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Sample records for active site aromatic

  1. Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase

    SciTech Connect

    Ghattyvenkatakrishna, Pavan K; Uberbacher, Edward C

    2013-01-01

    The presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase has been a topic of great interest. Flexibility of these residues has been suspected to be a key player in controlling ligand traversal in the gorge. This raises the question of whether the over representation of aromatic residues in the gorge implies higher than normal flexibility of those residues. The current study suggests that it does not. Large changes in the hydrophobic cross sectional area due to dihedral oscillations are probably the reason behind their presence in the gorge.

  2. The Unexpected Reactivity of the Carbon Sites on the Nanostructured Carbon Catalysts towards the C-H Bond Activation from the Analysis of the Aromaticity.

    PubMed

    Sun, XiaoYing; Li, Bo; Su, DangSheng

    2016-06-06

    It is believed that the oxygen groups on the carbon catalysts are responsible for the observed reactivity for C-H bond activations. On the other hand, the oxygen groups also reduce the aromaticity of the host. The loss of the aromaticity increases reactivities of the carbon atoms and they become the active sites for the C-H bond activation. The newly identified C-C site exhibits the comparable catalytic performance in the oxidative dehydrogenation (ODH) of propane compared with the conventional oxygen groups like quinone and ketone. A series of calculations indicate that the aromaticity might be a useful descriptor for the carbon catalysts.

  3. Subway construction activity influence on polycyclic aromatic hydrocarbons in fine particles: Comparison with a background mountainous site

    NASA Astrophysics Data System (ADS)

    Kong, Shaofei; Li, Xuxu; Li, Qi; Yin, Yan; Li, Li; Chen, Kui; Liu, Dantong; Yuan, Liang; Pang, Xiaobing

    2015-07-01

    Intensive construction activities worsened the surrounding atmospheric environment in China. Eighteen polycyclic aromatic hydrocarbons (PAHs) in fine particles (PM2.5) were collected at a subway construction site (SC) of Nanjing and compared with a regional background mountainous site (BM) to examine the influence of anthropogenic activities on concentrations, sources and health risks of PAHs. Average PAH concentrations at SC were higher than BM at a factor of about 5.9. All PAH species at SC were higher than BM, with the SC/BM ratios ranging from 1.3 (NaP) to 10.3 (BaP). PAH profiles differed for the two sites. The SC site had higher mass fractions of PAHs from coal combustion and vehicle emission, while the BM site held higher mass percentages of PAHs from long-range transported wood combustion and industrial activities. Lower temperature at BM may lead to the higher mass percentages of low ring PAHs. Coal combustion, traffic emissions and biomass burning were the common sources for PAHs at both SC and BM. Construction workers were exposed to higher BaPeq concentrations, nearly ten times of the background site and their lifetime cancer risk reached to 0.6 per 1,000,000 exposed worker, owing to the influence of coal combustion, vehicle emission and industrial activities at the surroundings of SC.

  4. Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12

    PubMed Central

    Zhang, Xiaomei; Wang, Shuai; Wu, Xiuyun; Liu, Shijia; Li, Dandan; Xu, Hao; Gao, Peiji; Chen, Guanjun; Wang, Lushan

    2015-01-01

    The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the −4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the −2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs. PMID:26670009

  5. Aromatic-Aromatic Interactions in Biological System: Structure Activity Relationships

    SciTech Connect

    Rajagopal, Appavu; Deepa, Mohan; Govindaraju, Munisamy

    2016-02-26

    While, intramolecular hydrogen bonds have attracted the greatest attention in studies of peptide conformations, the recognition that several other weakly polar interactions may be important determinants of folded structure has been growing. Burley and Petsko provided a comprehensive overview of the importance of weakly polar interactions, in shaping protein structures. The interactions between aromatic rings, which are spatially approximate, have attracted special attention. A survey of the proximal aromatic residue pairs in proteins, allowed Burley and Petsko to suggest that, “phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 Å, and dihedral angles approximately 90° are most common”.

  6. Praziquantel derivatives with antischistosomal activity: aromatic ring modification.

    PubMed

    Wang, Zhi-xia; Chen, Jing-lei; Qiao, Chunhua

    2013-08-01

    A series of aromatic ring-modified praziquantel derivatives were prepared and evaluated against juvenile and adult stage of Schistosoma japonicumin. Several analogs comparable in activity to the drug praziquantel have been identified based on in vitro and in vivo japonuicum schistosomes worm viability assay. Structure and activity relationship of these praziquantel aromatic ring-modified compounds was revealed. Specifically, a compound in which a bromine has been introduced in the aromatic ring of praziquantel demonstrated close antischistosomal activity to praziquantel in vivo.

  7. Constitutive Activation of the Aromatic Hydrocarbon Receptor

    PubMed Central

    Chang, Ching-Yi; Puga, Alvaro

    1998-01-01

    The ligand-activated aromatic hydrocarbon receptor (AHR) dimerizes with the AHR nuclear translocator (ARNT) to form a functional complex that transactivates expression of the cytochrome P-450 CYP1A1 gene and other genes in the dioxin-inducible [Ah] gene battery. Previous work from this laboratory has shown that the activity of the CYP1A1 enzyme negatively regulates this process. To study the relationship between CYP1A1 activity and Ah receptor activation we used CYP1A1-deficient mouse hepatoma c37 cells and CYP1A1- and AHR-deficient African green monkey kidney CV-1 cells. Using gel mobility shift and luciferase reporter gene expression assays, we found that c37 cells that had not been exposed to exogenous Ah receptor ligands already contained transcriptionally active AHR-ARNT complexes, a finding that we also observed in wild-type Hepa-1 cells treated with Ellipticine, a CYP1A1 inhibitor. In CV-1 cells, transient expression of AHR and ARNT leads to high levels of AHR–ARNT-dependent luciferase gene expression even in the absence of an agonist. Using a green fluorescent protein-tagged AHR, we showed that elevated reporter gene expression correlates with constitutive nuclear localization of the AHR. Transcriptional activation of the luciferase reporter gene observed in CV-1 cells is significantly decreased by (i) expression of a functional CYP1A1 enzyme, (ii) competition with chimeric or truncated AHR proteins containing the AHR ligand-binding domain, and (iii) treatment with the AHR antagonist α-naphthoflavone. These results suggest that a CYP1A1 substrate, which accumulates in cells lacking CYP1A1 enzymatic activity, is an AHR ligand responsible for endogenous activation of the Ah receptor. PMID:9418899

  8. Biochemical Evaluation of the Decarboxylation and Decarboxylation-Deamination Activities of Plant Aromatic Amino Acid Decarboxylases*

    PubMed Central

    Torrens-Spence, Michael P.; Liu, Pingyang; Ding, Haizhen; Harich, Kim; Gillaspy, Glenda; Li, Jianyong

    2013-01-01

    Plant aromatic amino acid decarboxylase (AAAD) enzymes are capable of catalyzing either decarboxylation or decarboxylation-deamination on various combinations of aromatic amino acid substrates. These two different activities result in the production of arylalkylamines and the formation of aromatic acetaldehydes, respectively. Variations in product formation enable individual enzymes to play different physiological functions. Despite these catalytic variations, arylalkylamine and aldehyde synthesizing AAADs are indistinguishable without protein expression and characterization. In this study, extensive biochemical characterization of plant AAADs was performed to identify residues responsible for differentiating decarboxylation AAADs from aldehyde synthase AAADs. Results demonstrated that a tyrosine residue located on a catalytic loop proximal to the active site of plant AAADs is primarily responsible for dictating typical decarboxylase activity, whereas a phenylalanine at the same position is primarily liable for aldehyde synthase activity. Mutagenesis of the active site phenylalanine to tyrosine in Arabidopsis thaliana and Petroselinum crispum aromatic acetaldehyde synthases primarily converts the enzymes activity from decarboxylation-deamination to decarboxylation. The mutation of the active site tyrosine to phenylalanine in the Catharanthus roseus and Papaver somniferum aromatic amino acid decarboxylases changes the enzymes decarboxylation activity to a primarily decarboxylation-deamination activity. Generation of these mutant enzymes enables the production of unusual AAAD enzyme products including indole-3-acetaldehyde, 4-hydroxyphenylacetaldehyde, and phenylethylamine. Our data indicates that the tyrosine and phenylalanine in the catalytic loop region could serve as a signature residue to reliably distinguish plant arylalkylamine and aldehyde synthesizing AAADs. Additionally, the resulting data enables further insights into the mechanistic roles of active site

  9. List 9 - Active CERCLIS Sites:

    EPA Pesticide Factsheets

    The List 9 displays the sequence of activities undertaken at active CERCLIS sites. An active site is one at which site assessment, removal, remedial, enforcement, cost recovery, or oversight activities are being planned or conducted.

  10. Facile Formation of Redox-Active Totally Organic Nanoparticles in Water by In Situ Reduction of Organic Precursors Stabilized through Aromatic-Aromatic Interactions by Aromatic Polyelectrolytes.

    PubMed

    Flores, Mario E; Garcés-Jerez, Pablo; Fernández, Daniel; Aros-Perez, Gustavo; González-Cabrera, Diego; Álvarez, Eduardo; Cañas, Ignacio; Oyarzun-Ampuero, Felipe; Moreno-Villoslada, Ignacio

    2016-11-01

    The formation of redox-active, totally organic nanoparticles in water is achieved following a strategy similar to that used to form metal nanoparticles. It is based on two fundamental concepts: i) complexation through aromatic-aromatic interactions of a water-soluble precursor aromatic molecule with polyelectrolytes bearing complementary charged aromatic rings, and ii) reduction of the precursor molecule to achieve stabilized nanoparticles. Thus, formazan nanoparticles are synthesized by reduction of a tetrazolium salt with ascorbic acid using polyelectrolytes bearing benzene sulfonate residues of high linear aromatic density, but cannot be formed in the presence of nonaromatic polyelectrolytes. The red colored nanoparticles are efficiently encapsulated in calcium alginate beads, showing macroscopic homogeneity. Bleaching kinetics with chlorine show linear rates on the order of tenths of milli-meters per minute. A linear behavior of the dependence of the rate of bleaching on the chlorine concentration is found, showing the potential of the nanoparticles for chlorine sensing.

  11. The emissions of major aromatic VOC as landfill gas from urban landfill sites in Korea.

    PubMed

    Kim, Ki-Hyun; Baek, Sung Ok; Choi, Ye-Jin; Sunwoo, Young; Jeon, Eui-Chan; Hong, J H

    2006-07-01

    In this study, concentrations of major aromatic VOCs were determined from landfill gas (LFG) at a total of five municipal landfill sites in Korea including Nan Ji (NJ), Woon Jung (WJ), Sam Poong (SP), Hoei Chun (HC), and No Hyung (NH). The concentration levels of those VOC were found to be significantly different, mainly as a function of such a parameter as landfill aging. The VOC concentrations measured from the unclosed landfill sites (e.g., WJ) were characterized by exceedingly high values above a few tens of ppm. However, the results of the abandoned site (e.g., SP) were about three orders of magnitude lower than the others so as to merely exceed the typical ambient concentration levels. It was most striking to find a systematic dominance of toluene over other aromatic VOC under most circumstances. The LFG flux values of all aromatic VOC and the four specific major ones (termed as BTEX: benzene, toluene, ethylbenzene, and xylene) were also computed for each vent pipe from all study sites using their concentrations and the concurrently determined environmental parameters. The results, if calculated in terms of the average BTEX quantity emitted per vent pipe, showed that the magnitude of their emissions can vary substantially, with the values ranging from 0.05 (SP) to 49.2 kg yr(-1) (WJ in wintertime). The LFG flux values of aromatic VOC, when compared to the contribution of non-methane hydrocarbons (NMHC), were able to explain a constant, but minor, proportion of the LFG carbon budget.

  12. Characterization of subsurface polycyclic aromatic hydrocarbons at the Deepwater Horizon site

    NASA Astrophysics Data System (ADS)

    Diercks, Arne-R.; Highsmith, Raymond C.; Asper, Vernon L.; Joung, DongJoo; Zhou, Zhengzhen; Guo, Laodong; Shiller, Alan M.; Joye, Samantha B.; Teske, Andreas P.; Guinasso, Norman; Wade, Terry L.; Lohrenz, Steven E.

    2010-10-01

    Here, we report the initial observations of distributions of polycyclic aromatic hydrocarbons (PAH) in subsurface waters near the Deepwater Horizon oil well site (also referred to as the Macondo, Mississippi Canyon Block 252 or MC252 well). Profiles of in situ fluorescence and beam attenuation conducted during 9-16 May 2010 were characterized by distinct peaks at depths greater than 1000 m, with highest intensities close to the wellhead and decreasing intensities with increasing distance from the wellhead. Gas chromatography/mass spectrometry (GC/MS) analyses of water samples coinciding with the deep fluorescence and beam attenuation anomalies confirmed the presence of polycyclic aromatic hydrocarbons (PAH) at concentrations reaching 189 μg L-1 (ppb). Subsurface exposure to PAH at levels considered to be toxic to marine organisms would have occurred in discrete depth layers between 1000 and 1400 m in the region southwest of the wellhead site and extending at least as far as 13 km.

  13. Xenoestrogenic gene expression: structural features of active polycyclic aromatic hydrocarbons.

    PubMed

    Schultz, T Wayne; Sinks, Glendon D

    2002-04-01

    Estrogenicity was assessed using the Saccharomyces cerevisiae-based Lac-Z reporter assay and was reported as the logarithm of the inverse of the 50% molar beta-galactosidase activity (log[EC50(-1)]). In an effort to quantify the relationship between molecular structure of polycyclic aromatic hydrocarbons (PAHs) and estrogenic gene expression, a series of PAHs were evaluated. With noted exceptions, the results of these studies indicate that the initial two-dimensional structural warning for estrogenicity, the superpositioning of a hydroxylated aromatic system on the phenolic A-ring of 17-beta-estradiol, can be extended to the PAHs. This two-dimensional-alignment criterion correctly identified estrogenicity of 22 of the 29 PAHs evaluated. Moreover, the estrogenic potency of these compounds was directly related to the size of the hydrophobic backbone. The seven compounds classified incorrectly by this structural feature were either dihydroxylated naphthalenes or aromatic nitrogen-heterocyclic compounds; all such compounds were false positives. Results with dihydroxylated naphthalenes reveal derivatives that were nonestrogenic when superimposed on the phenolic A-ring of 17-beta-estradiol had the second hydroxyl group in the position of the C-ring or were catechol-like in structure. Structural alerts for nitrogen-heterocyclic compounds must take into account the position of the hydroxyl group and the in-ring nitrogen atom; compounds with the hydroxyl group and nitrogen atom involved with the same ring were observed to be nonactive.

  14. ANSID: a Solid-Phase Proteomic Approach for Identification and Relative Quantification of Aromatic Nitration Sites

    NASA Astrophysics Data System (ADS)

    Nuriel, Tal; Whitehouse, Julia; Ma, Yuliang; Mercer, Emily; Brown, Neil; Gross, Steven

    2015-12-01

    Nitration of tyrosine and other aromatic amino acid residues in proteins occurs in the setting of inflammatory, neurodegenerative and cardiovascular diseases - importantly, this modification has been implicated in the pathogenesis of diverse diseases and the physiological process of tissue aging. To understand the biological consequences of aromatic nitration in both health and disease, it is critical to molecularly identify the proteins that undergo nitration, specify their cognate modification sites and quantify their extent of nitration. To date, unbiased identification of nitrated proteins has painstakingly employed 2D-gel electrophoresis followed by Western Blotting with an anti-nitrotyrosine antibody for detection. Apart from being relatively slow and laborious, this method suffers from limited coverage, the potential for false-positive identifications and failure to reveal specific amino acid modification sites. To overcome these shortcomings, we have developed a solid-phase, chemical-capture approach for unbiased and high-throughput discovery of nitrotyrosine and nitrotryptophan sites in proteins. Utilizing this method, we have successfully identified several endogenously nitrated proteins in rat brain and a total of 244 nitrated peptides from 145 proteins following in vitro exposure of rat brain homogenates to the nitrating agent peroxynitrite (1 mM). As expected, Tyr residues constituted the great majority of peroxynitrite-mediated protein nitration sites; however, we were surprised to discover several brain proteins that contain nitrated Trp residues. By incorporating a stable-isotope labeling step, this new Aromatic Nitrtion Site IDentification (ANSID) method was also adapted for relative quantification of nitration site abundances in proteins. Application of the quantitative ANSID method offers great potential to advance our understanding of the role of protein nitration in disease pathogenesis and normal physiology.

  15. ANSID: A Solid-Phase Proteomic Approach for Identification and Relative Quantification of Aromatic Nitration Sites

    PubMed Central

    Nuriel, Tal; Whitehouse, Julia; Ma, Yuliang; Mercer, Emily J.; Brown, Neil; Gross, Steven S.

    2016-01-01

    Nitration of tyrosine and other aromatic amino acid residues in proteins occurs in the setting of inflammatory, neurodegenerative, and cardiovascular diseases—importantly, this modification has been implicated in the pathogenesis of diverse diseases and the physiological process of aging. To understand the biological consequences of aromatic nitration in both health and disease, it is critical to molecularly identify the proteins that undergo nitration, specify their cognate modification sites and quantify their extent of nitration. To date, unbiased identification of nitrated proteins has often involved painstaking 2D-gel electrophoresis followed by Western Blotting with an anti-nitrotyrosine antibody for detection. Apart from being relatively slow and laborious, this method suffers from limited coverage, the potential for false-positive identifications, and failure to reveal specific amino acid modification sites. To overcome these shortcomings, we have developed a solid-phase, chemical-capture approach for unbiased and high-throughput discovery of nitrotyrosine and nitrotryptophan sites in proteins. Utilizing this method, we have successfully identified several endogenously nitrated proteins in rat brain and a total of 244 nitrated peptides from 145 proteins following in vitro exposure of rat brain homogenates to the nitrating agent peroxynitrite (1 mM). As expected, Tyr residues constituted the great majority of peroxynitrite-mediated protein nitration sites; however, we were surprised to discover several brain proteins that contain nitrated Trp residues. By incorporating a stable-isotope labeling step, this new Aromatic Nitration Site IDentification (ANSID) method was also adapted for relative quantification of nitration site abundances in proteins. Application of the ANSID method offers great potential to advance our understanding of the role of protein nitration in disease pathogenesis and normal physiology. PMID:26779476

  16. Lactoperoxidase-catalyzed activation of carcinogenic aromatic and heterocyclic amines.

    PubMed

    Gorlewska-Roberts, Katarzyna M; Teitel, Candee H; Lay, Jackson O; Roberts, Dean W; Kadlubar, Fred F

    2004-12-01

    Lactoperoxidase, an enzyme secreted from the human mammary gland, plays a host defensive role through antimicrobial activity. It has been implicated in mutagenic and carcinogenic activation in the human mammary gland. The potential role of heterocyclic and aromatic amines in the etiology of breast cancer led us to examination of the lactoperoxidase-catalyzed activation of the most commonly studied arylamine carcinogens: 2-amino-1-methyl-6-phenylimidazo[4,5-b]-pyridine (PhIP), benzidine, 4-aminobiphenyl (ABP), 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), and 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx). In vitro activation was performed with lactoperoxidase (partially purified from bovine milk or human milk) in the presence of hydrogen peroxide and calf thymus DNA. Products formed during enzymatic activation were monitored by HPLC with ultraviolet and radiometric detection. Two of these products were characterized as hydrazo and azo derivatives by means of mass spectrometry. The DNA binding level of 3H- and 14C-radiolabeled amines after peroxidase-catalyzed activation was dependent on the hydrogen peroxide concentration, and the highest levels of carcinogen binding to DNA were observed at 100 microM H2O2. Carcinogen activation and the level of binding to DNA were in the order of benzidine > ABP > IQ > MeIQx > PhIP. One of the ABP adducts was identified, and the level at which it is formed was estimated to be six adducts/10(5) nucleotides. The susceptibility of aromatic and heterocyclic amines for lactoperoxidase-catalyzed activation and the binding levels of activated products to DNA suggest a potential role of lactoperoxidase-catalyzed activation of carcinogens in the etiology of breast cancer.

  17. Biodegradation, bioaccessibility, and genotoxicity of diffuse polycyclic aromatic hydrocarbon (PAH) pollution at a motorway site.

    PubMed

    Johnsen, Anders R; De Lipthay, Julia R; Reichenberg, Fredrik; Sørensen, Søren J; Andersen, Ole; Christensen, Peter; Binderup, Mona-lise; Jacobsen, Carsten S

    2006-05-15

    Diffuse pollution of surface soil with polycyclic aromatic hydrocarbons (PAHs) is problematic in terms of the large areas and volumes of polluted soil. The levels and effects of diffuse PAH pollution at a motorway site were investigated. Surface soil was sampled with increasing distance from the asphalt pavement and tested for total amounts of PAHs, amounts of bioaccessible PAHs, total bacterial populations, PAH degrader populations, the potential for mineralization of 14C-PAHs, and mutagenicity. Elevated PAH concentrations were found in the samples taken 1-8 m from the pavement. Soil sampled at greater distances (12-24 m) contained only background levels of PAHs. The total bacterial populations (CFU and numbers of 16S rDNA genes) were similar for all soil samples, whereas the microbial degrader populations (culturable PAH degraders and numbers of PAH dioxygenase genes) were most abundant in the most polluted samples close to the pavement. Hydroxypropyl-beta-cyclodextrin extraction of soil PAHs, as a direct estimate of the bioaccessibility, indicated that only 1-5% of the PAHs were accessible to soil bacteria. This low bioaccessibility is suggested to be due to sorption to traffic soot particles. The increased PAH level close to the pavement was reflected in slightly increased mutagenic activity (1 m, 0.32 +/- 0.08 revertants g(-1) soil; background/ 24 m: 0.08 +/- 0.04), determined by the Salmonella/ microsome assay of total extractable PAHs activated by liver enzymes. The potential for lighter molecular weight PAH degradation in combination with low bioaccessibility of heavier PAHs is proposed to lead to a likely increase in concentration of heavier PAHs over time. These residues are, however, likely to be of low biological significance.

  18. Aromatic nitrogen mustard-based prodrugs: activity, selectivity, and the mechanism of DNA cross-linking.

    PubMed

    Chen, Wenbing; Han, Yanyan; Peng, Xiaohua

    2014-06-10

    Three novel H2O2-activated aromatic nitrogen mustard prodrugs (6-8) are reported. These compounds contain a DNA alkylating agent connected to a H2O2-responsive trigger by different electron-withdrawing linkers so that they are inactive towards DNA but can be triggered by H2O2 to release active species. The activity and selectivity of these compounds towards DNA were investigated by measuring DNA interstrand cross-link (ICL) formation in the presence or absence of H2O2. An electron-withdrawing linker unit, such as a quaternary ammonia salt (6), a carboxyamide (7), and a carbonate group (8), is sufficient to deactivate the aromatic nitrogen mustard resulting in less than 1.5 % cross-linking formation. However, H2O2 can restore the activity of the effectors by converting a withdrawing group to a donating group, therefore increasing the cross-linking efficiency (>20 %). The stability and reaction sites of the ICL products were determined, which revealed that alkylation induced by 7 and 8 not only occurred at the purine sites but also at the pyrimidine site. For the first time, we isolated and characterized the monomer adducts formed between the canonical nucleosides and the aromatic nitrogen mustard (15) which supported that nitrogen mustards reacted with dG, dA, and dC. The activation mechanism was studied by NMR spectroscopic analysis. An in vitro cytotoxicity assay demonstrated that compound 7 with a carboxyamide linker dramatically inhibited the growth of various cancer cells with a GI50 of less than 1 μM, whereas compound 6 with a charged linker did not show any obvious toxicity in all cell lines tested. These data indicated that a neutral carboxyamide linker is preferable for developing nitrogen mustard prodrugs. Our results showed that 7 is a potent anticancer prodrug that can serve as a model compound for further development. We believe these novel aromatic nitrogen mustards will inspire further and effective applications.

  19. Microbial degradation of polycyclic aromatic hydrocarbon and cyanide in soils from manufactured gas plant sites

    SciTech Connect

    Ho, YiFong.

    1993-01-01

    The microbial clean-up of cyanide and polycyclic aromatic hydrocarbon (PAH) in soils from manufactured gas plant (MGP) sites is the subject of this study. Cyanide was examined for its inhibition on microbial PAH degradation by an MGP-soil isolate identified as a strain of Pseudomonas aeruginosa by classical differential methods as well as 16S rRNA oligonucleotide probes. A strong cyanide-degrading Bacillus pumilus (ATCC No. 7061) strain was used for facilitating cyanide degradation thereby enhancing PAH biodegradation in this soil. This research has validated cyanide interference with the PAH degrader and shown that adding Bacillus pumilus accomplishes the removal of cyanide which subsequently allows Pseudomonas aeruginosa to metabolize PAHs. In addition to the biodegradation of cyanide and lower ring numbered PAHs, the microbial degradation of 4-ring polycyclic aromatic hydrocarbons (PAHs) by using a mixed culture obtained from another former coal tar contaminated site was also studied. The rate of biotransformation and the abiotic loss due to volatilization were monitored. The 3-ring PAH used in this project was phenanthrene and the 4-ring PAHs used were fluoranthene and pyrene. The results showed that volatilization loss of naphthalene in the control system was substantial while volatilization of higher molecular weight PAH compounds (fluoranthene and pyrene) was negligible. The biodegradation rates of phenanthrene, fluoranthene and pyrene are 6.56, 1.59 and 0.82 mg/L/day, respectively or 65.6, 15.9, 8.2 mg/gram of cells/day assuming 100 mg cells/L in the system. This study indicates that biodegradation of 3- and 4-ring PAHs by mixed cultures obtained from PAH contaminated sites is very promising. These studies will contribute to the understanding of PAH and cyanide removal from MGP and provide information for the design of a bioremediation project to reclaim unusable land that was contaminated through the previous coal gasification process.

  20. Probing the role of aromatic residues at the secondary saccharide binding sites of human salivary α-amylase in substrate hydrolysis and bacterial binding

    PubMed Central

    Ragunath, Chandran; Manuel, Suba G.A.; Venkataraman, Venkat; Sait, Hameetha B.R.; Kasinathan, Chinnasamy; Ramasubbu, Narayanan

    2008-01-01

    SUMMARY Human salivary α-amylase (HSAmy) has three distinct functions relevant to oral health: 1) hydrolysis of starch; 2) binding to hydroxyapatite; and 3) binding to bacteria (e.g. viridans streptococci). Although the active site of HSAmy for starch hydrolysis is well characterized, the regions responsible for the bacterial binding are yet to be defined. Since HSAmy possesses several secondary saccharide-binding sites in which aromatic residues are prominently located, we hypothesized that one or more of the secondary saccharide binding sites harboring the aromatic residues may play an important role in bacterial binding. To test this hypothesis, the aromatic residues at five secondary binding sites were mutated to alanine to generate six mutants representing either single (W203A, Y276A and W284A), double (Y276A/W284A and W316A/W388A) or multiple (HSAmy-ar; W134A/W203A/Y276A/W284A/W316A/W388A) mutations. The crystal structure of HSAmy-ar was determined at a resolution of 1.5 Å as an acarbose complex and compared with the existing wild type acarbose complex. The wild type and the mutant enzymes were characterized for their abilities to exhibit enzyme activity, starch binding, hydroxyapatite and bacterial binding activities. Our results clearly showed that 1) mutation of aromatic residues does not alter the overall conformation of the molecule; 2) the single or double mutants showed either moderate or minimal changes in both starch and bacterial binding activities activity whereas the HSAmy-ar showed significant reduction in these activities; 3) the starch hydrolytic activity was reduced 10-fold in HSAmy-ar; 4) oligosaccharide hydrolytic activity was reduced in all the mutants but the action pattern was similar to that of the wild type enzyme; and 5) the hydroxyaptite binding was unaffected in HSAmy-ar. These results clearly show that the aromatic residues at the secondary saccharide binding sites in HSAmy play a critical role in bacterial binding and starch

  1. Polycyclic aromatic hydrocarbons from U.S. and Antarctic sites analyzed with synchronous fluorescence spectrometry

    SciTech Connect

    Amick, E.N.; Pollard, J.E.; Engelmann, W.H.; Brown, K.W.; Alarie, J.P.; Watts, W.; Vo-Dinh, T.; Akindele, F.M.; Crockett, A.B.

    1995-12-31

    Synchronous ultraviolet-visible (UV-vis) fluorescence spectrometry is currently being evaluated as a field screening technology by the US Environmental Protection Agency`s (EPA) Environmental Monitoring Systems Laboratory in Las Vegas, Nevada (EMSL-LV). This method can provide compound or class-selective results on site at a reasonable cost. A prototype field-portable spectrofluorometer capable of excitation, emission, and synchronous scans was field tested at the American Creosote Works Superfund Site (a wood preservation facility) in Jackson, Tennessee. The instrument was also tested in the laboratory with sediment samples collected from Antarctica. The UV-vis fluorescence spectra of various polycyclic aromatic hydrocarbons (PAHs) were clearly seen in the synchronous spectra of soil samples extracted on site at American Creosote Works. The spectra for the Antarctic sediment samples were nearly identical to that of motor oil. The results of this study demonstrate the utility of synchronous fluorescence to provide evidence of the presence and identity of hydrocarbon contamination in environmental samples. The technique allows flexibility in selection of optimum extraction and instrumental procedures for site-specific matrices.

  2. Temporal variability of Polycyclic Aromatic Hydrocarbons in a receptor site of Puebla -Tlaxcala Valley.

    NASA Astrophysics Data System (ADS)

    Padilla Barrera, Zuhelen; Torres Jardón, Ricardo; Gerardo Ruiz, Luis; Castro, Telma

    2015-04-01

    The Puebla-Tlaxcala Valley is a region with high population scattered over two states, where emissions from combustion of a variety of materials and fuels represent a major problem in the deterioration of air quality. Polycyclic aromatic hydrocarbons (PAHs) are a class of semi-volatile organic compounds that are formed during combustion. PAH are present in large amounts in the particulate matter comes from the combustion and no combustion. The particle-bound PAHs are formed by accumulation and condensation mechanisms in the particle. In its condensed form are mainly associated with fine particles (< 0.10 um). The major emission sources of PAHs are open burning, industrial boilers and emission from cars and trucks. Emission rates of PAHs vary significantly depending on vehicle use: fuel type, engine type and catalytic converter, and once emitted into the atmosphere, particulate PAHs may undergo transformation by photo-oxidation. The measurements were made with a photoelectric aerosol sensor (PAS 2000 CE) and a diffusion charger (DC 2000 CE), the first determines the concentration of PAHs, while the second determines the active surface of particles. The use of these two sensors in parallel is a useful tool to identify quantitatively the greatest source of emission, describe the physical and chemical characteristics of the particles. Correlations between PAHs with the active surface (DC), NOy and CO, together with an analysis of weather atmospheric transport to approximate the possible origin of these particles. The coefficient PAHs / DC associated with the backward trajectory analysis is a tool to identify potential areas of emission. The correlation between PAHs and NOx reflects emissions associated with diesel combustion, while the correlation between PAHs and CO, combustion of gasoline. Concentration patterns were recorded over 24 hours in both PAHs and DC. The average concentration of PAHs was 4.9 ng/m3 and the maximum of 81.9 ng/m3 , while the average active

  3. PHOTOACTIVATED TOXICITY IN AMPHIPODS COLLECTED FROM POLYCYCLIC AROMATIC HYDROCARBON-CONTAMINATED SITES

    EPA Science Inventory

    The risk of photo-activated PAH toxicity in contaminated aquatic systems has not been well characterized. To better indicate this potential, amphipods (Gammarus spp.) were collected from two PAH contaminated sites (Hog Island and USX), as well as a reference site (Chipmunk Cove)...

  4. Salt site performance assessment activities

    SciTech Connect

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

    1983-01-01

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

  5. Mild and Efficient Palladium-Catalyzed Direct Trifluoroethylation of Aromatic Systems by C-H Activation.

    PubMed

    Tóth, Balázs L; Kovács, Szabolcs; Sályi, Gergő; Novák, Zoltán

    2016-02-05

    The introduction of trifluoroalkyl groups into aromatic molecules is an important transformation in the field of organic and medicinal chemistry. However, the direct installation of fluoroalkyl groups onto aromatic molecules still represents a challenging and highly demanding synthetic task. Herein, a simple trifluoroethylation process that relies on the palladium-catalyzed C-H activation of aromatic compounds is described. With the utilization of a highly active trifluoroethyl(mesityl)iodonium salt, the developed catalytic method enables the first highly efficient and selective trifluoroethylation of aromatic compounds. The robust catalytic procedure provides the desired products in up to 95 % yield at 25 °C in 1.5 to 3 hours and tolerates a broad range of functional groups. The utilization of hypervalent reagents opens new synthetic possibilities for direct alkylations and fluoroalkylations in the field of transition-metal-catalyzed C-H activation.

  6. Annulation of Aromatic Imines via Directed C-H BondActivation

    SciTech Connect

    Thalji, Reema K.; Ahrendt, Kateri A.; Bergman, Robert G.; Ellman,Jonathan A.

    2005-04-14

    A directed C-H bond activation approach to the synthesis of indans, tetralins, dihydrofurans, dihydroindoles, and other polycyclic aromatic compounds is presented. Cyclization of aromatic ketimines and aldimines containing alkenyl groups tethered at the meta position relative to the imine directing group has been achieved using (PPh{sub 3}){sub 3}RhCl (Wilkinson's catalyst). The cyclization of a range of aromatic ketimines and aldimines provides bi- and tricyclic ring systems with good regioselectivity. Different ring sizes and substitution patterns can be accessed through the coupling of monosubstituted, 1,1- or 1,2-disubstituted, and trisubstituted alkenes bearing both electron-rich and electron-deficient functionality.

  7. Seawater Polluted with Highly Concentrated Polycyclic Aromatic Hydrocarbons Suppresses Osteoblastic Activity in the Scales of Goldfish, Carassius auratus.

    PubMed

    Suzuki, Nobuo; Sato, Masayuki; Nassar, Hossam F; Abdel-Gawad, Fagr Kh; Bassem, Samah M; Yachiguchi, Koji; Tabuchi, Yoshiaki; Endo, Masato; Sekiguchi, Toshio; Urata, Makoto; Hattori, Atsuhiko; Mishima, Hiroyuki; Shimasaki, Youhei; Oshima, Yuji; Hong, Chun-Sang; Makino, Fumiya; Tang, Ning; Toriba, Akira; Hayakawa, Kazuichi

    2016-08-01

    We have developed an original in vitro bioassay using teleost scale, that has osteoclasts, osteoblasts, and bone matrix as each marker: alkaline phosphatase (ALP) for osteoblasts and tartrate-resistant acid phosphatase (TRAP) for osteoclasts. Using this scale in vitro bioassay, we examined the effects of seawater polluted with highly concentrated polycyclic aromatic hydrocarbons (PAHs) and nitro-polycyclic aromatic hydrocarbons (NPAHs) on osteoblastic and osteoclastic activities in the present study. Polluted seawater was collected from two sites (the Alexandria site on the Mediterranean Sea and the Suez Canal site on the Red Sea). Total levels of PAHs in the seawater from the Alexandria and Suez Canal sites were 1364.59 and 992.56 ng/l, respectively. We were able to detect NPAHs in both seawater samples. Total levels of NPAHs were detected in the seawater of the Alexandria site (12.749 ng/l) and the Suez Canal site (3.914 ng/l). Each sample of polluted seawater was added to culture medium at dilution rates of 50, 100, and 500, and incubated with the goldfish scales for 6 hrs. Thereafter, ALP and TRAP activities were measured. ALP activity was significantly suppressed by both polluted seawater samples diluted at least 500 times, but TRAP activity did not change. In addition, mRNA expressions of osteoblastic markers (ALP, osteocalcin, and the receptor activator of the NF-κB ligand) decreased significantly, as did the ALP enzyme activity. In fact, ALP activity decreased on treatment with PAHs and NPAHs. We conclude that seawater polluted with highly concentrated PAHs and NPAHs influences bone metabolism in teleosts.

  8. Risk Assessment Related to Atmospheric Polycyclic Aromatic Hydrocarbons in Gas and Particle Phases near Industrial Sites

    PubMed Central

    Ramírez, Noelia; Cuadras, Anna; Marcé, Rosa Maria

    2011-01-01

    Background: Inhalation is one of the main means of human exposure to polycyclic aromatic hydrocarbons (PAHs) because of their ubiquitous presence in the atmosphere. However, most studies have considered only PAHs found in the particle phase and have omitted the contribution of the gas-phase PAHs to the risk. Objective: We estimated the lifetime lung cancer risk from PAH exposure by inhalation in people living next to the largest chemical site in Southern Europe and the Mediterranean area. Methods: We determined 18 PAHs in the atmospheric gas and particle phase. We monitored the PAHs for 1 year in three locations near the chemical site in different seasons. We used toxic equivalence factors to calculate benzo[a]pyrene (BaP) equivalents (BaP-eq) for individual PAHs and applied the World Health Organization unit risk (UR) for BaP (UR = 8.7 × 10–5) to estimate lifetime cancer risks due to PAH exposures. Results: We observed some spatial and seasonal variability in PAH concentrations. The contribution of gas-phase PAHs to the total BaP-eq value was between 34% and 86%. The total estimated average lifetime lung cancer risk due to PAH exposure in the study area was 1.2 × 10–4. Conclusions: The estimated risk was higher than values recommended by the World Health Organization and U.S. Environmental Protection Agency but lower than the threshold value of 10–3 that is considered an indication of definite risk according to similar risk studies. The results also showed that risk may be underestimated if the contributions of gas-phase PAHs are not considered. PMID:21478082

  9. DEPENDENCY OF POLYCHLORINATED BIPHENYL AND POLYCYCLIC AROMATIC HYDROCARBON BIOACCUMULATION IN MYA ARENARIA ON BOTH WATER COLUMN AND SEDIMENT BED CHEMICAL ACTIVITIES

    EPA Science Inventory

    The bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) by the filter-feeding soft-shell clam Mya arenaria was evaluated at three sites near Boston (MA, USA) by assessing the chemical activities of those hydrophobic organic compounds (H...

  10. Thiolates Chemically Induce Redox Activation of BTZ043 and Related Potent Nitro Aromatic Anti-Tuberculosis Agents

    PubMed Central

    Tiwari, Rohit; Moraski, Garrett C.; Krchňák, Viktor; Miller, Patricia A.; Colon-Martinez, Mariangelli; Herrero, Eliza; Oliver, Allen G.; Miller, Marvin J.

    2013-01-01

    The development of multidrug resistant (MDR) and extensively drug resistant (XDR) forms of tuberculosis (TB) has stimulated research efforts globally to expand the new drug pipeline. Nitro aromatic compounds, including 1, 3-Benzothiazin-4-ones (BTZs) and related agents, are a promising new class for the treatment of TB. Research has shown that the nitroso intermediates of BTZs that are generated in vivo cause suicide inhibition of decaprenylphosphoryl-β-D-ribose 2′ oxidase (DprE1), which is responsible for cell wall arabinogalactan biosynthesis. We have designed and synthesized novel anti-TB agents inspired from BTZs and other nitroaromatic compounds. Computational studies indicated that the unsubstituted aromatic carbons of BTZ043 and related nitroaromatic compounds are the most electron deficient and might be prone to nucleophilic attack. Our chemical studies on BTZ043 and the additional nitro aromatic compounds synthesized by us and the others confirmed the postulated reactivity. The results indicate that nucleophiles such as thiolates, cyanide and hydride induce non-enzymatic reduction of the nitro groups present in these compounds to the corresponding nitroso intermediates by addition at the unsubstituted electron deficient aromatic carbon present in these compounds. Furthermore we demonstrate here that these compounds are good candidates for the classical von Richter reaction. These chemical studies offer an alternate hypotheses for the mechanism of action of nitro aromatic anti-TB agents in that the cysteine thiol(ate) or a hydride source at the active site of DprE1 may trigger the reduction of the nitro groups in a manner similar to the von Richter reaction to the nitroso intermediates, to initiate the inhibition of DprE1. PMID:23402278

  11. Heterolytic Activation of Hydrogen Promoted by Ruthenium Nanoparticles immobilized on Basic Supports and Hydrogenation of Aromatic Compounds

    NASA Astrophysics Data System (ADS)

    Fang, Minfeng

    Despite the aggressive development and deployment of new renewable and nuclear technologies, petroleum-derived transportation fuels---gasoline, diesel and jet fuels---will continue to dominate the markets for decades. Environmental legislation imposes severe limits on the tolerable proportion of aromatics, sulfur and nitrogen contents in transportation fuels, which is difficult to achieve with current refining technologies. Catalytic hydrogenation plays an important role in the production of cleaner fuels, both as a direct means to reduce the aromatics and as a key step in the hydrodenitrogenation (HDN) and hydrodesulfurization (HDS) processes. However, conventional catalysts require drastic conditions and/or are easily poisoned by S or N aromatics. Therefore, there is still a need for new efficient catalysts for hydrogenation reactions relevant to the production of cleaner fossil fuels. Our catalyst design involves metallic nanoparticles intimately associated with a basic support, with the aim of creating a nanostructure capable of promoting the heterolytic activation of hydrogen and ionic hydrogenation mechanisms, as a strategy to avoid catalyst poisoning and enhance catalytic activity. We have designed and prepared a new nanostructured catalytic material composed of RuNPs immobilized on the basic polymer P4VPy. We have demonstrated that the Ru/P4VPy catalyst can promote heterolytic hydrogen activation and a unique surface ionic hydrogenation mechanism for the efficient hydrogenation of N-aromatics. This is the first time these ionic hydrogenation pathways have been demonstrated on solid surfaces. For the RuNPs surfaces without basic sites in close proximity, the conventional homolytic H2 splitting is otherwise involved. Using the mechanistic concepts from Ru/P4VPy, we have designed and prepared the Ru/MgO catalyst, with the aim to improve the catalytic efficiency for the hydrogenation of heteroatom aromatics operating by the ionic hydrogenation mechanism. The Ru

  12. Catalytic activity of in situ synthesized MoWNi sulfides in hydrogenation of aromatic hydrocarbons

    NASA Astrophysics Data System (ADS)

    Topolyuk, Yu. A.; Maksimov, A. L.; Kolyagin, Yu. G.

    2017-02-01

    MoWNi-sulfide catalysts were obtained in situ by thermal decomposition of metal-polymer precursors based on the copolymers of polymaleic anhydride in a hydrocarbon raw material. The activity of the synthesized catalysts in hydrogenation of bicyclic aromatic hydrocarbons was studied, and the composition and structure of active phase nanoparticles were determined.

  13. Ion mobility spectrometry-mass spectrometry analysis for the site of aromatic hydroxylation.

    PubMed

    Shimizu, Atsushi; Chiba, Masato

    2013-07-01

    Hydroxylated metabolites often retain the pharmacological activity of parent compound, and the position of hydroxylation determines the formation of chemically reactive intermediates, such as quinones and analogs, from para- and/or ortho-hydroxylation of phenols or arylamines. Therefore, the identification of exact position of hydroxylation is often required at the early development stage of new drug candidates. In many cases, liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides identical MS/MS spectra among isomeric hydroxylated metabolites, and therefore, it alone cannot unequivocally identify the exact position(s) of hydroxylation. Ion mobility spectrometry (IMS), integrated with LC-MS/MS, recently showed the capability of separating isomeric species based on differences in their drift times from IMS, which are linearly proportional to the collision cross-section (CCS) reflecting physical size and shape. In the present study, a chemical derivatization of isomeric hydroxylated metabolites with 2-fluoro-N-methyl pyridinium p-toluenesulfonate was found to confer distinct theoretical CCS value on each isomer by forming corresponding N-methyl pyridine (NMP) derivative. The regression lines established by the comparison between theoretical CCS values and observed drift times from IMS for each set of parent compound (labetalol, ezetimibe, atorvastatin, and warfarin) and its MS/MS product ions accurately and selectively projected the actual drift times of NMP derivatives of corresponding aromatic or isomeric hydroxylated metabolites. The established method was used for the accurate assignment of predominant formation of 2-hydroxylated metabolite from imipramine in NADPH- fortified human liver microsomes. The present application expands the versatility of LC-IMS-MS technique to the structure identification of isomeric hydroxylated metabolites at the early stage for drug development.

  14. Induction of aromatic catabolic activity in Sphingomonas aromaticivorans strain F199.

    PubMed

    Romine, M F; Fredrickson, J K; Li, S-M W

    1999-10-01

    Enzyme induction studies with Sphingomonas aromaticivorans F199 demonstrated that both toluene and naphthalene induced expression of both naphthalene and toluene catabolic enzymes. However, neither aromatic compound induced expression of all the enzymes required for complete mineralization of either naphthalene or toluene. Activity measurements in combination with gene sequence analyses indicate that growth on either aromatic substrate in the absence of the other is, therefore, sub-optimal and is predicted to lead to the build-up of metabolites due to imbalance in toluene or naphthalene catabolic enzyme activities. Growth on toluene may be further inhibited by the co-expression of two toluene catabolic pathways, as predicted from gene sequence analyses. One of these pathways may potentially result in the formation of a dead-end intermediate, possibly benzaldehyde. In contrast, either p-cresol or benzoate can support high levels of growth. Analyses of promoter region sequences on the F199 aromatic catabolic plasmid, pNL1, suggest that additional regulatory events are modulated through the interaction of BphR with Sigma54 type promoters and through the binding of a regulator upstream of p-cresol catabolic genes and xylM. We hypothesize that the unusual gene clustering in strain F199 is optimized for simultaneous degradation of multiple aromatic compound classes, possibly in response to the heterogeneous composition of aromatic structures in the fossil organic matter present in the deep Atlantic Coastal Plain sediments from which this bacterium was isolated.

  15. Heterocyclic aromatic hydrocarbons show estrogenic activity upon metabolization in a recombinant transactivation assay.

    PubMed

    Brinkmann, Markus; Maletz, Sibylle; Krauss, Martin; Bluhm, Kerstin; Schiwy, Sabrina; Kuckelkorn, Jochen; Tiehm, Andreas; Brack, Werner; Hollert, Henner

    2014-05-20

    Heterocyclic aromatic hydrocarbons (hetero-PAHs) are increasingly studied at contaminated sites; especially at former industrial facilities where coal tar-oil was handled, e.g., wood treatment plants, high concentrations of hetero-PAHs are frequently detected in groundwater plumes. In previous studies, fractions of groundwater with high estrogenic activity contained hetero-PAHs and their hydroxylated metabolites. To evaluate this preliminary evidence, selected hetero-PAHs were screened for their estrogenic activity in lyticase yeast estrogen screen (LYES) and ER CALUX. All tested substances were inactive in the LYES. Hetero-PAHs such as acridine, xanthene, indole, 2-methylbenzofuran, 2,3-dimethylbenzofuran, dibenzofuran, dibenzothiophene, quinoline, and 6-methylquinoline were positive in the ER CALUX, with estradiol equivalence factors (EEFs) from 2.85 × 10(-7) to 3.18 × 10(-5). The EEF values of these substances were comparable to those of other xenoestrogens (e.g., alkylphenols or bisphenol A) that are sometimes found in surface water. Chemical analyses revealed that T47Dluc cells could metabolize most of the substances. Among the metabolites (tentatively) identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were hydroxides and their keto tautomers, sulfates, sulfoxides, and N-oxides. Because of their high concentrations measured in groundwater, we conclude that hetero-PAHs and metabolites may be a potential risk and should be the subject of further research.

  16. Bacterial Degradation of Aromatic Compounds

    PubMed Central

    Seo, Jong-Su; Keum, Young-Soo; Li, Qing X.

    2009-01-01

    Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms. PMID:19440284

  17. Structure-activity relationships of 2alpha-substituted androstenedione analogs as aromatase inhibitors and their aromatization reactions.

    PubMed

    Numazawa, Mitsuteru; Handa, Wakako; Hasegawa, Chie; Takahashi, Madoka

    2005-12-01

    Aromatase catalyzes the conversion of androstenedione (1a, AD) to estrone through three sequential oxygenations of the 19-methyl group. To gain insight into the spatial nature of the AD binding (active) site of aromatase in relation to the catalytic function of the enzyme, we tested for the ability of 2alpha-substituted (halogeno, alkyl, hydroxy, and alkoxy) ADs (1b-1i) to inhibit aromatase in human placental microsomes as well as their ability to serve as a substrate for the enzyme. All of the steroids inhibited the enzyme in a competitive manner with the apparent K(i)'s ranging from 45 to 1150 nM. 2alpha-Halogeno (F, Cl, and Br) and 2alpha-alkyl (CH3 and CH2CH3) steroids 1b-1f were powerful to good inhibitors (Ki=45-171 nM) whereas steroids 1g-1i, having an oxygen function (hydroxy or alkoxy) at C-2alpha, were poor inhibitors (Ki=670-1150 nM). Aromatization of some of the steroids with placental microsomes was analyzed by gas chromatography-mass spectrometry, indicating that the aromatization rate of the bromide 1d was about two-fold that of the natural substrate AD and that of 2alpha-methoxide 1h was similar to that of AD. Kinetic analysis of the aromatization of androgens revealed that a good substrate was not essentially a good inhibitor for aromatase.

  18. Spatiotemporal patterns and source implications of aromatic hydrocarbons at six rural sites across China's developed coastal regions

    NASA Astrophysics Data System (ADS)

    Zhang, Zhou; Zhang, Yanli; Wang, Xinming; Lü, Sujun; Huang, Zhonghui; Huang, Xinyu; Yang, Weiqiang; Wang, Yuesi; Zhang, Qiang

    2016-06-01

    Aromatic hydrocarbons are important anthropogenic precursors of tropospheric ozone and secondary organic aerosols. Here we measured ambient aromatic hydrocarbons from March 2012 to February 2014 at six rural sites in China's developed coastal regions. On average, benzene (B) comprised > 50% of total benzene (B), toluene (T), ethylbenzene (E), and xylenes (X) (BTEX) at sites in the Northeast China Plain (NECP) or in the North China Plain (NCP), whereas T, E, and X accounted for > 77% of total BTEX at sites in the Yangtze River Delta (YRD) and the Pearl River Delta in the south. BTEX at the northern sites was significantly correlated (p < 0.01) with combustion tracer-carbon monoxide (CO) but weakly correlated with traffic marker-methyl tert-butyl ether (MTBE), suggesting that their main sources were coal and biofuel/biomass burning with substantially elevated B levels during the winter heating period. In contrast, BTEX at the southern sites originated mainly from traffic-related and/or industrial emission sources, as indicated by the poor correlations with CO but highly significant (p < 0.01) correlations with MTBE and tetrachloroethylene, an industrial emission tracer. The B/CO emission ratios from measurement agreed within a factor of 2 with that of a previous widely used emission inventory of China, but the T/CO ratio at the NECP site and the o-X/CO ratio at the NCP site were 29% and 38% of that in the inventory, respectively; the E/CO and X/CO ratios at the YRD site were 3.2-3.5 fold that in the emission inventory.

  19. Mosquito repellent activity of volatile oils from selected aromatic plants.

    PubMed

    Lalthazuali; Mathew, Nisha

    2017-02-01

    Essential oils from fresh leaves of four aromatic plants viz., Ocimum sanctum, Mentha piperita, Eucalyptus globulus and Plectranthus amboinicus were extracted by hydrodistillation. The test solutions were prepared as 20% essential oil in ethanol and positive control as 20% DEET in ethanol. Essential oil blend was prepared as 5% concentration. Nulliparous, 3-5-day-old female adult Aedes aegypti mosquitoes were used for repellency screening as per ICMR protocol. The study showed that the repellency of 20% essential oil of O. sanctum, M. piperita and P. amboinicus were comparable with that of the standard DEET (20%) as no mosquito landing on the test was observed up to 6 h. The E. globulus oil exhibited mosquito repellency only upto 1½ h. Considerable mosquito landing and feeding was displayed in negative control. In the case of the oil blend, no landing of mosquitoes was seen up to 6 h as that of positive control. The results showed that the essential oil blend from O. sanctum, M. piperita, E. globulus and P. amboinicus could repel Ae. aegypti mosquitoes or prevent from feeding as in the case of DEET even at a lower concentration of 5%. This study demonstrates the potential of essential oils from O. sanctum, M. piperita, E. globulus and P. amboinicus and their blend as mosquito repellents against Ae. aegypti, the vector of dengue, chikungunya and yellow fever.

  20. Normal Modes Expose Active Sites in Enzymes

    PubMed Central

    Glantz-Gashai, Yitav; Samson, Abraham O.

    2016-01-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

  1. Polycyclic aromatic hydrocarbons in sediments at dredged material disposal sites around England: concentrations in 2013 and time trend information at selected sites 2008-2013.

    PubMed

    Rumney, Heather S; Bolam, Stefan G; Law, Robin J

    2015-03-15

    The maintenance of navigation channels to ports and the development of their facilities present a need to conduct dredging operations, and the subsequent disposal of dredged material at sea. Contaminant concentrations in candidate dredged material are determined and their possible impacts considered during the licensing process, which can result in the exclusion of some material from sea disposal. Monitoring of disposal sites is conducted in order to ensure that no undesirable impacts are occurring. In this study we consider the levels of polycyclic aromatic hydrocarbons (PAHs) in sediments at a number of disposal sites monitored in 2013 and variations in concentrations over time at three sites during the period 2008-2013. These were assessed using established sediment quality guidelines. Elevated PAH concentrations were generally observed only within the boundaries of the disposal sites studied.

  2. PAH RIS{reg_sign} soil test - a rapid, on-site screening test for polynuclear aromatic hydrocarbons in soil

    SciTech Connect

    McDonald, P.P.; Almond, R.E.; Friedman, S.B.

    1994-03-01

    Polynuclear aromatic hydrocarbons (PAHs) are chemicals of concern when they contaminate the environment. Current detection methods (gas chromatography and liquid chromatography) are laborious, time consuming, and expensive. As an alternative, we developed a competitive enzyme-linked immunosorbent assay kit that can be used on site for the detection of PAHs at 1 ppm in soil. The immunoassay kit includes all the components necessary to conduct the analysis in the field. The test consists of 3 major steps: (1) sample treatment; (2) immunoassay, in which the target compound is bound by a specific antibody followed by the development of an indicator color; and (3) interpretation of results. A sample the develops less color than the standard is interpreted as positive (soil sample contaminated with PAHs at {ge}1 ppm). Validation studies demonstrated that the assay is sensitive and specific. The assay detects PAH contamination in soil at 1 ppm or greater and specifically detects the 3- and 4-ringed aromatics and most of the 5- and 6-ringed aromatics. PAH-free soil samples gave negative results in the assay at a confidence level of >95%. Matrix effects, interperson, and interlot variations were minimal. The test requires <25 min to complete. The test kit is field compatible and provides a cost effective method for screening soils at risk for PAH contamination. 8 refs., 2 figs., 5 tabs.

  3. Atmospheric behaviors of polycyclic aromatic hydrocarbons at a Japanese remote background site, Noto peninsula, from 2004 to 2014

    NASA Astrophysics Data System (ADS)

    Tang, Ning; Hakamata, Mariko; Sato, Kousuke; Okada, Yumi; Yang, Xiaoyang; Tatematsu, Michiya; Toriba, Akira; Kameda, Takayuki; Hayakawa, Kazuichi

    2015-11-01

    Total suspended particulates were collected at a Japanese remote background site (Noto Air Monitoring Station; NAMS) on the Noto Peninsula from September 2004 to June 2014. Nine polycyclic aromatic hydrocarbons (PAHs) in the particulates (fluoranthene, pyrene, benz[a]anthracene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, benzo[ghi]perylene and indeno[1,2,3-cd]pyrene) were determined by HPLC with fluorescence detection. The mean total concentrations of the nine PAHs in the cold season (November to May for the years 2004-2014) was 670 pg m-3 (range 37-4100 pg m-3). The mean total concentration in the warm season (June to October for the same period) was 170 pg m-3 (range 31-960 pg m-3). The atmospheric PAH level at NAMS decreased in recent years, although no significant change was found in the warm season. An analysis of meteorological conditions showed that the atmospheric PAHs at NAMS were long range transported from Northeast China in the cold seasons and were contributed to by Japanese domestic sources in the warm seasons. Lower concentration ratios of reactive PAHs to their isomers at NAMS also supported these results. Activities associated with the Beijing Olympic and Paralympic Games in 2008 and reconstruction after the 2007 Noto Hanto earthquake may have contributed to the yearly variations of atmospheric PAH levels at NAMS during the period 2007-2009. Source control measures implemented by the Chinese and Japanese governments appear to have been effective in decreasing the atmospheric PAH levels at NAMS in recent years.

  4. Analysis of polycyclic aromatic hydrocarbons in tree-rings of Masson pine (Pinus massoniana L.) from two industrial sites in the Pearl River Delta, south China.

    PubMed

    Kuang, Yuan-wen; Zhou, Guo-yi; Wen, Da-zhi; Li, Jiong; Sun, Fang-fang

    2011-09-01

    Concentrations of polycyclic aromatic hydrocarbons (PAHs) were examined and potential sources of PAHs were identified from the dated tree-rings of Masson pine (Pinus massoniana L.) near two industrial sites (Danshuikeng, DSK and Xiqiaoshan, XQS) in the Pearl River Delta of south China. Total concentrations of PAHs (∑PAHs) were revealed with similar patterns of temporal trends in the tree-rings at both sites, suggesting tree-rings recorded the historical variation in atmospheric PAHs. The differences of individual PAHs and of ∑PAHs detected in the tree-rings between the two sites reflected the historical differences of airborne PAHs. Regional changes in industrial activities might contribute to the site-specific and period-specific patterns of the tree-ring PAHs. The diagnostic PAH ratios of Ant/(Ant + PA), FL/(FL + Pyr), and BaA/(BaA + Chr)) revealed that PAHs in the tree-rings at both sites mainly stemmed from the combustion process (pyrogenic sources). Principal component analysis further confirmed that wood burning, coal combustion, diesel, and gasoline-powered vehicular emissions were the dominant contributors of PAHs sources at DSK, while diesel combustion, gasoline and natural gas combustion, and incomplete coal combustion were responsible for the main origins of PAHs at XQS. Tree-ring analysis of PAHs was indicative of PAHs from a mixture of sources of combustion, thus minimizing the bias of short-term active air sampling.

