Sample records for catalytic domain directed

  1. Altered sugar donor specificity and catalytic activity of pteridine glycosyltransferases by domain swapping or site-directed mutagenesis

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    Hye-Lim Kim


    Full Text Available CY-007 and CY-049 pteridine glycosyltransferases (PGTs thatdiffer in sugar donor specificity to catalyze either glucose orxylose transfer to tetrahydrobiopterin were studied here touncover the structural determinants necessary for the specificity.The importance of the C-terminal domain and its residues 218and 258 that are different between the two PGTs was assessed viastructure-guided domain swapping or single and dual amino acidsubstitutions. Catalytic activity and selectivity were altered in allthe mutants (2 chimeric and 6 substitution to accept bothUDP-glucose and UDP-xylose. In addition, the wild typeactivities were improved 1.6-4.2 fold in 4 substitution mutantsand activity was observed towards another substrate UDP-Nacetylglucosaminein all the substitution mutants from CY-007PGT. The results strongly support essential role of the C-terminaldomain and the two residues for catalysis as well as sugar donorspecificity, bringing insight into the structural features of thePGTs. [BMB Reports 2013; 46(1: 37-40

  2. Direct binding of syndecan-4 cytoplasmic domain to the catalytic domain of protein kinase C alpha (PKC alpha) increases focal adhesion localization of PKC alpha

    DEFF Research Database (Denmark)

    Lim, Ssang-Taek; Longley, Robert L; Couchman, John R; Woods, Anne


    Syndecan-4 is a transmembrane heparan sulfate proteoglycan that acts as a coreceptor with integrins in focal adhesion formation. The central region of syndecan-4 cytoplasmic domain (4V; LGKKPIYKK) binds phosphatidylinositol 4,5-bisphosphate, and together they regulate protein kinase C alpha (PKC......, overexpression of syndecan-4 in rat embryo fibroblast cells, but not expression of the YF mutant, increased PKC alpha localization to focal adhesions. The data support a mechanism where syndecan-4 binds PKC alpha and localizes it to focal adhesions, whose assembly may be regulated by the kinase....

  3. Fluorescent fusion proteins of soluble guanylyl cyclase indicate proximity of the heme nitric oxide domain and catalytic domain.

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    Tobias Haase

    Full Text Available BACKGROUND: To examine the structural organisation of heterodimeric soluble guanylyl cyclase (sGC Förster resonance energy transfer (FRET was measured between fluorescent proteins fused to the amino- and carboxy-terminal ends of the sGC beta1 and alpha subunits. METHODOLOGY/PRINCIPAL FINDINGS: Cyan fluorescent protein (CFP was used as FRET donor and yellow fluorescent protein (YFP as FRET acceptor. After generation of recombinant baculovirus, fluorescent-tagged sGC subunits were co-expressed in Sf9 cells. Fluorescent variants of sGC were analyzed in vitro in cytosolic fractions by sensitized emission FRET. Co-expression of the amino-terminally tagged alpha subunits with the carboxy-terminally tagged beta1 subunit resulted in an enzyme complex that showed a FRET efficiency of 10% similar to fluorescent proteins separated by a helix of only 48 amino acids. Because these findings indicated that the amino-terminus of the alpha subunits is close to the carboxy-terminus of the beta1 subunit we constructed fusion proteins where both subunits are connected by a fluorescent protein. The resulting constructs were not only fluorescent, they also showed preserved enzyme activity and regulation by NO. CONCLUSIONS/SIGNIFICANCE: Based on the ability of an amino-terminal fragment of the beta1 subunit to inhibit activity of an heterodimer consisting only of the catalytic domains (alphacatbetacat, Winger and Marletta (Biochemistry 2005, 44:4083-90 have proposed a direct interaction of the amino-terminal region of beta1 with the catalytic domains. In support of such a concept of "trans" regulation of sGC activity by the H-NOX domains our results indicate that the domains within sGC are organized in a way that allows for direct interaction of the amino-terminal regulatory domains with the carboxy-terminal catalytic region. In addition, we constructed "fluorescent-conjoined" sGC's by fusion of the alpha amino-terminus to the beta1 carboxy-terminus leading to a

