestis topoisomerase I (YTOP) was the only substitution at this position found to induce the SOS response in Escherichia coli. Overexpression of the M326R mutant YTOP resulted in ∼4 log loss of viability. Biochemical analysis of purified Y. pestis and E. coli mutant topoisomerase I s...

  19. Experimental study of the residual activity induced by 950 MeV/u uranium ions in stainless steel and copper

    As a preparatory work for constructing the FAIR facility at GSI, samples of stainless steel and copper were irradiated by 950 MeV/u 238U ions and depth-profiles of residual activity were measured by gamma-ray spectroscopy. The isotopes with dominating contribution to the residual activity were identified and their contributions were quantified. In contrast to the previous study performed at lower energies, the activities could no longer be determined from the full-assembly target measurements. Depth-profiling of residual activity of all identified isotopes had to be completed by measurements of individual target foils. The activity contributions were then obtained by integration of the depth-profiles

  20. ZnCl2-activated biochar from biogas residue facilitates aqueous As(III) removal

    Xia, Dong; Tan, Fen; Zhang, Chuanpan; Jiang, Xiuli; Chen, Zheng; Li, Heng; Zheng, Yanmei; Li, Qingbiao; Wang, Yuanpeng

    2016-07-01

    Biochars prepared from biogas residue using different chemical activators were investigated for their As(III) adsorption properties. The results indicated that the original biochars did not exhibit significant As(III) adsorption. However, ZnCl2-activated biochar, which possessed the largest specific surface area, 516.67 cm2/g, and exhibited a perfectly porous texture, showed excellent performance in a 500 μgL-1 solution of As(III). Fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy were utilized to identify the mechanism of As(III) adsorption by ZnCl2-activated biochar. Adsorption was found to occur mainly through ligand exchange of the hydroxyl in Zn-OH to form Zn-O-As(III), as well as through porous adsorption. As a low-cost adsorbent, the adsorption process was well fitted using a pseudo-second-order model, with an R2 > 0.993. The adsorption process was fast, requiring nearly 90 min to reach adsorption equilibrium. Batch adsorption experimental results indicated that ZnCl2-activated biochar has a maximum adsorption capacity of 27.67 mg/g at pH 7.0, and the adsorption process followed the Freundlich isotherm model well, with an R2 > 0.994. In addition, the current work demonstrated the efficiency of using ZnCl2-activated biochar adsorbent to treat As(III)-contaminated water.

  1. TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues

    Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

    2014-01-01

    microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents ...

  2. Role of the tryptophan residue in the vicinity of the catalytic center of exonuclease III family AP endonucleases: AP site recognition mechanism

    Kaneda, Kohichi; Sekiguchi, Junichi; Shida, Toshio

    2006-01-01

    The mechanisms by which AP endonucleases recognize AP sites have not yet been determined. Based on our previous study with Escherichia coli exonuclease III (ExoIII), the ExoIII family AP endonucleases probably recognize the DNA-pocket formed at an AP site. The indole ring of a conserved tryptophan residue in the vicinity of the catalytic site presumably intercalates into this pocket. To test this hypothesis, we constructed a series of mutants of ExoIII and human APE1. Trp-212 of ExoIII and Tr...

  3. Kinetic model of ethopropazine interaction with horse serum butyrylcholinesterase and its docking into the active site.

    Golicnik, Marko; Sinko, Goran; Simeon-Rudolf, Vera; Grubic, Zoran; Stojan, Jure

    2002-02-01

    The action of a potent tricyclic cholinesterase inhibitor ethopropazine on the hydrolysis of acetylthiocholine and butyrylthiocholine by purified horse serum butyrylcholinesterase (EC 3.1.1.8) was investigated at 25 and 37 degrees C. The enzyme activities were measured on a stopped-flow apparatus and the analysis of experimental data was done by applying a six-parameter model for substrate hydrolysis. The model, which was introduced to explain the kinetics of Drosophila melanogaster acetylcholinesterase [Stojan et al. (1998) FEBS Lett. 440, 85-88], is defined with two dissociation constants and four rate constants and can describe both cooperative phenomena, apparent activation at low substrate concentrations and substrate inhibition by excess of substrate. For the analysis of the data in the presence of ethopropazine at two temperatures, we have enlarged the reaction scheme to allow primarily its competition with the substrate at the peripheral site, but the competition at the acylation site was not excluded. The proposed reaction scheme revealed, upon analysis, competitive effects of ethopropazine at both sites; at 25 degrees C, three enzyme-inhibitor dissociation constants could be evaluated; at 37 degrees C, only two constants could be evaluated. Although the model considers both cooperative phenomena, it appears that decreased enzyme sensitivity at higher temperature, predominantly for the ligands at the peripheral binding site, makes the determination of some expected enzyme substrate and/or inhibitor complexes technically impossible. The same reason might also account for one of the paradoxes in cholinesterases: activities at 25 degrees C at low substrate concentrations are higher than at 37 degrees C. Positioning of ethopropazine in the active-site gorge by molecular dynamics simulations shows that A328, W82, D70, and Y332 amino acid residues stabilize binding of the inhibitor. PMID:11811945

  4. Procedure of Active Residual Heat Removal after Emergency Shutdown of High-Temperature-Gas-Cooled Reactor

    Xingtuan Yang

    2014-01-01

    Full Text Available After emergency shutdown of high-temperature-gas-cooled reactor, the residual heat of the reactor core should be removed. As the natural circulation process spends too long period of time to be utilized, an active residual heat removal procedure is needed, which makes use of steam generator and start-up loop. During this procedure, the structure of steam generator may suffer cold/heat shock because of the sudden load of coolant or hot helium at the first few minutes. Transient analysis was carried out based on a one-dimensional mathematical model for steam generator and steam pipe of start-up loop to achieve safety and reliability. The results show that steam generator should be discharged and precooled; otherwise, boiling will arise and introduce a cold shock to the boiling tubes and tube sheet when coolant began to circulate prior to the helium. Additionally, in avoiding heat shock caused by the sudden load of helium, the helium circulation should be restricted to start with an extreme low flow rate; meanwhile, the coolant of steam generator (water should have flow rate as large as possible. Finally, a four-step procedure with precooling process of steam generator was recommended; sensitive study for the main parameters was conducted.

  5. Antihyperlipidemic and hepatoprotective activities of residue polysaccharide from Cordyceps militaris SU-12.

    Wang, Liqin; Xu, Nuo; Zhang, Jianjun; Zhao, Huajie; Lin, Lin; Jia, Shouhua; Jia, Le

    2015-10-20

    Cordyceps militaris has been artificially cultivated in China, and the great amounts of produced medium residue were discarded after the harvest. The aims of this work were to analyze the structure of the residue polysaccharide (RPS) of C. militaris SU-12, and to investigate the pharmacological effects of RPS on lipid metabolism and oxidative stress. RPS was composed of glucose, arabinose and mannose with a ratio of 62:1.6:1 by gas chromatography analysis, and the Mw (weight-average molecular weight), Mn (number-average molecular weight) and Mz (z-average molecular weight) of RPS were 2.86×10(3), 6.85×10(2), and 1.97×10(4)Da, respectively. The mice experiments demonstrated that RPS could reduce the levels of blood and liver lipid, and improve the glutamate pyruvate transaminase and antioxidant activity. The histopathological observations of mice livers indicated that RPS could attenuate liver cell injury. Results suggest that the RPS might be used as a potential antihyperlipidemic, hepatoprotective and antioxidant product. PMID:26256194

  6. Reaction of argininosuccinase with bromomesaconic acid: role of an essential lysine in the active site

    We have undertaken studies on bovine liver argininosuccinase (L-argininosuccinate arginine-lyase with the active site-directed reagent bromo[U-14C]mesaconic acid, an analogue of fumaric acid. Reactivity, measured by enzyme inactivation, followed pseudo-first-order kinetics, and the rate increased with reagent concentration. Argininosuccinate completely protected the enzyme against inactivation, but neither arginine nor fumarate was protective. A plot of the degree of inactivation as a function of alkyl groups incorporated was extrapolated to 4 mol per mol of enzyme, or 1 mol per active site. After large-scale alkylation of the enzyme (and digestion with trypsin), two 14C-labeled tryptic peptides were isolated. These were chemically sequenced by the Edman method. The amino acid sequences proved to be identical with regions of the deduced amino acid sequences or argininosuccinases from human and yeast sources The 14C-labeled tryptic peptide in the active site region had the sequence Gly-Leu-Glu-Xaa-Ala-Gly-Leu-Leu-Thr-Lys; Xaa represents an unknown phenylthiohydantoin derivative detected in cycle 4. The corresponding amino acid was identified as lysine-51 on the basis of sequence similarity with human and yeast amino acid sequences in this region. The reaction of the enzyme with the alkylating agent and the specific protection against inactivation by argininosuccinate suggest that this lysine residue has an essential role in the binding of argininosuccinate to the enzyme and, consequently, is essential for catalysis

  7. Site-specific Interaction Mapping of Phosphorylated Ubiquitin to Uncover Parkin Activation.

    Yamano, Koji; Queliconi, Bruno B; Koyano, Fumika; Saeki, Yasushi; Hirokawa, Takatsugu; Tanaka, Keiji; Matsuda, Noriyuki

    2015-10-16

    Damaged mitochondria are eliminated through autophagy machinery. A cytosolic E3 ubiquitin ligase Parkin, a gene product mutated in familial Parkinsonism, is essential for this pathway. Recent progress has revealed that phosphorylation of both Parkin and ubiquitin at Ser(65) by PINK1 are crucial for activation and recruitment of Parkin to the damaged mitochondria. However, the mechanism by which phosphorylated ubiquitin associates with and activates phosphorylated Parkin E3 ligase activity remains largely unknown. Here, we analyze interactions between phosphorylated forms of both Parkin and ubiquitin at a spatial resolution of the amino acid residue by site-specific photo-crosslinking. We reveal that the in-between-RING (IBR) domain along with RING1 domain of Parkin preferentially binds to ubiquitin in a phosphorylation-dependent manner. Furthermore, another approach, the Fluoppi (fluorescent-based technology detecting protein-protein interaction) assay, also showed that pathogenic mutations in these domains blocked interactions with phosphomimetic ubiquitin in mammalian cells. Molecular modeling based on the site-specific photo-crosslinking interaction map combined with mass spectrometry strongly suggests that a novel binding mechanism between Parkin and ubiquitin leads to a Parkin conformational change with subsequent activation of Parkin E3 ligase activity. PMID:26260794

  8. Efficacy of drinking-water treatment residual in controlling off-site phosphorus losses: a field study in Florida.

    Agyin-Birikorang, S; Oladeji, O O; O'Connor, G A; Obreza, T A; Capece, J C

    2009-01-01

    Land application of drinking-water treatment residuals (WTR) has been shown to control excess soil soluble P and can reduce off-site P losses to surface and ground water. To our knowledge, no field study has directly evaluated the impacts of land application of WTRs on ground water quality. We monitored the effects of three organic sources of P (poultry manure, Boca Raton biosolids, Pompano biosolids) or triple superphosphate co-applied with an aluminum-based WTR (Al-WTR) on soil and ground water P and Al concentrations under natural field conditions for 20 mo in a soil with limited P sorption capacity. The P sources were applied at two rates (based on P or nitrogen [N] requirement of bahiagrass) with or without Al-WTR amendment and replicated three times. Without WTR application, applied P sources increased surface soil soluble P concentrations regardless of the P source or application rate. Co-applying the P sources with Al-WTR prevented increases in surface soil soluble P concentrations and reduced P losses to shallow ground water. Total dissolved P and orthophosphate concentrations of shallow well ground water of the N-based treatments were greater (>0.9 and 0.3 mg L(-1), respectively) in the absence than in the presence ( approximately 0.6 and 0.2 mg L(-1), respectively) of Al-WTR. The P-based application rate did not increase ground water P concentrations relative to background concentrations. Notwithstanding, Al-WTR amendment decreased ground water P concentrations from soil receiving treatments with P-based application rates. Ground water total dissolved Al concentrations were unaffected by soil Al-WTR application. We conclude that, at least for the study period, Al-WTR can be safely used to reduce P leaching into ground water without increasing the Al concentration of ground water. PMID:19329695

  9. SU-E-T-534: Level of Residual Radioactivity of Activated Parts of a Decommissioned Cyclotron

    Choi, HHF; Leung, TM; Chiu, TL; Yang, B; Wu, PM; Cheung, KY; Yu, SK [Hong Kong Sanatorium and Hospital, Happy Valley (Hong Kong)

    2015-06-15

    Purpose: CTI cyclotron RDS-111 was used at the Hong Kong Sanatorium and Hospital (HKSH) to produce radiopharmaceuticals and radioactive tracers for diagnostic scans between 1999 and 2007. During the operation, some machine components became radioactive by activation. For the safety of staff, decommissioning took place in 2009, two years after the cyclotron had stopped operation. This study investigates the residual radioactivity and radionuclides found in different cyclotron components in 2014 in compliance with the local regulations in Hong Kong for transfer of radioactive waste. Methods: A representative sample of each part was counted using a high-purity germanium detector (manufacturer: ORTECT) for at least four hours. GammaVision, a multichannel analyzer software, was used to identify the radionuclides found in the cyclotron components, as well as the associated activities. A standard library and a Mariscotti peak search algorithm were used to identify the present radionuclides. Only radionuclides with half-life greater than 180 days were considered. Results: Among the components, the Havar target foil has the highest specific activity ((4.6±0.6)×10{sup 2} Bq/g), with Co-60 being the most prominent ((3.8±0.5)×10{sup 2} Bq/g). The total activity of the target foil, however, is still low due to its small mass of 0.04 g. Radioisotopes Mn-54 (46±6 Bq/g), Na-22 (6.8±0.8 Bq/g), Co-57 (7.3±0.9 Bq/g), and Fe-59 (6.0±0.9 Bq/g) have also been detected in the target foil. The target window holder and the vacuum window register a specific activity of 88.3±0.6 Bq/g and 48.6±0.1 Bq/g, respectively. Other components, such as the collimator, the target tube, the valve body and the beamline, are also found with trace amounts of radionuclides. Conclusion: Even seven years after the cyclotron had stopped operation, some components still exhibited residual radioactivity from activation exceeding the IAEA clearance levels. Special consideration for radiological

  10. Role of conserved cysteine residues in Herbaspirillum seropedicae NifA activity.

    Oliveira, Marco A S; Baura, Valter A; Aquino, Bruno; Huergo, Luciano F; Kadowaki, Marco A S; Chubatsu, Leda S; Souza, Emanuel M; Dixon, Ray; Pedrosa, Fábio O; Wassem, Roseli; Monteiro, Rose A

    2009-01-01

    Herbaspirillum seropedicae is an endophytic diazotrophic bacterium that associates with economically important crops. NifA protein, the transcriptional activator of nif genes in H. seropedicae, binds to nif promoters and, together with RNA polymerase-sigma(54) holoenzyme, catalyzes the formation of open complexes to allow transcription initiation. The activity of H. seropedicae NifA is controlled by ammonium and oxygen levels, but the mechanisms of such control are unknown. Oxygen sensitivity is attributed to a conserved motif of cysteine residues in NifA that spans the central AAA+ domain and the interdomain linker that connects the AAA+ domain to the C-terminal DNA binding domain. Here we mutagenized this conserved motif of cysteines and assayed the activity of mutant proteins in vivo. We also purified the mutant variants of NifA and tested their capacity to bind to the nifB promoter region. Chimeric proteins between H. seropedicae NifA, an oxygen-sensitive protein, and Azotobacter vinelandii NifA, an oxygen-tolerant protein, were constructed and showed that the oxygen response is conferred by the central AAA+ and C-terminal DNA binding domains of H. seropedicae NifA. We conclude that the conserved cysteine motif is essential for NifA activity, although single cysteine-to-serine mutants are still competent at binding DNA. PMID:19573596

  11. The determination of pesticide residues in local vegetables by means of neutron activation technique

    Analytical methods based on neutron activation have been developed for studying pesticides residues of bromine, arsenic and mercury in local vegetables and fruits. The concentration of bromine, arsenic and mercury in samples are enriched prior to neutron irradiations by a technique of dry-ashing and freeze-drying for the determination of arsenic, bromine and mercury respectively. The element bromine is determined instrumentally while arsenic and mercury are determined destructively using a distillation technique. The limit of detection under the conditions used for bromine, arsenic and mercury as obtained are 0.01, 0.001 and 0.0001 microgram respectively. A total of 45 varieties of vegetables and 20 varieties of fruits are analyzed. The results of the investigation and the concentration range in part per million of bromine, arsenic and mercury are also presented

  12. PEPIN, Methodology for Computing Concentrations, Activities, Gamma-Ray Spectra, and Residual Heat from Fission Products

    1 - Description of program or function: The concentrations, activities, gamma-ray spectra and residual heat from fission products can be calculated as a function of time for instantaneous fission or for one or more irradiation steps. 2 - Methods: Using the basic data in the libraries, the PEPIN code solves the differential equations satisfied by the fission product concentrations. Data Libraries: Independent Yields Library: 8 independent yields for 235U, 238U, 239U, 232U, 233U. Chain library: Precursor chain file for 635 nuclides. Gamma-Ray Energies Library: Average beta and gamma-ray energies in increasing order. 3 - Restrictions on the complexity of the problem: The number of nuclides must not exceed 650. The number of Gamma-Rays must not exceed 8500. The number of decay times must not exceed 59. The number of irradiation steps must not exceed 40

  13. Reassessment of atomic bomb neutron dosimetry of Hiroshima by using residual activity of rock

    The neutron dose reassessment of atomic bomb at Hiroshima was done by using residual activity of 152Eu of granite rock specimen taken out from 41.5cm depth position inside the Motoyasu bridge pillar. The neutron dose (tissue Kerma in air) at a point of 132m of SSW direction from the hypocenter was experimentally evaluated to be 15.5Gy. The obtained value shows that it is needed to argue and include the anisotropic performance of Hiroshima atomic bomb warhead. After the correction of anisotropic effect of warhead, the source yield of Hiroshima atomic bomb is estimated to be 17.7Kt by combining the measured value obtained here with DS86 calculated value

  14. Removal of dyes from aqueous solutions using activated carbon prepared from rice husk residue.

    Li, Yaxin; Zhang, Xian; Yang, Ruiguang; Li, Guiying; Hu, Changwei

    2016-01-01

    The treatment of dye wastewater by activated carbon (AC) prepared from rice husk residue wastes was studied. Batch adsorption studies were conducted to investigate the effects of contact time, initial concentration (50-450 mg/L), pH (3-11) and temperature (30-70 °C) on the removal of methylene blue (MB), neutral red, and methyl orange. Kinetic investigation revealed that the adsorption of dyes followed pseudo-second-order kinetics. The results suggested that AC was effective to remove dyes, especially MB, from aqueous solutions. Desorption studies found that chemisorption by the adsorbent might be the major mode of dye removal. Fourier transform infrared results suggested that dye molecules were likely to combine with the O-H and P=OOH groups of AC. PMID:26942535

  15. Purification and sequencing of the active site tryptic peptide from penicillin-binding protein 1b of Escherichia coli

    This paper reports the sequence of the active site peptide of penicillin-binding protein 1b from Escherichia coli. Purified penicillin-binding protein 1b was labeled with [14C]penicillin G, digested with trypsin, and partially purified by gel filtration. Upon further purification by high-pressure liquid chromatography, two radioactive peaks were observed, and the major peak, representing over 75% of the applied radioactivity, was submitted to amino acid analysis and sequencing. The sequence Ser-Ile-Gly-Ser-Leu-Ala-Lys was obtained. The active site nucleophile was identified by digesting the purified peptide with aminopeptidase M and separating the radioactive products on high-pressure liquid chromatography. Amino acid analysis confirmed that the serine residue in the middle of the sequence was covalently bonded to the [14C]penicilloyl moiety. A comparison of this sequence to active site sequences of other penicillin-binding proteins and beta-lactamases is presented

  16. Methodology for contaminated sites of military activity territories restoration

    Major part of Eastern Europe countries meet environmental problems related to sites of military activity. Major part of these sites is characterised with degradation of natural landscapes and contamination of geological environment with toxic and hazardous waste representing actual and potential danger for population and environment. Actual danger is caused with localisation of toxic waste, hazardous materials and waste which are preventing normal land use. Potential danger is related to successive dispersion of contamination in biosphere as well as origin of new derivatives and products having toxic and hazardous properties. The list of such sites and objects comprises bases of land, air and naval forces. These objects include a network of infrastructures: storages of fuels and lubricants (surface, underground), filling stations, pipe lines, reparation stations, garages, decontamination stations, underground storages of different purposes, depots (for ammunition, chemical products), hospitals, constructions, firing grounds (tank, artillery, aircraft bombing etc.) and waste disposal sites. Special programs aimed at military industries and bases contaminated sites remediation have been carrying out in developed countries (USA, United Kingdom, Germany etc.). This experience was used in the frames of joint programs having been founded in several countries of Central and Eastern Europe (Chesh Republic, Slovakia, Lithuania etc.). (author)

  17. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid

    Shaya, D.; Hahn, Bum-Soo; Bjerkan, Tonje Marita; Kim, Wan Seok; Park, Nam Young; Sim, Joon-Soo; Kim, Yeong-Shik; Cygler, M. (Catholic Univ of Korea); (NUST); (McGill); (Nat); (Natural Products Res Inst, Korea)

    2008-03-19

    Enzymes have evolved as catalysts with high degrees of stereospecificity. When both enantiomers are biologically important, enzymes with two different folds usually catalyze reactions with the individual enantiomers. In rare cases a single enzyme can process both enantiomers efficiently, but no molecular basis for such catalysis has been established. The family of bacterial chondroitin lyases ABC comprises such enzymes. They can degrade both chondroitin sulfate (CS) and dermatan sulfate (DS) glycosaminoglycans at the nonreducing end of either glucuronic acid (CS) or its epimer iduronic acid (DS) by a {beta}-elimination mechanism, which commences with the removal of the C-5 proton from the uronic acid. Two other structural folds evolved to perform these reactions in an epimer-specific fashion: ({alpha}/{alpha}){sub 5} for CS (chondroitin lyases AC) and {beta}-helix for DS (chondroitin lyases B); their catalytic mechanisms have been established at the molecular level. The structure of chondroitinase ABC from Proteus vulgaris showed surprising similarity to chondroitinase AC, including the presence of a Tyr-His-Glu-Arg catalytic tetrad, which provided a possible mechanism for CS degradation but not for DS degradation. We determined the structure of a distantly related Bacteroides thetaiotaomicron chondroitinase ABC to identify additional structurally conserved residues potentially involved in catalysis. We found a conserved cluster located {approx}12 {angstrom} from the catalytic tetrad. We demonstrate that a histidine in this cluster is essential for catalysis of DS but not CS. The enzyme utilizes a single substrate-binding site while having two partially overlapping active sites catalyzing the respective reactions. The spatial separation of the two sets of residues suggests a substrate-induced conformational change that brings all catalytically essential residues close together.

  18. Exploiting Innocuous Activity for Correlating Users Across Sites

    Goga, Oana; Lei, Howard; Parthasarathi, Sree Hari Krishnan; Friedland, Gerald; Sommer, Robin; Teixeira, Renata

    2013-01-01

    International audience We study how potential attackers can identify accounts on different social network sites that all belong to the same user, exploiting only innocuous activity that inherently comes with posted content. We examine three specific features on Yelp, Flickr, and Twitter: the geo-location attached to a user's posts, the timestamp of posts, and the user's writing style as captured by language models. We show that among these three features the location of posts is the most po...

  19. Active sites in char gasification: Final technical report

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  20. Resolving the Structure of Active Sites on Platinum Catalytic Nanoparticles

    Chang, Lan Yun; Barnard, Amanda S.; Gontard, Lionel Cervera; Dunin-Borkowski, Rafal E.