  5. Adsorption of aromatic compounds by carbonaceous adsorbents: a comparative study on granular activated carbon, activated carbon fiber, and carbon nanotubes.

    PubMed

    Zhang, Shujuan; Shao, Ting; Kose, H Selcen; Karanfil, Tanju

    2010-08-15

    Adsorption of three aromatic organic compounds (AOCs) by four types of carbonaceous adsorbents [a granular activated carbon (HD4000), an activated carbon fiber (ACF10), two single-walled carbon nanotubes (SWNT, SWNT-HT), and a multiwalled carbon nanotube (MWNT)] with different structural characteristics but similar surface polarities was examined in aqueous solutions. Isotherm results demonstrated the importance of molecular sieving and micropore effects in the adsorption of AOCs by carbonaceous porous adsorbents. In the absence of the molecular sieving effect, a linear relationship was found between the adsorption capacities of AOCs and the surface areas of adsorbents, independent of the type of adsorbent. On the other hand, the pore volume occupancies of the adsorbents followed the order of ACF10 > HD4000 > SWNT > MWNT, indicating that the availability of adsorption site was related to the pore size distributions of the adsorbents. ACF10 and HD4000 with higher microporous volumes exhibited higher adsorption affinities to low molecular weight AOCs than SWNT and MWNT with higher mesopore and macropore volumes. Due to their larger pore sizes, SWNTs and MWNTs are expected to be more efficient in adsorption of large size molecules. Removal of surface oxygen-containing functional groups from the SWNT enhanced adsorption of AOCs.

  6. Estrogenic Activity of Mineral Oil Aromatic Hydrocarbons Used in Printing Inks

    PubMed Central

    Tarnow, Patrick; Hutzler, Christoph; Grabiger, Stefan; Schön, Karsten; Tralau, Tewes; Luch, Andreas

    2016-01-01

    The majority of printing inks are based on mineral oils (MOs) which contain complex mixtures of saturated and aromatic hydrocarbons. Consumer exposure to these oils occurs either through direct skin contacts or, more frequently, as a result of MO migration into the contents of food packaging that was made from recycled newspaper. Despite this ubiquitous and frequent exposure little is known about the potential toxicological effects, particularly with regard to the aromatic MO fractions. From a toxicological point of view the huge amount of alkylated and unsubstituted compounds therein is reason for concern as they can harbor genotoxicants as well as potential endocrine disruptors. The aim of this study was to assess both the genotoxic and estrogenic potential of MOs used in printing inks. Mineral oils with various aromatic hydrocarbon contents were tested using a battery of in vitro assays selected to address various endpoints such as estrogen-dependent cell proliferation, activation of estrogen receptor α or transcriptional induction of estrogenic target genes. In addition, the comet assay has been applied to test for genotoxicity. Out of 15 MOs tested, 10 were found to potentially act as xenoestrogens. For most of the oils the effects were clearly triggered by constituents of the aromatic hydrocarbon fraction. From 5 oils tested in the comet assay, 2 showed slight genotoxicity. Altogether it appears that MOs used in printing inks are potential endocrine disruptors and should thus be assessed carefully to what extent they might contribute to the total estrogenic burden in humans. PMID:26771904

  7. Estrogenic Activity of Mineral Oil Aromatic Hydrocarbons Used in Printing Inks.

    PubMed

    Tarnow, Patrick; Hutzler, Christoph; Grabiger, Stefan; Schön, Karsten; Tralau, Tewes; Luch, Andreas

    2016-01-01

    The majority of printing inks are based on mineral oils (MOs) which contain complex mixtures of saturated and aromatic hydrocarbons. Consumer exposure to these oils occurs either through direct skin contacts or, more frequently, as a result of MO migration into the contents of food packaging that was made from recycled newspaper. Despite this ubiquitous and frequent exposure little is known about the potential toxicological effects, particularly with regard to the aromatic MO fractions. From a toxicological point of view the huge amount of alkylated and unsubstituted compounds therein is reason for concern as they can harbor genotoxicants as well as potential endocrine disruptors. The aim of this study was to assess both the genotoxic and estrogenic potential of MOs used in printing inks. Mineral oils with various aromatic hydrocarbon contents were tested using a battery of in vitro assays selected to address various endpoints such as estrogen-dependent cell proliferation, activation of estrogen receptor α or transcriptional induction of estrogenic target genes. In addition, the comet assay has been applied to test for genotoxicity. Out of 15 MOs tested, 10 were found to potentially act as xenoestrogens. For most of the oils the effects were clearly triggered by constituents of the aromatic hydrocarbon fraction. From 5 oils tested in the comet assay, 2 showed slight genotoxicity. Altogether it appears that MOs used in printing inks are potential endocrine disruptors and should thus be assessed carefully to what extent they might contribute to the total estrogenic burden in humans.

  8. Polycyclic aromatic hydrocarbons, aliphatic hydrocarbons, trace elements and monooxygenase activity in birds nesting on the North Platte River, Casper, Wyoming, USA

    USGS Publications Warehouse

    Custer, T.W.; Custer, Christine M.; Dickerson, K.; Allen, K.; Melancon, M.J.; Schmidt, L.J.

    2001-01-01

    Tree swallow (Tachycineta bicolor) and house wren (Troglodytes aedon) eggs and chicks were collected near a refinery site on the North Platte River, Casper, Wyoming, USA and at a reference site 10 km upstream. Total polycylic aromatic hydrocarbon (PAH) concentrations in swallow and wren chicks were higher at the refinery site than at the reference site. Polycylic aromatic hydrocarbon concentrations in sediment and chick dietary samples were consistent with these findings. The general lack of methylated PAHs in sediment, diet, and bird carcasses suggested that the PAHs were derived from combustion and not from petroleum. The predominance of odd numbered aliphatic hydrocarbons and the low ratios (≤ 0.25) of pristane: n-C17 and phytane: n-C18 in chick and diet samples also suggested that swallow and wren chicks were not being chronically exposed to petroleum. Mean ethoxyresorufin-O-dealkylase and benzyloxyresorufin-O-dealkylase activities in tree swallow livers averaged nine times higher at the refinery site than at the reference site and were probably induced by exposure to PAHs. Trace element concentrations in eggs and livers of swallows and wrens were similar or greater at the reference site than at the refinery site. Selenium, strontium, and boron concentrations were elevated in eggs and livers of swallows and wrens at both the refinery and reference sites.

  9. Polycyclic aromatic hydrocarbons in sediments, mussels and crustacea around a former gasworks site in Shoreham-by-Sea, UK.

    PubMed

    Law, R J; Kelly, C A; Baker, K L; Langford, K H; Bartlett, T

    2002-09-01

    Concentrations of polycyclic aromatic hydrocarbons have been determined in sediments, mussels and crustacea in the vicinity of a former gasworks site by Shoreham Harbour, UK. Very high concentrations of PAH were found in the substrate, an ash-like material deposited on the former gasworks site, which exhibited a profile consistent with the major source of contamination being coal or coke tar produced during the period of gas production at the site. Elevated PAH concentrations were also found in mussels both from the beach below the former gasworks site, and from sites further to the east in Portslade and Hove. The significance of these concentrations were assessed using an approach which involved the calculation of benzo[a]pyrene equivalent conoentrations (BaPEs), summing concentrations of individual PAH on the basis of their comparative potency as carcinogens. BaPE ranged from values of, or close to, zero for crustacea, to 336 microg kg(-1) wet weight in mussels from Southwick Beach. The contaminated mussels are not exploited commercially but may be taken by casual gatherers, and notices have been posted to warn potential consumers.

  10. Activation of group IVC phospholipase A2 by polycyclic aromatic hydrocarbons induces apoptosis of human coronary artery endothelial cells

    PubMed Central

    Richards, Sean M.; Elgayyar, Mona A.; Menn, Fu-Minn; Vulava, Vijay M.; McKay, Larry; Sanseverino, John; Sayler, Gary; Tucker, Dawn E.; Leslie, Christina C.; Lu, Kim P.; Ramos, Kenneth S.

    2016-01-01

    Exposure to environmental pollutants, such as polycyclic aromatic hydrocarbons (PAHs) found in coal tar mixtures and tobacco sources, is considered a significant risk factor for the development of heart disease in humans. The goal of this study was to determine the influence of PAHs present at a Superfund site on human coronary artery endothelial cell (HCAEC) phospholipase A2 (PLA2) activity and apoptosis. Extremely high levels of 12 out of 15 EPA high-priority PAHs were present in both the streambed and floodplain sediments at a site where an urban creek and its adjacent floodplain were extensively contaminated by PAHs and other coal tar compounds. Nine of the 12 compounds and a coal tar mixture (SRM 1597A) activated group IVC PLA2 in HCAECs, and activation of this enzyme was associated with histone fragmentation and poly (ADP) ribose polymerase (PARP) cleavage. Genetic silencing of group IVC PLA2 inhibited both 3H-fatty acid release and histone fragmentation by PAHs and SRM 1597A, indicating that individual PAHs and a coal tar mixture induce apoptosis of HCAECs via a mechanism that involves group IVC PLA2. Western blot analysis of aortas isolated from feral mice (Peromyscus leucopus) inhabiting the Superfund site showed increased PARP and caspase-3 cleavage when compared to reference mice. These data suggest that PAHs induce apoptosis of HCAECs via activation of group IVC PLA2. PMID:21132278

  11. Asymmetric Intramolecular Alkylation of Chiral Aromatic Imines via Catalytic C-H Bond Activation

    SciTech Connect

    Watzke, Anja; Wilson, Rebecca; O'Malley, Steven; Bergman, Robert; Ellman, Jonathan

    2007-04-16

    The asymmetric intramolecular alkylation of chiral aromatic aldimines, in which differentially substituted alkenes are tethered meta to the imine, was investigated. High enantioselectivities were obtained for imines prepared from aminoindane derivatives, which function as directing groups for the rhodium-catalyzed C-H bond activation. Initial demonstration of catalytic asymmetric intramolecular alkylation also was achieved by employing a sterically hindered achiral imine substrate and catalytic amounts of a chiral amine.

  12. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

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

    2015-01-01

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

  13. Plant activation of aromatic amines mediated by cytochromes P450 and flavin-containing monooxygenases.

    PubMed

    Chiapella, C; Radovan, R D; Moreno, J A; Casares, L; Barbé, J; Llagostera, M

    2000-10-31

    To know the mechanisms involved in the activation of promutagenic aromatic amines mediated by plants, we used Persea americana S117 system (S117) for the activation of 2-aminofluorene (2-AF) and m-phenylenediamine (m-PDA) in Ames assays. In these assays, the effect of the diphenylene iodonium (DPI), an inhibitor of flavin-containing monooxygenases (FMOs), of the 1-aminobenzotriazole (1-ABT), an inhibitor of cytochromes P450 (cyt-P450s) and of the methimazole, a high-affinity substrate for FMOs, was studied. The efficacy of both inhibitors and of the methimazole was verified to find that they did partially inhibit the mutagenesis of both aromatic amines, activated with rat liver S9. Similarly, both inhibitors and methimazole did produce a significant decrease in 2-AF and m-PDA mutagenesis, when the activation system was S117, indicating that, similar to what occurs in mammalian systems, plant FMOs and cyt-P450s can metabolize aromatic amines to mutagenic product(s). However, the affinity of both FMOs and cyt-P450s of plant for 2-AF and m-PDA was different. Data obtained indicate that the activities of plant FMOs must be the main enzymatic system of m-PDA activation while, in 2-AF activation, plant cyt-P450s have the most relevant activities. In addition, peroxidases of the S117 system must contribute to 2-AF activation and some isoforms of FMOs and/or cyt-P450s of the S117 system, uninhibited by the inhibitors used, must be the responsible for a partial activation of m-PDA.

  14. Effect of Polarity of Activated Carbon Surface, Solvent and Adsorbate on Adsorption of Aromatic Compounds from Liquid Phase.

    PubMed

    Goto, Tatsuru; Amano, Yoshimasa; Machida, Motoi; Imazeki, Fumio

    2015-01-01

    In this study, introduction of acidic functional groups onto a carbon surface and their removal were carried out through two oxidation methods and outgassing to investigate the adsorption mechanism of aromatic compounds which have different polarity (benzene and nitrobenzene). Adsorption experiments for these aromatics in aqueous solution and n-hexane solution were conducted in order to obtain the adsorption isotherms for commercial activated carbon (BAC) as a starting material, its two types of oxidized BAC samples (OXs), and their outgassed samples at 900 °C (OGs). Adsorption and desorption kinetics of nitrobenzene for the BAC, OXs and OGs in aqueous solution were also examined. The results showed that the adsorption of benzene molecules was significantly hindered by abundant acidic functional groups in aqueous solution, whereas the adsorbed amount of nitrobenzene on OXs gradually increased as the solution concentration increased, indicating that nitrobenzene can adsorb favourably on a hydrophilic surface due to its high dipole moment, in contrast to benzene. In n-hexane solution, it was difficult for benzene to adsorb on any sample owing to the high affinity between benzene and n-hexane solvent. On the other hand, adsorbed amounts of nitrobenzene on OXs were larger than those of OGs in n-hexane solution, implying that nitrobenzene can adsorb two adsorption sites, graphene layers and surface acidic functional groups. The observed adsorption and desorption rate constants of nitrobenzene on the OXs were lower than those on the BAC due to disturbance of diffusion by the acidic functional groups.

  15. Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library*

    PubMed Central

    Kiefer, Jonathan D.; Srinivas, Raja R.; Lobner, Elisabeth; Tisdale, Alison W.; Mehta, Naveen K.; Yang, Nicole J.; Tidor, Bruce; Wittrup, K. Dane

    2016-01-01

    The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation. PMID:27582495

  16. Gas-particle partitioning of polycyclic aromatic hydrocarbons in urban, adjacent coastal, and continental background sites of western Greece.

    PubMed

    Terzi, Eleni; Samara, Constantini

    2004-10-01

    Particle- and gas-phase polycyclic aromatic hydrocarbons (PAHs) were collected from an urban, an adjacent coastal, and a continental background site located in Eordea basin, western Greece, to investigate their gas/ particle distributions. Thirteen two- to six-ring PAHs, included in the U.S. EPA priority pollutant list, were determined in 24-h integrated glass fiber filters and polyurethane foam samples. At the prevailing ambient temperature levels, the three-ringed species (phenanthrene, anthracene) and the four-ringed fluoranthene and pyrene were primarily found in the gas phase. Conversely, the five- and six-ring PAHs were mainly associated with the particle phase. Gas/particle partitioning coefficients, Kp, were calculated, and their relationship with the subcooled liquid vapor pressure p degrees L of individual PAHs was investigated. Despite the large variability among samples, a good linear relationship between log Kp and log p degrees L was obtained for all sampling sites following the equation log Kp = m(r) log p degrees L + b(r). In the majority of sampling events, particularly in the adjacent coastal and the continental background sites, slopes (m(r)) were found to be shallower than the value of -1, which has been suggested as reflecting equilibrium partitioning. The deviations from predicted aerosol behavior observed in the present study may be attributed to several reasons, such as the presence of nonexchangeable PAH fraction, nonequilibrium as well as different particle characteristics.

  17. Validated ligand mapping of ACE active site

    NASA Astrophysics Data System (ADS)

    Kuster, Daniel J.; Marshall, Garland R.

    2005-08-01

    Crystal structures of angiotensin-converting enzyme (ACE) complexed with three inhibitors (lisinopril, captopril, enalapril) provided experimental data for testing the validity of a prior active site model predicting the bound conformation of the inhibitors. The ACE active site model - predicted over 18 years ago using a series of potent ACE inhibitors of diverse chemical structure - was recreated using published data and commercial software. Comparison between the predicted structures of the three inhibitors bound to the active site of ACE and those determined experimentally yielded root mean square deviation (RMSD) values of 0.43-0.81 Å, among the distances defining the active site map. The bound conformations of the chemically relevant atoms were accurately deduced from the geometry of ligands, applying the assumption that the geometry of the active site groups responsible for binding and catalysis of amide hydrolysis was constrained. The mapping of bound inhibitors at the ACE active site was validated for known experimental compounds, so that the constrained conformational search methodology may be applied with confidence when no experimentally determined structure of the enzyme yet exists, but potent, diverse inhibitors are available.

  18. Validation of a computational model for predicting the site for electrophilic substitution in aromatic systems.

    PubMed

    Liljenberg, Magnus; Brinck, Tore; Herschend, Björn; Rein, Tobias; Rockwell, Glen; Svensson, Mats

    2010-07-16

    We have investigated the scope and limitations of a method for predicting the regioisomer distribution in electrophilic aromatic substitution reactions that are under kinetic control. This method is based on calculation of the relative stabilities of the sigma-complex intermediates using density functional theory. Predictions from this method can be used quantitatively for halogenations; it agreed to an accuracy of about 1 kcal/mol with experimental observations in 10 of the 11 investigated halogenation reactions. For nitrations, the method gave useful predictions for heterocyclic substrates. The method failed for nitration of monosubstituted benzenes, and we expect that more elaborate model systems, including explicit solvent molecules, will be necessary to obtain quantitatively useful predictions for such cases. For Lewis acid promoted Friedel-Crafts acylations, the method can be expected to give qualitatively correct predictions, that is, to point out the dominating isomer. For substrates where the regioisomeric outcome is highly dependent on the reaction conditions, the method can only be of qualitative use if the concentration of the free Lewis acid is high during the reaction. We have also compared the predictive capacity of the method to that of a modern reactivity index, the average local ionization energy, I(r). The latter method is found to predict the regisolectivity in halogenations and nitrations qualitatively correctly if the positions for the I(r) minima (I(S,min)) are not too sterically hindered but fails for qualitative predictions of F-C reactions. The downscaled I(S,min) values also perform well for the quantitative prediction of regioisomer distributions of halogenations. The accuracy is slightly lower than that for the new method.

  19. Relating aromatic hydrocarbon-induced DNA adducts and c-H-ras mutations in mouse skin papillomas: the role of apurinic sites.

    PubMed Central

    Chakravarti, D; Pelling, J C; Cavalieri, E L; Rogan, E G

    1995-01-01

    Mouse skin tumors contain activated c-H-ras oncogenes, often caused by point mutations at codons 12 and 13 in exon 1 and codons 59 and 61 in exon 2. Mutagenesis by the noncoding apurinic sites can produce G-->T and A-->T transversions by DNA misreplication with more frequent insertion of deoxyadenosine opposite the apurinic site. Papillomas were induced in mouse skin by several aromatic hydrocarbons, and mutations in the c-H-ras gene were determined to elucidate the relationship among DNA adducts, apurinic sites, and ras oncogene mutations. Dibenzo[a,l]pyrene (DB[a,l]P), DB[a,l]P-11,12-dihydrodiol, anti-DB[a,l]P-11,12-diol-13,14-epoxide, DB[a,l]P-8,9-dihydrodiol, 7,12-dimethylbenz[a]anthracene (DMBA), and 1,2,3,4-tetrahydro-DMBA consistently induced a CAA-->CTA mutation in codon 61 of the c-H-ras oncogene. Benzo[a]pyrene induced a GGC-->GTC mutation in codon 13 in 54% of tumors and a CAA-->CTA mutation in codon 61 in 15%. The pattern of mutations induced by each hydrocarbon correlated with its profile of DNA adducts. For example, both DB[a,l]P and DMBA primarily form DNA adducts at the N-3 and/or N-7 of deoxyadenosine that are lost from the DNA by depurination, generating apurinic sites. Thus, these results support the hypothesis that misreplication of unrepaired apurinic sites generated by loss of hydrocarbon-DNA adducts is responsible for transforming mutations leading to papillomas in mouse skin. PMID:7479797

  20. Identification and quantification of biomarkers and polycyclic aromatic hydrocarbons (PAHs) in an aged mixed contaminated site: from source to soil.

    PubMed

    Kao, Nien-Hsin; Su, Ming-Chien; Fan, Jheng-Rong; Chung, Ying-Yung

    2015-05-01

    The sources of the spill and the contaminated soils of an aged oil spill contaminated site with unknown mixed pollutants were investigated by using a set of developed forensic chemical procedures which include analysis of oil products, site investigation, gas chromatography/mass spectrometry (GC/MS) screening, biomarker identification, and finally, the confirmation of pollutants. Adamantanes (17 compounds), 10 bicyclic sesquiterpanes, 6 newly detected compounds, 16 polycyclic aromatic hydrocarbons, and 10 alkylated naphthalenes compounds in several gasoline, diesel oil samples, and contaminated soil samples were examined and quantified. GC/MS method, retention indices, relative response factors, and diagnostic ratio were used to identify and quantify pollutant compounds. The study revealed the key factors for distinguishing among gasoline and diesel oil products in the market, created a new set of retention indices for 10 bicyclic sesquiterpane compounds, and discovered 6 quantifiable compounds in analysis of fresh oil products. The suggested diagnostic ratios for BSs and the new compounds in the analysis of the biomarker show the differences among diesel products, link between the source of pollutants with contaminated soil, and the recognition of the signs of an aged spill, and the indications of weathering effects.

  1. Role of weathered coal tar pitch in the partitioning of polycyclic aromatic hydrocarbons in manufactured gas plant site sediments.

    PubMed

    Khalil, Muhammad F; Ghosh, Upal; Kreitinger, Joseph P

    2006-09-15

    Polycyclic aromatic hydrocarbons (PAHs) in manufactured gas plant (MGP) site sediments are often associated with carbonaceous particles that reduce contaminant bioavailability. Although black carbon inclusive partitioning models have been proposed to describe elevated PAH partitioning behavior, questions remain on the true loading and association of PAHs in different particle types in industrially impacted sediments. In the studied MGP sediments, the light density organic particles (coal, coke, wood, and coal tar pitch) comprised 10-20% of the total mass and 70-95% of the PAHs. The remainder of the PAHs in sediment was associated with the heavy density particles (i.e., sand, silt, and clays). Among the different particle types, coal tar pitch (quantified by a quinoline extraction method) contributed the most to the bulk sediment PAH concentration. Aqueous partition coefficients for PAHs measured using a weathered pitch sample from the field were generally an order of magnitude higher than reported for natural organic matter partitioning, and match well with theoretical predictions based on a coal tar-water partitioning model. A pitch-partitioning inclusive model is proposed that gives better estimates of the measured site-specific PAH aqueous equilibrium values than standard estimation based on natural organic matter partitioning only. Thus, for MGP impacted sediments containing weathered pitch particles, the partitioning behavior may be dominated by the sorption characteristics of pitch and not by natural organic matter or black carbon.

  2. Role of weathered coal tar pitch in the partitioning of polycyclic aromatic hydrocarbons in manufactured gas plant site sediments

    SciTech Connect

    Muhammad F. Khalil; Upal Ghosh; Joseph P. Kreitinger

    2006-09-15

    Polycyclic aromatic hydrocarbons (PAHs) in manufactured gas plant (MGP) site sediments are often associated with carbonaceous particles that reduce contaminant bioavailability. Although black carbon inclusive partitioning models have been proposed to describe elevated PAH partitioning behavior, questions remain on the true loading and association of PAHs in different particle types in industrially impacted sediments. In the studied MGP sediments, the light density organic particles (coal, coke, wood, and coal tar pitch) comprised 10-20% of the total mass and 70-95% of the PAHs. The remainder of the PAHs in sediment was associated with the heavy density particles (i.e., sand, silt, and clays). Among the different particle types, coal tar pitch (quantified by a quinoline extraction method) contributed the most to the bulk sediment PAH concentration. Aqueous partition coefficients for PAHs measured using a weathered pitch sample from the field were generally an order of magnitude higher than reported for natural organic matter partitioning, and match well with theoretical predictions based on a coal tar-water partitioning model. A pitch-partitioning inclusive model is proposed that gives better estimates of the measured site-specific PAH aqueous equilibrium values than standard estimation based on natural organic matter partitioning only. Thus, for MGP impacted sediments containing weathered pitch particles, the partitioning behavior may be dominated by the sorption characteristics of pitch and not by natural organic matter or black carbon. 25 refs., 5 figs., 1 tab.

  3. Assessment of polycyclic aromatic hydrocarbons (PAHs) contamination in surface soil of coal stockpile sites in South Kalimantan, Indonesia.

    PubMed

    Mizwar, Andy; Priatmadi, Bambang Joko; Abdi, Chairul; Trihadiningrum, Yulinah

    2016-03-01

    Concentrations, spatial distribution, and sources of 16 polycyclic aromatic hydrocarbons (PAHs), listed as priority pollutants by the United States Environmental Protection Agency (USEPA), were investigated in surface soils of three different coal stockpile, agricultural, and residential sites in South Kalimantan Province, Indonesia. Total PAHs concentration ranged from 4.69 to 22.67 mg kg(-1)-dw. PAHs concentrations in soil of coal stockpile sites were higher than those in agricultural and residential soil. A complex of petrogenic origin and pyrolytic sources was found within the study area, as suggested by the isomeric ratios of PAHs. The results of principal component analysis and multiple linear regressions (PCA/MLR) showed that three sources contributed to the PAHs in the study area, including biomass and coal combustion (48.46%), raw coal (35.49%), and vehicular emission (16.05%). The high value of total benzo[a]pyrene equivalent concentration (B[a]Peq) suggests that local residents are exposed to a high carcinogenic potential.

  4. Antimicrobial activity of essential oils from Mediterranean aromatic plants against several foodborne and spoilage bacteria.

    PubMed

    Silva, Nuno; Alves, Sofia; Gonçalves, Alexandre; Amaral, Joana S; Poeta, Patrícia

    2013-12-01

    The antimicrobial activity of essential oils extracted from a variety of aromatic plants, often used in the Portuguese gastronomy was studied in vitro by the agar diffusion method. The essential oils of thyme, oregano, rosemary, verbena, basil, peppermint, pennyroyal and mint were tested against Gram-positive (Listeria monocytogenes, Clostridium perfringens, Bacillus cereus, Staphylococcus aureus, Enterococcus faecium, Enterococcus faecalis, and Staphylococcus epidermidis) and Gram-negative strains (Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa). For most essential oils examined, S. aureus, was the most susceptible bacteria, while P. aeruginosa showed, in general, least susceptibility. Among the eight essential oils evaluated, thyme, oregano and pennyroyal oils showed the greatest antimicrobial activity, followed by rosemary, peppermint and verbena, while basil and mint showed the weakest antimicrobial activity. Most of the essential oils considered in this study exhibited a significant inhibitory effect. Thyme oil showed a promising inhibitory activity even at low concentration, thus revealing its potential as a natural preservative in food products against several causal agents of foodborne diseases and food spoilage. In general, the results demonstrate that, besides flavoring the food, the use of aromatic herbs in gastronomy can also contribute to a bacteriostatic effect against pathogens.

  5. Antitumor and antiparasitic activity of novel ruthenium compounds with polycyclic aromatic ligands.

    PubMed

    Miserachs, Helena Guiset; Cipriani, Micaella; Grau, Jordi; Vilaseca, Marta; Lorenzo, Julia; Medeiros, Andrea; Comini, Marcelo A; Gambino, Dinorah; Otero, Lucía; Moreno, Virtudes

    2015-09-01

    Five novel ruthenium(II)-arene complexes with polycyclic aromatic ligands were synthesized, comprising three compounds of the formula [RuCl(η(6)-p-cym)(L)][PF6], where p-cym = 1-isopropyl-4-methylbenzene and L are the bidentate aromatic ligands 1,10-phenanthroline-5,6-dione, 1, 5-amine-1,10-phenanthroline, 4, or 5,6-epoxy-5,6-dihydro-phenanthroline, 5. In the other two complexes [RuCl2(η(6)-p-cym)(L')], the metal is coordinated to a monodentate ligand L', where L' is phenanthridine, 2, or 9-carbonylanthracene, 3. All compounds were fully characterized by mass spectrometry and elemental analysis, as well as NMR and IR spectroscopic techniques. Obtained ruthenium compounds as well as their respective ligands were tested for their antiparasitic and antitumoral activities. Even though all compounds showed lower Trypanosoma brucei activity than the free ligands, they also resulted less toxic on mammalian cells. Cytotoxicity assays on HL60 cells showed a moderate antitumoral activity for all ruthenium compounds. Compound 1 was the most potent antitumoral (IC50 = 1.26±0.78 μM) and antiparasitic (IC50 = 0.19 ± 0.05 μM) agent, showing high selectivity towards the parasites (selectivity index >100). As complex 1 was the most promising antitumoral compound, its interaction with ubiquitin as potential target was also studied. In addition, obtained ruthenium compounds were found to bind DNA, and they are thought to interact with this macromolecule mainly through intercalation of the aromatic ligand.

  6. Evidence for segmental mobility in the active site of pepsin

    SciTech Connect

    Pohl, J.; Strop, P.; Senn, H.; Foundling, S.; Kostka, V.

    1986-05-01

    The low hydrolytic activity (k/sub cat/ < 0.001 s/sup -1/) of chicken pepsin (CP) towards tri- and tetrapeptides is enhanced at least 100 times by modification of its single sulfhydryl group of Cys-115, with little effect on K/sub m/-values. Modification thus simulates the effect of secondary substrate binding on pepsin catalysis. The rate of Cys-115 modification is substantially decreased in the presence of some competitive inhibitors, suggesting its active site location. Experiments with CP alkylated at Cys-115 with Acrylodan as a fluorescent probe or with N-iodoacetyl-(4-fluoro)-aniline as a /sup 19/F-nmr probe suggest conformation change around Cys-115 to occur on substrate or substrate analog binding. The difference /sup 1/H-nmr spectra (500 MHz) of unmodified free and inhibitor-complexed CP reveal chemical shifts almost exclusively in the aromatic region. The effects of Cu/sup + +/ on /sup 19/F- and /sup 1/H-nmr spectra have been studied. Examination of a computer graphics model of CP based on E. parasitica pepsin-inhibitor complex X-ray coordinates suggests that Cys-115 is located near the S/sub 3//S/sub 5/ binding site. The results are interpreted in favor of segmental mobility of this region important for pepsin substrate binding and catalysis.

  7. Antifertility activity and toxicity of alpha-chlorohydrin aromatic ketal analogues in male rats.

    PubMed

    Brown-Woodman, P D; White, I G; Ridley, D D

    1986-01-01

    The antifertility activity and toxicity of alpha-chlorohydrin and seven aromatic ketal derivatives were investigated in male rats. At a dose of 5 mg/kg injected intraperitoneally each day for 14 days, alpha-chlorohydrin and the methoxy benzaldehyde derivative (compound 2) produced complete infertility. The benzaldehyde derivative (compound 1) was 89% effective and the other five compounds 71-25% effective. All compounds except the least effective antifertility agent, the methylbenzaldehyde derivative (compound 3), reduced the motility of sperm recovered from the epididymis. None of the compounds caused a decrease in body or testes weight but some increased adrenal weight.

  8. Aromatic glycosyl disulfide derivatives: evaluation of their inhibitory activities against Trypanosoma cruzi.

    PubMed

    Gutiérrez, Bessy; Muñoz, Christian; Osorio, Luis; Fehér, Krisztina; Illyés, Tünde-Zita; Papp, Zsuzsa; Kumar, Ambati Ashok; Kövér, Katalin E; Sagua, Hernán; Araya, Jorge E; Morales, Patricio; Szilágyi, László; González, Jorge

    2013-06-15

    Aromatic oligovalent glycosyl disulfides and some diglycosyl disulfides were tested against three different Trypanosoma cruzi strains. Di-(β-D-galactopyranosyl-dithiomethylene) benzenes 2b and 4b proved to be the most active derivatives against all three strains of cell culture-derived trypomastigotes with IC50 values ranging from 4 to 11 μM at 37 °C. The inhibitory activities were maintained, although somewhat lowered, at a temperature of 4 °C as well. Three further derivatives displayed similar activities against at least one of the three strains. Low cytotoxicities of the active compounds, tested on confluent HeLa, Vero and peritoneal macrophage cell cultures, resulted in significantly higher selectivity indices (SI) than that of the reference drug benznidazole. Remarkably, several molecules of the tested panel strongly inhibited the parasite release from T. cruzi infected HeLa cell cultures suggesting an effect against the intracellular development of T. cruzi amastigotes as well.

  9. Patterns and sources of particle-phase aliphatic and polycyclic aromatic hydrocarbons in urban and rural sites of western Greece

    NASA Astrophysics Data System (ADS)

    Kalaitzoglou, Maria; Terzi, Eleni; Samara, Constantini

    Particle-bound aliphatic and polycyclic aromatic hydrocarbons (AHs and PAHs, respectively) were determined in the ambient air of the Eordea basin, in western Greece, where intensive coal burning for power generation takes place. Thirteen PAHs, n-alkanes (C 14-C 35), hopanes, and isoprenoid hydrocarbons (pristane and phytane) were determined in the total suspended particles collected from the atmosphere of four sites within the basin receiving potential impacts from various sources, such as fly ash, coal mining, automobile traffic, domestic heating, and agricultural or refuse burning. The same organic species were also determined in the fly ash generated in power stations, and in particulate emissions from open burning of biomass (dry corn leaves) and refuse burning. Organic particle sources were resolved using concentration diagnostic ratios and factor analysis (FA). A multivariate statistical receptor model (Absolute Principal Component Analysis, APCA) was finally employed to estimate the contribution of identified sources to the measured concentrations of organic pollutants. Four major sources for ambient PAHs and AHs were identified displaying variable contribution in different sites: (a) fossil fuel combustion, (b) biogenic emissions, (c) refuse burning, and (d) oil residues. Fuel combustion was the major source of ambient PAHs and an important source of n-alkanes in the range C 21-C 28. Oil residues were found to be the major source of low molecular weight n-alkanes (particularly the C 14-C 16), and an important source of pristane, phytane and UCM. Biogenic sources were primarily responsible for the high molecular weight n-alkanes explaining almost the entire concentration levels of homologues >C 32. Biomass burning was particularly important for the C 23-C 26n-alkanes. Despite the vicinity of certain sampling sites to power stations, coal fly ash was not identifiable as a source for ambient PAHs and AHs.

  10. Concentrations of polycyclic aromatic hydrocarbons: Their potential health risks and sources at three non-urban sites in Japan.

    PubMed

    Jadoon, Waqar A; Sakugawa, Hiroshi

    2016-09-18

    This investigation was undertaken to monitor particulate polycyclic aromatic hydrocarbons (PAHs) concentrations in order to determine their emission sources and potential human health risks in remote and rural areas of Japan. Seventeen PAHs in aerosol samples collected in remote (Kamihaya), coastal (Hiki) and inland (Higashi-Hiroshima) areas of Japan during 2013-2014 were analyzed using gas chromatography/mass spectrometry. Total PAH (Σ17PAH) concentrations in aerosol samples were in the range of 0.08-6.51 ng m(-3), 0.09-4.74 ng m(-3), and 0.21-6.53 ng m(-3) at Kamihaya, Hiki, and Higashi-Hiroshima sites, with mean concentrations of 1.63, 1.18, and 2.43 ng m(-3), respectively. Significant seasonal variation in concentrations occurred at Hiki and Higashi-Hiroshima, while no significant variation occurred at Kamihaya. Ambient air temperature greatly affected PAH concentrations in Higashi-Hiroshima, but had only moderate effects in Kamihaya and Hiki. Wind direction also influenced the concentrations of PAHs. Vehicle exhaust, industrial emissions, biomass combustion, and domestic heating and cooking were identified as the main PAH emission sources using principal component analysis. Backward trajectory calculations showed that domestically generated PAHs were significant in Kamihaya and Hiki, while in Higashi-Hiroshima concentrations were mainly influenced by long-range transport. The incremental lifetime lung cancer risk had values of 3.38 × 10(-5) and 1.84 × 10(-5) at Higashi-Hiroshima and Hiki, which are greater than the US EPA acceptable level (10(-6)). Typically, 5-6-ring PAHs contributed 95% to this overall health risk, of which benzo(a)pyrene was the largest contributor, followed by dibenz(a,h)anthracene at both residential sites. Clearly, stricter guidelines for PAHs need to be implemented at these sites to protect the population.

  11. Spatial distribution of polycyclic aromatic hydrocarbons in soil, sediment, and combusted residue at an e-waste processing site in southeast China.

    PubMed

    Leung, Anna O W; Cheung, Kwai Chung; Wong, Ming Hung

    2015-06-01

    The environmental pollution and health impacts caused by the primitive and crude recycling of e-waste have become urgent global issues. Guiyu, China is a major hotspot of e-waste recycling. In this study, the levels and distribution of polycyclic aromatic hydrocarbons in soil in Guiyu were determined to investigate the effect of e-waste activities on the environment and to identify possible sources of these pollutants. Sediment samples from a local duck pond, water gullies, a river tributary, and combusted residue from e-waste burning sites were also investigated. The general trend found in soil (Σ16 PAHs) was acid leaching site > duck pond > rice field > printer roller dump site > reservoir (control site) and ranged from 95.2 ± 54.2 to 5,210 ± 89.6 ng/g (dry wt). The highest average total PAH concentrations were found in combusted residues of wires, cables, and other computer electrical components located at two e-waste open burning sites (18,600 and 10,800 ± 3,940 ng/g). These were 195- and 113-fold higher than the PAH concentrations of soil at the control site. Sediment PAH concentrations ranged from 37.2 ± 6 to 534 ± 271 ng/g. Results of this study provide further evidence of significant input of PAHs to the environment attributed to crude e-waste recycling.

  12. Polycyclic aromatic hydrocarbon bioaccumulation by meiobenthic copepods inhabiting a superfund site: techniques for micromass body burden and total lipid analysis.

    PubMed

    Klosterhaus, Susan L; Ferguson, P Lee; Chandlert, G Thomas

    2002-11-01

    Microtechniques for polycyclic aromatic hydrocarbon (PAH) body burden and total lipid analysis were developed and applied to determine the first lipid-normalized bioaccumulation factors for a hydrophobic organic toxicant in a meiobenthic organism (0.063-0.500 mm) living in field-contaminated sediments. The total lipid microtechnique combines the standard Bligh-Dyer extraction method with a colorimetric quantification method for analysis of samples containing I to 50 microg lipid. The microtechnique for body burden analysis quantifies PAHs from tissue samples containing as little as 10 pg PAH. Fluoranthene, benz[a]anthracene, and benzo[a]pyrene biota-sediment accumulation factors (BSAFs) were determined for the meiobenthic copepod Microarthridion littorale living in an estuarine U.S. Environmental Protection Agency Superfund site. Gravid female, nongravid female, and male BSAFs were 0.82, 0.54, and 0.36, respectively, for fluoranthene; 0.50, 0.44, and 0.40, respectively, for benz[a]anthracene; and 0.09, 0.12, and 0.15, respectively, for benzo[a]pyrene. Comparison of nonlipid-normalized bioaccumulation factors (BAFs) to BSAFs indicates that M. littorale bioaccumulated PAHs on a gram lipid basis. The BSAFs declined consistently with increasing PAH log K(ow) for all copepod sex and reproductive stages. Sex- and stage-specific comparisons of BSAFs suggest that differences in lipid content and quality may lead to differences in BSAF values depending on PAH molecular weight and/or hydrophobicity.

  13. Greatly reduced bioavailability and toxicity of polycyclic aromatic hydrocarbons to Hyalella azteca in sediments from manufactured-gas plant sites.

    PubMed

    Kreitinger, Joseph P; Neuhauser, Edward F; Doherty, Francis G; Hawthorne, Steven B

    2007-06-01

    The toxicity of polycyclic aromatic hydrocarbons (PAHs) to Hyalella azteca, was measured in 34 sediment samples collected from four manufactured-gas plant (MGP) sites ranging in total PAH16 (sum of 16 U.S. Environmental Protection Agency priority pollutant PAHs) concentrations from 4 to 5700 mg/kg, total organic carbon content from 0.6 to 11%, and soot carbon from 0.2 to 5.1%. The survival and growth of H. azteca in 28-d bioassays were unrelated to total PAH concentration, with 100% survival in one sediment having 1,730 mg/kg total PAH16, whereas no survival was observed in sediment samples with concentrations as low as 54 mg/kg total PAH16. Twenty-five of the 34 sediment samples exceeded the probable effects concentration screening value of 22.8 mg/kg total PAH13 (sum of 13 PAHs) and equilibrium partitioning sediment benchmarks for PAH mixtures (on the basis of the measurement of 18 parent PAHs and 16 groups of alkylated PAHs, [PAH34]); yet, 19 (76%) of the 25 samples predicted to be toxic were not toxic to H. azteca. However, the toxicity of PAHs to H. azteca was accurately predicted when either the rapidly released concentrations as determined by mild supercritical fluid extraction (SFE) or the pore-water concentrations were used to establish the bioavailability of PAHs. These results demonstrate that the PAHs present in many sediments collected from MGP sites have low bioavailability and that both the measurement of the rapidly released PAH concentrations with mild SFE and the dissolved pore-water concentrations of PAHs are useful tools for estimating chronic toxicity to H. azteca.

  14. Accumulation and bioconcentration of polycyclic aromatic hydrocarbons in a nearshore estuarine environment near a Pensacola (Florida) creosote contamination site

    USGS Publications Warehouse

    Elder, J.F.; Dresler, P.V.

    1988-01-01

    Long-term accumulation of creosote wastes at a wood-preserving facility near Pensacola, Florida, has produced high levels of organic contamination of groundwaters near Pensacola Bay. Impacts of this contamination on the nearshore environment of the bay were examined by analysis of water, sediment and tissues of two mollusc species. One of the species (Thais haemastoma) was native to the study area. Individuals of the other test species (Crassostrea virginica) were placed in cages at the test sites for a 6-week period. Contamination at the nearshore estuarine sites was assessed by comparison to a control site in an uncontaminated area of the bay, as well as a small stream which forms a direct surface-water link between the creosote storage ponds and the bay. The study focused on polycyclic aromatic hydrocarbons (PAH), the primary components of creosote. Very little PAH in water or in the surface layer of estuarine sediments was detected, despite heavy pollution of the stream sediments. This is attributed to various degradation processes which attack the PAH compounds once they discharge into the estuary, and to the likelihood of intermittent and localised release of contaminants to the estuary. Examination of sediment cores and mollusc tissues, which provide a record integrated over time and space, revealed some accumulation of a few PAH, notably fluoranthene, pyrene, benzo(a)anthracene, chrysene and phenanthrene. In the sediments, the highest concentrations of these compounds appeared below the surface, within a depth range of 8-13 cm. Bioaccumulation of fluoranthene, pyrene and phenanthrene in both mollusc species was up to ten times greater at test sites than at the control site. This contrasts with naphthalene, the bioaccumulation of which was no greater at test sites than at the control site. These differences in bioaccumulation factors relate to structural chemistry of the compounds which control their solubility, bioavailability, susceptibility to degradation

  15. Design, synthesis and biological activity of aromatic diketone derivatives as HIV-1 integrase inhibitors.

    PubMed

    Hu, Liming; Li, Zhipeng; Wang, Zhanyang; Liu, Gengxin; He, Xianzhuo; Wang, Xiaoli; Zeng, Chengchu

    2015-01-01

    A series of aromatic diketone derivatives were designed and synthesized as potential HIV-1 integrase (IN) inhibitors and evaluated to determine their ability to inhibit the strand transfer process of HIV-1 integrase. The results indicate that (Z)-1-(3-acetyl-2-hydroxy-4,6-dimethoxyphenyl)-3-hydroxy-3-(substituted)phenylprop-2-en-1-one (5a-5d) can moderately inhibit HIV-1 integrase. The cyclization and condensation products (6a-6c and 7e-7f) of compounds 5a-5d show poor inhibitory activity against HIV-1 integrase. The molecular docking results indicate that the different types of compounds act on HIV-1 integrase in different ways, and these results can explain the differences in the inhibitory activities.

  16. Virucidal activity of essential oils from aromatic plants of San Luis, Argentina.

    PubMed

    García, C C; Talarico, L; Almeida, N; Colombres, S; Duschatzky, C; Damonte, E B

    2003-11-01

    Essential oils obtained from eight aromatic plants of San Luis Province, Argentina, were screened for virucidal activity against herpes simplex virus type 1 (HSV-1), Junin virus (JUNV) and dengue virus type 2 (DEN-2). The most potent inhibition was observed with the essential oil of Lippia junelliana and Lippia turbinata against JUNV with virucidal concentration 50% (VC(50)) values in the range 14-20 ppm, whereas Aloysia gratissima, Heterotheca latifolia and Tessaria absinthioides inhibited JUNV in the range 52-90 ppm. The virucidal activity was time- and temperature-dependent. The essential oils of A. gratissima, Artemisia douglasiana, Eupatorium patens and T. absinthioides inactivated HSV-1 at 65-125 ppm. However, only A. douglasiana and E. patens had any discernible effect on DEN-2 infectivity with VC(50) values of 60 and 150 ppm, respectively.

  17. Reaction of active uranium and thorium with aromatic carbonyls and pinacols in hydrocarbon solvents

    SciTech Connect

    Kahn, B.E.; Rieke, R.D.

    1988-02-01

    Highly reactive uranium and thorium metal powders have been prepared by reduction of the anhydrous metal(IV) chlorides in hydrocarbon solvents. The reduction employs the crystalline hydrocarbon-soluble reducing agent ((TMEDA)Li)/sub 2/(Nap) (TMEDA = N,N,N',N'-tetramethylethylenediamine, Nap = naphthalene). The resulting active metal powders have been shown to be extremely reactive with oxygen-containing compounds and have been used in the reductive coupling of aromatic ketones giving tetra-arylethylenes. Reactions with pinacols have given some mechanistic insight into the ketone coupling reaction. These finely divided metal powders activate very weakly acidic C-H bonds forming metal hydrides, which can be transferred to organic substrates.

  18. Effect of different solvent on the photocatalytic activity of ZnIn2S4 for selective oxidation of aromatic alcohols to aromatic aldehydes under visible light irradiation

    NASA Astrophysics Data System (ADS)

    Su, Li; Ye, Xiangju; Meng, Sugang; Fu, Xianliang; Chen, Shifu

    2016-10-01

    A series of ternary chalcogenides, zinc indium sulphide (ZnIn2S4), were synthesized by a simple solvothermal method with different solvents. The structure, textural, and optical properties of the resulting materials were thoroughly characterized by several techniques. The as-prepared ZnIn2S4 samples could all be employed as excellent photocatalysts to activate O2 for selective oxidation of aromatic alcohols to aromatic aldehydes under visible light illumination. The results showed that ZnIn2S4 prepared in ethanol solvent (ZIS-EtOH) exhibited the highest photocatalytic activity among the screened samples. The differences of photocatalytic performance for ZnIn2S4 samples prepared in different media were mainly attributed to the different levels of exposed {0001} special facets caused by the exposure extent of the basic crystal plane. In addition, rad O2- and positive holes were proved to be the main active species during the photocatalytic process. Combined with the previous reports, a possible photocatalytic mechanism for the selective oxidation of benzyl alcohol to benzaldehyde over ZnIn2S4 sample was proposed.

  19. PHOTOACTIVATED POLYCYCLIC AROMATIC HYDROCARBON TOXICITY IN MEDAKA (ORYZIAS LATIPES) EMBRYOS: RELEVANCE TO ENVIRONMENTAL RISK IN CONTAMINATED SITES

    EPA Science Inventory

    The hazard for photoactivated toxicity of polycyclic aromatic hydrocarbons (PAHs) has been clearly demonstrated; however, to our knowledge, the risk in contaminated systems has not been characterized. To address this question, a median lethal dose (LD50) for fluoranthene photoa...

  20. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site

    PubMed Central

    Butler, Jessica E; He, Qiang; Nevin, Kelly P; He, Zhili; Zhou, Jizhong; Lovley, Derek R

    2007-01-01

    Background Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. Results The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation

  1. Passive dosing of soil invertebrates with polycyclic aromatic hydrocarbons: limited chemical activity explains toxicity cutoff.

    PubMed

    Mayer, Philipp; Holmstrup, Martin

    2008-10-01

    The partitioning of organic soil pollutants into soil organisms is driven by their chemical activity, which normally does not exceed that of the pure pollutant. Passive dosing with the silicone poly(dimethylsiloxane) (PDMS) was used to initiate and maintain the maximum chemical activity of 10 polycyclic aromatic hydrocarbons (PAHs) in toxicity tests with the springtail Folsomia candida. The test animals could move freely on the PDMS saturated with PAHs, resulting in direct contact and exposure to saturated air. After 7 days, springtail lethality correlated neither with the octanol-water partition coefficients of the PAHs nor with their molecular size, but with their melting point All low-melting PAHs (T(M) < or = 110 degrees C) caused 100% lethality, whereas all high-melting PAHs (TM > or = 180 degrees C) caused no significant lethality. The lethality was successfully fitted to one chemical activity response curve for all PAHs tested, with effective chemical activity causing 50% lethality (Ea-50) of 0.058. It was also fitted to the PAH concentration in the PDMS, resulting in an EC(PDMS)-50 of 8.7 mM. Finally, the combined exposure to anthracene and pyrene was described by the sum of chemical activities causing lethality, in good agreement with the chemical activity-response curve obtained.

  2. Depth heterogeneity of fully aromatic polyamide active layers in reverse osmosis and nanofiltration membranes.

    PubMed

    Coronell, Orlando; Mariñas, Benito J; Cahill, David G

    2011-05-15

    We studied the depth heterogeneity of fully aromatic polyamide (PA) active layers in commercial reverse osmosis (RO) and nanofiltration (NF) membranes by quantifying near-surface (i.e., top 6 nm) and volume-averaged properties of the active layers using X-ray photoelectron spectrometry (XPS) and Rutherford backscattering spectrometry (RBS), respectively. Some membranes (e.g., ESPA3 RO) had active layers that were depth homogeneous with respect to the concentration and pK(a) distribution of carboxylic groups, degree of polymer cross-linking, concentration of barium ion probe that associated with ionized carboxylic groups, and steric effects experienced by barium ion. Other membranes (e.g., NF90 NF) had active layers that were depth heterogeneous with respect to the same properties. Our results therefore support the existence of both depth-homogeneous and depth-heterogeneous active layers. It remains to be assessed whether the depth heterogeneity consists of gradually changing properties throughout the active layer depth or of distinct sublayers with different properties.

  3. [Assessment of exposure to cancerogenic aromatic hydrocarbon during controlled-access highways management activities].

    PubMed

    Martinotti, I; Cirla, A M; Cottica, D; Cirla, P E

    2011-01-01

    The purpose of this study was an integrated assessment of exposure to benzene and Polycyclic Aromatic Hydrocarbons (PAH) in 29 workers employed to manage a controlled-access highways. A campaign was performed in summertime by environmental monitoring (active and passive airborne personal sampler), as well as by biological monitoring (urine samples of the beginning and of the end of daily shift, baseline after two days of vacation). The measured environmental levels did not differ from background environmental concentrations found in a metropolitan area (i.e. benzo[a]pyrene < 1 ng/m3; benzene < 5 mcg/m3), and the results of biological monitoring were in agreement and were compatible with extra-professional habits of the investigated subjects (1-hydroxipyrene 50-990 ng/g creatinine; unmetabolized benzene 15-2010 ng/I; t-t muconic acid < 4-222 mcg/g creatinine).

  4. Antioxidant activity of a new aromatic geranyl derivative of the resinous exudates from Heliotropium glutinosum Phil.

    PubMed

    Modak, Brenda; Rojas, Macarena; Torres, René; Rodilla, Jesús; Luebert, Federico

    2007-05-21

    Heliotropium glutinosum Phil. (Heliotropiceae) is a resinous bush that grows at a height of 2000 m in Chañaral, Chile. From the resinous exudates of Heliotropium glutinosum Phil. a new aromatic geranyl derivative: 4-methoxy-3-[(2)-7'-methyl-3'-hydroxymethyl-2',6'-octadienyl] phenol (1) and three flavonoids: 5,3'-dihydroxy-7,4'-dimethoxyflavanone (2), 5,4'-dihydroxy-7-methoxyflavanone (3) and 4'-acetyl-5-hydroxy-7-methoxyflavanone (4) were isolated and their structures were determined. Their antioxidant activity were evaluated using the bleaching of ABTS and DPPH derived cation radical methods and expressed in terms of FRE (fast reacting equivalents) and TRE (total reacting equivalents), where FRE is a good measure of the quick protection of a given compound against oxidants and TRE measures the degree of long-term protection of the antioxidant, or how effective it is against a strong oxidative stress.

  5. Corrosion Research And Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2001-01-01

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

  6. Corrosion Research and Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2002-01-01

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

  7. Chemical composition and antimicrobial activity of the essential oil from the edible aromatic plant Aristolochia delavayi.

    PubMed

    Li, Zhi-Jian; Njateng, Guy S S; He, Wen-Jia; Zhang, Hong-Xia; Gu, Jian-Long; Chen, Shan-Na; Du, Zhi-Zhi

    2013-11-01

    The essential oil obtained by hydrodistillation from the aerial parts of Aristolochia delavayi Franch. (Aristolochiaceae), a unique edible aromatic plant consumed by the Nakhi (Naxi) people in Yunnan, China, was investigated using GC/MS analysis. In total, 95 components, representing more than 95% of the oil composition, were identified, and the main constituents found were (E)-dec-2-enal (52.0%), (E)-dodec-2-enal (6.8%), dodecanal (3.35%), heptanal (2.88%), and decanal (2.63%). The essential oil showed strong inhibitory activity (96% reduction) of the production of bacterial volatile sulfide compounds (VSC) by Klebsiella pneumoniae, an effect that was comparable with that of the reference compound citral (91% reduction). Moreover, the antimicrobial activity of the essential oil and the isolated major compound against eight bacterial and six fungal strains were evaluated. The essential oil showed significant antibacterial activity against Providencia stuartii and Escherichia coli, with minimal inhibitory concentrations (MIC) ranging from 3.9 to 62.5 μg/ml. The oil also showed strong inhibitory activity against the fungal strains Trichophyton ajelloi, Trichophyton terrestre, Candida glabrata, Candida guilliermondii, and Cryptococcus neoformans, with MIC values ranging from 3.9 to 31.25 μg/ml, while (E)-dec-2-enal presented a lower antifungal activity than the essential oil.

  8. Interspecies quantitative structure-activity-activity relationships (QSAARs) for prediction of acute aquatic toxicity of aromatic amines and phenols.

    PubMed

    Furuhama, A; Hasunuma, K; Aoki, Y

    2015-01-01

    We propose interspecies quantitative structure-activity-activity relationships (QSAARs), that is, QSARs with descriptors, to estimate species-specific acute aquatic toxicity. Using training datasets consisting of more than 100 aromatic amines and phenols, we found that the descriptors that predicted acute toxicities to fish (Oryzias latipes) and algae were daphnia toxicity, molecular weight (an indicator of molecular size and uptake) and selected indicator variables that discriminated between the absence or presence of various substructures. Molecular weight and the selected indicator variables improved the goodness-of-fit of the fish and algae toxicity prediction models. External validations of the QSAARs proved that algae toxicity could be predicted within 1.0 log unit and revealed structural profiles of outlier chemicals with respect to fish toxicity. In addition, applicability domains based on leverage values provided structural alerts for the predicted fish toxicity of chemicals with more than one hydroxyl or amino group attached to an aromatic ring, but not for fluoroanilines, which were not included in the training dataset. Although these simple QSAARs have limitations, their applicability is defined so clearly that they may be practical for screening chemicals with molecular weights of ≤364.9.

  9. Complete σ* intramolecular aromatic hydroxylation mechanism through O2 activation by a Schiff base macrocyclic dicopper(I) complex.

    PubMed

    Poater, Albert; Solà, Miquel

    2013-01-01

    In this work we analyze the whole molecular mechanism for intramolecular aromatic hydroxylation through O2 activation by a Schiff hexaazamacrocyclic dicopper(I) complex, [Cu(I) 2(bsH2m)](2+). Assisted by DFT calculations, we unravel the reaction pathway for the overall intramolecular aromatic hydroxylation, i.e., from the initial O2 reaction with the dicopper(I) species to first form a Cu(I)Cu(II)-superoxo species, the subsequent reaction with the second Cu(I) center to form a μ-η(2):η(2)-peroxo-Cu(II) 2 intermediate, the concerted peroxide O-O bond cleavage and C-O bond formation, followed finally by a proton transfer to an alpha aromatic carbon that immediately yields the product [Cu(II) 2(bsH2m-O)(μ-OH)](2+).

  10. Carbon-hydrogen bond activation of aromatic imines by (Cp{sup *}{sub 2}SmH){sub 2}

    SciTech Connect

    Radu, N.S.; Buchwald, S.L.; Scott, B.; Burns, C.J.

    1996-09-17

    Treatment of (Cp{sup *}{sub 2}SmH){sub 2} with 2-phenyl-1-pyrroline forms product 1, via ortho-metalation. Complex 1 was characterized spectroscopically and by single-crystal X-ray diffraction. The C-H bond activation reaction also occurs for acyclic aromatic ketimines and aldimines. 30 refs., 1 fig.

  11. Sorption kinetics of polycyclic aromatic hydrocarbons removal using granular activated carbon: intraparticle diffusion coefficients.

    PubMed

    Valderrama, C; Gamisans, X; de las Heras, X; Farrán, A; Cortina, J L

    2008-09-15

    Granular activated carbon (GAC) was evaluated as a suitable sorbent for polycyclic aromatic hydrocarbons (PAHs) removal from aqueous solutions. For this purpose, kinetic measurements on the extraction of a family of six PAHs were taken. A morphology study was performed by means of a scanning electron microscopy (SEM) analysis of GAC samples. Analyses of the batch rate data for each PAH were carried out using two kinetic models: the homogenous particle diffusion model (HPDM) and the shell progressive model (SPM). The process was controlled by diffusion rate the solutes (PAHs) that penetrated the reacted layer at PAH concentrations in the range of 0.2-10 mg L(-1). The effective particle diffusion coefficients (D(eff)) derived from the two models were determined from the batch rate data. The Weber and Morris intraparticle diffusion model made a double contribution to the surface and pore diffusivities in the sorption process. The D(eff) values derived from both the HPMD and SPM equations varied from 1.1 x 10(-13) to 6.0 x 10(-14) m(2) s(-1). The simplest model, the pore diffusion model, was applied first for data analysis. The model of the next level of complexity, the surface diffusion model, was applied in order to gain a deeper understanding of the diffusion process. This model is able to explain the data, and the apparent surface diffusivities are in the same order of magnitude as the values for the sorption of functionalized aromatic hydrocarbons (phenols and sulphonates) that are described in the literature.

  12. Theoretical studies of chemical reactivity of metabolically activated forms of aromatic amines toward DNA.

    PubMed

    Shamovsky, Igor; Ripa, Lena; Blomberg, Niklas; Eriksson, Leif A; Hansen, Peter; Mee, Christine; Tyrchan, Christian; O'Donovan, Mike; Sjö, Peter

    2012-10-15

    The metabolism of aromatic and heteroaromatic amines (ArNH₂) results in nitrenium ions (ArNH⁺) that modify nucleobases of DNA, primarily deoxyguanosine (dG), by forming dG-C8 adducts. The activated amine nitrogen in ArNH⁺ reacts with the C8 of dG, which gives rise to mutations in DNA. For the most mutagenic ArNH₂, including the majority of known genotoxic carcinogens, the stability of ArNH⁺ is of intermediate magnitude. To understand the origin of this observation as well as the specificity of reactions of ArNH⁺ with guanines in DNA, we investigated the chemical reactivity of the metabolically activated forms of ArNH₂, that is, ArNHOH and ArNHOAc, toward 9-methylguanine by DFT calculations. The chemical reactivity of these forms is determined by the rate constants of two consecutive reactions leading to cationic guanine intermediates. The formation of ArNH⁺ accelerates with resonance stabilization of ArNH⁺, whereas the formed ArNH⁺ reacts with guanine derivatives with the constant diffusion-limited rate until the reaction slows down when ArNH⁺ is about 20 kcal/mol more stable than PhNH⁺. At this point, ArNHOH and ArNHOAc show maximum reactivity. The lowest activation energy of the reaction of ArNH⁺ with 9-methylguanine corresponds to the charge-transfer π-stacked transition state (π-TS) that leads to the direct formation of the C8 intermediate. The predicted activation barriers of this reaction match the observed absolute rate constants for a number of ArNH⁺. We demonstrate that the mutagenic potency of ArNH₂ correlates with the rate of formation and the chemical reactivity of the metabolically activated forms toward the C8 atom of dG. On the basis of geometric consideration of the π-TS complex made of genotoxic compounds with long aromatic systems, we propose that precovalent intercalation in DNA is not an essential step in the genotoxicity pathway of ArNH₂. The mechanism-based reasoning suggests rational design strategies to

  13. Aromatic amino acid mutagenesis at the substrate binding pocket of Yarrowia lipolytica lipase Lip2 affects its activity and thermostability.

    PubMed

    Wang, Guilong; Liu, Zimin; Xu, Li; Yan, Yunjun

    2014-01-01

    The lipase2 from Yarrowia lipolytica (YLLip2) is a yeast lipase exhibiting high homologous to filamentous fungal lipase family. Though its crystal structure has been resolved, its structure-function relationship has rarely been reported. By contrast, there are two amino acid residues (V94 and I100) with significant difference in the substrate binding pocket of YLLip2; they were subjected to site-directed mutagenesis (SDM) to introduce aromatic amino acid mutations. Two mutants (V94W and I100F) were created. The enzymatic properties of the mutant lipases were detected and compared with the wild-type. The activities of mutant enzymes dropped to some extent towards p-nitrophenyl palmitate (pNPC16) and their optimum temperature was 35°C, which was 5°C lower than that of the wild-type. However, the thermostability of I100F increased 22.44% after incubation for 1 h at 40°C and its optimum substrate shifted from p-nitrophenyl laurate (pNPC12) to p-nitrophenyl caprate (pNPC10). The above results demonstrated that the two substituted amino acid residuals have close relationship with such enzymatic properties as thermostability and substrate selectivity.

  14. Structure-activity relationships for vitamin D3-based aromatic a-ring analogues as hedgehog pathway inhibitors.

    PubMed

    Deberardinis, Albert M; Madden, Daniel J; Banerjee, Upasana; Sail, Vibhavari; Raccuia, Daniel S; De Carlo, Daniel; Lemieux, Steven M; Meares, Adam; Hadden, M Kyle

    2014-05-08

    A structure-activity relationship study for a series of vitamin D3-based (VD3) analogues that incorporate aromatic A-ring mimics with varying functionality has provided key insight into scaffold features that result in potent, selective Hedgehog (Hh) pathway inhibition. Three analogue subclasses containing (1) a single substitution at the ortho or para position of the aromatic A-ring, (2) a heteroaryl or biaryl moiety, or (3) multiple substituents on the aromatic A-ring were prepared and evaluated. Aromatic A-ring mimics incorporating either single or multiple hydrophilic moieties on a six-membered ring inhibited the Hh pathway in both Hh-dependent mouse embryonic fibroblasts and cultured cancer cells (IC50 values 0.74-10 μM). Preliminary studies were conducted to probe the cellular mechanisms through which VD3 and 5, the most active analogue, inhibit Hh signaling. These studies suggested that the anti-Hh activity of VD3 is primarily attributed to the vitamin D receptor, whereas 5 affects Hh inhibition through a separate mechanism.

  15. Aromatic lipoxin A4 and lipoxin B4 analogues display potent biological activities.

    PubMed

    O'Sullivan, Timothy P; Vallin, Karl S A; Shah, Syed Tasadaque Ali; Fakhry, Jérôme; Maderna, Paola; Scannell, Michael; Sampaio, Andre L F; Perretti, Mauro; Godson, Catherine; Guiry, Patrick J

    2007-11-29

    Lipoxins are a group of biologically active eicosanoids typically formed by transcellular lipoxygenase activity. Lipoxin A4 (LXA4) and Lipoxin B4 (LXB4) biosynthesis has been detected in a variety of inflammatory conditions. The native lipoxins LXA4 and LXB4 demonstrate potent antiinflammatory and proresolution bioactions. However, their therapeutic potential is compromised by rapid metabolic inactivation by PG dehydrogenase-mediated oxidation and reduction. Here we report on the stereoselective synthesis of aromatic LXA4 and LXB4 analogues by employing Sharpless epoxidation, Pd-mediated Heck coupling, and diastereoselective reduction as the key transformations. Subsequent biological testing has shown that these analogues display potent biological activities. Phagocytic clearance of apoptotic leukocytes plays a critical role in the resolution of inflammation. Both LXA4 analogues (1R)-3a and (1S)-3a were found to stimulate a significant increase in phagocytosis of apoptotic polymorphonuclear leukocytes (PMN) by macrophages, with comparable efficacy to the effect of native LXA4, albeit greater potency, while the LXB4 analogue also stimulated phagocytosis with a maximum effect observed at 10-11 M. LX-stimulated phagocytosis was associated with rearrangement of the actin cytoskeleton consistent with that reported for native lipoxins. Using zymosan-induced peritonitis as a murine model of acute inflammation (1R)-3a significantly reduced PMN accumulation.

  16. Antioxidant and Anti-Osteoporotic Activities of Aromatic Compounds and Sterols from Hericium erinaceum.

    PubMed

    Li, Wei; Lee, Sang Hyun; Jang, Hae Dong; Ma, Jin Yeul; Kim, Young Ho

    2017-01-11

    Hericium erinaceum, commonly called lion's mane mushroom, is a traditional edible mushroom widely used in culinary applications and herbal medicines in East Asian countries. In this study, a new sterol, cerevisterol 6-cinnamate (6), was isolated from the fruiting bodies of H. erinaceum together with five aromatic compounds 1-5 and five sterols 7-11. The chemical structures of these compounds were elucidated using chemical and physical methods and comparison of HRESIMS, ¹D-NMR (¹H, (13)C, and DEPT) and 2D-NMR (COSY, HMQC, HMBC, and NOESY) spectra with previously reported data. The antioxidant and anti-osteoporotic activities of extracts and the isolated compounds 1-11 were investigated. All compounds exhibited peroxyl radical-scavenging capacity but only compounds 1, 3, and 4 showed potent reducing capacity. Moreover, compounds 1, 2, 4, and 5 showed moderate effects on cellular antioxidant activity and inhibited the receptor activator of nuclear factor κB ligand (RANKL)-induced osteoclastic differentiation. These results suggested that H. erinaceum could be utilized in the development of natural antioxidant and anti-osteoporotic nutraceuticals and functional foods.

  17. Antitumor and antimicrobial activities of some hetero aromatic benzofurans derived from naturally occurring visnagin.

    PubMed

    El-Nakkady, Sally S; Roaiah, Hanaa F; El-Serwy, Weam S; Soliman, Abdel Mohsen; El-Moez, Sherein I Abd; Abdel-Rahman, Adel A H

    2012-01-01

    Bromination of visnaginone (1) yielded the dibromo derivative (2), which upon methylation with methyl iodide gave 1-(2,7-dibromo-4,6-dimethoxybenzofuran-5-yl) ethanone (3). Compound (3) reacted with dimethylformamide dimethylacetal to give (4). The reaction of (3) with aromatic aldehydes namely (vanillin, benzaldehyde and 3-anisaldehyde) in ammonium acetate, malononitrile and/or butyric cyanoanhydride gave the 2-amino substituted nicotinonitriles (5a-c) and the 2-hydroxyl substituted nicotinonitriles (7a-c), respectively, while in piperidine gave (E)-1-(2,7-dibromo-4,6-dimethoxybenzofuran-5-yl)-3-(substituted)prop-2-en-l-one (11a-c). (5a) was hydrolyzed with sulfuric acid on cold to give the nicotinic acid derivative (6a). When compound (3) reacted with hydrazines and aromatic amines, it gave the Schiff bases (8a,b) and (10a,b), respectively. (8b) reacted with thioglycolic acid to give the thiazolidin-4-one (9b). When (11a-c) reacted with thiourea, it gave the pyrimidine derivatives (12a-c). (11a,b) also reacted with butyric cyanoanhydride and hydroxylamine hydrochloride to give (13a,b) and (15a,b), respectively. When the carboxylate (13a) was treated with 2,4-dinitroaniline, it gave the carboxamide (14a). Compounds (11b,c) reacted with hydrazine derivatives (hydrazine hydrate and phenylhydrazine) yielding the substituted pyrazole derivatives (16b,c) and (17b,c), respectively. All the structures of the synthesized compounds were elucidated by elemental analyses and spectral data. The newly synthesized benzofuran compounds showed a strong to moderate cytotoxicity against liver HEPG2 cancer cell line compared to 5-fluorouracil and doxorubicin (the anticancer agents). Compounds (2, 6a, 13a, 14a, 16c and 17b) were the most active compounds in descending order. The synthesized compounds were also tested for their antimicrobial activity. Compound (10b) showed the highest activity against all the tested strains followed by 6, 10a, 5a, 8b and 7a in descending order.

  18. Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

    PubMed

    Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

    2015-12-11

    Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases.

  19. Antimicrobial Activity of Seven Essential Oils From Iranian Aromatic Plants Against Common Causes of Oral Infections

    PubMed Central

    Zomorodian, Kamiar; Ghadiri, Pooria; Saharkhiz, Mohammad Jamal; Moein, Mohammad Reza; Mehriar, Peiman; Bahrani, Farideh; Golzar, Tahereh; Pakshir, Keyvan; Fani, Mohammad Mehdi

    2015-01-01

    Background: Over the past two decades, there has been a growing trend in using oral hygienic products originating from natural resources such as essential oils (EOs) and plant extracts. Seven aromatic plants used in this study are among popular traditional Iranian medicinal plants with potential application in modern medicine as anti-oral infectious diseases. Objectives: This study was conducted to determine the chemical composition and antimicrobial activities of essential oils from seven medicinal plants against pathogens causing oral infections. Materials and Methods: The chemical compositions of EOs distilled from seven plants were analyzed by gas chromatography/mass spectrometry (GC/MS). These plants included Satureja khuzestanica, S. bachtiarica, Ocimum sanctum, Artemisia sieberi, Zataria multiflora, Carum copticum and Oliveria decumbens. The antimicrobial activity of the essential oils was evaluated by broth micro-dilution in 96 well plates as recommended by the Clinical and Laboratory Standards Institute (CLSI) methods. Results: The tested EOs inhibited the growth of examined oral pathogens at concentrations of 0.015-16 µL/mL. Among the examined oral pathogens, Enterococcus faecalis had the highest Minimum Inhibitory Concentrations (MICs) and Minimum Microbicidal Concentrations (MMCs). Of the examined EOs, S. khuzestanica, Z. multiflora and S. bachtiarica, showed the highest antimicrobial activities, respectively, while Artemisia sieberi exhibited the lowest antimicrobial activity. Conclusions: The excellent antimicrobial activities of the tested EOs might be due to their major phenolic or alcoholic monoterpenes with known antimicrobial activities. Hence, these EOs can be possibly used as an antimicrobial agent in treatment and control of oral pathogens. PMID:25793100

  20. Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity

    SciTech Connect

    Johnson, Christopher W.; Salvachua, Davinia; Khanna, Payal; Smith, Holly; Peterson, Darren J.; Beckham, Gregg T.

    2016-04-22

    The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCA decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92+/-0.48 g/L muconate. Furthermore, this study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions.

  1. Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity

    DOE PAGES

    Johnson, Christopher W.; Salvachua, Davinia; Khanna, Payal; ...

    2016-04-22

    The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCAmore » decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92+/-0.48 g/L muconate. Furthermore, this study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions.« less

  2. Possible Mechanism of Liver Necrosis Caused by Aromatic Organic Compounds

    PubMed Central

    Brodie, Bernard B.; Reid, Watson D.; Cho, Arthur K.; Sipes, Glenn; Krishna, Gopal; Gillette, James R.

    1971-01-01

    Treatment of rats with phenobarbital, which stimulates the activity of the drug-metabolizing enzymes in the liver, potentiates hepatic necrosis elicited by bromobenzene and a number of other chemically inert halogenated aromatic hydrocarbons. Radioautographic studies indicate that [14C]bromobenzene is covalently bound at the sites of necrosis. From these results, it is inferred that the hepatotoxic effects of the halogenated aromatic hydrocarbons are mediated by chemically active metabolites formed in hepatocytes. In accord with this view, a number of aromatic halogenated hydrocarbons are converted by microsomes in vitro to active intermediates which form covalent complexes with glutathione (GSH). Images PMID:4395686

  3. THE CONNECTION BETWEEN 3.3 {mu}m POLYCYCLIC AROMATIC HYDROCARBON EMISSION AND ACTIVE GALACTIC NUCLEUS ACTIVITY

    SciTech Connect

    Woo, Jong-Hak; Park, Dawoo; Kim, Ji Hoon; Imanishi, Masatoshi

    2012-02-15

    We investigate the connection between starburst and active galactic nucleus (AGN) activity by comparing 3.3 {mu}m polycyclic aromatic hydrocarbon (PAH) emission with AGN properties. Utilizing the slitless spectroscopic capability of the AKARI space telescope, we observe a moderate-luminosity Type I AGN at z {approx} 0.4 to measure global starburst activity. The 3.3 {mu}m PAH emissions are detected for 7 out of 26 target galaxies. We find no strong correlation between the 3.3 {mu}m PAH emission and AGN luminosity in the limited range of the observed AGN luminosity, suggesting that global star formation may not be closely related to AGN activity. Combining our measurements with previous 3.3 {mu}m measurements of low-redshift Type I AGNs in the literature, we investigate the connection between nuclear starburst and AGN activity. In contrast to global star formation, the 3.3 {mu}m PAH luminosity measured from the central part of galaxies correlates with AGN luminosity, implying that starburst activity and AGN activity are directly connected in the nuclear region.

  4. Effect of aromatic cedar mulch on Argentine ant (Hymenoptera: Formicidae) foraging activity and nest establishment.

    PubMed

    Meissner, Heike E; Silverman, Jules

    2003-06-01

    In the laboratory, Argentine ant, Linepithema humile (Mayr), mortality was positively correlated to the length of an aromatic cedar mulch section that had to be crossed before food could be reached. When ants could access food without crossing the mulch, mortality was not correlated to mulch section length. In the field, Argentine ants showed a tendency to avoid aromatic cedar mulch as a nesting substrate. In plant beds alongside buildings the number of ant nests (pockets containing brood) found was not significantly different between aromatic cedar and cypress mulch. However, when pine straw mulch around oak trees was replaced with aromatic cedar or cypress mulch, a similar number of ant nests was found in the cypress mulch as in the original pine straw, whereas numbers in aromatic cedar mulch were significantly lower. Also, fewer ants were trailing on the trees surrounded by aromatic cedar mulch compared with cypress mulch or the original pine straw. The number of ants attracted to apple jelly baits placed alongside the buildings did not differ between mulch types; neither did the number of ant trails crossing the mulch beds around the buildings. We suggest that aromatic cedar mulch may help control Argentine ants and reduce insecticide input when applied in combination with conventional control methods.

  5. Human Aldo-Keto Reductases and the Metabolic Activation of Polycyclic Aromatic Hydrocarbons

    PubMed Central

    2015-01-01

    Aldo-keto reductases (AKRs) are promiscuous NAD(P)(H) dependent oxidoreductases implicated in the metabolic activation of polycyclic aromatic hydrocarbons (PAH). These enzymes catalyze the oxidation of non-K-region trans-dihydrodiols to the corresponding o-quinones with the concomitant production of reactive oxygen species (ROS). The PAH o-quinones are Michael acceptors and can form adducts but are also redox-active and enter into futile redox cycles to amplify ROS formation. Evidence exists to support this metabolic pathway in humans. The human recombinant AKR1A1 and AKR1C1–AKR1C4 enzymes all catalyze the oxidation of PAH trans-dihydrodiols to PAH o-quinones. Many human AKRs also catalyze the NADPH-dependent reduction of the o-quinone products to air-sensitive catechols, exacerbating ROS formation. Moreover, this pathway of PAH activation occurs in a panel of human lung cell lines, resulting in the production of ROS and oxidative DNA damage in the form of 8-oxo-2′-deoxyguanosine. Using stable-isotope dilution liquid chromatography tandem mass spectrometry, this pathway of benzo[a]pyrene (B[a]P) metabolism was found to contribute equally with the diol-epoxide pathway to the activation of this human carcinogen in human lung cells. Evaluation of the mutagenicity of anti-B[a]P-diol epoxide with B[a]P-7,8-dione on p53 showed that the o-quinone produced by AKRs was the more potent mutagen, provided that it was permitted to redox cycle, and that the mutations observed were G to T transversions, reminiscent of those observed in human lung cancer. It is concluded that there is sufficient evidence to support the role of human AKRs in the metabolic activation of PAH in human lung cell lines and that they may contribute to the causation of human lung cancer. PMID:25279998

  6. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

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

    1992-02-01

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

  7. Factors that Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase†‡

    PubMed Central

    Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Carrell, Christopher J.; Mathews, F. Scott; Jorns, Marilyn Schuman

    2009-01-01

    NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative 2-electron oxidation of P2C but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single 2-electron oxidation step. Wild-type and mutant enzyme exhibit identical rate constants for P2C oxidation to dihydropicolinate and isomerization of a reduced enzyme•dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Picolinate release from Tyr258Phe is 100-fold faster than turnover. The presence of bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10- to 75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate or 1-cyclohexenoate, a 1-deaza P2C analog. The reduced Tyr258Phe•1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD. PMID:19702312

  8. Crystallographic Analysis of Active Site Contributions to Regiospecificity in the Diiron Enzyme Toluene 4-Monooxygenase

    SciTech Connect

    Bailey, Lucas J.; Acheson, Justin F.; McCoy, Jason G.; Elsen, Nathaniel L.; Phillips, Jr., George N.; Fox, Brian G.

    2014-10-02

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric {mu}-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH{sub 2}-benzoate and p-Br-benzoate showed a {mu}-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a {pi}-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 {angstrom}) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential

  9. [Structural regularities in activated cleavage sites of thrombin receptors].

    PubMed

    Mikhaĭlik, I V; Verevka, S V

    1999-01-01

    Comparison of thrombin receptors activation splitting sites sequences testifies to their similarity both in activation splitting sites of protein precursors and protein proteinase inhibitors reactive sites. In all these sites corresponded to effectory sites P2'-positions are placed by hydrophobic amino-acids only. The regularity defined conforms with previous thesis about the role of effectory S2'-site in regulation of the processes mediated by serine proteinases.

  10. Analogues of capsaicin with agonist activity as novel analgesic agents; structure-activity studies. 1. The aromatic "A-region".

    PubMed

    Walpole, C S; Wrigglesworth, R; Bevan, S; Campbell, E A; Dray, A; James, I F; Perkins, M N; Reid, D J; Winter, J

    1993-08-06

    A series of analogues of capsaicin, the pungent principle of chilli peppers, was synthesized and tested in assays for capsaicin-like agonism in vitro. The results of these assays were compared with activities in an acute nociceptive model and a correlation was observed which established that the results of these in vitro assays were predictive of analgesia. Using a modular approach the structure-activity profile of specific regions of capsaicin congeners was established using an in vitro assay measuring 45Ca2+ uptake into neonatal rat dorsal root ganglia neurones. Substituted benzylnonanamides 2a-z and N-octyl-substituted phenylacetamides 4a-v were made to test the requirements for activity in the aromatic "A-region" of the molecule. Compounds with the natural substitution pattern (2b and 4c) and the corresponding catechols (2i and 4g) were the most potent, although the catechols were less potent in vivo. Other substitution patterns have reduced activity. These results have established stringent structural requirements for capsaicin-like activity in this part of the molecule.

  11. Polybenzimidazole via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G. (Inventor)

    1994-01-01

    Di(hydroxyphenyl)benzimidazole monomers were prepared from phenyl-4-hydroxybenzoate and aromatic bis(o-diamine)s. These monomers were used in the synthesis of soluble polybenzimidazoles. The reaction involved the aromatic nucleophilic displacement of various di(hydroxyphenyl)benzimidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds in the presence of an alkali metal base. These polymers exhibited lower glass transition temperatures, improved solubility, and better compression moldability over their commercial counterparts.

  12. Targeting of arenavirus RNA synthesis by a carboxamide-derivatized aromatic disulfide with virucidal activity.

    PubMed

    Sepúlveda, Claudia S; García, Cybele C; Levingston Macleod, Jesica M; López, Nora; Damonte, Elsa B

    2013-01-01

    Several arenaviruses can cause severe hemorrhagic fever (HF) in humans, representing a public health threat in endemic areas of Africa and South America. The present study characterizes the potent virucidal activity of the carboxamide-derivatized aromatic disulfide NSC4492, an antiretroviral zinc finger-reactive compound, against Junín virus (JUNV), the causative agent of Argentine HF. The compound was able to inactivate JUNV in a time and temperature-dependent manner, producing more than 99 % reduction in virus titer upon incubation with virions at 37 °C for 90 min. The ability of NSC4492-treated JUNV to go through different steps of the multiplication cycle was then evaluated. Inactivated virions were able to bind and enter into the host cell with similar efficiency as control infectious particles. In contrast, treatment with NSC4492 impaired the capacity of JUNV to drive viral RNA synthesis, as measured by quantitative RT-PCR, and blocked viral protein expression, as determined by indirect immunofluorescence. These results suggest that the disulfide NSC4492 targets on the arenavirus replication complex leading to impairment in viral RNA synthesis. Additionally, analysis of VLP produced in NSC4492-treated cells expressing JUNV matrix Z protein revealed that the compound may interact with Z resulting in an altered aggregation behavior of this protein, but without affecting its intrinsic self-budding properties. The potential perspectives of NSC4492 as an inactivating vaccinal compound for pathogenic arenaviruses are discussed.

  13. Targeting of Arenavirus RNA Synthesis by a Carboxamide-Derivatized Aromatic Disulfide with Virucidal Activity

    PubMed Central

    Sepúlveda, Claudia S.; García, Cybele C.; Levingston Macleod, Jesica M.

    2013-01-01

    Several arenaviruses can cause severe hemorrhagic fever (HF) in humans, representing a public health threat in endemic areas of Africa and South America. The present study characterizes the potent virucidal activity of the carboxamide-derivatized aromatic disulfide NSC4492, an antiretroviral zinc finger-reactive compound, against Junín virus (JUNV), the causative agent of Argentine HF. The compound was able to inactivate JUNV in a time and temperature-dependent manner, producing more than 99 % reduction in virus titer upon incubation with virions at 37°C for 90 min. The ability of NSC4492-treated JUNV to go through different steps of the multiplication cycle was then evaluated. Inactivated virions were able to bind and enter into the host cell with similar efficiency as control infectious particles. In contrast, treatment with NSC4492 impaired the capacity of JUNV to drive viral RNA synthesis, as measured by quantitative RT-PCR, and blocked viral protein expression, as determined by indirect immunofluorescence. These results suggest that the disulfide NSC4492 targets on the arenavirus replication complex leading to impairment in viral RNA synthesis. Additionally, analysis of VLP produced in NSC4492-treated cells expressing JUNV matrix Z protein revealed that the compound may interact with Z resulting in an altered aggregation behavior of this protein, but without affecting its intrinsic self-budding properties. The potential perspectives of NSC4492 as an inactivating vaccinal compound for pathogenic arenaviruses are discussed. PMID:24278404

  14. Mineralisation and primary biodegradation of aromatic organophosphorus flame retardants in activated sludge.

    PubMed

    Jurgens, Sharona S; Helmus, Rick; Waaijers, Susanne L; Uittenbogaard, Dirk; Dunnebier, Dorien; Vleugel, Melissa; Kraak, Michiel H S; de Voogt, Pim; Parsons, John R

    2014-09-01

    Halogen-free flame retardants (HFFRs), such as the aromatic organophosphorus flame retardants (OPFRs) triphenyl phosphate (TPHP), resorcinol bis(diphenylphosphate) (PBDPP) and bisphenol A bis(diphenylphosphate) (BPA-BDPP) have been proposed as potential replacements for brominated flame retardants in polymers and textiles. Although these OPFRs are already marketed, their environmental fate and effects are poorly characterised. The aim of this study was therefore to determine the mineralisation and primary biodegradation of these OPFRs by activated sludge. Mineralisation was monitored by measuring CO2 production by means of GC analysis, whereas primary biodegradation was monitored by LC-MS/MS analysis of the OPFRs and their potential metabolites. TPHP was biodegraded and mineralised most rapidly and achieved the requirement for ready biodegradability (60% of theoretical maximum mineralisation). Primary biodegradation was also rapid for PBDPP, but 60% mineralisation was not achieved within the time of the test, suggesting that transformation products of PBDPP may accumulate. Primary degradation of BPA-BDPP was very slow and very low CO2 production was also observed. Based on these results, TPHP and to a lesser extent PBDPP appear to be suitable replacements for the more environmentally persistent brominated flame retardants.

  15. Extraction of sediment-associated polycyclic aromatic hydrocarbons with granular activated carbon.

    PubMed

    Rakowska, M I; Kupryianchyk, D; Grotenhuis, T; Rijnaarts, H H M; Koelmans, A A

    2013-02-01

    Addition of activated carbon (AC) to sediments has been proposed as a method to reduce ecotoxicological risks of sediment-bound contaminants. The present study explores the effectiveness of granular AC (GAC) in extracting polycyclic aromatic hydrocarbon (PAH) from highly contaminated sediments. Four candidate GAC materials were screened in terms of PAH extraction efficiency using single-step 24-h GAC extractions, with traditional 24-h Tenax extraction as a reference. Subsequently, sorption of native PAHs to the best performing GAC 1240W (0.45-1.70 mm) was studied for sediment only and for GAC-sediment mixtures at different GAC-sediment weight ratios, using 76-µm polyoxymethylene (POM) passive samplers. Granular AC sorption parameters for PAHs were determined by subtracting the contribution of PAH sorption to sediment from PAH sorption to the GAC-sediment mixture. It appears that the binding of PAHs and the effectiveness of GAC to reduce sediment porewater concentrations were highly dependent on the GAC-sediment mixing ratio and hydrophobicity of the PAH. Despite the considerable fouling of GAC by organic matter and oil, 50 to 90% of the most available PAH was extracted by the GAC during a 28-d contact time, at a dose as low as 4%, which also is a feasible dose in field-scale applications aimed at cleaning the sediment by GAC addition and removal.

  16. A quantum chemical study for exploring the inhibitory effect of nitrogen containing species on the adsorption of polynuclear aromatic hydrocarbons over a Bronsted acid site

    NASA Astrophysics Data System (ADS)

    Celis-Cornejo, C. M.; Garnica Mantilla, M. M.; Baldovino-Medrano, V. G.; Ramírez-Caballero, G. E.

    2016-08-01

    The analysis of the inhibitory effect of nitrogenated compounds on the hydroprocessing and hydropurification of oil derived fuels is important to produce cleaner fuels. In this work, density functional theory calculations were performed to investigate the effect of the nitrogen containing molecules on the adsorption of Polynuclear Aromatic Hydrocarbons (PAHs). Mordenite was chosen as a zeolitic structure for simulating a Bronsted acid site. The character of the acid site was confirmed by both a vibrational frequency calculation and a Bader charge analysis. From the adsorption calculations, it was found that the adsorption energy of PAHs increases with the number of aromatic rings in the structure. Also, the nitrogen containing species possibly inhibit more extensively two and three rings PAHs because of their lower adsorption energies. Finally, it was observed that the nitrogen species tend to drag the proton from the mordenite acid site. This explains the inhibitory effect in the adsorption of PAHs and contributes to understanding the dynamics of hydrocarbon hydroprocessing in refineries.

  17. Evaluation of heavy metal and polycyclic aromatic hydrocarbons accumulation in plants from typical industrial sites: potential candidate in phytoremediation for co-contamination.

    PubMed

    Sun, Lu; Liao, Xiaoyong; Yan, Xiulan; Zhu, Ganghui; Ma, Dong

    2014-11-01

    The heavy metal and polycyclic aromatic hydrocarbons (PAHs) contents were evaluated in surface soil and plant samples of 18 wild species collected from 3 typical industrial sites in South Central China. The accumulative characteristics of the plant species for both heavy metal and PAHs were discussed. The simultaneous accumulation of heavy metal and PAHs in plant and soil was observed at all the investigated sites, although disparities in spatial distributions among sites occurred. Both plant and soil samples were characterized by high accumulation for heavy metal at smelting site, moderate enrichment at coke power and coal mining sites, whereas high level of PAHs (16 priority pollutants according to US Environmental Protection Agency) at coke power site, followed sequentially by coal mining and smelting sites. Based on the differences of heavy metal and PAH accumulation behaviors of the studied plant species, heavy metal and PAH accumulation strategies were suggested: Pteris vittata L. and Pteris cretica L. for As and PAHs, Boehmeria nivea (L.) Gaud for Pb, As, and PAHs, and Miscanthus floridulu (Labnll.) Warb for Cu and PAHs. These native plant species could be proposed as promising materials for heavy metal and PAHs combined pollution remediation.

  18. Activation of the cnidarian oxidative stress response by ultraviolet radiation, polycyclic aromatic hydrocarbons and crude oil

    PubMed Central

    Tarrant, A. M.; Reitzel, A. M.; Kwok, C. K.; Jenny, M. J.

    2014-01-01

    Organisms are continuously exposed to reactive chemicals capable of causing oxidative stress and cellular damage. Antioxidant enzymes, such as superoxide dismutases (SODs) and catalases, are present in both prokaryotes and eukaryotes and provide an important means of neutralizing such oxidants. Studies in cnidarians have previously documented the occurrence of antioxidant enzymes (transcript expression, protein expression and/or enzymatic activity), but most of these studies have not been conducted in species with sequenced genomes or included phylogenetic analyses, making it difficult to compare results across species due to uncertainties in the relationships between genes. Through searches of the genome of the sea anemone Nematostella vectensis Stephenson, one catalase gene and six SOD family members were identified, including three copper/zinc-containing SODs (CuZnSODs), two manganese-containing SODs (MnSODs) and one copper chaperone of SOD (CCS). In 24 h acute toxicity tests, juvenile N. vectensis showed enhanced sensitivity to combinations of ultraviolet radiation (UV) and polycyclic aromatic hydrocarbons (PAHs, specifically pyrene, benzo[a]pyrene and fluoranthene) relative to either stressor alone. Adult N. vectensis exhibited little or no mortality following UV, benzo[a]pyrene or crude oil exposure but exhibited changes in gene expression. Antioxidant enzyme transcripts were both upregulated and downregulated following UV and/or chemical exposure. Expression patterns were most strongly affected by UV exposure but varied between experiments, suggesting that responses vary according to the intensity and duration of exposure. These experiments provide a basis for comparison with other cnidarian taxa and for further studies of the oxidative stress response in N. vectensis. PMID:24436378

  19. Aromatic plants essential oils activity on Fusarium verticillioides Fumonisin B(1) production in corn grain.

    PubMed

    López, A G; Theumer, M G; Zygadlo, J A; Rubinstein, H R

    2004-10-01

    The minimum inhibitory concentration (MIC) of Origanum vulgare, Aloysia triphylla, Aloysia polystachya and Mentha piperita essential oils (EOs) against Fusarium verticillioides M 7075 (F. moniliforme, Sheldon) were assessed, using the semisolid agar antifungal susceptibility (SAAS) technique. O. vulgare, A. triphylla, A. polystachya and M. piperita EOs were evaluated at final concentrations of 10, 20, 40, 50, 100, 200, 250, 500, 1000 and 1500 epsilonl per litre (epsilonl/l) of culture medium. A. triphylla and O. vulgare EOs showed the highest inhibitory effects on F. verticillioides mycelial development. This inhibition was observed at 250 and 500 epsilonl/l for EOs coming from Aloysia triphylla and O. vulgare, respectively. Thus, the effects of EOs on FB(1) production were evaluated using corn grain (Zea mays) as substrate. The EOs were inserted on the 5th, 10th, 15th and 20th day of maize postinoculation with a conidia suspension of F. verticillioides. O. vulgare and A. triphylla were applied to give final concentrations of 30 ppm and 45 ppm, respectively. Different effects were observed in the toxicogenicity at the 20th day treatment. The O. vulgare EO decreased the production level of FB(1) (P < 0.01) while A. triphyla EO increased it (P < 0.001) with respect to those obtained in the inoculated maize, not EOs treated. Results obtained in the present work indicate that fumonisin production could be inhibited or stimulated by some constituents of EOs coming from aromatic plants. Further studies should be performed to identify the components of EOs with modulatory activity on the growth and fumonisins production of Fusarium verticillioides.

  20. GC-MS-olfactometric characterization of the most aroma-active components in a representative aromatic extract from Iranian saffron (Crocus sativus L.).

    PubMed

    Amanpour, Asghar; Sonmezdag, A Salih; Kelebek, Hasim; Selli, Serkan

    2015-09-01

    Aroma and aroma-active compounds of Iranian saffron (Crocus sativus L.) were analyzed by gas chromatography-mass spectrometry-olfactometry. The saffron aromatic extracts were obtained by four different extraction techniques including solvent-assisted flavour evaporation (SAFE), liquid-liquid extraction (LLE), solid phase extraction (SPE), and simultaneous distillation extraction (SDE) and compared to achieve a representative aromatic extract from saffron. According to sensory analysis, the aromatic extract obtained by SAFE was the most representative of saffron odour. A total of 28 aroma compounds were identified in saffron. Ketones were quantitatively the most dominant volatiles in saffron, followed by aldehydes and acids. Aroma extract dilution analysis (AEDA) was used for the determination of aroma-active compounds of saffron. A total of nine aroma-active compounds were detected in the aromatic extract. On the basis of the flavour dilution (FD) factor, the most powerful aroma active compounds were safranal (FD = 512), 4-ketoisophorone (FD = 256) and dihydrooxophorone (FD = 128).

  1. MYST protein acetyltransferase activity requires active site lysine autoacetylation.

    PubMed

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-04

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases.

  2. MYST protein acetyltransferase activity requires active site lysine autoacetylation

    PubMed Central

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-01

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases. PMID:22020126

  3. Synthesis of high specific activity (+)- and (-)-6-( sup 18 F)fluoronorepinephrine via the nucleophilic aromatic substitution reaction

    SciTech Connect

    Ding, Y.S.; Fowler, J.S.; Gatley, S.J.; Dewey, S.L.; Wolf, A.P. )

    1991-02-01

    The first example of a no-carrier-added {sup 18}F-labeled catecholamine, 6-({sup 18}F)fluoronorepinephrine (6-({sup 18}F)FNE), has been synthesized via nucleophilic aromatic substitution. The racemic mixture was resolved on a chiral HPLC column to obtain pure samples of (-)-6-({sup 18}F)FNE and (+)6-({sup 18}F)FNE. Radiochemical yields of 20% at the end of bombardment (EOB) for the racemic mixture (synthesis time 93 min), 6% for each enantiomer (synthesis time 128 min) with a specific activity of 2-5 Ci/mumol at EOB were obtained. Chiral HPLC peak assignment for the resolved enantiomers was achieved by using two independent methods: polarimetric determination and reaction with dopamine beta-hydroxylase. Positron emission tomography (PET) studies with racemic 6-({sup 18}F)FNE show high uptake and retention in the baboon heart. This work demonstrates that nucleophilic aromatic substitution by ({sup 18}F)fluoride ion is applicable to systems having electron-rich aromatic rings, leading to high specific activity radiopharmaceuticals. Furthermore, the suitably protected dihydroxynitrobenzaldehyde 1 may serve as a useful synthetic precursor for the radiosynthesis of other complex {sup 18}F-labeled radiotracers.

  4. POLYCYCLIC AROMATIC HYDROCARBON AND EMISSION LINE RATIOS IN ACTIVE GALACTIC NUCLEI AND STARBURST GALAXIES

    SciTech Connect

    Sales, Dinalva A.; Pastoriza, M. G.; Riffel, R. E-mail: pastoriza@ufrgs.b

    2010-12-10

    We study the polycyclic aromatic hydrocarbon (PAH) bands, ionic emission lines, and mid-infrared continuum properties in a sample of 171 emission line galaxies taken from the literature plus 15 new active galactic nucleus (AGN) Spitzer spectra. We normalize the spectra at {lambda} = 23 {mu}m and grouped them according to the type of nuclear activity. The continuum shape steeply rises for longer wavelengths and can be fitted with a warm blackbody distribution of T {approx} 150-300 K. The brightest PAH spectral bands (6.2, 7.7, 8.6, 11.3, and 12.7 {mu}m) and the forbidden emission lines of [Si II] 34.8 {mu}m, [Ar II] 6.9 {mu}m, [S III] 18.7 and 33.4 {mu}m were detected in all the starbursts and in {approx}80% of the Seyfert 2. Taking under consideration only the PAH bands at 7.7 {mu}m, 11.3 {mu}m, and 12.7 {mu}m, we find that they are present in {approx}80% of the Seyfert 1, while only half of this type of activity show the 6.2 {mu}m and 8.6 {mu}m PAH bands. The observed intensity ratios for neutral and ionized PAHs (6.2 {mu}m/7.7 {mu}m x 11.3 {mu}m/7.7 {mu}m) were compared to theoretical intensity ratios, showing that AGNs have higher ionization fraction and larger PAH molecules ({>=}180 carbon atoms) than SB galaxies. The ratio between the ionized (7.7 {mu}m) and the neutral PAH bands (8.6 {mu}m and 11.3 {mu}m) are distributed over different ranges for AGNs and SB galaxies, suggesting that these ratios could depend on the ionization fraction, as well as on the hardness of the radiation field. The ratio between the 7.7 {mu}m and 11.3 {mu}m bands is nearly constant with the increase of [Ne III]15.5 {mu}m/[Ne II] 12.8 {mu}m, indicating that the fraction of ionized to neutral PAH bands does not depend on the hardness of the radiation field. The equivalent width of both PAH features show the same dependence (strongly decreasing) with [Ne III]/[Ne II], suggesting that the PAH molecules, emitting either ionized (7.7 {mu}m) or neutral (11.3 {mu}m) bands, may be destroyed

  5. Mutagenic activation of aromatic amines by molluscs as a biomarker of marine pollution.

    PubMed

    Díaz-Méndez, F M; Rodríguez-Ariza, A; Usero-García, J; Pueyo, C; López-Barea, J

    1998-01-01

    Mutagenic activation of arylamines by mollusc S9 fractions was evaluated as a biomarker for marine pollution. Two bivalve species were used as bioindicators, the common mussel (Mytilus edulis) and the striped venus (Chameleo gallina). A strain of Salmonella typhimurium overproducing O-acetyltransferase was used as indicator of mutagenicity. Mussels from an area of the North Atlantic Spanish zone that was exposed to an accidental crude oil spill were compared to bivalves from a reference area. C. gallina samples were from low polluted and highly polluted areas of the South Atlantic Spanish littoral. The promutagen 2-aminoanthracene (2-AA) was activated to mutagenic derivative(s) by S9 fractions from both C. gallina and M. edulis. Animals from contaminated sites showed higher arylamine activation capabilities than reference animals. This was further correlated with the mutagenic activities of corresponding cyclopentone-dichloromethane animal extracts. 2-AA activation by mollusc S9 was potentiated by alpha-naphthoflavone (ANF), known to inhibit PAH-inducible CYP1A cytochromes from vertebrates, but inhibited by methimazole (MZ), a substrate of the flavin monooxygenase (FMO) system. 2-AA-activating enzymes were mainly cytosolic; this localization clearly suggests that such activity could be attributed to soluble enzymes, different from the CYP1A or FMO systems. In conclusion, mutagenic activation of arylamines by mollusc S9, using as indicator a strain of Salmonella typhimurium that overproduces O-acetyltransferase, could be a reliable biomarker for marine pollution.

  6. Characterization of polycyclic aromatic compounds in diesel exhaust particulate extract responsible for aryl hydrocarbon receptor activity

    NASA Astrophysics Data System (ADS)

    Soontjens, Carol D.; Holmberg, Kristina; Westerholm, Roger N.; Rafter, Joseph J.

    Chemical fractions of a model diesel exhaust particulate extract, notably the fraction containing polycyclic aromatic hydrocarbons (PAH) (Fraction II), mono-nitro PAH (Fraction III), and dinitro-PAH (Fraction IV) have been shown to displace binding of 2,3,7,8-tetrachloro[1,6-[ 3H

  7. Nucleophilic Aromatic Substitution.

    ERIC Educational Resources Information Center

    Avila, Walter B.; And Others

    1990-01-01

    Described is a microscale organic chemistry experiment which demonstrates one feasible route in preparing ortho-substituted benzoic acids and provides an example of nucleophilic aromatic substitution chemistry. Experimental procedures and instructor notes for this activity are provided. (CW)

  8. In vitro and in vivo activities of T4 endonuclease V mutants altered in the C-terminal aromatic region

    SciTech Connect

    Ishida, M.; Kanamori, Y.; Hori, N.; Inaoka, T.; Ohtsuka, E. )

    1990-04-24

    Genes encoding mutants of the thymine photodimer repair enzyme from bacteriophage T4 (T4 endonuclease V) having an amino acid substitution (T127M, W128A, W128S, Y129A, K130L, Y131A, Y132A) were constructed by use of a previously obtained synthetic gene and expressed in Escherichia coli under the control of the E. coli tryptophan promoter. An in vitro assay of partially fractionated mutant proteins for glycosylase activity was performed with chemically synthesized substrates containing a thymine photodimer. T127M and K130L showed almost the same activity as the wild-type protein. Although W128S, Y131A, and Y132A were slightly active, W128A and Y129A lost activity. The results indicated that the aromatic amino acids around position 130 may be important for the glycosylase activity. Mutant T127M was purified, and the Km value was found to be of the same order as that of the wild type (10(-8) M). In vivo activities for all mutants were characterized with UV-sensitive E. coli. The results showed that substitution of Thr-127 with Met or Lys-130 with Leu did not have an effect on the survival of the bacteria but substitution of aromatic amino acids (128-132) had various effects on survival.

  9. Integrating geophysical data for mapping the contamination of industrial sites by polycyclic aromatic hydrocarbons: A geostatistical approach

    SciTech Connect

    Colin, P.; Nicoletis, S.; Froidevaux, R.; Garcia, M.

    1996-12-31

    A case study is presented of building a map showing the probability that the concentration in polycyclic aromatic hydrocarbon (PAH) exceeds a critical threshold. This assessment is based on existing PAH sample data (direct information) and on an electrical resistivity survey (indirect information). Simulated annealing is used to build a model of the range of possible values for PAH concentrations and of the bivariate relationship between PAH concentrations and electrical resistivity. The geostatistical technique of simple indicator kriging is then used, together with the probabilistic model, to infer, at each node of a grid, the range of possible values which the PAH concentration can take. The risk map is then extracted for this characterization of the local uncertainty. The difference between this risk map and a traditional iso-concentration map is then discussed in terms of decision-making.

  10. The effect of wind direction on the observed size distribution of particle adsorbed polycyclic aromatic hydrocarbons on an inner city sampling site.

    PubMed

    Schnelle-Kreis, J; Jänsch, T; Wolf, K; Gebefügi, I; Kettrup, A

    1999-08-01

    An investigation of the variability in the size distribution of particle adsorbed polycyclic aromatic hydrocarbons (PAHs) on an inner city sampling site showed differences depending on the wind direction. Particle size distributions of PAHs from outdoor air sampling were measured in Munich from 1994 to 1997. The sampling site is located northeast of a crossing with heavy traffic and southwest of a large inner city park. Depending on the wind direction, three different size distributions of particle adsorbed PAHs were observed. The maximum PAH concentration on very small particles (geometric mean diameter 75 nm) was observed with wind from west to southwest coming directly from the crossing area or the roads with heavy traffic. The maximum PAH concentration on particles with geometric mean diameter of 260 nm was found on days with wind from the built-up area north of the sampling site. On particles with geometric mean diameter of 920 nm the maximum PAH concentration was found on days with main wind directions from northeast to east. On these days the wind is blowing from the direction of the city park nearby. The distribution of particle adsorbed PAHs within different particle size classes is substantially influenced by the distance of the sampling site from strong sources of PAH loaded particulate matter.

  11. Synthesis and antifungal activity of C-21 steroids with an aromatic D ring.

    PubMed

    Sonego, Juan M; Cirigliano, Adriana M; Cabrera, Gabriela M; Burton, Gerardo; Veleiro, Adriana S

    2013-07-01

    Six analogues of salpichrolides with a simplified side chain (6-11) were synthesized using a new methodology to obtain steroids with an aromatic D-ring. The key step was the elimination of HBr in a vicinal dibromo D-homosteroid by treatment with 1,4-diazabicyclo[2.2.2]octane (DABCO). All new compounds were completely characterized by 2D NMR techniques and tested on two fungal pathogenic species, Fusarium virguliforme and Fusarium solani.

  12. Membrane position of a basic aromatic peptide that sequesters phosphatidylinositol 4,5 bisphosphate determined by site-directed spin labeling and high-resolution NMR.

    PubMed

    Ellena, Jeffrey F; Moulthrop, Jason; Wu, Jing; Rauch, Michelle; Jaysinghne, Sajith; Castle, J David; Cafiso, David S

    2004-11-01

    The membrane interactions and position of a positively charged and highly aromatic peptide derived from a secretory carrier membrane protein (SCAMP) are examined using magnetic resonance spectroscopy and several biochemical methods. This peptide (SCAMP-E) is shown to bind to membranes containing phosphatidylinositol 4,5-bisphosphate, PI(4,5)P2, and sequester PI(4,5)P2 within the plane of the membrane. Site-directed spin labeling of the SCAMP-E peptide indicates that the position and structure of membrane bound SCAMP-E are not altered by the presence of PI(4,5)P2, and that the peptide backbone is positioned within the lipid interface below the level of the lipid phosphates. A second approach using high-resolution NMR was used to generate a model for SCAMP-E bound to bicelles. This approach combined oxygen enhancements of nuclear relaxation with a computational method to dock the SCAMP-E peptide at the lipid interface. The model for SCAMP generated by NMR is consistent with the results of site-directed spin labeling and places the peptide backbone in the bilayer interfacial region and the aromatic side chains within the lipid hydrocarbon region. The charged side chains of SCAMP-E lie well within the interface with two arginine residues lying deeper than a plane defined by the position of the lipid phosphates. These data suggest that SCAMP-E interacts with PI(4,5)P2 through an electrostatic mechanism that does not involve specific lipid-peptide contacts. This interaction may be facilitated by the position of the positively charged side chains on SCAMP-E within a low-dielectric region of the bilayer interface.

  13. Quantitative structure-activity relationship modeling of polycyclic aromatic hydrocarbon mutagenicity by classification methods based on holistic theoretical molecular descriptors.

    PubMed

    Gramatica, Paola; Papa, Ester; Marrocchi, Assunta; Minuti, Lucio; Taticchi, Aldo

    2007-03-01

    Various polycyclic aromatic hydrocarbons (PAHs), ubiquitous environmental pollutants, are recognized mutagens and carcinogens. A homogeneous set of mutagenicity data (TA98 and TA100,+S9) for 32 benzocyclopentaphenanthrenes/chrysenes was modeled by the quantitative structure-activity relationship classification methods k-nearest neighbor and classification and regression tree, using theoretical holistic molecular descriptors. Genetic algorithm provided the selection of the best subset of variables for modeling mutagenicity. The models were validated by leave-one-out and leave-50%-out approaches and have good performance, with sensitivity and specificity ranges of 90-100%. Mutagenicity assessment for these PAHs requires only a few theoretical descriptors of their molecular structure.

  14. Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism.

    PubMed

    Guo, H; Cui, Q; Lipscomb, W N; Karplus, M

    2001-07-31

    Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer.

  15. Increased concentrations of polycyclic aromatic hydrocarbons in Alpine streams during annual snowmelt: investigating effects of sampling method, site characteristics, and meteorology.

    PubMed

    Shahpoury, Pourya; Hageman, Kimberly J; Matthaei, Christoph D; Alumbaugh, Robert E; Cook, Michelle E

    2014-10-07

    Silicone passive samplers and macroinvertebrates were used to measure time-integrated concentrations of polycyclic aromatic hydrocarbons (PAHs) in alpine streams during annual snowmelt. The three sampling sites were located near a main highway in Arthur's Pass National Park in the Southern Alps of New Zealand. A similar set of PAH congeners, composed of 2-4 rings, were found in silicone passive samplers and macroinvertebrates. The background PAH concentrations were similar at all sites, implying that proximity to the highway did not affect concentrations. In passive samplers, an increase of PAH concentrations by up to seven times was observed during snowmelt. In macroinvertebrates, the concentration changes were moderate; however, macroinvertebrate sampling did not occur during the main pulse observed in the passive samplers. The extent of vegetation in the catchment appeared to affect the concentration patterns seen at the different stream sites. A strong correlation was found between PAH concentrations in passive samplers and the amount of rainfall in the study area, indicating that the washout of contaminants from snowpack by rainfall was an important process.

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

    SciTech Connect

    Hartman, F.C.

    1991-01-01

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

  17. Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase

    PubMed Central

    Piontek, Klaus; Strittmatter, Eric; Ullrich, René; Gröbe, Glenn; Pecyna, Marek J.; Kluge, Martin; Scheibner, Katrin; Hofrichter, Martin; Plattner, Dietmar A.

    2013-01-01

    Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio- and stereoselectivities. When compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons. Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO. PMID:24126915

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

    SciTech Connect

    Not Available

    1990-07-01

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

  19. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

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

  20. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

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

  1. Activation of Aromatic C-C Bonds of 2,2'-Bipyridine Ligands.

    PubMed

    Fombona, Sergio; Espinal-Viguri, Maialen; Huertos, Miguel A; Díaz, Jesús; López, Ramón; Menéndez, M Isabel; Pérez, Julio; Riera, Lucía

    2016-11-21

    4,4'-Disubstituted-2,2'-bipyridine ligands coordinated to Mo(II) and Re(I) cationic fragments become dearomatized by an intramolecular nucleophilic attack from a deprotonated N-alkylimidazole ligand in cis disposition. The subsequent protonation of these neutral complexes takes place on a pyridine carbon atom rather than at nitrogen, weakening an aromatic C-C bond and affording a dihydropyridyl moiety. Computational calculations allowed for the rationalization of the formation of the experimentally obtained products over other plausible alternatives.

  2. Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

    PubMed Central

    Lim, Sung In; Yang, Byungseop; Jung, Younghan; Cha, Jaehyun; Cho, Jinhwan; Choi, Eun-Sil; Kim, Yong Hwan; Kwon, Inchan

    2016-01-01

    Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other. PMID:28004799

  3. Polyimidazoles via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor)

    1991-01-01

    Polyimidazoles (Pl) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl)imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethylacetamide, sulfolane, N-methylpyrroldinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperature under nitrogen. The di(hydroxyphenyl)imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl)imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxyphenyl)imidazole monomer. This synthetic route has provided high molecular weight Pl of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

  4. Polyimidazoles via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor)

    1992-01-01

    Polyimidazoles (PI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethyl acetamide, sulfolane, N-methylpyrrolidinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl) imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxphenyl) imidazole monomer. This synthetic route has provided high molecular weight PI of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

  5. Effects of heterocyclic aromatic substituents on binding affinities at two distinct sites of somatostatin receptors. Correlation with the electrostatic potential of the substituents.

    PubMed

    Prasad, Vidya; Birzin, Elizabeth T; McVaugh, Cheryl T; Van Rijn, Rachel D; Rohrer, Susan P; Chicchi, Gary; Underwood, Dennis J; Thornton, Edward R; Smith, Amos B; Hirschmann, Ralph

    2003-05-08

    In our continuing program exploring glucose-based peptidomimetics of somatostatin (SRIF-14), we sought to improve the water solubility of our glycosides. This led to insights into the nature of the ligand binding sites at the SRIF receptor. Replacement of the C4 benzyl substituent in glucoside (+)-2 with pyridinylmethyl or pyrazin-2-ylmethyl congeners increased water solubility and enhanced affinity for the human SRIF subtype receptor 4 (sst4). We attribute this effect to hydrogen bond formation. The pyridin-3-ylmethyl substituent at C4, when combined with the imidazol-4-ylmethyl group at C2, generated (-)-19, which has the highest affinity of a glucose-based peptidomimetic at a human SRIF receptor to date (K(i) 53 +/- 23 nM, n = 6 at sst4). The C4 heterocyclic congeners of glucosides bearing a 1-methoxy substituent rather than an indole side chain at the anomeric carbon, such as (+)-16, also provided information about the Trp(8) binding pocket. We correlated the SARs at both the C4 and the Trp(8) binding pockets with calculations of the electrostatic potentials of the diverse C4 aromatic substituents using Spartan 3-21G(*) MO analysis. These calculations provide an approximate analysis of a molecule's ability to interact within a receptor binding site. Our binding studies show that benzene and indole rings, but not pyridinylmethyl nor pyrazin-2-ylmethyl rings, can bind the hydrophobic Trp(8) binding pocket of sst4. The Spartan 3-21G(*) MO analysis reveals significant negative electrostatic potential in the region of the pi-clouds for the benzene and indole rings but not for the pyridinylmethyl or pyrazin-2-ylmethyl congeners. Our data further demonstrate that the replacement of benzene or indole side chains by heterocyclic aromatic rings typified by pyridine and pyrazine not only enhances water solubility and hydrogen bonding capacity as expected, but can also profoundly diminish the ability of the pi-cloud of the aromatic substituent to interact with side chains

  6. DELTA-13C VALUES OF POLYCYCLIC AROMATIC HYDROCARBONS (PAHS) COLLECTED FROM TWO CREOSOTE-CONTAMINATED WASTE SITES

    EPA Science Inventory

    Groundwater samples were collected from the American Creosote Works (ACW) Superfund site in Pensacola, Florida in June and September 1994. Sampling wells were located along a transect leading away from the most contaminated area. PAHs were extracted from the groundwater samples w...

  7. Temporal variability of Polycyclic Aromatic Hydrocarbons (PAHs) in a receptor site of the Puebla-Tlaxcala Valley

    NASA Astrophysics Data System (ADS)

    Padilla, Z. V.; Torres, R.; Ruiz Suarez, L.; Molina, L. T.

    2013-05-01

    This contribution documents the presence and possible origin of PAHs, their temporal concentration patterns and correlations with other air pollutants in the so-called Puebla-Tlaxcala valley. This valley is located to the east of the Mexico City Metropolitan Area and is a very populated region which suffers of air pollution problems. Emission sources of PAHs include open burning, industrial boilers, automobiles and trucks, but vehicle emissions vary significantly depending on the use of: fuel, engine type and catalytic converter. An important emission source in the Puebla-Tlaxcala region is wood burning for cooking. Therefore, it is expected to have contributions of PAHS from this type of sources. PAHs measurements were performed in an air pollution semi-rural receptor site (Chipilo) southwest the City of Puebla, using an aerosol photoelectric sensor (PAS 2000 CE) to measure the concentration of PAHs and a diffuser charger (DC 2000 CE) to evaluate the active surface (DC) of the particles. The measuring period included March and April of 2012 during the ozne season in central Mexico. The use of these two sensors in parallel has been identified as a fingerprint technique to identify different types of particles from several combustion processes and is a useful tool to identify quantitatively the major source of emissions, as well as to describe thephysical and chemical characteristics of the particles. Correlations between PAHs and DC, with NOx and CO, together with an analysis of atmospheric transport may approximate the possible origin of these particles. The coefficient PAHs / DC associated with backward trajectory analysis represents a tool to identify potential areas of emission. The correlation between PAHs and NOx emissions reflects association with diesel combustion, while the correlation between PAHs and CO, the combustion of gasoline. The results show that vehicle emissions are the major source of PAHs with an associated increase in the concentration of

  8. Perspective: On the active site model in computational catalyst screening

    NASA Astrophysics Data System (ADS)

    Reuter, Karsten; Plaisance, Craig P.; Oberhofer, Harald; Andersen, Mie

    2017-01-01

    First-principles screening approaches exploiting energy trends in surface adsorption represent an unparalleled success story in recent computational catalysis research. Here we argue that our still limited understanding of the structure of active sites is one of the major bottlenecks towards an ever extended and reliable use of such computational screening for catalyst discovery. For low-index transition metal surfaces, the prevalently chosen high-symmetry (terrace and step) sites offered by the nominal bulk-truncated crystal lattice might be justified. For more complex surfaces and composite catalyst materials, computational screening studies will need to actively embrace a considerable uncertainty with respect to what truly are the active sites. By systematically exploring the space of possible active site motifs, such studies might eventually contribute towards a targeted design of optimized sites in future catalysts.