    2010-01-01

    Accurate understanding of the structure of active sites is fundamentally important in predicting catalytic properties of heterogeneous nanocatalysts. We present an accurate determination of both experimental and theoretical atomic structures of surface monatomic steps on industrial platinum...... nanoparticles. This comparison reveals that the edges of nanoparticles can significantly alter the atomic positions of monatomic steps in their proximity, which can lead to substantial deviations in the catalytic properties compared with the extended surfaces....

  1. The purification of affinity-labelled active-site peptides

    The isolation of the labelled peptide from the protein digest, following the affinity labelling of the active sites of enzymes or antibodies, is described. Single-step affinity chromatography utilises the affinity of the native enzymes or antibody for the ligand used to label the same protein. The labelled peptide is the only one in the digest that displays affinity for the immobilised protein and can be released with eluants that dissociate the protein-ligand complex. (Auth.)

  2. Brownian aggregation rate of colloid particles with several active sites

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure

  3. Antioxidant, Anti-Tyrosinase and Anti-Inflammatory Activities of Oil Production Residues from Camellia tenuifloria

    Shu-Yuan Chiou

    2015-12-01

    Full Text Available Camellia tenuifloria is an indigenous Camellia species used for the production of camellia oil in Taiwan. This study investigated for the first time the potential antioxidant, anti-tyrosinase and anti-inflammatory activities of oil production byproducts, specifically those of the fruit shell, seed shell, and seed pomace from C. tenuifloria. It was found that the crude ethanol extract of the seed shell had the strongest DPPH scavenging and mushroom tyrosinase inhibitory activities, followed by the fruit shell, while seed pomace was the weakest. The IC50 values of crude extracts and fractions on monophenolase were smaller than diphenolase. The phenolic-rich methanol fraction of seed shell (SM reduced nitric oxide (NO production, and inducible nitric oxide synthase (iNOS expression in lipopolysaccharide (LPS-stimulated RAW 264.7 cells. It also repressed the expression of IL-1β, and secretion of prostaglandin E2 (PGE2 and IL-6 in response to LPS. SM strongly stimulated heme oxygenase 1 (HO-1 expression and addition of zinc protoporphyrin (ZnPP, a HO-1 competitive inhibitor, reversed the inhibition of NO production, indicating the involvement of HO-1 in its anti-inflammatory activity. The effects observed in this study provide evidence for the reuse of residues from C. tenuifloria in the food additive, medicine and cosmetic industries.

  4. Site characterization techniques used in environmental remediation activities

    As a result of decades of nuclear energy research, weapons production, as well as ongoing operations, a significant amount of radioactive contamination has occurred throughout the United States Department of Energy (DOE) complex. DOE facility are in the process of assessing and potentially remediating various sites according to the regulations imposed by a Federal Facility Agreement and Consent order (FFA/CO) between DOE, the state in which the facility is located, and the U.S. Environmental Protection Agency (EPA). In support of these active site remediation efforts, the DOE has devoted considerable resources towards the development of innovative site characterization techniques that support environmental restoration activities. These resources and efforts have focused on various aspects of this complex problem. Research and technology development conducted at the Idaho National Engineering and Environmental Laboratory (INEEL) has resulted in the ability and state-of-the-art equipment required to obtain real-time, densely spaced, in situ characterization data (i.e. detection, speciation, and location) of various radionuclides and contaminants. The Remedial Action Monitoring System (RAMS), developed by the INEEL, consists of enhanced sensor technology, measurement modeling and interpretation techniques, and a suite of deployment platforms which can be interchanged to directly support remedial cleanup and site verification operations. In situ characterization techniques have advanced to the point where they are being actively deployed in support of remedial operations. The INEEL has deployed its system at various DOE and international sites. The deployment of in situ characterization systems during environmental restoration operations has shown that this approach results in several significant benefits versus conventional sampling techniques. A flexible characterization system permits rapid modification to satisfy physical site conditions, available site resources

  5. A Coevolutionary Residue Network at the Site of a Functionally Important Conformational Change in a Phosphohexomutase Enzyme Family

    Lee, Yingying; Mick, Jacob; Furdui, Cristina; Beamer, Lesa J

    2012-01-01

    Coevolution analyses identify residues that co-vary with each other during evolution, revealing sequence relationships unobservable from traditional multiple sequence alignments. Here we describe a coevolutionary analysis of phosphomannomutase/phosphoglucomutase (PMM/PGM), a widespread and diverse enzyme family involved in carbohydrate biosynthesis. Mutual information and graph theory were utilized to identify a network of highly connected residues with high significance. An examination of th...

  6. Residues in the alternative reading frame tumor suppressor that influence its stability and p53-independent activities

    The Alternative Reading Frame (ARF) protein suppresses tumorigenesis through p53-dependent and p53-independent pathways. Most of ARF's anti-proliferative activity is conferred by sequences in its first exon. Previous work showed specific amino acid changes occurred in that region during primate evolution, so we programmed those changes into human p14ARF to assay their functional impact. Two human p14ARF residues (Ala14 and Thr31) were found to destabilize the protein while two others (Val24 and Ala41) promoted more efficient p53 stabilization and activation. Despite those effects, all modified p14ARF forms displayed robust p53-dependent anti-proliferative activity demonstrating there are no significant biological differences in p53-mediated growth suppression associated with simian versus human p14ARF residues. In contrast, p53-independent p14ARF function was considerably altered by several residue changes. Val24 was required for p53-independent growth suppression whereas multiple residues (Val24, Thr31, Ala41 and His60) enabled p14ARF to block or reverse the inherent chromosomal instability of p53-null MEFs. Together, these data pinpoint specific residues outside of established p14ARF functional domains that influence its expression and signaling activities. Most intriguingly, this work reveals a novel and direct role for p14ARF in the p53-independent maintenance of genomic stability.

  7. A split active site couples cap recognition by Dcp2 to activation

    Floor, Stephen N.; Jones, Brittnee N.; Hernandez, Gail A.; Gross, John D.

    2010-01-01

    Decapping by Dcp2 is an essential step in 5′-3′ mRNA decay. In yeast, decapping requires an open-to-closed transition in Dcp2, though the link between closure and catalysis remains elusive. Here we show using NMR that cap binds conserved residues on both the catalytic and regulatory domains of Dcp2. Lesions in the cap-binding site on the regulatory domain reduce the catalytic step two orders of magnitude and block formation of the closed state whereas Dcp1 enhances the catalytic step by a fac...

  8. Seismic activity parameters of the Finnish potential repository sites

    Posiva Oy has started a project for estimating the possible earthquake induced rock movements on the deposition holes containing canisters of spent nuclear fuel. These estimates will be made for the four investigation sites, Romuvaara, Kivetty, Olkiluoto and Haestholmen. This study deals with the current and future seismicity associated with the above mentioned sites. Seismic belts that participate the seismic behaviour of the studied sites have been identified and the magnitude-frequency distributions of these belts have been estimated. The seismic activity parameters of the sites have been deduced from the characteristics of the seismic belts in order to forecast the seismicity during the next 100,000 years. The report discusses the possible earthquakes induced by future glaciation. The seismic interpretation seems to indicate that the previous postglacial faults in Finnish Lapland have been generated in compressional environment. The orientation of the rather uniform compression has been NW-SE, which coincide with the current stress field. It seems that, although the impact of postglacial crustal rebound must have been significant, the impact of plate tectonics has been dominant. A major assumption of this study has been that future seismicity will generally resemble the current seismicity. However, when the postglacial seismicity is concerned, the magnitude-frequency distribution is likely different and the expected maximum magnitude will be higher. Maximum magnitudes of future postglacial earthquakes have been approximated by strain release examinations. Seismicity has been examined within the framework of the lineament maps, in order to associate the future significant earthquakes with active fault zones in the vicinity of the potential repository sites. (orig.)

  9. Seismic activity parameters of the Finnish potential repository sites

    Saari, J. [Fortum Engineering Oy, Vantaa (Finland)

    2000-10-01

    Posiva Oy has started a project for estimating the possible earthquake induced rock movements on the deposition holes containing canisters of spent nuclear fuel. These estimates will be made for the four investigation sites, Romuvaara, Kivetty, Olkiluoto and Haestholmen. This study deals with the current and future seismicity associated with the above mentioned sites. Seismic belts that participate the seismic behaviour of the studied sites have been identified and the magnitude-frequency distributions of these belts have been estimated. The seismic activity parameters of the sites have been deduced from the characteristics of the seismic belts in order to forecast the seismicity during the next 100,000 years. The report discusses the possible earthquakes induced by future glaciation. The seismic interpretation seems to indicate that the previous postglacial faults in Finnish Lapland have been generated in compressional environment. The orientation of the rather uniform compression has been NW-SE, which coincide with the current stress field. It seems that, although the impact of postglacial crustal rebound must have been significant, the impact of plate tectonics has been dominant. A major assumption of this study has been that future seismicity will generally resemble the current seismicity. However, when the postglacial seismicity is concerned, the magnitude-frequency distribution is likely different and the expected maximum magnitude will be higher. Maximum magnitudes of future postglacial earthquakes have been approximated by strain release examinations. Seismicity has been examined within the framework of the lineament maps, in order to associate the future significant earthquakes with active fault zones in the vicinity of the potential repository sites. (orig.)

  10. Elimination of textile dyes using activated carbons prepared from vegetable residues and their characterization.

    Peláez-Cid, Alejandra-Alicia; Herrera-González, Ana-María; Salazar-Villanueva, Martín; Bautista-Hernández, Alejandro

    2016-10-01

    In this study, three mesoporous activated carbons prepared from vegetable residues were used to remove acid, basic, and direct dyes from aqueous solutions, and reactive and vat dyes from textile wastewater. Granular carbons obtained by chemical activation at 673 K with phosphoric acid from prickly pear peels (CarTunaQ), broccoli stems (CarBrocQ), and white sapote seeds (CarZapQ) were highly efficient for the removal of dyes. Adsorption equilibrium studies were carried out in batch systems and treated with Langmuir and Freundlich isotherms. The maximum adsorption capacities calculated from the Langmuir isotherms ranged between 131.6 and 312.5 mg/g for acid dyes, and between 277.8 and 500.0 mg/g for basic dyes at 303 K. Our objective in this paper was to show that vegetable wastes can serve as precursors for activated carbons that can be used for the adsorption of dyes. Specifically CarBrocQ was the best carbon produced for the removal of textile dyes. The color removal of dyes present in textile wastewaters was compared with that of a commercial powdered carbon, and it was found that the carbons produced using waste material reached similar efficiency levels. Carbon samples were characterized by bulk density, point of zero charge, thermogravimetric analysis, elemental analysis, Fourier transform infrared spectroscopy, scanning electron microscopy, methylene blue adsorption isotherms at 303 K, and nitrogen adsorption isotherms at 77 K (SBET). The results show that the activated carbons possess a large specific surface area (1025-1177 m(2)/g) and high total pore volume (1.06-2.16 cm(3)/g) with average pore size diameters between 4.1 and 8.4 nm. Desorption and regeneration tests were made to test the viability of reusing the activated carbons. PMID:27372249

  11. Characterization of the interactions between the active site of a protein tyrosine kinase and a divalent metal activator

    Ayrapetov Marina K

    2005-11-01

    Full Text Available Abstract Background Protein tyrosine kinases are important enzymes for cell signalling and key targets for anticancer drug discovery. The catalytic mechanisms of protein tyrosine kinase-catalysed phosphorylation are not fully understood. Protein tyrosine kinase Csk requires two Mg2+ cations for activity: one (M1 binds to ATP, and the other (M2 acts as an essential activator. Results Experiments in this communication characterize the interaction between M2 and Csk. Csk activity is sensitive to pH in the range of 6 to 7. Kinetic characterization indicates that the sensitivity is not due to altered substrate binding, but caused by the sensitivity of M2 binding to pH. Several residues in the active site with potential of binding M2 are mutated and the effect on metal activation studied. An active mutant of Asn319 is generated, and this mutation does not alter the metal binding characteristics. Mutations of Glu236 or Asp332 abolish the kinase activity, precluding a positive or negative conclusion on their role in M2 coordination. Finally, the ability of divalent metal cations to activate Csk correlates to a combination of ionic radius and the coordination number. Conclusion These studies demonstrate that M2 binding to Csk is sensitive to pH, which is mainly responsible for Csk activity change in the acidic arm of the pH response curve. They also demonstrate critical differences in the metal activator coordination sphere in protein tyrosine kinase Csk and a protein Ser/Thr kinase, the cAMP-dependent protein kinase. They shed light on the physical interactions between a protein tyrosine kinase and a divalent metal activator.

  12. Active site histidine in spinach ribulosebisphosphate carboxylase/oxygenase modified by diethyl pyrocarbonate

    [3H] Diethyl pyrocarbonate was synthesized from [3H] ethanol prepared by the reduction of acetaldehyde by NaB3H4. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from spinach was inactivated with this reagent at pH 7.0 the presence of 20 mM Mg2+, and tryptic peptides that contained modified histidine residues were isolated by reverse-phase high-performance liquid chromatography. Labeling of the enzyme was conducted in the presence and absence of the competitive inhibitor sedoheptulose 1,7-bisphosphate. The amount of one peptide that was heavily labeled in the absence of this compound was reduced 10-fold in its presence. The labeled residue was histidine-298. This result, in combination with earlier experiments, suggests that His-298 in spinach RuBisCO is located in the active site domain and is essential to enzyme activity. This region of the primary structure is strongly conserved in seven other ribulosebisphosphate carboxylases from divergent sources

  13. Oxygen reduction and evolution at single-metal active sites

    Calle-Vallejo, F.; Martínez, J.I.; García Lastra, Juan Maria;

    2013-01-01

    A worldwide spread of clean technologies such as low-temperature fuel cells and electrolyzers depends strictly on their technical reliability and economic affordability. Currently, both conditions are hardly fulfilled mainly due to the same reason: the oxygen electrode, which has large overpotent......A worldwide spread of clean technologies such as low-temperature fuel cells and electrolyzers depends strictly on their technical reliability and economic affordability. Currently, both conditions are hardly fulfilled mainly due to the same reason: the oxygen electrode, which has large...... overpotentials and is made of precious materials. A possible solution is the use of non-noble electrocatalysts with single-metal active sites. Here, on the basis of DFT calculations of adsorbed intermediates and a thermodynamic analysis, we compare the oxygen reduction (ORR) and evolution (OER) activities of...... functionalized graphitic materials and gas-phase porphyrins with late transition metals. We find that both kinds of materials follow approximately the same activity trends, and active sites with transition metals from groups 7 to 9 may be good ORR and OER electrocatalysts. However, spin analyses show more...

  14. Effect of site-directed mutagenic alterations on ADP-ribosyltransferase activity of the A subunit of Escherichia coli heat-labile enterotoxin.

    Lobet, Y; Cluff, C W; Cieplak, W

    1991-01-01

    Previous studies of the S1 subunit of pertussis toxin, an NAD(+)-dependent ADP-ribosyltransferase, suggested that a small amino-terminal region of amino acid sequence similarity to the active fragments of both cholera toxin and Escherichia coli heat-labile enterotoxin represents a region containing critical active-site residues that might be involved in the binding of the substrate NAD+. Other studies of two other bacterial toxins possessing ADP-ribosyltransferase activity, diphtheria toxin and Pseudomonas exotoxin A, have revealed the presence of essential glutamic acid residues vicinal to the active site. To help determine the relevance of these observations to activities of the enterotoxins, the A-subunit gene of the E. coli heat-labile enterotoxin was subjected to site-specific mutagenesis in the region encoding the amino-terminal region of similarity to the S1 subunit of pertussis toxin delineated by residues 6 through 17 and at two glutamic acid residues, 110 and 112, that are conserved in the active domains of all of the heat-labile enterotoxin variants and in cholera toxin. Mutant proteins in which arginine 7 was either deleted or replaced with lysine exhibited undetectable levels of ADP-ribosyltransferase activity. However, limited trypsinolysis of the arginine 7 mutants yielded fragmentation kinetics that were different from that yielded by the wild-type recombinant subunit or the authentic A subunit. In contrast, mutant proteins in which glutamic acid residues at either position 110 or 112 were replaced with aspartic acid responded like the wild-type subunit upon limited trypsinolysis, while exhibiting severely depressed, but detectable, ADP-ribosyltransferase activity. The latter results may indicate that either glutamic acid 110 or glutamic acid 112 of the A subunit of heat-labile enterotoxin is analogous to those active-site glutamic acids identified in several other ADP-ribosylating toxins. Images PMID:1908825

  15. Inducible nitric oxide synthase (NOS2) expressed in septic patients is nitrated on selected tyrosine residues: implications for enzymic activity.

    Lanone, Sophie; Manivet, Philippe; Callebert, Jacques; Launay, Jean-Marie; Payen, Didier; Aubier, Michel; Boczkowski, Jorge; Mebazaa, Alexandre

    2002-01-01

    Tyrosine nitration is a post-translational protein modification with potentially significant biological implications. In the present study we demonstrate, for the first time, that tyrosine residues of human inducible nitric oxide synthase (NOS2) can be nitrated by peroxynitrite in vitro, leading to a decreased activity. Moreover, we show that NOS2 expressed in a skeletal muscle from septic patients is nitrated on selective tyrosine residues belonging to a canonic sequence. This phenomenon could be an endogenous mechanism of in vivo modulation of NOS2 enzymic activity. PMID:12097137

  16. Insilco analysis of functionally important residues in folate receptors

    Ramamoorthy, Kalidoss; Potala, Sirisha; Verma, Rama Shanker

    2007-01-01

    Lack of crystal structure data of folate binding proteins has left so many questions unanswered (for example, important residues in active site, binding domain, important amino acid residues involved in interactions between ligand and receptor). With sequence alignment and PROSITE motif identification, we attempted to answer evolutionarily significant residues that are of functional importance for ligand binding and that form catalytic sites. We have analyzed 46 different FRs and FBP sequence...

  17. Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

    Kevin A James

    Full Text Available The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD motif in the catalytic loop and the Asp-Phe-Gly (DFG motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not

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

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

    2011-12-31

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

  19. HDAC Inhibitors without an Active Site Zn2+-Binding Group

    Vickers, Chris J.; Olsen, Christian Adam; Leman, Luke J.;

    2012-01-01

    Natural and synthetic histone deacetylase (HDAC) inhibitors generally derive their strong binding affinity and high potency from a key functional group that binds to the Zn2+ ion within the enzyme active site. However, this feature is also thought to carry the potential liability of undesirable off......-target interactions with other metalloenzymes. As a step toward mitigating this issue, here, we describe the design, synthesis, and structure−activity characterizations of cyclic α3β-tetrapeptide HDAC inhibitors that lack the presumed indispensable Zn2+-binding group. The lead compounds (e.g., 15 and 26) display good...... potency against class 1 HDACs and are active in tissue culture against various human cancer cell lines. Importantly, enzymological analysis of 26 indicates that the cyclic α3β-tetrapeptide is a fast-on/ off competitive inhibitor of HDACs 1−3 with Ki values of 49, 33, and 37 nM, respectively. Our proof...

  20. A single mutation in the hepta-peptide active site of Aspergillus niger PhyA phytase leads to myriad of biochemical changes

    The active site motif of proteins belonging to ‘Histidine Acid Phosphatase’ (HAP) contains a hepta-peptide region, RHGXRXP. A close comparison among fungal and yeast HAPs has revealed the fourth residue of the hepta-peptide to be E instead of A, which is the case with A. niger phyA phytase. However,...

  1. Current activities handbook: formerly utilized sites remedial action program

    None

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  2. Overview of the activities carried out at the FEBEX site

    Missana, T.; Buil, B.; Garralon, A.; Gomez, P. [CIEMAT, Dept. de Medioambien te, 28040 Madrid (Spain); Perez-Estaun, A.; Carbonell, R. [Inst. Jaume Almera, CSIC (Spain); Suso, J.; Carretero, G.; Bueno, J.; Martinez, L. [AITEMIN (Spain) ; Hernan, P. [ENRESA (Spain)

    2007-06-15

    One of the main aim of WP 4.1 and 4.2 is to study solute migration mechanisms in crystalline host-rock in realistic conditions. Many organisations are participating in a joint study that is being performed in the FEBEX gallery (NAGRA's Grimsel Test Site, GTS, Switzerland). The FEBEX experiment reproduces at a real scale a high-level waste repository in granite and was installed more than 9 years ago. At moment, it represents the most realistic environment where the processes affecting radionuclide migration from the bentonite to granite can be studied. This paper summarises the main activities carried out at the FEBEX site during the second year of the project.

  3. Current activities handbook: formerly utilized sites remedial action program

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified

  4. Unique Residues Involved in Activation of the Multitasking Protease/Chaperone HtrA from Chlamydia trachomatis

    Huston, Wilhelmina M.; Joel D. A. Tyndall; Lott, William B.; Stansfield, Scott H.; Timms, Peter

    2011-01-01

    DegP, a member of the HtrA family of proteins, conducts critical bacterial protein quality control by both chaperone and proteolysis activities. The regulatory mechanisms controlling these two distinct activities, however, are unknown. DegP activation is known to involve a unique mechanism of allosteric binding, conformational changes and oligomer formation. We have uncovered a novel role for the residues at the PDZ1:protease interface in oligomer formation specifically for chaperone substrat...

  5. Removal of reactive blue 19 from aqueous solution by pomegranate residual-based activated carbon: optimization by response surface methodology

    Radaei, Elham; Alavi Moghaddam, Mohammad Reza; Arami, Mokhtar

    2014-01-01

    Background In this research, response surface methodology (RSM) was applied to optimize Reactive Blue 19 removal by activated carbon from pomegranate residual. A 24 full factorial central composite design (CCD) was applied to evaluate the effects of initial pH, adsorbent dose, initial dye concentration, and contact time on the dye removal efficiency. Methodology The activated carbon prepared by 50 wt.% phosphoric acid activation under air condition at 500°C. The range of pH and initial dye co...

  6. Atividade residual de diuron, oxyfluorfen e prometryne no controle de Euphorbia heterophylla Residual activity of diuron, oxyfluorfen, and prometryne for Euphorbia heterophylla control

    R.S. Oliveira Jr.

    2012-09-01

    Full Text Available As aplicações de herbicidas em pré-emergência têm por finalidade a obtenção da atividade residual no início do ciclo das culturas. Assim, o objetivo deste trabalho foi avaliar a atividade residual dos herbicidas diuron, oxyfluorfen e prometryne, aplicados isoladamente ou em misturas, no controle de Euphorbia heterophylla. Oito experimentos foram conduzidos em casa de vegetação, aplicando-se doses dos herbicidas ou das misturas aos 30, 20, 10 e 0 dias antes da semeadura da planta daninha (DAS. Com o diuron e prometryne, foram observados controles satisfatórios até 20 DAS nas doses a partir de 1,07 e 1,6 kg ha-1, respectivamente. Quanto ao oxyfluorfen, foi registrado um período residual inferior, obtendo-se controle mínimo de 80% até 10 DAS nas doses a partir de 0,324 kg ha-1. Em relação às misturas dos herbicidas, a mistura diuron+prometryne promoveu controle superior a 85% por períodos de até 30 dias, quando aplicada na menor dose (1+2 kg ha-1, e de 20 dias, quando aplicada na dose de 2+1 kg ha-1. Visando obter esse mesmo patamar de controle por 30 dias, foi necessário 1+0,288 kg ha-1 da mistura diuron+oxyfluorfen. A mistura prometryne+oxyfluorfen apresentou um mínimo de 80% de controle no período de 10 dias, quando utilizada a dose de 1+0,192 kg ha-1.Pre-emergence herbicide applications are designed to obtain residual activity at the beginning of the crop cycle. The objective of this study was to evaluate the residual activity of diuron, oxyfluorfen, and prometryne, applied alone or in mixture, to control Euphorbia heterophylla. Eight experiments were conducted under greenhouse conditions, by applying herbicide doses or mixtures at 30, 20, 10, and 0 days before weed sowing (DBWS.With diuron and prometryne, satisfactory controls were observed at doses up to 20 DBWS, from 1.07 to 1.6 kg ha-1, respectively. As for oxyfluorfen, a lower residual period was verified, with a minimum gaining control of at least 80% being obtained

  7. Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis

    Tian, Li; Liu, Shijia; Wang, Shuai; Wang, Lushan

    2016-01-01

    Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes. PMID:27009476

  8. Unique residues involved in activation of the multitasking protease/chaperone HtrA from Chlamydia trachomatis.

    Wilhelmina M Huston

    Full Text Available DegP, a member of the HtrA family of proteins, conducts critical bacterial protein quality control by both chaperone and proteolysis activities. The regulatory mechanisms controlling these two distinct activities, however, are unknown. DegP activation is known to involve a unique mechanism of allosteric binding, conformational changes and oligomer formation. We have uncovered a novel role for the residues at the PDZ1:protease interface in oligomer formation specifically for chaperone substrates of Chlamydia trachomatis HtrA (DegP homolog. We have demonstrated that CtHtrA proteolysis could be activated by allosteric binding and oligomer formation. The PDZ1 activator cleft was required for the activation and oligomer formation. However, unique to CtHtrA was the critical role for residues at the PDZ1:protease interface in oligomer formation when the activator was an in vitro chaperone substrate. Furthermore, a potential in vivo chaperone substrate, the major outer membrane protein (MOMP from Chlamydia, was able to activate CtHtrA and induce oligomer formation. Therefore, we have revealed novel residues involved in the activation of CtHtrA which are likely to have important in vivo implications for outer membrane protein assembly.