  9. Diffusional correlations among multiple active sites in a single enzyme.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2014-04-07

    Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

  10. Occurrence and distribution of polycyclic aromatic hydrocarbons in organo-mineral particles of alluvial sandy soil profiles at a petroleum-contaminated site.

    PubMed

    Lu, Zhe; Zeng, Fangang; Xue, Nandong; Li, Fasheng

    2012-09-01

    The occurrence and the distribution of 16 USEPA priority pollutants polycyclic aromatic hydrocarbons (PAHs) were investigated in two alluvial sandy soil profiles and in their four sizes of organo-mineral particles (<2 μm clay, 2-20 μm silt, 20-200 μm fine sand, and >200 μm coarse sand) beside a typical oil sludge storage site in eastern China. PAHs were mainly enriched in the surface soil (0-20 cm) and the concentrations declined in deeper soils, from 3.68 to 0.128 μg/g in profile 1 and 10.8 to 0.143 μg/g in profile 2 (dry wt.). The PAHs in the upper soil layers of this study site mainly came from combustion pollution, whereas in the lower soil layers petroleum contamination became the major source of PAHs. The content of different sized organo-mineral particles of this alluvial sandy soil decreased in the following order: fine sand>coarse sand>silt>clay. X-ray diffraction (XRD) results showed that all the different sized soil fractions of this study site were dominated by quartz, calcite and feldspar. The particle surface became smoother with size increasing as shown by scanning electron microscope (SEM) images. PAH concentrations varied largely in different sized soil fractions. The highest PAH concentration was associated with clay and decreased in the order: clay>silt>coarse sand>fine sand. Soil organic matter (SOM) content, mineral composition and particle surface characteristics were suggested as three main factors affecting the distribution of PAHs in different sized organo-mineral particles. This study will help to understand the distribution and transport characteristics of PAHs in soil profiles at petroleum-contaminated sites.

  11. Size-dependent distribution and inhalation cancer risk of particle-bound polycyclic aromatic hydrocarbons at a typical e-waste recycling and an urban site.

    PubMed

    Luo, Pei; Bao, Lian-Jun; Li, Shao-Meng; Zeng, Eddy Y

    2015-05-01

    Atmospheric particle size distribution of polycyclic aromatic hydrocarbons (PAHs) in a typical e-waste recycling zone and an urban site (Guangzhou) in southern China featured a unimodal peak in 0.56-1.8 μm for 4-6 ring PAHs but no obvious peak for 2-3 ring PAHs at both sites. The atmospheric deposition fluxes of PAHs were estimated at 5.4 ± 2.3 μg m(-2) d(-1) in the e-waste recycling zone and 3.1 ± 0.6 μg m(-2) d(-1) in Guangzhou. In addition, dry and wet deposition fluxes of PAHs were dominated by coarse (Dp > 1.8 μm) and fine particles (Dp < 1.8 μm), respectively. Fine particles predominated the deposition of PAHs in the lung. The results estimated by incremental inhalation cancer risk suggested that particle-bound PAHs posed serious threat to human health within the e-waste recycling zone and Guangzhou.

  12. Health risks of polycyclic aromatic hydrocarbons via fish consumption in Haimen bay (China), downstream of an e-waste recycling site (Guiyu).

    PubMed

    Shi, Jingchun; Zheng, Gene Jin-Shu; Wong, Ming-Hung; Liang, Hong; Li, Yuelin; Wu, Yinglin; Li, Ping; Liu, Wenhua

    2016-05-01

    Guiyu, China has been one of the largest e-waste recycling sites of the world for more than 20 years. Abundant data show that local dwellers there suffered from severe health risks from e-waste contaminants. In this study, polycyclic aromatic hydrocarbons (PAHs) were used as candidates to test the contamination levels and their possible adverse effects on residents in Haimen Bay, the estuary of Lian River (less than 30km from Guiyu), which has been totally neglected. The concentrations of 16PAHs were determined in collected marine fish with a median ΣPAH concentration of 1478ng/g (wet weight), and the contamination may be mainly influenced by Lian River runoff, specifically from Guiyu. The lifetime excess cancer risk for local dwellers was much higher than the serious risk level (10(-4)). More seriously, outflows of PAHs from the e-waste recycling site (Guiyu) seemed to exert health risks of a much larger scale of population downstream.

  13. Distribution and sources of polycyclic aromatic hydrocarbons in sediments of the Mai Po Inner Deep Bay Ramsar Site in Hong Kong.

    PubMed

    Zhao, Zhen-Ye; Chu, Yan-ling; Gu, Ji-Dong

    2012-08-01

    The concentration of total polycyclic aromatic hydrocarbons (∑PAHs) and the 16 US EPA priority individual PAH compounds were analyzed in surface sediments from the Mai Po Inner Deep Bay, Ramsar Site of Hong Kong from December 2001 to Jun 2005, to investigate the spatial variability of anthropogenic pollutants. ∑PAHs concentrations ranged from 36.5 to 256.3 ng g(-1) dry weight with an average of 148.9 ng g(-1), comparable to other urbanized areas of the world, and there was little difference among different sampling times from December 2001 to June 2005. Based on comparison to the results from earlier study, it appears that a decrease of total PAHs concentration has occurred since 1992. Meanwhile, the concentrations of ∑PAHs were positive correlated with total organic carbon contents except sites F and G, suggesting the characteristics of the sediment influences the distribution and concentration of PAHs. There was relatively a good relationship among the individual PAHs and the compounds of fluorene, phenanthrene, anthracene, fluoranthene, pyrene, benzo[a]pyrene and indeno[cd]pyrene yielded a good correlation (r(2) > 0.5) with total PAHs. Principal component analysis and specific PAHs compound ratios (Phe/Ant vs. Flt/Pyr) indicate the pyrogenic origins, especially traffic exhausts, are the dominant sources of PAHs in the Mai Po Inner Deep Bay Nature Reserve.

  14. Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency.

    PubMed

    Armstrong, Michelle; van Hoorebeke, Christopher; Horn, Thomas; Deschamps, Joshua; Freedman, J Cody; Kalyanaraman, Chakrapani; Jacobson, Matthew P; Holman, Theodore

    2016-11-01

    Human 15-lipoxygenase-1 (h15-LOX-1 or h12/15-LOX) reacts with polyunsaturated fatty acids and produces bioactive lipid derivatives that are implicated in many important human diseases. One such disease is stroke, which is the fifth leading cause of death and the first leading cause of disability in America. The discovery of h15-LOX-1 inhibitors could potentially lead to novel therapeutics in the treatment of stroke, however, little is known about the inhibitor/active site interaction. This study utilizes site-directed mutagenesis, guided in part by molecular modeling, to gain a better structural understanding of inhibitor interactions within the active site. We have generated eight mutants (R402L, R404L, F414I, F414W, E356Q, Q547L, L407A, I417A) of h15-LOX-1 to determine whether these active site residues interact with two h15-LOX-1 inhibitors, ML351 and an ML094 derivative, compound 18. IC50 values and steady-state inhibition kinetics were determined for the eight mutants, with four of the mutants affecting inhibitor potency relative to wild type h15-LOX-1 (F414I, F414W, E356Q and L407A). The data indicate that ML351 and compound 18, bind in a similar manner in the active site to an aromatic pocket close to F414 but have subtle differences in their specific binding modes. This information establishes the binding mode for ML094 and ML351 and will be leveraged to develop next-generation inhibitors.

  15. Robotics at Savannah River site: activity report

    SciTech Connect

    Byrd, J.S.

    1984-09-01

    The objectives of the Robotics Technology Group at the Savannah River Laboratory are to employ modern industrial robots and to develop unique automation and robotic systems to enhance process operations at the Savannah River site (SRP and SRL). The incentives are to improve safety, reduce personnel radiation exposure, improve product quality and productivity, and to reduce operating costs. During the past year robotic systems have been installed to fill chemical dilution vials in a SRP laboratory at 772-F and remove radioactive waste materials in the SRL Californium Production Facility at 773-A. A robotic system to lubricate an extrusion press has been developed and demonstrated in the SRL robotics laboratory and is scheduled for installation at the 321-M fuel fabrication area. A mobile robot was employed by SRP for a radiation monitoring task at a waste tank top in H-Area. Several other robots are installed in the SRL robotics laboratories and application development programs are underway. The status of these applications is presented in this report.

  16. Involvement of a surface-active high molecular weight factor in degradation of polycyclic aromatic hydrocarbons by Pseudomonas marginalis.

    PubMed

    Burd, G; Ward, O P

    1996-08-01

    A strain of Pseudomonas marginalis PD-14B, isolated from polycyclic aromatic hydrocarbon (PAH) contaminated soil, produced an extracellular surface-active factor of high molecular weight containing protein and lipopolysaccharide. A crude preparation of the factor, obtained from the culture both of cells grown in mineral salts (MS) medium with succinate and yeast extract, affected the extent of PAH degradation by the bacterial cells and prevented flocculation of PAHs in an aqueous suspension. A washed suspension of P. marginalis cells also prevented flocculation of PAH suspensions and emulsified liquid hydrocarbons. Incubation of the factor and the factor-producing strain in the presence of different PAHs resulted in gradual increase of turbidity of the PAH dispersions. The factor markedly stimulated rate and extent of turbidity generation by bacterial cells. The surface-active factor may promote infection of lettuce and other plants by this known pathogen and may also have application in bioremediation.

  17. Effect of torrefaction on the properties of rice straw high temperature pyrolysis char: Pore structure, aromaticity and gasification activity.

    PubMed

    Chen, Handing; Chen, Xueli; Qin, Yueqiang; Wei, Juntao; Liu, Haifeng

    2017-03-01

    The influence of torrefaction on the physicochemical characteristics of char during raw and water washed rice straw pyrolysis at 800-1200°C is investigated. Pore structure, aromaticity and gasification activity of pyrolysis chars are compared between raw and torrefied samples. For raw straw, BET specific surface area decreases with the increased torrefaction temperature at the same pyrolysis temperature and it approximately increases linearly with weight loss during pyrolysis. The different pore structure evolutions relate to the different volatile matters and pore structures between raw and torrefied straw. Torrefaction at higher temperature would bring about a lower graphitization degree of char during pyrolysis of raw straw. Pore structure and carbon crystalline structure evolutions of raw and torrefied water washed straw are different from these of raw straw during pyrolysis. For both raw and water washed straw, CO2 gasification activities of pyrolysis chars are different between raw and torrefied samples.

  18. Aromatics saturation over hydrotreating catalysts: Reactivity and susceptibility to poisons

    SciTech Connect

    Kokayeff, P.

    1994-12-31

    Aromatics saturation over hydrotreating catalysts has been investigated by processing a synthetic feedstock to which naphthalene, biphenyl, tetralin, and cyclohexylbenzene have been added as model aromatic compounds. The saturation reactions were successfully correlated with a kinetic model of consecutive first order reactions. The rates of saturation of the di-aromatics, naphthalene and biphenyl, were approximately 5--40 times faster than the rate of saturation of the mono-aromatics, tetralin and cyclohexylbenzene. The nature of the di-aromatic is a significant determinant of its reactivity for saturation. The rate of saturation of naphthalene is 10--20 times faster than the rate of saturation of biphenyl. The two mono-aromatics, tetralin and cyclohexylbenzene, exhibited nearly identical reactivities for saturation. An investigation of the effect of organo-nitrogen compounds on saturation activity revealed a very severe poisoning and attenuation of saturation activity. Since activity was recoverable upon the removal of the poisoning agent the chemical effect was conjectured to be due to adsorption of the poison on the active sites of the catalyst. The adsorption constants were determined for three model nitrogen compounds--quinoline, indole, and tert-butylamine. The poisoning action of an organo-nitrogen compound was found to be dependent on both basicity and chemical structure.

  19. Mosquito repellent activity of essential oils of aromatic plants growing in Argentina.

    PubMed

    Gillij, Y G; Gleiser, R M; Zygadlo, J A

    2008-05-01

    Mosquitoes are important vectors of diseases and nuisance pests. Repellents minimize contact with mosquitoes. Repellents based on essential oils (EO) are being developed as an alternative to DEET (N,N-diethyl-m-methylbenzamide), an effective compound that has disadvantages including toxic reactions, and damage to plastic and synthetic fabric. This work evaluated the repellency against Aedes aegypti of EO from aromatic plants that grow in Argentina: Acantholippia seriphioides, Achyrocline satureioides, Aloysia citriodora, Anemia tomentosa, Baccharis spartioides, Chenopodium ambrosioides, Eucalyptus saligna, Hyptis mutabilis, Minthostachys mollis, Rosmarinus officinalis, Tagetes minuta and Tagetes pusilla. Most EO were effective. Variations depending on geographic origin of the plant were detected. At a 90% EO concentration, A. satureoides and T. pusilla were the least repellent. At concentrations of 12.5% B. spartioides, R. officinalis and A. citriodora showed the longest repellency times. Comparisons of the principal components of each EO suggest that limonene and camphor were the main components responsible for the repellent effects.

  20. The Toluene o-Xylene Monooxygenase Enzymatic Activity for the Biosynthesis of Aromatic Antioxidants

    PubMed Central

    Pizzo, Elio; Notomista, Eugenio; Pezzella, Alessandro; Di Cristo, Carlo; De Lise, Federica; Di Donato, Alberto; Izzo, Viviana

    2015-01-01

    Monocyclic phenols and catechols are important antioxidant compounds for the food and pharmaceutic industries; their production through biotransformation of low-added value starting compounds is of major biotechnological interest. The toluene o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 is a bacterial multicomponent monooxygenase (BMM) that is able to hydroxylate a wide array of aromatic compounds and has already proven to be a versatile biochemical tool to produce mono- and dihydroxylated derivatives of aromatic compounds. The molecular determinants of its regioselectivity and substrate specificity have been thoroughly investigated, and a computational strategy has been developed which allows designing mutants able to hydroxylate non-natural substrates of this enzyme to obtain high-added value compounds of commercial interest. In this work, we have investigated the use of recombinant ToMO, expressed in cells of Escherichia coli strain JM109, for the biotransformation of non-natural substrates of this enzyme such as 2-phenoxyethanol, phthalan and 2-indanol to produce six hydroxylated derivatives. The hydroxylated products obtained were identified, isolated and their antioxidant potential was assessed both in vitro, using the DPPH assay, and on the rat cardiomyoblast cell line H9c2. Incubation of H9c2 cells with the hydroxylated compounds obtained from ToMO-catalyzed biotransformation induced a differential protective effect towards a mild oxidative stress induced by the presence of sodium arsenite. The results obtained confirm once again the versatility of the ToMO system for oxyfunctionalization reactions of biotechnological importance. Moreover, the hydroxylated derivatives obtained possess an interesting antioxidant potential that encourages the use of the enzyme for further functionalization reactions and their possible use as scaffolds to design novel bioactive molecules. PMID:25915063

  1. The Toluene o-Xylene Monooxygenase Enzymatic Activity for the Biosynthesis of Aromatic Antioxidants.

    PubMed

    Donadio, Giuliana; Sarcinelli, Carmen; Pizzo, Elio; Notomista, Eugenio; Pezzella, Alessandro; Di Cristo, Carlo; De Lise, Federica; Di Donato, Alberto; Izzo, Viviana

    2015-01-01

    Monocyclic phenols and catechols are important antioxidant compounds for the food and pharmaceutic industries; their production through biotransformation of low-added value starting compounds is of major biotechnological interest. The toluene o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 is a bacterial multicomponent monooxygenase (BMM) that is able to hydroxylate a wide array of aromatic compounds and has already proven to be a versatile biochemical tool to produce mono- and dihydroxylated derivatives of aromatic compounds. The molecular determinants of its regioselectivity and substrate specificity have been thoroughly investigated, and a computational strategy has been developed which allows designing mutants able to hydroxylate non-natural substrates of this enzyme to obtain high-added value compounds of commercial interest. In this work, we have investigated the use of recombinant ToMO, expressed in cells of Escherichia coli strain JM109, for the biotransformation of non-natural substrates of this enzyme such as 2-phenoxyethanol, phthalan and 2-indanol to produce six hydroxylated derivatives. The hydroxylated products obtained were identified, isolated and their antioxidant potential was assessed both in vitro, using the DPPH assay, and on the rat cardiomyoblast cell line H9c2. Incubation of H9c2 cells with the hydroxylated compounds obtained from ToMO-catalyzed biotransformation induced a differential protective effect towards a mild oxidative stress induced by the presence of sodium arsenite. The results obtained confirm once again the versatility of the ToMO system for oxyfunctionalization reactions of biotechnological importance. Moreover, the hydroxylated derivatives obtained possess an interesting antioxidant potential that encourages the use of the enzyme for further functionalization reactions and their possible use as scaffolds to design novel bioactive molecules.

  2. Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog

    PubMed Central

    Englert, Markus; Nakamura, Akiyoshi; Wang, Yane-Shih; Eiler, Daniel; Söll, Dieter; Guo, Li-Tao

    2015-01-01

    Genetically encoded non-canonical amino acids are powerful tools of protein research and engineering; in particular they allow substitution of individual chemical groups or atoms in a protein of interest. One such amino acid is the tryptophan (Trp) analog 3-benzothienyl-l-alanine (Bta) with an imino-to-sulfur substitution in the five-membered ring. Unlike Trp, Bta is not capable of forming a hydrogen bond, but preserves other properties of a Trp residue. Here we present a pyrrolysyl-tRNA synthetase-derived, engineered enzyme BtaRS that enables efficient and site-specific Bta incorporation into proteins of interest in vivo. Furthermore, we report a 2.1 Å-resolution crystal structure of a BtaRS•Bta complex to show how BtaRS discriminates Bta from canonical amino acids, including Trp. To show utility in protein mutagenesis, we used BtaRS to introduce Bta to replace the Trp28 residue in the active site of Staphylococcus aureus thioredoxin. This experiment showed that not the hydrogen bond between residues Trp28 and Asp58, but the bulky aromatic side chain of Trp28 is important for active site maintenance. Collectively, our study provides a new and robust tool for checking the function of Trp in proteins. PMID:26582921

  3. Active sites of thioredoxin reductases: why selenoproteins?

    PubMed

    Gromer, Stephan; Johansson, Linda; Bauer, Holger; Arscott, L David; Rauch, Susanne; Ballou, David P; Williams, Charles H; Schirmer, R Heiner; Arnér, Elias S J

    2003-10-28

    Selenium, an essential trace element for mammals, is incorporated into a selected class of selenoproteins as selenocysteine. All known isoenzymes of mammalian thioredoxin (Trx) reductases (TrxRs) employ selenium in the C-terminal redox center -Gly-Cys-Sec-Gly-COOH for reduction of Trx and other substrates, whereas the corresponding sequence in Drosophila melanogaster TrxR is -Ser-Cys-Cys-Ser-COOH. Surprisingly, the catalytic competence of these orthologous enzymes is similar, whereas direct Sec-to-Cys substitution of mammalian TrxR, or other selenoenzymes, yields almost inactive enzyme. TrxRs are therefore ideal for studying the biology of selenocysteine by comparative enzymology. Here we show that the serine residues flanking the C-terminal Cys residues of Drosophila TrxRs are responsible for activating the cysteines to match the catalytic efficiency of a selenocysteine-cysteine pair as in mammalian TrxR, obviating the need for selenium. This finding suggests that the occurrence of selenoenzymes, which implies that the organism is selenium-dependent, is not necessarily associated with improved enzyme efficiency. Our data suggest that the selective advantage of selenoenzymes is a broader range of substrates and a broader range of microenvironmental conditions in which enzyme activity is possible.

  4. Concentration profiles, source apportionment and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in dumpsite soils from Agbogbloshie e-waste dismantling site, Accra, Ghana.

    PubMed

    Daso, Adegbenro P; Akortia, Eric; Okonkwo, Jonathan O

    2016-06-01

    The concentrations of eighteen (18) polycyclic aromatic hydrocarbons (PAHs), including the 16 USEPA's priority PAHs as well as two alkyl-substituted naphthalenes were determined in dumpsite soils collected from different sampling sites within the Agbogbloshie e-waste dismantling site in Accra, Ghana. Following their isolation with ultrasonic-assisted extraction technique, the concentrations of the PAHs were determined by gas chromatography mass spectrometry (GC-MS). Loss-on-ignition (LOI) method was employed for the determination of total organic carbon (TOC) of the soil samples. The mean Σ18PAHs obtained were 3006, 5627, 3046, 5555, and 7199 ng g(-1) dry weight (dw) for sampling sites A (mosque), B (dismantling site), C (residential house/police station), D (personal computer repairers' shop) and E (e-waste open burning area), respectively. In all cases, the prevalence of phenanthrene, fluoranthene and pyrene was generally observed across the sampling sites. In this study, PAHs with two to three rings and four to six rings exhibited strong positive correlations, whereas BbF and BkF showed weak positive and negative correlations with other PAHs investigated. With the exception of BbF and BkF, all the PAHs had moderate to strong positive correlations with the TOC. Benzo[a]pyrene equivalent (BaPeq) concentration is a useful indicator of the carcinogenic potency of environmental matrices and these ranged between 111 and 454 ng g(-1), which are generally below the 'safe' level of 600 ng g(-1) established for the protection of the environment and human health. Interestingly, the seven carcinogenic PAHs were the major contributors to the BaPeq concentrations accounting between 97.7 and 98.3 %. Despite the minimal risk to cancer via exposure to the investigated dumpsite soil as indicated in the present study, the prolonged exposure to these pollutants via various exposure pathways may result in increased risk to cancer over time. The application of several

  5. Community Update on Site Activities, July 19, 2013

    EPA Pesticide Factsheets

    In an effort to engage and inform community members interested in the New Bedford Harbor Superfund Site cleanup, EPA will be issuing periodic topic-based fact sheets that will provide background information and updates about ongoing activities.

  6. Super oxidation and solidification of organic solvents, polycyclic aromatic hydrocarbons and pesticides at an abandoned chemical factory site

    SciTech Connect

    Yao, Kevin; Xu, Paul; Loo, Walter

    2013-07-01

    Large quantities of organic chemical such as VOCs, SVOCs and POPs were found in the soil of land at an abandoned Chemical Plant. Technology of super oxidation was applied to the soil for cleanup. Fenton process was utilized to treat soil contaminated heavily by BHC, benzene, chlorobenzene, dichlorobenzene, hexachlorobenzene, dichloroethane, dichloropropane, trichlorobenzene and dichloroether, etc. Super oxidation was coupled with method of stabilization for this case to enhance the remediation effect, which proved to be successful. Concentration of concerned pollutants was brought down below the national regulation level by approximately 8 folds. To make the treated soil strong and effective layer preventing pollutants breaking through, Iron powder was mixed in the soil, forming PBR (Permeable Barrier Reactor), to lower the risk to human health. The site after enhanced super oxidation above was totally safe to be developed into a residential community and/or commercial area. (authors)

  7. {Polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons in gas and particle phases in two sites of Mexico: MILAGRO project}

    NASA Astrophysics Data System (ADS)

    Amador-Muñoz, O.; Villalobos-Pietrini, R.; Castro, T.; Gaspariano-Larino, R.

    2009-04-01

    Aliphatic hydrocarbons are markers of anthropogenic and biogenic emission sources1; meanwhile PAHs are generated by incomplete combustion sources2. The last ones are important compounds due to their carcinogenic and mutagenic properties3,4. The aim of this study was to identify and quantify aliphatic hydrocarbons and PAHs in gas and particles phases of the atmospheric aerosol and to determine the day and night time behavior during the MILAGRO (Megacity Initiative: Local Global and Research Observations) campaign. The gas phase was collected on polyurethane foam, while particles less than 2.5 m (PM2.5) were collected on glass fiber filters covered with Teflon (TIGF, pallflex) of 8x10 in. Samplings were carried out with a high volume sampler (Tisch) with a flow of 1.13 m3 min-1 at two sites: Instituto Mexicano del Petróleo (T0) and Tecamac (T1) located at North and Northeast of Mexico City, respectively during day (7:00 am-7:00 pm) and night time (7:00 pm-7:00 am) from 1 to 29 of March, 2006. Ninteen PAHs and 23 aliphatic hydrocarbons from n-C13H28 to n-C35H72 were analyzed by gas chromatography coupled to mass spectrometry in impact mode. The samples were spiked with deuterads PAHs and aliphatics hydrocarbons before ultrasound extraction. Medians comparisons were made with Mann-Whitney U test. PAHs with molecular weight (MW) less than 228 g mol-1 were distributed in the gas phase, in both sites. Higher concentrations of PAHs ≥ 228 g mol-1 in PM2.5, were observed during night period (p

  8. Influence of urban activities on polycyclic aromatic hydrocarbons in precipitation: distribution, sources and depositional flux in a developing metropolis, Fortaleza, Brazil.

    PubMed

    Cavalcante, Rivelino M; Sousa, Francisco W; Nascimento, Ronaldo F; Silveira, Edilberto R; Viana, Rommel B

    2012-01-01

    We measured polycyclic aromatic hydrocarbons (PAHs) in bulk precipitation in the Fortaleza metropolitan area, Ceará, Brazil, for the first time. Because little information is available concerning PAHs in tropical climatic regions, we assessed their spatial distribution and possible sources and the influence of urban activities on the depositional fluxes of PAHs in bulk precipitation. The concentrations of individual and total PAHs (Σ(PAHs)) in bulk precipitation ranged from undetectable to 133.9 ng.L(-1) and from 202.6 to 674.8 ng.L(-1), respectively. The plume of highest concentrations was most intense in a zone with heavy automobile traffic and favorable topography for the concentration of emitted pollutants. The depositional fluxes of PAHs in bulk precipitation calculated in this study (undetectable to 0.87 μg.m(-2).month(-1)) are 4 to 27 times smaller than those reported from tourist sites and industrial and urban areas in the Northern Hemisphere. Diagnostic ratio analyses of PAH samples showed that the major source of emissions is gasoline exhaust, with a small percentage originating from diesel fuel. Contributions from coal and wood combustion were also found. Major economic activities appear to contribute to pollutant emissions.

  9. Polycyclic Aromatic Hydrocarbons in Galaxies at z ~ 0.1: The Effect of Star Formation and Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    O'Dowd, Matthew J.; Schiminovich, David; Johnson, Benjamin D.; Treyer, Marie A.; Martin, Christopher D.; Wyder, Ted K.; Charlot, S.; Heckman, Timothy M.; Martins, Lucimara P.; Seibert, Mark; van der Hulst, J. M.

    2009-11-01

    We present the analysis of the polycyclic aromatic hydrocarbon (PAH) spectra of a sample of 92 typical star-forming galaxies at 0.03 < z < 0.2 observed with the Spitzer intensified Reticon spectrograph (IRS). We compare the relative strengths of PAH emission features with Sloan Digital Sky Survey optical diagnostics to probe the relationship between PAH grain properties and star formation and active galactic nuclei (AGNs) activity. Short-to-long wavelength PAH ratios, and in particular the 7.7 μm-to-11.3 μm feature ratio, are strongly correlated with the star formation diagnostics Dn (4000) and Hα equivalent width, increasing with younger stellar populations. This ratio also shows a significant difference between active and non-active galaxies, with the active galaxies exhibiting weaker 7.7 μm emission. A hard radiation field as measured by [O III]/Hβ and [Ne III]_{15.6 μm}/[Ne II]_{12.8 μm} effects PAH ratios differently depending on whether this field results from starburst activity or an AGN. Our results are consistent with a picture in which larger PAH molecules grow more efficiently in richer media and in which smaller PAH molecules are preferentially destroyed by the AGN.

  10. POLYCYCLIC AROMATIC HYDROCARBONS IN GALAXIES AT z approx 0.1: THE EFFECT OF STAR FORMATION AND ACTIVE GALACTIC NUCLEI

    SciTech Connect

    O'Dowd, Matthew J.; Schiminovich, David; Johnson, Benjamin D.; Treyer, Marie A.; Martin, Christopher D.; Wyder, Ted K.; Charlot, S.; Heckman, Timothy M.; Martins, Lucimara P.; Seibert, Mark; Van der Hulst, J. M.

    2009-11-01

    We present the analysis of the polycyclic aromatic hydrocarbon (PAH) spectra of a sample of 92 typical star-forming galaxies at 0.03 < z < 0.2 observed with the Spitzer intensified Reticon spectrograph (IRS). We compare the relative strengths of PAH emission features with Sloan Digital Sky Survey optical diagnostics to probe the relationship between PAH grain properties and star formation and active galactic nuclei (AGNs) activity. Short-to-long wavelength PAH ratios, and in particular the 7.7 mum-to-11.3 mum feature ratio, are strongly correlated with the star formation diagnostics D{sub n} (4000) and Halpha equivalent width, increasing with younger stellar populations. This ratio also shows a significant difference between active and non-active galaxies, with the active galaxies exhibiting weaker 7.7 mum emission. A hard radiation field as measured by [O{sub III}]/Hbeta and [Ne{sub III}]{sub 15.6m}u{sub m}/[Ne{sub II}]{sub 12.8m}u{sub m} effects PAH ratios differently depending on whether this field results from starburst activity or an AGN. Our results are consistent with a picture in which larger PAH molecules grow more efficiently in richer media and in which smaller PAH molecules are preferentially destroyed by the AGN.

  11. Seasonal changes of polycyclic aromatic hydrocarbons in response to hydrology and anthropogenic activities in the Pearl River estuary, China.

    PubMed

    Liu, Feng; Niu, Lixia; Chen, Hui; Li, Ping; Tian, Feng; Yang, Qingshu

    2017-02-07

    The behaviours of PAHs (containing 2-6 aromatic rings) in the Pearl River estuary were examined each month in 2011. This study was designed to investigate the abundance of 16 priority PAHs and their response to the seasonal dynamics of anthropogenic activities and hydrological cycles. Monthly mean concentrations of ∑16PAHs in water and suspended particulate matter (SPM) were 88.31ng/L and 252.31ng/L respectively, with higher concentrations in the wet season (April to September). Heavy precipitation in the wet season resulted in relatively increased PAH input via riverine discharges and atmospheric deposition. Seasonal variations in suspended sediment concentration (SSC), temperature and salinity have considerably affected the PAH phase association. Higher SSC in the wet season contributed to higher concentration of the PAHs in SPM, and higher temperature and lower salinity facilitated desorption from SPM. The PAH sources were largely attributed to vehicular emissions, coal combustion and coke ovens.

  12. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

    PubMed

    Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  13. Function and the biosynthesis of unusual corrinoids by a novel activation mechanism of aromatic compounds in anaerobic bacteria

    NASA Astrophysics Data System (ADS)

    Stupperich, E.; Eisinger, H. J.

    A corrinoid screening of several phylogenetically diverse ``archaebacteria'' revealed vitamin B12-like corrinoids. This indicates an optimized structure and function relationship of the corrinoids under different bacterial growth conditions during the early evolution of live. Some of these corrinoids have been substituted by modified corrinoids in growing cells without affecting the generation times of the bacteria. In this respect, the discovery of the unique para-cresolyl cobamide from the eubacterium Sporomusa ovata attracted attention. The unusual structure of this corrinoid was achieved by a biosynthesis proceeding via a novel and stereospecific activation mechanism of aromatic compounds. The corrinoid was detected both in the membrane fraction and in the soluble fraction of the cells. Methyltransfer is one of the probable functions of the para-cresolyl cobamide in Sporomusa.

  14. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  15. [Studies by means of 1H NMR spectroscopy of complex formation of aromatic biologically active compounds with antibiotic topotecan].

    PubMed

    Mosunov, A A; Kostiukov, V V; Evstigneev, M P

    2012-01-01

    The analysis of heteroassociation of antibiotic topotecan (TPT) with aromatic biologically active compounds (BAC): caffeine, mutagens ethidium bromide and proflavine, antibiotic daunomycin, vitamins flavin-mononucleotide and nicotinamide, has been carried out in the work using 1H NMR spectroscopy data. The equilibrium constants of heteroassociation and induced chemical shifts of the protons have been obtained in the complexes with BAC. It is found that the complex formation TPT-BAC has the nature of stacking of the chromophores, additionally stabilized in the case of proflavine by intermolecular hydrogen bond. Calculation of the basic components of the Gibbs free energy of the complexation reactions is carried out, and the factors which stabilize and destabilize the heterocomplexes of molecules are revealed.

  16. Simultaneous removal of sulfur dioxide and polycyclic aromatic hydrocarbons from incineration flue gas using activated carbon fibers.

    PubMed

    Liu, Zhen-Shu; Li, Wen-Kai; Hung, Ming-Jui

    2014-09-01

    Incineration flue gas contains polycyclic aromatic hydrocarbons (PAHs) and sulfur dioxide (SO2). The effects of SO2 concentration (0, 350, 750, and 1000 ppm), reaction temperature (160, 200, and 280 degrees C), and the type of activated carbon fibers (ACFs) on the removal of SO2 and PAHs by ACFs were examined in this study. A fluidized bed incinerator was used to simulate practical incineration flue gas. It was found that the presence of SO2 in the incineration flue gas could drastically decrease removal of PAHs because of competitive adsorption. The effect of rise in the reaction temperature from 160 to 280 degrees C on removal of PAHs was greater than that on SO2 removal at an SO2 concentration of 750 ppm. Among the three ACFs studied, ACF-B, with the highest microporous volume, highest O content, and the tightest structure, was the best adsorbent for removing SO2 and PAHs when these gases coexisted in the incineration flue gas. Implications: Simultaneous adsorption of sulfur dioxide (SO2) and polycyclic aromatic hydrocarbons (PAHs) emitted from incineration flue gas onto activated carbon fibers (ACFs) meant to devise a new technique showed that the presence of SO2 in the incineration flue gas leads to a drastic decrease in removal of PAHs because of competitive adsorption. Reaction temperature had a greater influence on PAHs removal than on SO2 removal. ACF-B, with the highest microporous volume, highest O content, and tightest structure among the three studied ACFs, was found to be the best adsorbent for removing SO2 and PAHs.

  17. Airborne particulate polycyclic aromatic hydrocarbon (PAH) pollution in a background site in the North China Plain: concentration, size distribution, toxicity and sources.

    PubMed

    Zhu, Yanhong; Yang, Lingxiao; Yuan, Qi; Yan, Chao; Dong, Can; Meng, Chuanping; Sui, Xiao; Yao, Lan; Yang, Fei; Lu, Yaling; Wang, Wenxing

    2014-01-01

    The size-fractionated characteristics of particulate polycyclic aromatic hydrocarbons (PAHs) were studied from January 2011 to October 2011 using a Micro-orifice Uniform Deposit Impactor (MOUDI) at the Yellow River Delta National Nature Reserve (YRDNNR), a background site located in the North China Plain. The average annual concentration of total PAHs in the YRDNNR (18.95 ± 16.51 ng/m(3)) was lower than that in the urban areas of China; however, it was much higher than that in other rural or remote sites in developed countries. The dominant PAHs, which were found in each season, were fluorene (5.93%-26.80%), phenanthrene (8.17%-26.52%), fluoranthene (15.23%-27.12%) and pyrene (9.23%-16.31%). A bimodal distribution was found for 3-ring PAHs with peaks at approximately 1.0-1.8 μm and 3.2-5.6 μm; however, 4-6 ring PAHs followed a nearly unimodal distribution, with the highest peak in the 1.0-1.8 μm range. The mass median diameter (MMD) values for the total PAHs averaged 1.404, 1.467, 1.218 and 0.931 μm in spring, summer, autumn and winter, respectively. The toxicity analysis indicated that the carcinogenic potency of particulate PAHs existed primarily in the <1.8 μm size range. Diagnostic ratios and PCA analysis indicated that the PAHs in aerosol particles were mainly derived from coal combustion. In addition, back-trajectory calculations demonstrated that atmospheric PAHs were produced primarily by local anthropogenic sources.

  18. Identification of putative active site residues of ACAT enzymes.

    PubMed

    Das, Akash; Davis, Matthew A; Rudel, Lawrence L

    2008-08-01

    In this report, we sought to determine the putative active site residues of ACAT enzymes. For experimental purposes, a particular region of the C-terminal end of the ACAT protein was selected as the putative active site domain due to its high degree of sequence conservation from yeast to humans. Because ACAT enzymes have an intrinsic thioesterase activity, we hypothesized that by analogy with the thioesterase domain of fatty acid synthase, the active site of ACAT enzymes may comprise a catalytic triad of ser-his-asp (S-H-D) amino acid residues. Mutagenesis studies revealed that in ACAT1, S456, H460, and D400 were essential for activity. In ACAT2, H438 was required for enzymatic activity. However, mutation of D378 destabilized the enzyme. Surprisingly, we were unable to identify any S mutations of ACAT2 that abolished catalytic activity. Moreover, ACAT2 was insensitive to serine-modifying reagents, whereas ACAT1 was not. Further studies indicated that tyrosine residues may be important for ACAT activity. Mutational analysis showed that the tyrosine residue of the highly conserved FYXDWWN motif was important for ACAT activity. Furthermore, Y518 was necessary for ACAT1 activity, whereas the analogous residue in ACAT2, Y496, was not. The available data suggest that the amino acid requirement for ACAT activity may be different for the two ACAT isozymes.

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

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

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

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

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

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

  1. Species difference among experimental rodents in the activity and induction of cytochrome P-450 isozymes for mutagenic activation of carcinogenic aromatic amines.

    PubMed

    Degawa, M; Agatsuma, T; Hashimoto, Y

    1990-12-01

    The expressions of hepatic microsomal cytochrome P-450 isozymes in male rats, mice, hamsters and guinea pigs were studied comparatively with or without an ip injection of a cytochrome P-450 inducer. The activity and quantity of microsomal cytochrome P-450 isozymes were determined respectively by a bacterial mutation assay with Salmonella typhimurium TA98 and immunochemical assays using monoclonal antibodies against rat cytochrome P-450 isozymes. 3-Methoxy-4-aminoazobenzene (3-MeO-AAB), 2-amino-3-methyl-9H-pyrido[2,3-b]indole acetate (MeA alpha C) and 3-methylcholanthrene were used as cytochrome P-450 inducers, and 7 carcinogenic aromatic amines including 3-MeO-AAB and MeA alpha C were used as substrates for the mutation assay. By means of these assays, we examined the species differences among rodents in the activity and induction rate of hepatic cytochrome P-450 isozymes responsible for the mutagenic activation of carcinogenic aromatic amines.

  2. Activation of octopaminergic receptors by essential oil constituents isolated from aromatic plants: possible mode of action against insect pests.

    PubMed

    Kostyukovsky, Moshe; Rafaeli, Ada; Gileadi, Carina; Demchenko, Nataly; Shaaya, Eli

    2002-11-01

    As a result of screening a large number of essential oils from Israeli aromatic plants and their biologically active constituents, we isolated two oils with high activity against several stored-product insects. In this study the effect of these compounds on the acetylcholinesterase and the octopamine systems in insects was studied in order to elucidate their mode of action. Inhibition of acetylcholinesterase activity in vitro was evident only at high concentrations (10(-3) M) and could not account effectively for the low-dose mortality for some stored-product insects observed in vivo. However, the essential oil constituents were found to cause a significant increase in the levels of the intracellular messenger, cyclic AMP of abdominal epidermal tissue in the model insect, Helicoverpa armigera Hübn. The effect was significant even at low, physiological concentrations (10(-8) M) when tested directly on abdominal epidermal tissue preparations in vitro. This intracellular response was found to resemble closely the significant increases in the levels of the cyclic AMP of abdominal epidermal tissue due to treatment with the neurotransmitter/neuromodulator, octopamine. Subsequent treatment with the octopaminergic antagonist, phentolamine, effectively inhibited the cyclic AMP levels induced by essential oil treatment, indicating possible competitive activation of octopaminergic receptors by essential oil constituents.

  3. Uptake and toxicity of polycyclic aromatic hydrocarbons in terrestrial springtails--studying bioconcentration kinetics and linking toxicity to chemical activity.

    PubMed

    Schmidt, Stine Nørgaard; Smith, Kilian Eric Christopher; Holmstrup, Martin; Mayer, Philipp

    2013-02-01

    Passive dosing applies a polymer loaded with test compound(s) to establish and maintain constant exposure in laboratory experiments. Passive dosing with the silicone poly(dimethylsiloxane) was used to control exposure of the terrestrial springtail Folsomia candida to six polycyclic aromatic hydrocarbons (PAHs) in bioconcentration and toxicity experiments. Folsomia candida could move freely on the PAH-loaded silicone, resulting in exposure via air and direct contact. The bioconcentration kinetics indicated efficient uptake of naphthalene, anthracene, and pyrene through air and (near) equilibrium partitioning of these PAHs to lipids and possibly the waxy layer of the springtail cuticle. Toxicities of naphthalene, phenanthrene, and pyrene were related to chemical activity, which quantifies the energetic level and drives spontaneous processes including diffusive biouptake. Chemical activity-response relationships yielded effective lethal chemical activities (La50s) well within the expected range for baseline toxicity (0.01-0.1). Effective lethal body burdens for naphthalene and pyrene exceeded the expected range of 2 to 8 mmol kg(-1) fresh weight, which again indicated the waxy layer to be a sorbing phase. Finally, chemical activities were converted into equilibrium partitioning concentrations in lipids yielding effective lethal concentrations for naphthalene and phenanthrene in good correspondence with the lethal membrane burden for baseline toxicity (40-160 mmol kg(-1) lipid). Passive dosing was a practical approach for tightly controlling PAH exposure, which in turn provided new experimental possibilities and findings.

  4. The Luminous Polycyclic Aromatic Hydrocarbon Emission Features: Applications to High Redshift Galaxies and Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Shipley, Heath; Papovich, Casey

    2015-08-01

    We provide a new robust star-formation rate (SFR) calibration using the luminosity from polycyclic aromatic hydrogen (PAH) molecules. The PAH features emit strongly in the mid-infrared (mid-IR; 3-19μm), mitigating dust extinction, and they are very luminous, containing 5-10% of the total IR luminosity in galaxies. We derive the calibration of the PAH luminosity as a SFR indicator using a sample of 105 star-forming galaxies covering a range of total IR luminosity, LIR = L(8-1000μm) = 109 - 1012 L⊙ and redshift 0 < z < 0.6. The PAH luminosity correlates linearly with the SFR as measured by the dust-corrected Hα luminosity (using the sum of the Hα and rest-frame 24μm luminosity from Kennicutt et al. 2009), with tight scatter of ~0.15 dex, comparable to the scatter in the dust-corrected Hα SFRs and Paα SFRs. We show this relation is sensitive to galaxy metallicity, where the PAH luminosity of galaxies with Z < 0.7 Z⊙ departs from the linear SFR relationship but in a behaved manor. We derive for this a correction to galaxies below solar metallicity. As a case study for observations with JWST, we apply the PAH SFR calibration to a sample of lensed galaxies at 1 < z < 3 with Spitzer Infrared Spectrograph (IRS) data, and we demonstrate the utility of PAHs to derive SFRs as accurate as those available from any other indicator. This new SFR indicator will be useful for probing the peak of the SFR density of the universe (1 < z < 3) and for studying the coevolution of star-formation and supermassive blackhole accretion contemporaneously in a galaxy.

  5. Experimental warming differentially affects microbial structure and activity in two contrasted moisture sites in a Sphagnum-dominated peatland.

    PubMed

    Delarue, Frédéric; Buttler, Alexandre; Bragazza, Luca; Grasset, Laurent; Jassey, Vincent E J; Gogo, Sébastien; Laggoun-Défarge, Fatima

    2015-04-01

    Several studies on the impact of climate warming have indicated that peat decomposition/mineralization will be enhanced. Most of these studies deal with the impact of experimental warming during summer when prevalent abiotic conditions are favorable to decomposition. Here, we investigated the effect of experimental air warming by open-top chambers (OTCs) on water-extractable organic matter (WEOM), microbial biomasses and enzymatic activities in two contrasted moisture sites named Bog and Fen sites, the latter considered as the wetter ones. While no or few changes in peat temperature and water content appeared under the overall effect of OTCs, we observed that air warming smoothed water content differences and led to a decrease in mean peat temperature at the warmed Bog sites. This thermal discrepancy between the two sites led to contrasting changes in microbial structure and activities: a rise in hydrolytic activity at the warmed Bog sites and a relative enhancement of bacterial biomass at the warmed Fen sites. These features were not associated with any change in WEOM properties namely carbon and sugar contents and aromaticity, suggesting that air warming did not trigger any shift in OM decomposition. Using various tools, we show that the use of single indicators of OM decomposition can lead to fallacious conclusions. Lastly, these patterns may change seasonally as a consequence of complex interactions between groundwater level and air warming, suggesting the need to improve our knowledge using a high time-resolution approach.

  6. Multiple, Ligand-Dependent Routes from the Active Site of Cytochrome P450 2C9

    SciTech Connect

    Cojocaru, Vlad; Winn, Peter J.; Wade, Rebecca C.

    2012-02-13

    The active site of liver-specific, drug-metabolizing cytochrome P450 (CYP) monooxygenases is deeply buried in the protein and is connected to the protein surface through multiple tunnels, many of which were found open in different CYP crystal structures. It has been shown that different tunnels could serve as ligand passage routes in different CYPs. However, it is not understood whether one CYP uses multiple routes for substrate access and product release and whether these routes depend on ligand properties. From 300 ns of molecular dynamics simulations of CYP2C9, the second most abundant CYP in the human liver we found four main ligand exit routes, the occurrence of each depending on the ligand type and the conformation of the F-G loop, which is likely to be affected by the CYP-membrane interaction. A non-helical F-G loop favored exit towards the putative membrane-embedded region. Important protein features that direct ligand exit include aromatic residues that divide the active site and whose motions control access to two pathways. The ligands interacted with positively charged residues on the protein surface through hydrogen bonds that appear to select for acidic substrates. The observation of multiple, ligand-dependent routes in a CYP aids understanding of how CYP mutations affect drug metabolism and provides new possibilities for CYP inhibition.

  7. Polycyclic aromatic hydrocarbons (PAHs) mediate transcriptional activation of the ATP binding cassette transporter ABCB6 gene via the aryl hydrocarbon receptor (AhR).

    PubMed

    Chavan, Hemantkumar; Krishnamurthy, Partha

    2012-09-14

    Liver is endowed with a mechanism to induce hepatic cytochromes P450 (CYP450s) in response to therapeutic drugs and environmental contaminants, leading to increased detoxification and elimination of the xenobiotics. Each CYP450 is composed of an apoprotein moiety and a heme prosthetic group, which is required for CYP450 activity. Thus, under conditions of CYP450 induction, there is a coordinate increase in heme biosynthesis to compensate for the increased expression of CYP450s. ABCB6, a mitochondrial ATP binding cassette transporter, which regulates coproporphyrinogen transport from the cytoplasm into the mitochondria to complete heme biosynthesis, represents a previously unrecognized rate-limiting step in heme biosynthesis. However, it is not known if exposure to drugs and environmental contaminants induces ABCB6 expression, to assure an adequate and apparently coordinated supply of heme for the generation of functional cytochrome holoprotein. In the present study, we demonstrate that polycyclic aromatic hydrocarbons (PAHs), the widely distributed environmental toxicants shown to induce porphyrin accumulation causing hepatic porphyria, up-regulate ABCB6 expression in both mice and humans. Using siRNA technology and Abcb6 knock-out mice, we demonstrate that PAH-mediated increase in hepatic porphyrins is compromised in the absence of ABCB6. Moreover, in vivo studies in aryl hydrocarbon receptor (AhR) knock-out mice demonstrate that PAH induction of ABCB6 is mediated by AhR. Promoter activation studies combined with electrophoretic mobility shift assay and chromatin immunoprecipitation assay demonstrate direct interactions between the AhR binding sites in the ABCB6 promoter and the AhR receptor, implicating drug activation mechanisms for ABCB6 similar to those found in inducible cytochrome P450s. These studies are the first to describe direct transcriptional activation of both mouse and human ABCB6 by xenobiotics.

  8. Therapeutic agents with dramatic antiretroviral activity and little toxicity at effective doses: aromatic polycyclic diones hypericin and pseudohypericin.

    PubMed Central

    Meruelo, D; Lavie, G; Lavie, D

    1988-01-01

    Two aromatic polycyclic diones hypericin and pseudohypericin have potent antiretroviral activity; these substances occur in plants of the Hypericum family. Both compounds are highly effective in preventing viral-induced manifestations that follow infections with a variety of retroviruses in vivo and in vitro. Pseudohypericin and hypericin probably interfere with viral infection and/or spread by direct inactivation of the virus or by preventing virus shedding, budding, or assembly at the cell membrane. These compounds have no apparent activity against the transcription, translation, or transport of viral proteins to the cell membrane and also no direct effect on the polymerase. This property distinguishes their mode of action from that of the major antiretro-virus group of nucleoside analogues. Hypericin and pseudohypericin have low in vitro cytotoxic activity at concentrations sufficient to produce dramatic antiviral effects in murine tissue culture model systems that use radiation leukemia and Friend viruses. Administration of these compounds to mice at the low doses sufficient to prevent retroviral-induced disease appears devoid of undesirable side effects. This lack of toxicity at therapeutic doses extends to humans, as these compounds have been tested in patients as antidepressants with apparent salutary effects. Our observations to date suggest that pseudohypericin and hypericin could become therapeutic tools against retroviral-induced diseases such as acquired immunodeficiency syndrome (AIDS). Images PMID:2839837

  9. Crude oil polycyclic aromatic hydrocarbons removal via clay-microbe-oil interactions: Effect of acid activated clay minerals.

    PubMed

    Ugochukwu, Uzochukwu C; Fialips, Claire I

    2017-03-09

    Acid treatment of clay minerals is known to modify their properties such as increase their surface area and surface acidity, making them suitable as catalysts in many chemical processes. However, the role of these surface properties during biodegradation processes of polycyclic aromatic hydrocarbons (PAHs) is only known for mild acid (0.5 M Hydrochloric acid) treated clays. Four different clay minerals were used for this study: a montmorillonite, a saponite, a palygorskite and a kaolinite. They were treated with 3 M hydrochloric acid to produce acid activated clay minerals. The role of the acid activated montmorillonite, saponite, palygorskite and kaolinite in comparison with the unmodified clay minerals in the removal of PAHs during biodegradation was investigated in microcosm experiments. The microcosm experiments contained micro-organisms, oil, and clays in aqueous medium with a hydrocarbon degrading microorganism community predominantly composed of Alcanivorax spp. Obtained results indicated that acid activated clays and unmodified kaolinite did not enhance the biodegradation of the PAHs whereas unmodified montmorillonite, palygorskite and saponite enhanced their biodegradation. In addition, unmodified palygorskite adsorbed the PAHs significantly due to its unique channel structure.

  10. The Luminous Polycyclic Aromatic Hydrocarbon Emission Features: Applications to High Redshift Galaxies and Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Shipley, Heath V.

    2016-01-01

    For decades, significant work has been applied to calibrating emission from the ultra-violet, nebular emission lines, far-infrared, X-ray and radio as tracers of the star-formation rate (SFR) in distant galaxies. Understanding the exact rate of star-formation and how it evolves with time and galaxy mass has deep implications for how galaxies form. The co-evolution of star-formation and supermassive black hole (SMBH) accretion is one of the key problems in galaxy formation theory. But, many of these SFR indicators are influenced by SMBH accretion in galaxies and result in unreliable SFRs. Utilizing the luminous polycyclic aromatic hydrocarbon (PAH) emission features, I provide a new robust SFR calibration using the luminosity emitted from the PAHs at 6.2μm, 7.7μm and 11.3μm to solve this. The PAH features emit strongly in the mid-infrared (mid-IR; 5-25μm) mitigating dust extinction, containing on average 5-10% of the total IR luminosity in galaxies. I use a sample of 105 star-forming galaxies covering a range of total IR luminosity, LIR = L(8-1000μm) = 109 - 1012 L⊙ and redshift 0 < z < 0.4, with mid-IR spectroscopy from the Spitzer Infrared Spectrograph (IRS), and data covering other SFR indicators (Hα emission and rest-frame 24μm continuum emission). The PAH luminosity correlates linearly with the SFR as measured by the Hα luminosity (corrected for attenuation using the mono-chromatic rest-frame 24μm emission), with a tight scatter of <0.15 dex. The scatter is comparable to that between SFRs derived from the Paα and dust-corrected Hα emission lines. We present a case study in advance of JWST, which will be capable of measuring SFRs (from 8μm rest-frame photometry, i.e. PAHs) in distant galaxies (z ≤ 2) with JWST/MIRI to SFRs as low as ~10 M⊙yr-1, because the PAH features are so bright. We use Spitzer/IRS observations of PAH features in lensed star-forming galaxies at 1 < z < 3 to demonstrate the utility of the PAHs to derive SFRs that agree with

  11. Promoter-proximal polyadenylation sites reduce transcription activity

    PubMed Central

    Andersen, Pia K.; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites on 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 base pairs of the promoter. In contrast, promoter-proximal positioning of a pA site-independent histone gene terminator supports high transcription levels. We propose that optimal communication between a pA site-dependent gene terminator and its promoter critically depends on gene length and that short RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels. PMID:23028143

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

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

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

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

    SciTech Connect

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

    1991-10-01

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

  14. Active and regulatory sites of cytosolic 5'-nucleotidase.

    PubMed

    Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

    2010-12-01

    Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation.

  15. Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.

    PubMed

    Neshat, Armin; Mentz, Almut; Rückert, Christian; Kalinowski, Jörn

    2014-11-20

    The Gram-positive bacterium Corynebacterium glutamicum belongs to the order Corynebacteriales and is used as a producer of amino acids at industrial scales. Due to its economic importance, gene expression and particularly the regulation of amino acid biosynthesis has been investigated extensively. Applying the high-resolution technique of transcriptome sequencing (RNA-seq), recently a vast amount of data has been generated that was used to comprehensively analyze the C. glutamicum transcriptome. By analyzing RNA-seq data from a small RNA cDNA library of C. glutamicum, short transcripts in the known transcriptional attenuators sites of the trp operon, the ilvBNC operon and the leuA gene were verified. Furthermore, whole transcriptome RNA-seq data were used to elucidate the transcriptional organization of these three amino acid biosynthesis operons. In addition, we discovered and analyzed the novel attenuator aroR, located upstream of the aroF gene (cg1129). The DAHP synthase encoded by aroF catalyzes the first step in aromatic amino acid synthesis. The AroR leader peptide contains the amino acid sequence motif F-Y-F, indicating a regulatory effect by phenylalanine and tyrosine. Analysis by real-time RT-PCR suggests that the attenuator regulates the transcription of aroF in dependence of the cellular amount of tRNA loaded with phenylalanine when comparing a phenylalanine-auxotrophic C. glutamicum mutant fed with limiting and excess amounts of a phenylalanine-containing dipeptide. Additionally, the very interesting finding was made that all analyzed attenuators are leaderless transcripts.

  16. Control of Substrate Specificity by Active-Site Residues in Nitrobenzene Dioxygenase

    PubMed Central

    Ju, Kou-San; Parales, Rebecca E.

    2006-01-01

    Nitrobenzene 1,2-dioxygenase from Comamonas sp. strain JS765 catalyzes the initial reaction in nitrobenzene degradation, forming catechol and nitrite. The enzyme also oxidizes the aromatic rings of mono- and dinitrotoluenes at the nitro-substituted carbon, but the basis for this specificity is not understood. In this study, site-directed mutagenesis was used to modify the active site of nitrobenzene dioxygenase, and the contribution of specific residues in controlling substrate specificity and enzyme performance was evaluated. The activities of six mutant enzymes indicated that the residues at positions 258, 293, and 350 in the α subunit are important for determining regiospecificity with nitroarene substrates and enantiospecificity with naphthalene. The results provide an explanation for the characteristic specificity with nitroarene substrates. Based on the structure of nitrobenzene dioxygenase, substitution of valine for the asparagine at position 258 should eliminate a hydrogen bond between the substrate nitro group and the amino group of asparagine. Up to 99% of the mononitrotoluene oxidation products formed by the N258V mutant were nitrobenzyl alcohols rather than catechols, supporting the importance of this hydrogen bond in positioning substrates in the active site for ring oxidation. Similar results were obtained with an I350F mutant, where the formation of the hydrogen bond appeared to be prevented by steric interference. The specificity of enzymes with substitutions at position 293 varied depending on the residue present. Compared to the wild type, the F293Q mutant was 2.5 times faster at oxidizing 2,6-dinitrotoluene while retaining a similar Km for the substrate based on product formation rates and whole-cell kinetics. PMID:16517627

  17. BAX Activation is Initiated at a Novel Interaction Site

    PubMed Central

    Gavathiotis, Evripidis; Suzuki, Motoshi; Davis, Marguerite L.; Pitter, Kenneth; Bird, Gregory H.; Katz, Samuel G.; Tu, Ho-Chou; Kim, Hyungjin; Cheng, Emily H.-Y.; Tjandra, Nico; Walensky, Loren D.

    2008-01-01

    BAX is a pro-apoptotic protein of the BCL-2 family stationed in the cytosol until activated by a diversity of stress stimuli to induce cell death. Anti-apoptotic proteins such as BCL-2 counteract BAX-mediated cell death. Although an interaction site that confers survival functionality has been defined for anti-apoptotic proteins, an activation site has not been identified for BAX, rendering its explicit trigger mechanism unknown. We previously developed Stabilized Alpha-Helix of BCL-2 domains (SAHBs) that directly initiate BAX-mediated mitochondrial apoptosis. Here we demonstrate by NMR analysis that BIM SAHB binds BAX at an interaction site that is distinct from the canonical binding groove characterized for anti-apoptotic proteins. The specificity of the BIM SAHB-BAX interaction is highlighted by point mutagenesis that abrogates functional activity, confirming that BAX activation is initiated at this novel structural location. Thus, we have now defined a BAX interaction site for direct activation, establishing a new target for therapeutic modulation of apoptosis. PMID:18948948

  18. A critical evaluation of magnetic activated carbon's potential for the remediation of sediment impacted by polycyclic aromatic hydrocarbons.

    PubMed

    Han, Zhantao; Sani, Badruddeen; Akkanen, Jarkko; Abel, Sebastian; Nybom, Inna; Karapanagioti, Hrissi K; Werner, David

    2015-04-09

    Addition of activated carbon (AC) or biochar (BC) to sediment to reduce the chemical and biological availability of organic contaminants is a promising in-situ remediation technology. But concerns about leaving the adsorbed pollutants in place motivate research into sorbent recovery methods. This study explores the use of magnetic sorbents. A coal-based magnetic activated carbon (MAC) was identified as the strongest of four AC and BC derived magnetic sorbents for polycyclic aromatic hydrocarbons (PAHs) remediation. An 8.1% MAC amendment (w/w, equal to 5% AC content) was found to be as effective as 5% (w/w) pristine AC in reducing aqueous PAHs within three months by 98%. MAC recovery from sediment after three months was 77%, and incomplete MAC recovery had both, positive and negative effects. A slight rebound of aqueous PAH concentrations was observed following the MAC recovery, but aqueous PAH concentrations then dropped again after six months, likely due to the presence of the 23% unrecovered MAC. On the other hand, the 77% recovery of the 8.1% MAC dose was insufficient to reduce ecotoxic effects of fine grained AC or MAC amendment on the egestion rate, growth and reproduction of the AC sensitive species Lumbriculus variegatus.

  19. Polycyclic aromatic hydrocarbon-induced CYP1B1 activity is suppressed by perillyl alcohol in MCF-7 cells

    SciTech Connect

    Chan, Nelson L.S.; Wang Huan; Wang Yun; Leung, H.Y.; Leung, Lai K. . E-mail: laikleung@yahoo.com

    2006-06-01

    Perillyl alcohol (POH) is a dietary monoterpene with potential applications in chemoprevention and chemotherapy. Although clinical trials are under way, POH's physiological and pharmacological properties are still unclear. In the present study, the effect of POH on polycyclic aromatic hydrocarbon (PAH)-induced genotoxicity, and the related expression were examined in MCF-7 cells. Exposure to environmental toxicant increases the risk of cancer. Many of these compounds are pro-carcinogens and are biotransformed into their ultimate genotoxic structures by xenobiotic metabolizing enzymes. CYP1A1 and 1B1 are enzymes that catalyze the biotransformation of dimethylbenz[a]anthracene (DMBA). Our data revealed that 0.5 {mu}M of POH was effective in blocking DMBA-DNA binding. Ethoxyresorufin-O-deethylase (EROD) assay indicated that the administration of POH inhibited the DMBA-induced enzyme activity in MCF-7 cells. Enzyme kinetic analysis revealed that POH inhibited CYP1B1 but not CYP1A1 activity. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assay also demonstrated that the monoterpene reduced CYP1B1 mRNA abundance induced by DMBA. The present study illustrated that POH might inhibit and downregulate CYP1B1, which could protect against PAH-induced carcinogenesis.

  20. Metal catalysts supported on activated carbon fibers for removal of polycyclic aromatic hydrocarbons from incineration flue gas.

    PubMed

    Lin, Chiou-Liang; Cheng, Yu-Hsiang; Liu, Zhen-Shu; Chen, Jian-Yuan

    2011-12-15

    The aim of this research was to use metal catalysts supported on activated carbon fibers (ACFs) to remove 16 species of polycyclic aromatic hydrocarbons (PAHs) from incineration flue gas. We tested three different metal loadings (0.11 wt%, 0.29 wt%, and 0.34 wt%) and metals (Pt, Pd, and Cu), and two different pretreatment solutions (HNO(3) and NaOH). The results demonstrated that the ACF-supported metal catalysts removed the PAHs through adsorption and catalysis. Among the three metals, Pt was most easily adsorbed on the ACFs and was the most active in oxidation of PAHs. The mesopore volumes and density of new functional groups increased significantly after the ACFs were pretreated with either solutions, and this increased the measured metal loading in HNO(3)-0.48% Pd/ACFs and NaOH-0.52% Pd/ACFs. These data confirm that improved PAH removal can be achieved with HNO(3)-0.48% Pd/ACFs and NaOH-0.52% Pd/ACFs.

  1. Enantio-selective optrode for optical isomers of biologically active amines using a new lipophilic aromatic carrier

    NASA Astrophysics Data System (ADS)

    He, Huarui; Uray, Georg; Wolfbeis, Otto S.

    1991-09-01

    This paper presents a method for optically sensing enantiomers (optical isomers) of biological amines such as norephedrine, and drugs such as the (Beta) -blocker propranolol. It is based on the use of a new lipophilic aromatic ammonium ion carrier (DODD) and a highly fluorescent lipophilic proton carrier (DZ 49) dissolved in a pvc membrane. Recognition of one of the enantiomers is accomplished by specific interaction of the amine with the optically active lipophilic substrate in a pvc membrane. The amine, which is present as an ammonium ion at physiological pH, is carried into the pvc membranes. Simultaneously, a proton is released from the proton carrier (a lipophilic xanthene dye) that thereby undergoes a change in both color and fluorescence intensity. The sensors respond to three analytes in the concentration range from 0.01 to 10 mM for propranolol, 0.3 to 100 mM for norephedrine, and 1 to 100 mM for 1-phenylethylamine. The selectivity coefficients (Kopt) are 0.8, 0.7, and 0.8 for propranolol, norephedrine,a nd 1-phenylethylamine, respectively. It is of potential utility for specifically recognizing one out of several isomers, in particular bioactive amines, where one form usually is active only. The carrier showed stronger affinity for compounds which contain naphthyl rather than phenyl substituents.

  2. Involvement of novel autophosphorylation sites in ATM activation.

    PubMed

    Kozlov, Sergei V; Graham, Mark E; Peng, Cheng; Chen, Philip; Robinson, Phillip J; Lavin, Martin F

    2006-08-09

    ATM kinase plays a central role in signaling DNA double-strand breaks to cell cycle checkpoints and to the DNA repair machinery. Although the exact mechanism of ATM activation remains unknown, efficient activation requires the Mre11 complex, autophosphorylation on S1981 and the involvement of protein phosphatases and acetylases. We report here the identification of several additional phosphorylation sites on ATM in response to DNA damage, including autophosphorylation on pS367 and pS1893. ATM autophosphorylates all these sites in vitro in response to DNA damage. Antibodies against phosphoserine 1893 revealed rapid and persistent phosphorylation at this site after in vivo activation of ATM kinase by ionizing radiation, paralleling that observed for S1981 phosphorylation. Phosphorylation was dependent on functional ATM and on the Mre11 complex. All three autophosphorylation sites are physiologically important parts of the DNA damage response, as phosphorylation site mutants (S367A, S1893A and S1981A) were each defective in ATM signaling in vivo and each failed to correct radiosensitivity, genome instability and cell cycle checkpoint defects in ataxia-telangiectasia cells. We conclude that there are at least three functionally important radiation-induced autophosphorylation events in ATM.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  4. Aromatic graphene

    NASA Astrophysics Data System (ADS)

    Das, D. K.; Sahoo, S.

    2016-04-01

    In recent years graphene attracts the scientific and engineering communities due to its outstanding electronic, thermal, mechanical and optical properties and many potential applications. Recently, Popov et al. [1] have studied the properties of graphene and proved that it is aromatic but without fragrance. In this paper, we present a theory to prepare graphene with fragrance. This can be used as scented pencils, perfumes, room and car fresheners, cosmetics and many other useful household substances.

  5. Spectral Response and Diagnostics of Biological Activity of Hydroxyl-Containing Aromatic Compounds

    NASA Astrophysics Data System (ADS)

    Tolstorozhev, G. B.; Mayer, G. V.; Bel'kov, M. V.; Shadyro, O. I.

    2016-08-01

    Using IR Fourier spectra and employing quantum-chemical calculations of electronic structure, spectra, and proton-acceptor properties, synthetic derivatives of aminophenol exhibiting biological activity in the suppression of herpes, influenza, and HIV viruses have been investigated from a new perspective, with the aim of establishing the spectral response of biological activity of the molecules. It has been experimentally established that the participation of the aminophenol hydroxyl group in intramolecular hydrogen bonds is characteristic of structures with antiviral properties. A quantum-chemical calculation of the proton-acceptor ability of the investigated aminophenol derivatives has shown that biologically active structures are characterized by a high proton-acceptor ability of oxygen of the hydroxyl group. A correlation that has been obtained among the formation of an intramolecular hydrogen bond, high proton-acceptor ability, and antiviral activity of substituted aminophenols enables us to predict the pharmacological properties of new medical preparations of the given class of compounds.

  6. Antimicrobial, Antioxidant, and Anti-Inflammatory Activities of Essential Oils of Selected Aromatic Plants from Tajikistan

    PubMed Central

    Sharopov, Farukh; Braun, Markus Santhosh; Gulmurodov, Isomiddin; Khalifaev, Davlat; Isupov, Salomiddin; Wink, Michael

    2015-01-01

    Antimicrobial, antioxidant, and anti-inflammatory activities of the essential oils of 18 plant species from Tajikistan (Central Asia) were investigated. The essential oil of Origanum tyttanthum showed a strong antibacterial activity with both minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 312.5 µg/mL for E. coli, 625 µg/mL (MIC) and 1250 µg/mL (MBC) for MRSA (methicillin-resistant Staphylococcus aureus), respectively. The essential oil of Galagania fragrantissima was highly active against MRSA at concentrations as low as 39.1 µg/mL and 78.2 µg/mL for MIC and MBC, respectively. Origanum tyttanthum essential oil showed the highest antioxidant activity with IC50 values of 0.12 mg/mL for ABTS (2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid)) and 0.28 mg/mL for DPPH (2,2-diphenyl-1-picrylhydrazyl). Galagania fragrantissima and Origanum tyttanthum essential oils showed the highest anti-inflammatory activity; IC50 values of 5-lipoxygenase (5-LOX) inhibition were 7.34 and 14.78 µg/mL, respectively. In conclusion, essential oils of Origanum tyttanthum and Galagania fragrantissima exhibit substantial antimicrobial, antioxidant, and anti-inflammatory activities. They are interesting candidates in phytotherapy. PMID:28231227

  7. Volatile profiling of aromatic traditional medicinal plant, Polygonum minus in different tissues and its biological activities.

    PubMed

    Ahmad, Rafidah; Baharum, Syarul Nataqain; Bunawan, Hamidun; Lee, Minki; Mohd Noor, Normah; Rohani, Emelda Roseleena; Ilias, Norashikin; Zin, Noraziah Mohamad

    2014-11-20

    The aim of this research was to identify the volatile metabolites produced in different organs (leaves, stem and roots) of Polygonum minus, an important essential oil producing crop in Malaysia. Two methods of extraction have been applied: Solid Phase Microextraction (SPME) and hydrodistillation coupled with Gas Chromatography-Mass Spectrometry (GC-MS). Approximately, 77 metabolites have been identified and aliphatic compounds contribute significantly towards the aroma and flavour of this plant. Two main aliphatic compounds: decanal and dodecanal were found to be the major contributor. Terpenoid metabolites were identified abundantly in leaves but not in the stem and root of this plant. Further studies on antioxidant, total phenolic content, anticholinesterase and antimicrobial activities were determined in the essential oil and five different extracts. The plant showed the highest DPPH radical scavenging activity in polar (ethanol) extract for all the tissues tested. For anti-acetylcholinesterase activity, leaf in aqueous extract and methanol extract showed the best acetylcholinesterase inhibitory activities. However, in microbial activity, the non-polar extracts (n-hexane) showed high antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA) compared to polar extracts. This study could provide the first step in the phytochemical profiles of volatile compounds and explore the additional value of pharmacology properties of this essential oil producing crop Polygonum minus.

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

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

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

  9. Spectroscopic studies of the active site of galactose oxidase

    SciTech Connect

    Knowles, P.F.; Brown, R.D. III; Koenig, S.H.

    1995-07-19

    X-ray absorption and EPR spectroscopy have been used to probe the copper site structure in galactose oxidase at pH 4.5 and 7.0. the results suggest that there are no major differences in the structure of the tetragonal Cu(II) site at these pH values. Analysis of the extended X-ray absorption fine structure (EXAFS) indicates that four N,O scatterers are present at approximately 2 {Angstrom}; these are presumably the equatorial ligands. In addition, the EXAFS data establish that oxidative activation to produce the active-site tyrosine radical does not cause major changes in the copper coordination environment. Therefore results obtained on the one-electron reduced enzyme, containing Cu(II) but not the tyrosine radical, probably also apply to the catalytically active Cu(II)/tyrosine radical state. Solvent water exchange, inhibitor binding, and substrate binding have been probed via nuclear magnetic relaxation dispersion (NMRD) measurements. The NMRD profile of galactose oxidase is quantitatively consistent with the rapid exchange of a single, equatorial water ligand with a Cu(II)-O separation of about 2.4 {Angstrom}. Azide and cyanide displace this coordinated water. The binding of azide and the substrate dihydroxyacetone produce very similar effects on the NMRD profile of galactose oxidase, indicating that substrates also bind to the active site Cu(II) in an equatorial position.

  10. Energy transfer at the active sites of heme proteins

    SciTech Connect

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

    1995-12-31

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

  11. The bioflavonoid galangin blocks aryl hydrocarbon receptor activation and polycyclic aromatic hydrocarbon-induced pre-B cell apoptosis.

    PubMed

    Quadri, S A; Qadri, A N; Hahn, M E; Mann, K K; Sherr, D H

    2000-09-01

    Bioflavonoids are plant compounds touted for their potential to treat or prevent several diseases including cancers induced by common environmental chemicals. Much of the biologic activity of one such class of pollutants, polycyclic aromatic hydrocarbons (PAH), is mediated by the aryl hydrocarbon receptor/transcription factor (AhR). For example, the AhR regulates PAH immunotoxicity that manifests as pre-B cell apoptosis in models of B cell development. Because bioflavonoids block PAH-induced cell transformation and are structurally similar to AhR ligands, it was postulated that some of them would suppress PAH-induced, AhR-dependent immunotoxicity, possibly through a direct AhR blockade. This hypothesis was tested using a model of B cell development in which pre-B cells are cultured with and are dependent on bone marrow stromal or hepatic parenchymal cell monolayers. Of seven bioflavonoids screened, galangin (3,5,7-trihydroxyflavone) blocked PAH-induced but not C(2)-ceramide- or H(2)O(2)-induced pre-B cell apoptosis. Because galangin blocked AhR-dependent reporter gene expression, AhR complex-DNA binding, and AhR nuclear translocation, inhibition of a relatively early step in AhR signaling was implicated. This hypothesis was supported by the ability of galangin to bind the AhR and stabilize AhR-90-kDa heat shock protein complexes in the presence of AhR agonists. These studies demonstrate the utility of pre-B cell culture systems in identifying compounds capable of blocking PAH immunotoxicity, define at least one mechanism of galangin activity (i.e., repression of AhR activation), and motivate the use of this and similar dietary bioflavonoids as relatively nontoxic inhibitors of AhR agonist activity and as pharmacologic agents with which to dissect AhR signaling pathways.

  12. A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism.

    PubMed

    Sánchez-Reyez, Ayixon; Batista-García, Ramón Alberto; Valdés-García, Gilberto; Ortiz, Ernesto; Perezgasga, Lucía; Zárate-Romero, Andrés; Pastor, Nina; Folch-Mallol, Jorge Luis

    2017-03-09

    Activated sludge is produced during the treatment of sewage and industrial wastewaters. Its diverse chemical composition allows growth of a large collection of microbial phylotypes with very different physiologic and metabolic profiles. Thus, activated sludge is considered as an excellent environment to discover novel enzymes through functional metagenomics, especially activities related with degradation of environmental pollutants. Metagenomic DNA was isolated and purified from an activated sludge sample. Metagenomic libraries were subsequently constructed in Escherichia coli. Using tributyrin hydrolysis, a screening by functional analysis was conducted and a clone that showed esterase activity was isolated. Blastx analysis of the sequence of the cloned DNA revealed, among others, an ORF that encodes a putative thioesterase with 47-64% identity to GenBank CDS reported genes, similar to those in the hotdog fold thioesterase superfamily. On the basis of its amino acid similarity and its homology-modelled structure we deduced that this gene encodes an enzyme (ThYest_ar) that belongs to family TE13, with a preference for aryl-CoA substrates and a novel catalytic residue constellation. Plasmid retransformation in E. coli confirmed the clone's phenotype, and functional complementation of a paaI E. coli mutant showed preference for phenylacetate over chlorobenzene as a carbon source. This work suggests a role for TE13 family thioesterases in swimming and degradation approaches for phenyl acetic acid. Proteins 2017. © 2017 Wiley Periodicals, Inc.

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

    PubMed

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

    2014-12-16

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

  14. New aromatic activated dihalides and bisphenol monomers for the preparation of novel poly(arylene ethers)

    NASA Technical Reports Server (NTRS)

    Wolfe, James F.

    1993-01-01

    The goal of this research program was to synthesize a series of unique monomers of type I to be utilized at NASA-Langley in the preparation of new poly(arylene ether ketones), poly(arylene ether ketosulfones), and poly(arylene ether ketophosphine oxides). These A-A and A-B monomer systems, which possess activated aryl halide and/or phenolic end groups, are accessible via condensation reactions of appropriately substituted aryl acetonitrile carbanions with activated aryl dihalides followed by oxidative decyanation.

  15. Catalytic co-aromatization of ethanol and methane

    SciTech Connect

    Wang, Aiguo; He, Peng; Yung, Matthew; Zeng, Hongbo; Qian, Hui; Song, Hua

    2016-06-06

    This study demonstrates the technical feasibility of simultaneously converting ethanol and methane into liquid hydrocarbons at mild reaction conditions (400 °C and 1 atm) over silver and/or zinc modified zeolite catalysts. After GC-MS analysis, it is worth noting that aromatics are the major compounds contained in the liquid product collected from the run when 1%Ag/ZSM-5, particularly after H2 pretreatment, is charged. Compared to the performance exhibited from the run with pure HZSM-5 support engaged, Ag addition into the HZSM-5 framework favors aromatics formation, which might be closely associated with better Ag dispersion and more abundance of strong surface acidic sites where aromatization might take place while Zn loading exerts a detrimental effect on the production of aromatics but promotes the ether generation possibly through dehydration reaction. Referred to that from its N2 counterpart, the increased aromatics formation of the collected liquid product when methane is present indicates that methane existence might facilitate ethanol aromatization. Moreover, combined with the increased carbon number in the formed aromatics from CH4 run when H2 run is referred and zero liquid formation from CH4-alone test as well as more prominent endothermic feature of methane run and more importantly the notably increased 13C signals in 13C NMR spectra of the liquid product collected during ethanol conversion under 13CH4 environment, all the observations suggest that methane might be activated nonoxidatively and converted into higher hydrocarbons, preferentially into aromatics if suitable catalyst is charged under the assistance of co-existing oxygenated hydrocarbon. Lastly, the reported synergetic effect could potentially lead to the more economic utilization of abundant natural gas and cellulosic ethanol.

  16. Methyl-beta-cyclodextrin enhanced biodegradation of polycyclic aromatic hydrocarbons and associated microbial activity in contaminated soil.

    PubMed

    Sun, Mingming; Luo, Yongming; Christie, Peter; Jia, Zhongjun; Li, Zhengao; Teng, Ying

    2012-01-01

    The contamination of soils by polycyclic aromatic hydrocarbons (PAHs) is a widespread environmental problem and the remediation of PAHs from these areas has been a major concern. The effectiveness of many in situ bioremediation systems may be constrained by low contaminant bioavailability due to limited aqueous solubility or a large magnitude of sorption. The objective of this research was to evaluate the effect of methyl-beta-cyclodextrin (MCD) on bioaugmentation by Paracoccus sp. strain HPD-2 of an aged PAH-contaminated soil. When 10% (W/W) MCD amendment was combined with bioaugmentation by the PAH-degrading bacterium Paracoccus sp. strain HPD-2, the percentage degradation of total PAHs was significantly enhanced up to 34.8%. Higher counts of culturable PAH-degrading bacteria and higher soil dehydrogenase and soil polyphenol oxidase activities were observed in 10% (W/W) MCD-assisted bioaugmentation soil. This MCD-assisted bioaugmentation strategy showed significant increases (p < 0.05) in the average well color development (AWCD) obtained by the BIOLOG Eco plate assay, Shannon-Weaver index (H) and Simpson index (lambda) compared with the controls, implying that this strategy at least partially restored the microbiological functioning of the PAH-contaminated soil. The results suggest that MCD-aided bioaugmentation by Paracoccus sp. strain HPD-2 may be a promising practical bioremediation strategy for aged PAH-contaminated soils.

  17. Prenatal Polycyclic Aromatic Hydrocarbon, Adiposity, Peroxisome Proliferator-Activated Receptor (PPAR) γ Methylation in Offspring, Grand-Offspring Mice

    PubMed Central

    Yan, Zhonghai; Zhang, Hanjie; Maher, Christina; Arteaga-Solis, Emilio; Champagne, Frances A.; Wu, Licheng; McDonald, Jacob D.; Yan, Beizhan; Schwartz, Gary J.; Miller, Rachel L.

    2014-01-01

    Rationale Greater levels of prenatal exposure to polycyclic aromatic hydrocarbon (PAH) have been associated with childhood obesity in epidemiological studies. However, the underlying mechanisms are unclear. Objectives We hypothesized that prenatal PAH over-exposure during gestation would lead to weight gain and increased fat mass in offspring and grand-offspring mice. Further, we hypothesized that altered adipose gene expression and DNA methylation in genes important to adipocyte differentiation would be affected. Materials and Methods Pregnant dams were exposed to a nebulized PAH mixture versus negative control aerosol 5 days a week, for 3 weeks. Body weight was recorded from postnatal day (PND) 21 through PND60. Body composition, adipose cell size, gene expression of peroxisome proliferator-activated receptor (PPAR) γ, CCAAT/enhancer-binding proteins (C/EBP) α, cyclooxygenase (Cox)-2, fatty acid synthase (FAS) and adiponectin, and DNA methylation of PPAR γ, were assayed in both the offspring and grand-offspring adipose tissue. Findings Offspring of dams exposed to greater PAH during gestation had increased weight, fat mass, as well as higher gene expression of PPAR γ, C/EBP α, Cox2, FAS and adiponectin and lower DNA methylation of PPAR γ. Similar differences in phenotype and DNA methylation extended through the grand-offspring mice. Conclusions Greater prenatal PAH exposure was associated with increased weight, fat mass, adipose gene expression and epigenetic changes in progeny. PMID:25347678

  18. Purification of Pseudomonas putida acyl coenzyme A ligase active with a range of aliphatic and aromatic substrates.

    PubMed Central

    Fernández-Valverde, M; Reglero, A; Martinez-Blanco, H; Luengo, J M

    1993-01-01

    Acyl coenzyme A (acyl-CoA) ligase (acyl-CoA synthetase [ACoAS]) from Pseudomonas putida U was purified to homogeneity (252-fold) after this bacterium was grown in a chemically defined medium containing octanoic acid as the sole carbon source. The enzyme, which has a mass of 67 kDa, showed maximal activity at 40 degrees C in 10 mM K2PO4H-NaPO4H2 buffer (pH 7.0) containing 20% (wt/vol) glycerol. Under these conditions, ACoAS showed hyperbolic behavior against acetate, CoA, and ATP; the Kms calculated for these substrates were 4.0, 0.7, and 5.2 mM, respectively. Acyl-CoA ligase recognizes several aliphatic molecules (acetic, propionic, butyric, valeric, hexanoic, heptanoic, and octanoic acids) as substrates, as well as some aromatic compounds (phenylacetic and phenoxyacetic acids). The broad substrate specificity of ACoAS from P. putida was confirmed by coupling it with acyl-CoA:6-aminopenicillanic acid acyltransferase from Penicillium chrysogenum to study the formation of several penicillins. Images PMID:8476289

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

    PubMed

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

    2016-09-06

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

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

    PubMed Central

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

    2016-01-01

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

  1. Metabolism and Biomarkers of Heterocyclic Aromatic Amines in Molecular Epidemiology Studies: Lessons Learned from Aromatic Amines

    PubMed Central

    2011-01-01

    Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group, to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs and, thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review article, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and

  2. Bioassay of polycyclic aromatic hydrocarbons

    SciTech Connect

    Van Kirk, E.A.

    1980-08-01

    A positive relationship was found between the photodynamic activity of 24 polycyclic aromatic hydrocarbons versus published results on the mutagenicity, carcinogenicity, and initiation of unscheduled DNA synthesis. Metabolic activation of benzo(a)pyrene resulted in detection of increased mutagenesis in Paramecium tetraurelia as found also in the Ames Salmonella assay. The utility of P. tetraurelia as a biological detector of hazardous polycyclic aromatic hydrocarbons is discussed.

  3. Probing the promiscuous active site of myo-inositol dehydrogenase using synthetic substrates, homology modeling, and active site modification.

    PubMed

    Daniellou, Richard; Zheng, Hongyan; Langill, David M; Sanders, David A R; Palmer, David R J

    2007-06-26

    The active site of myo-inositol dehydrogenase (IDH, EC 1.1.1.18) from Bacillus subtilis recognizes a variety of mono- and disaccharides, as well as 1l-4-O-substituted inositol derivatives. It catalyzes the NAD+-dependent oxidation of the axial alcohol of these substrates with comparable kinetic constants. We have found that 4-O-p-toluenesulfonyl-myo-inositol does not act as a substrate for IDH, in contrast to structurally similar compounds such as those bearing substituted benzyl substituents in the same position. X-ray crystallographic analysis of 4-O-p-toluenesulfonyl-myo-inositol and 4-O-(2-naphthyl)methyl-myo-inositol, which is a substrate for IDH, shows a distinct difference in the preferred conformation of the aryl substituent. Conformational analysis of known substrates of IDH suggests that this conformational difference may account for the difference in reactivity of 4-O-p-toluenesulfonyl-myo-inositol in the presence of IDH. A sequence alignment of IDH with the homologous glucose-fructose oxidoreductase allowed the construction of an homology model of inositol dehydrogenase, to which NADH and 4-O-benzyl-scyllo-inosose were docked and the active site energy minimized. The active site model is consistent with all experimental results and suggests that a conserved tyrosine-glycine-tyrosine motif forms the hydrophobic pocket adjoining the site of inositol recognition. Y233F and Y235F retain activity, while Y233R and Y235R do not. A histidine-aspartate pair, H176 and D172, are proposed to act as a dyad in which H176 is the active site acid/base. The enzyme is inactivated by diethyl pyrocarbonate, and the mutants H176A and D172N show a marked loss of activity. Kinetic isotope effect experiments with D172N indicate that chemistry is rate-determining for this mutant.

  4. Activation of Ca2+ uptake and inhibition of reversal of the sarcoplasmic reticulum Ca2+ pump by aromatic compounds.

    PubMed

    Petretski, J H; Wolosker, H; de Meis, L

    1989-12-05

    The effects of aromatic compounds in sarcoplasmic reticulum Ca2+-ATPase were investigated. The solubility of the drugs in various organic solvents and water was measured. The ratio between the solubility in organic solvents and that in water (distribution coefficient) was used as an index of their hydrophobicity. The order found was triphenylphosphine greater than diphenylamine greater than 3-nitrophenol greater than 4-nitrophenol greater than 1,3-dihydroxybenzene. The effects observed on the Ca2+-ATPase were correlated with hydrophobicity of the drugs, activation and inhibition being obtained at a lower concentration the greater the distribution coefficient of the drug into organic solvent. In leaky vesicles, the effects of each compound on the ATPase activity varied depending on the Ca2+ concentration in the medium: it inhibited in the presence of 5 microM Ca2+ and activated when the Ca2+ concentration was raised to 2 mM. In intact vesicles, 3- and 4-nitrophenol, diphenylamine, and triphenylphosphine enhanced both the rate of ATP hydrolysis and the amount of Ca2+ accumulated by the vesicles. These four drugs inhibited Ca2+ uptake when ITP was used as substrate. 1,3-Dihydroxybenzene enhanced the amount of Ca2+ accumulated by the vesicles regardless of whether ATP or ITP was the substrate. All five compounds inhibited the phosphorylation of the enzyme by Pi, the efflux of Ca2+, and the synthesis of ATP measured during the reversal of the Ca2+ pump. The results indicate that the hydrophobic character of various organic compounds determines their access to sensitive domains of the membrane-bound calcium pump. Additional specific effects are then produced, depending on the structure of each compound.

  5. Exploring the Influence of the Aromaticity on the Anticancer and Antivascular Activities of Organoplatinum(II) Complexes.

    PubMed

    Zamora, Ana; Pérez, Sergio A; Rothemund, Matthias; Rodríguez, Venancio; Schobert, Rainer; Janiak, Christoph; Ruiz, José

    2017-03-09

    A series of new organometallic Pt(II) complexes of the type [Pt(C^N)Cl(DMSO)] (C^N=N,N-dimethyl-1-(2-aryl)methanamine-κ(2) C2,N; aryl=phenyl 2 a, biphenyl 2 b, p-terphenyl 2 c, naphthyl 2 d, anthracenyl 2 e, or pyrenyl 2 f) have been synthesized to explore the influence of the aromaticity on their anticancer activity. The best performers, 2 b and d, are more active than cisplatin (CDDP) in epithelial ovarian carcinoma cells A2780, with 2 d having a higher selectivity factor than CDDP in all the tested cell lines. In addition, all the new compounds overcome the acquired resistance in A2780cisR cells and interestingly, show low micromolar IC50 values towards the triple negative breast cancer cell line MDA-MB-231 and the highly metastatic 518A2 melanoma cells. This study shows that the hydrophobicity, accumulation into cells, and metal levels on nuclear DNA for the complexes are consistent with their cytotoxicity. Complexes 2 b and d induce apoptosis in a caspase-independent manner and suppress the intracellular ROS generation without modifying the mitochondria membrane potential. In addition, 2 a-f effectively inhibit angiogenesis in the endothelial cell line EA.hy926 at sub-cytotoxic concentrations and 2 b and d show in vivo antivascular effects on the chorioallantoic membrane (CAM) of fertilized SPF-eggs (SPF=specific-pathogen-free). Inhibition of tubulin polymerization and degeneration of cytoskeleton organization in 518A2 melanoma cells are presented as a preliminary mechanism of its antimetastatic activity.

  6. The active site structure and mechanism of phosphoenolpyruvate utilizing enzymes

    SciTech Connect

    Cheng, K.C.

    1989-01-01

    Arginine specific reagents showed irreversible inhibition of avian liver mitochondrial phosphoenolpyruvate carboxykinase. Potent protection against modification was elicited by CO{sub 2} or CO{sub 2} in the presence of other substrates. Labeling of enzyme with (7-{sup 14}C) phenylglyoxal showed that 1 or 2 arginines are involved in CO{sub 2} binding and activation. Peptide map studies showed this active site arginine residues is located at position 289. Histidine specific reagents showed pseudo first order inhibition of avian mitochondrial phosphoenolpyruvate carboxykinase activity. The best protection against modification was elicited by IDP or IDP and Mn{sup +2}. One histidine residue is at or near the phosphoenolpyruvate binding site as demonstrated in the increased absorbance at 240 nm and proton relaxation rate studies. Circular dichroism studies reveal that enzyme structure was perturbed by diethylpyrocarbonate modification. Metal binding studies suggest that this enzyme has only one metal binding site. The putative binding sites from several GTP and phosphoenolpyruvate utilizing enzymes are observed in P-enolpyruvate carboxykinase from different species.

  7. Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

    SciTech Connect

    Not Available

    2012-07-01

    NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for

  8. Enhanced Activity of Supported Ni Catalysts Promoted by Pt for Rapid Reduction of Aromatic Nitro Compounds

    PubMed Central

    Shang, Huishan; Pan, Kecheng; Zhang, Lu; Zhang, Bing; Xiang, Xu

    2016-01-01

    To improve the activities of non-noble metal catalysts is highly desirable and valuable to the reduced use of noble metal resources. In this work, the supported nickel (Ni) and nickel-platinum (NiPt) nanocatalysts were derived from a layered double hydroxide/carbon composite precursor. The catalysts were characterized and the role of Pt was analysed using X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS) mapping, and X-ray photoelectron spectroscopy (XPS) techniques. The Ni2+ was reduced to metallic Ni0 via a self-reduction way utilizing the carbon as a reducing agent. The average sizes of the Ni particles in the NiPt catalysts were smaller than that in the supported Ni catalyst. The electronic structure of Ni was affected by the incorporation of Pt. The optimal NiPt catalysts exhibited remarkably improved activity toward the reduction of nitrophenol, which has an apparent rate constant (Ka) of 18.82 × 10−3 s−1, 6.2 times larger than that of Ni catalyst and also larger than most of the reported values of noble-metal and bimetallic catalysts. The enhanced activity could be ascribed to the modification to the electronic structure of Ni by Pt and the effect of exposed crystal planes. PMID:28335231

  9. Adsorption of aromatic organic contaminants by graphene nanosheets: comparison with carbon nanotubes and activated carbon.

    PubMed

    Apul, Onur Guven; Wang, Qiliang; Zhou, Yang; Karanfil, Tanju

    2013-03-15

    Adsorption of two synthetic organic compounds (SOCs; phenanthrene and biphenyl) by two pristine graphene nanosheets (GNS) and one graphene oxide (GO) was examined and compared with those of a coal base activated carbon (HD4000), a single-walled carbon nanotube (SWCNT), and a multi-walled carbon nanotube (MWCNT) in distilled and deionized water and in the presence of natural organic matter (NOM). Graphenes exhibited comparable or better adsorption capacities than carbon nanotubes (CNTs) and granular activated carbon (GAC) in the presence of NOM. The presence of NOM reduced the SOC uptake of all adsorbents. However, the impact of NOM on the SOC adsorption was smaller on graphenes than CNTs and activated carbons. Furthermore, the SOC with its flexible molecular structure was less impacted from NOM preloading than the SOC with planar and rigid molecular structure. The results indicated that graphenes can serve as alternative adsorbents for removing SOCs from water. However, they will also, if released to environment, adsorb organic contaminants influencing their fate and impact in the environment.

  10. Enhanced Activity of Supported Ni Catalysts Promoted by Pt for Rapid Reduction of Aromatic Nitro Compounds.

    PubMed

    Shang, Huishan; Pan, Kecheng; Zhang, Lu; Zhang, Bing; Xiang, Xu

    2016-06-04

    To improve the activities of non-noble metal catalysts is highly desirable and valuable to the reduced use of noble metal resources. In this work, the supported nickel (Ni) and nickel-platinum (NiPt) nanocatalysts were derived from a layered double hydroxide/carbon composite precursor. The catalysts were characterized and the role of Pt was analysed using X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS) mapping, and X-ray photoelectron spectroscopy (XPS) techniques. The Ni(2+) was reduced to metallic Ni⁰ via a self-reduction way utilizing the carbon as a reducing agent. The average sizes of the Ni particles in the NiPt catalysts were smaller than that in the supported Ni catalyst. The electronic structure of Ni was affected by the incorporation of Pt. The optimal NiPt catalysts exhibited remarkably improved activity toward the reduction of nitrophenol, which has an apparent rate constant (Ka) of 18.82 × 10(-3) s(-1), 6.2 times larger than that of Ni catalyst and also larger than most of the reported values of noble-metal and bimetallic catalysts. The enhanced activity could be ascribed to the modification to the electronic structure of Ni by Pt and the effect of exposed crystal planes.

  11. Anti-plasmodial and insecticidal activities of the essential oils of aromatic plants growing in the Mediterranean area

    PubMed Central

    2012-01-01

    Background Sardinia is a Mediterranean area endemic for malaria up to the last century. During a screening study to evaluate the anti-plasmodial activity of some aromatic plants traditionally used in Sardinia, Myrtus communis (myrtle, Myrtaceae), Satureja thymbra (savory, Lamiaceae), and Thymus herba-barona (caraway thyme, Lamiaceae) were collected in three vegetative periods: before, during and after flowering. Methods The essential oils were obtained by steam distillation, fractionated by silica gel column chromatography and analysed by GC-FID-MS. Total oil and three main fractions were tested on D10 and W2 strains of Plasmodium falciparum in vitro. Larvicidal and adulticidal activities were tested on Anopheles gambiae susceptible strains. Results The essential oil of savory, rich in thymol, was the most effective against P. falciparum with an inhibitory activity independent from the time of collection (IC50 17–26 μg/ml on D10 and 9–11 μg/ml on W2). Upon fractionation, fraction 1 was enriched in mono-sesquiterpenoid hydrocarbons; fraction 2 in thymol (73-83%); and fraction 3 contained thymol, carvacrol and terpinen-4-ol, with a different composition depending on the time of collection. Thymol-enriched fractions were the most active on both strains (IC50 20–22 μg/ml on D10 and 8–10 μg/ml on W2) and thymol was confirmed as mainly responsible for this activity (IC50 19.7± 3.0 and 10.6 ± 2.0 μg/ml on D10 and W2, respectively). The essential oil of S. thymbra L. showed also larvicidal and adulticidal activities. The larvicidal activity, expressed as LC50, was 0.15 ± 0.002; 0.21 ± 0.13; and 0.15 ± 0.09 μg/ml (mean ± sd) depending on the time of collection: before, during and after flowering, respectively. Conclusions This study provides evidence for the use of essential oils for treating malaria and fighting the vector at both the larval and adult stages. These findings open the possibility for further investigation aimed at

  12. Characteristics, identification, and potential risk of polycyclic aromatic hydrocarbons in road dusts and agricultural soils from industrial sites in Shanghai, China.

    PubMed

    Jia, Jinpu; Bi, Chunjuan; Guo, Xue; Wang, Xueping; Zhou, Xiaoxiao; Chen, Zhenlou

    2017-01-01

    Road dusts and agricultural soil samples were collected from eight sites close to steel mills, chemical plants, and municipal solid waste incinerator in suburban Shanghai. Sixteen polycyclic aromatic hydrocarbons (PAHs) in the United States Environmental Protection Agency (US EPA) priority controlled list were analyzed quantitatively using GC-MS. The total PAH concentrations ranged from 0.79 to 6.2 μg g(-1) in road dust samples with a mean value of 2.38 μg g(-1) and 0.26 to 0.54 μg g(-1) in agricultural soils with an average of 0.36 μg g(-1). The most abundant individual PAHs were phenanthrene, fluoranthene, pyrene, chrysene, and benzo(b)fluoranthene in dust samples and phenanthrene, fluoranthene, chrysene, and benzo(b)fluoranthene, benzo (k) fluoranthene in soil samples. Dominant compounds were four-ring and five- to six-ring PAHs, which accounted for 41.5 and 31.5 % in dusts and 33.9 and 41.1 % in soils. The spatial distribution of PAHs in dusts and soils was consistent. The wind direction could affect the spatial distribution of PAHs. Organic matter contents were found to be significantly positively correlated with PAH concentrations in both dusts and soils while grain size of particles had no correlation with PAH concentrations and could not significantly influence the distribution of PAH concentrations. PAH isomer ratios showed that combustion of grass, wood, and coal was important sources of PAHs in road dusts and agricultural soils. Toxic equivalent concentrations indicated seven kinds of carcinogenetic PAHs were major toxic equivalent concentration (TEQ) contributors, accounting for 98 % of TEQ, in the road dusts and agricultural soils. Incremental lifetime cancer risk (ILCR) estimation results showed that the PAHs in the dusts and soils had potential cancer risk for both children and adults only by direct ingestion exposure. The TEQ and ILCR values of PAHs in road dusts were much higher than those in soils, which suggested that PAHs in road

  13. [Estimation inventory of polycyclic aromatic hydrocarbons (PAHs) from anthropogenic sources and its impacts within the Yanghe Watershed, an important water-source site of Beijing, China].

    PubMed

    Gao, Jia-Jia; Luo, Wei; Xi, Xiao-Xia

    2014-12-01

    The Yanghe Watershed, situated at the upwind of Beijing, is an important water-source site and ecologic protection barrier for Beijing and Zhangjiakou cities. The Yanghe Watershed is also a farming-pastoral transitional area and an ecologically vulnerable and sensitive region, as well as the place applying for Winter Olympic Game in 2022. Establishment of atmospheric emissions inventory of polycyclic aromatic hydrocarbons (PAHs) and identification of its sources within the Yanghe Watershed and its possible transportation paths to Beijing can help us get a better understanding of regional environmental pollution (especially air environmental pollution) in Beijing-Zhangjiakou area. In the present study, PAHs emission from different counties and cities within the Yanghe Watershed in 2012 was calculated based on the statistical data of local industries, agriculture and resident living while PAHs emission factors were estimated. According to the cluster analysis for air transport trajectories, main categories of air masses were obtained. Results indicated that total emission of PAHs in 2012 was 4.4 x 10(2) t. Coal combustion and crop-straw burning were the most important emission sources of PAHs, accounting for 76% and 16% of total emission of PAHs, respectively. Xuanhua county had the greatest emission of PAHs (49 t), followed by Xinghe (36 t), Tianzhen (32 t), Huailai (24 t) and Wanquan (15 t). In emission of 16 isomers of PAHs, the emission of high molecular weight isomers containing 4-6 rings was approximate to that of low molecular weight isomers containing 2-3 rings, accounting for approximately 50% of total emission of PAHs. Emission of PAHs had positive correlations with gross industrial production (GIP) (r = 0.96, P < 0.05) and resident income (RI) (r = 0.94, P < 0.05) and population density (PD) (r = 0.92, P < 0.05), but negatively correlated with land area (LA) (r = - 0.9, P < 0.05) and no significant correlationship with gross output value of agriculture

  14. Antimicrobial Activity and Chemical Composition of Three Essential Oils Extracted from Mediterranean Aromatic Plants.

    PubMed

    Elshafie, Hazem S; Sakr, Shimaa; Mang, Stefania M; Belviso, Sandra; De Feo, Vincenzo; Camele, Ippolito

    2016-11-01

    There is a growing interest in essential oils (EOs) as possible alternatives for traditional chemical pesticides. This study was carried out to characterize the chemical composition of the three EOs extracted from Verbena officinalis, Majorana hortensis, and Salvia officinalis using gas chromatography (GC) and GC-mass spectrometry (GC-MS) and to evaluate in vitro their efficacy against some phyto or human pathogens. The antifungal activity was investigated against Colletotrichum acutatum and Botrytis cinerea in comparison with Azoxystrobin as a large spectrum fungicide. Antibacterial activity was evaluated against Bacillus megaterium, Bacillus mojavensis, and Clavibacter michiganensis (G+ve) and Escherichia coli, Xanthomonas campestris, Pseudomonas savastanoi, and P. syringae pv. phaseolicola (G-ve) compared to a synthetic antibiotic tetracycline. Minimum inhibitory concentration was evaluated against the above tested fungi using 96-well microplate method. Results showed that the chemical structure of the three studied EOs was mainly composed of monoterpene compounds and all oils belong to the chemotype carvacrol/thymol. Results of GC analysis identified 64 compounds, which were identified based on their mass to charge ratio. Furthermore, the different concentrations of studied EOs inhibited the growth of tested microorganism in a dose-dependent manner.

  15. Effect of cyclic aromatics on sodium active transport in frog skin

    SciTech Connect

    Blankemeyer, J.T.; Bowerman, M.C. )

    1993-01-01

    A modified glass Ussing-chamber was used to mount the skin. The electrical potential difference (PD) was measured by two 3% agar-frog Ringer's bridges. Current (i.e. short-circuit current, or ISC) was passed by Ag-AgCl electrodes placed so that current density was uniform across the skin. Ringer's solution, bathing each side of the frog skin, was stirred and aerated by gas-lift pumps. The effect of toxicants on the ISC was determined by using the 15 min prior to toxicant administration as a control period, then calculating the change in ISC during the toxicant period as a percent of the control ISC. Phenol and benzene are components of crude oil and crude oil waste. These hydrocarbons and phenanthrene were tested for their effect on frog skin. The results show that the effect of organics on sodium active transport of an epithelium is to alter the active transport of sodium ions. 5 refs., 3 figs., 1 tab.

  16. Oxidation of polycyclic aromatic hydrocarbons using Bacillus subtilis CotA with high laccase activity and copper independence.

    PubMed

    Zeng, Jun; Zhu, Qinghe; Wu, Yucheng; Lin, Xiangui

    2016-04-01

    Bacterial laccase CueO from Escherichia coli can oxidize polycyclic aromatic hydrocarbons (PAHs); however, its application in the remediation of PAH-contaminated soil mainly suffers from a low oxidation rate and copper dependence. It was reported that a laccase with a higher redox potential tended to have a higher oxidation rate; thus, the present study investigated the oxidation of PAHs using another bacterial laccase CotA from Bacillus subtilis with a higher redox potential (525 mV) than CueO (440 mV). Recombinant CotA was overexpressed in E. coli and partially purified, exhibiting a higher laccase-specific activity than CueO over a broad pH and temperature range. CotA exhibited moderate thermostability at high temperatures. CotA oxidized PAHs in the absence of exogenous copper. Thereby, secondary heavy metal pollution can be avoided, another advantage of CotA over CueO. Moreover, this study also evaluated some unexplained phenomena in our previous study. It was observed that the oxidation of PAHs with bacterial laccases can be promoted by copper. The partially purified bacterial laccase oxidized only two of the 15 tested PAHs, i.e., anthracene and benzo[a]pyrene, indicating the presence of natural redox mediators in crude cell extracts. Overall, the recombinant CotA oxidizes PAHs with high laccase activity and copper independence, indicating that CotA is a better candidate for the remediation of PAHs than CueO. Besides, the findings here provide a better understanding of the oxidation of PAHs using bacterial laccases.

  17. Phytochemical profiles and antimicrobial activity of aromatic Malaysian herb extracts against food-borne pathogenic and food spoilage microorganisms.

    PubMed

    Aziman, Nurain; Abdullah, Noriham; Noor, Zainon Mohd; Kamarudin, Wan Saidatul Syida Wan; Zulkifli, Khairusy Syakirah

    2014-04-01

    Preliminary phytochemical and flavonoid compounds of aqueous and ethanolic extracts of 6 aromatic Malaysian herbs were screened and quantified using Reverse-Phase High Performance Liquid Chromatography (RP-HPLC). The herbal extracts were tested for their antimicrobial activity against 10 food-borne pathogenic and food spoilage microorganisms using disk diffusion assay. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC)/minimum fungicidal concentration (MFC) of herbal extracts were determined. In the phytochemical screening process, both aqueous and ethanolic extracts of P. hydropiper exhibited presence of all 7 tested phytochemical compounds. Among all herbal extracts, the aqueous P. hydropiper and E. elatior extracts demonstrated the highest antibacterial activity against 7 tested Gram-positive and Gram-negative bacteria with diameter ranging from 7.0 to 18.5 mm and 6.5 to 19 mm, respectively. The MIC values for aqueous and ethanolic extracts ranged from 18.75 to 175 mg/mL and 0.391 to 200 mg/mL, respectively while the MBC/MFC values for aqueous and ethanolic extracts ranged from 25 to 200 mg/mL and 3.125 to 50 mg/mL, respectively. Major types of bioactive compounds in aqueous P. hydropiper and E. elatior extracts were identified using RP-HPLC instrument. Flavonoids found in these plants were epi-catechin, quercetin, and kaempferol. The ability of aqueous Persicaria hydropiper (L.) H. Gross and Etlingera elatior (Jack) R.M. Sm. extracts to inhibit the growth of bacteria is an indication of its broad spectrum antimicrobial potential. Hence these herbal extracts may be used as natural preservative to improve the safety and shelf-life of food and pharmaceutical products.

  18. Identification of Ice Nucleation Active Sites on Silicate Dust Particles

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts [1-3]. Nevertheless, among those structures K-feldspar showed by far the highest ice nucleation activity. In this study, the reasons for its activity and the difference in the activity of the different feldspars were investigated in closer details. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. We give a potential explanation of the increased ice nucleation activity of K-feldspar. The ice nucleating sites are very much dependent on the alkali ion present by altering the water structure and the feldspar surface. The higher activity of K-feldspar can be attributed to the presence of potassium ions on the surface and surface bilayer. The alkali-ions have different hydration shells and thus an influence on the ice nucleation activity of feldspar. Chaotropic behavior of Calcium and Sodium ions are lowering the ice nucleation potential of the other feldspars, while kosmotropic Potassium has a neutral or even positive effect. Furthermore we investigated the influence of milling onto the ice nucleation of quartz particles. The ice nucleation activity can be increased by mechanical milling, by introducing more molecular, nucleation active defects to the particle surface. This effect is larger than expected by plane surface increase. [1] Atkinson et al. The Importance of Feldspar for Ice Nucleation by Mineral Dust in Mixed-Phase Clouds. Nature 2013, 498, 355-358. [2] Yakobi-Hancock et al.. Feldspar Minerals as Efficient Deposition Ice Nuclei. Atmos. Chem. Phys. 2013, 13, 11175-11185. [3] Zolles et al. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles. J. Phys. Chem. A 2015 accepted.

  19. Evaluation of the mutagenic activity of chrysin, a flavonoid inhibitor of the aromatization process.

    PubMed

    Oliveira, G A R; Ferraz, E R A; Souza, A O; Lourenço, R A; Oliveira, D P; Dorta, D J

    2012-01-01

    Chrysin is one of the natural flavonoids present in plants, and large amounts are present in honey and propolis. In addition to anticancer, antioxidation, and anti-inflammatory activities, chrysin has also been reported to be an inhibitor of aromatase, an enzyme converting testosterone into estrogen. The present study evaluated the mutagenicity of this flavonoid using micronucleus (MN) with HepG2 cells and Salmonella. Cell survival after exposure to different concentrations of chrysin was also determined using sulforhodamine B (SRB) colorimetric assay in HepG2 cells and the influence of this flavonoid on growth of cells in relation to the cell cycle and apoptosis. The MN test showed that from 1 to 15 μM of this flavonoid mutagenic activity was noted in HepG2 cells. The Salmonella assay demonstrated a positive response to the TA100 Salmonella strain in the presence or absence of S9, suggesting that this compound acted on DNA, inducing base pair substitution before or after metabolism via cytochrome P-450. The SRB assay illustrated that chrysin promoted growth inhibition of HepG2 cells in both periods studied (24 and 48 h). After 24 h of exposure it was noted that the most significant results were obtained with a concentration of 50 μM, resulting in 83% inhibition and SubG0 percentage of 12%. After 48 h of incubation cell proliferation inhibition rates (97% at 50 μM) were significantly higher. Our results showed that chrysin is a mutagenic and cytotoxic compound in cultured human HepG2 cells and Salmonella typhimurium. Although it is widely accepted that flavonoids are substances beneficial to health, one must evaluate the risk versus benefit relationship and concentrations of these substances to which an individual may be exposed.

  20. Face the Edges: Catalytic Active Sites of Nanomaterials

    PubMed Central

    Ni, Bing

    2015-01-01

    Edges are special sites in nanomaterials. The atoms residing on the edges have different environments compared to those in other parts of a nanomaterial and, therefore, they may have different properties. Here, recent progress in nanomaterial fields is summarized from the viewpoint of the edges. Typically, edge sites in MoS2 or metals, other than surface atoms, can perform as active centers for catalytic reactions, so the method to enhance performance lies in the optimization of the edge structures. The edges of multicomponent interfaces present even more possibilities to enhance the activities of nanomaterials. Nanoframes and ultrathin nanowires have similarities to conventional edges of nanoparticles, the application of which as catalysts can help to reduce the use of costly materials. Looking beyond this, the edge structures of graphene are also essential for their properties. In short, the edge structure can influence many properties of materials. PMID:27980960

  1. Active sites in char gasification: Final technical report

    SciTech Connect

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

    1987-09-01

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

  2. Treatment of soil eluate containing nitro aromatic compounds by adsorption on activated coke (AC).

    PubMed

    Zhang, Yiping; Jiang, Zhenming; Zhao, Quanlin; Zhang, Zhenzhong; Su, Hongping; Gao, Xuewen; Ye, Zhengfang

    2016-01-01

    Soil washing is a kind of physical method to remove organic matters from contaminated soil. However, its eluate after washing may result in secondary pollution to the environment. In this study, activated coke (AC) was used to remove organic pollutants from contaminated soil eluate. The effect of temperature, initial chemical oxygen demand (COD) and AC dosage on COD removal efficiency was investigated. The results showed that the organic matter can be removed in the eluate because the COD dropped a lot. When the AC dosage was 20 g·L(-1), 88.92% of COD decreased after 480 min of adsorption at 50 °C. The process of adsorption can be described by the Redlich-Peterson isotherm. The adsorption was spontaneous and endothermic. The pseudo-second-order model can be used to describe the adsorption process. After adsorption, the acute toxicity of the eluate was reduced by 76%, and the water qualities were in agreement with Chinese discharge standard GB 14470.1-2002, which means the eluate could be discharged to the environment.

  3. In vitro antimicrobial activity of essential oils from aromatic plants against selected foodborne pathogens.

    PubMed

    Rota, C; Carramiñana, J J; Burillo, J; Herrera, A

    2004-06-01

    The purpose of this study was to examine the effectiveness of selected essential oils for the control of growth and survival of pathogenic microorganisms of significant importance in food hygiene and to determine whether the antimicrobial effect was due to the major compounds of the oils. MIC and MBC were determined by the tube dilution method. Essential oils from Thymus vulgaris from Spain and France, Salvia sclarea, Salvia officinalis, Salvia lavandulifolia, Lavandula latifolia, Lavandula angustifolia, three hybrids of Lavandula latifolia x Lavandula angustifolia (Lavandin 'Super', Lavandin 'Abrialis', and Lavandin 'Grosso'), Rosmarinus officinalis, Hissopus officinalis, and Satureja montana were evaluated. Inhibition ranged from the strong activity of Satureja montana and Thymus vulgaris (France) to no inhibition with Salvia sclarea and Hissopus officinalis for each of the test strains: Salmonella Enteritidis, Salmonella Typhimurium, Escherichia coli O157:H7, Yersinia enterocolitica, Shigella flexneri, Listeria monocytogenes serovar 4b, and Staphylococcus aureus. Because some of the essential oils were highly inhibitory in small quantities to selected pathogenic microorganisms, they may provide alternatives to conventional antimicrobial additives in foods.

  4. Visible-Light-Induced Olefin Activation Using 3D Aromatic Boron-Rich Cluster Photooxidants.

    PubMed

    Messina, Marco S; Axtell, Jonathan C; Wang, Yiqun; Chong, Paul; Wixtrom, Alex I; Kirlikovali, Kent O; Upton, Brianna M; Hunter, Bryan M; Shafaat, Oliver S; Khan, Saeed I; Winkler, Jay R; Gray, Harry B; Alexandrova, Anastassia N; Maynard, Heather D; Spokoyny, Alexander M

    2016-06-08

    We report a discovery that perfunctionalized icosahedral dodecaborate clusters of the type B12(OCH2Ar)12 (Ar = Ph or C6F5) can undergo photo-excitation with visible light, leading to a new class of metal-free photooxidants. Excitation in these species occurs as a result of the charge transfer between low-lying orbitals located on the benzyl substituents and an unoccupied orbital delocalized throughout the boron cluster core. Here we show how these species, photo-excited with a benchtop blue LED source, can exhibit excited-state reduction potentials as high as 3 V and can participate in electron-transfer processes with a broad range of styrene monomers, initiating their polymerization. Initiation is observed in cases of both electron-rich and electron-deficient styrene monomers at cluster loadings as low as 0.005 mol%. Furthermore, photo-excitation of B12(OCH2C6F5)12 in the presence of a less activated olefin such as isobutylene results in the production of highly branched poly(isobutylene). This work introduces a new class of air-stable, metal-free photo-redox reagents capable of mediating chemical transformations.

  5. Limiting activity coefficients of some aromatic and aliphatic nitro compounds in water

    SciTech Connect

    Benes, M.; Dohnal, V.

    1999-09-01

    Limiting activity coefficients of nine nitroaromatic compounds and four nitroalkanes in water were determined in the range of environmentally related temperatures by measuring suitable phase equilibria. For liquid and solid nitroaromatics (nitrobenzene, 2-nitrotoluene, 3-nitrotoluene, 4-nitrotoluene, 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 1-chloro-2-nitrobenzene, and 1-chloro-4-nitrobenzene) the aqueous solubilities were measured by a conventional batch contacting method with UV spectrophotometric analysis, while for nitroalkanes (nitromethane, nitroethane, 1-nitropropane, and 2-nitropropane) the air-water partitioning (Henry`s law constant H{sub 12} or air-water partition coefficient K{sub aw}) was determined by the inert gas stripping method employing gas chromatography. Whenever possible, results were compared to literature values. Calculation of H{sub 12} or K{sub aw} for nitroaromatics from the measured solubilities is hindered by the lack of reliable vapor pressure data. On the basis of the temperature dependences of the solubilities measured, the enthalpies of solution at infinite dilution for the nitroaromatics in water were evaluated.

  6. Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis

    PubMed Central

    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

  7. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  8. Nest predation increases with parental activity: separating nest site and parental activity effects.

    PubMed Central

    Martin, T E; Scott, J; Menge, C

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection. PMID:11413645

  9. Active site amino acid sequence of human factor D.

    PubMed

    Davis, A E

    1980-08-01

    Factor D was isolated from human plasma by chromatography on CM-Sephadex C50, Sephadex G-75, and hydroxylapatite. Digestion of reduced, S-carboxymethylated factor D with cyanogen bromide resulted in three peptides which were isolated by chromatography on Sephadex G-75 (superfine) equilibrated in 20% formic acid. NH2-Terminal sequences were determined by automated Edman degradation with a Beckman 890C sequencer using a 0.1 M Quadrol program. The smallest peptide (CNBr III) consisted of the NH2-terminal 14 amino acids. The other two peptides had molecular weights of 17,000 (CNBr I) and 7000 (CNBr II). Overlap of the NH2-terminal sequence of factor D with the NH2-terminal sequence of CNBr I established the order of the peptides. The NH2-terminal 53 residues of factor D are somewhat more homologous with the group-specific protease of rat intestine than with other serine proteases. The NH2-terminal sequence of CNBr II revealed the active site serine of factor D. The typical serine protease active site sequence (Gly-Asp-Ser-Gly-Gly-Pro was found at residues 12-17. The region surrounding the active site serine does not appear to be more highly homologous with any one of the other serine proteases. The structural data obtained point out the similarities between factor D and the other proteases. However, complete definition of the degree of relationship between factor D and other proteases will require determination of the remainder of the primary structure.