  9. Flexible and Adhesive Surface Enhance Raman Scattering Active Tape for Rapid Detection of Pesticide Residues in Fruits and Vegetables.

    Chen, Jiaming; Huang, Youju; Kannan, Palanisamy; Zhang, Lei; Lin, Zhenyu; Zhang, Jiawei; Chen, Tao; Guo, Longhua

    2016-02-16

    The efficient extraction of targets from complex surfaces is vital for technological applications ranging from environmental pollutant monitoring to analysis of explosive traces and pesticide residues. In our present study, we proposed a proof-of-concept surface enhance Raman scattering (SERS) active substrate serving directly to the rapid extraction and detection of target molecules. The novel substrate was constructed by decorating the commercial tape with colloidal gold nanoparticles (Au NPs), which simultaneously provides SERS activity and "sticky" of adhesive. The utility of SERS tape was demonstrated by directly extracting pesticide residues in fruits and vegetables via a simple and viable "paste and peel off" approach. The obtained strong and easily distinguishable SERS signals allow us to detect various pesticide residues such as parathion-methyl, thiram, and chlorpyrifos in the real samples with complex surfaces including green vegetable, cucumber, orange, and apple. PMID:26810698

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

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

    2013-01-01

    Removal of the 5′ cap structure by Dcp2 is a major step in several 5′–3′ mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base ...

  11. Effect of site-directed mutagenic alterations on ADP-ribosyltransferase activity of the A subunit of Escherichia coli heat-labile enterotoxin.

    Lobet, Y; Cluff, C W; Cieplak, W

    1991-01-01

    Previous studies of the S1 subunit of pertussis toxin, an NAD(+)-dependent ADP-ribosyltransferase, suggested that a small amino-terminal region of amino acid sequence similarity to the active fragments of both cholera toxin and Escherichia coli heat-labile enterotoxin represents a region containing critical active-site residues that might be involved in the binding of the substrate NAD+. Other studies of two other bacterial toxins possessing ADP-ribosyltransferase activity, diphtheria toxin a...

  12. 10 CFR 63.16 - Review of site characterization activities. 2

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Review of site characterization activities. 2 63.16... site characterization activities. 2 2 In addition to the review of site characterization activities... investigation and site characterization, to allow early identification of potential licensing issues for...

  13. Analysis of the technical capabilities of DOE sites for disposal of residuals from the treatment of mixed low-level waste

    Waters, R.D.; Gruebel, M.M.; Langkopf, B.S.; Kuehne, P.B.

    1997-04-01

    The US Department of Energy (DOE) has stored or expects to generate over the next five years more than 130,000 m{sup 3} of mixed low-level waste (MLLW). Before disposal, MLLW is usually treated to comply with the land disposal restrictions of the Resource Conservation and Recovery Act. Depending on the type of treatment, the original volume of MLLW and the radionuclide concentrations in the waste streams may change. These changes must be taken into account in determining the necessary disposal capacity at a site. Treatment may remove the characteristic in some waste that caused it to be classified as mixed. Treatment of some waste may, by reduction of the mass, increase the concentrations of some transuranic radionuclides sufficiently so that it becomes transuranic waste. In this report, the DOE MLLW streams were analyzed to determine after-treatment volumes and radionuclide concentrations. The waste streams were reclassified as residual MLLW or low-level or transuranic waste resulting from treatment. The volume analysis indicated that about 89,000 m{sup 3} of waste will require disposal as residual MLLW. Fifteen DOE sites were then evaluated to determine their capabilities for hosting disposal facilities for some or all of the residual MLLW. Waste streams associated with about 90% of the total residual MLLW volume are likely to present no significant issues for disposal and require little additional analysis. Future studies should focus on the remaining waste streams that are potentially problematic by examining site-specific waste acceptance criteria, alternative treatment processes, alternative waste forms for disposal, and pending changes in regulatory requirements.

  14. Analysis of the technical capabilities of DOE sites for disposal of residuals from the treatment of mixed low-level waste

    The US Department of Energy (DOE) has stored or expects to generate over the next five years more than 130,000 m3 of mixed low-level waste (MLLW). Before disposal, MLLW is usually treated to comply with the land disposal restrictions of the Resource Conservation and Recovery Act. Depending on the type of treatment, the original volume of MLLW and the radionuclide concentrations in the waste streams may change. These changes must be taken into account in determining the necessary disposal capacity at a site. Treatment may remove the characteristic in some waste that caused it to be classified as mixed. Treatment of some waste may, by reduction of the mass, increase the concentrations of some transuranic radionuclides sufficiently so that it becomes transuranic waste. In this report, the DOE MLLW streams were analyzed to determine after-treatment volumes and radionuclide concentrations. The waste streams were reclassified as residual MLLW or low-level or transuranic waste resulting from treatment. The volume analysis indicated that about 89,000 m3 of waste will require disposal as residual MLLW. Fifteen DOE sites were then evaluated to determine their capabilities for hosting disposal facilities for some or all of the residual MLLW. Waste streams associated with about 90% of the total residual MLLW volume are likely to present no significant issues for disposal and require little additional analysis. Future studies should focus on the remaining waste streams that are potentially problematic by examining site-specific waste acceptance criteria, alternative treatment processes, alternative waste forms for disposal, and pending changes in regulatory requirements

  15. Identification of covalent active site inhibitors of dengue virus protease

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  16. Identification of covalent active site inhibitors of dengue virus protease.

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  17. Multiple autophosphorylation sites of the epidermal growth factor receptor are essential for receptor kinase activity and internalization. Contrasting significance of tyrosine 992 in the native and truncated receptors

    Sorkin, A; Helin, K; Waters, C M; Carpenter, G; Beguinot, L

    1992-01-01

    similar to a kinase-negative receptor. Mutation of tyrosine residue Y992 alone in the context of full length EGF receptor, however, did not affect receptor internalization or kinase activity toward phospholipase C-gamma 1. These data indicate that tyrosine 992 is critical for substrate phosphorylation and...... internalization only in the context of the truncated receptor, and that minor autophosphorylation sites, such as Y992, may act as compensatory regulatory sties in the absence of the major EGF receptor autophosphorylation sites....

  18. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

    Warren, Ean; Bekins, Barbara A.

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  19. Conformational study reveals amino acid residues essential for hemagglutinating and anti-proliferative activities of Clematis montana lectin.

    Lu, Bangmin; Zhang, Bin; Qi, Wei; Zhu, Yanan; Zhao, Yan; Zhou, Nan; Sun, Rong; Bao, Jinku; Wu, Chuanfang

    2014-11-01

    Clematis montana lectin (CML), a novel mannose-binding lectin purified from C. montana Buch.-Ham stem (Ranunculaceae), has been proved to have hemagglutinating activity in rabbit erythrocytes and apoptosis-inducing activity in tumor cells. However, the biochemical properties of CML have not revealed and its structural information still needs to be elucidated. In this study, it was found that CML possessed quite good thermostability and alkaline resistance, and its hemagglutinating activity was bivalent metal cation dependent. In addition, hemagglutination test and fluorescence spectroscopy proved that GuHCl, urea, and sodium dodecyl sulfate could change the conformation of CML and further caused the loss of hemagglutination activity. Moreover, the changes of fluorescence spectrum indicated that the tryptophan (Trp) microenvironment conversion might be related to the conformation and bioactivities of CML. In addition, it was also found that Trp residues, arginine (Arg) residues, and sulfhydryl were important for the hemagglutinating activity of CML, but only Trp was proved to be crucial for the CML conformation. Furthermore, the Trp, Arg, and sulfhydryl-modified CML exhibited 97.17%, 76.99%, and 49.64% loss of its anti-proliferative activity, respectively, which was consistent with the alterations of its hemagglutinating activity. Given these findings, Trp residues on the surface of CML are essential for the active center to form substrate-accessible conformation and suitable environment for carbohydrate binding. PMID:25239139

  20. Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation

    Boudreaux, David A.; Maiti, Tushar K.; Davies, Christopher W.; Das, Chittaranjan (Purdue)

    2010-07-06

    Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a Parkinson disease-associated, putative cysteine protease found abundantly and selectively expressed in neurons. The crystal structure of apo UCHL1 showed that the active-site residues are not aligned in a canonical form, with the nucleophilic cysteine being 7.7 {angstrom} from the general base histidine, an arrangement consistent with an inactive form of the enzyme. Here we report the crystal structures of the wild type and two Parkinson disease-associated variants of the enzyme, S18Y and I93M, bound to a ubiquitin-based suicide substrate, ubiquitin vinyl methyl ester. These structures reveal that ubiquitin vinyl methyl ester binds primarily at two sites on the enzyme, with its carboxy terminus at the active site and with its amino-terminal {beta}-hairpin at the distal site - a surface-exposed hydrophobic crevice 17 {angstrom} away from the active site. Binding at the distal site initiates a cascade of side-chain movements in the enzyme that starts at a highly conserved, surface-exposed phenylalanine and is relayed to the active site resulting in the reorientation and proximal placement of the general base within 4 {angstrom} of the catalytic cysteine, an arrangement found in productive cysteine proteases. Mutation of the distal-site, surface-exposed phenylalanine to alanine reduces ubiquitin binding and severely impairs the catalytic activity of the enzyme. These results suggest that the activity of UCHL1 may be regulated by its own substrate.

  1. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  2. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  3. Biosorption of lead (II) ions by NaOH-activated apple (Malus domestica) juice residue

    Arimurti, Devita Dwi; Heraldy, Eddy; Lestari, Witri Wahyu

    2016-02-01

    This research studied the removal of Pb(II) ions from aqueous solutions using NaOH-activated apple (Malus domestica) juice residue. Biosorbent was characterized with Fourier Transform Infrared Spectrophotometer (FTIR), and Surface Area Analyzer (SAA). The effects of biosorbent dosage, pH, contact time and initial metal ion concentration had been investigated in batch-adsorption method. The biosorption kinetic data were analyzed by pseudo-first-order and pseudo-second-order kinetics model. Freundlich and Langmuir's isotherm were used to describe the biosorption process. The optimum conditions of Pb(II) adsorption was observed at 60 min of contact time, pH 4, and 0.1 g biosorbent dosage in 25 ml solution. The biosorption kinetics followed the pseudo-second-order kinetic model, resulted biosorption constant rate of 0.184 g.mg-1.min-1. The Langmuir isotherm model exhibited the best fit to experimental data. The maximum biosorption capacity of Pb(II) determined according to the Langmuir model was 90.90 mg.g-1 at 302 K, with the adsorption energy of 26.429 kJ.mol-1.

  4. Determination of barium and antimony in gun shot residues by neutron activation analysis

    The antimony contents on both hands of 7 persons before and after firing an automatic pistol were determined by instrumental neutron activation analysis. The gun shot residues were removed from hands by a 4% solution of cellulose acetate in acetone. The average content of antimony on both hands before firing obtained from 70 measurements (35 from each hand) was 0.040 ± 0.010 micro gram, whereas the average contents on the right and the left hands after 1 firing were 0.385 ± 0.036 and 0.144 ± 0.029 micro gram respectively. The ration of the antimony contents after 1 firing to the normal level (before firing) was 9.9 for the right and 3.6 for the left. No significant difference was observed between male and female, smoker and non-smoker. The antimony content after several firings was not much different from that of 1 firing and it reduced to the normal level within 2 days after firing. The barium contents before and after firing were studied from one person. Barium was precipitated as Ba SO4 before counting. An average contents of 0.936 ± 0.551 micro gram for both hands before firing, 4.092 ± 2.687 micro gram for the right hand and 1.363 ± 0.879 micro gram for the left hand after 1 firing were found

  5. Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site.

    Sandeep Chakraborty

    Full Text Available The pathways of proton abstraction (PA, a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive. We present a push button methodology--Proton abstraction Simulation (PRISM--to enumerate the possible pathways of PA in a protein with known 3D structure based on the spatial and electrostatic properties of residues in the proximity of a given nucleophilic residue. Proton movements are evaluated in the vicinity of this nucleophilic residue based on distances, potential differences, spatial channels and characteristics of the individual residues (polarity, acidic, basic, etc. Modulating these parameters eliminates their empirical nature and also might reveal pathways that originate from conformational changes. We have validated our method using serine proteases and concurred with the dichotomy in PA in Class A β-lactamases, both of which are hydrolases. The PA mechanism in a transferase has also been corroborated. The source code is made available at www.sanchak.com/prism.

  6. Study on residual radioactivity measurement method for site release of nuclear facilities. In-situ radioactivity measurement test with the use of portable Ge semiconductor detector (Contract research)

    Nuclear facility sites after decommissioning are allowed to be released from nuclear safety regulations after confirming that sites have been decontaminated to acceptable levels. In-situ measurement with the use of a portable pure-germanium semiconductor detector (Ge detector) is a suitable technology for confirmatory survey. A method to conservatively evaluate residual radioactivity on the sites was proposed in this study. In the evaluation method concept, the radionuclide (Cs-137, etc.), which are in reality distributed across the area of interest, is assumed to be the single point source located at the furthest position on the ground surface of the area from the Ge detector. Based on this assumption, the detectable minimum time of the interest radionuclide was predicted by the calculation. If radiation from the point source is not detected for longer than the predicted detectable time, it can be proven that the radioactivity remaining in the interest area is lower than the radioactivity corresponding to the assumed point source. Results of the field test in JAEA site indicated that the proposed evaluation method was reasonable for the conservative evaluation of residual radioactivity. (author)

  7. Mechanism of removal of undesirable residual amylase, insoluble starch, and select colorants from refinery streams by powdered activated carbons

    There is a need in the world-wide sugar industry to find a practical and economical solution to remove or inactivate residual alpha-amylase that are high temperature stable from factory or refinery streams. A survey of refineries that used amylase and had activated carbon systems for decolorization,...

  8. Study the active site of flavonoid applying radiation chemistry

    Flavonoid are a large and important class of naturally occurring, low molecular weight benzo-γ-pyrone derivatives which are reported to have a myriad of biological activities, but the study on the active sites of flavonoids is still ambiguous. In this paper, rutin, quercetin and baicalin have been selected as model compounds. It is well known that rutin is used in inhibiting arteriosclerosis and baicalin is antibacterial and antiviral. They have similar basic structure, but their medicinal properties are so different, why? As most flavonoids contain carbonyl group, which can capture electron effectively, we predict that flavonoids can capture electron to form radical anion. The formation of anion radical may have influence on the mitochondrial electron transport chain. The difference in the ability of forming anion radical may cause the difference in their medicinal effects. (author)

  9. Structural Basis for the Inhibition of RNase H Activity of HIV-1 Reverse Transcriptase by RNase H Active Site-Directed Inhibitors

    Su, Hua-Poo; Yan, Youwei; Prasad, G. Sridhar; Smith, Robert F.; Daniels, Christopher L.; Abeywickrema, Pravien D.; Reid, John C.; Loughran, H. Marie; Kornienko, Maria; Sharma, Sujata; Grobler, Jay A.; Xu, Bei; Sardana, Vinod; Allison, Timothy J.; Williams, Peter D.; Darke, Paul L.; Hazuda, Daria J.; Munshi, Sanjeev (Merck)

    2010-09-02

    HIV/AIDS continues to be a menace to public health. Several drugs currently on the market have successfully improved the ability to manage the viral burden in infected patients. However, new drugs are needed to combat the rapid emergence of mutated forms of the virus that are resistant to existing therapies. Currently, approved drugs target three of the four major enzyme activities encoded by the virus that are critical to the HIV life cycle. Although a number of inhibitors of HIV RNase H activity have been reported, few inhibit by directly engaging the RNase H active site. Here, we describe structures of naphthyridinone-containing inhibitors bound to the RNase H active site. This class of compounds binds to the active site via two metal ions that are coordinated by catalytic site residues, D443, E478, D498, and D549. The directionality of the naphthyridinone pharmacophore is restricted by the ordering of D549 and H539 in the RNase H domain. In addition, one of the naphthyridinone-based compounds was found to bind at a second site close to the polymerase active site and non-nucleoside/nucleotide inhibitor sites in a metal-independent manner. Further characterization, using fluorescence-based thermal denaturation and a crystal structure of the isolated RNase H domain reveals that this compound can also bind the RNase H site and retains the metal-dependent binding mode of this class of molecules. These structures provide a means for structurally guided design of novel RNase H inhibitors.

  10. The Role of Putative Phosphatidylserine-Interactive Residues of Tissue Factor on Its Coagulant Activity at the Cell Surface.

    Shabbir A Ansari

    Full Text Available Exposure of phosphatidylserine (PS on the outer leaflet of the cell membrane is thought to play a critical role in tissue factor (TF decryption. Recent molecular dynamics simulation studies suggested that the TF ectodomain may directly interact with PS. To investigate the potential role of TF direct interaction with the cell surface phospholipids on basal TF activity and the enhanced TF activity following the decryption, one or all of the putative PS-interactive residues in the TF ectodomain were mutated and tested for their coagulant activity in cell systems. Out of the 9 selected TF mutants, five of them -TFS160A, TFS161A, TFS162A, TFK165A, and TFD180A- exhibited a similar TF coagulant activity to that of the wild-type TF. The specific activity of three mutants, TFK159A, TFS163A, and TFK166A, was reduced substantially. Mutation of the glycine residue at the position 164 markedly abrogated the TF coagulant activity, resulting in ~90% inhibition. Mutation of all nine lipid binding residues together did not further decrease the activity of TF compared to TFG164A. A similar fold increase in TF activity was observed in wild-type TF and all TF mutants following the treatment of THP-1 cells with either calcium ionomycin or HgCl2, two agents that are commonly used to decrypt TF. Overall, our data show that a few select TF residues that are implicated in interacting with PS contribute to the TF coagulant activity at the cell surface. However, our data also indicate that TF regions outside of the putative lipid binding region may also contribute to PS-dependent decryption of TF.

  11. The Role of Putative Phosphatidylserine-Interactive Residues of Tissue Factor on Its Coagulant Activity at the Cell Surface.

    Ansari, Shabbir A; Pendurthi, Usha R; Sen, Prosenjit; Rao, L Vijaya Mohan

    2016-01-01

    Exposure of phosphatidylserine (PS) on the outer leaflet of the cell membrane is thought to play a critical role in tissue factor (TF) decryption. Recent molecular dynamics simulation studies suggested that the TF ectodomain may directly interact with PS. To investigate the potential role of TF direct interaction with the cell surface phospholipids on basal TF activity and the enhanced TF activity following the decryption, one or all of the putative PS-interactive residues in the TF ectodomain were mutated and tested for their coagulant activity in cell systems. Out of the 9 selected TF mutants, five of them -TFS160A, TFS161A, TFS162A, TFK165A, and TFD180A- exhibited a similar TF coagulant activity to that of the wild-type TF. The specific activity of three mutants, TFK159A, TFS163A, and TFK166A, was reduced substantially. Mutation of the glycine residue at the position 164 markedly abrogated the TF coagulant activity, resulting in ~90% inhibition. Mutation of all nine lipid binding residues together did not further decrease the activity of TF compared to TFG164A. A similar fold increase in TF activity was observed in wild-type TF and all TF mutants following the treatment of THP-1 cells with either calcium ionomycin or HgCl2, two agents that are commonly used to decrypt TF. Overall, our data show that a few select TF residues that are implicated in interacting with PS contribute to the TF coagulant activity at the cell surface. However, our data also indicate that TF regions outside of the putative lipid binding region may also contribute to PS-dependent decryption of TF. PMID:27348126

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

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

    2008-04-02

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

  13. Identification of covalent active site inhibitors of dengue virus protease

    Koh-Stenta X

    2015-12-01

    Full Text Available Xiaoying Koh-Stenta,1 Joma Joy,1 Si Fang Wang,1 Perlyn Zekui Kwek,1 John Liang Kuan Wee,1 Kah Fei Wan,2 Shovanlal Gayen,1 Angela Shuyi Chen,1 CongBao Kang,1 May Ann Lee,1 Anders Poulsen,1 Subhash G Vasudevan,3 Jeffrey Hill,1 Kassoum Nacro11Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR, Singapore; 2Novartis Institute for Tropical Diseases, Singapore; 3Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, SingaporeAbstract: Dengue virus (DENV protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.Keywords: flavivirus protease, small molecule optimization, covalent inhibitor, active site binding, pyrazole ester derivatives

  14. Maxey Flats low-level waste disposal site closure activities

    The Maxey Flats Radioactive Waste Disposal Facility in Fleming County, Kentucky is in the process of being closed. The facility opened for commercial business in the spring of 1963 and received approximately 4.75 million cubic feet of radioactive waste by the time it was closed in December of 1977. During fourteen years of operation approximately 2.5 million curies of by-product material, 240,000 kilograms of source material, and 430 kilograms of special nuclear material were disposed. The Commonwealth purchased the lease hold estate and rights in May 1978 from the operating company. This action was taken to stabilize the facility and prepare it for closure consisting of passive care and monitoring. To prepare the site for closure, a number of remedial activities had to be performed. The remediation activities implemented have included erosion control, surface drainage modifications, installation of a temporary plastic surface cover, leachate removal, analysis, treatment and evaporation, US DOE funded evaporator concentrates solidification project and their on-site disposal in an improved disposal trench with enhanced cover for use in a humid environment situated in a fractured geology, performance evaluation of a grout injection demonstration, USGS subsurface geologic investigation, development of conceptual closure designs, and finally being added to the US EPA National Priority List for remediation and closure under Superfund. 13 references, 3 figures

  15. An active site aromatic triad in Escherichia coli DNA Pol IV coordinates cell survival and mutagenesis in different DNA damaging agents.

    Ryan W Benson

    Full Text Available DinB (DNA Pol IV is a translesion (TLS DNA polymerase, which inserts a nucleotide opposite an otherwise replication-stalling N(2-dG lesion in vitro, and confers resistance to nitrofurazone (NFZ, a compound that forms these lesions in vivo. DinB is also known to be part of the cellular response to alkylation DNA damage. Yet it is not known if DinB active site residues, in addition to aminoacids involved in DNA synthesis, are critical in alkylation lesion bypass. It is also unclear which active site aminoacids, if any, might modulate DinB's bypass fidelity of distinct lesions. Here we report that along with the classical catalytic residues, an active site "aromatic triad", namely residues F12, F13, and Y79, is critical for cell survival in the presence of the alkylating agent methyl methanesulfonate (MMS. Strains expressing dinB alleles with single point mutations in the aromatic triad survive poorly in MMS. Remarkably, these strains show fewer MMS- than NFZ-induced mutants, suggesting that the aromatic triad, in addition to its role in TLS, modulates DinB's accuracy in bypassing distinct lesions. The high bypass fidelity of prevalent alkylation lesions is evident even when the DinB active site performs error-prone NFZ-induced lesion bypass. The analyses carried out with the active site aromatic triad suggest that the DinB active site residues are poised to proficiently bypass distinctive DNA lesions, yet they are also malleable so that the accuracy of the bypass is lesion-dependent.