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

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

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

  11. [Mechanism of arginine deiminase activity by site-directed mutagenesis].

    PubMed

    Li, Lifeng; Ni, Ye; Sun, Zhihao

    2012-04-01

    Arginine deiminase (ADI) has been studied as a potential anti-cancer agent for inhibiting arginine-auxotrophic tumors (such as melanomas and hepatocellular carcinomas) in phase III clinical trials. In this work, we studied the molecular mechanism of arginine deiminase activity by site-directed mutagenesis. Three mutation sites, A128, H404 and 1410, were introduced into wild-type ADI gene by QuikChange site-directed mutagenesis method, and four ADI mutants M1 (A128T), M2 (H404R), M3 (I410L), and M4 (A128T, H404R) were obtained. The ADI mutants were individually expressed in Escherichia coli BL21 (DE3), and the enzymatic properties of the purified mutant proteins were determined. The results show that both A128T and H404R had enhanced optimum pH, higher activity and stability of ADI under physiological condition (pH 7.4), as well as reduced K(m) value. This study provides an insight into the molecular mechanism of the ADI activity, and also the experimental evidence for the rational protein evolution in the future.

  12. Potential sites of CFTR activation by tyrosine kinases

    PubMed Central

    Billet, Arnaud; Jia, Yanlin; Jensen, Timothy J.; Hou, Yue-Xian; Chang, Xiu-Bao; Riordan, John R.; Hanrahan, John W.

    2016-01-01

    ABSTRACT The CFTR chloride channel is tightly regulated by phosphorylation at multiple serine residues. Recently it has been proposed that its activity is also regulated by tyrosine kinases, however the tyrosine phosphorylation sites remain to be identified. In this study we examined 2 candidate tyrosine residues near the boundary between the first nucleotide binding domain and the R domain, a region which is important for channel function but devoid of PKA consensus sequences. Mutating tyrosines at positions 625 and 627 dramatically reduced responses to Src or Pyk2 without altering the activation by PKA, suggesting they may contribute to CFTR regulation. PMID:26645934

  13. 1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

    NASA Astrophysics Data System (ADS)

    Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

    2004-07-01

    NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

  14. Polybenzimidazoles via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

    1995-01-01

    Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl) benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl) benzimidazoles are synthesizedby reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

  15. Polybenzimidazoles Via Aromatic Nucleophilic Displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergerrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

    1997-01-01

    Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenylbenzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl)benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl)benzimidazoles are synthesized by reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

  16. MSK1 activity is controlled by multiple phosphorylation sites

    PubMed Central

    McCOY, Claire E.; Campbell, David G.; Deak, Maria; Bloomberg, Graham B.; Arthur, J. Simon C.

    2004-01-01

    MSK1 (mitogen- and stress-activated protein kinase) is a kinase activated in cells downstream of both the ERK1/2 (extracellular-signal-regulated kinase) and p38 MAPK (mitogen-activated protein kinase) cascades. In the present study, we show that, in addition to being phosphorylated on Thr-581 and Ser-360 by ERK1/2 or p38, MSK1 can autophosphorylate on at least six sites: Ser-212, Ser-376, Ser-381, Ser-750, Ser-752 and Ser-758. Of these sites, the N-terminal T-loop residue Ser-212 and the ‘hydrophobic motif’ Ser-376 are phosphorylated by the C-terminal kinase domain of MSK1, and their phosphorylation is essential for the catalytic activity of the N-terminal kinase domain of MSK1 and therefore for the phosphorylation of MSK1 substrates in vitro. Ser-381 is also phosphorylated by the C-terminal kinase domain, and mutation of Ser-381 decreases MSK1 activity, probably through the inhibition of Ser-376 phosphorylation. Ser-750, Ser-752 and Ser-758 are phosphorylated by the N-terminal kinase domain; however, their function is not known. The activation of MSK1 in cells therefore requires the activation of the ERK1/2 or p38 MAPK cascades and does not appear to require additional signalling inputs. This is in contrast with the closely related RSK (p90 ribosomal S6 kinase) proteins, whose activity requires phosphorylation by PDK1 (3-phosphoinositide-dependent protein kinase 1) in addition to phosphorylation by ERK1/2. PMID:15568999

  17. Rapid microwave hydrothermal synthesis of ZnGa{sub 2}O{sub 4} with high photocatalytic activity toward aromatic compounds in air and dyes in liquid water

    SciTech Connect

    Sun Meng; Li Danzhen; Zhang Wenjuan; Chen Zhixin; Huang Hanjie; Li Wenjuan; He Yunhui; Fu Xianzhi

    2012-06-15

    ZnGa{sub 2}O{sub 4} was synthesized from Ga(NO{sub 3}){sub 3} and ZnCl{sub 2} via a rapid and facile microwave-assisted hydrothermal method. The photocatalytic properties of the as-prepared ZnGa{sub 2}O{sub 4} were evaluated by the degradation of pollutants in air and aqueous solution under ultraviolet (UV) light illumination. The results demonstrated that ZnGa{sub 2}O{sub 4} had exhibited efficient photocatalytic activities higher than that of commercial P25 (Degussa Co.) in the degradation of benzene, toluene, and ethylbenzene, respectively. In the liquid phase degradation of dyes (methyl orange, Rhodamine B, and methylene blue), ZnGa{sub 2}O{sub 4} has also exhibited remarkable activities higher than that of P25. After 32 min of UV light irradiation, the decomposition ratio of methyl orange (10 ppm, 150 mL) over ZnGa{sub 2}O{sub 4} (0.06 g) was up to 99%. The TOC tests revealed that the mineralization ratio of MO (10 ppm, 150 mL) was 88.1% after 90 min of reaction. A possible mechanism of the photocatalysis over ZnGa{sub 2}O{sub 4} was also proposed. - Graphical abstract: In the degradation of RhB under UV light irradiation, ZnGa{sub 2}O{sub 4} had exhibited efficient photo-activity, and after only 24 min of irradiation the decomposition ratio was up to 99.8%. Highlights: Black-Right-Pointing-Pointer A rapid and facile M-H method to synthesize ZnGa{sub 2}O{sub 4} photocatalyst. Black-Right-Pointing-Pointer The photocatalyst exhibits high activity toward benzene and dyes. Black-Right-Pointing-Pointer The catalyst possesses more surface hydroxyl sites than TiO{sub 2} (P25). Black-Right-Pointing-Pointer Deep oxidation of different aromatic compounds and dyes over catalyst.

  18. Polyphenylquinoxalines via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

    1990-01-01

    Polyphenylquinoxalines are prepared by the nucleophilic displacement reaction of di(hydroxyphenyl)quinoxaline monomers with activated aromatic dihalides or dinitro compounds. The reactions are carried out in polar aprotic solvents using alkali metal bases at elevated temperatures under nitrogen. The di(hydroxyphenyl)quinoxaline monomers are prepared either by reacting stoichiometric quantities of aromatic bis(o-diamines) with a hydroxybenzil or by reacting o-phenylenediamine with a dihydroxybenzil or bis(hydroxyphenylglyoxylyl)benzene.

  19. Polyphenylquinoxalines via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

    1991-01-01

    Polyphenylquinoxalines are prepared by the nucleophilic displacement reaction of di(hydroxyphenyl)quinoxaline monomers with activated aromatic dihalides or dinitro compounds. The reactions are carried out in polar aprotic solvents during alkali metal bases at elevated temperatures under nitrogen. The di(hydroxyphenyl)quinoxaline monomers are prepared either by reacting stoichiometric quantities of aromatic bis(o-diamines) with a hydroxybenzil or by reacting o-phenylenediamine with a dihydroxybenzil or bis(hydroxyphenylglyoxylyl)benzene.

  20. Manganese peroxidase mRNA and enzyme activity levels during bioremediation of polycyclic aromatic hydrocarbon-contaminated soil with Phanerochaete chrysosporium.

    PubMed Central

    Bogan, B W; Schoenike, B; Lamar, R T; Cullen, D

    1996-01-01

    mRNA extraction from soil and quantitation by competitive reverse transcription-PCR were combined to study the expression of three manganese peroxidase (MnP) genes during removal of polycyclic aromatic hydrocarbons from cultures of Phanerochaete chrysosporium grown in presterilized soil. Periods of high mnp transcript levels and extractable MnP enzyme activity were temporally correlated, although separated by a short (1- to 2-day) lag period. This time frame also coincided with maximal rates of fluorene oxidation and chrysene disappearance in soil cultures, supporting the hypothesis that high ionization potential polycyclic aromatic hydrocarbons are oxidized in soil via MnP-dependent mechanisms. The patterns of transcript abundance over time in soil-grown P. chrysosporium were similar for all three of the mnp mRNAs studied, indicating that transcription of this gene family may be coordinately regulated under these growth conditions. PMID:8779576

  1. Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

    PubMed Central

    2015-01-01

    The class I terpenoid cyclase epi-isozizaene synthase (EIZS) utilizes the universal achiral isoprenoid substrate, farnesyl diphosphate, to generate epi-isozizaene as the predominant sesquiterpene cyclization product and at least five minor sesquiterpene products, making EIZS an ideal platform for the exploration of fidelity and promiscuity in a terpenoid cyclization reaction. The hydrophobic active site contour of EIZS serves as a template that enforces a single substrate conformation, and chaperones subsequently formed carbocation intermediates through a well-defined mechanistic sequence. Here, we have used the crystal structure of EIZS as a guide to systematically remold the hydrophobic active site contour in a library of 26 site-specific mutants. Remolded cyclization templates reprogram the reaction cascade not only by reproportioning products generated by the wild-type enzyme but also by generating completely new products of diverse structure. Specifically, we have tripled the overall number of characterized products generated by EIZS. Moreover, we have converted EIZS into six different sesquiterpene synthases: F96A EIZS is an (E)-β-farnesene synthase, F96W EIZS is a zizaene synthase, F95H EIZS is a β-curcumene synthase, F95M EIZS is a β-acoradiene synthase, F198L EIZS is a β-cedrene synthase, and F96V EIZS and W203F EIZS are (Z)-γ-bisabolene synthases. Active site aromatic residues appear to be hot spots for reprogramming the cyclization cascade by manipulating the stability and conformation of critical carbocation intermediates. A majority of mutant enzymes exhibit only relatively modest 2–100-fold losses of catalytic activity, suggesting that residues responsible for triggering substrate ionization readily tolerate mutations deeper in the active site cavity. PMID:24517311

  2. Structure-activity study on the spatial arrangement of the third aromatic ring of endomorphins 1 and 2 using an atypical constrained C terminus.

    PubMed

    Yu, Ye; Shao, Xuan; Cui, Yun; Liu, Hong-mei; Wang, Chang-ling; Fan, Ying-zhe; Liu, Jing; Dong, Shou-liang; Cui, Yu-xing; Wang, Rui

    2007-03-01

    The discovery of endomorphins (EMs) has opened the possibility of searching for new analgesics. However, the design of peptide analgesics has proven to be very difficult as a result of their conformational flexibility and a lack of clarity in structure-activity relationships (SAR). In EMs, the amino acid side chains exhibit considerable conformational flexibility, especially in the third aromatic ring, which is free to adopt a bioactive conformation. To resolve these problems, a series of C terminus EM analogues, [Xaa(4)-R]EMs, modified through the substitution of Phe(4) with nonaromatic residues and termination with benzyl groups, were designed to generate conformational constrains of the third aromatic ring by amide bond and torsion angles (phi(4) and psi(4)) of Xaa(4). Introduction of (S)-alpha-methyl or (S)/(R)-alpha-carboxamide on the methylene unit of the benzyl group was designed to produce an atypical topographical constraint (phi(5)) of the third aromatic ring rotation. Interestingly, some EM derivatives, with elimination of the C-terminal carboxamide group and significant changes in the address sequence (Phe(4)-NH(2)), still exhibited higher mu-opioid receptor (MOR) affinity than unmodified EMs. In contrast, some analogues with incorrectly constrained C termini displayed very low affinity and pharmacological activities. Thus, our results indicate that these EM analogues, with atypical constrained C termini, provide model compounds with potent MOR agonism. They also give evidence that the proper spatial orientation and conformational restriction of the third aromatic ring are crucial for the interaction of EMs with MOR.

  3. A Hydrophobic Pocket in the Active Site of Glycolytic Aldolase Mediates Interactions with Wiskott-Aldrich Syndrome Protein

    SciTech Connect

    St-Jean,M.; Izard, T.; Sygusch, J.

    2007-01-01

    Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C-terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, 4-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds about the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues, Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C-terminus with its active site, and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure a novel naphthol phosphate-based inhibitor of aldolase was identified and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

  4. Polycyclic aromatic hydrocarbons (PAHs) in soils and vegetation near an e-waste recycling site in South China: concentration, distribution, source, and risk assessment.

    PubMed

    Wang, Yan; Tian, Zhongjing; Zhu, Haolin; Cheng, Zhineng; Kang, Meiling; Luo, Chunling; Li, Jun; Zhang, Gan

    2012-11-15

    This study determined the concentrations of PAHs generated from e-waste recycling activities and their potential impacts on soil, vegetation, and human health. The total PAH concentrations in soils and plants ranged from 127 to 10,600 and 199 to 2420 ng/g, respectively. Samples from an e-waste burning site had higher PAH concentrations than samples from adjacent locations. The PAHs in plants varied with plant species and tissue, and Lactuca sativa L. contained the highest PAHs of all the vegetable species. Various land use types showed different PAH concentrations in soils, with vegetable fields showing higher concentrations than paddy fields. Low molecular weight PAHs, such as phenanthrene, were the predominant congeners in soils, whereas high molecular weight PAHs, such as fluoranthene, pyrene, and benzo[a]anthracene, were enriched in plants relative to soils. Dissimilar PAH profiles in soil and the corresponding vegetation indicated that the uptake of PAHs by plants was selective. A source analysis showed that the contamination by PAHs originated primarily from the open burning of e-waste. The total daily intakes of PAHs and carcinogenic PAHs through vegetables at the e-waste dismantling site were estimated to be 279 and 108 ng/kg/d, respectively, indicating that the consumption of vegetables grown near e-waste recycling sites is risky and should be completely avoided.

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

    SciTech Connect

    1981-02-27

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

  6. Vitamin K epoxide reductase: homology, active site and catalytic mechanism.

    PubMed

    Goodstadt, Leo; Ponting, Chris P

    2004-06-01

    Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1, a subunit of the VKOR complex, has recently been shown to possess this activity. Here, we show that VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologues the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases. These might reduce disulfide bonds of VKORC1-like enzymes as a prerequisite for their catalytic activities.

  7. Noncomparative scaling of aromaticity through electron itinerancy

    SciTech Connect

    Paul, Satadal; Goswami, Tamal; Misra, Anirban

    2015-10-15

    Aromaticity is a multidimensional concept and not a directly observable. These facts have always stood in the way of developing an appropriate theoretical framework for scaling of aromaticity. In the present work, a quantitative account of aromaticity is developed on the basis of cyclic delocalization of π-electrons, which is the phenomenon leading to unique features of aromatic molecules. The stabilization in molecular energy, caused by delocalization of π-electrons is obtained as a second order perturbation energy for archetypal aromatic systems. The final expression parameterizes the aromatic stabilization energy in terms of atom to atom charge transfer integral, onsite repulsion energy and the population of spin orbitals at each site in the delocalized π-electrons. An appropriate computational platform is framed to compute each and individual parameter in the derived equation. The numerical values of aromatic stabilization energies obtained for various aromatic molecules are found to be in close agreement with available theoretical and experimental reports. Thus the reliable estimate of aromaticity through the proposed formalism renders it as a useful tool for the direct assessment of aromaticity, which has been a long standing problem in chemistry.

  8. Anti-prion activity of a panel of aromatic chemical compounds: in vitro and in silico approaches.

    PubMed

    Ferreira, Natalia C; Marques, Icaro A; Conceição, Wesley A; Macedo, Bruno; Machado, Clarice S; Mascarello, Alessandra; Chiaradia-Delatorre, Louise Domeneghini; Yunes, Rosendo Augusto; Nunes, Ricardo José; Hughson, Andrew G; Raymond, Lynne D; Pascutti, Pedro G; Caughey, Byron; Cordeiro, Yraima

    2014-01-01

    The prion protein (PrP) is implicated in the Transmissible Spongiform Encephalopathies (TSEs), which comprise a group of fatal neurodegenerative diseases affecting humans and other mammals. Conversion of cellular PrP (PrP(C)) into the scrapie form (PrP(Sc)) is the hallmark of TSEs. Once formed, PrP(Sc) aggregates and catalyzes PrP(C) misfolding into new PrP(Sc) molecules. Although many compounds have been shown to inhibit the conversion process, so far there is no effective therapy for TSEs. Besides, most of the previously evaluated compounds failed in vivo due to poor pharmacokinetic profiles. In this work we propose a combined in vitro/in silico approach to screen for active anti-prion compounds presenting acceptable drugability and pharmacokinetic parameters. A diverse panel of aromatic compounds was screened in neuroblastoma cells persistently infected with PrP(Sc) (ScN2a) for their ability to inhibit PK-resistant PrP (PrP(Res)) accumulation. From ∼200 compounds, 47 were effective in decreasing the accumulation of PrP(Res) in ScN2a cells. Pharmacokinetic and physicochemical properties were predicted in silico, allowing us to obtain estimates of relative blood brain barrier permeation and mutagenicity. MTT reduction assays showed that most of the active compounds were non cytotoxic. Compounds that cleared PrP(Res) from ScN2a cells, were non-toxic in the MTT assay, and presented a good pharmacokinetic profile were investigated for their ability to inhibit aggregation of an amyloidogenic PrP peptide fragment (PrP(109-149)). Molecular docking results provided structural models and binding affinities for the interaction between PrP and the most promising compounds. In summary, using this combined in vitro/in silico approach we have identified new small organic anti-scrapie compounds that decrease the accumulation of PrP(Res) in ScN2a cells, inhibit the aggregation of a PrP peptide, and possess pharmacokinetic characteristics that support their drugability. These

  9. Anti-Prion Activity of a Panel of Aromatic Chemical Compounds: In Vitro and In Silico Approaches

    PubMed Central

    Ferreira, Natalia C.; Marques, Icaro A.; Conceição, Wesley A.; Macedo, Bruno; Machado, Clarice S.; Mascarello, Alessandra; Chiaradia-Delatorre, Louise Domeneghini; Yunes, Rosendo Augusto; Nunes, Ricardo José; Hughson, Andrew G.; Raymond, Lynne D.; Pascutti, Pedro G.; Caughey, Byron; Cordeiro, Yraima

    2014-01-01

    The prion protein (PrP) is implicated in the Transmissible Spongiform Encephalopathies (TSEs), which comprise a group of fatal neurodegenerative diseases affecting humans and other mammals. Conversion of cellular PrP (PrPC) into the scrapie form (PrPSc) is the hallmark of TSEs. Once formed, PrPSc aggregates and catalyzes PrPC misfolding into new PrPSc molecules. Although many compounds have been shown to inhibit the conversion process, so far there is no effective therapy for TSEs. Besides, most of the previously evaluated compounds failed in vivo due to poor pharmacokinetic profiles. In this work we propose a combined in vitro/in silico approach to screen for active anti-prion compounds presenting acceptable drugability and pharmacokinetic parameters. A diverse panel of aromatic compounds was screened in neuroblastoma cells persistently infected with PrPSc (ScN2a) for their ability to inhibit PK-resistant PrP (PrPRes) accumulation. From ∼200 compounds, 47 were effective in decreasing the accumulation of PrPRes in ScN2a cells. Pharmacokinetic and physicochemical properties were predicted in silico, allowing us to obtain estimates of relative blood brain barrier permeation and mutagenicity. MTT reduction assays showed that most of the active compounds were non cytotoxic. Compounds that cleared PrPRes from ScN2a cells, were non-toxic in the MTT assay, and presented a good pharmacokinetic profile were investigated for their ability to inhibit aggregation of an amyloidogenic PrP peptide fragment (PrP109–149). Molecular docking results provided structural models and binding affinities for the interaction between PrP and the most promising compounds. In summary, using this combined in vitro/in silico approach we have identified new small organic anti-scrapie compounds that decrease the accumulation of PrPRes in ScN2a cells, inhibit the aggregation of a PrP peptide, and possess pharmacokinetic characteristics that support their drugability. These compounds are

  10. Identification of covalent active site inhibitors of dengue virus protease

    PubMed Central

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  11. Gallium Zeolites for Light Paraffin Aromatization

    SciTech Connect

    Price, G.L.; Dooley, K.M.

    1999-02-10

    The primary original goal of this project was to investigate the active state of gallium-containing MFI catalysts for light paraffin aromatization, in particular the state of gallium in the active material. Our original hypothesis was that the most active and selective materials were those which contained gallium zeolitic cations, and that previously reported conditions for the activation of gallium-containing catalysts served to create these active centers. We believed that in high silica materials such as MFI, ion-exchange is most effectively accomplished with metals in their 1+ oxidation state, both because of the sparsity of the anionic ion-exchange sites associated with the zeolite, and because the large hydration shells associated with aqueous 3+ cations hinder transport. Metals such as Ga which commonly exist in higher oxidation states need to be reduced to promote ion-exchange and this is the reason that reduction of gallium-containing catalysts for light paraffin aromatization often yields a dramatic enhancement in catalytic activity. We have effectively combined reduction with ion-exchange and we term this combined process ''reductive solid-state ion-exchange''. Our hypothesis has largely been proven true, and a number of the papers we have published directly address this hypothesis.

  12. Removal of Intermediate Aromatic Halogenated DBPs by Activated Carbon Adsorption: A New Approach to Controlling Halogenated DBPs in Chlorinated Drinking Water.

    PubMed

    Jiang, Jingyi; Zhang, Xiangru; Zhu, Xiaohu; Li, Yu

    2017-03-21

    During chlorine disinfection of drinking water, chlorine may react with natural organic matter (NOM) and bromide ion in raw water to generate halogenated disinfection byproducts (DBPs). To mitigate adverse effects from DBP exposure, granular activated carbon (GAC) adsorption has been considered as one of the best available technologies for removing NOM (DBP precursor) in drinking water treatment. Recently, we have found that many aromatic halogenated DBPs form in chlorination, and they act as intermediate DBPs to decompose and form commonly known DBPs including trihalomethanes and haloacetic acids. In this work, we proposed a new approach to controlling drinking water halogenated DBPs by GAC adsorption of intermediate aromatic halogenated DBPs during chlorination, rather than by GAC adsorption of NOM prior to chlorination (i.e., traditional approach). Rapid small-scale column tests were used to simulate GAC adsorption in the new and traditional approaches. Significant reductions of aromatic halogenated DBPs were observed in the effluents with the new approach; the removals of total organic halogen, trihalomethanes, and haloacetic acids by the new approach always exceeded those by the traditional approach; and the effluents with the new approach were considerably less developmentally toxic than those with the traditional approach. Our findings indicate that the new approach is substantially more effective in controlling halogenated DBPs than the traditional approach.

  13. Polycyclic Aromatic Hydrocarbon Affects Acetic Acid Production during Anaerobic Fermentation of Waste Activated Sludge by Altering Activity and Viability of Acetogen.

    PubMed

    Luo, Jingyang; Chen, Yinguang; Feng, Leiyu

    2016-07-05

    Till now, almost all the studies on anaerobic fermentation of waste activated sludge (WAS) for bioproducts generation focused on the influences of operating conditions, pretreatment methods and sludge characteristics, and few considered those of widespread persistent organic pollutants (POPs) in sludge, for example, polycyclic aromatic hydrocarbons (PAHs). Herein, phenanthrene, which was a typical PAH and widespread in WAS, was selected as a model compound to investigate its effect on WAS anaerobic fermentation for short-chain fatty acids (SCFAs) accumulation. Experimental results showed that the concentration of SCFAs derived from WAS was increased in the presence of phenanthrene during anaerobic fermentation. The yield of acetic acid which was the predominant SCFA in the fermentation reactor with the concentration of 100 mg/kg dry sludge was 1.8 fold of that in the control. Mechanism exploration revealed that the present phenanthrene mainly affected the acidification process of anaerobic fermentation and caused the shift of the microbial community to benefit the accumulation of acetic acid. Further investigation showed that both the activities of key enzymes (phosphotransacetylase and acetate kinase) involved in acetic acid production and the quantities of their corresponding encoding genes were enhanced in the presence of phenanthrene. Viability tests by determining the adenosine 5'-triphosphate content and membrane potential confirmed that the acetogens were more viable in anaerobic fermentation systems with phenanthrene, which resulted in the increased production of acetic acid.

  14. Target-classification approach applied to active UXO sites

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  15. Inhibition of peripheral aromatization in baboons by an enzyme-activated aromatase inhibitor (MDL 18,962)

    SciTech Connect

    Longcope, C.; Femino, A.; Johnston, J.O.

    1988-05-01

    The peripheral aromatization ((rho)BM) of androstenedione (A) and testosterone (T) was measured before and after administration of the aromatase inhibitor 10-(2 propynyl)estr-4-ene-3,17-dione (MDL-18,962) to five mature female baboons, Papio annubis. The measurements were made by infusing (3H)androstenedione/(14C)estrone or (3H)testosterone/(14C)estradiol for 3.5 h and collecting blood samples during the infusions and all urine for 96 h from the start of the infusion. Blood samples were analyzed for radioactivity as infused and product steroids, and the data were used to calculate MCRs. An aliquot of the pooled urine was analyzed for the glucuronides of estrone and estradiol and used to calculate the (rho)BM. MDL-18,962 was administered as a pulse in polyethylene glycol-400 (1-5 ml) either iv or via gastric tube 30 min before administration of the radiolabeled steroids. Control studies were done with and without polyethylene glycol-400 administration. When MDL-18,962 was given iv at 4 mg/kg, the aromatization of A was decreased 91.8 +/- 0.9% from the control value of 1.23 +/- 0.13% to 0.11 +/- 0.01%. At the same dose, aromatization of T was decreased 82.0 +/- 7.1%, from a control value of 0.20 +/- 0.03% to 0.037 +/- 0.018%. When MDL-18,962 was given iv at doses of 0.4, 0.1, 0.04, and 0.01 mg/kg, the values for aromatization of A were 0.16 +/- 0.03%, 0.18 +/- 0.06%, 0.37 +/- 11%, and 0.65 +/- 0.09%, respectively. The administration of MDL-18,962 via gastric tube at 4 mg/kg as a pulse decreased the aromatization of A from 1.35 +/- 0.06% to 0.43 +/- 0.12%, an inhibition of 67.2 +/- 10.7%. When administered via gastric tube daily for 5 days at 4 mg/kg, the aromatization of A fell from 1.35 +/- 0.06% to 0.063 +/- 0.003%, an inhibition of 84.4 +/- 0.5%.

  16. Identification of Phosphorylation Sites Altering Pollen Soluble Inorganic Pyrophosphatase Activity.

    PubMed

    Eaves, Deborah J; Haque, Tamanna; Tudor, Richard L; Barron, Yoshimi; Zampronio, Cleidiane G; Cotton, Nicholas P J; de Graaf, Barend H J; White, Scott A; Cooper, Helen J; Franklin, F Christopher H; Harper, Jeffery F; Franklin-Tong, Vernonica E

    2017-03-01

    Protein phosphorylation regulates numerous cellular processes. Identifying the substrates and protein kinases involved is vital to understand how these important posttranslational modifications modulate biological function in eukaryotic cells. Pyrophosphatases catalyze the hydrolysis of inorganic phosphate (PPi) to inorganic phosphate Pi, driving biosynthetic reactions; they are essential for low cytosolic inorganic phosphate. It was suggested recently that posttranslational regulation of Family I soluble inorganic pyrophosphatases (sPPases) may affect their activity. We previously demonstrated that two pollen-expressed sPPases, Pr-p26.1a and Pr-p26.1b, from the flowering plant Papaver rhoeas were inhibited by phosphorylation. Despite the potential significance, there is a paucity of data on sPPase phosphorylation and regulation. Here, we used liquid chromatographic tandem mass spectrometry to map phosphorylation sites to the otherwise divergent amino-terminal extensions on these pollen sPPases. Despite the absence of reports in the literature on mapping phosphorylation sites on sPPases, a database survey of various proteomes identified a number of examples, suggesting that phosphorylation may be a more widely used mechanism to regulate these enzymes. Phosphomimetic mutants of Pr-p26.1a/b significantly and differentially reduced PPase activities by up to 2.5-fold at pH 6.8 and 52% in the presence of Ca(2+) and hydrogen peroxide over unmodified proteins. This indicates that phosphoregulation of key sites can inhibit the catalytic responsiveness of these proteins in concert with key intracellular events. As sPPases are essential for many metabolic pathways in eukaryotic cells, our findings identify the phosphorylation of sPPases as a potential master regulatory mechanism that could be used to attenuate metabolism.

  17. First Principles Computational Study of the Active Site of Arginase

    SciTech Connect

    Ivanov, Ivaylo; Klien, Micheal

    2004-01-14

    Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible -1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

  18. C-H Activation on Co,O Sites: Isolated Surface Sites versus Molecular Analogs.

    PubMed

    Estes, Deven P; Siddiqi, Georges; Allouche, Florian; Kovtunov, Kirill V; Safonova, Olga V; Trigub, Alexander L; Koptyug, Igor V; Copéret, Christophe

    2016-11-16

    The activation and conversion of hydrocarbons is one of the most important challenges in chemistry. Transition-metal ions (V, Cr, Fe, Co, etc.) isolated on silica surfaces are known to catalyze such processes. The mechanisms of these processes are currently unknown but are thought to involve C-H activation as the rate-determining step. Here, we synthesize well-defined Co(II) ions on a silica surface using a metal siloxide precursor followed by thermal treatment under vacuum at 500 °C. We show that these isolated Co(II) sites are catalysts for a number of hydrocarbon conversion reactions, such as the dehydrogenation of propane, the hydrogenation of propene, and the trimerization of terminal alkynes. We then investigate the mechanisms of these processes using kinetics, kinetic isotope effects, isotopic labeling experiments, parahydrogen induced polarization (PHIP) NMR, and comparison with a molecular analog. The data are consistent with all of these reactions occurring by a common mechanism, involving heterolytic C-H or H-H activation via a 1,2 addition across a Co-O bond.

  19. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

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

    SciTech Connect

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

    1992-02-01

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

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

    SciTech Connect

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

    2008-04-02

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

  2. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  3. An active site water network in the plasminogen activator pla from Yersinia pestis.

    PubMed

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-07-14

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 A. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  4. Studies on the Simultaneous Formation of Aroma-Active and Toxicologically Relevant Vinyl Aromatics from Free Phenolic Acids during Wheat Beer Brewing.

    PubMed

    Langos, Daniel; Granvogl, Michael

    2016-03-23

    During the brewing process of wheat beer, the desired aroma-active vinyl aromatics 2-methoxy-4-vinylphenol and 4-vinylphenol as well as the undesired and toxicologically relevant styrene are formed from their respective precursors, free ferulic acid, p-coumaric acid, and cinnamic acid, deriving from the malts. Analysis of eight commercial wheat beers revealed high concentrations of 2-methoxy-4-vinylphenol and 4-vinylphenol always in parallel with high concentrations of styrene or low concentrations of the odorants in parallel with low styrene concentrations, suggesting a similar pathway. To better understand the formation of these vinyl aromatics, each process step of wheat beer brewing and the use of different strains of Saccharomyces cerevisiae were evaluated. During wort boiling, only a moderate decarboxylation of free phenolic acids and formation of desired and undesired vinyl aromatics were monitored due to the thermal treatment. In contrast, this reaction mainly occurred enzymatically catalyzed during fermentation with S. cerevisiae strain W68 with normal Pof(+) activity (phenolic off-flavor) resulting in a wheat beer eliciting the typical aroma requested by consumers due to high concentrations of 2-methoxy-4-vinylphenol (1790 μg/L) and 4-vinylphenol (937 μg/L). Unfortunately, also a high concentration of undesired styrene (28.3 μg/L) was observed. Using a special S. cerevisiae strain without Pof(+) activity resulted in a significant styrene reduction (

  5. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    SciTech Connect

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; Nash, Connor; Steirer, K. Xerxes; Clark, Jared; Robichaud, David J.; Ruddy, Daniel A.

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, an abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.

  6. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    DOE PAGES

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; ...

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, anmore » abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

  7. Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

    PubMed

    Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

    2012-01-01

    The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

  8. Graphene stabilized ultra-small CuNi nanocomposite with high activity and recyclability toward catalysing the reduction of aromatic nitro-compounds

    NASA Astrophysics Data System (ADS)

    Fang, Hao; Wen, Ming; Chen, Hanxing; Wu, Qingsheng; Li, Weiying

    2015-12-01

    Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (~2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s-1, with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime because it could be recycled over 25 times without obvious performance decay or even a morphology change. This work showed the promise and great potential of noble-metal-free catalysts in green chemistry.Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (~2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s-1, with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime

  9. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  10. Characterization of the active site of ADP-ribosyl cyclase.

    PubMed

    Munshi, C; Thiel, D J; Mathews, I I; Aarhus, R; Walseth, T F; Lee, H C

    1999-10-22

    ADP-ribosyl cyclase synthesizes two Ca(2+) messengers by cyclizing NAD to produce cyclic ADP-ribose and exchanging nicotinic acid with the nicotinamide group of NADP to produce nicotinic acid adenine dinucleotide phosphate. Recombinant Aplysia cyclase was expressed in yeast and co-crystallized with a substrate, nicotinamide. x-ray crystallography showed that the nicotinamide was bound in a pocket formed in part by a conserved segment and was near the central cleft of the cyclase. Glu(98), Asn(107) and Trp(140) were within 3.5 A of the bound nicotinamide and appeared to coordinate it. Substituting Glu(98) with either Gln, Gly, Leu, or Asn reduced the cyclase activity by 16-222-fold, depending on the substitution. The mutant N107G exhibited only a 2-fold decrease in activity, while the activity of W140G was essentially eliminated. The base exchange activity of all mutants followed a similar pattern of reduction, suggesting that both reactions occur at the same active site. In addition to NAD, the wild-type cyclase also cyclizes nicotinamide guanine dinucleotide to cyclic GDP-ribose. All mutant enzymes had at least half of the GDP-ribosyl cyclase activity of the wild type, some even 2-3-fold higher, indicating that the three coordinating amino acids are responsible for positioning of the substrate but not absolutely critical for catalysis. To search for the catalytic residues, other amino acids in the binding pocket were mutagenized. E179G was totally devoid of GDP-ribosyl cyclase activity, and both its ADP-ribosyl cyclase and the base exchange activities were reduced by 10,000- and 18,000-fold, respectively. Substituting Glu(179) with either Asn, Leu, Asp, or Gln produced similar inactive enzymes, and so was the conversion of Trp(77) to Gly. However, both E179G and the double mutant E179G/W77G retained NAD-binding ability as shown by photoaffinity labeling with [(32)P]8-azido-NAD. These results indicate that both Glu(179) and Trp(77) are crucial for catalysis and

  11. SEDIMENT-ASSOCIATED REACTIONS OF AROMATIC AMINES: QSAR DEVELOPMENT

    EPA Science Inventory

    Despite the common occurrence of the aromatic amine functional group in environmental contaminants, few quantitative structure-activity relationships (QSARs) have been developed to predict sorption kinetics for aromatic amines in natural soils and sediments. Towards the goal of d...

  12. Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity.

    PubMed

    Lipski, Alexandra; Watzlawick, Hildegard; Ravaud, Stéphanie; Robert, Xavier; Rhimi, Moez; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2013-02-01

    Sucrose isomerase is an enzyme that catalyzes the production of sucrose isomers of high biotechnological and pharmaceutical interest. Owing to the complexity of the chemical synthesis of these isomers, isomaltulose and trehalulose, enzymatic conversion remains the preferred method for obtaining these products. Depending on the microbial source, the ratio of the sucrose-isomer products varies significantly. In studies aimed at understanding and explaining the underlying molecular mechanisms of these reactions, mutations obtained using a random-mutagenesis approach displayed a major hydrolytic activity. Two of these variants, R284C and F164L, of sucrose isomerase from Rhizobium sp. were therefore crystallized and their crystal structures were determined. The three-dimensional structures of these mutants allowed the identification of the molecular determinants that favour hydrolytic activity compared with transferase activity. Substantial conformational changes resulting in an active-site opening were observed, as were changes in the pattern of water molecules bordering the active-site region.

  13. Contributions of Selected Biogenic and Aromatic Compounds to the Formation of Tropospheric Secondary Organic Aerosol over Several Sites in the United States

    NASA Astrophysics Data System (ADS)

    Jaoui, M.; Kleindienst, T. E.; Lewandowski, M.; Offenberg, J. H.; Corse, E. W.; Gerald, T.; Edney, E.

    2009-12-01

    The National Exposure Research Laboratory of the U.S. Environmental Protection Agency recently undertook an integrated laboratory and field research effort to better understand the contribution of biogenic and aromatic hydrocarbons to the formation of submicron ambient secondary organic aerosol (SOA). In the laboratory, isoprene, α-pinene, β-caryophyllene, 1,3-butadiene, 2-methyl-3-buten-2-ol, benzene, and toluene were individually irradiated under a wide range of conditions in a photochemical reaction chamber in the presence of nitrogen oxide (NOx). These hydrocarbons are thought to contribute to ambient SOA formation. In field studies conducted in Research Triangle Park, NC; Duke Forest in Chapel Hill, NC; Atlanta, GA; Pensacola, FL; Birmingham and Centerville, AL; Riverside, CA; Detroit, MI; Northbrook, East St. Louis and Bondville, IL; and Cincinnati, OH, ambient PM2.5 samples were collected for various periods between 2003 and 2006. The SOA collected from these laboratory experiments and the ambient PM2.5 samples were analyzed for organic carbon (OC) concentration and for organic tracer compounds by GC-MS using BSTFA derivatization for their identification and quantification. An organic tracer-based method was developed for estimating ambient SOA concentrations from individual SOA precursors to allow an assessment of SOA model predictions with ambient data. The results show that several major reaction products detected in SOA formed in the laboratory photooxidations were among the major compounds detected in field samples, effectively connecting laboratory and field results. Using the tracer-based method, the contributions of isoprene and monoterpenes to SOA formation show strong seasonal dependencies. However, no clear seasonal variations were observed for sesquiterpenes and aromatic hydrocarbons. The contribution of 2-methyl-3-buten-2-ol to ambient SOA was found to be not only season dependent but also higher in locations dominated by conifers, which are

  14. SiRNAs conjugated with aromatic compounds induce RISC-mediated antisense strand selection and strong gene-silencing activity

    SciTech Connect

    Kubo, Takanori; Yanagihara, Kazuyoshi; Takei, Yoshifumi; Mihara, Keichiro; Sato, Yuichiro; Seyama, Toshio

    2012-10-05

    Highlights: Black-Right-Pointing-Pointer SiRNAs conjugated with aromatic compounds (Ar-siRNAs) at 5 Prime -sense strand were synthesized. Black-Right-Pointing-Pointer Ar-siRNAs increased resistance against nuclease degradation. Black-Right-Pointing-Pointer Ar-siRNAs were thermodynamically stable compared with the unmodified siRNA. Black-Right-Pointing-Pointer High levels of cellular uptake and cytoplasmic localization were found. Black-Right-Pointing-Pointer Strong gene-silencing efficacy was exhibited in the Ar-siRNAs. -- Abstract: Short interference RNA (siRNA) is a powerful tool for suppressing gene expression in mammalian cells. In this study, we focused on the development of siRNAs conjugated with aromatic compounds in order to improve the potency of RNAi and thus to overcome several problems with siRNAs, such as cellular delivery and nuclease stability. The siRNAs conjugated with phenyl, hydroxyphenyl, naphthyl, and pyrenyl derivatives showed strong resistance to nuclease degradation, and were thermodynamically stable compared with unmodified siRNA. A high level of membrane permeability in HeLa cells was also observed. Moreover, these siRNAs exhibited enhanced RNAi efficacy, which exceeded that of locked nucleic acid (LNA)-modified siRNAs, against exogenous Renilla luciferase in HeLa cells. In particular, abundant cytoplasmic localization and strong gene-silencing efficacy were found in the siRNAs conjugated with phenyl and hydroxyphenyl derivatives. The novel siRNAs conjugated with aromatic compounds are promising candidates for a new generation of modified siRNAs that can solve many of the problems associated with RNAi technology.

  15. Site-specific PEGylation of lidamycin and its antitumor activity

    PubMed Central

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-01-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (Mw 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  16. Polycyclic aromatic hydrocarbons and metals in transplanted lichen (Pseudovernia furfuracea) at sites adjacent to a solid-waste landfill in central Italy.

    PubMed

    Protano, C; Guidotti, M; Owczarek, M; Fantozzi, L; Blasi, G; Vitali, M

    2014-05-01

    The aim of the study was to evaluate the airborne contamination by polycyclic aromatic hydrocarbons (PAHs) and some heavy metals (arsenic [As], cadmium [Cd], chromium [Cr], copper [Cu], nickel [Ni], lead [Pb], and zinc [Zn]) of different pollution scenarios around a solid-waste landfill in central Italy using the lichen Pseudovernia furfuracea as a monitoring tool. For this purpose, eight stations around a landfill characterized by different air pollution sources (industrial, agricultural, residential areas, and roads with different traffic intensities), together with three stations far from the landfill (control areas), were monitored using a set of 22 lichen samples (11 samples analysed for PAHs and metals after 4 months, and 11 samples analysed for metals after 8 months). After 4 months of exposure, the lichen content of all of the analysed elements was greater than that in the pre-exposed lichens. In addition, the Cu and Pb concentration after 8 months was greater than the level after 4 months. The order of metal concentration was Zn > Pb > Cu (or Cu > Pb) > Cr > Ni > As > Cd in all cases. The range of ∑11PAHs concentration was 634-1,371 ng/g dw (three to seven times greater than the amount in the pre-exposed lichens). The ∑11PAHs were dominated (>70 %) by compounds with three aromatic rings. The comparison of the levels of air pollutants among the monitored stations shows nonrelevant spatial patterns between the landfill stations and the control areas; the levels of PAHs and metals found in the lichen samples around the landfill seemed to be more related to the general diffusion of these pollutants in that area.

  17. Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

    PubMed

    Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

    2016-08-01

    Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

  18. Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis.

    PubMed

    Chi, Gamma; Manos-Turvey, Alexandra; O'Connor, Patrick D; Johnston, Jodie M; Evans, Genevieve L; Baker, Edward N; Payne, Richard J; Lott, J Shaun; Bulloch, Esther M M

    2012-06-19

    MbtI is the salicylate synthase that catalyzes the first committed step in the synthesis of the iron chelating compound mycobactin in Mycobacterium tuberculosis. We previously developed a series of aromatic inhibitors against MbtI based on the reaction intermediate for this enzyme, isochorismate. The most potent of these inhibitors had hydrophobic substituents, ranging in size from a methyl to a phenyl group, appended to the terminal alkene of the enolpyruvyl group. These compounds exhibited low micromolar inhibition constants against MbtI and were at least an order of magnitude more potent than the parental compound for the series, which carries a native enolpyruvyl group. In this study, we sought to understand how the substituted enolpyruvyl group confers greater potency, by determining cocrystal structures of MbtI with six inhibitors from the series. A switch in binding mode at the MbtI active site is observed for inhibitors carrying a substituted enolpyruvyl group, relative to the parental compound. Computational studies suggest that the change in binding mode, and higher potency, is due to the effect of the substituents on the conformational landscape of the core inhibitor structure. The crystal structures and fluorescence-based thermal shift assays indicate that substituents larger than a methyl group are accommodated in the MbtI active site through significant but localized flexibility in the peptide backbone. These findings have implications for the design of improved inhibitors of MbtI, as well as other chorismate-utilizing enzymes from this family.

  19. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

    PubMed Central

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

  20. The Role of Human Aldo-Keto Reductases in the Metabolic Activation and Detoxication of Polycyclic Aromatic Hydrocarbons: Interconversion of PAH Catechols and PAH o-Quinones.

    PubMed

    Zhang, Li; Jin, Yi; Huang, Meng; Penning, Trevor M

    2012-01-01

    Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants. They are procarcinogens requiring metabolic activation to elicit their deleterious effects. Aldo-keto reductases (AKR) catalyze the oxidation of proximate carcinogenic PAH trans-dihydrodiols to yield electrophilic and redox-active PAH o-quinones. AKRs are also found to be capable of reducing PAH o-quinones to form PAH catechols. The interconversion of o-quinones and catechols results in the redox-cycling of PAH o-quinones to give rise to the generation of reactive oxygen species and subsequent oxidative DNA damage. On the other hand, PAH catechols can be intercepted through phase II metabolism by which PAH o-quinones could be detoxified and eliminated. The aim of the present review is to summarize the role of human AKRs in the metabolic activation/detoxication of PAH and the relevance of phase II conjugation reactions to human lung carcinogenesis.

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

    PubMed Central

    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 factor of ten and promotes closure. We conclude that closure occurs during the rate-limiting catalytic step of decapping, juxtaposing the cap-binding region of each domain to form a composite active site. This work suggests a model for regulation of decapping, where coactivators trigger decapping by stabilizing a labile composite active site. PMID:20711189

  2. X-ray structure of human aromatase reveals an androgen-specific active site.

    PubMed

    Ghosh, Debashis; Griswold, Jennifer; Erman, Mary; Pangborn, Walter

    2010-02-28

    Aromatase is a unique cytochrome P450 that catalyzes the removal of the 19-methyl group and aromatization of the A-ring of androgens for the synthesis of estrogens. All human estrogens are synthesized via this enzymatic aromatization pathway. Aromatase inhibitors thus constitute a frontline therapy for estrogen-dependent breast cancer. Despite decades of intense investigation, this enzyme of the endoplasmic reticulum membrane has eluded all structure determination efforts. We have determined the crystal structure of the highly active aromatase purified from human placenta, in complex with its natural substrate androstenedione. The structure shows the binding mode of androstenedione in the catalytically active oxidized high-spin ferric state of the enzyme. Hydrogen bond-forming interactions and tight packing hydrophobic side chains that complement the puckering of the steroid backbone provide the molecular basis for the exclusive androgenic specificity of aromatase. Locations of catalytic residues and water molecules shed new light on the mechanism of the aromatization step. The structure also suggests a membrane integration model indicative of the passage of steroids through the lipid bilayer.

  3. Characterization of Active Site Residues of Nitroalkane Oxidase†

    PubMed Central

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

    2010-01-01

    The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitrolkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Serl71 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by ~5-fold and decreases in the rate constant for product release of ~2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. PMID:20056514

  4. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    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.

  5. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems.

  6. Polyphenylquinoxalines via Aromatic Nucleophilic Displacement

    NASA Technical Reports Server (NTRS)

    Hergenrother, Paul M.; Connell, John W.

    1988-01-01

    Polyphenylquinoxalines are produced by an aromatic nucleophilic displacement reaction involving an activated aromatic dihalide with an appropriate quinoxaline monomer. Polyphenylquinoxalines are high temperature thermoplastics used as adhesives, coatings, films and composite matrices. The novelty of this invention is threefold: (1) some of the quinoxaline monomers are new compositions of matter; (2) the phenylquinoxaline polymers which are the end products of the invention are new compositions of matter; and (3) the method of forming the polymers is novel, replacing a more costly prior art process, which is also limited in the kinds of products prepared therefrom.

  7. Polybenzimidazoles Via Aromatic Nucleophilic Displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W.; Hergenrother, Paul M.; Smith, Joseph G.

    1994-01-01

    Soluble polybenzimidazoles (PBI's) synthesized by nucleophilic displacement reaction of di(hydroxyphenyl)-benzimidazole monomers with activated aromatic difluoride compounds in presence of anhydrous potassium carbonate. These polymers exhibit good thermal, thermo-oxidative, and chemical stability, and high mechanical properties. Using benzimidazole monomers, more economical, and new PBI's processed more easily than commercial PBI, without loss of desirable physical properties.

  8. Binuclear Phthalocyanines with Aromatic Bridges

    DTIC Science & Technology

    1989-03-01

    successful. (Scheme 2) Synthesis of Binuclear Phthalocyanines Covalently Bridged by Anthracene The coupling reaction of aromatic halides using elemental...available (16), it Is not active enough to undergo the desired cross coupling reaction . Less electropositive arylzinc derivatives can tolerate various electro...philic functional groups such as nitriles and esters (17). These organo- metallic reagents readily undergo cross coupling reaction with aryl halides

  9. The presence and distribution of polycyclic aromatic hydrocarbons and inorganic elements in water and lakebed materials and the potential for bioconcentration in biota at established sampling sites on Lake Powell, Utah and Arizona

    USGS Publications Warehouse

    Schonauer, Kurt T.; Hart, Robert J.; Antweiler, Ronald C.

    2014-01-01

    The National Park Service is responsible for monitoring the effects of visitor use on the quality of water, lakebed material (bottom sediments), and biota, in Lake Powell, Utah and Arizona. A sampling program was begun in 2010 to assess the presence, distribution, and concentrations of organic and inorganic compounds in the water column and bottom sediment. In response to an Environmental Impact Statement regarding personal watercraft and as a continuation from previous studies by the U.S. Geological Survey and the National Park Service, Glen Canyon National Recreation Area, water samples were collected and analyzed for polycyclic aromatic hydrocarbons (PAHs) using semipermeable membrane devices and inorganic elements using a fixed-bottle sampler deployed at established monitoring sites during 2010 and 2011. Lakebed material samples were also analyzed for polycyclic aromatic hydrocarbons and inorganic elements, some of which could be harmful to aquatic biota if present at concentrations above established aquatic life criteria. Of the 44 PAH compounds analyzed, 26 individual compounds were detected above the censoring limit in the water column by semipermeable membrane devices. The highest number of compounds detected were at Lone Rock Beach, Wahweap Marina, Rainbow Bridge National Monument, and Antelope Marina which are all located in the southern part of Lake Powell where visitation and boat use is high. Because PAHs can remain near their source, the potential for bioconcentration is highest near these sites. The PAH compound found in the highest concentration was phenol (5,902 nanograms per liter), which is included in the U.S. Environmental Protection Agency’s priority pollutants list. The dissolved inorganic chemistry of water samples measured at the sampling sites in Lake Powell defined three different patterns of elements: (1) concentrations were similar between sites in the upper part of the lake near Farley Canyon downstream to Halls Crossing Marina, a

  10. Biodegradation of polycyclic aromatic hydrocarbons by an acidophilic Stenotrophomonas maltophilia strain AJH1 isolated from a mineral mining site in Saudi Arabia.

    PubMed

    Arulazhagan, P; Al-Shekri, K; Huda, Q; Godon, J J; Basahi, J M; Jeyakumar, D

    2017-01-01

    The present study aims at analyzing the degradation of polycyclic aromatic hydrocarbons (PAHs) at acidic conditions (pH = 2) by acidophilic Stenotrophomonas maltophilia strain AJH1 (KU664513). The strain AJH1 was obtained from an enrichment culture obtained from soil samples of mining area in the presence of PAH as sole sources of carbon and energy. Strain AJH1was able to degrade low (anthracene, phenanthrene, naphthalene, fluorene) and high (pyrene, benzo(e)pyrene and benzo(k)fluoranthene) molecular weight PAHs in acidophilic mineral salt medium at pH 2, with removal rates of up to 95% (LMW PAH) and 80% (HMW PAH), respectively. In addition, strain AJH1 treated petroleum wastewater with 89 ± 1.1% COD removal under acidic condition (pH 2) in a continuously stirred reactor. Acidophilic S. maltophilia strain AJH1, hence holds the promise as an effective degrader for biological treatment of PAHs contaminated wastewater at acidic pH.

  11. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  12. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  13. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  14. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  15. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  16. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  17. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  18. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    SciTech Connect

    Teese, G.D.

    1995-09-28

    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.

  19. Contorted polycyclic aromatics.

    PubMed

    Ball, Melissa; Zhong, Yu; Wu, Ying; Schenck, Christine; Ng, Fay; Steigerwald, Michael; Xiao, Shengxiong; Nuckolls, Colin

    2015-02-17

    CONSPECTUS: This Account describes a body of research in the design, synthesis, and assembly of molecular materials made from strained polycyclic aromatic molecules. The strain in the molecular subunits severely distorts the aromatic molecules away from planarity. We coined the term "contorted aromatics" to describe this class of molecules. Using these molecules, we demonstrate that the curved pi-surfaces are useful as subunits to make self-assembled electronic materials. We have created and continue to study two broad classes of these "contorted aromatics": discs and ribbons. The figure that accompanies this conspectus displays the three-dimensional surfaces of a selection of these "contorted aromatics". The disc-shaped contorted molecules have well-defined conformations that create concave pi-surfaces. When these disc-shaped molecules are substituted with hydrocarbon side chains, they self-assemble into columnar superstructures. Depending on the hydrocarbon substitution, they form either liquid crystalline films or macroscopic cables. In both cases, the columnar structures are photoconductive and form p-type, hole- transporting materials in field effect transistor devices. This columnar motif is robust, allowing us to form monolayers of these columns attached to the surface of dielectrics such as silicon oxide. We use ultrathin point contacts made from individual single-walled carbon nanotubes that are separated by a few nanometers to probe the electronic properties of short stacks of a few contorted discs. We find that these materials have high mobility and can sense electron-deficient aromatic molecules. The concave surfaces of these disc-shaped contorted molecules form ideal receptors for the molecular recognition and assembly with spherical molecules such as fullerenes. These interfaces resemble ball-and-socket joints, where the fullerene nests itself in the concave surface of the contorted disc. The tightness of the binding between the two partners can be

  20. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  1. Lidar research activities and observations at NARL site, Gadanki, India

    NASA Astrophysics Data System (ADS)

    Yellapragada, Bhavani Kumar

    2016-05-01

    The National Atmospheric Research Laboratory (NARL), a unit of Department of Space (DOS), located at Gadanki village (13.5°N, 79.2°E, 370 m AMSL) in India, is involved in the development of lidar remote sensing technologies for atmospheric research. Several advanced lidar technologies employing micropulse, polarization, Raman and scanning have been developed at this site and demonstrated for atmospheric studies during the period between 2008 and 2015. The technology of micropulse lidar, operates at 532 nm wavelength, was successfully transferred to an industry and the commercial version has been identified for Indian Lidar network (I-LINK) programme. Under this lidar network activity, several lidar units were installed at different locations in India to study tropospheric aerosols and clouds. The polarization sensitive lidar technology was realized using a set of mini photomultiplier tube (PMT) units and has the capability to operate during day and night without a pause. The lidar technology uses a compact flashlamp pumped Qswitched laser and employs biaxial configuration between the transmitter and receiver units. The lidar technology has been utilized for understanding the polarization characteristics of boundary layer aerosols during the mixed layer development. The demonstrated Raman lidar technology, uses the third harmonic wavelength of Nd:YAG laser, provides the altitude profiles of aerosol backscattering, extinction and water vapor covering the boundary layer range and allows operation during nocturnal periods. The Raman lidar derived height profiles of aerosol backscattering and extinction coefficient, lidar ratio, and watervapor mixing ratio inform the tropical boundary layer aerosol characteristics. The scanning lidar technology uses a near infrared laser wavelength for probing the lower atmosphere and has been utilized for high resolution cloud profiling during convective periods. The lidar technology is also used for rain rate measurement during

  2. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  3. Synthesis of tetra- and octa-aurated heteroaryl complexes towards probing aromatic indoliums

    PubMed Central

    Yuan, Jun; Sun, Tingting; He, Xin; An, Ke; Zhu, Jun; Zhao, Liang

    2016-01-01

    Polymetalated aromatic compounds are particularly challenging synthetic goals because of the limited thermodynamic stability of polyanionic species arising from strong electrostatic repulsion between adjacent carbanionic sites. Here we describe a facile synthesis of two polyaurated complexes including a tetra-aurated indole and an octa-aurated benzodipyrrole. The imido trinuclear gold(I) moiety exhibits nucleophilicity and undergoes an intramolecular attack on a gold(I)-activated ethynyl to generate polyanionic heteroaryl species. Their computed magnetic properties reveal the aromatic character in the five-membered ring. The incorporation of the aurated substituents at the nitrogen atom can convert non-aromaticity in the parent indolium into aromaticity in the aurated one because of hyperconjugation. Thus, the concept of hyperconjugative aromaticity is extended to heterocycles with transition metal substituents. More importantly, further analysis indicates that the aurated substituents can perform better than traditional main-group substituents. This work highlights the difference in aromaticity between polymetalated aryls and their organic prototypes. PMID:27186982

  4. Active-site zinc ligands and activated H2O of zinc enzymes.

    PubMed Central

    Vallee, B L; Auld, D S

    1990-01-01

    The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families. Universally, H2O is a ligand and critical component of the catalytically active zinc sites. In addition, three protein side chains bind to the catalytic zinc atom, whereas four protein ligands bind to the structural zinc atom. The geometry and coordination number of zinc can vary greatly to accommodate particular ligands. Zinc forms complexes with nitrogen and oxygen just as readily as with sulfur, and this is reflected in catalytic zinc sites having a binding frequency of His much greater than Glu greater than Asp = Cys, three of which bind to the metal atom. The systematic spacing between the ligands is striking. For all catalytic zinc sites except the coenzyme-dependent alcohol dehydrogenase, the first two ligands are separated by a "short-spacer" consisting of 1 to 3 amino acids. These ligands are separated from the third ligand by a "long spacer" of approximately 20 to approximately 120 amino acids. The spacer enables formation of a primary bidentate zinc complex, whereas the long spacer contributes flexibility to the coordination sphere, which can poise the zinc for catalysis as well as bring other catalytic and substrate binding groups into apposition with the active site. The H2O is activated by ionization, polarization, or poised for displacement. Collectively, the data imply that the preferred mechanistic pathway for activating the water--e.g., zinc hydroxide or Lewis acid catalysis--will be determined by the identity of the other three ligands and their spacing. Images PMID:2104979

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

    PubMed Central

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

    1998-01-01

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

  6. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.

    PubMed

    Xiang, Kehui; Manley, James L; Tong, Liang

    2012-07-10

    The activity of RNA polymerase II (Pol II) is controlled in part by the phosphorylation state of the C-terminal domain (CTD) of its largest subunit. Recent reports have suggested that yeast regulator of transcription protein, Rtr1, and its human homologue RPAP2, possess Pol II CTD Ser5 phosphatase activity. Here we report the crystal structure of Kluyveromyces lactis Rtr1, which reveals a new type of zinc finger protein and does not have any close structural homologues. Importantly, the structure does not show evidence of an active site, and extensive experiments to demonstrate its CTD phosphatase activity have been unsuccessful, suggesting that Rtr1 has a non-catalytic role in CTD dephosphorylation.

  7. Functional soil metagenomics: Elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.

    PubMed

    Duarte, Márcia; Nielsen, Agnes; Camarinha-Silva, Amélia; Vilchez-Vargas, Ramiro; Bruls, Thomas; Wos-Oxley, Melissa L; Jauregui, Ruy; Pieper, Dietmar H

    2017-04-12

    A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422,750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds. This article is protected by copyright. All rights reserved.

  8. Atmospheric Concentrations, Gas/Particle Partitioning And Exposure Risk Of Polycyclic Aromatic Hydrocarbons (PAHs) At Background, Rural Village And Urban Sites In The North China Plain

    NASA Astrophysics Data System (ADS)

    Wang, W.; Simonich, S.; Zhao, J.; Xue, M.; Wang, W.; Tao, S.

    2009-05-01

    Particle- and gas-phase PAHs were measured in air collected from a background site (Xiaolongmen), two rural village sites (Gubeikou and Donghe), and an urban site (Beijing) located in the North China Plain for four seasons from September 2007 to August 2008 in order to evaluate their concentrations, relative abundance, and gas/particle partitioning. Sixteen PAHs, included in the U.S.EPA priority pollutant list, were determined in the particle (PM10) and gas phases. The annual average 15 PAH concentration in Donghe was 730.7±608.0 ng/m3, which was 18.2, 3.0, 1.8 times higher than Xiaolongmen, Gubeikou and Beijing, respectively. A good linear relationship between gas/particle partitioning coefficients, Kp and subcooled liquid vapor pressure, pl was obtained. At the rural and urban sites, the regression slopes were much steeper than -1, indicating that adsorption of PAH to particulate matter dominated over absorption possibly because, at these sites, the freshly emitted particulate matter and PAHs had not yet reached equilibrium. However, gas/particle partitioning of PAHs approached equilibrium at the background site because of long- range transport of PAHs. In addition, the gas/particle partitioning was studied according to three different models: The Junge-Pankow adsorption model, the Koa absorption model, and the dual organic matter absorption model combined with the soot carbon adsorption model. The Junge-Pankow model and Koa model both under-predicted our experimental Kp values. However, the dual model fit our experimental Kp values well suggesting that the main partitioning mechanism was PAH adsorption onto soot carbon in this region of China. The different particulate matter characteristics (including organic matter and elemental carbon fraction and available adsorption sites), temperature variation during sampling, the presence of a non- exchangeable PAH fraction and non-equilibrium were considered possible reasons for why our experimental Kp values deviated

  9. Heterogeneous photocatalytic reactions of sulfur aromatic compounds.

    PubMed

    Samokhvalov, Alexander

    2011-11-18

    Sulfur aromatic compounds, such as mono-, di-, tri-, and tetraalkyl-substituted thiophene, benzothiophenes, dibenzothiophenes, are the molecular components of many fossils (petroleum, oil shale, tar sands, bitumen). Structural units of natural, cross-linked heteroaromatic polymers present in brown coals, turf, and soil are similar to those of sulfur aromatic compounds. Many sulfur aromatic compounds are found in the streams of petroleum refining and upgrading (naphthas, gas oils) and in the consumer products (gasoline, diesel, jet fuels, heating fuels). Besides fossils, the structural fragments of sulfur aromatic compounds are present in molecules of certain organic semiconductors, pesticides, small molecule drugs, and in certain biomolecules present in human body (pheomelanin pigments). Photocatalysis is the frontier area of physical chemistry that studies chemical reactions initiated by absorption of photons by photocatalysts, that is, upon electronic rather than thermal activation, under "green" ambient conditions. This review provides systematization and critical review of the fundamental chemical and physicochemical information on heterogeneous photocatalysis of sulfur aromatic compounds accumulated in the last 20-30 years. Specifically, the following topics are covered: physicochemical properties of sulfur aromatic compounds, major classes of heterogeneous photocatalysts, mechanisms and reactive intermediates of photocatalytic reactions of sulfur aromatic compounds, and the selectivity of these reactions. Quantum chemical calculations of properties and structures of sulfur aromatic compounds, their reactive intermediates, and the structure of adsorption complexes formed on the surface of the photocatalysts are also discussed.

  10. Kinetic Modeling of Paraffin Aromatization over Zeolites: A Design Perspective

    NASA Astrophysics Data System (ADS)

    Bhan, Aditya; Katare, Santhoji; Caruthers, James; Lauterbach, Jochen; Venkatasubramanian, Venkat; Delgass, Nicholas

    2002-03-01

    A generic framework for catalyst design involving the solution of a forward predictive problem using hybrid models and the inverse problem using evolutionary algorithms has been proposed. In that context, we investigate the aromatization of light paraffins over HZSM-5 to obtain the catalyst descriptors and associated kinetic parameters that predict performance. A detailed kinetic model that can fundamentally quantify the catalytic properties of acid sites in terms of intrinsic parameters such as rate constants and activation energies of elementary steps is developed on the basis of the following types of reactions: adsorption/desorption, oligomerization/ beta-scission, hydride transfer, protolysis and aromatization. The reaction network so generated has been grouped under various reaction families taking into account the different stabilities and reactivities of the adsorbed carbenium/carbonium ions. The detailed parameterization of each reaction type, optimizing fits to data, linking catalyst descriptors to performance, and means of improving the robustness of the model will be presented.

  11. Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase - The importance of accommodating the active site water.

    PubMed

    Heyes, Logan C; Reichau, Sebastian; Cross, Penelope J; Jameson, Geoffrey B; Parker, Emily J

    2014-12-01

    3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, which produces the aromatic amino acids as well as many other aromatic metabolites. DAH7PS catalyses an aldol-like reaction between phosphoenolpyruvate and erythrose 4-phosphate. Three phosphoenolpyruvate mimics, (R)-phospholactate, (S)-phospholactate and vinyl phosphonate [(E)-2-methyl-3-phosphonoacrylate], were found to competitively inhibit DAH7PS from Neisseria meningitidis, which is the pathogen responsible for bacterial meningitis. The most potent inhibitor was the vinyl phosphonate with a Ki value of 3.9±0.4μM. We report for the first time crystal structures of these compounds bound in the active site of a DAH7PS enzyme which reveals that the inhibitors bind to the active site of the enzyme in binding modes that mimic those of the predicted oxocarbenium and tetrahedral intermediates of the enzyme-catalysed reaction. Furthermore, the inhibitors accommodate the binding of a key active site water molecule. Together, these observations provide strong evidence that this active site water participates directly in the DAH7PS reaction, enabling the facial selectivity of the enzyme-catalysed reaction sequence to be delineated.

  12. Extreme Modulation Properties of Aromatic Fluorine

    SciTech Connect

    Burnett, Michael N; Gakh, Andrei A

    2011-01-01

    Thorough examination of the current literature as well as publicly available databases allowed us to qualify aromatic fluorine as a unique modulator of biological properties of organic compounds. In some rare cases, introduction of fluorine increased biological activity 100,000 times and even higher. We have also identified several examples where aromatic fluorine substantially reduced biological activity. Selected individual cases of extreme modulation are presented and discussed in the paper.

  13. A NOVEL METABOLIC ACTIVATION PATHWAY FOR POLYCYCLIC AROMATIC HYDROCARBONS: REACTIVE OXYGEN SPECIES-MEDIATED DNA DAMAGE AND MORPHOLOGICAL CELL TRANSFORMATION IN MOUSE EMBRYO CELLS BY K-REGION DIOL METABOLITES

    EPA Science Inventory

    Benzo[ a ]pyrene (BP) is a well-studied polycyclic aromatic hydrocarbon (P AH) .Many
    mechanisms have been suggested to explain its carcinogenic activity, yet many questions still
    remain. K-region dihydrodiols (diols) ofPAHs are common metabolites and some are genotoxic. W...

  14. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  15. Development of highly potent phosphodiesterase 4 inhibitors with anti-neuroinflammation potential: Design, synthesis, and structure-activity relationship study of catecholamides bearing aromatic rings.

    PubMed

    Zhou, Zhong-Zhen; Ge, Bing-Chen; Zhong, Qiu-Ping; Huang, Chang; Cheng, Yu-Fang; Yang, Xue-Mei; Wang, Hai-Tao; Xu, Jiang-Ping

    2016-11-29

    In this study, catecholamides (7a-l) bearing different aromatic rings (such as pyridine-2-yl, pyridine-3-yl, phenyl, and 2-chlorophenyl groups) were synthesized as potent phosphodiesterase (PDE) 4 inhibitors. The inhibitory activities of these compounds were evaluated against the core catalytic domains of human PDE4 (PDE4CAT), full-length PDE4A4, PDE4B1, PDE4C1, and PDE4D7 enzymes, and other PDE family members. Eight of the synthesized compounds were identified as having submicromolar IC50 values in the mid-to low-nanomolar range. Careful analysis on the structure-activity relationship of compounds 7a-l revealed that the replacement of the 4-methoxy group with the difluoromethoxy group improved inhibitory activities. More interesting, 4-difluoromethoxybenzamides 7i and 7j exhibited preference for PDE4 with higher selectivities of about 3333 and 1111-fold over other PDEs, respectively. In addition, compound 7j with wonderful PDE4D7 inhibitory activities inhibited LPS-induced TNF-α production in microglia.

  16. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification

    PubMed Central

    Keating, David H.; Zhang, Yaoping; Ong, Irene M.; McIlwain, Sean; Morales, Eduardo H.; Grass, Jeffrey A.; Tremaine, Mary; Bothfeld, William; Higbee, Alan; Ulbrich, Arne; Balloon, Allison J.; Westphall, Michael S.; Aldrich, Josh; Lipton, Mary S.; Kim, Joonhoon; Moskvin, Oleg V.; Bukhman, Yury V.; Coon, Joshua J.; Kiley, Patricia J.; Bates, Donna M.; Landick, Robert

    2014-01-01

    Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts. PMID:25177315

  17. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    SciTech Connect

    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.

  18. Revealing the nature of the active site on the carbon catalyst for C-H bond activation.

    PubMed

    Sun, XiaoYing; Li, Bo; Su, Dangsheng

    2014-09-28

    A reactivity descriptor for the C-H bond activation on the nanostructured carbon catalyst is proposed. Furthermore the calculations reveal that the single ketone group can be an active site in ODH reaction.

  19. Cellular Active N-Hydroxyurea FEN1 Inhibitors Block Substrate Entry to the Active Site

    PubMed Central

    Exell, Jack C.; Thompson, Mark J.; Finger, L. David; Shaw, Steven J.; Debreczeni, Judit; Ward, Thomas A.; McWhirter, Claire; Siöberg, Catrine L. B.; Martinez Molina, Daniel; Mark Abbott, W.; Jones, Clifford D.; Nissink, J. Willem M.; Durant, Stephen T.; Grasby, Jane A.

    2016-01-01

    The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the first crystal structure of inhibitor-bound hFEN1 and show a cyclic N-hydroxyurea bound in the active site coordinated to two magnesium ions. Three such compounds had similar IC50 values but differed subtly in mode of action. One had comparable affinity for protein and protein–substrate complex and prevented reaction by binding to active site catalytic metal ions, blocking the unpairing of substrate DNA necessary for reaction. Other compounds were more competitive with substrate. Cellular thermal shift data showed engagement of both inhibitor types with hFEN1 in cells with activation of the DNA damage response evident upon treatment. However, cellular EC50s were significantly higher than in vitro inhibition constants and the implications of this for exploitation of hFEN1 as a drug target are discussed. PMID:27526030

  20. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  1. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  2. Eaton's reagent-mediated domino π-cationic arylations of aromatic carboxylic acids to Iasi-red polymethoxylated polycyclic aromatic hydrocarbons: products with unprecedented biological activities as tubulin polymerization inhibitors.

    PubMed

    Ghinet, Alina; Gautret, Philippe; Hijfte, Nathalie Van; Ledé, Bertrand; Hénichart, Jean-Pierre; Bîcu, Elena; Darbost, Ulrich; Rigo, Benoît; Daïch, Adam

    2014-08-04

    A rapid domino π-cationic arylation of aromatic carboxylic acids, mediated by Eaton's reagent, has been developed for the synthesis of Iasi-red polymethoxylated polycyclic aromatic hydrocarbons (PAHs). This route is currently the easiest method to obtain such popular PAH compounds, which bear in addition numerous methoxy groups. The domino process was generalized, the structure of the obtained red products and the mechanism of their formations were elucidated, and some of their photophysical properties were determined. Newly synthesized polymethoxylated-PAHs were tested for their interaction with tubulin polymerization as well as for their cytotoxicity on a panel of NCI-60 human cancer cell lines. Interestingly, one of these rubicene derivatives exhibited remarkable cytotoxicity in vitro, including inhibition of leukemia, colon, melanoma, CNS, and ovarian cancer cell lines with GI50 values in the low nanomolar range (GI50 < 10 nM).

  3. Activation of ERK1/2 and p38 kinases by polycyclic aromatic hydrocarbons in rat liver epithelial cells is associated with induction of apoptosis

    SciTech Connect

    Andrysik, Zdenek; Machala, Miroslav; Chramostova, Katerina; Hofmanova, Jirina; Kozubik, Alois; Vondracek, Jan . E-mail: vondracek@ibp.cz

    2006-03-15

    Deregulation of various signaling pathways, linked either to induction of cell proliferation or to modulation of cellular differentiation and apoptosis, has been proposed to contribute to carcinogenicity of polycyclic aromatic hydrocarbons (PAHs). In the present study, we investigated effects of the PAHs previously shown to induce cell proliferation and/or apoptosis in contact-inhibited rat liver epithelial WB-F344 cells, with an aim to define the role of mitogen-activated protein kinases in both events. We found that only strong genotoxin dibenzo[a,l]pyrene (DBalP) activated extracellular signal-regulated kinases 1 and 2 (ERK1/2) and p38 kinase, but not c-Jun N-terminal kinases (JNKs), at concentrations inducing both apoptosis and phosphorylation of p53 tumor suppressor at serine 15 residue. In contrast, the PAHs stimulating cell proliferation in WB-F344 cell line had no effect on activation of ERK1/2, p38 or JNKs. Synthetic inhibitors of ERK1/2 activation (U0126) or p38 kinase activity (SB203580) prevented both apoptosis and induction of p53 phosphorylation by DBalP. Pifithrin-{alpha}, inhibitor of p53 transcriptional activity, prevented induction of apoptosis and activation of ERK1/2 and p38. Taken together, our data suggest that both ERK1/2 and p38 are activated in response to DBalP and that they might be involved in regulation of cellular response to DNA damage induced by DBalP, while neither kinase is involved in the release from contact inhibition induced by PAHs.

  4. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    NASA Astrophysics Data System (ADS)

    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.

  5. Polycyclic aromatic hydrocarbons in carcinogenesis.

    PubMed Central

    Warshawsky, D

    1999-01-01

    A symposium on "Polycyclic Aromatic Hydrocarbons (PAHs) in Carcinogenesis" was presented at the third International Congress of Pathophysiology held in Lathi, Finland, 28 June-3 July 1998. The congress was also sponsored by the International Union of Biological Sciences and the International Society of Free Radical Research. Institutional support for the symposium included the Electric Power Research Institute, National Center for Toxicological Research, and EPA/National Health and Environmental Effects Research Laboratory and the Office of Solid Waste and Emergency Response. The symposium focused on the sources, carcinogenicity, genotoxicity, and risk assessment of individual and mixtures of PAHs that are found in solid wastes, Superfund sites, and other hazardous waste sites. Based on the occurrence of PAHs at numerous Superfund sites and the significant data gaps on the toxic potential of certain PAHs, the information developed during this symposium would be of value in assessing health risks of these chemicals at Superfund and other hazardous waste sites. PMID:10090712

  6. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    SciTech Connect

    Not Available

    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.

  7. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins

    PubMed Central

    Yamada, Kazunori D.; Nishi, Hafumi; Nakata, Junichi; Kinoshita, Kengo

    2016-01-01

    Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations. PMID:27924270

  8. Lamellipodial actin mechanically links myosin activity with adhesion site formation

    PubMed Central

    Giannone, Gregory; Dubin-Thaler, Benjamin; Rossier, Olivier; Cai, Yunfei; Chaga, Oleg; Jiang, Guoying; Beaver, William; Döbereiner, Hans-Günther; Freund, Yoav; Borisy, Gary; Sheetz, Michael P.

    2013-01-01

    Summary Cell motility proceeds by cycles of edge protrusion, adhesion and retraction. Whether these functions are coordinated by biochemical or biomechanical processes is unknown. We find that myosin II pulls the rear of the lamellipodial actin network, causing upward bending, edge retraction and initiation of new adhesion sites. The network then separates from the edge and condenses over the myosin. Protrusion resumes as lamellipodial actin regenerates from the front and extends rearward until it reaches newly assembled myosin, initiating the next cycle. Upward bending, observed by evanescence and electron microscopy, results in ruffle formation when adhesion strength is low. Correlative fluorescence and electron microscopy shows that the regenerating lamellipodium forms a cohesive, separable layer of actin above the lamellum. Thus, actin polymerization periodically builds a mechanical link, the lamellipodium, connecting myosin motors with the initiation of adhesion sites, suggesting that the major functions driving motility are coordinated by a biomechanical process. PMID:17289574

  9. In vitro and in vivo characterization of opioid activities of endomorphins analogs with novel constrained C-terminus: evidence for the important role of proper spatial disposition of the third aromatic ring.

    PubMed

    Yu, Ye; Shao, Xuan; Wang, Chang-Lin; Liu, Hong-Mei; Cui, Yun; Fan, Ying-Zhe; Liu, Jing; Wang, Rui

    2007-04-01

    In the present study, the C-terminus of endomorphin (Tyr(1)-Pro(2)-Trp/Phe(3)-Phe(4)-NH(2), EMs) analogs [Xaa(4)-R]EMs, modified by substitution of a non-aromatic residue for Phe(4) and ending up with -NH-benzyl, were designed to generate an atypical conformationally constrained peptide set. We investigated the effects of these analogs on the opioid receptors affinity, guinea pig ileum (GPI) and mouse vas deferens (MVD) activity, system arterial pressure (SAP), heart rate (HR), antinociception and colonic motility. Analogs 5 ([D-V(4)-Bzl]EM1) and 10 ([D-V(4)-Bzl]EM2), which exhibit appropriate spatial orientations of the third aromatic ring, were about 3-4 times more potent than their parents both in vivo and in vitro. However, a drastic loss of activity was found in analogs 2 ([A(4)-Bzl]EM1) and 7 ([A(4)-Bzl]EM2), which possess improper spatial orientations of the third aromatic ring. Interestingly, analog 7 or 3 ([G(4)-Bzl]EM1), when injected intravenously (i.v.), produced significantly different changes in SAP from their parents. Surprisingly, analog 4 displayed relatively higher vasodepressor activity but significantly less potent colonic contractile activity than analog 5. This may be elicited by the differences in the spatial disposition of the third aromatic ring, which were verified by molecular modeling. Our results indicate that the proper spatial disposition of the third aromatic ring plays an important role in the regulation of pharmacological activities of EMs.

  10. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.

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

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

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

  12. Quantitative structure-activity relationship investigation of the role of hydrophobicity in regulating mutagenicity in the Ames test: 2. Mutagenicity of aromatic and heteroaromatic nitro compounds in Salmonella typhimurium TA100

    SciTech Connect

    Debnath, A.K.; Hansch, C. ); Shusterman, A.J. ); Lopez de Compadre, R.L. )

    1992-01-01

    A quantitative structure-activity relationship (QSAR) has been derived for the mutagenic activity of 117 aromatic and heteroaromatic nitro compounds acting on Salmonella typhimurium TA100. Relative mutagenic activity is bilinearly dependent on hydrophobicity, with an optimal log P of 5.44, and is linearly dependent on the energy of the lowest unoccupied molecular orbital of the nitro compound. The dependence of mutagenic activity on hydrophobicity and electronic effects is very similar for TA98 and TA100. Mutagenic activity in TA100 does not depend on the size of the aromatic ring system, as it does in TA98. The effect of the choice of assay organism, TA98 versus TA100, on nitroarene QSAR is seen to be similar to the effect previously found for aminoarenes. Lateral verification of QSARs is presented as a tool for establishing the significance of a new QSAR.

  13. Aryl hydrocarbon receptor-mediated and estrogenic activities of oxygenated polycyclic aromatic hydrocarbons and azaarenes originally identified in extracts of river sediments.

    PubMed

    Machala, M; Ciganek, M; Bláha, L; Minksová, K; Vondráck, J

    2001-12-01

    Reproductive dysfunction in wildlife populations can be a result of environmental contaminants binding to aryl hydrocarbon receptor (AhR) or estrogenic receptors. Signaling by both types of receptors can be affected by polycyclic aromatic hydrocarbons (PAHs), which are potential endocrine disruptors. However, our knowledge regarding the effects of oxygenated (oxy)-PAHs and azaarenes on AhR-mediated and estrogenic activities is incomplete. In the present study, we have identified 9-fluorenone, anthrone, anthraquinone, benzanthrone, benz[a]anthracene-7,12-dione, benz[c]acridine, and dibenz[a,h]acridine as prevalent oxy-PAHs and azaarenes found in river sediments. Their concentrations in sediment samples ranged from 2.1 to 165.2 ng g(-1) for oxy-PAHs and up to 27.3 ng g(-1) for azaarenes. Their relative AhR-inducing and estrogenic potencies were quantified in vitro using two cell lines that were stably transfected with a luciferase reporter gene system and expressed as induction equivalency factors (IEFs). The only oxy-PAHs with detectable levels of in vitro AhR-mediated activity were benzanthrone and benz[a]anthracene-7,12-dione. However, their IEFs were approximately three to four orders of magnitude lower than those of benzo[a]pyrene. On the other hand, azaarenes showed a strong AhR-mediated activity, with dibenzo[a,h]acridine being a far more potent inducer of activity than benzo[a]pyrene. Benzanthrone, benz[a]anthracene-7,12-dione, anthraquinone, and benz[a]acridine were weak inducers of in vitro estrogenic activity, with IEFs similar to that of benzo[a]pyrene. Based on concentrations and relative potencies, our results suggest that dibenzo[a,h]acridine can significantly contribute to the overall AhR-mediated activity in river sediments, whereas the remaining compounds do not. No studied compound was found to contribute significantly to estrogen receptor-mediated activity in vitro.

  14. Exposure to Solute Stress Affects Genome-Wide Expression but Not the Polycyclic Aromatic Hydrocarbon-Degrading Activity of Sphingomonas sp. Strain LH128 in Biofilms

    PubMed Central

    Fida, Tekle Tafese; Breugelmans, Philip; Lavigne, Rob; Coronado, Edith; Johnson, David R.; van der Meer, Jan Roelof; Mayer, Antonia P.; Heipieper, Hermann J.; Hofkens, Johan

    2012-01-01

    Members of the genus Sphingomonas are important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degrading Sphingomonas sp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity. PMID:23001650

  15. Studies of the Active Sites for Methane Dehydroaromatization Using Ultrahigh-Field Solid-State Mo95 NMR Spectroscopy

    SciTech Connect

    Hu, Jian Z.; Kwak, Ja Hun; Wang, Yong; Peden, Charles HF; Zheng, Heng; Ma, Ding; Bao, Xinhe

    2009-01-26

    Abstract It is found that the spin-lattice relaxation time, T1, corresponding to the surface exchanged molybdenum species in Mo/HZSM-5 catalysts is short, i.e., less than about 100ms at 21.1 T while the value of T1 for the crystallite MoO3 molecules is longer, i.e., about 30 s. Such a difference, more than two orders in magnitude, is utilized to differentiate the exchanged Mo species from the agglomerate MoO3 in Mo/HZSM-5 catalyst. An approximately linear correlation between the amount of exchanged species and the aromatics formation rate is obtained. This result significantly strengthens our prior conclusion that the exchanged Mo species are the active centers for the methane dehydroaromatization reaction on Mo/HZSM-5 catalysts (J. Am. Chem. Soc. 2008, 130, 3722-3723). Our results also suggest that one exchanged Mo atom anchors on two ion exchange sites and the exchanged Mo species on catalysts are possibly monomeric. Analyzing the linshapes obtained from both the 95Mo MAS and the static spectra indicates that the exchanged sites are heterogeneous, resulting in a significantly broadened MAS spectrum and essentially a featureless but nearly symmetric static lineshape for the exchanged Mo species. Furthermore, for crystallite MoO3 powder sample, the parameters related to the electric-field-gradient (EFG) tensor, the chemical shift anisotropy (CSA) and the three Euler angles required to align the CSA principal axis system with the quadrupolar principal axis system are determined by analyzing both the 95Mo MAS and the static spectra obtained at ultra-high field of 21.1 T. The new results obtained from this study on crystallite MoO3 powders should help to clarify some of the contradictions in prior literature reports from other groups. Key words: 95Mo NMR, MAS, relaxation, surface exchanged species, HZSM-5, electric-field-gradient (EFG), chemical shift anisotropy (CSA), active centers.

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

    PubMed

    Stec, Boguslaw

    2012-11-13

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO(2). We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O(2) and CO(2) bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO(2) defines an elusive, preactivation complex that contains a metal cation Mg(2+) surrounded by three H(2)O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming.

  17. Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites

    DTIC Science & Technology

    2013-08-01

    Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites Edward W. Malin, MD, Chaya M. Galin, BSN, RN... microcurrent in comparison to silver-coated dressing with sham microcurrent on wound-closure time for autogenous skin donor sites. Methods: Four...hundred five patients were screened for treatment of their donor sites using a silver-coated nylon dressing with either sham or active microcurrent

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

    PubMed Central

    2015-01-01

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

  19. 76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-26

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  20. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    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...). Title X requires DOE to reimburse eligible uranium and thorium licensees for certain costs...

  1. A model of the rabies virus glycoprotein active site.

    PubMed

    Rustici, M; Bracci, L; Lozzi, L; Neri, P; Santucci, A; Soldani, P; Spreafico, A; Niccolai, N

    1993-06-01

    The glycoprotein from the neurotropic rabies virus shows a significant homology with the alpha neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the alpha neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection.

  2. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

    PubMed Central

    2016-01-01

    Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

  3. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

    PubMed

    Dingerdissen, Hayley; Motwani, Mona; Karagiannis, Konstantinos; Simonyan, Vahan; Mazumder, Raja

    2013-03-01

    An enzyme's active site is essential to normal protein activity such that any disruptions at this site may lead to dysfunction and disease. Nonsynonymous single-nucleotide variations (nsSNVs), which alter the amino acid sequence, are one type of disruption that can alter the active site. When this occurs, it is assumed that enzyme activity will vary because of the criticality of the site to normal protein function. We integrate nsSNV data and active site annotations from curated resources to identify all active-site-impacting nsSNVs in the human genome and search for all pathways observed to be associated with this data set to assess the likely consequences. We find that there are 934 unique nsSNVs that occur at the active sites of 559 proteins. Analysis of the nsSNV data shows an over-representation of arginine and an under-representation of cysteine, phenylalanine and tyrosine when comparing the list of nsSNV-impacted active site residues with the list of all possible proteomic active site residues, implying a potential bias for or against variation of these residues at the active site. Clustering analysis shows an abundance of hydrolases and transferases. Pathway and functional analysis shows several pathways over- or under-represented in the data set, with the most significantly affected pathways involved in carbohydrate metabolism. We provide a table of 32 variation-substrate/product pairs that can be used in targeted metabolomics experiments to assay the effects of specific variations. In addition, we report the significant prevalence of aspartic acid to histidine variation in eight proteins associated with nine diseases including glycogen storage diseases, lacrimo-auriculo-dento-digital syndrome, Parkinson's disease and several cancers.

  4. Passive dosing of polycyclic aromatic hydrocarbon (PAH) mixtures to terrestrial springtails: linking mixture toxicity to chemical activities, equilibrium lipid concentrations, and toxic units.

    PubMed

    Schmidt, Stine N; Holmstrup, Martin; Smith, Kilian E C; Mayer, Philipp

    2013-07-02

    A 7-day mixture toxicity experiment with the terrestrial springtail Folsomia candida was conducted, and the effects were linked to three different mixture exposure parameters. Passive dosing from silicone was applied to tightly control exposure levels and compositions of 12 mixture treatments, containing the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, and pyrene. Springtail lethality was then linked to sum chemical activities (∑a), sum equilibrium lipid concentrations (∑C(lipid eq.)), and sum toxic units (∑TU). In each case, the effects of all 12 mixture treatments could be fitted to one sigmoidal exposure-response relationship. The effective lethal chemical activity (La50) of 0.027 was well within the expected range for baseline toxicity of 0.01-0.1. Linking the effects to the lipid-based exposure parameter yielded an effective lethal concentration (LC(lipid eq 50)) of 133 mmol kg(-1) lipid in good correspondence with the lethal membrane burden for baseline toxicity (40-160 mmol kg(-1) lipid). Finally, the effective lethal toxic unit (LTU50) of 1.20 was rather close to the expected value of 1. Altogether, passive dosing provided tightly controlled mixture exposure in terms of both level and composition, while ∑a, ∑C(lipid eq.), and ∑TU allowed baseline toxicity to be linked to mixture exposure.

  5. Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae.

    PubMed

    Jendresen, Christian Bille; Stahlhut, Steen Gustav; Li, Mingji; Gaspar, Paula; Siedler, Solvej; Förster, Jochen; Maury, Jérôme; Borodina, Irina; Nielsen, Alex Toftgaard

    2015-07-01

    Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit(-1) in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases.

  6. Assessment and management of human health risk from toxic metals and polycyclic aromatic hydrocarbons in urban stormwater arising from anthropogenic activities and traffic congestion.

    PubMed

    Ma, Yukun; Liu, An; Egodawatta, Prasanna; McGree, James; Goonetilleke, Ashantha

    2017-02-01

    Toxic metals (TMs) and polycyclic aromatic hydrocarbons (PAHs) in urban stormwater pose risk to human health, thereby constraining its reuse potential. Based on the hypothesis that stormwater quality is primarily influenced by anthropogenic activities and traffic congestion, the primary focus of the research study was to analyse the impacts on human health risk from TMs and PAHs in urban stormwater and thereby develop a quantitative risk assessment model. The study found that anthropogenic activities and traffic congestion exert influence on the risk posed by TMs and PAHs in stormwater from commercial and residential areas. Motor vehicle related businesses (FVS) and traffic congestion (TC) were identified as two parameters which need to be included as independent variables to improve the model. Based on the study outcomes, approaches for mitigating the risk associated with TMs and PAHs in urban stormwater are discussed. Additionally, a roadmap is presented for the assessment and management of the risk arising from these pollutants. The study outcomes are expected to contribute to reducing the human health risk associated urban stormwater pollution and thereby enhance its reuse potential.

  7. Assessment of activation products in the Savannah River Site environment

    SciTech Connect

    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.

  8. All the catalytic active sites of MoS2 for hydrogen evolution

    DOE PAGES

    Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5more » s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

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

    PubMed Central

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

    2015-01-01

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

  10. Iridium(I)-catalyzed regioselective C-H activation and hydrogen-isotope exchange of non-aromatic unsaturated functionality.

    PubMed

    Kerr, William J; Mudd, Richard J; Paterson, Laura C; Brown, Jack A

    2014-11-03

    Isotopic labelling is a key technology of increasing importance for the investigation of new CH activation and functionalization techniques, as well as in the construction of labelled molecules for use within both organic synthesis and drug discovery. Herein, we report for the first time selective iridium-catalyzed CH activation and hydrogen-isotope exchange at the β-position of unsaturated organic compounds. The use of our highly active [Ir(cod)(IMes)(PPh3 )][PF6 ] (cod=1,5-cyclooctadiene) catalyst, under mild reaction conditions, allows the regioselective β-activation and labelling of a range of α,β-unsaturated compounds with differing steric and electronic properties. This new process delivers high levels of isotope incorporation over short reaction times by using low levels of catalyst loading.

  11. Biodegradation of Aromatic Compounds by Escherichia coli

    PubMed Central

    Díaz, Eduardo; Ferrández, Abel; Prieto, María A.; García, José L.

    2001-01-01

    Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications. PMID:11729263

  12. Biodegradation of aromatic compounds by Escherichia coli.

    PubMed

    Díaz, E; Ferrández, A; Prieto, M A; García, J L

    2001-12-01

    Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications.

  13. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  14. An active site mutation increases the polymerase activity of the guinea pig-lethal Marburg virus.

    PubMed

    Koehler, Alexander; Kolesnikova, Larissa; Becker, Stephan

    2016-10-01

    Marburg virus (MARV) causes severe, often fatal, disease in humans and transient illness in rodents. Sequential passaging of MARV in guinea pigs resulted in selection of a lethal virus containing 4 aa changes. A D184N mutation in VP40 (VP40D184N), which leads to a species-specific gain of viral fitness, and three mutations in the active site of viral RNA-dependent RNA polymerase L, which were investigated in the present study for functional significance in human and guinea pig cells. The transcription/replication activity of L mutants was strongly enhanced by a substitution at position 741 (S741C), and inhibited by other substitutions (D758A and A759D) in both species. The polymerase activity of L carrying the S741C substitution was eightfold higher in guinea pig cells than in human cells upon co-expression with VP40D184N, suggesting that the additive effect of the two mutations provides MARV a replicative advantage in the new host.

  15. Catalytic Mechanism of Aromatic Prenylation by NphB

    PubMed Central

    Yang, Yue; Miao, Yipu; Wang, Bing; Cui, Guanglei; Merz, Kenneth M.

    2012-01-01

    NphB is an aromatic prenyltransferase that catalyzes the attachment of a 10-carbon geranyl group to aromatic substrates. Importantly, NphB exhibits a rich substrate selectivity and product regioselectivity. A systematic computational study has been conducted in order to address several question associated with NphB catalyzed geranylation. The reaction mechanism of the prenylation step has been characterized as a SN1 type dissociative mechanism with a weakly stable carbocation intermediate. A novel π-chamber composed of Tyr121, Tyr216 and 1,6-DHN is found to be important in stabilizing the carbocation. The observed difference in the rates of product formation from 5 and 2-prenylation arises from the differing orientations of the aromatic substrate in the resting state. 4-prenylation shares the same resting state with 5-prenylation, but the lower free energy barrier for carbocation formation makes the latter reaction more facile. The high free energy barrier associated with 7-prenylation is caused by the unfavorable orientation of 1,6-DHN in active site pocket, along with the difficulty of proton elimination after the prenylation step. A water mediated proton transfer facilitates the loss of hydrogen at the prenylation site to form the final prenylated product. Interestingly, the same crystallographically observed water molecule has been found to be responsible for proton loss in all three experimentally identified products. After proton transfer, the relaxation of the final product from a sp3 carbon center to a sp2 center triggers a “spring-loaded” product release mechanism which pushes the final product out of the binding pocket towards the edge of the active site. The hydrogen bond interactions between the two hydroxyl groups of the aromatic product and the sidechains of Ser214 and Tyr288 help to “steer” the movement of the product. In addition, mutagenesis studies identify these same two sidechains as being responsible for the observed regioselectivity

  16. Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions.

    PubMed

    Pathak, Arup Kumar; Bandyopadhyay, Tusar

    2016-01-01

    Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.

  17. Encroachment of Human Activity on Sea Turtle Nesting Sites

    NASA Astrophysics Data System (ADS)

    Ziskin, D.; Aubrecht, C.; Elvidge, C.; Tuttle, B.; Baugh, K.; Ghosh, T.

    2008-12-01

    The encroachment of anthropogenic lighting on sea turtle nesting sites poses a serious threat to the survival of these animals [Nicholas, 2001]. This danger is quantified by combining two established data sets. The first is the Nighttime Lights data produced by the NOAA National Geophysical Data Center [Elvidge et al., 1997]. The second is the Marine Turtle Database produced by the World Conservation Monitoring Centre (WCMC). The technique used to quantify the threat of encroachment is an adaptation of the method described in Aubrecht et al. [2008], which analyzes the stress on coral reef systems by proximity to nighttime lights near the shore. Nighttime lights near beaches have both a direct impact on turtle reproductive success since they disorient hatchlings when they mistake land-based lights for the sky-lit surf [Lorne and Salmon, 2007] and the lights are also a proxy for other anthropogenic threats. The identification of turtle nesting sites with high rates of encroachment will hopefully steer conservation efforts to mitigate their effects [Witherington, 1999]. Aubrecht, C, CD Elvidge, T Longcore, C Rich, J Safran, A Strong, M Eakin, KE Baugh, BT Tuttle, AT Howard, EH Erwin, 2008, A global inventory of coral reef stressors based on satellite observed nighttime lights, Geocarto International, London, England: Taylor and Francis. In press. Elvidge, CD, KE Baugh, EA Kihn, HW Kroehl, ER Davis, 1997, Mapping City Lights with Nighttime Data from the DMSP Operational Linescan System, Photogrammatic Engineering and Remote Sensing, 63:6, pp. 727-734. Lorne, JK, M Salmon, 2007, Effects of exposure to artificial lighting on orientation of hatchling sea turtles on the beach and in the ocean, Endangered Species Research, Vol. 3: 23-30. Nicholas, M, 2001, Light Pollution and Marine Turtle Hatchlings: The Straw that Breaks the Camel's Back?, George Wright Forum, 18:4, p77-82. Witherington, BE, 1999, Reducing Threats To Nesting Habitat, Research and Management Techniques for

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

    SciTech Connect

    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.

  19. Identification of inhibitors against the potential ligandable sites in the active cholera toxin.

    PubMed

    Gangopadhyay, Aditi; Datta, Abhijit

    2015-04-01

    The active cholera toxin responsible for the massive loss of water and ions in cholera patients via its ADP ribosylation activity is a heterodimer of the A1 subunit of the bacterial holotoxin and the human cytosolic ARF6 (ADP Ribosylation Factor 6). The active toxin is a potential target for the design of inhibitors against cholera. In this study we identified the potential ligandable sites of the active cholera toxin which can serve as binding sites for drug-like molecules. By employing an energy-based approach to identify ligand binding sites, and comparison with the results of computational solvent mapping, we identified two potential ligandable sites in the active toxin which can be targeted during structure-based drug design against cholera. Based on the probe affinities of the identified ligandable regions, docking-based virtual screening was employed to identify probable inhibitors against these sites. Several indole-based alkaloids and phosphates showed strong interactions to the important residues of the ligandable region at the A1 active site. On the other hand, 26 top scoring hits were identified against the ligandable region at the A1 ARF6 interface which showed strong hydrogen bonding interactions, including guanidines, phosphates, Leucopterin and Aristolochic acid VIa. This study has important implications in the application of hybrid structure-based and ligand-based methods against the identified ligandable sites using the identified inhibitors as reference ligands, for drug design against the active cholera toxin.

  20. Barium ions selectively activate BK channels via the Ca2+-bowl site.

    PubMed

    Zhou, Yu; Zeng, Xu-Hui; Lingle, Christopher J

    2012-07-10

    Activation of Ca(2+)-dependent BK channels is increased via binding of micromolar Ca(2+) to two distinct high-affinity sites per BK α-subunit. One site, termed the Ca(2+) bowl, is embedded within the second RCK domain (RCK2; regulator of conductance for potassium) of each α-subunit, while oxygen-containing residues in the first RCK domain (RCK1) have been linked to a separate Ca(2+) ligation site. Although both sites are activated by Ca(2+) and Sr(2+), Cd(2+) selectively favors activation via the RCK1 site. Divalent cations of larger ionic radius than Sr(2+) are thought to be ineffective at activating BK channels. Here we show that Ba(2+), better known as a blocker of K(+) channels, activates BK channels and that this effect arises exclusively from binding at the Ca(2+)-bowl site. Compared with previous estimates for Ca(2+) bowl-mediated activation by Ca(2+), the affinity of Ba(2+) to the Ca(2+) bowl is reduced about fivefold, and coupling of binding to activation is reduced from ∼3.6 for Ca(2+) to about ∼2.8 for Ba(2+). These results support the idea that ionic radius is an important determinant of selectivity differences among different divalent cations observed for each Ca(2+)-binding site.

  1. Activation of brown adipose tissue mitochondrial GDP binding sites

    SciTech Connect

    Swick, A.G.

    1987-01-01

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of (/sup 3/H)-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time.

  2. Structure and Reactivity of the Phosphotriesterase Active Site

    DTIC Science & Technology

    2002-01-01

    characterize different catalytic conformations for chorismate mutase . Preliminary evidence for water binding in phosphotriesterase suggests that activity in...MD/QM study of the chorismate mutase catalyzed Claisen rearrangement reaction. 2001.subm. J.Phys.Chem.B 22.Day, P.N.J., J.H.; Gordon,M.S.; Webb,S.P...Claisen rearrangement of an unusual substrate in chorismate mutase . 2001.subm. J.Phys.Chem.B 38.Stevens, W.J., Basch,H., Krauss,M., Compact effective

  3. Nematicidal activity of essential oils and volatiles derived from Portuguese aromatic flora against the pinewood nematode, Bursaphelenchus xylophilus

    PubMed Central

    Barbosa, P.; Lima, A. S.; Vieira, P.; Dias, L. S.; Tinoco, M. T.; Barroso, J. G.; Pedro, L. G.; Figueiredo, A. C.

    2010-01-01

    Twenty seven essential oils, isolated from plants representing 11 families of Portuguese flora, were screened for their nematicidal activity against the pinewood nematode (PWN), Bursaphelenchus xylophilus. The essential oils were isolated by hydrodistillation and the volatiles by distillation-extraction, and both were analysed by GC and GC-MS. High nematicidal activity was achieved with essential oils from Chamaespartium tridentatum, Origanum vulgare, Satureja montana, Thymbra capitata, and Thymus caespititius. All of these essential oils had an estimated minimum inhibitory concentration ranging between 0.097 and 0.374 mg/ml and a lethal concentration necessary to kill 100% of the population (LC100) between 0.858 and 1.984 mg/ml. Good nematicidal activity was also obtained with the essential oil from Cymbopogon citratus. The dominant components of the effective oils were 1–octen-3-ol (9%), n–nonanal, and linalool (both 7%) in C. tridentatum, geranial (43%), neral (29%), and β-myrcene (25%) in C. citratus, carvacrol (36% and 39%), γ-terpinene (24% and 40%), and p-cymene (14% and 7%) in O. vulgare and S. montana, respectively, and carvacrol (75% and 65%, respectively) in T. capitata and T. caespititius. The other essential oils obtained from Portuguese flora yielded weak or no activity. Five essential oils with nematicidal activity against PWN are reported for the first time. PMID:22736831

  4. Nematicidal activity of essential oils and volatiles derived from Portuguese aromatic flora against the pinewood nematode, Bursaphelenchus xylophilus.

    PubMed

    Barbosa, P; Lima, A S; Vieira, P; Dias, L S; Tinoco, M T; Barroso, J G; Pedro, L G; Figueiredo, A C; Mota, M

    2010-03-01

    Twenty seven essential oils, isolated from plants representing 11 families of Portuguese flora, were screened for their nematicidal activity against the pinewood nematode (PWN), Bursaphelenchus xylophilus. The essential oils were isolated by hydrodistillation and the volatiles by distillation-extraction, and both were analysed by GC and GC-MS. High nematicidal activity was achieved with essential oils from Chamaespartium tridentatum, Origanum vulgare, Satureja montana, Thymbra capitata, and Thymus caespititius. All of these essential oils had an estimated minimum inhibitory concentration ranging between 0.097 and 0.374 mg/ml and a lethal concentration necessary to kill 100% of the population (LC(100)) between 0.858 and 1.984 mg/ml. Good nematicidal activity was also obtained with the essential oil from Cymbopogon citratus. The dominant components of the effective oils were 1-octen-3-ol (9%), n-nonanal, and linalool (both 7%) in C. tridentatum, geranial (43%), neral (29%), and β-myrcene (25%) in C. citratus, carvacrol (36% and 39%), γ-terpinene (24% and 40%), and p-cymene (14% and 7%) in O. vulgare and S. montana, respectively, and carvacrol (75% and 65%, respectively) in T. capitata and T. caespititius. The other essential oils obtained from Portuguese flora yielded weak or no activity. Five essential oils with nematicidal activity against PWN are reported for the first time.

  5. Fruits and vegetables protect against the genotoxicity of heterocyclic aromatic amines activated by human xenobiotic-metabolizing enzymes expressed in immortal mammalian cells.

    PubMed

    Platt, K L; Edenharder, R; Aderhold, S; Muckel, E; Glatt, H

    2010-12-21

    Heterocyclic aromatic amines (HAAs) can be formed during the cooking of meat and fish at elevated temperatures and are associated with an increased risk for cancer. On the other hand, epidemiological findings suggest that foods rich in fruits and vegetables can protect against cancer. In the present study three teas, two wines, and the juices of 15 fruits and 11 vegetables were investigated for their protective effect against the genotoxic effects of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). To closely mimic the enzymatic activation of these HAAs in humans, genetically engineered V79 Chinese hamster fibroblasts were employed that express human cytochrome P450-dependent monooxygenase (hCYP) 1A2 (responsible for the first step of enzymatic activation) and human N(O)-acetyltransferase (hNAT) 2*4 or human sulfotransferase (hSULT)1A1*1 (responsible for the second step of enzymatic activation): V79-hCYP1A2-hNAT2*4 for IQ activation and V79-hCYP1A2-hSULT1A1*1 for PhIP activation. HAA genotoxicity was determined by use of the comet assay. Black, green and rooibos tea moderately reduced the genotoxicity of IQ (IC(50)=0.8-0.9%), whereas red and white wine were less active. From the fruit juices, sweet cherry juice exhibited the highest inhibitory effect on IQ genotoxicity (IC(50)=0.17%), followed by juices from kiwi fruit, plum and blueberry (IC(50)=0.48-0.71%). The juices from watermelon, blackberry, strawberry, black currant, and Red delicious apple showed moderate suppression, whereas sour cherry, grapefruit, red currant, and pineapple juices were only weakly active. Granny Smith apple juice and orange juice proved inactive. Of the vegetable juices, strong inhibition of IQ genotoxicity was only seen with spinach and onion juices (IC(50)=0.42-0.54%). Broccoli, cauliflower, beetroot, sweet pepper, tomato, chard, and red-cabbage juices suppressed IQ genotoxicity only moderately, whereas cucumber juice was

  6. Nucleophilic fluorination of aromatic compounds

    SciTech Connect

    Satyamurthy, Nagichettiar; Barrio, Jorge R

    2014-03-18

    Iodylbenzene derivatives substituted with electron donating as well as electron withdrawing groups on the aromatic ring are used as precursors in aromatic nucleophilic substitution reactions. The iodyl group (IO.sub.2) is regiospecifically substituted by nucleophilic fluoride to provide the corresponding fluoroaryl derivatives. No-carrier-added [F-18]fluoride ion derived from anhydrous [F-18](F/Kryptofix, [F-18]CsF or a quaternary ammonium fluoride (e.g., Me.sub.4NF, Et.sub.4NF, n-Bu.sub.4NF, (PhCH.sub.2).sub.4NF) exclusively substitutes the iodyl moiety in these derivatives and provides high specific activity F-18 labeled fluoroaryl analogs. Iodyl derivatives of a benzothiazole analog and 6-iodyl-L-dopa derivatives have been synthesized as precursors and have been used in the preparation of no-carrier-added [F-18]fluorobenzothiazole as well as 6-[F-18]fluoro-L-dopa.

  7. Active site proton delivery and the lyase activity of human CYP17A1

    SciTech Connect

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    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.

  8. Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase

    PubMed Central

    Teixeira, Vitor H.; Baptista, António M.; Soares, Cláudio M.

    2006-01-01

    Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H2), but little is known about the diffusion of H2 toward the active site. Here we analyze pathways for H2 permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H2 easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H2 molecules that reach the active site made their approach from the side of the Ni ion. H2 is able to reach distances of <4 Å from the active site, although after 6 Å permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H2 inside the protein and at lower distances from the active site. This valine can be a control point in the H2 access to the active center. PMID:16731562

  9. Activation of electrophilicity of stable Y-delocalized carbamate cations in intramolecular aromatic substitution reaction: evidence for formation of diprotonated carbamates leading to generation of isocyanates.

    PubMed

    Kurouchi, Hiroaki; Kawamoto, Kyoko; Sugimoto, Hiromichi; Nakamura, Satoshi; Otani, Yuko; Ohwada, Tomohiko

    2012-10-19

    Although cations with three heteroatoms, such as monoprotonated guanidine and urea, are stabilized by Y-shaped conjugation and such Y-conjugated cations are sufficiently basic to be further protonated (or protosolvated) to dications in strongly acid media, only O-monoprotonated species have been detected in the case of carbamates even in magic acid. We found that the trifluoromethanesulfonic acid-catalyzed cyclization of arylethylcarbamates proceeds to afford dihydroisoquinolones in high yield. In strong acids, methyl carbamates are fully O-monoprotonated, and these monocations do not undergo cyclization even under heating. But, as the acidity of the reaction medium is further increased, the cyclization reaction of methyl phenethylcarbamates starts to proceed as a first-order reaction, with a linear relationship between rate and acidity. The sign and magnitude of the entropy of activation ΔS(‡) were found to be similar to those of other A(Ac)1 reactions. These results strongly support the idea that further protonation of the O-protonated carbamates is involved in the cyclization, but the concentration of the dications is very low and suggests that the rate-determining step is dissociation of methanol from the diprotonated carbamate to generate protonated isocyanate, which reacts with the aromatic ring. Therefore, O-protonated carbamates are weak bases in sharp contrast to other Y-shaped monocations.

  10. Removal of Aromatic Pollutant Surrogate from Water by Recyclable Magnetite-Activated Carbon Nanocomposite: An Experiment for General Chemistry

    ERIC Educational Resources Information Center

    Furlan, Ping Y.; Melcer, Michael E.

    2014-01-01

    A general chemistry laboratory experiment using readily available chemicals is described to introduce college students to an exciting class of nanocomposite materials. In a one-step room temperature synthetic process, magnetite nanoparticles are embedded onto activated carbon matrix. The resultant nanocomposite has been shown to combine the…

  11. Maintenance of plastid RNA editing activities independently of their target sites.

    PubMed

    Tillich, Michael; Poltnigg, Peter; Kushnir, Sergei; Schmitz-Linneweber, Christian

    2006-03-01

    RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.

  12. Assessment of the aryl hydrocarbon receptor-mediated activities of polycyclic aromatic hydrocarbons in a human cell-based reporter gene assay.

    PubMed

    Vondráček, Jan; Pěnčíková, Kateřina; Neča, Jiří; Ciganek, Miroslav; Grycová, Aneta; Dvořák, Zdeněk; Machala, Miroslav

    2017-01-01

    Activation of the aryl hydrocarbon receptor (AhR)-mediated activity is one of key events in toxicity of polycyclic aromatic hydrocarbons (PAHs). Although various classes of AhR ligands may differentially activate human and rodent AhR, there is presently a lack of data on the human AhR-inducing relative potencies (REPs) of PAHs. Here, we focused on estimation of the AhR-mediated activities of a large set of environmental PAHs in human gene reporter AZ-AhR cell line, with an aim to develop the human AhR-based REP values with potential implications for risk assessment of PAHs. The previously identified weakly active PAHs mostly failed to activate the AhR in human cells. The order for REPs of individual PAHs in human cells largely corresponded with the available data from rodent-based experimental systems; nevertheless, we identified differences up to one order of magnitude in REP values of PAHs between human and rodent cells. Higher REP values were found in human cells for some important environmental contaminants or suspected carcinogens, such as indeno[1,2,3-cd]pyrene, benz[a]anthracene or benzo[b]fluoranthene, while lower REP values were determined for methyl-substituted PAHs. Our results also indicate that a different rate of metabolism for individual PAHs in human vs. rodent cells may affect estimation of REP values in human cell-based assay, and potentially alter toxicity of some compounds, such as benzofluoranthenes, in humans. We applied the AZ-AhR assay to evaluation of the AhR-mediated activity of complex mixtures of organic compounds associated with diesel exhaust particles, and we identified the polar compounds present in these mixtures as being particularly highly active in human cells, as compared with rodent cells. The present data suggest that differences may exist between the AhR-mediated potencies of PAHs in human and rodent cells, and that the AhR-mediated effects of polar PAH derivatives and metabolites in human cell models deserve further

  13. A Processive Carbohydrate Polymerase That Mediates Bifunctional Catalysis Using a Single Active Site

    PubMed Central

    May, John F.; Levengood, Matthew R.; Splain, Rebecca A.; Brown, Christopher D.; Kiessling, Laura L.

    2012-01-01

    Even in the absence of a template, glycosyltransferases can catalyze the synthesis of carbohydrate polymers of specific sequence. The paradigm has been that one enzyme catalyzes the formation of one type of glycosidic linkage, yet certain glycosyltransferases generate polysaccharide sequences composed of two distinct linkage types. In principle, bifunctional glycosyltransferases can possess separate active sites for each catalytic activity or one active site with dual activities. We encountered the fundamental question of one or two distinct active sites in our investigation of the galactosyltransferase GlfT2. GlfT2 catalyzes the formation of mycobacterial galactan, a critical cell-wall polymer composed of galactofuranose residues connected with alternating, regioisomeric linkages. We found that GlfT2 mediates galactan polymerization using only one active site that manifests dual regioselectivity. Structural modeling of the bifunctional glycosyltransferases hyaluronan synthase and cellulose synthase suggests that these enzymes also generate multiple glycosidic linkages using a single active site. These results highlight the versatility of glycosyltransferases for generating polysaccharides of specific sequence. We postulate that a hallmark of processive elongation of a carbohydrate polymer by a bifunctional enzyme is that one active site can give rise to two separate types of glycosidic bonds. PMID:22217153

  14. Activation of Ca sup 2+ uptake and inhibition of reversal of the sarcoplasmic reticulum Ca sup 2+ pump by aromatic compounds

    SciTech Connect

    Petretski, J.H.; Wolosker, H.; de Meis, L. )

    1989-12-05

    The effects of aromatic compounds in sarcoplasmic reticulum Ca2+-ATPase were investigated. The solubility of the drugs in various organic solvents and water was measured. The ratio between the solubility in organic solvents and that in water (distribution coefficient) was used as an index of their hydrophobicity. The order found was triphenylphosphine greater than diphenylamine greater than 3-nitrophenol greater than 4-nitrophenol greater than 1,3-dihydroxybenzene. The effects observed on the Ca2+-ATPase were correlated with hydrophobicity of the drugs, activation and inhibition being obtained at a lower concentration the greater the distribution coefficient of the drug into organic solvent. In leaky vesicles, the effects of each compound on the ATPase activity varied depending on the Ca2+ concentration in the medium: it inhibited in the presence of 5 microM Ca2+ and activated when the Ca2+ concentration was raised to 2 mM. In intact vesicles, 3- and 4-nitrophenol, diphenylamine, and triphenylphosphine enhanced both the rate of ATP hydrolysis and the amount of Ca2+ accumulated by the vesicles. These four drugs inhibited Ca2+ uptake when ITP was used as substrate. 1,3-Dihydroxybenzene enhanced the amount of Ca2+ accumulated by the vesicles regardless of whether ATP or ITP was the substrate. All five compounds inhibited the phosphorylation of the enzyme by Pi, the efflux of Ca2+, and the synthesis of ATP measured during the reversal of the Ca2+ pump. The results indicate that the hydrophobic character of various organic compounds determines their access to sensitive domains of the membrane-bound calcium pump. Additional specific effects are then produced, depending on the structure of each compound.

  15. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors*

    PubMed Central

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M.; Kenny, Paul J.; Lindstrom, Jon

    2015-01-01

    Neuronal nicotinic acetylcholine receptors containing α4, β2, and sometimes other subunits (α4β2* nAChRs) regulate addictive and other behavioral effects of nicotine. These nAChRs exist in several stoichiometries, typically with two high affinity acetylcholine (ACh) binding sites at the interface of α4 and β2 subunits and a fifth accessory subunit. A third low affinity ACh binding site is formed when this accessory subunit is α4 but not if it is β2. Agonists selective for the accessory ACh site, such as 3-[3-(3-pyridyl)-1,2,4-oxadiazol-5-yl]benzonitrile (NS9283), cannot alone activate a nAChR but can facilitate more efficient activation in combination with agonists at the canonical α4β2 sites. We therefore suggest categorizing agonists according to their site selectivity. NS9283 binds to the accessory ACh binding site; thus it is termed an accessory site-selective agonist. We expressed (α4β2)2 concatamers in Xenopus oocytes with free accessory subunits to obtain defined nAChR stoichiometries and α4/accessory subunit interfaces. We show that α2, α3, α4, and α6 accessory subunits can form binding sites for ACh and NS9283 at interfaces with α4 subunits, but β2 and β4 accessory subunits cannot. To permit selective blockage of the accessory site, α4 threonine 126 located on the minus side of α4 that contributes to the accessory site, but not the α4β2 sites, was mutated to cysteine. Alkylation of this cysteine with a thioreactive reagent blocked activity of ACh and NS9283 at the accessory site. Accessory agonist binding sites are promising drug targets. PMID:25869137

  16. Structural insights into the regulation of aromatic amino acid hydroxylation.

    PubMed

    Fitzpatrick, Paul F

    2015-12-01

    The aromatic amino acid hydroxylases phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase are homotetramers, with each subunit containing a homologous catalytic domain and a divergent regulatory domain. The solution structure of the regulatory domain of tyrosine hydroxylase establishes that it contains a core ACT domain similar to that in phenylalanine hydroxylase. The isolated regulatory domain of tyrosine hydroxylase forms a stable dimer, while that of phenylalanine hydroxylase undergoes a monomer-dimer equilibrium, with phenylalanine stabilizing the dimer. These solution properties are consistent with the regulatory mechanisms of the two enzymes, in that phenylalanine hydroxylase is activated by phenylalanine binding to an allosteric site, while tyrosine hydroxylase is regulated by binding of catecholamines in the active site.