  16. Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase

    Li DU; Ya-xue ZHAO; Liu-meng YANG; Yong-tang ZHENG; Yun TANG; Xu SHEN; Hua-liang JIANG

    2008-01-01

    Aim:To characterize the functional and pharmacological features of a symmetrical 1-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide,as a new anti-HIV compound which could competitively inhibit HIV-1 integrase (IN) binding to viral DNA.Methods:A surface plasma resonance (SPR)-based competitive assay was employed to determine the compound's inhibitory activity,and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell assay was used to qualify the antiviral activity.The potential binding sites were predicted by molecular modeling and determined by site-directed mutagenesis and a SPR binding assay.Results:l-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide could competitively inhibit IN binding to viral DNA with a 50% inhibitory concentration (IC50) value of 7.29±0.68 μmol/L as investigated by SPR-based investigation.Another antiretroviral activity assay showed that this compound exhibited inhibition against HⅣ-Ⅰ(ⅢB) replication with a 50% effective concentration (EC50) value of 40.54 μmol/L in C8166 cells,and cytotoxicity with a cytotoxic concentration value of 173.84 μmol/L in mock-infected C8166 cells.Molecular docking predicted 3 potential residues as 1-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene)bis-1-pyrrolidineacetamide binding sites.The importance of 3 key amino acid residues (Lys103,Lys173,and Thr174) involved in the binding was further identified by site-directed mutagenesis and a SPR binding assay.Conclusion:This present work identified a new anti-HIV compound through a new IN-binding site which is expected to supply new potential drug-binding site information for HIV-1 integrase inhibitor discovery and development.

  17. Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites.

    Simon, Bertrand; Huart, Anne-Sophie; Temmerman, Koen; Vahokoski, Juha; Mertens, Haydyn D T; Komadina, Dana; Hoffmann, Jan-Erik; Yumerefendi, Hayretin; Svergun, Dmitri I; Kursula, Petri; Schultz, Carsten; McCarthy, Andrew A; Hart, Darren J; Wilmanns, Matthias

    2016-06-01

    The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation. PMID:27133022

  18. Identification of tyrosine residues within the intracellular domain of the erythropoietin receptor crucial for STAT5 activation.

    Gobert, S.; Chretien, S; Gouilleux, F; Muller, O.; Pallard, C; Dusanter-Fourt, I; Groner, B; Lacombe, C.; Gisselbrecht, S; Mayeux, P

    1996-01-01

    FDCP-1 cells are hematopoietic progenitor cells which require interleukin-3 for survival and proliferation. FDCP-1 cells stably transfected with the murine erythropoietin receptor cDNA survive and proliferate in the presence of erythropoietin. Erythropoietin induces the activation of the short forms (80 kDa) of STAT5 in the cells. Erythropoietin-induced activation of STAT5 was strongly reduced in cells expressing mutated variants of the erythropoietin receptors in which tyrosine residues in t...

  19. Antibacterial and residual antimicrobial activities against Enterococcus faecalis biofilm: A comparison between EDTA, chlorhexidine, cetrimide, MTAD and QMix

    Zhang, Rui; Chen, Min; Lu, Yan; Guo, Xiangjun; Qiao, Feng; Wu, Ligeng

    2015-01-01

    We compared the antibacterial and residual antimicrobial activities of five root canal irrigants (17% EDTA,2% chlorhexidine,0.2% cetrimide, MTAD, and QMix) in a model of Enterococcus faecalis biofilm formation. Sixty dentin blocks with 3-week E. faecalis biofilm were divided into six equal groups and flushed with irrigant for 2 min or left untreated. A blank control group was also established. Antibacterial activities of the irrigants were evaluated by counting colony forming units. To test r...

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

    Yu Zhang

    Full Text Available Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL from Geobacillus kaustophilus HTA426 (GkaP exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  1. Residual dose rate monitoring for future machine activation control at J-PARC MR

    Since July 11, 2012, to investigate the beam loss mechanism, we have been monitoring the residual dose rate on the accelerator components like Q and B magnets, RF components, and collimators after beam stop. As for the collimator area, residual dose rate change was measured up to 300hrs cooling time after beam stop, and these data were estimated by using the Sullivan-Overton equation. The equation well reproduces the measured data within ±50% and the fitting parameters were obtained. By using the parameters we have estimated the future residual dose rate level at the collimator area within the factor of 2. These calculations show that the 1000W injection beam loss during an 11 months/year continuous beam operation will make residual dose rate of over 2.4mSv/h during the next 1 month maintenance stage after 15 years repetition. (author)

  2. Conserved charged amino acid residues in the extracellular region of sodium/iodide symporter are critical for iodide transport activity

    Liang Ji-An

    2010-11-01

    Full Text Available Abstract Background Sodium/iodide symporter (NIS mediates the active transport and accumulation of iodide from the blood into the thyroid gland. His-226 located in the extracellular region of NIS has been demonstrated to be critical for iodide transport in our previous study. The conserved charged amino acid residues in the extracellular region of NIS were therefore characterized in this study. Methods Fourteen charged residues (Arg-9, Glu-79, Arg-82, Lys-86, Asp-163, His-226, Arg-228, Asp-233, Asp-237, Arg-239, Arg-241, Asp-311, Asp-322, and Asp-331 were replaced by alanine. Iodide uptake abilities of mutants were evaluated by steady-state and kinetic analysis. The three-dimensional comparative protein structure of NIS was further modeled using sodium/glucose transporter as the reference protein. Results All the NIS mutants were expressed normally in the cells and targeted correctly to the plasma membrane. However, these mutants, except R9A, displayed severe defects on the iodide uptake. Further kinetic analysis revealed that mutations at conserved positively charged amino acid residues in the extracellular region of NIS led to decrease NIS-mediated iodide uptake activity by reducing the maximal rate of iodide transport, while mutations at conserved negatively charged residues led to decrease iodide transport by increasing dissociation between NIS mutants and iodide. Conclusions This is the first report characterizing thoroughly the functional significance of conserved charged amino acid residues in the extracellular region of NIS. Our data suggested that conserved charged amino acid residues, except Arg-9, in the extracellular region of NIS were critical for iodide transport.

  3. Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase

    Peters, Günther H.j.; Svendsen, A.; Langberg, H.; Vind, J.; Patkar, S.A.; Toxvaerd, S.; Kinnunen, P.K.J.

    1998-01-01

    reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S 146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to...

  4. Pb2+ adsorption from aqueous solutions on activated carbons obtained from lignocellulosic residues

    L. Giraldo

    2008-03-01

    Full Text Available Activated carbons obtained from cane sugar bagasse (ACB, African palm pit (ACP and sawdust (ACS were prepared through an impregnated with HNO3 and thermal treatment in an atmosphere in N2/steam water at 1173 K. Adsorption isotherms of N2 at 77 K and of CO2 at 273 K were determined for the activated carbons for which surface area and pore volume values were from 868 to 1100 m²g-1 and from 0.27 to 0.55cm³ g-1, respectively. These results were correlated, with the ones obtained for adsorption the adsorption isotherms of Pb2+ in aqueous solutions. Impregnation of the lignocellulosic materials with nitric acid produced acid-type activated carbons with total acid site contents between 4.13 and 6.93 mmol g-1 and pH at the point of zero charge values between 2.7 and 4.1, which were within range of the adsorption, at different pH values, since they determined, the surface charge of the activated carbons. Adsorption isotherms of Pb2+ at different pH values (2-8 at 298 K were determined. The ion adsorption capacity on ACB, ACP and ACS were 13.7, 15.2 and 17.5 mg.g-1, respectively. Experimental data were fitted to the Langmuir and Freundlich models and all cases the former fit better. The highest values for the quantity adsorbed on the monolayer, qm, were at pH 4, whereas the surface, charge of activated carbons was negative and the lead species mainly present was Pb2+. For higher pHs, the quantity of Pb2+ adsorbed decreased, and this had an important effect on adsorption, the surface characteristics of the solids and the hydroxilated lead species that were formed in the system.

  5. Dissecting the active site of the collagenolytic cathepsin L3 protease of the invasive stage of Fasciola hepatica.

    Ileana Corvo

    Full Text Available BACKGROUND: A family of secreted cathepsin L proteases with differential activities is essential for host colonization and survival in the parasitic flatworm Fasciola hepatica. While the blood feeding adult secretes predominantly FheCL1, an enzyme with a strong preference for Leu at the S2 pocket of the active site, the infective stage produces FheCL3, a unique enzyme with collagenolytic activity that favours Pro at P2. METHODOLOGY/PRINCIPAL FINDINGS: Using a novel unbiased multiplex substrate profiling and mass spectrometry methodology (MSP-MS, we compared the preferences of FheCL1 and FheCL3 along the complete active site cleft and confirm that while the S2 imposes the greatest influence on substrate selectivity, preferences can be indicated on other active site subsites. Notably, we discovered that the activity of FheCL1 and FheCL3 enzymes is very different, sharing only 50% of the cleavage sites, supporting the idea of functional specialization. We generated variants of FheCL1 and FheCL3 with S2 and S3 residues by mutagenesis and evaluated their substrate specificity using positional scanning synthetic combinatorial libraries (PS-SCL. Besides the rare P2 Pro preference, FheCL3 showed a distinctive specificity at the S3 pocket, accommodating preferentially the small Gly residue. Both P2 Pro and P3 Gly preferences were strongly reduced when Trp67 of FheCL3 was replaced by Leu, rendering the enzyme incapable of digesting collagen. In contrast, the inverse Leu67Trp substitution in FheCL1 only slightly reduced its Leu preference and improved Pro acceptance in P2, but greatly increased accommodation of Gly at S3. CONCLUSIONS/SIGNIFICANCE: These data reveal the significance of S2 and S3 interactions in substrate binding emphasizing the role for residue 67 in modulating both sites, providing a plausible explanation for the FheCL3 collagenolytic activity essential to host invasion. The unique specificity of FheCL3 could be exploited in the design of

  6. A light-dependent complementation system for analysis of NADPH:protochlorophyllide oxidoreductase: Identification and mutagenesis of two conserved residues that are essential for enzyme activity

    Wilks, H.M.; Timko, M.P. [Univ. of Virginia, Charlottesville, VA (United States)

    1995-01-31

    Protochlorophyllide reductase (NADPH:protochlorophyllide oxidoreductase; EC 1.6.99.1) catalyzes the light-dependent reduction of protochlorophyllide to chlorophyllide, a key regulatory step in the chlorophyll biosynthetic pathway. We have developed an expression system in which the protochlorophyllide reductase from pea (Pisum sativum L.) is used to complement protochlorophyllide reduction mutants in the photosynthetic bacterium Rhodobacter capsulatus, allowing analysis of wild-type and mutant forms of the enzyme. By protein sequence comparisons, we have identified the plant protochlorophyllide reductases as belonging to the family of short-chain alcohol dehydrogenases. Based on our protein sequence alignments, we have identified and mutated two conserved residues (Tyr-275 and Lys-279) within the proposed active site of the enzyme and shown that they are critical for activity. A model of the enzyme reaction mechanism for light-dependent protochlorophyllide reduction is proposed. 33 refs., 5 figs.

  7. Fat residue and use-wear found on Acheulian biface and scraper associated with butchered elephant remains at the site of Revadim, Israel.

    Natalya Solodenko

    Full Text Available The archaeological record indicates that elephants must have played a significant role in early human diet and culture during Palaeolithic times in the Old World. However, the nature of interactions between early humans and elephants is still under discussion. Elephant remains are found in Palaeolithic sites, both open-air and cave sites, in Europe, Asia, the Levant, and Africa. In some cases elephant and mammoth remains indicate evidence for butchering and marrow extraction performed by humans. Revadim Quarry (Israel is a Late Acheulian site where elephant remains were found in association with characteristic Lower Palaeolithic flint tools. In this paper we present results regarding the use of Palaeolithic tools in processing animal carcasses and rare identification of fat residue preserved on Lower Palaeolithic tools. Our results shed new light on the use of Palaeolithic stone tools and provide, for the first time, direct evidence (residue of animal exploitation through the use of an Acheulian biface and a scraper. The association of an elephant rib bearing cut marks with these tools may reinforce the view suggesting the use of Palaeolithic stone tools in the consumption of large game.

  8. Acute and Chronic Effects of Dietary Lactose in Adult Rats Are not Explained by Residual Intestinal Lactase Activity

    Bert J. M. van de Heijning

    2015-07-01

    Full Text Available Neonatal rats have a high intestinal lactase activity, which declines around weaning. Yet, the effects of lactose-containing products are often studied in adult animals. This report is on the residual, post-weaning lactase activity and on the short- and long-term effects of lactose exposure in adult rats. Acutely, the postprandial plasma response to increasing doses of lactose was studied, and chronically, the effects of a 30% lactose diet fed from postnatal (PN Day 15 onwards were evaluated. Intestinal lactase activity, as assessed both in vivo and in vitro, was compared between both test methods and diet groups (lactose vs. control. A 50%–75% decreased digestive capability towards lactose was observed from weaning into adulthood. Instillation of lactose in adult rats showed disproportionally low increases in plasma glucose levels and did not elicit an insulin response. However, gavages comprising maltodextrin gave rise to significant plasma glucose and insulin responses, indicative of a bias of the adult GI tract to digest glucose polymers. Despite the residual intestinal lactase activity shown, a 30% lactose diet was poorly digested by adult rats: the lactose diet rendered the animals less heavy and virtually devoid of body fat, whereas their cecum tripled in size, suggesting an increased bacterial fermentation. The observed acute and chronic effects of lactose exposure in adult rats cannot be explained by the residual intestinal lactase activity assessed.

  9. Direct contacts between conserved motifs of different subunits provide major contribution to active site organization in human and mycobacterial dUTPases.

    Takács, Eniko; Nagy, Gergely; Leveles, Ibolya; Harmat, Veronika; Lopata, Anna; Tóth, Judit; Vértessy, Beáta G

    2010-07-16

    dUTP pyrophosphatases (dUTPases) are essential for genome integrity. Recent results allowed characterization of the role of conserved residues. Here we analyzed the Asp/Asn mutation within conserved Motif I of human and mycobacterial dUTPases, wherein the Asp residue was previously implicated in Mg(2+)-coordination. Our results on transient/steady-state kinetics, ligand binding and a 1.80 A resolution structure of the mutant mycobacterial enzyme, in comparison with wild type and C-terminally truncated structures, argue that this residue has a major role in providing intra- and intersubunit contacts, but is not essential for Mg(2+) accommodation. We conclude that in addition to the role of conserved motifs in substrate accommodation, direct subunit interaction between protein atoms of active site residues from different conserved motifs are crucial for enzyme function. PMID:20493855

  10. Metavanadate at the active site of the phosphatase VHZ.

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  11. Accommodation of GDP-Linked Sugars in the Active Site of GDP-Perosamine Synthase

    Cook, Paul D.; Carney, Amanda E.; Holden, Hazel M. (UW)

    2009-01-12

    Perosamine (4-amino-4,6-dideoxy-d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 {angstrom} resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K{sub m} for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k{sub cat} was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy-d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.

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

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

  13. Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme

    Berezniak, Tomasz [University of Heidelberg; Zahran, Mai [ORNL; Imhof, Petra [University of Heidelberg; Jaeschke, Andres [Free University of Berlin; Smith, Jeremy C [ORNL

    2010-10-01

    The Diels-Alderase ribozyme, an in vitro-evolved ribonucleic acid enzyme, accelerates the formation of carbon-carbon bonds between an anthracene diene and a maleimide dienophile in a [4 + 2] cycloaddition, a reaction with broad application in organic chemistry. Here, the Diels-Alderase ribozyme is examined via molecular dynamics (MD) simulations in both crystalline and aqueous solution environments. The simulations indicate that the catalytic pocket is highly dynamic. At low Mg(2+) ion concentrations, inactive states with the catalytic pocket closed dominate. Stabilization of the enzymatically active, open state of the catalytic pocket requires a high concentration of Mg(2+) ions (e.g., 54 mM), with cations binding to specific phosphate sites on the backbone of the residues bridging the opposite strands of the pocket. The free energy profile for pocket opening at high Mg(2+) cation concentration exhibits a double minimum, with a barrier to opening of approximately 5.5 kJ/mol and the closed state approximately 3 kJ/mol lower than the open state. Selection of the open state on substrate binding leads to the catalytic activity of the ribozyme. The simulation results explain structurally the experimental observation that full catalytic activity depends on the Mg(2+) ion concentration

  14. Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

    Tekpinar, Mustafa; Yildirim, Ahmet; Wassenaar, Tsjerk A

    2015-12-01

    The protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is involved in the quorum sensing of several bacterial species, including Helicobacter pylori. In particular, these bacteria depend on MTAN for synthesis of vitamin K2 homologs. The residue D198 in the active site of MTAN seems to be of crucial importance, by acting as a hydrogen-bond acceptor for the ligand. In this study, we investigated the conformation and dynamics of apo and holo H. pylori MTAN (HpMTAN), and assessed the effect of protonation of D198 by use of molecular dynamics simulations. Our results show that protonation of the active site of HpMTAN can cause a conformational transition from a closed state to an open state even in the absence of substrate, via inter-chain mechanical coupling. PMID:26254213

  15. Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase.

    Law, Brian J C; Bennett, Matthew R; Thompson, Mark L; Levy, Colin; Shepherd, Sarah A; Leys, David; Micklefield, Jason

    2016-02-18

    Catechol-O-methyltransferase (COMT), an important therapeutic target in the treatment of Parkinson's disease, is also being developed for biocatalytic processes, including vanillin production, although lack of regioselectivity has precluded its more widespread application. By using structural and mechanistic information, regiocomplementary COMT variants were engineered that deliver either meta- or para-methylated catechols. X-ray crystallography further revealed how the active-site residues and quaternary structure govern regioselectivity. Finally, analogues of AdoMet are accepted by the regiocomplementary COMT mutants and can be used to prepare alkylated catechols, including ethyl vanillin. PMID:26797714

  16. Fluconazole Binding and Sterol Demethylation in Three CYP51 Isoforms Indicate Differences in Active Site Topology

    Bellamine, A.; Lepesheva, Galina I.; Waterman, Mike (Vanderbilt)

    2010-11-16

    14{alpha}-Demethylase (CYP51) is a key enzyme in all sterol biosynthetic pathways (animals, fungi, plants, protists, and some bacteria), catalyzing the removal of the C-14 methyl group following cyclization of squalene. Based on mutations found in CYP51 genes from Candida albicans azole-resistant isolates obtained after fluconazole treatment of fungal infections, and using site-directed mutagenesis, we have found that fluconazole binding and substrate metabolism vary among three different CYP51 isoforms: human, fungal, and mycobacterial. In C. albicans, the Y132H mutant from isolates shows no effect on fluconazole binding, whereas the F145L mutant results in a 5-fold increase in its IC{sub 50} for fluconazole, suggesting that F145 (conserved only in fungal 14{alpha}-demethylases) interacts with this azole. In C. albicans, F145L accounts, in part, for the difference in fluconazole sensitivity reported between mammals and fungi, providing a basis for treatment of fungal infections. The C. albicans Y132H and human Y145H CYP51 mutants show essentially no effect on substrate metabolism, but the Mycobacterium tuberculosis F89H CYP51 mutant loses both its substrate binding and metabolism. Because these three residues align in the three isoforms, the results indicate that their active sites contain important structural differences, and further emphasize that fluconazole and substrate binding are uncoupled properties.

  17. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase.

    Cyril Moccand

    Full Text Available The prevalent de novo biosynthetic pathway of vitamin B6 involves only two enzymes (Pdx1 and Pdx2 that form an ornate multisubunit complex functioning as a glutamine amidotransferase. The synthase subunit, Pdx1, utilizes ribose 5-phosphate and glyceraldehyde 3-phosphate, as well as ammonia derived from the glutaminase activity of Pdx2 to directly form the cofactor vitamer, pyridoxal 5'-phosphate. Given the fact that a single enzyme performs the majority of the chemistry behind this reaction, a complicated mechanism is anticipated. Recently, the individual steps along the reaction co-ordinate are beginning to be unraveled. In particular, the binding of the pentose substrate and the first steps of the reaction have been elucidated but it is not known if the latter part of the chemistry, involving the triose sugar, takes place in the same or a disparate site. Here, we demonstrate through the use of enzyme assays, enzyme kinetics, and mutagenesis studies that indeed a second site is involved in binding the triose sugar and moreover, is the location of the final vitamin product, pyridoxal 5'-phosphate. Furthermore, we show that product release is triggered by the presence of a PLP-dependent enzyme. Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery.

  18. 10 CFR 60.18 - Review of site characterization activities. 2

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Review of site characterization activities. 2 60.18... IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.18 Review of site characterization activities. 2 2 In addition to the review of site characterization activities specified in this section,...

  19. JAK2 V617F constitutive activation requires JH2 residue F595: a pseudokinase domain target for specific inhibitors.

    Alexandra Dusa

    Full Text Available The JAK2 V617F mutation present in over 95% of Polycythemia Vera patients and in 50% of Essential Thrombocythemia and Primary Myelofibrosis patients renders the kinase constitutively active. In the absence of a three-dimensional structure for the full-length protein, the mechanism of activation of JAK2 V617F has remained elusive. In this study, we used functional mutagenesis to investigate the involvement of the JH2 alphaC helix in the constitutive activation of JAK2 V617F. We show that residue F595, located in the middle of the alphaC helix of JH2, is indispensable for the constitutive activity of JAK2 V617F. Mutation of F595 to Ala, Lys, Val or Ile significantly decreases the constitutive activity of JAK2 V617F, but F595W and F595Y are able to restore it, implying an aromaticity requirement at position 595. Substitution of F595 to Ala was also able to decrease the constitutive activity of two other JAK2 mutants, T875N and R683G, as well as JAK2 K539L, albeit to a lower extent. In contrast, the F595 mutants are activated by erythropoietin-bound EpoR. We also explored the relationship between the dimeric conformation of EpoR and several JAK2 mutants. Since residue F595 is crucial to the constitutive activation of JAK2 V617F but not to initiation of JAK2 activation by cytokines, we suggest that small molecules that target the region around this residue might specifically block oncogenic JAK2 and spare JAK2 wild-type.

  20. Identification of residues in the heme domain of soluble guanylyl cyclase that are important for basal and stimulated catalytic activity.

    Padmamalini Baskaran

    Full Text Available Nitric oxide signals through activation of soluble guanylyl cyclase (sGC, a heme-containing heterodimer. NO binds to the heme domain located in the N-terminal part of the β subunit of sGC resulting in increased production of cGMP in the catalytic domain located at the C-terminal part of sGC. Little is known about the mechanism by which the NO signaling is propagated from the receptor domain (heme domain to the effector domain (catalytic domain, in particular events subsequent to the breakage of the bond between the heme iron and Histidine 105 (H105 of the β subunit. Our modeling of the heme-binding domain as well as previous homologous heme domain structures in different states point to two regions that could be critical for propagation of the NO activation signal. Structure-based mutational analysis of these regions revealed that residues T110 and R116 in the αF helix-β1 strand, and residues I41 and R40 in the αB-αC loop mediate propagation of activation between the heme domain and the catalytic domain. Biochemical analysis of these heme mutants allows refinement of the map of the residues that are critical for heme stability and propagation of the NO/YC-1 activation signal in sGC.

  1. Hexavalent chromium removal from aqueous solution by algal bloom residue derived activated carbon: Equilibrium and kinetic studies

    Zhang Hong; Tang Yi; Cai Dongqing; Liu Xianan; Wang Xiangqin [Key Laboratory of Ion Beam Bioengineering, Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Huang Qing, E-mail: huangq@ipp.ac.cn [Key Laboratory of Ion Beam Bioengineering, Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Yu Zengliang, E-mail: zlyu@ipp.ac.cn [Key Laboratory of Ion Beam Bioengineering, Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China)

    2010-09-15

    A novel approach to prepare activated carbon from blue-green algal bloom residue has been tried for first time and its adsorption capability to remove hexavalent chromium Cr(VI) from aqueous solution has been examined. For this algal bloom residue derived activated carbon, the physical characters regarding adsorption capability were analyzed by scanning electron microscope (SEM), energy dispersive X-ray spectroscope (EDS) and Fourier transform infrared (FTIR) spectroscopy. Batch studies showed that initial pH, absorbent dosage, and initial concentration of Cr(VI) were important parameters for Cr(VI) absorption. It was found that initial pH of 1.0 was most favorable for Cr(VI) removal. The adsorption process followed the pseudo-second-order equation and Freundlich isotherm. The maximum adsorption capacity for Cr(VI) was 155.52 mg g{sup -1} in an acidic medium, which is comparable to best result from activated carbons derived from biomass. Therefore, this work put forward a nearly perfect solution which on one hand gets rid of environment-unfriendly algae residue while on the other hand produces high-quality activated carbon that is in return advantageous to environment protection.

  2. Multiple transport-active binding sites are available for a single substrate on human P-glycoprotein (ABCB1).

    Chufan, Eduardo E; Kapoor, Khyati; Sim, Hong-May; Singh, Satyakam; Talele, Tanaji T; Durell, Stewart R; Ambudkar, Suresh V

    2013-01-01

    P-glycoprotein (Pgp, ABCB1) is an ATP-Binding Cassette (ABC) transporter that is associated with the development of multidrug resistance in cancer cells. Pgp transports a variety of chemically dissimilar amphipathic compounds using the energy from ATP hydrolysis. In the present study, to elucidate the binding sites on Pgp for substrates and modulators, we employed site-directed mutagenesis, cell- and membrane-based assays, molecular modeling and docking. We generated single, double and triple mutants with substitutions of the Y307, F343, Q725, F728, F978 and V982 residues at the proposed drug-binding site with cys in a cysless Pgp, and expressed them in insect and mammalian cells using a baculovirus expression system. All the mutant proteins were expressed at the cell surface to the same extent as the cysless wild-type Pgp. With substitution of three residues of the pocket (Y307, Q725 and V982) with cysteine in a cysless Pgp, QZ59S-SSS, cyclosporine A, tariquidar, valinomycin and FSBA lose the ability to inhibit the labeling of Pgp with a transport substrate, [(125)I]-Iodoarylazidoprazosin, indicating these drugs cannot bind at their primary binding sites. However, the drugs can modulate the ATP hydrolysis of the mutant Pgps, demonstrating that they bind at secondary sites. In addition, the transport of six fluorescent substrates in HeLa cells expressing triple mutant (Y307C/Q725C/V982C) Pgp is also not significantly altered, showing that substrates bound at secondary sites are still transported. The homology modeling of human Pgp and substrate and modulator docking studies support the biochemical and transport data. In aggregate, our results demonstrate that a large flexible pocket in the Pgp transmembrane domains is able to bind chemically diverse compounds. When residues of the primary drug-binding site are mutated, substrates and modulators bind to secondary sites on the transporter and more than one transport-active binding site is available for each

  3. Multiple transport-active binding sites are available for a single substrate on human P-glycoprotein (ABCB1.

    Eduardo E Chufan

    Full Text Available P-glycoprotein (Pgp, ABCB1 is an ATP-Binding Cassette (ABC transporter that is associated with the development of multidrug resistance in cancer cells. Pgp transports a variety of chemically dissimilar amphipathic compounds using the energy from ATP hydrolysis. In the present study, to elucidate the binding sites on Pgp for substrates and modulators, we employed site-directed mutagenesis, cell- and membrane-based assays, molecular modeling and docking. We generated single, double and triple mutants with substitutions of the Y307, F343, Q725, F728, F978 and V982 residues at the proposed drug-binding site with cys in a cysless Pgp, and expressed them in insect and mammalian cells using a baculovirus expression system. All the mutant proteins were expressed at the cell surface to the same extent as the cysless wild-type Pgp. With substitution of three residues of the pocket (Y307, Q725 and V982 with cysteine in a cysless Pgp, QZ59S-SSS, cyclosporine A, tariquidar, valinomycin and FSBA lose the ability to inhibit the labeling of Pgp with a transport substrate, [(125I]-Iodoarylazidoprazosin, indicating these drugs cannot bind at their primary binding sites. However, the drugs can modulate the ATP hydrolysis of the mutant Pgps, demonstrating that they bind at secondary sites. In addition, the transport of six fluorescent substrates in HeLa cells expressing triple mutant (Y307C/Q725C/V982C Pgp is also not significantly altered, showing that substrates bound at secondary sites are still transported. The homology modeling of human Pgp and substrate and modulator docking studies support the biochemical and transport data. In aggregate, our results demonstrate that a large flexible pocket in the Pgp transmembrane domains is able to bind chemically diverse compounds. When residues of the primary drug-binding site are mutated, substrates and modulators bind to secondary sites on the transporter and more than one transport-active binding site is available

  4. Hazardous Material Storage Facilities and Sites - WASTE_SOLID_ACTIVE_PERMITTED_IDEM_IN: Active Permitted Solid Waste Sites in Indiana (Indiana Department of Environmental Management, Point Shapefile)

    NSGIC GIS Inventory (aka Ramona) — WASTE_SOLID_ACTIVE_PERMITTED_IDEM_IN is a point shapefile that contains active permitted solid waste site locations in Indiana, provided by personnel of Indiana...

  5. Human uroporphyrinogen III synthase: NMR-based mapping of the active site.

    Cunha, Luis; Kuti, Miklos; Bishop, David F; Mezei, Mihaly; Zeng, Lei; Zhou, Ming-Ming; Desnick, Robert J

    2008-05-01

    Uroporphyrinogen III synthase (URO-synthase) catalyzes the cyclization and D-ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO-synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein-protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane-synthase (HMB-synthase) and/or uroporphyrinogen-decarboxylase (URO-decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically-labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO-synthase backbone (13)C(alpha) (100%), (1)H(alpha) (99.6%), and nonproline (1)H(N) and (15)N resonances (94%) was achieved as well as 85% of the side-chain (13)C and (1)H resonances. NMR analyses of URO-synthase titrated with competitive inhibitors N(D)-methyl-1-formylbilane (NMF-bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO-synthase crystal structure with NMF-bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme-inhibitor complex. The absence of chemical shift changes in the (15)N spectrum of URO-synthase mixed with the homogeneous HMB-synthase holoenzyme or URO-decarboxylase precluded occurrence of a stable cytosolic enzyme complex. PMID:18004775

  6. Prediction and Simulation the Breakthrough of Residual Chlorine Removal by Granular Activated Carbon Adsorbent Using Artificial Neural Networks

    Rusul Naseer

    2012-07-01

    Full Text Available This study has included two parts. The first part has dealt with carbon production whereas the date Palm was used to produce Granular Activated Carbon (GAC with specific physical characteristics. The new produced of GAC is used to adsorbate the Residual chlorine from water by deep bed filter column. In the second part, the experimental results of the breakthrough of residual chlorine curves is predicted and simulated using artificial neural network with back propagation algorithm whereas the optimum number of neuron was investigated based on RMSE. The removal of residual chlorine has been used as target function in ANN while the other properties of adsorption process such as operation conditions, chlorine concentration in raw water and GAC characteristics has been used as input parameters. The results showed that ANN with back propagation algorithm is a good tool that can be used to predict the best operating parameter for designing GAC layer in multimedia filter whereas 35 neuron gave the best fitting with experimental data. In addition to that, the simulation result was showed that the predictions of breakthrough curve model has been coincided well with the measured values which explained that the depth 25 cm with grain size 1.5 mm of GAC filter bed will be give the optimum removal of residual chlorine from chlorinated water.

  7. Selective effects of charge on G protein activation by FSH-receptor residues 551-555 and 650-653.

    Grasso, P; Deziel, M R; Reichert, L E

    1995-01-01

    Two cytosolic regions of the rat testicular FSH receptor (FSHR), residues 533-555 and 645-653, have been identified as G protein-coupling domains. We localized the activity in these domains to their C-terminal sequences, residues 551-555 (KIAKR, net charge +3) and 650-653 (RKSH, net charge +3), and examined the effects of charge on G protein activation by the C-terminal peptides, using synthetic analogs containing additions, through alanine (A) linkages, of arginine (R, +), histidine (H, +) or both. RA-KIAKR (net charge +4) mimicked the effect of FSHR-(551-555) on guanine nucleotide exchange in rat testis membranes, but reduced its ability to inhibit FSH-stimulated estradiol biosynthesis in cultured rat Sertoli cells. Further increasing net charge by the addition of H (HARA-KIAKR, net charge +5) increased guanosine 5'-triphosphate (GTP) binding, but eliminated FSHR-(551-555) effects on FSH-stimulated steroidogenesis. HA-RKSH (net charge +4) significantly inhibited guanine nucleotide exchange in rat testis membranes, but stimulated basal and potentiated FSH-induced estradiol biosynthesis in cultured rat Sertoli cells. Addition of two H residues (HAHA-RKSH, net charge +5) restored GTP binding and further potentiated basal and FSH-stimulated steroidogenesis. These results suggest that positive charges in G protein-coupling domains of the FSHR play a role in modulating G protein activation and postbinding effects of FSH, such as steroidogenesis. PMID:8589550

  8. Arsenic stabilization by zero-valent iron, bauxite residue, and zeolite at a contaminated site planting Panax notoginseng.

    Yan, X L; Lin, L Y; Liao, X Y; Zhang, W B; Wen, Y

    2013-10-01

    Panax notoginseng (Burk.) F.H. Chen, a rare traditional Chinese medicinal herb, is a widely used phytomedicine used all over the world. In recent years, the arsenic contamination of the herb and its relative products becomes a serious problem due to elevated soil As concentration. This study aimed to evaluate the effects of different types and dosages of amendments on As stabilization in soil and its uptake by P. notoginseng. Results showed that comparing to control treatment, the As concentrations of P. notoginseng declined by 49-63%, 43-61% and 52-66% in 0.25% zero-valent iron (Fe(0)), 0.5% bauxite residue, and 1% zeolite treatment, respectively; whereas the biomasses were elevated by 62-116%, 45-152% and 114-265%, respectively. The As(III) proportions of P. notoginseng increased by 8%, 9%, and 8%, and the transfer factors of As from root to shoot increased by 37%, 42% and 84% in the optimal treatments of Fe(0), bauxite residue, and zeolite. For soil As, all the three amendments could transform the non-specifically adsorbed As fraction to hydrous oxides Fe/Al fractions (by Fe(0) and red mud) or specifically adsorbed As fraction (by zeolite), therefore reduced the bioavailability of soil As. With a comprehensive consideration of stabilization efficiency, plant growth, environmental influence, and cost, Fe(0) appeared to be the best amendment, and zeolite could also be a good choice. In conclusion, this study was of significance in developing As contamination control in P. notoginseng planting areas, and even other areas for medicinal herb growing. PMID:23871591

  9. Structure and Active Stie Residues of Pg1D, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter jejuni

    Rangarajan,E.; Ruane, K.; Sulea, T.; Watson, D.; Proteau, A.; Leclerc, S.; Cygler, M.; Matte, A.; Young, N.

    2008-01-01

    Campylobacter jejuni is highly unusual among bacteria in forming N-linked glycoproteins. The heptasaccharide produced by its pgl system is attached to protein Asn through its terminal 2, 4-diacetamido-2, 4,6-trideoxy-d-Glc (QuiNAc4NAc or N, N'-diacetylbacillosamine) moiety. The crucial, last part of this sugar's synthesis is the acetylation of UDP-2-acetamido-4-amino-2, 4,6-trideoxy-d-Glc by the enzyme PglD, with acetyl-CoA as a cosubstrate. We have determined the crystal structures of PglD in CoA-bound and unbound forms, refined to 1.8 and 1.75 Angstroms resolution, respectively. PglD is a trimer of subunits each comprised of two domains, an N-terminal {alpha}/{beta}-domain and a C-terminal left-handed {beta}-helix. Few structural differences accompany CoA binding, except in the C-terminal region following the {beta}-helix (residues 189-195), which adopts an extended structure in the unbound form and folds to extend the {beta}-helix upon binding CoA. Computational molecular docking suggests a different mode of nucleotide-sugar binding with respect to the acetyl-CoA donor, with the molecules arranged in an 'L-shape', compared with the 'in-line' orientation in related enzymes. Modeling indicates that the oxyanion intermediate would be stabilized by the NH group of Gly143', with His125' the most likely residue to function as a general base, removing H+ from the amino group prior to nucleophilic attack at the carbonyl carbon of acetyl-CoA. Site-specific mutations of active site residues confirmed the importance of His125', Glu124', and Asn118. We conclude that Asn118 exerts its function by stabilizing the intricate hydrogen bonding network within the active site and that Glu124' may function to increase the pKa of the putative general base, His125'.

  10. TAR CREEK SUPERFUND SITE REMEDIATION: COMBINED ROLES FOR BIOMASS, POULTRY LITTER, FLY ASH AND FLU GAS DESULFURIZATION RESIDUES

    The Tar Creek Superfund site in Northeastern Oklahoma is a large area contaminated from 100 years of lead and zinc mining. In this proposal we focus on developing surface coverage and remediation methods for the 45 million cubic yards of mine tailings, known as chat. The chat h...

  11. First results of an experimental study of the residual activity induced by high-energy uranium ions in steel and copper

    First results of an experimental study of the residual activity induced by high-energy uranium ions are presented. As a preparatory work for constructing the FAIR facility at GSI, samples of stainless steel and copper were irradiated by 500 MeV/u 238U ions and investigated by gamma-ray spectroscopy. The isotopes that contribute dominantly to the residual activity have been identified and their contributions have been quantified. Depth-profiles of residual activity of individual isotopes have shown that target activation due to projectile fragments and neutrons extends far beyond the range of primary particles and reaches the same level as in the region irradiated by primary particles

  12. Detection limit for activation measurements in ultralow background sites

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  13. Molecular recognition at the active site of subtilisin BPN': crystallographic studies using genetically engineered proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor).

    Takeuchi, Y; Noguchi, S; Satow, Y; Kojima, S; Kumagai, I; Miura, K; Nakamura, K T; Mitsui, Y

    1991-06-01

    Unlike trypsin-like serine proteases having only one conspicuous binding pocket in the active site, subtilisin BPN' has two such pockets, the S1 and S4 pockets, which accommodate the P1 and P4 residues of ligands (after Schechter and Berger notation) respectively. Using computer graphics, the geometrical nature of the two pockets was carefully examined and strategies for site-directed mutagenesis studies were set up against a protein SSI (Streptomyces subtilisin inhibitor), which is a strong proteinaceous inhibitor (or a substrate analogue) of subtilisin BPN'. It was decided to convert the P1 residue, methionine 73, into lysine (M73K) with or without additional conversion of the P4 residue, methionine 70, into glycine (M70G). The crystal structures of the two complexes of subtilisin BPN', one with the single mutant SSI (M73K) and the other with the double mutant SSI (M73K, M70G) were solved showing that (i) small 'electrostatic induced-fit movement' occurs in the S1 pocket upon introducing the terminal plus charge of the lysine side chain, and (ii) large 'mechanical induced-fit movement' occurs in the S4 pocket upon reducing the size of the P4 side chain from methionine to glycine. In both (i) and (ii), the induced-fit movement occurred in a concerted fashion involving both the enzyme and 'substrate' amino acid residues. The term 'substrate-assisted stabilization' was coined to stress the cooperative nature of the induced-fit movements. PMID:1891457

  14. Active-Site α-Helix in Papain and the Stability of the Ion Pair RS- · · · ImH+. Ab initio Molecular Orbital Study

    Duijnen, P.Th. van; Thole, B.Th.; Broer, Ria; Nieuwpoort, W. C.

    1980-01-01

    Ab initio MO calculations, using both minimal (STO-3G) and extended (Roos-Siegbahn) basis sets are reported for the systems methanethiol-imidazole, methanethiol-imidazole-formaldehyde, and methanethiol-imidazole-formamide, which, together with a point-change representation of a long α-helix, form models for the active site of papain. It is shown that the large electric field exerted by the helix in the active-site region is responsible for the presence of the essential residues Cys 25 and His...

  15. Finnsjoen study site. Scope of activities and main results

    The Finnsjoen study site was selected in 1977 to provide input to the KBS-1 and KBS-2 performance assessments. The site was later used as a test site for testing new instruments and new site characterization methods, as well as a research site for studying mainly groundwater flow and groundwater transport. All together, the Finnsjoen studies have involved 11 cored boreholes, down to max 700 m depth, and extensive borehole geophysical, geochemical and geohydraulic measurements, as well as rock stress measurements and tracer tests. This report presents the scope of the Finnsjoen studies together with main results. Conceptual uncertainties in assumptions and models are discussed with emphasis on the models used for the performance assessment SKB91. Of special interest for the Finnsjoen study site is the strong influence caused by a subhorizontal fracture zone on groundwater flow, transport and chemistry

  16. The active site of hen egg-white lysozyme: flexibility and chemical bonding

    Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C

  17. An atypical residue in the pore of Varroa destructor GABA-activated RDL receptors affects picrotoxin block and thymol modulation.

    Price, Kerry L; Lummis, Sarah C R

    2014-12-01

    GABA-activated RDL receptors are the insect equivalent of mammalian GABAA receptors, and play a vital role in neurotransmission and insecticide action. Here we clone the pore lining M2 region of the Varroa mite RDL receptor and show that it has 4 atypical residues when compared to M2 regions of most other insects, including bees, which are the major host of Varroa mites. We create mutant Drosophila RDL receptors containing these substitutions and characterise their effects on function. Using two electrode voltage clamp electrophysiology we show that one substitution (T6'M) ablates picrotoxin inhibition and increases the potency of GABA. This mutation also alters the effect of thymol, which enhances both insect and mammalian GABA responses, and is widely used as a miticide. Thymol decreases the GABA EC50 of WT receptors, enhancing responses, but in T6'M-containing receptors it is inhibitory. The other 3 atypical residues have no major effects on either the GABA EC50, the picrotoxin potency or the effect of thymol. In conclusion we show that the RDL 6' residue is important for channel block, activation and modulation, and understanding its function also has the potential to prove useful in the design of Varroa-specific insecticidal agents. PMID:25460510

  18. The Arabidopsis KS-type dehydrin recovers lactate dehydrogenase activity inhibited by copper with the contribution of His residues.

    Hara, Masakazu; Monna, Shuhei; Murata, Takae; Nakano, Taiyo; Amano, Shono; Nachbar, Markus; Wätzig, Hermann

    2016-04-01

    Dehydrin, which is one of the late embryogenesis abundant (LEA) proteins, is involved in the ability of plants to tolerate the lack of water. Although many reports have indicated that dehydrins bind heavy metals, the physiological role of this metal binding has not been well understood. Here, we report that the Arabidopsis KS-type dehydrin (AtHIRD11) recovered the lactate dehydrogenase (LDH) activity denatured by Cu(2+). The LDH activity was partially inhibited by 0.93 μM Cu(2+) but totally inactivated by 9.3 μM Cu(2+). AtHIRD11 recovered the activity of LDH treated with 9.3 μM Cu(2+) in a dose-dependent manner. The recovery activity of AtHIRD11 was significantly higher than those of serum albumin and lysozyme. The conversion of His residues to Ala in AtHIRD11 resulted in the loss of the Cu(2+) binding of the protein as well as the disappearance of the conformational change induced by Cu(2+) that is observed by circular dichroism spectroscopy. The mutant protein showed lower recovery activity than the original AtHIRD11. These results indicate that AtHIRD11 can reactivate LDH inhibited by Cu(2+) via the His residues. This function may prevent physiological damage to plants due to heavy-metal stress. PMID:26940498

  19. Leucine residues in conserved region of 33K protein of bovine adenovirus - 3 are important for binding to major late promoter and activation of late gene expression.

    Kulshreshtha, Vikas; Islam, Azharul; Ayalew, Lisanework E; Tikoo, Suresh K

    2015-09-01

    The L6 region of bovine adenovirus 3 (BAdV-3) encode 33K (spliced) and 22K (unspliced) proteins. Earlier, anti-33K serum detected five major and three minor proteins in BAdV-3 infected cells. Here, we demonstrate that anti-sera raised against L6-22K protein detected two proteins of 42 and 37 kDa in BAdV-3 infected cells and one protein of 42 kDa in transfected cells expressing splice-site variant 22K protein (pC.22K containing substituted splice acceptor/donor sequence). Unlike 22K, 33K stimulated the transcription from the major late promoter (MLP) by binding to the downstream sequence elements (DE). Analysis of the variant proteins demonstrated that amino acids 201-240 of the conserved C-terminus of 33K containing the potential leucine zipper and RS repeat are required for the activation of MLP. Furthermore, amino acid substitution analysis demonstrated that unlike arginine residues of RS repeat, the leucine residues (217, 224, 232 and 240) of the conserved leucine zipper appear required for the binding of 33K to the MLP. PMID:25974868

  20. Accelerator production of tritium activities at the Savannah River Site

    The Savannah River site (SRS) has been chosen as the site to host the accelerator production of tritium (APT). This facility, which will produce tritium for national defense purposes, is a natural extension of the site's original mission. All of the tritium for U.S. weapons needs has been produced at SRS in the heavy water reactors (now shut down) that operated until 1988. Much of the tritium-handling infrastructure still exists at SRS, and the tritium recycling and purification facilities are new and fully operational. This paper summarizes the reasons for the choice of the site and describes some of the early SRS efforts to learn the new technology, to weave into it a strong operations/production ethic, and to prepare the site to host the APT

  1. Health physics and public health activities at hazardous wastes sites

    The Agency for Toxic Substances and Disease Registry (ATSDR) has worked with the U.S. Environmental Protection Agency (EPA) at several sites contaminated with radioactive materials. The Navajo Brown Vandever (B-V) uranium mine site near Bluewater, New Mexico, and the Austin Avenue Radiation Site (AAR) in Lansdowne, Pennsylvania were the subject of ATSDR health advisories. The sites were contamined with uranium or uranium byproducts but the identification of potential health effects and actions taken to prevent or reduce exposures were approached from different perspectives. At B-V contaminants included uranium and mine tailings, radium, and radon. Contaminants at the site and physical hazards were removed. At AAR, radium and radon were located in residential settings. Residents who might have had annual exposures greater than accepted standards or recommendations were relocated and contaminated building demolished

  2. Rapid photometric detection of thymine residues partially flipped out of double helix as a method for direct scanning of point mutations and apurinic DNA sites.

    Logvina, N A; Yakubovskaya, M G; Dolinnaya, N G

    2011-02-01

    A spectroscopic assay for detection of extrahelical thymine residues in DNA heteroduplexes under their modification by potassium permanganate has been developed. The assay is based on increase in absorbance at 420 nm due to accumulation of thymidine oxidation intermediates and soluble manganese dioxide. The analysis was carried out using a set of 19-bp DNA duplexes containing unpaired thymidines opposite tetrahydrofuranyl derivatives mimicking a widespread DNA damage (apurinic (AP) sites) and a library of 50-bp DNA duplexes containing all types of base mismatches in different surroundings. The relation between the selectivity of unpaired T oxidation and the thermal stability of DNA double helix was investigated. The method described here was shown to discriminate between DNA duplexes with one or two AP sites and to reveal thymine-containing mismatches and all noncanonical base pairs in AT-surroundings. Comparative results of CCM analysis and the rapid photometric assay for mismatch detection are demonstrated for the first time in the same model system. The chemical reactivity of target thymines was shown to correlate with local disturbance of double helix at the mismatch site. As the spectroscopic assay does not require the DNA cleavage reaction and gel electrophoresis, it can be easily automated and used for primary screening of somatic mutations. PMID:21568858

  3. Antibacterial and residual antimicrobial activities against Enterococcus faecalis biofilm: A comparison between EDTA, chlorhexidine, cetrimide, MTAD and QMix

    Zhang, Rui; Chen, Min; Lu, Yan; Guo, Xiangjun; Qiao, Feng; Wu, Ligeng

    2015-08-01

    We compared the antibacterial and residual antimicrobial activities of five root canal irrigants (17% EDTA,2% chlorhexidine,0.2% cetrimide, MTAD, and QMix) in a model of Enterococcus faecalis biofilm formation. Sixty dentin blocks with 3-week E. faecalis biofilm were divided into six equal groups and flushed with irrigant for 2 min or left untreated. A blank control group was also established. Antibacterial activities of the irrigants were evaluated by counting colony forming units. To test residual antimicrobial activities, 280 dentin blocks were divided into seven equal groups and flushed with irrigant for 2 min or left untreated and then incubated with E. faecalis suspension for 48 h, or used as a blank. No bacteria were observed in the blank control group. The number of viable E. faecalis was significantly fewer in the irrigant-treated groups compared with the untreated control (P root canal irrigants were effective to some extent against E. faecalis, but QMix and CHX had the strongest, and CHX the longest (up to 36 h), antimicrobial activity.