  17. Comparative Study of Composition, Antioxidant, and Antimicrobial Activities of Essential Oils of Selected Aromatic Plants from Balkan Peninsula.

    PubMed

    Stanković, Nemanja; Mihajilov-Krstev, Tatjana; Zlatković, Bojan; Matejić, Jelena; Stankov Jovanović, Vesna; Kocić, Branislava; Čomić, Ljiljana

    2016-05-01

    The objective of the present study to perform a comparative analysis of the chemical composition, antioxidant, and antimicrobial activities of the essential oils of plant species Hyssopus officinalis, Achillea grandifolia, Achillea crithmifolia, Tanacetum parthenium, Laserpitium latifolium, and Artemisia absinthium from Balkan Peninsula. The chemical analysis of essential oils was performed by using gas chromatography and gas chromatography-mass spectrometry. Monoterpenes were dominant among the recorded components, with camphor in T. parthenium, A. grandifolia, and A. crithmifolia (51.4, 45.4, and 25.4 %, respectively), 1,8-cineole in H. officinalis, A. grandifolia, and A. crithmifolia (49.1, 16.4, and 14.8 %, respectively), and sabinene in L. latifolium and A. absinthium (47.8 and 21.5 %). The antiradical and antioxidant activities were determined by using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) and 2,2-diphenyl-1-picrylhydrazyl radical scavenging methods. The essential oil of A. grandifolia has shown the highest antioxidant activity [IC50 of 33.575 ± 0.069 mg/mL for 2,2-diphenyl-1-picrylhydrazyl and 2.510 ± 0.036 mg vitamin C/g for the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) assay]. The antimicrobial activity against 16 multiresistant pathogenic bacteria isolated from human source material was tested by the broth microdilution assay. The resulting minimum inhibitory concentration/minimum bactericidal concentration values ranged from 4.72 to 93.2 mg/mL. Therefore, the essential oils of the plant species included in this study may be considered to be prospective natural sources of antimicrobial substances, and may contribute as effective agents in the battle against bacterial multiresistance.

  18. Constituents and Pharmacological Activities of Myrcia (Myrtaceae): A Review of an Aromatic and Medicinal Group of Plants

    PubMed Central

    Cascaes, Márcia Moraes; Guilhon, Giselle Maria Skelding Pinheiro; Andrade, Eloisa Helena de Aguiar; Zoghbi, Maria das Graças Bichara; Santos, Lourivaldo da Silva

    2015-01-01

    Myrcia is one of the largest genera of the economically important family Myrtaceae. Some of the species are used in folk medicine, such as a group known as “pedra-hume-caá” or “pedra-ume-caá” or “insulina vegetal” (insulin plant) that it is used for the treatment of diabetes. The species are an important source of essential oils, and most of the chemical studies on Myrcia describe the chemical composition of the essential oils, in which mono- and sesquiterpenes are predominant. The non-volatile compounds isolated from Myrcia are usually flavonoids, tannins, acetophenone derivatives and triterpenes. Anti-inflammatory, antinociceptive, antioxidant, antimicrobial activities have been described to Myrcia essential oils, while hypoglycemic, anti-hemorrhagic and antioxidant activities were attributed to the extracts. Flavonoid glucosides and acetophenone derivatives showed aldose reductase and α-glucosidase inhibition, and could explain the traditional use of Myrcia species to treat diabetes. Antimicrobial and anti-inflammatory are some of the activities observed for other isolated compounds from Myrcia. PMID:26473832

  19. The role of aryl hydrocarbon receptor in regulation of enzymes involved in metabolic activation of polycyclic aromatic hydrocarbons in a model of rat liver progenitor cells.

    PubMed

    Vondrácek, Jan; Krcmár, Pavel; Procházková, Jirina; Trilecová, Lenka; Gavelová, Martina; Skálová, Lenka; Szotáková, Barbora; Buncek, Martin; Radilová, Hana; Kozubík, Alois; Machala, Miroslav

    2009-07-15

    In contrast to hepatocytes, there is only limited information about the expression and activities of enzymes participating in metabolic activation of environmental mutagens, including polycyclic aromatic hydrocarbons (PAHs), in liver progenitor cells. In rat liver "stem-like" WB-F344 cell line, sharing many characteristics with rat liver progenitor cells, PAHs are efficiently activated to their ultimate genotoxic metabolites forming DNA adducts. The present study aimed to characterize expression/activities of enzymes of two major pathways involved in the metabolism of benzo[a]pyrene (BaP): cytochrome P450 (CYP) family 1 enzymes and cytosolic aldo-keto reductases (AKRs). We report here that, apart from induction of CYP1A1 and CYP1B1 expression and the corresponding enzymatic activity, both BaP and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induced rat 3alpha-hydroxysteroid dehydrogenase (AKR1C9) expression and activity. In contrast, the aldehyde reductase AKR1A1 was not induced by either treatment. Thus, both CYP1 and AKR metabolic pathways were inducible in the model of liver progenitor cells. BaP and TCDD were efficient inducers of NAD(P)H:quinone oxidoreductase 1 (NQO1) expression and activity in WB-F344 cells, a principal enzyme of cellular antioxidant defense. Both compounds also induced expression of transcription factor NRF2, involved in control of enzymes protecting cells from oxidative stress. However, although BaP induced a significant formation of reactive oxygen species, it did not induce expression of heme oxygenase-1, suggesting that induction of oxidative stress by BaP was limited. Using shRNA against the aryl hydrocarbon receptor (AhR), we found that similar to CYP1A1 and CYP1B1, the AKR1C9 induction was AhR-dependent. Moreover, constitutive AKR1C9 levels in AhR-deficient rat BP8 hepatoma cells were significantly lower than in their AhR-positive 5L variant, thus supporting possible role of AhR in regulation of AKR1C9 expression. Taken together, both

  20. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  1. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  2. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...). (e) For all asbestos-containing waste material received, the owner or operator of the active waste... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  3. Trimerization of aromatic nitriles

    NASA Technical Reports Server (NTRS)

    Hsu, L. C. (Inventor)

    1977-01-01

    Triazine compounds and cross-linked polymer compositions were made by heating aromatic nitriles to a temperature in the range of about 100 C to about 700 C, in the presence of a catalyst or mixture of catalysts. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers were made which were trimerized with or without a filler by the aforementioned catalytic trimerization process.

  4. Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

    PubMed

    Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

    2003-05-13

    Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate

  5. Structure and nuclearity of active sites in Fe-zeolites: comparison with iron sites in enzymes and homogeneous catalysts.

    PubMed

    Zecchina, Adriano; Rivallan, Mickaël; Berlier, Gloria; Lamberti, Carlo; Ricchiardi, Gabriele

    2007-07-21

    Fe-ZSM-5 and Fe-silicalite zeolites efficiently catalyse several oxidation reactions which find close analogues in the oxidation reactions catalyzed by homogeneous and enzymatic compounds. The iron centres are highly dispersed in the crystalline matrix and on highly diluted samples, mononuclear and dinuclear structures are expected to become predominant. The crystalline and robust character of the MFI framework has allowed to hypothesize that the catalytic sites are located in well defined crystallographic positions. For this reason these catalysts have been considered as the closest and best defined heterogeneous counterparts of heme and non heme iron complexes and of Fenton type Fe(2+) homogeneous counterparts. On this basis, an analogy with the methane monooxygenase has been advanced several times. In this review we have examined the abundant literature on the subject and summarized the most widely accepted views on the structure, nuclearity and catalytic activity of the iron species. By comparing the results obtained with the various characterization techniques, we conclude that Fe-ZSM-5 and Fe-silicalite are not the ideal samples conceived before and that many types of species are present, some active and some other silent from adsorptive and catalytic point of view. The relative concentration of these species changes with thermal treatments, preparation procedures and loading. Only at lowest loadings the catalytically active species become the dominant fraction of the iron species. On the basis of the spectroscopic titration of the active sites by using NO as a probe, we conclude that the active species on very diluted samples are isolated and highly coordinatively unsaturated Fe(2+) grafted to the crystalline matrix. Indication of the constant presence of a smaller fraction of Fe(2+) presumably located on small clusters is also obtained. The nitrosyl species formed upon dosing NO from the gas phase on activated Fe-ZSM-5 and Fe-silicalite, have been analyzed

  6. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    SciTech Connect

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; Nørskov, Jens K.; Studt, Felix

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidation reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.

  7. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    DOE PAGES

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; ...

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidationmore » reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.« less

  8. Molten salt-supported polycondensation of optically active diacid monomers with an aromatic thiazole-bearing diamine using microwave irradiation

    PubMed Central

    Mallakpour, Shadpour; Zadehnazari, Amin

    2013-01-01

    Microwave heating was used to prepare optically active thiazole-bearing poly(amide-imide)s. Polymerization reactions were carried out in the molten tetrabutylammonium bromide as a green molten salt medium and triphenyl phosphite as the homogenizer. Structural elucidation of the compounds was performed by Fourier transform infrared and NMR spectroscopic data and elemental analysis results. The polymeric samples were readily soluble in various organic solvents, forming low-colored and flexible thin films via solution casting. They showed high thermal stability with decomposition temperature being above 360 °C. They were assembled randomly in a nanoscale size. PMID:25685498

  9. Aromatic Polyimide Foam

    NASA Technical Reports Server (NTRS)

    Weiser, Erik S. (Inventor); St.Clair, Terry L. (Inventor); Echigo, Yoshiaki (Inventor); Kaneshiro, Hisayasu (Inventor)

    2000-01-01

    A mechanically undensified aromatic polyimide foam is made from an aromatic polyimide precursor solid residuum and has the following combination of properties: a density according to ASTM D-3574A of about 0.5 pounds/cu.ft to about 20 pounds/cu.ft; a compression strength according to ASTM D-3574C of about 1.5 psi to about 1500 psi; and a limiting oxygen index according to ASTM D-2863 of about 35% oxygen to about 75% oxygen at atmospheric pressure. The aromatic polyimide foam has no appreciable solid inorganic contaminants which are residues of inorganic blowing agents. The aromatic polyimide which constitutes the aromatic polyimide foam has a glass transition temperature (Tg) by differential scanning calorimetry of about 235 C to about 400 C; and a thermal stability of 0 to about 1% weight loss at 204 C as determined by thermogravinietric analysis (TGA). The aromatic polyimide foam has utility as foam insulation and as structural foam, for example, for aeronautical, aerospace and maritime applications.

  10. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    SciTech Connect

    Not Available

    1994-02-01

    This report is a detailed listing of all of the Hazardous Waste activities occurring at Martin Marietta`s K-25 site. Contained herein are hazardous waste notification forms, waste stream reports, generator fee forms and various TSDR reports.

  11. An investigation into the occurrence and distribution of polycyclic aromatic hydrocarbons in two soil size fractions at a former industrial site in NE England, UK using in situ PFE-GC-MS.

    PubMed

    Lorenzi, Damien; Cave, Mark; Dean, John R

    2010-12-01

    Polycyclic aromatic hydrocarbon (PAH) concentrations were determined in 16 topsoils (0-10 cm) collected across the site of a former tar works in NE England. The soils were prepared in the laboratory to two different particle size fractions: <250 μm (fraction A) and >250 μm to <2 mm (fraction B). Sixteen priority PAHs were analysed in the soils using in situ pressurised fluid extraction (PFE) followed by gas chromatography-mass spectrometry (GC-MS). The average total PAH concentration in the soils ranged from 9.0 to 1,404 mg/kg (soil fraction A) and from 6.6 to 872 mg/kg (soil fraction B). These concentrations are high compared with other industrially contaminated soils reported in the international literature, indicating that the tar works warrants further investigation/remediation. A predominance of higher-molecular-weight compounds was determined in the samples, suggesting that the PAHs were of pyrogenic (anthropogenic) origin. Statistical comparison (t-test) of the mean total PAH concentrations in soil fractions A and B indicated that there was a significant difference (95% confidence interval) between the fractions in all but two of the soil samples. Additionally, comparisons of the distributions of individual PAHs (i.e. 16 PAHs × 16 soil samples) in soil fractions A and B demonstrated generally higher PAH concentrations in fraction A (i.e. 65.8% of all individual PAH concentrations were higher in soil fraction A). This is important because fraction A corresponds to the particle size thought to be most important in terms of human contact with soils and potential threats to human health.

  12. Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae

    PubMed Central

    Stahlhut, Steen Gustav; Li, Mingji; Gaspar, Paula; Siedler, Solvej; Förster, Jochen; Maury, Jérôme; Borodina, Irina

    2015-01-01

    Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit−1 in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases. PMID:25911487

  13. The surface chemistry of heterogeneous catalysis: mechanisms, selectivity, and active sites.

    PubMed

    Zaera, Francisco

    2005-01-01

    The role of chemical kinetics in defining the requirements for the active sites of heterogeneous catalysts is discussed. A personal view is presented, with specific examples from our laboratory to illustrate the role of the chemical composition, structure, and electronic properties of specific surface sites in determining reaction activity and selectivity. Manipulation of catalytic behavior via the addition of chemical modifiers and by tuning of the reaction conditions is also introduced.

  14. Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase YopH Exhibit Impaired WPD-Loop Function and Crystallize with Divanadate Esters in Their Active Sites

    PubMed Central

    Moise, Gwendolyn; Gallup, Nathan M.; Alexandrova, Anastassia N.; Hengge, Alvan C.; Johnson, Sean J.

    2016-01-01

    Catalysis in protein tyrosine phosphatases (PTPs) involves movement of a protein loop called the WPD loop that brings a conserved aspartic acid into the active site to function as a general acid. Mutation of the tryptophan in the WPD loop of the PTP YopH to any other residue with a planar, aromatic side chain (phenylalanine, tyrosine, or histidine) disables general acid catalysis. Crystal structures reveal these conservative mutations leave this critical loop in a catalytically unproductive, quasi-open position. Although the loop positions in crystal structures are similar for all three conservative mutants, the reasons inhibiting normal loop closure differ for each mutant. In the W354F and W354Y mutants, steric clashes result from six-membered rings occupying the position of the five-membered ring of the native indole side chain. The histidine mutant dysfunction results from new hydrogen bonds stabilizing the unproductive position. The results demonstrate how even modest modifications can disrupt catalytically important protein dynamics. Crystallization of all the catalytically compromised mutants in the presence of vanadate gave rise to vanadate dimers at the active site. In W354Y and W354H, a divanadate ester with glycerol is observed. Such species have precedence in solution and are known from the small molecule crystal database. Such species have not been observed in the active site of a phosphatase, as a functional phosphatase would rapidly catalyze their decomposition. The compromised functionality of the mutants allows the trapping of species that undoubtedly form in solution and are capable of binding at the active sites of PTPs, and, presumably, other phosphatases. In addition to monomeric vanadate, such higher-order vanadium-based molecules are likely involved in the interaction of vanadate with PTPs in solution. PMID:26445170

  15. Ultrahigh gas storage both at low and high pressures in KOH-activated carbonized porous aromatic frameworks.

    PubMed

    Li, Yanqiang; Ben, Teng; Zhang, Bingyao; Fu, Yao; Qiu, Shilun

    2013-01-01

    The carbonized PAF-1 derivatives formed by high-temperature KOH activation showed a unique bimodal microporous structure located at 0.6 nm and 1.2 nm and high surface area. These robust micropores were confirmed by nitrogen sorption experiment and high-resolution transmission electron microscopy (TEM). Carbon dioxide, methane and hydrogen sorption experiments indicated that these novel porous carbon materials have significant gas sorption abilities in both low-pressure and high-pressure environments. Moreover the methane storage ability of K-PAF-1-750 is among the best at 35 bars, and its low-pressure gas adsorption abilities are also comparable to the best porous materials in the world. Combined with excellent physicochemical stability, these materials are very promising for industrial applications such as carbon dioxide capture and high-density clean energy storage.

  16. Nuclear waste: Status of DOE`s nuclear waste site characterization activities

    SciTech Connect

    1987-12-31

    Three potential nuclear waste repository sites have been selected to carry out characterization activities-the detailed geological testing to determine the suitability of each site as a repository. The sites are Hanford in south-central Washington State, Yucca Mountain in southern Nevada, and Deaf Smith in the Texas Panhandle. Two key issues affecting the total program are the estimations of the site characterization completion data and costs and DOE`s relationship with the Nuclear Regulatory Commission which has been limited and its relations with affected states and Indian tribes which continue to be difficult.

  17. Number and locations of agonist binding sites required to activate homomeric Cys-loop receptors.

    PubMed

    Rayes, Diego; De Rosa, María José; Sine, Steven M; Bouzat, Cecilia

    2009-05-06

    Homo-pentameric Cys-loop receptors contain five identical agonist binding sites, each formed at a subunit interface. To determine the number and locations of binding sites required to generate a stable active state, we constructed a receptor subunit with a mutation that disables the agonist binding site and a reporter mutation that alters unitary conductance and coexpressed mutant and nonmutant subunits. Although receptors with a range of different subunit compositions are produced, patch-clamp recordings reveal that the amplitude of each single-channel opening event reports the number and, for certain subunit combinations, the locations of subunits with intact binding sites. We find that receptors with three binding sites at nonconsecutive subunit interfaces exhibit maximal mean channel open time, receptors with binding sites at three consecutive or two nonconsecutive interfaces exhibit intermediate open time, and receptors with binding sites at two consecutive or one interface exhibit brief open time. Macroscopic recordings after rapid application of agonist reveal that channel activation slows and the extent of desensitization decreases as the number of binding sites per receptor decreases. The overall results provide a framework for defining mechanisms of activation and drug modulation for homo-pentameric Cys-loop receptors.

  18. Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons.

    PubMed

    Lipińska, Aneta; Wyszkowska, Jadwiga; Kucharski, Jan

    2015-12-01

    Polycyclic aromatic hydrocarbons are organic compounds with highly toxic, carcinogenic, and mutagenic properties, which adversely affect the basic biological parameters of the soil, including the count of microorganisms, and the enzymatic activity. In addition to disturbances to the biological activity of the soil, PAHs may also exhibit toxic effects on plants. In view of the above, the study involved testing aimed at the determination of the effects of polycyclic aromatic hydrocarbons in a form of naphthalene, phenanthrene, anthracene and pyrene on the count, colony development (CD) index, ecophysiological (EP) diversity index of organotrophic bacteria, and the activity of soil dehydrogenases and soil urease. Moreover, an attempt was made to determine the soil's resistance based on the activity of the above-listed enzymes, and the effect of polycyclic aromatic hydrocarbons on seed germination and root growth was assessed by Lepidium sativum, Sorghum saccharatum, and Sinapis alba. In addition, the species of bacteria found in a soil subjected to strong pressure of polycyclic aromatic hydrocarbons were isolated. The experiment was performed in a laboratory on samples of loamy sand. Polycyclic aromatic hydrocarbons were introduced into the soil in an amount of 0, 1000, 2000, and 4000 mg kg(-1) of soil dry matter. Germination and growth of cress (L. sativum), white mustard (S. alba), and sweet sorghum (S. saccharatum) were determined using Phytotoxkit tests. It was found that the tested PAHs increased the average colony counts of organotrophic soil bacteria; pyrene did so to the greatest extent (2.2-fold relative to non-contaminated soil), phenanthrene to the smallest extent (1.4-fold relative to non-contaminated soil). None of the PAHs changed the value of the bacterial colony development (CD) index, while anthracene and pyrene increased the value of the eco-physiological (EP) diversity indicator. PAHs lowered the activity of the tested enzymes. The activity of

  19. Equilibrium adsorption studies of some aromatic pollutants from dilute aqueous solutions on activated carbon at different temperatures

    SciTech Connect

    Khan, A.R.; Ataullah, R.; Al-Haddad, A.

    1997-10-01

    Aqueous solutions of phenol, p-chlorophenol, and p-nitrophenol have been used to determine the adsorption isotherm for single solute systems on activated carbon at different temperatures. The experimental program has been conducted to investigate the influence of concentration and temperature. All the reported equilibrium isotherm equations have been tried on present and published experimental data. A generalized isotherm equation which was proposed by Khan et al. and tested for bi-solute adsorption data has been modified for single-solute system. The temperature dependency has also been incorporated into a generalized equation. It has been noticed that the Radke and Prausnitz and generalized isotherm equations could represent the entire data with a minimum average percentage error. The influence of different adsorbents, sorbate concentrations, and pH of aqueous solutions has also been discussed in detail. The temperature dependency has been investigated using both the Dubinin-Astakov and the modified generalized equation. The generalized equation describes the experimental and published data adequately and provides a single value of differential molar heat of adsorption, {Delta}H{sub ads}, for a single solute adsorption system. The Dubinin-Astakov isotherm equation has shown an increasing trend of {Delta}H{sub ads} as the loading of adsorbent has increased.

  20. Simultaneous monitoring method of polycyclic aromatic hydrocarbons and persistent organic pollutants in the atmosphere using activated carbon fiber filter paper.

    PubMed

    Yagoh, Hiroaki; Murayama, Hitoshi; Suzuki, Takahiro; Tominaga, Yasuko; Shibuya, Nobuo; Masuda, Yoshio

    2006-04-01

    In order to simultaneously monitor the concentrations of PAHs and POPs in the atmosphere, an activated carbon fiber filter paper (ACFP) was used as the adsorbing material in this study. The pressurized liquid extraction method (PLE method) was used to extract PAHs and POPs collected on the ACFP. Toluene was an effective solvent to extract them from ACFP using the PLE method, but some of PAHs, such as benzo(a)pyrene, benzo(g,h,i)perylene, dibenzo(a,h)anthracene and indeno(1,2,3-cd)pyrene, were hardly extracted. These PAHs were adsorbed on the particulate matter in the atmosphere. In general, these forms of particulate matter could be collected using a quartz fiber paper (QFP); these PAHs were efficiently extracted from the QFP using the PLE method with toluene. In this study, the collecting method of the PAHs was modified by using QFP overlapped in front of the ACFP. Atmospheric monitoring of PAHs and POPs in Niigata area was performed using this method, and most of the target compounds were detected. However, some of the POPs, such as aldrin, endrin, mirex, could not be detected. The POPs, such as hexachlorobenzene, alpha-hexachlorocyclohexane and chlordanes, and most of the PAHs were detected from all of the samples collected throughout the monitoring period. It was confirmed that these methods were effective to simultaneously monitor the concentrations of the PAHs and POPs in the atmosphere.

  1. Polycyclic aromatic hydrocarbons in rock oysters: a baseline study.

    PubMed

    Kagi, R; Alexander, R; Cumbers, M

    1985-01-01

    Coral-rock oysters were collected in September 1982 from six locations in the area of Mermaid Sound in North-Western Australia. Analysis was carried out by digestion of the samples, followed by solvent extraction and analysis of the extracts using HPLC-UVF and GC-MS. The levels of two- and three-ring aromatics ranged from very low for the site outside Mermaid Sound and for one site within the Sound, to low for the four other sites within the Sound. The PAH values at the latter four sites are attributed to occasional petroleum release episodes related to small boat activities and large-scale salt and iron ore shipping and general cargo activities of the Port of Dampier. The levels of PAHs with four or more rings were found to be low or very low at all sites; in fact, in most cases values measured for specific PAHs were below the limits of detection of even the very sensitive methods used in this study. Samples from sites within Mermaid Sound closest to the town and port of Dampier showed noticeably higher levels than those from outside; the present study does not allow the source of the PAHs to be determined. It is interesting to note, however, that the parent PAHs appear to form a greater proportion of the total PAH assemblage in these cases, indicating contributions from material which has been subjected to high temperature processing prior to release into the Sound.

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

    PubMed

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

    2015-04-21

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

  3. Purification of aromatic hydrocarbons via fibrous activated carbon/photocatalytic composite coupled with UV light-emitting diodes.

    PubMed

    Jo, Wan-Kuen

    2013-01-01

    In the present study, the applicability of light-emitting diodes (LEDs) to a fibrous activated carbon (FAC)/titania (TiO2) composite used for the purification of gas-phase benzene, toluene, ethyl benzene and xylene was evaluated. The surface and morphological properties of the FAC and prepared FAC/TiO2 composite were investigated by X-ray diffraction and scanning electron microscopy. The study protocol included two different tests, comparison of FAC and the FAC/TiO2 composite for BTEX removal efficiency and evaluation of the FAC/TiO2 composite for benzene and toluene removal efficiency under differing operation conditions. The time-series ratios obtained with the FAC/TiO2 composite showed longer removal times for all target compounds when compared to those of FAC alone. For both benzene and toluene, the breakthrough time decreased with the stream flow rate, whereas it increased with increasing light intensity under the experimental conditions employed in this study. The breakthrough time of benzene and toluene increased as increasing amounts of TiO2 were coated onto the surface of FAC between 11 and 229 mg-TiO2 (g-FAC)(-1), but decreased as the amount of TiO2 increased to 451 mg (g-FAC)(-1). These findings indicate that the optimal TiO2 weight for the removal process of benzene and toluene via the FAC/TiO2 composite is between 229 and 451 mg-TiO2 (g-FAC)(-1).

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

    SciTech Connect

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

    2011-09-18

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

  5. Research on Aromatic Poly

    NASA Astrophysics Data System (ADS)

    Kiebooms, Rafael Hugo Ludo

    1995-11-01

    A detailed analysis of the literature indicated that substituents can only be used at the level of improving properties during processing, that end groups are only important for those polymers where the energy difference between the aromatic and quinoid structure is very small, and that stability of pi delocalisation is the most important tool for the design of low bandgap polymers. From our research it appeared that, based on a detailed NMR and FT-Raman analysis of oligomers and model compounds, the low band gap of PITN could be associated with the quinoid structure. However, a theoretical analysis of the UV-vis data of a series of aromatic isothianaphthene oligomers indicates that a substantial lowering of the band gap can be obtained in planar aromatic isothianaphthene systems. A parallel investigation of PTFITN, a soluble isothianaphthene analogue, gave some indications that this polymer should possess an aromatic structure. The aromatic structure makes it possible that the fluorines probably induce non planarity such that inter ring pi -conjugation is lowered to a considerable extent. This could explain the increased band gap of 2.1eV observed by Swann et al.^{[1] }. Analysis of a series of aza-analogues of PITN revealed that in these materials it should be possible to combine a planar aromatic geometry with enhanced processability. The 4,5-diaza and 4,7-diaza isothianaphthene polymers can therefore be considered as very promising low band gap materials. Finally, we showed that it is possible to combine the aromatic isothianaphthene ring system with another heterocycle such as thiophene in a formal copolymer. Through the development of a highly specific and efficient synthesis route to 1,3-dithienylisothianaphthene (DTI, 4), we established the basis for the further synthesis and study of formal copolymers with tailor-made electronic properties. ftn ^{[1]}M. J. Swann, G. Brooke, D. Bloor. Synth.Met., 55-57, 281-286, (1993).

  6. Two interacting binding sites for quinacrine derivatives in the active site of trypanothione reductase – a template for drug design

    PubMed Central

    Saravanamuthu, Ahilan; Vickers, Tim J.; Bond, Charles S.; Peterson, Mark R.; Hunter, William N.; Fairlamb, Alan H.

    2012-01-01

    SUMMARY Trypanothione reductase is a key enzyme in the trypanothione-based redox metabolism of pathogenic trypanosomes. Since this system is absent in humans, being replaced with glutathione and glutathione reductase, it offers a target for selective inhibition. The rational design of potent inhibitors requires accurate structures of enzyme-inhibitor complexes, but this is lacking for trypanothione reductase. We therefore used quinacrine mustard, an alkylating derivative of the competitive inhibitor quinacrine, to probe the active site of this dimeric flavoprotein. Quinacrine mustard irreversibly inactivates Trypanosoma cruzi trypanothione reductase, but not human glutathione reductase, in a time-dependent manner with a stoichiometry of two inhibitors bound per monomer. The rate of inactivation is dependent upon the oxidation state of trypanothione reductase, with the NADPH-reduced form being inactivated significantly faster than the oxidised form. Inactivation is slowed by clomipramine and a melarsen oxide-trypanothione adduct (both are competitive inhibitors) but accelerated by quinacrine. The structure of the trypanothione reductase-quinacrine mustard adduct was determined to 2.7 Å, revealing two molecules of inhibitor bound in the trypanothione-binding site. The acridine moieties interact with each other through π-stacking effects, and one acridine interacts in a similar fashion with a tryptophan residue. These interactions provide a molecular explanation for the differing effects of clomipramine and quinacrine on inactivation by quinacrine mustard. Synergism with quinacrine occurs as a result of these planar acridines being able to stack together in the active site cleft, thereby gaining an increased number of binding interactions, whereas antagonism occurs with non-planar molecules, such as clomipramine, where stacking is not possible. PMID:15102853

  7. The three Mycobacterium tuberculosis antigen 85 isoforms have unique substrates and activities determined by non-active site regions.

    PubMed

    Backus, Keriann M; Dolan, Michael A; Barry, Conor S; Joe, Maju; McPhie, Peter; Boshoff, Helena I M; Lowary, Todd L; Davis, Benjamin G; Barry, Clifton E

    2014-09-05

    The three isoforms of antigen 85 (A, B, and C) are the most abundant secreted mycobacterial proteins and catalyze transesterification reactions that synthesize mycolated arabinogalactan, trehalose monomycolate (TMM), and trehalose dimycolate (TDM), important constituents of the outermost layer of the cellular envelope of Mycobacterium tuberculosis. These three enzymes are nearly identical at the active site and have therefore been postulated to exist to evade host immunity. Distal to the active site is a second putative carbohydrate-binding site of lower homology. Mutagenesis of the three isoforms at this second site affected both substrate selectivity and overall catalytic activity in vitro. Using synthetic and natural substrates, we show that these three enzymes exhibit unique selectivity; antigen 85A more efficiently mycolates TMM to form TDM, whereas C (and to a lesser extent B) has a higher rate of activity using free trehalose to form TMM. This difference in substrate selectivity extends to the hexasaccharide fragment of cell wall arabinan. Mutation of secondary site residues from the most active isoform (C) into those present in A or B partially interconverts this substrate selectivity. These experiments in combination with molecular dynamics simulations reveal that differences in the N-terminal helix α9, the adjacent Pro(216)-Phe(228) loop, and helix α5 are the likely cause of changes in activity and substrate selectivity. These differences explain the existence of three isoforms and will allow for future work in developing inhibitors.

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

    SciTech Connect

    Carra,J.; McHugh, C.; Mulligan, S.; Machiesky, L.; Soares, A.; Millard, C.

    2007-01-01

    We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding to a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.

  9. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    SciTech Connect

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  10. All the catalytic active sites of MoS2 for hydrogen evolution

    SciTech Connect

    Li, Guoqing; Zhang, Du; Qiao, Qiao; Yu, Yifei; Peterson, David; Zafar, Abdullah; Kumar, Raj; Curtarolo, Stefano; Hunte, Frank; Shannon, Steve; Zhu, Yimei; Yang, Weitao; Cao, Linyou

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5 s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.

  11. Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole

    PubMed Central

    Zhang, Xuwang; Qu, Yuanyuan; Ma, Qiao; Zhang, Zhaojing; Li, Duanxing; Wang, Jingwei; Shen, Wenli; Shen, E; Zhou, Jiti

    2015-01-01

    Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole. PMID:25928424

  12. Application of toxicity-based fractionation techniques and structure-activity relationship models for the identification of phototoxic polycyclic aromatic hydrocarbons in sediment pore water

    SciTech Connect

    Kosian, P.A.; Makynen, E.A.; Monson, P.D.; Mount, D.R.; Ankley, G.T.; Spacie, A.; Mekenyan, O.G.

    1998-06-01

    Recent studies conducted at their laboratory have shown that sediments contaminated with complex mixtures of polycyclic aromatic hydrocarbons (PAHs) can exhibit enhanced toxicity (lethality) to a variety of aquatic species when the samples are tested under ultraviolet (UV) light designed to mimic the wavelengths present in sunlight. However, because these contaminated sediments can contain literally thousands of chemicals, it is difficult to use conventional analytical techniques to identify those compounds responsible for photo-induced toxicity. The purpose of this study was to adapt existing toxicity identification evaluation methods to attempt to identify those compounds contributing to the phototoxicity observed in their sediment samples. Pore water obtained from sediments collected near an oil refinery discharge was toxic to Lumbriculus variegatus following exposure to UV light, while organisms exposed to the same pore water, but without subsequent UV treatment, showed no toxic effect. Solid-phase extraction disks and high-performance liquid chromatography were used, in conjunction with toxicity tests with L. variegatus, to extract and fractionate phototoxic chemicals from the pore water. Phototoxic fractions analyzed by gas chromatography-mass spectrometry revealed the presence of a number of aliphatic hydrocarbons, substituted PAHs, and PAHs containing heteroatoms. Chemicals were screened for their phototoxic potential based on empirical data and predictive models. A refined list of PAHs was then evaluated on the basis of their phototoxic potency as defined by a recently developed quantitative structure-activity relationship model and estimates of their bioaccumulation potential. Based on the model predictions of potency and bioaccumulation, nine likely phototoxic chemicals were identified.

  13. The aromatic ene reaction

    PubMed Central

    Niu, Dawen; Hoye, Thomas R.

    2014-01-01

    The ene reaction is a pericyclic process in which an alkene having an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed π-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (≤6%). Here we show efficient aromatic ene reactions in which a thermally generated aryne engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (i) hexadehydro-Diels-Alder (for aryne generation), (ii) intramolecular aromatic ene, and (iii) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multi-stage, reagent- and byproduct-free, single-pot transformations. PMID:24345944

  14. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

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

    SciTech Connect

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

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  16. Synergistic effect between defect sites and functional groups on the hydrolysis of cellulose over activated carbon.

    PubMed

    Foo, Guo Shiou; Sievers, Carsten

    2015-02-01

    The chemical oxidation of activated carbon by H2 O2 and H2 SO4 is investigated, structural and chemical modifications are characterized, and the materials are used as catalysts for the hydrolysis of cellulose. Treatment with H2 O2 enlarges the pore size and imparts functional groups such as phenols, lactones, and carboxylic acids. H2 SO4 treatment targets the edges of carbon sheets primarily, and this effect is more pronounced with a higher temperature. Adsorption isotherms demonstrate that the adsorption of oligomers on functionalized carbon is dominated by van der Waals forces. The materials treated chemically are active for the hydrolysis of cellulose despite the relative weakness of most of their acid sites. It is proposed that a synergistic effect between defect sites and functional groups enhances the activity by inducing a conformational change in the glucan chains if they are adsorbed at defect sites. This activates the glycosidic bonds for hydrolysis by in-plane functional groups.

  17. Denaturation studies of active-site labeled papain using electron paramagnetic resonance and fluorescence spectroscopy.

    PubMed Central

    Ping, Z A; Butterfiel, D A

    1991-01-01

    A spin-labeled p-chloromercuribenzoate (SL-PMB) and a fluorescence probe, 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan), both of which bind to the single SH group located in the active site of papain, were used to investigate the interaction of papain (EC 3.4.22.2) with two protein denaturants. It was found that the active site of papain was highly stable in urea solution, but underwent a large conformational change in guanidine hydrochloride solution. Electron paramagnetic resonance and fluorescence results were in agreement and both paralleled enzymatic activity of papain with respect to both the variation in pH and denaturation. These results strongly suggest that SL-PMB and Acrylodan labels can be used to characterize the physical state of the active site of the enzyme. PMID:1657229

  18. In situ microbial metabolism of aromatic-hydrocarbon environmental pollutants.

    PubMed

    Jeon, Che Ok; Madsen, Eugene L

    2013-06-01

    Microbial processes that eliminate organic environmental contamination are important. Progress in the biotechnology of biodegradation relies upon the underlying sciences of environmental microbiology and analytical geochemistry. Recent key discoveries advancing knowledge of biodegradation (in general) and the aromatic-hydrocarbon biodegradation (in particular) have relied upon characterization of microorganisms: pure-culture isolates, laboratory enrichment cultures, and in contaminated field sites. New analytical and molecular tools (ranging from sequencing the DNA of biodegrading microorganisms to assessing changes in the isotopic ratios of 13C to 12C and 2H to 1H in contaminant pools in field sites) have deepened our insights into the mechanisms (how), the occurrence (what), and the identity (who) of active players that effect biodegradation of organic environmental pollutants.

  19. 1,N6-etheno-AMP and 1,N6-etheno-2'-deoxy-AMP as probes of the activator site of glycogen phosphorylase from rabbit skeletal muscle.

    PubMed Central

    Vandenbunder, B; Morange, M; Buc, H

    1976-01-01

    Both 1,N6-etheno-AMP and 1,N6-etheno-2'-deoxy-AMP bind at the AMP site of phosphorylase b (1,4-alpha-D-glucan:orthophosphate alpha-glucosyltransferase, EC 2.4.1.1). Etheno-AMP induces the same activation as AMP, about 30-fold higher than the activation induced by etheno-dAMP. The fluorescence of etheno-AMP and etheno-dAMP is associated with the base moiety; therefore, when free in solution, the two derivatives have identical fluorescence properties. However, when bound to phosphorylase, the fluorescence of etheno-AMP is quenched more efficiently than the fluorescence of etheno-dAMP. This difference between the fluorescence properties of the bound nucleotides suggests that a modification in the ribose ring affects the position of the adenine in the AMP site of phosphorylase b. The observed quenching may be due to a stacking interaction between an aromatic residue and the base moiety of the bound nucleotide. PMID:1066682

  20. Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site

    PubMed Central

    Ma, Yi; Zhang, Beilei; Wang, Meng; Ou, Yanghui

    2016-01-01

    The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) with 5′-3′ DNA polymerase activity while in absence of 5′-3′ exonuclease activity possesses high thermal stability and polymerase activity. Bst DNA polymerase was employed in isothermal multiple self-matching initiated amplification (IMSA) which amplified the interest sequence with high selectivity and was widely applied in the rapid detection of human epidemic diseases. However, the detailed information of commercial Bst DNA polymerase is unpublished and well protected by patents, which makes the high price of commercial kits. In this study, wild-type Bst DNA polymerase (WT) and substitution mutations for improving the efficiency of DNA polymerization were expressed and purified in E. coli. Site-directed substitutions of four conserved residues (Gly310, Arg412, Lys416, and Asp540) in the activity site of Bst DNA polymerase influenced efficiency of polymerizing dNTPs. The substitution of residue Gly310 by alanine or leucine and residue Asp540 by glutamic acid increased the efficiency of polymerase activity. All mutants with higher polymerizing efficiency were employed to complete the rapid detection of EV71-associated hand, foot, and mouth disease (HFMD) by IMSA approach with relatively shorter period which is suitable for the primary diagnostics setting in rural and underdeveloped areas. PMID:27981047

  1. The Crystal Structure of a Cardiovirus RNA-Dependent RNA Polymerase Reveals an Unusual Conformation of the Polymerase Active Site

    PubMed Central

    Vives-Adrian, Laia; Lujan, Celia; Oliva, Baldo; van der Linden, Lonneke; Selisko, Barbara; Coutard, Bruno; Canard, Bruno; van Kuppeveld, Frank J. M.

    2014-01-01

    ABSTRACT Encephalomyocarditis virus (EMCV) is a member of the Cardiovirus genus within the large Picornaviridae family, which includes a number of important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for viral genome replication. In this study, we report the X-ray structures of two different crystal forms of the EMCV RdRp determined at 2.8- and 2.15-Å resolution. The in vitro elongation and VPg uridylylation activities of the purified enzyme have also been demonstrated. Although the overall structure of EMCV 3Dpol is shown to be similar to that of the known RdRps of other members of the Picornaviridae family, structural comparisons show a large reorganization of the active-site cavity in one of the crystal forms. The rearrangement affects mainly motif A, where the conserved residue Asp240, involved in ribonucleoside triphosphate (rNTP) selection, and its neighbor residue, Phe239, move about 10 Å from their expected positions within the ribose binding pocket toward the entrance of the rNTP tunnel. This altered conformation of motif A is stabilized by a cation-π interaction established between the aromatic ring of Phe239 and the side chain of Lys56 within the finger domain. Other contacts, involving Phe239 and different residues of motif F, are also observed. The movement of motif A is connected with important conformational changes in the finger region flanked by residues 54 to 63, harboring Lys56, and in the polymerase N terminus. The structures determined in this work provide essential information for studies on the cardiovirus RNA replication process and may have important implications for the development of new antivirals targeting the altered conformation of motif A. IMPORTANCE The Picornaviridae family is one of the largest virus families known, including many important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for picornavirus genome replication and a validated

  2. Aryl hydrocarbon receptor mediated activities in road dust from a metropolitan area, Hanoi-Vietnam: contribution of polycyclic aromatic hydrocarbons (PAHs) and human risk assessment.

    PubMed

    Tuyen, Le Huu; Tue, Nguyen Minh; Suzuki, Go; Misaki, Kentaro; Viet, Pham Hung; Takahashi, Shin; Tanabe, Shinsuke

    2014-09-01

    Dioxin-Responsive Chemical-Activated LUciferase gene eXpression assay (DR-CALUX) was applied to assess the total toxic activity of the mixture of PAHs and related compounds as well as dioxin-related compounds in road dust from urban areas of Hanoi, Vietnam. Road dust from Hanoi contained significantly higher DR-CALUX activities (3 to 39, mean 20 ng CALUX-TEQ/g dw) than those from a rural site (2 to 13, mean 5 ng CALUX-TEQ/g dw). The total concentrations of 24 major PAHs (Σ24PAHs) in urban road dust (0.1 to 5.5, mean 2.5 μg/g dw) were also 6 times higher than those in rural road dust (0.08 to 1.5, mean 0.4 μg/g dw). Diagnostic ratios of PAHs indicated vehicular engine combustion as the major PAH emission source in both sites. PAHs accounted for 0.8 to 60% (mean 10%) and 2 to 76% (mean 20%) of the measured CALUX-TEQs in road dust for Hanoi the rural site, respectively. Benzo[b]-/benzo[k]fluoranthenes were the major TEQ contributors among PAHs, whereas DRCs contributed <0.1% to CALUX-TEQs for both rural and urban sites. These results suggest TEQ contribution of other aryl hydrocarbon receptor agonists in road dust. Significant PAH concentrations in urban dust indicated high mutagenic and carcinogenic potencies. Estimated results of incremental life time cancer risk (ILCR) indicated that Vietnamese populations, especially those in urban areas such as Hanoi, are potentially exposed to high cancer risk via both dust ingestion and dermal contact. This is the first study on the exposure risk of AhR agonists, including PAHs and DRCs, in urban road dust from a developing country using a combined bio-chemical analytical approach.

  3. Superconductivity in aromatic hydrocarbons

    NASA Astrophysics Data System (ADS)

    Kubozono, Yoshihiro; Goto, Hidenori; Jabuchi, Taihei; Yokoya, Takayoshi; Kambe, Takashi; Sakai, Yusuke; Izumi, Masanari; Zheng, Lu; Hamao, Shino; Nguyen, Huyen L. T.; Sakata, Masafumi; Kagayama, Tomoko; Shimizu, Katsuya

    2015-07-01

    'Aromatic hydrocarbon' implies an organic molecule that satisfies the (4n + 2) π-electron rule and consists of benzene rings. Doping solid aromatic hydrocarbons with metals provides the superconductivity. The first discovery of such superconductivity was made for K-doped picene (Kxpicene, five benzene rings). Its superconducting transition temperatures (Tc's) were 7 and 18 K. Recently, we found a new superconducting Kxpicene phase with a Tc as high as 14 K, so we now know that Kxpicene possesses multiple superconducting phases. Besides Kxpicene, we discovered new superconductors such as Rbxpicene and Caxpicene. A most serious problem is that the shielding fraction is ⩽15% for Kxpicene and Rbxpicene, and it is often ∼1% for other superconductors. Such low shielding fractions have made it difficult to determine the crystal structures of superconducting phases. Nevertheless, many research groups have expended a great deal of effort to make high quality hydrocarbon superconductors in the five years since the discovery of hydrocarbon superconductivity. At the present stage, superconductivity is observed in certain metal-doped aromatic hydrocarbons (picene, phenanthrene and dibenzopentacene), but the shielding fraction remains stubbornly low. The highest priority research area is to prepare aromatic superconductors with a high superconducting volume-fraction. Despite these difficulties, aromatic superconductivity is still a core research target and presents interesting and potentially breakthrough challenges, such as the positive pressure dependence of Tc that is clearly observed in some phases of aromatic hydrocarbon superconductors, suggesting behavior not explained by the standard BCS picture of superconductivity. In this article, we describe the present status of this research field, and discuss its future prospects.

  4. Quantitative structure-activity relationships for polycyclic aromatic hydrocarbons: correlation between molecular connectivity, physico-chemical properties, bioconcentration and toxicity in Daphnia pulex

    SciTech Connect

    Govers, H.; Ruepert, C.; Aiking, H.

    1984-01-01

    High correlation coefficients were calculated for the linear one-parameter correlation between molecular weight, molecular connectivity indices, HPLC and TLC retention indices, partition coefficients between n-octanol or sediment and water, and bioconcentration factors or lethal concentrations in Daphnia Pulex of unsubstituted polycyclic aromatic hydrocarbons.

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

    PubMed

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

    2012-05-01

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

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

    PubMed

    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.

  7. Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen

    PubMed Central

    Phillips, John D.; Warby, Christy A.; Whitby, Frank G.; Kushner, James P.; Hill, Christopher P.

    2009-01-01

    Summary Uroporphyrinogen Decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of the four acetate side chains on the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer with the active site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single chain protein (scURO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposible with wild-type activity and have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of scURO-D resulted in approximately half of wild-type activity. The distribution of reaction intermediates was the same for mutant and wild-type sequences, and was unaltered in a competition experiment using the I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function, and suggest that the dimeric structure of URO-D is required to achieve conformational stability and create a large active site cleft. PMID:19362562

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

    SciTech Connect

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

    2009-01-01

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

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

    SciTech Connect

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

    2009-11-10

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

  10. Transcriptional activation by LR1 at the Eµ enhancer and switch region sites

    PubMed Central

    Hanakahi, L. A.; Maizels, Nancy

    2000-01-01

    LR1 is a B cell-specific, sequence-specific duplex DNA binding activity which is induced in B cells carrying out class switch recombination. Here we identify several properties of LR1 which enable it to function in transcriptional regulation. We show that LR1 contributes to transcriptional activation by the Eµ immunoglobulin heavy chain intron enhancer by binding to a site within the enhancer core. We further show that LR1 bends DNA upon binding. In addition, we show that LR1 is itself a bona fide transcriptional activator, as multimerized LR1 sites produce an element which can enhance transcription from a minimal promoter. In order for class switch recombination to occur, an activating signal must be transmitted via the Eµ core, and both S regions targeted for recombination must be actively transcribed. The properties of LR1 that we have identified suggest distinct potential functions of LR1 duplex DNA binding activity in class switch recombination. First, LR1 may contribute to recombinational activation by the Eµ core. Second, there are multiple potential LR1 duplex binding sites in each of the G-rich switch regions, and LR1 bound at contiguous sites may enhance recombination by stimulating transcription of the S regions. PMID:10908319

  11. Regulation of Dpp activity by tissue-specific cleavage of an upstream site within the prodomain

    PubMed Central

    Sopory, Shailaja; Kwon, Sunjong; Wehrli, Marcel; Christian, Jan L.

    2010-01-01

    BMP4 is synthesized as an inactive precursor that is cleaved at two sites during maturation: initially at a site (S1) adjacent to the ligand domain, and then at an upstream site (S2) within the prodomain. Cleavage at the second site regulates the stability of mature BMP4 and this in turn influences its signaling intensity and range of action. The Drosophila ortholog of BMP4, Dpp, functions as a long- or short-range signaling molecule in the wing disc or embryonic midgut, respectively but mechanisms that differentially regulate its bioactivity in these tissues have not been explored. In the current studies we demonstrate, by dpp mutant rescue, that cleavage at the S2 site of proDpp is required for development of the wing and leg imaginal discs, whereas cleavage at the S1 site is sufficient to rescue Dpp function in the midgut. Both the S1 and S2 site of proDpp are cleaved in the wing disc, and S2-cleavage is essential to generate sufficient ligand to exceed the threshold for pMAD activation at both short- and long-range in most cells. By contrast, proDpp is cleaved at the S1 site alone in the embryonic mesoderm and this generates sufficient ligand to activate physiological target genes in neighboring cells. These studies provide the first biochemical and genetic evidence that that selective cleavage of the S2 site of proDPP provides a tissue-specific mechanism for regulating Dpp activity, and that differential cleavage can contribute to, but is not an absolute determinant of signaling range. PMID:20659445

  12. Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR).

    PubMed

    Menon, Binuraj R K; Hardman, Samantha J O; Scrutton, Nigel S; Heyes, Derren J

    2016-08-01

    Protochlorophyllide oxidoreductase (POR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), an essential, regulatory step in chlorophyll biosynthesis. The unique requirement of the enzyme for light has provided the opportunity to investigate how light energy can be harnessed to power biological catalysis and enzyme dynamics. Excited state interactions between the Pchlide molecule and the protein are known to drive the subsequent reaction chemistry. However, the structural features of POR and active site residues that are important for photochemistry and catalysis are currently unknown, because there is no crystal structure for POR. Here, we have used static and time-resolved spectroscopic measurements of a number of active site variants to study the role of a number of residues, which are located in the proposed NADPH/Pchlide binding site based on previous homology models, in the reaction mechanism of POR. Our findings, which are interpreted in the context of a new improved structural model, have identified several residues that are predicted to interact with the coenzyme or substrate. Several of the POR variants have a profound effect on the photochemistry, suggesting that multiple residues are important in stabilizing the excited state required for catalysis. Our work offers insight into how the POR active site geometry is finely tuned by multiple active site residues to support enzyme-mediated photochemistry and reduction of Pchlide, both of which are crucial to the existence of life on Earth.

  13. An Electromagnetic Interference Study of Potential Transmitter Sites for the HF Active Auroral Research Program (HAARP)

    DTIC Science & Technology

    1993-07-19

    heating . The measurements described in this report were conducted at a number of candidate HAARP transmitter sites in the vicinity of Fairbanks...employ the High Power Auroral Stimulation (HIPAS) RF heating facility [1], located in the Chena River valley area near Fairbanks. HAARP will be an...Potential Transmitter Sites for the HF Active Auroral Research Program ( HAARP ) JOSEP11 A. GOLDSTEIN EDWARD 1. KENNEDY ADRIAN S. ELEY 4 IMICHlAEL A. RuPAR C

  14. Two novel ternary dicopper(II) μ-guanazole complexes with aromatic amines strongly activated by quantum dots for DNA cleavage.

    PubMed

    Hernández-Gil, Javier; Ferrer, Sacramento; Castiñeiras, Alfonso; Liu-González, Malva; Lloret, Francesc; Ribes, Angela; Coga, Lucija; Bernecker, Anja; Mareque-Rivas, Juan C

    2014-01-06

    Two novel (μ-guanazole)-bridged binuclear copper(II) complexes with 1,10-phenanthroline (phen) or 2,2'-bipyridine (bipy), [Cu2(μ-N2,N4-Hdatrz)(phen)2(H2O)(NO3)4] (1) and [Cu2(μ-N1,N2-datrz)2(μ-OH2)(bipy)2](ClO4)2 (2) (Hdatrz = 3,5-diamino-1,2,4-triazole = guanazole), have been prepared and characterized by X-ray diffraction, spectroscopy, and susceptibility measurements. Compounds 1 and 2 differ in the aromatic amine, which acts as a coligand, and in the Cu···Cu'-bridging system. Compound 1, which contains two mono-bridged copper ions, represents the first example of a discrete Cu-(NCN-trz)-Cu' complex. Compound 2, with two triply bridged copper ions, is one of the few compounds featuring a Cu-[(NN-trz)2 + (O-aquo)]-Cu' unit. Both compounds display antiferromagnetic coupling but of different magnitude: J (μ2,4-triazole) = -52 cm(-1) for 1 and J (μ1,2-triazolate) = -115 cm(-1) for 2. The DNA binding and cleavage properties of the two compounds have been investigated. Fluorescence, viscosimetry, and thermal denaturation studies reveal that both complexes have high affinity for DNA (1 > 2) and that only 1 acts as an intercalator. In the presence of a reducing agent like 3-mercaptopropionic acid, 1 produces significant oxidative DNA cleavage, whereas 2 is inactive. However, in the presence of very small quantities of micelles filled with core-shell CdSe-ZnS quantum dots (15 nM), 1 and 2 are considerably more active and become highly efficient nucleases as a result of the different possible mechanisms for promoting cooperative catalysis (metal-metal, metal-hydrogen bonding, metal-intercalation, and metal-nanoparticle). Electrophoresis DNA-cleavage inhibition experiments, X-ray photoelectron spectroscopy studies, and fluorescence ethidium bromide displacement assays reveal that in these novel nucleases the QDs act as redox-active protein-like nanoparticle structures that bind to the DNA and deliver electrons to the copper(II) centers for the generation of Cu

  15. Poly(1,3,4-oxadiazoles) via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Wolf, Peter (Inventor)

    1992-01-01

    Poly(1,3,4-oxadiazoles) (POX) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) 1,3,4-oxadiazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as sulfolane or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) 1,3,4-oxadiazole monomers are synthesized by reacting 4-hydroxybenzoic hydrazide with phenyl 4-hydrobenzoate in the melt and also by reacting aromatic dihydrazides with two moles of phenyl 4-hydroxybenzoate in the melt. This synthetic route has provided high molecular weight POX of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the large variety of activated aromatic dihalides which are available.

  16. Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues.

    PubMed

    Kuhn, Isabelle; Kellenberger, Esther; Cakir-Kiefer, Céline; Muller-Steffner, Hélène; Schuber, Francis

    2014-07-01

    Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.

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

    PubMed

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

    2016-09-01

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

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

    SciTech Connect

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

    2015-03-27

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

  19. Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.

    PubMed

    Wang, Beibei; Sexton, Rachel E; Feig, Michael

    2017-04-01

    During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.

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

    PubMed Central

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

    2016-01-01

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

  1. Gamma exposure rates due to neutron activation of soil: site of Hood detonation, Operation Plumbbob

    SciTech Connect

    Auxier, J.A.; Ohnesorge, W.F.

    1980-06-01

    This paper is the result of some recent discussions of exposure rates within the first few hours of the Hood detonation of the Plumbbob series due to neutron activation of soil. We estimated the exposure rates from 1/2 to 3 h after the detonation from ground zero to 1000 yards from ground zero. The area was assumed to be uncontaminated by fallout. Soil samples from the area of the Nevada Test Site at which the Hood device was detonated were sent to ORNL by Dr. John Malik of Los Alamos and by Mr. Gordon Jacks of the Nevada Test Site. These samples were irradiated at the DOSAR facility and the resulting activity analyzed. Calculations of exposure rates were then made based on the analyzed activity and the measured thermal neutron fluences at DOSAR and at the Hood Site.

  2. Systematic mutagenesis of the active site omega loop of TEM-1 beta-lactamase.

    PubMed Central

    Petrosino, J F; Palzkill, T

    1996-01-01

    Beta-Lactamase is a bacterial protein that provides resistance against beta-lactam antibiotics. TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Normally, this enzyme has high levels of hydrolytic activity for penicillins, but mutant beta-lactamases have evolved with activity toward a variety of beta-lactam antibiotics. It has been shown that active site substitutions are responsible for changes in the substrate specificity. Since mutant beta-lactamases pose a serious threat to antimicrobial therapy, the mechanisms by which mutations can alter the substrate specificity of TEM-1 beta-lactamase are of interest. Previously, screens of random libraries encompassing 31 of 55 active site amino acid positions enabled the identification of the residues responsible for maintaining the substrate specificity of TEM-1 beta-lactamase. In addition to substitutions found in clinical isolates, many other specificity-altering mutations were also identified. Interestingly, many nonspecific substitutions in the N-terminal half of the active site omega loop were found to increase ceftazidime hydrolytic activity and decrease ampicillin hydrolytic activity. To complete the active sight study, eight additional random libraries were constructed and screened for specificity-altering mutations. All additional substitutions found to alter the substrate specificity were located in the C-terminal half of the active site loop. These mutants, much like the N-terminal omega loop mutants, appear to be less stable than the wild-type enzyme. Further analysis of a 165-YYG-167 triple mutant, selected for high levels of ceftazidime hydrolytic activity, provides an example of the correlation which exists between enzyme instability and increased ceftazidime hydrolytic activity in the ceftazidime-selected omega loop mutants. PMID:8606154

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

    PubMed

    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.

  4. A mutational analysis of the active site of human type II inosine 5'-monophosphate dehydrogenase.

    PubMed

    Futer, Olga; Sintchak, Michael D; Caron, Paul R; Nimmesgern, Elmar; DeCenzo, Maureen T; Livingston, David J; Raybuck, Scott A

    2002-01-31

    The oxidation of IMP to XMP is the rate-limiting step in the de novo synthesis of guanine ribonucleotides. This NAD-dependent reaction is catalyzed by the enzyme inosine monophosphate dehydrogenase (IMPDH). Based upon the recent structural determination of IMPDH complexed to oxidized IMP (XMP*) and the potent uncompetitive inhibitor mycophenolic acid (MPA), we have selected active site residues and prepared mutants of human type II IMPDH. The catalytic parameters of these mutants were determined. Mutations G326A, D364A, and the active site nucleophile C331A all abolish enzyme