  4. Radiation dosimetry by neutron or X ray fluorescence activation of residual silver in ionographic emulsions

    A global measuring technique which is sensitive enough to detect small silver contents in films for dosimetry applications is presented. The applications studied are neutron dosimetry by measuring residual silver due to recoil protons in developed emulsions and high dose dosimetry by the detection of photolytic silver in fixed emulsions. An individual fast neutron dosimeter which can be used in radiation protection was developed, along with an automatic data analysis and readout system. Application of this technique to the measurement of high radiation doses (100 to 1 million Gy) via the measurement of photolytic silver in fixed, but undeveloped, emulsions confirms the usefulness of the method

  5. Biochemical characteristics of an alkaline pectate lyase PelA from Volvariella volvacea: roles of the highly conserved N-glycosylation site in its secretion and activity.

    Shi, Aiqin; Hu, Hang; Zheng, Fei; Long, Liangkun; Ding, Shaojun

    2015-04-01

    Alkaline pectate lyases have great application potential in the bioscouring of textiles. They are isolated predominantly from bacteria and a few fungi. Here, we report the biochemical characteristics of a novel alkaline pectate lyase PelA from the basidiomycete Volvariella volvacea. The full-length pelA encodes a 321-amino-acid polypeptide containing a putative 18-residue signal peptide and a pectate lyase family 1 catalytic domain. It contains one conserved and one non-conserved potential N-glycosylation site (N-X-S/T) at the residues N95 and N198, respectively. The enzyme showed optimal activity at 60 °C and pH 10, although it was stable between pH 4 and pH 11. Additional Ca(2+) was not required to measure PelA activity in vitro, but it could significantly enhance its activity and thermal stability. The V max values using polygalacturonic acid as substrate were increased from 50.71 to 89.96 IU mg(-1) by the addition of 0.1 mM Ca(2+), whereas the K m values were decreased from 0.681 to 0.514 mg ml(-1). Site-directed mutagenesis revealed PelA has only one N-glycan attached to the residue N95. This N-glycan is crucial to its efficient secretion and activity possibly due to its role in maintaining the secondary structure of PelA. Amino acid substitution at the residue N198 had no effect on PelA secretion, but resulted in a slight (5.16 %) to modest (27.37 %) decrease in specific activity and less thermal stability, indicating the amino acid itself is also important for activity due to it being highly conserved and because of its proximity to the catalytic site. PMID:25341402

  6. Simple, High-Yield Syntheses of DNA Duplexes Containing Interstrand DNA-DNA Cross-Links Between an N(4) -Aminocytidine Residue and an Abasic Site.

    Gamboa Varela, Jacqueline; Gates, Kent S

    2016-01-01

    The protocol describes the preparation and purification of interstrand DNA-DNA cross-links derived from the reaction of an N(4) -aminocytidine residue with an abasic site in duplex DNA. The procedures employ inexpensive, commercially available chemicals and enzymes to carry out post-synthetic modification of commercially available oligodeoxynucleotides. The yield of cross-linked duplex is typically better than 90%. If purification is required, the cross-linked duplex can be readily separated from single-stranded DNA starting materials by denaturing gel electrophoresis. The resulting covalent hydrazone-based cross-links are stable under physiologically relevant conditions and may be useful for biophysical studies, structural analyses, DNA repair studies, and materials science applications. © 2016 by John Wiley & Sons, Inc. PMID:27248783

  7. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers

  8. Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study.

    Prabhakar, Rajeev; Vreven, Thom; Frisch, Michael J; Morokuma, Keiji; Musaev, Djamaladdin G

    2006-07-13

    In this ONIOM(QM:MM) study, we evaluate the role of the protein surroundings in the mechanism of H2O2 reduction catalyzed by the glutathione peroxidase enzyme, using the whole monomer (3113 atoms in 196 amino acid residues) as a model. A new optimization scheme that allows the full optimization of transition states for large systems has been utilized. It was found that in the presence of the surrounding protein the optimized active site structure bears a closer resemblance to the one in the X-ray structure than that without the surrounding protein. H2O2 reduction occurs through a two-step mechanism. In the first step, the selenolate anion (E-Se(-)) formation occurs with a barrier of 16.4 kcal/mol and is endothermic by 12.0 kcal/mol. The Gln83 residue plays the key role of the proton abstractor, which is in line with the experimental suggestion. In the second step, the O-O bond is cleaved, and selenenic acid (R-Se-OH) and a water molecule are formed. The calculated barrier for this process is 6.0 kcal/mol, and it is exothermic by 80.9 kcal/mol. The overall barrier of 18.0 kcal/mol for H2O2 reduction is in reasonable agreement with the experimentally measured barrier of 14.9 kcal/mol. The protein surroundings has been calculated to exert a net effect of only 0.70 kcal/mol (in comparison to the "active site only" model including solvent effects) on the overall barrier, which is most likely due to the active site being located at the enzyme surface. PMID:16821888

  9. Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase.

    Du, Juan; Say, Rafael F; Lü, Wei; Fuchs, Georg; Einsle, Oliver

    2011-10-27

    Fructose-1,6-bisphosphate (FBP) aldolase/phosphatase is a bifunctional, thermostable enzyme that catalyses two subsequent steps in gluconeogenesis in most archaea and in deeply branching bacterial lineages. It mediates the aldol condensation of heat-labile dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP) to FBP, as well as the subsequent, irreversible hydrolysis of the product to yield the stable fructose-6-phosphate (F6P) and inorganic phosphate; no reaction intermediates are released. Here we present a series of structural snapshots of the reaction that reveal a substantial remodelling of the active site through the movement of loop regions that create different catalytic functionalities at the same location. We have solved the three-dimensional structures of FBP aldolase/phosphatase from thermophilic Thermoproteus neutrophilus in a ligand-free state as well as in complex with the substrates DHAP and FBP and the product F6P to resolutions up to 1.3 Å. In conjunction with mutagenesis data, this pinpoints the residues required for the two reaction steps and shows that the sequential binding of additional Mg(2+) cations reversibly facilitates the reaction. FBP aldolase/phosphatase is an ancestral gluconeogenic enzyme optimized for high ambient temperatures, and our work resolves how consecutive structural rearrangements reorganize the catalytic centre of the protein to carry out two canonical reactions in a very non-canonical type of bifunctionality. PMID:21983965

  10. Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry.

    Kumar, Gnanesh; Mishra, Padmanabh; Anantharam, Vellareddy; Surolia, Avadhesha

    2015-12-01

    A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W102) in the activity of the lectin. PMID:26597132

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

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

    2016-08-01

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

  12. Probing the effect of the non-active-site mutation Y229W in New Delhi metallo-β-lactamase-1 by site-directed mutagenesis, kinetic studies, and molecular dynamics simulations.

    Jiao Chen

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

  13. Effects of the substitution of amino acid residues, through chemical synthesis, on the conformation and activity of antimicrobial peptides

    Regina C. Adão

    2012-06-01

    Full Text Available Antimicrobial peptides make up an assorted group of molecules which contain from 12 to 50 amino acid residues and which may be produced by microorganisms, plants and animals. From the discovery that these biomolecules are lethal to bacteria, inhibiting the pathogenic organism’s growth, and are also related to innate and adapted defense mechanisms, the investigation of such molecules came to be an emergent research field, in which more than 1800 antimicrobial peptides have so far been discovered throughout the last three decades. These molecules are potential representatives of a new generation of antibiotic agents and the main motivation for such use is their activity against a wide variety of pathogens, including Gram-positive and Gram-negative bacteria as well as fungi and viruses. An important class of comprising some of these peptides may be found in anurans, from which it has been isolated, a considerable number of antimicrobial peptides with diverse sequences and structures, including linear and dimeric ones. In this work monomeric chains (CH1 e CH2 of the heterodimeric antimicrobial peptide distinctin (isolated in 1999 from Phyllomedusa distincta anurans, as well as its mutated monomers (CH1-S and CH2-S and the heterodimer itself were synthesized. The distinctin is the peptide with two chains of different sequences (Table 1 bound each other by disulfide bond from the cystein residues constituting the heterodimer. To investigate the effects on the biological activity by amino acids substitution at normal distinctin CH1 and CH2 chains, both were synthesized as well as their similar chains (CH1-S and CH2-S in which the cystein (Fig.1 a residues of each chain were changed by serin residues (Fig. 1 b. The new chains were named mutants. The synthesis was carried out in solid phase, using Fmoc strategy. The heterodimer distinctin was obtained from CH1 and CH2 chains coupling through cystein residues air oxidation. The results from HPLC

  14. The deviant ATP-binding site of the multidrug efflux pump Pdr5 plays an active role in the transport cycle.

    Furman, Christopher; Mehla, Jitender; Ananthaswamy, Neeti; Arya, Nidhi; Kulesh, Bridget; Kovach, Ildiko; Ambudkar, Suresh V; Golin, John

    2013-10-18

    Pdr5 is the founding member of a large subfamily of evolutionarily distinct, clinically important fungal ABC transporters containing a characteristic, deviant ATP-binding site with altered Walker A, Walker B, Signature (C-loop), and Q-loop residues. In contrast to these motifs, the D-loops of the two ATP-binding sites have similar sequences, including a completely conserved aspartate residue. Alanine substitution mutants in the deviant Walker A and Signature motifs retain significant, albeit reduced, ATPase activity and drug resistance. The D-loop residue mutants D340A and D1042A showed a striking reduction in plasma membrane transporter levels. The D1042N mutation localized properly had nearly WT ATPase activity but was defective in transport and was profoundly hypersensitive to Pdr5 substrates. Therefore, there was a strong uncoupling of ATPase activity and drug efflux. Taken together, the properties of the mutants suggest an additional, critical intradomain signaling role for deviant ATP-binding sites. PMID:24019526

  15. SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.

    Del Rizzo, Paul A; Couture, Jean-François; Dirk, Lynnette M A; Strunk, Bethany S; Roiko, Marijo S; Brunzelle, Joseph S; Houtz, Robert L; Trievel, Raymond C

    2010-10-01

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ε-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ε-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ε-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes. PMID:20675860

  16. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation*

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M. A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C.

    2010-01-01

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ϵ-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ϵ-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ϵ-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes. PMID:20675860

  17. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C. (Michigan); (NWU); (Kentucky)

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  18. Atividade residual de diuron, oxyfluorfen e prometryne no controle de Euphorbia heterophylla Residual activity of diuron, oxyfluorfen, and prometryne for Euphorbia heterophylla control

    R.S. Oliveira Jr; J.C. Carneiro; Constantin, J; G. Santos; A.C. Francischini; A.M Oliveira Neto

    2012-01-01

    As aplicações de herbicidas em pré-emergência têm por finalidade a obtenção da atividade residual no início do ciclo das culturas. Assim, o objetivo deste trabalho foi avaliar a atividade residual dos herbicidas diuron, oxyfluorfen e prometryne, aplicados isoladamente ou em misturas, no controle de Euphorbia heterophylla. Oito experimentos foram conduzidos em casa de vegetação, aplicando-se doses dos herbicidas ou das misturas aos 30, 20, 10 e 0 dias antes da semeadura da planta daninha (DAS)...

  19. LRRK2 Kinase Activity and Biology are Not Uniformly Predicted by its Autophosphorylation and Cellular Phosphorylation Site Status

    April Reynolds

    2014-06-01

    Full Text Available Missense mutations in the Leucine Rich Repeat protein Kinase 2 (LRRK2 gene are the most common genetic predisposition to develop Parkinson’s disease (PD LRRK2 is a large multi-domain phosphoprotein with a GTPase domain and a serine/threonine protein kinase domain whose activity is implicated in neuronal toxicity; however the precise mechanism is unknown. LRRK2 autophosphorylates on several serine/threonine residues across the enzyme and is found constitutively phosphorylated on Ser910, Ser935, Ser955 and Ser973, which are proposed to be regulated by upstream kinases. Here we investigate the phosphoregulation at these sites by analyzing the effects of disease-associated mutations Arg1441Cys, Arg1441Gly, Ala1442Pro, Tyr1699Cys, Ile2012Thr, Gly2019Ser, and Ile2020Thr. We also studied alanine substitutions of phosphosite serines 910, 935, 955 and 973 and specific LRRK2 inhibition on autophosphorylation of LRRK2 Ser1292, Thr1491, Thr2483 and phosphorylation at the cellular sites. We found that mutants in the Roc-COR domains, including Arg1441Cys, Arg1441His, Ala1442Pro and Tyr1699Cys, can positively enhance LRRK2 kinase activity while concomitantly inducing the dephosphorylation of the cellular sites. Mutation of the cellular sites individually did not affect LRRK2 intrinsic kinase activity; however, Ser910/935/955/973Ala mutations trended toward increased kinase activity of LRRK2. Increased cAMP levels did not lead to increased LRRK2 cellular site phosphorylation, 14-3-3 binding or kinase activity. In cells, inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser1292 by Calyculin A and okadaic acid sensitive phosphatases, while the cellular sites are dephosphorylated by Calyculin A sensitive phosphatases. These findings indicate that comparative analysis of both Ser1292 and Ser910/935/955/973 phosphorylation sites will provide important and distinct measures of LRRK2 kinase and biological activity in vitro and in vivo.

  20. Human population and activities in Forsmark. Site description

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced.The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations.The data in this description is essential for future evaluations of the impact on the environment and its human population (Environmental Impact Assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments.The actual area for the study is in this report called 'the Forsmark area', an area of 19.5 km2 near Forsmark nuclear power plant. The land use in the Forsmark area differs notably from the land use in Uppsala laen (laen = county). Only 0.04% of the total area is developed (built-up) compared to 4.9% in Uppsala laen and only 4% is agricultural land compared to 25% in the county. Furthermore, there are far more forest, wetlands and water areas in the Forsmark area. The forest area represents as much as 72.5% of the total area.The Forsmark area is uninhabited, and its surroundings are very sparsely populated. In 2002, the population density in Forsmark was 1.8 inhabitants per square kilometre, which was 24 times lower than in Uppsala laen. The population density in the parish has been

  1. Human population and activities in Forsmark. Site description

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced.The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations.The data in this description is essential for future evaluations of the impact on the environment and its human population (Environmental Impact Assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments.The actual area for the study is in this report called 'the Forsmark area', an area of 19.5 km{sup 2} near Forsmark nuclear power plant. The land use in the Forsmark area differs notably from the land use in Uppsala laen (laen = county). Only 0.04% of the total area is developed (built-up) compared to 4.9% in Uppsala laen and only 4% is agricultural land compared to 25% in the county. Furthermore, there are far more forest, wetlands and water areas in the Forsmark area. The forest area represents as much as 72.5% of the total area.The Forsmark area is uninhabited, and its surroundings are very sparsely populated. In 2002, the population density in Forsmark was 1.8 inhabitants per square kilometre, which was 24 times lower than in Uppsala laen. The population density in the

  2. Maize, Sunflower and Barley Sensitivity to the Residual Activity of Clomazone in Soil

    Jelena Gajić Umiljendić

    2012-01-01

    Full Text Available Sensitivity of maize, sunflower and barley to clomazone residues in loamy soil wasassessed in the study using bioassay. Clomazone was applied at a series of concentrationsfrom 0.12 to 12 mg a.i./kg of soil. After 14 days, morphological (shoot height, fresh and dryweight and physiological (content of carotenoids, chlorophyll a and chlorophyll b parameterswere measured. The results showed that morphological parameters are not valid indicatorsof clomazone sensitivity. Based on the results showing inhibition of the physiologicalparameters, I50 values were calculated and used to estimate the difference in sensitivitybetween the species tested. Sunflower was the most sensitive species, while the differencein sensitivity between maize and barley was not significant.Nomenclature: clomazone (2-(2-chlorbenzyl-4,4-dimethyl-1,2-oxazolidin-3-one, maize(Zea mays L., sunflower (Helianthus annuus L., barley (Hordeum vulgare L.

  3. Analysis of binding behavior between dynamic structures of a papain and the peptide consisting of 10 GLY residues

    Nishiyama, Katsuhiko

    2010-07-01

    The binding of 10GLY to dynamic structures of papain was investigated by molecular dynamics and docking simulations. The binding free energies and sites were greatly fluctuated depending on the time and the binding was more stable and existed at the near site of active center when the structural changes in the highly flexible residues in papain were larger. Binding stability and sites would be significantly influenced by the highly flexible residues. Analysis of such residues would provide an important guideline for clarification of enzymatic activities and modification of structural dynamics of such residues would allow us to control enzymatic activities.

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

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

    2015-12-15

    Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg(2+). A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg(2+) from Ca(2+). Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution. PMID:26450964

  5. A comparative study of drug resistance mechanism associated with active site and non-active site mutations: I388N and D425G mutants of acetyl-coenzyme-A carboxylase.

    Zhu, Xiao-Lei; Yang, Guang-Fu

    2012-03-01

    A major concern in the development of acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides is the emergence of resistance as a result of the selection of distinct mutations within the CT domain. Mutations associated with resistance have been demonstrated to include both active sites and non-active sites, including Ile-1781-Leu, Trp- 2027-Cys, Ile-2041-Asn, Asp-2078-Gly, and Gly-2096-Ala (numbered according to the Alopecurus myosuroides plastid ACCase). In the present study, extensive computational simulations, including molecular dynamics (MD) simulations and molecular mechanics-Poisson-Boltzmann surface area (MM/PBSA) calculations, were carried out to compare the molecular mechanisms of active site mutation (I388N) and non-active site mutation (D425G) in Alopecurus myosuroides resistance to some commercial herbicides targeting ACCase, including haloxyfop (HF), diclofop (DF) and fenoxaprop (FR). All of the computational model and energetic results indicated that both I388N and D425G mutations have effects on the conformational change of the binding pocket. The π-π interaction between ligand and Phe377 and Tyr161' residues, which make an important contribution to the binding affinity, was decreased after mutation. As a result, the mutant-type ACCase has a lower affinity for the inhibitor than the wild-type enzyme, which accounts for the molecular basis of herbicidal resistance. The structural and mechanistic insights obtained from the present study will deepen our understanding of the interactions between ACCase and herbicides, which provides a molecular basis for the future design of a promising inhibitor with low resistance risk. PMID:22242795

  6. Neu1 desialylation of sialyl alpha-2,3-linked beta-galactosyl residues of TOLL-like receptor 4 is essential for receptor activation and cellular signaling.

    Amith, Schammim Ray; Jayanth, Preethi; Franchuk, Susan; Finlay, Trisha; Seyrantepe, Volkan; Beyaert, Rudi; Pshezhetsky, Alexey V; Szewczuk, Myron R

    2010-02-01

    The ectodomain of TOLL-like receptors (TLR) is highly glycosylated with several N-linked gylcosylation sites located in the inner concave surface. The precise role of these sugar N-glycans in TLR receptor activation is unknown. Recently, we have shown that Neu1 sialidase and not Neu2, -3 and -4 forms a complex with TLR-2, -3 and -4 receptors on the cell-surface membrane of naïve and activated macrophage cells (Glycoconj J DOI 10.1007/s10719-009-9239-8). Activation of Neu1 is induced by TLR ligands binding to their respective receptors. Here, we show that endotoxin lipopolysaccharide (LPS)-induced MyD88/TLR4 complex formation and subsequent NFkappaB activation is dependent on the removal of alpha-2,3-sialyl residue linked to beta-galactoside of TLR4 by the Neu1 activity associated with LPS-stimulated live primary macrophage cells, macrophage and dendritic cell lines but not with primary Neu1-deficient macrophage cells. Exogenous alpha-2,3 sialyl specific neuraminidase (Streptoccocus pneumoniae) and wild-type T. cruzi trans-sialidase (TS) but not the catalytically inactive mutant TSAsp98-Glu mediate TLR4 dimerization to facilitate MyD88/TLR4 complex formation and NFkappaB activation similar to those responses seen with LPS. These same TLR ligand-induced NFkappaB responses are not observed in TLR deficient HEK293 cells, but are re-established in HEK293 cells stably transfected with TLR4/MD2, and are significantly inhibited by alpha-2,3-sialyl specific Maackia amurensis (MAL-2) lectin, alpha-2,3-sialyl specific galectin-1 and neuraminidase inhibitor Tamiflu but not by alpha-2,6-sialyl specific Sambucus nigra lectin (SNA). Taken together, the findings suggest that Neu1 desialylation of alpha-2,3-sialyl residues of TLR receptors enables in removing a steric hinderance to receptor association for TLR activation and cellular signaling. PMID:19796680

  7. Multi-residue enantiomeric analysis of pharmaceuticals and their active metabolites in the Guadalquivir River basin (South Spain) by chiral liquid chromatography coupled with tandem mass spectrometry.

    López-Serna, Rebeca; Kasprzyk-Hordern, Barbara; Petrović, Mira; Barceló, Damià

    2013-07-01

    This paper describes the development and application of a multi-residue chiral liquid chromatography coupled with tandem mass spectrometry method for simultaneous enantiomeric profiling of 18 chiral pharmaceuticals and their active metabolites (belonging to several therapeutic classes including analgesics, psychiatric drugs, antibiotics, cardiovascular drugs and β-agonists) in surface water and wastewater. To the authors' knowledge, this is the first time an enantiomeric method including such a high number of pharmaceuticals and their metabolites has been reported. Some of the pharmaceuticals have never been studied before in environmental matrices. Among them are timolol, betaxolol, carazolol and clenbuterol. A monitoring programme of the Guadalquivir River basin (South Spain), including 24 sampling sites and five wastewater treatment plants along the basin, revealed that enantiomeric composition of studied pharmaceuticals is dependent on compound and sampling site. Several compounds such as ibuprofen, atenolol, sotalol and metoprolol were frequently found as racemic mixtures. On the other hand, fluoxetine, propranolol and albuterol were found to be enriched with one enantiomer. Such an outcome might be of significant environmental relevance as two enantiomers of the same chiral compound might reveal different ecotoxicity. For example, propranolol was enriched with S(-)-enantiomer, which is known to be more toxic to Pimephales promelas than R(+)-propranolol. Fluoxetine was found to be enriched with S(+)-enantiomer, which is more toxic to P. promelas than R(-)-fluoxetine. PMID:23579471

  8. 76 FR 7226 - Commercial Wind Lease Issuance and Site Characterization Activities; Atlantic Outer Continental...

    2011-02-09

    ... site characterization and assessment data the lessee may submit a construction and operations plan (COP... 30 CFR 285.620-.629. Although BOEMRE does not authorize site characterization activities (i.e... on the environmental effects of reasonably foreseeable site characterization surveys that may...

  9. The status of Yucca Mountain site characterization activities

    The U.S. Department of Energy (DOE) Office of Civilian Radioactive Waste Management is continuing its studies to determine if Yucca Mountain in Nevada can safely isolate high-level nuclear waste for the next ten thousand years. As mandated by Congress in 1987, DOE is studying the rocks, the climate, and the water table at Yucca Mountain to ensure that the site is suitable before building a repository about 305 meters (1,000 feet) below the surface. Yucca Mountain, located 161 kilometers (100 miles) northwest of Las Vegas, lies on the western edge of the Nevada Test Site. Nevada and DOE have been in litigation for almost two years over three environmental permits needed to conduct studies, but recent court decisions have allowed limited work to take place. This paper will examine progress made on the Yucca Mountain Site Characterization Project (YMP) during the past year and continuing into 1992, discuss the complex legal issues that are delaying progress, and describe new site drilling work. Title I and II design work on the underground exploratory studies facility (ESF) also will be discussed

  10. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  11. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria

  12. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    Goodenough, A. E.; Elliot, S. L.; Hart, A. G.

    2009-09-01

    Many widely-accepted ecological concepts are simplified assumptions about complex situations that remain largely untested. One example is the assumption that nest-building species choose nest sites actively when they are not resource limited. This assumption has seen little direct empirical testing: most studies on nest-site selection simply assume that sites are chosen actively (and seek explanations for such behaviour) without considering that sites may be selected randomly. We used 15 years of data from a nestbox scheme in the UK to test the assumption of active nest-site choice in three cavity-nesting bird species that differ in breeding and migratory strategy: blue tit ( Cyanistes caeruleus), great tit ( Parus major) and pied flycatcher ( Ficedula hypoleuca). Nest-site selection was non-random (implying active nest-site choice) for blue and great tits, but not for pied flycatchers. We also considered the relative importance of year-specific and site-specific factors in determining occupation of nest sites. Site-specific factors were more important than year-specific factors for the tit species, while the reverse was true for pied flycatchers. Our results show that nest-site selection, in birds at least, is not always the result of active choice, such that choice should not be assumed automatically in studies of nesting behaviour. We use this example to highlight the need to test key ecological assumptions empirically, and the importance of doing so across taxa rather than for single "model" species.

  13. Toxicity and Residual Activity of Insecticides Against Tamarixia triozae (Hymenoptera: Eulophidae), a Parasitoid of Bactericera cockerelli (Hemiptera: Triozidae).

    Luna-Cruz, Alfonso; Rodríguez-Leyva, Esteban; Lomeli-Flores, J Refugio; Ortega-Arenas, Laura D; Bautista-Martínez, Néstor; Pineda, Samuel

    2015-10-01

    Bactericera cockerelli (Sulc) (Hemiptera: Triozidae) is one of the most economically important pests of potato, tomato, and peppers in Central America, Mexico, the United States, and New Zealand. Its control is based on the use of insecticides; however, recently, the potential of the eulophid parasitoid Tamarixia triozae (Burks) (Hymenoptera: Eulophidae) for population regulation has been studied. Because T. triozae is likely to be exposed to insecticides on crops, the objective of this study was to explore the compatibility of eight insecticides with this parasitoid. The toxicity and residual activity (persistence) of spirotetramat, spiromesifen, beta-cyfluthrin, pymetrozine, azadirachtin, imidacloprid, abamectin, and spinosad against T. triozae adults were assessed using a method based on the residual contact activity of each insecticide on tomato leaf discs collected from treated plants growing under greenhouse conditions. All eight insecticides were toxic to T. triozae. Following the classification of the International Organization of Biological Control, the most toxic were abamectin and spinosad, which could be placed in toxicity categories 3 and 4, respectively. The least toxic were azadirachtin, pymetrozine, spirotetramat, spiromesifen, imidacloprid, and beta-cyfluthrin, which could be placed in toxicity category 2. In terms of persistence, by day 5, 6, 9, 11, 13, 24, and 41 after application, spirotetramat, azadirachtin, spiromesifen, pymetrozine, imidacloprid, beta-cyfluthrin, abamectin, and spinosad could be considered harmless, that is, placed in toxicity category 1 (pest management programs that include T. triozae. PMID:26453717

  14. Transcriptional activation domains stimulate initiation and elongation at different times and via different residues.

    Brown, S. A.; Weirich, C S; Newton, E M; Kingston, R E

    1998-01-01

    Transcriptional activators can stimulate multiple steps in the transcription process. We have used GAL4 fusion proteins to characterize the ability of different transcriptional activation domains to stimulate transcriptional elongation on the hsp70 gene in vitro. Stimulation of elongation apparently occurs via a mechanistic pathway different from that of stimulation of initiation: the herpes simplex virus VP16, heat shock factor 1 (HSF1) and amphipathic helix (AH) activation domains all stimu...

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

    Miao, Yinglong [ORNL; Baudry, Jerome Y [ORNL

    2011-01-01

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

  16. Human population and activities at Simpevarp. Site description

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km2 near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km2, three times lower than in Kalmar laen. The demography statistics show no

  17. Human population and activities at Simpevarp. Site description

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km{sup 2} near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km{sup 2}, three times lower than in Kalmar laen. The

  18. Human population and activities at Simpevarp. Site description

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km{sup 2} near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km{sup 2}, three times lower than in Kalmar laen. The

  19. Measurement of residual 60Co activity induced by atomic-bomb neutrons in Nagasaki and background contribution by environmental neutrons

    Residual 60Co activity in five steel samples induced by neutrons from the Nagasaki atomic bomb has been measured within about 1000 m from the hypocenter. The chemical separation of cobalt and nickel from steel samples was performed, and cobalt-enriched samples were prepared for all samples. Gamma-ray measurements were carried out with a low-background well-type germanium detector. The gamma-ray spectra for five samples were compared with the spectrum of a control sample to ensure that the observed 60Co was actually induced by A-bomb neutrons. The activation of cobalt by environmental neutrons was also investigated. It has been shown that the present 60Co data are consistent with earlier Hashizume's data. (author)

  20. Measurement of residual 60Co activity induced by atomic-bomb neutrons in Nagasaki and background contribution by environmental neutrons.

    Shizuma, Kiyoshi; Endo, Satoru; Hoshi, Masaharu; Takada, Jun; Iwatani, Kazuo; Hasai, Hiromi; Oka, Takamitsu; Shimazaki, Tatsuya; Okumura, Yutaka; Fujita, Shoichiro; Watanabe, Tadaaki; Imanaka, Tetsuji

    2002-12-01

    Residual 60Co activity in five steel samples induced by neutrons from the Nagasaki atomic bomb has been measured within about 1000 m from the hypocenter. The chemical separation of cobalt and nickel from steel samples was performed, and cobalt-enriched samples were prepared for all samples. Gamma-ray measurements were carried out with a low-background well-type germanium detector. The gamma-ray spectra for five samples were compared with the spectrum of a control sample to ensure that the observed 60Co was actually induced by A-bomb neutrons. The activation of cobalt by environmental neutrons was also investigated. It has been shown that the present 60Co data are consistent with earlier Hashizume's data. PMID:12674203

  1. An Examination by Site-Directed Mutagenesis of Putative Key Residues in the Determination of Coenzyme Specificity in Clostridial NAD+-Dependent Glutamate Dehydrogenase

    Joanna Griffin

    2011-01-01

    Full Text Available Sequence and structure comparisons of various glutamate dehydrogenases (GDH and other nicotinamide nucleotide-dependent dehydrogenases have potentially implicated certain residues in coenzyme binding and discrimination. We have mutated key residues in Clostridium symbiosum NAD+-specific GDH to investigate their contribution to specificity and to enhance acceptance of NADPH. Comparisons with E. coli NADPH-dependent GDH prompted design of mutants F238S, P262S, and F238S/P262S, which were purified and assessed at pH 6.0, 7.0, and 8.0. They showed markedly increased catalytic efficiency with NADPH, especially at pH 8.0 (∼170-fold for P262S and F238S/P262S with relatively small changes for NADH. A positive charge introduced through the D263K mutation also greatly increased catalytic efficiency with NADPH (over 100-fold at pH 8 and slightly decreased activity with NADH. At position 242, “P6” of the “core fingerprint,” where NAD+- and NADP+-dependent enzymes normally have Gly or Ala, respectively, clostridial GDH already has Ala. Replacement with Gly produced negligible shift in coenzyme specificity.

  2. Determination of activity by gamma spectrometry of radionuclides present in drums of residues generated in nuclear centrals

    The generation of radioactive residuals in nuclear centrals as CNA I (Atucha I Nuclear Central) and CNE (Embalse Nuclear Central) makes that the measurement of those radionuclides has been a previous stage to the waste management. A method used in those nuclear centrals it is the gamma spectrometry with HPGe detectors, previous to the immobilization of the residual in a cemented matrix, with this the contact with the external agents and its possible dispersion to the atmosphere in the short term is avoided. The ARN (Nuclear Regulatory Authority) of Argentina it carries out periodically intercomparisons and evaluations of the measurement and procedures systems used in the nuclear power stations for the correct measurement and determination of activity of radioactive residuals by gamma spectrometry. In this work an independent method of measurement is exposed to the nuclear power stations. To determine the activity of the residuals by gamma spectrometry deposited in drums, it is required of the precise knowledge of the efficiency curve for such geometry and matrix. Due to the RNA doesn't have a pattern of these characteristics, a mathematical model has been used to obtain this efficiency curve. For it, it is necessary to determine previously: 1) the geometric efficiency or solid angle sustained by the source-detector system (drum-detector) applying a mathematical model described in this work. 2) To estimate the auto-attenuation factor that present the photons in the cemented matrix, these calculations are carried out with a simple equation and its are verified with the Micro Shield 6.10 program. The container commonly used by these nuclear power stations its are drums for 220 liters constructed with SAE 1010 steel and with a thickness of 0.127 cm, with an approximate weight 7.73 Kg., internal diameter of 57.1 cm, and height: 87 cm. The results obtained until the moment register a discrepancy from 5 to 10% with relationship to the measurements carried out by the

  3. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S; Drakou, Evangelia G.; Pantis, John D.

    2013-01-01

    The Natura 2000 network was established across the European Union’s (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries...

  4. The mechanisms of substrates interaction with the active site of Mycobacterium tuberculosis tyrosyl-tRNA synthetase studied by molecular dynamics simulations

    Mykuliak V. V.

    2014-03-01

    Full Text Available Aim. To study the mechanisms of substrates interaction with the active site of Mycobacterium tuberculosis tyrosyl-tRNA synthetase (MtTyrRS. Methods. Complexes of MtTyrRS with tyrosine, ATP and tyrosyl adenylate were constructed by superposition of the MtTyrRS structure and crystallographic structures of bacterial TyrRS. All complexes of MtTyrRS with substrates were investigated by molecular dynamics (MD simulations in solution. Results. It was shown the formation of network of hydrogen bonds between substrates and the MtTyrRS active center, which were stable in the course of MD simulations. ATP binds in the active site both by hydrogen bonds and via electrostatic interactions with Lys231 and Lys234 of catalytic KFGKS motif. Conclusions. The L-tyrosine binding site in the enzyme active site is negatively charged, whereas the ATP binding site contains positive Lys231 and Lys234 residues of catalytic KFGKS motif. The occupancy of H-bonds between substrates and the enzyme evidences a significant conformational mobility of the active site.

  5. Active cancellation of residual amplitude modulation in a frequency-modulation based Fabry-Perot interferometer

    Yu, Yinan; Wang, Yicheng; Pratt, Jon R.

    2016-03-01

    Residual amplitude modulation (RAM) is one of the most common noise sources known to degrade the sensitivity of frequency modulation spectroscopy. RAM can arise as a result of the temperature dependent birefringence of the modulator crystal, which causes the orientation of the crystal's optical axis to shift with respect to the polarization of the incident light with temperature. In the fiber-based optical interferometer used on the National Institute of Standards and Technology calculable capacitor, RAM degrades the measured laser frequency stability and correlates with the environmental temperature fluctuations. We have demonstrated a simple approach that cancels out excessive RAM due to polarization mismatch between the light and the optical axis of the crystal. The approach allows us to measure the frequency noise of a heterodyne beat between two lasers individually locked to different resonant modes of a cavity with an accuracy better than 0.5 ppm, which meets the requirement to further determine the longitudinal mode number of the cavity length. Also, this approach has substantially mitigated the temperature dependency of the measurements of the cavity length and consequently the capacitance.

  6. Replacement of a phenylalanine by a tyrosine in the active site confers fructose-6-phosphate aldolase activity to the transaldolase of Escherichia coli and human origin.

    Schneider, Sarah; Sandalova, Tatyana; Schneider, Gunter; Sprenger, Georg A; Samland, Anne K

    2008-10-31

    Based on a structure-assisted sequence alignment we designed 11 focused libraries at residues in the active site of transaldolase B from Escherichia coli and screened them for their ability to synthesize fructose 6-phosphate from dihydroxyacetone and glyceraldehyde 3-phosphate using a newly developed color assay. We found one positive variant exhibiting a replacement of Phe(178) to Tyr. This mutant variant is able not only to transfer a dihydroxyacetone moiety from a ketose donor, fructose 6-phosphate, onto an aldehyde acceptor, erythrose 4-phosphate (14 units/mg), but to use it as a substrate directly in an aldolase reaction (7 units/mg). With a single amino acid replacement the fructose-6-phosphate aldolase activity was increased considerably (>70-fold compared with wild-type). Structural studies of the wild-type and mutant protein suggest that this is due to a different H-bond pattern in the active site leading to a destabilization of the Schiff base intermediate. Furthermore, we show that a homologous replacement has a similar effect in the human transaldolase Taldo1 (aldolase activity, 14 units/mg). We also demonstrate that both enzymes TalB and Taldo1 are recognized by the same polyclonal antibody. PMID:18687684

  7. Bioactive Properties of Phaseolus lunatus (Lima Bean) and Vigna unguiculata (Cowpea) Hydrolyzates Incorporated into Pasta. Residual Activity after Pasta Cooking.

    Drago, Silvina R; Franco-Miranda, Hanai; Cian, Raúl E; Betancur-Ancona, David; Chel-Guerrero, Luis

    2016-09-01

    The aims of the study were to study the inclusion of P. lunatus (PLH) and V. unguiculata (VUH) protein hydrolyzates with bioactive properties into a pasta-extruded product and determine residual activity after extrusion or pasta cooking. Both protein hydrolyzates showed angiotensin-converting enzyme inhibition (ACEI) and antioxidant activity (TEAC). PLH showed higher ACEI but lower TEAC than VUH (97.19 ± 0.23 vs. 91.95 ± 0.29 % and 244.7 ± 3.4 vs. 293.7 ± 3.3 μmol Trolox/g, respectively). They were included at 5 or 10 % into wheat pasta. Control pasta had the lowest ACEI activity or TEAC (22.01 ± 0.76 % or 14.14 ± 1.28 μmol Trolox/g, respectively). Higher activity remained in pasta with PLH than VUH after extrusion, and higher the level of addition, higher the ACEI was. Pasta had practically the same ACEI activity after cooking, thus active compounds were not lost by temperature or lixiviation. Regarding TEAC, higher activity remained in pasta with 10 % VUH (31.84 ± 0.17 μmol Trolox/g). Other samples with hydrolyzates had the same activity. After cooking, pasta with hydrolyzates had higher TEAC values than control, but these were not modified by the level of incorporation. Moreover, the profile changed because pasta with PLH had the highest TEAC values (21.39 ± 0.01 and 20.34 ± 0.15 for 5 or 10 % hydrolyzates, respectively). Cooking decreased this activity (~ 20 %), for all samples. Although a certain loss of antioxidant activity was observed, pasta could be a good vehicle for bioactive compounds becoming a functional food. PMID:27422785

  8. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    2011-05-03

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... from eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of 1992. DATES: In our Federal Register Notice of November 24, 2010, (75...

  9. Determination of platinum group metal catalyst residues in active pharmaceutical ingredients by means of total reflection X-ray spectrometry

    Marguí, Eva, E-mail: eva.margui@udg.edu [Department of Chemistry, University of Girona, Campus Montilivi, 17071 Girona (Spain); Queralt, Ignasi, E-mail: iqueralt@ictja.csic.es [Laboratory of X-ray Analytical Applications, Institute of Earth Sciences “Jaume Almera”, CSIC, Solé Sabarís s/n, 08028 Barcelona (Spain); Hidalgo, Manuela, E-mail: manuela.hidalgo@udg.edu [Department of Chemistry, University of Girona, Campus Montilivi, 17071 Girona (Spain)

    2013-08-01

    The control of metal catalyst residues (i.e., platinum group metals (PGMs)) in different stages of the manufacturing processes of the active pharmaceutical ingredients (APIs) and, especially, in the final product is crucial. For API specimens, there are strict guidelines to limit the levels of metal residues based on their individual levels of safety concern. For PGMs the concentration limit has been established at 10 mg/kg in the API. Therefore great effort is currently being devoted to the development of new and simple procedures to control metals in pharmaceuticals. In the present work, an analytical methodology based on benchtop total reflection X-ray fluorescence spectrometry (TXRF) has been developed for the rapid and simple determination of some PGM catalyst impurities (Rh, Pd, Ir and Pt) in different types of API samples. An evaluation of different sample treatments (dissolution and digestion of the solid pharmaceutical samples) has been carried out and the developed methodologies have been validated according to the analytical parameters to be considered and acceptance criteria for PGM determination according to the United States Pharmacopeia (USP). Limits of quantification obtained for PGM metals were in the range of 2–4 mg/kg which are satisfactory according to current legislation. From the obtained results it is shown that the developed TXRF method can be implemented in the pharmaceutical industries to increase productivity of the laboratory; offering an interesting and complementary analytical tool to other atomic spectroscopic methods. - Highlights: • A TXRF method for PGM catalyst residue determination in API samples is presented. • Analysis can be performed using 10 μL of the internal standardized dissolved API. • The method is rapid, simple and suitable according to the USP requirements.

  10. Determination of platinum group metal catalyst residues in active pharmaceutical ingredients by means of total reflection X-ray spectrometry

    The control of metal catalyst residues (i.e., platinum group metals (PGMs)) in different stages of the manufacturing processes of the active pharmaceutical ingredients (APIs) and, especially, in the final product is crucial. For API specimens, there are strict guidelines to limit the levels of metal residues based on their individual levels of safety concern. For PGMs the concentration limit has been established at 10 mg/kg in the API. Therefore great effort is currently being devoted to the development of new and simple procedures to control metals in pharmaceuticals. In the present work, an analytical methodology based on benchtop total reflection X-ray fluorescence spectrometry (TXRF) has been developed for the rapid and simple determination of some PGM catalyst impurities (Rh, Pd, Ir and Pt) in different types of API samples. An evaluation of different sample treatments (dissolution and digestion of the solid pharmaceutical samples) has been carried out and the developed methodologies have been validated according to the analytical parameters to be considered and acceptance criteria for PGM determination according to the United States Pharmacopeia (USP). Limits of quantification obtained for PGM metals were in the range of 2–4 mg/kg which are satisfactory according to current legislation. From the obtained results it is shown that the developed TXRF method can be implemented in the pharmaceutical industries to increase productivity of the laboratory; offering an interesting and complementary analytical tool to other atomic spectroscopic methods. - Highlights: • A TXRF method for PGM catalyst residue determination in API samples is presented. • Analysis can be performed using 10 μL of the internal standardized dissolved API. • The method is rapid, simple and suitable according to the USP requirements

  11. Effects of polyacrylamide, biopolymer, and biochar on decomposition of soil organic matter and 14C-labeled plant residues as determined by enzyme activities

    Mahmoud Awad, Yasser; Ok, Young Sik; Kuzyakov, Yakov

    2014-05-01

    Application of polymers for the improvement of aggregate structure and reduction of soil erosion may alter the availability and decomposition of plant residues. In this study, we assessed the effects of anionic polyacrylamide (PAM), synthesized biopolymer (BP), and biochar (BC) on the decomposition of 14C-labeled maize residue in sandy and sandy loam soils. Specifically, PAM and BP with or without 14C-labeled plant residue were applied at 400 kg ha-1, whereas BC was applied at 5000 kg ha-1, after which the soils were incubated for 80 days at 22 oC. Initially, plant residue decomposition was much higher in untreated sandy loam soil than in sandy soil. Nevertheless, the stimulating effects of BP and BC on the decomposition of plant residue were more pronounced in sandy soil, where it accounted for 13.4% and 23.4% of 14C input, respectively, whereas in sandy loam soil, the acceleration of plant residue decomposition by BP and BC did not exceed 2.6% and 14.1%, respectively, compared to untreated soil with plant residue. The stimulating effects of BP and BC on the decomposition of plant residue were confirmed based on activities of β-cellobiohydrolase, β-glucosidase, and chitinase in both soils. In contrast to BC and BP, PAM did not increase the decomposition of native or added C in both soils.

  12. Measurement of residual 152Eu activity induced by atomic bomb neutrons in Nagasaki and the contribution of environmental neutrons to this activity

    Residual 152Eu activities induced by neutrons from the Nagasaki atomic bomb were measured for nine mineral samples located up to 1,061 m in the slant range and one control sample at 2,850 m from the hypocenter. A chemical separation to prepare europium-enriched samples was performed for all samples, and gamma ray measurements were carried out with a low background well-type germanium detector. In this paper, the measured specific activities of 152Eu are compared with activation calculations based on the DS86 neutron fluence and the 93Rev one. The calculated-to-measured ratios are also compared with those of 60Co and 36Cl. The present results indicate that the measurements agree to the calculation within a factor of three as observed in the nuclear tests at Nevada. The activation level of environmental neutrons and the detection limit for 152Eu are also discussed. (author)

  13. Measurement of residual 152Eu activity induced by atomic bomb neutrons in Nagasaki and the contribution of environmental neutrons to this activity.

    Shizuma, Kiyoshi; Endo, Satoru; Hoshi, Masaharu; Takada, Jun; Ishikawa, Masayori; Iwatani, Kazuo; Hasai, Hiromi; Oka, Takamitsu; Fujita, Shoichiro; Watanabe, Tadaaki; Yamashita, Tomoaki; Imanaka, Tetsuji

    2003-06-01

    Residual 152Eu activities induced by neutrons from the Nagasaki atomic bomb were measured for nine mineral samples located up to 1,061 m in the slant range and one control sample at 2,850 m from the hypocenter. A chemical separation to prepare europium-enriched samples was performed for all samples, and gamma ray measurements were carried out with a low background well-type germanium detector. In this paper, the measured specific activities of 152Eu are compared with activation calculations based on the DS86 neutron fluence and the 93Rev one. The calculated-to-measured ratios are also compared with those of 60Co and 36Cl. The present results indicate that the measurements agree to the calculation within a factor of three as observed in the nuclear tests at Nevada. The activation level of environmental neutrons and the detection limit for 152Eu are also discussed. PMID:13678342

  14. Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae

    Daniel, Bastian; Wallner, Silvia; Steiner, Barbara; Oberdorfer, Gustav; Kumar, Prashant; van der Graaff, Eric; Roitsch, Thomas; Sensen, Christoph W.; Gruber, Karl; Macheroux, Peter

    2016-01-01

    Berberine bridge enzyme-like (BBE-like) proteins form a multigene family (pfam 08031), which is present in plants, fungi and bacteria. They adopt the vanillyl alcohol-oxidase fold and predominantly show bi-covalent tethering of the FAD cofactor to a cysteine and histidine residue, respectively. The Arabidopsis thaliana genome was recently shown to contain genes coding for 28 BBE-like proteins, while featuring four distinct active site compositions. We determined the structure of a member of the AtBBE-like protein family (termed AtBBE-like 28), which has an active site composition that has not been structurally and biochemically characterized thus far. The most salient and distinguishing features of the active site found in AtBBE-like 28 are a mono-covalent linkage of a histidine to the 8α-position of the flavin-isoalloxazine ring and the lack of a second covalent linkage to the 6-position, owing to the replacement of a cysteine with a histidine. In addition, the structure reveals the interaction of a glutamic acid (Glu426) with an aspartic acid (Asp369) at the active site, which appear to share a proton. This arrangement leads to the delocalization of a negative charge at the active site that may be exploited for catalysis. The structure also indicates a shift of the position of the isoalloxazine ring in comparison to other members of the BBE-like family. The dioxygen surrogate chloride was found near the C(4a) position of the isoalloxazine ring in the oxygen pocket, pointing to a rapid reoxidation of reduced enzyme by dioxygen. A T-DNA insertional mutant line for AtBBE-like 28 results in a phenotype, that is characterized by reduced biomass and lower salt stress tolerance. Multiple sequence analysis showed that the active site composition found in AtBBE-like 28 is only present in the Brassicaceae, suggesting that it plays a specific role in the metabolism of this plant family. PMID:27276217

  15. Definition of a physiologic aging autoantigen by using synthetic peptides of membrane protein band 3: localization of the active antigenic sites.

    Kay, M M; Marchalonis, J J; Hughes, J; Watanabe, K; Schluter, S F

    1990-08-01

    Senescent cell antigen (SCA), an aging antigen, is a protein that appears on old cells and marks them for removal by the immune system in mammals. It is derived from band 3, a ubiquitous membrane transport protein found in diverse cell types and tissues. We have used synthetic peptides to identify aging antigenic sites on band 3, using a competitive inhibition assay and immunoblotting with IgG directed against the aging antigen on old cells. Results indicate that: (i) the active antigenic sites of the aging antigen reside on membrane protein band 3 residues that are extracellular regions implicated in anion transport (residues 538-554 and 788-827); (ii) a putative ankyrin-binding-region peptide is not involved in SCA activity; and (iii) carbohydrate moieties are not required for the antigenicity or recognition of SCA because synthetic peptides alone abolish binding of senescent cell IgG to erythrocytes. One of the putative transport sites that contributes to the aging antigen is located toward the carboxyl terminus. A model of band 3 is presented. Localization of the active antigenic site on the band 3 molecule facilitates definition of the molecular changes occurring during aging that initiate molecular as well as cellular degeneration. PMID:1696010

  16. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  17. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation's energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization's ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization's commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans

  18. Redox-active tyrosine residue in the microcin J25 molecule

    Chalon, Miriam C. [Departamento de Bioquimica de la Nutricion, Instituto Superior de Investigaciones Biologicas (Consejo Nacional de Investigaciones Cientificas y Tecnicas-Universidad Nacional de Tucuman) and Instituto de Quimica Biologica ' Dr Bernabe Bloj' , Chacabuco 461, 4000 San Miguel de Tucuman, Tucuman (Argentina); Wilke, Natalia [CIQUIBIC, Dpto. de Quimica Biologica, Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Pabellon Argentina, Ciudad Universitaria, X5000HUA, Cordoba (Argentina); Pedersen, Jens; Rufini, Stefano [Department of Biology, University of Rome Tor Vergata 00133, Rome (Italy); Morero, Roberto D.; Cortez, Leonardo; Chehin, Rosana N.; Farias, Ricardo N. [Departamento de Bioquimica de la Nutricion, Instituto Superior de Investigaciones Biologicas (Consejo Nacional de Investigaciones Cientificas y Tecnicas-Universidad Nacional de Tucuman) and Instituto de Quimica Biologica ' Dr Bernabe Bloj' , Chacabuco 461, 4000 San Miguel de Tucuman, Tucuman (Argentina); Vincent, Paula A., E-mail: pvincent@fbqf.unt.edu.ar [Departamento de Bioquimica de la Nutricion, Instituto Superior de Investigaciones Biologicas (Consejo Nacional de Investigaciones Cientificas y Tecnicas-Universidad Nacional de Tucuman) and Instituto de Quimica Biologica ' Dr Bernabe Bloj' , Chacabuco 461, 4000 San Miguel de Tucuman, Tucuman (Argentina)

    2011-03-18

    Research highlights: {yields} Cyclic voltammetry measurements showed irreversible oxidation of MccJ25 and MccJ25 (Y9F). {yields} Infrared spectroscopy studies showed that only Tyr9 could be deprotonated upon chemical oxidation. {yields} Formation of a long-lived tyrosyl radical in the native MccJ25 oxidized by H{sub 2}O{sub 2} was demonstrated. {yields} Tyr9 but not Tyr20 can be easily oxidized and form a tyrosyl radical. -- Abstract: Microcin J25 (MccJ25) is a 21 amino acid lasso-peptide antibiotic produced by Escherichia coli and composed of an 8-residues ring and a terminal 'tail' passing through the ring. We have previously reported two cellular targets for this antibiotic, bacterial RNA polymerase and the membrane respiratory chain, and shown that Tyr9 is essential for the effect on the membrane respiratory chain which leads to superoxide overproduction. In the present paper we investigated the redox behavior of MccJ25 and the mutant MccJ25 (Y9F). Cyclic voltammetry measurements showed irreversible oxidation of both Tyr9 and Tyr20 in MccJ25, but infrared spectroscopy studies demonstrated that only Tyr9 could be deprotonated upon chemical oxidation in solution. Formation of a long-lived tyrosyl radical in the native MccJ25 oxidized by H{sub 2}O{sub 2} was demonstrated by Electron Paramagnetic Resonance Spectroscopy; this radical was not detected when the reaction was carried out with the MccJ25 (Y9F) mutant. These results show that the essential Tyr9, but not Tyr20, can be easily oxidized and form a tyrosyl radical.

  19. Redox-active tyrosine residue in the microcin J25 molecule

    Research highlights: → Cyclic voltammetry measurements showed irreversible oxidation of MccJ25 and MccJ25 (Y9F). → Infrared spectroscopy studies showed that only Tyr9 could be deprotonated upon chemical oxidation. → Formation of a long-lived tyrosyl radical in the native MccJ25 oxidized by H2O2 was demonstrated. → Tyr9 but not Tyr20 can be easily oxidized and form a tyrosyl radical. -- Abstract: Microcin J25 (MccJ25) is a 21 amino acid lasso-peptide antibiotic produced by Escherichia coli and composed of an 8-residues ring and a terminal 'tail' passing through the ring. We have previously reported two cellular targets for this antibiotic, bacterial RNA polymerase and the membrane respiratory chain, and shown that Tyr9 is essential for the effect on the membrane respiratory chain which leads to superoxide overproduction. In the present paper we investigated the redox behavior of MccJ25 and the mutant MccJ25 (Y9F). Cyclic voltammetry measurements showed irreversible oxidation of both Tyr9 and Tyr20 in MccJ25, but infrared spectroscopy studies demonstrated that only Tyr9 could be deprotonated upon chemical oxidation in solution. Formation of a long-lived tyrosyl radical in the native MccJ25 oxidized by H2O2 was demonstrated by Electron Paramagnetic Resonance Spectroscopy; this radical was not detected when the reaction was carried out with the MccJ25 (Y9F) mutant. These results show that the essential Tyr9, but not Tyr20, can be easily oxidized and form a tyrosyl radical.

  20. Residual 152Eu and 60Co activities induced by neutrons from the Hiroshima atomic bomb

    Specific activities of 152Eu:Eu in stone samples exposed to the Hiroshima atomic bomb were determined for 70 samples up to a 1,500-m slant range from the epicenter. The specific activities of 60Co:Co were also determined for six samples near the Hiroshima hypocenter. First, the 152Eu data were investigated to find out the directional dependence of neutron activation. Directional anisotropy was not definite; however, there was an indication that the activation in the west-southwest was lower than in other directions. Second, measured 152Eu and 60Co radioactivity data were compared with activation calculations based on DS86 neutrons. It is clearly shown that the measured data are lower than the calculation near the hypocenter and vice versa at long distances beyond 1,000 m. The calculated-to-measured ratios of 152Eu are 1.6 at the hypocenter, 1.0 at approximately 900 m, and 0.05 at a 1,500-m slant range. Present results indicate that systematic errors exist in the DS86 neutrons concerning the source-term spectrum, neutron transport calculations in air, and/or activation measurements

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

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

    2016-01-01

    Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with

  2. Assessment of former uranium sites and their ongoing remediation activities

    Carried out analysis on tailing's buildings operation shows that period for engineer barrier service, taking into account any catastrophic natural impacts, is too little in comparison with life-time of long-live radionuclides. Priorities should be defined by danger degree and isolation costs (protection optimization), therefore uncommon, non-traditional methods, developed taking into account natural factors for long-live waste (radionuclides) isolation are necessary. That's why, it is necessary to carry out specialized research and development, design and exploratory and other works on monitoring of social-ecological condition of these sites, as well as on demographic public diseases, living in these regions.

  3. Production of activated carbon from biodiesel solid residues: An alternative for hazardous metal sorption from aqueous solution.

    Ribeiro, Rita F L; Soares, Vitor C; Costa, Letícia M; Nascentes, Clésia C

    2015-10-01

    In this study, the potential for the sorption of Pb(2+) and Cd(2+) from aqueous solutions using HNO3-treated activated carbon (TAC) obtained from radish press cake (Raphanus sativus L.), a solid residue from biodiesel production, was investigated. Activated carbon (AC) was obtained by physical activation with CO2(g). Chemical modification with HNO3 was employed to increase the sorption capability of the AC. The sorption of Pb(2+) and Cd(2+) was studied in monometallic systems in equilibrium with different metal-ion concentrations (10-400 mg L(-1)). The experimental sorption equilibrium data were fit to the Langmuir and Freundlich isotherm models. The maximum sorption capacity (qmax) obtained for AC from the Langmuir isotherm was 45.5 mg g(-1) for Cd(2+) and 250 mg g(-1) for Pb(2+). Moreover, TAC presented qmax of 166.7 mg g(-1) (1.48 mmol g(-1)) for Cd(2+) and 500.0 mg g(-1) (2.41 mmol g(-1)) for Pb(2+)showing the effect of chemical modification. Sorption-desorption studies showed that the interaction between metals and TAC is reversible and this sorbent can be reused for several consecutive cycles. Furthermore, the sorption of Cd(2+) and Pb(2+) by TAC was not affected by the presence of competing ions. The experimental data obtained in this study indicated that this solid residue is viable for the production of sorbents that remove metals, such as cadmium and lead, from wastewaters and thereby contribute to the sustainable development of the production of biodiesel. PMID:26233585

  4. Life stage toxicity and residual activity of insecticides to codling moth and oriental fruit moth (Lepidoptera: Tortricidae).

    Magalhaes, Leonardo C; Walgenbach, James F

    2011-12-01

    The codling moth, Cydia pomonella (L.), and oriental fruit moth, Grapholita molesta (Busck), are two key pests of apple (Malus domestica Borkh.) in North Carolina. Growers extensively relied on organophosphate insecticides, primarily azinphosmethyl, for > 40 yr to manage these pests. Because of organophosphate resistance development and regulatory actions, growers are transitioning to management programs that use new, reduced-risk, and OP-replacement insecticides. This study evaluated the toxicity of a diversity of replacement insecticides to eggs, larvae, and adults, as well as an assessment of their residual activity, to codling moth and oriental fruit moth. Laboratory-susceptible strains of both species were used for all bioassays. Fresh field-harvested apples were used as a media for assessing the ovicidal activity of insecticides. For larval studies, insecticides were topically applied to the surface of lima bean-based diet, onto which neonates were placed. Toxicity was based on two measures of mortality; 5-d mortality and development to adult stage. Ovicidal bioassays showed that oriental fruit moth eggs were generally more tolerant than codling moth eggs to insecticides, with novaluron, acetamiprid, and azinphoshmethyl having the highest levels of toxicity to eggs of both species. In contrast, codling moth larvae generally were more tolerant than oriental fruit moth to most insecticides. Methoxyfenozide and pyriproxyfen were the only insecticides with lower LC50 values against codling moth than oriental fruit moth neonates. Moreover, a number of insecticides, particularly the IGRs methoxyfenozide and novaluron, the anthranilic diamide chlorantriliprole, and the spinosyn spinetoram, provided equal or longer residual activity against codling moth compared with azinphosmethyl in field studies. Results are discussed in relation to their use in devising field use patterns of insecticides and for insecticide resistance monitoring programs. PMID:22299357

  5. Determination of platinum group metal catalyst residues in active pharmaceutical ingredients by means of total reflection X-ray spectrometry

    Marguí, Eva; Queralt, Ignasi; Hidalgo, Manuela

    2013-08-01

    The control of metal catalyst residues (i.e., platinum group metals (PGMs)) in different stages of the manufacturing processes of the active pharmaceutical ingredients (APIs) and, especially, in the final product is crucial. For API specimens, there are strict guidelines to limit the levels of metal residues based on their individual levels of safety concern. For PGMs the concentration limit has been established at 10 mg/kg in the API. Therefore great effort is currently being devoted to the development of new and simple procedures to control metals in pharmaceuticals. In the present work, an analytical methodology based on benchtop total reflection X-ray fluorescence spectrometry (TXRF) has been developed for the rapid and simple determination of some PGM catalyst impurities (Rh, Pd, Ir and Pt) in different types of API samples. An evaluation of different sample treatments (dissolution and digestion of the solid pharmaceutical samples) has been carried out and the developed methodologies have been validated according to the analytical parameters to be considered and acceptance criteria for PGM determination according to the United States Pharmacopeia (USP). Limits of quantification obtained for PGM metals were in the range of 2-4 mg/kg which are satisfactory according to current legislation. From the obtained results it is shown that the developed TXRF method can be implemented in the pharmaceutical industries to increase productivity of the laboratory; offering an interesting and complementary analytical tool to other atomic spectroscopic methods.

  6. In vitro residual anti-bacterial activity of difloxacin, sarafloxacin and their photoproducts after photolysis in water

    Kusari, Souvik; Prabhakaran, Deivasigamani; Lamshoeft, Marc [Institut fuer Umweltforschung (INFU), Technische Universitaet Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund (Germany); Spiteller, Michael, E-mail: m.spiteller@infu.uni-dortmund.d [Institut fuer Umweltforschung (INFU), Technische Universitaet Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund (Germany)

    2009-10-15

    Fluoroquinolones like difloxacin (DIF) and sarafloxacin (SARA) are adsorbed in soil and enter the aquatic environment wherein they are subjected to photolytic degradation. To evaluate the fate of DIF and SARA, their photolysis was performed in water under stimulated natural sunlight conditions. DIF primarily degrades to SARA. On prolonged photodegradation, seven photoproducts were elucidated by HR-LC-MS/MS, three of which were entirely novel. The residual anti-bacterial activities of DIF, SARA and their photoproducts were studied against a group of pathogenic strains. DIF and SARA revealed potency against both Gram-positive and -negative bacteria. The photoproducts also exhibited varying degrees of efficacies against the tested bacteria. Even without isolating the individual photoproducts, their impact on the aquatic environment could be assessed. Therefore, the present results call for prudence in estimating the fate of these compounds in water and in avoiding emergence of resistance in bacteria caused by the photoproducts of DIF and SARA. - Assessment of the residual anti-bacterial efficacies of difloxacin, sarafloxacin and their photoproducts in water, and estimating their impact on the aquatic environment in inducing resistance to microorganisms.

  7. In vitro residual anti-bacterial activity of difloxacin, sarafloxacin and their photoproducts after photolysis in water

    Fluoroquinolones like difloxacin (DIF) and sarafloxacin (SARA) are adsorbed in soil and enter the aquatic environment wherein they are subjected to photolytic degradation. To evaluate the fate of DIF and SARA, their photolysis was performed in water under stimulated natural sunlight conditions. DIF primarily degrades to SARA. On prolonged photodegradation, seven photoproducts were elucidated by HR-LC-MS/MS, three of which were entirely novel. The residual anti-bacterial activities of DIF, SARA and their photoproducts were studied against a group of pathogenic strains. DIF and SARA revealed potency against both Gram-positive and -negative bacteria. The photoproducts also exhibited varying degrees of efficacies against the tested bacteria. Even without isolating the individual photoproducts, their impact on the aquatic environment could be assessed. Therefore, the present results call for prudence in estimating the fate of these compounds in water and in avoiding emergence of resistance in bacteria caused by the photoproducts of DIF and SARA. - Assessment of the residual anti-bacterial efficacies of difloxacin, sarafloxacin and their photoproducts in water, and estimating their impact on the aquatic environment in inducing resistance to microorganisms.

  8. Synthesis and characterization of 18F-labeled active site inhibited factor VII (ASIS)

    Erlandsson, Maria; Nielsen, Carsten Haagen; Jeppesen, Troels Elmer;

    2015-01-01

    Activated factor VII blocked in the active site with Phe-Phe-Arg-chloromethyl ketone (active site inhibited factor VII (ASIS)) is a 50-kDa protein that binds with high affinity to its receptor, tissue factor (TF). TF is a transmembrane glycoprotein that plays an important role in, for example......, thrombosis, metastasis, tumor growth, and tumor angiogenesis. The aim of this study was to develop an 18F-labeled ASIS derivative to assess TF expression in tumors. Active site inhibited factor VII was labeled using N-succinimidyl-4-[18F]fluorobenzoate, and the [18F]ASIS was purified on a PD-10 desalting...

  9. Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

    Pegan, Scott D. [Univ. of Denver, CO (United States); Rukseree, Kamolchanok [National Center for Genetic Engineering and Biotechnology (BIOTEC), Tha Khlong (Thailand); Capodagli, Glenn C. [Univ. of Denver, CO (United States); Baker, Erica A. [Univ. of Denver, CO (United States); Krasnykh, Olga [Univ. of Illinois, Chicago, IL (United States); Franzblau, Scott G. [Univ. of Illinois, Chicago, IL (United States); Mesecar, Andrew D. [Purdue Univ., West Lafayette, IN (United States)

    2013-01-08

    The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

  10. Enzyme catalysis via control of activation entropy: site-directed mutagenesis of 6,7-dimethyl-8-ribityllumazine synthase.

    Fischer, Markus; Haase, Ilka; Kis, Klaus; Meining, Winfried; Ladenstein, Rudolf; Cushman, Mark; Schramek, Nicholas; Huber, Robert; Bacher, Adelbert

    2003-02-21

    6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase) catalyses the penultimate step in the biosynthesis of riboflavin. In Bacillus subtilis, 60 lumazine synthase subunits form an icosahedral capsid enclosing a homotrimeric riboflavin synthase unit. The ribH gene specifying the lumazine synthase subunit can be expressed in high yield. All amino acid residues exposed at the surface of the active site cavity were modified by PCR assisted mutagenesis. Polar amino acid residues in direct contact with the enzyme substrates, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and 3,4-dihydroxy-2-butanone 4-phosphate, could be replaced with relative impunity with regard to the catalytic properties. Only the replacement of Arg127, which forms a salt bridge with the phosphate group of 3,4-dihydroxy-2-butanone 4-phosphate, reduced the catalytic rate by more than one order of magnitude. Replacement of His88, which is believed to assist in proton transfer reactions, reduced the catalytic activity by about one order of magnitude. Surprisingly, the activation enthalpy deltaH of the lumazine synthase reaction exceeds that of the uncatalysed reaction. On the other hand, the free energy of activation deltaG of the uncatalysed reaction is characterised by a large entropic term (TdeltaS) of -37.8 kJmol(-1), whereas the entropy of activation (TdeltaS) of the enzyme-catalysed reaction is -6.7 kJmol(-1). This suggests that the rate enhancement by the enzyme is predominantly achieved by establishing a favourable topological relation of the two substrates, whereas acid/base catalysis may play a secondary role. PMID:12581640

  11. Possibility of Independence in ADL (Activities of Daily Living) for Patients with Cervical Spinal Cord Injuries : An Evaluation based on the Zancolli Classification of Residual Arm Functions

    Yoshimura, Osamu; Takayanagi, Kiyomi; Kobayashi, Ryuji; Hosoda, Masataka; Minematsu, Akira; Sasaki, Hisato; Maejima, Hiroshi; Matsuda, Yuiti; Tanaka, Satiko; Matsuo, Akihisa; Kanemura, Naohiko

    1998-01-01

    For patients with cervical spinal cord injuries to become independent in their ADL (Activities of Daily Living), residual arm function is very important. Also, age, sex, physical strength, obesity, spasticity, pain, contracture and motivation are related. We investigated the possibility of independence in ADL for patients with cervical spinal cord injuries, carrying out our evaluation based on the Zancolli Classification of Residual Arm Functions. Zancolli classification C6BII is taken as the...

  12. Assessment of activation products in the Savannah River Site environment

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: 32P, 51Cr, 60C, and 65Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated

  13. Assessment of activation products in the Savannah River Site environment

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  14. Single molecule TPM analysis of the catalytic pentad mutants of Cre and Flp site-specific recombinases: contributions of the pentad residues to the pre-chemical steps of recombination

    Fan, Hsiu-Fang; Cheng, Yong-Song; Ma, Chien-Hui; Jayaram, Makkuni

    2015-01-01

    Cre and Flp site-specific recombinase variants harboring point mutations at their conserved catalytic pentad positions were characterized using single molecule tethered particle motion (TPM) analysis. The findings reveal contributions of these amino acids to the pre-chemical steps of recombination. They suggest functional differences between positionally conserved residues in how they influence recombinase-target site association and formation of ‘non-productive’, ‘pre-synaptic’ and ‘synaptic...

  15. Comparative estrogenic activity of wine extracts and organochlorine pesticide residues in food

    Gaido, K.; Dohme, L.; Wang, F.; Chen, I.; Blankvoort, B.; Ramamoorthy, K.; Safe, S.

    1998-01-01

    The human diet contains industrial-derived, endocrine-active chemicals and higher levels of naturally occurring compounds that modulate multiple endocrine pathways. Hazard and risk assessment of these mixtures is complicated by noadditive interactions between different endocrine-mediated responses.

  16. The landscape degradation in the mining sites with suspended activity

    Anca IONCE

    2009-01-01

    The extracting industry, through its extraction activities, of shipping the ores, of breaking the ores, of preparing the practical substances, of stowing the useless rock, of transporting the practical substances, etc. might modify the area’s relief and the quality of ground, of thesurface waters and of the air. Suceava County has an old tradition of mining, where the results of this activity are visible, especially the visual point of view, and where not taking certain measures of ecological...

  17. Active site proton delivery and the lyase activity of human CYP17A1

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G., E-mail: s-sligar@illinois.edu

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  18. Active site proton delivery and the lyase activity of human CYP17A1

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis

  19. Artemisolide is a typical inhibitor of IκB kinase β targeting cysteine-179 residue and down-regulates NF-κB-dependent TNF-α expression in LPS-activated macrophages

    Nuclear factor (NF)-κB regulates a central common signaling for immunity and cell survival. Artemisolide (ATM) was previously isolated as a NF-κB inhibitor from a plant of Artemisia asiatica. However, molecular basis of ATM on NF-κB activation remains to be defined. Here, we demonstrate that ATM is a typical inhibitor of IκB kinase β (IKKβ), resulting in inhibition of lipopolysaccharide (LPS)-induced NF-κB activation in RAW 264.7 macrophages. ATM inhibited the kinase activity of highly purified IKKβ and also LPS-induced IKK activity in the cells. Moreover, the effect of ATM on IKKβ activity was completely abolished by substitution of Cys-179 residue of IKKβ to Ala residue, indicating direct targeting site of ATM. ATM could inhibit IκBα phosphorylation in LPS-activated RAW 264.7 cells and subsequently prevent NF-κB activation. Further, we demonstrate that ATM down-regulates NF-κB-dependent TNF-α expression. Taken together, this study provides a pharmacological potential of ATM in NF-κB-dependent inflammatory disorders

  20. Baseline study of pesticide residues and toxic contaminants in environmental samples in Thailand by neutron activation technique

    The technique of neutron activation, both instrumental and radiochemical, is used for the investigation of pesticide residues and contaminants, viz. Hg, Se, As, Cd, Cu, Br, Co and Zn in rice and marine fish in Thailand. More than 500 samples of 6 species including squid of fish caught from polluted and non (less)-polluted areas in Thai waters, and of 17 varieties of non-glutinous rice and 6 varieties of glutinous rice of both brown and milled collected from 21 different rice experiment stations throughout the Kingdom are analyzed. The results of this study positively indicate that there is no contamination in fish and rice in Thailand. Additionally, the baseline concentration of studies trace toxic elements is established. (author)