  4. [Molecular engineering of cellulase catalytic domain based on glycoside hydrolase family]. (United States)

    Zhang, Xiaomei; Li, Dandan; Wang, Lushan; Zhao, Yue; Chen, Guanjun


    Molecular engineering of cellulases can improve enzymatic activity and efficiency. Recently, the Carbohydrate-Active enZYmes Database (CAZy), including glycoside hydrolase (GH) families, has been established with the development of Omics and structural measurement technologies. Molecular engineering based on GH families can obviously decrease the probing space of target sequences and structures, and increase the odds of experimental success. Besides, the study of cellulase active-site architecture paves the way toward the explanation of catalytic mechanism. This review focuses on the main GH families and the latest progresses in molecular engineering of catalytic domain. Based on the combination of analysis of a large amount of data in the same GH family and their conservative active-site architecture information, rational design will be an important direction for molecular engineering and promote the rapid development of the conversion of biomass. PMID:23894816

  5. Crystal structure of catalytic domain of the initiation factor 2B epsilon subunit

    DEFF Research Database (Denmark)

    Boesen, Thomas; Mohammad, Sarah S.; Pavitt, Graham D.; Andersen, Gregers Rom

    CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF THE INITIATION FACTOR 2B EPSILON SUBUNIT Thomas Boesen1,Sarah S. Mohammad2, Graham Pavitt2, and Gregers R. Andersen1* 1Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Århus C, Denmark 2Department of Biomolecular Science...... of residues important for catalytic function and the location of residues for which mutations in humans give rise the the fatal brain disorder leukoencephalopathy with vanishing white matter....

  6. Time domain computational modeling of viscothermal acoustic propagation in catalytic converter substrates with porous walls (United States)

    Dickey, N. S.; Selamet, A.; Miazgowicz, K. D.; Tallio, K. V.; Parks, S. J.


    Models for viscothermal effects in catalytic converter substrates are developed for time domain computational methods. The models are suitable for use in one-dimensional approaches for the prediction of exhaust system performance (engine tuning characteristics) and radiated sound levels. Starting with the ``low reduced frequency'' equations for viscothermal acoustic propagation in capillary tubes, time domain submodels are developed for the frequency-dependent wall friction, frequency-dependent wall heat transfer, and porous wall effects exhibited by catalytic converter substrates. Results from a time domain computational approach employing these submodels are compared to available analytical solutions for the low reduced frequency equations. The computational results are shown to agree well with the analytical solutions for capillary geometries representative of automotive catalytic converter substrates.

  7. Direct catalytic cross-coupling of organolithium compounds (United States)

    Giannerini, Massimo; Fañanás-Mastral, Martín; Feringa, Ben L.


    Catalytic carbon-carbon bond formation based on cross-coupling reactions plays a central role in the production of natural products, pharmaceuticals, agrochemicals and organic materials. Coupling reactions of a variety of organometallic reagents and organic halides have changed the face of modern synthetic chemistry. However, the high reactivity and poor selectivity of common organolithium reagents have largely prohibited their use as a viable partner in direct catalytic cross-coupling. Here we report that in the presence of a Pd-phosphine catalyst, a wide range of alkyl-, aryl- and heteroaryl-lithium reagents undergo selective cross-coupling with aryl- and alkenyl-bromides. The process proceeds quickly under mild conditions (room temperature) and avoids the notorious lithium halogen exchange and homocoupling. The preparation of key alkyl-, aryl- and heterobiaryl intermediates reported here highlights the potential of these cross-coupling reactions for medicinal chemistry and material science.

  8. Domain function dissection and catalytic properties of Listeria monocytogenes p60 protein with bacteriolytic activity. (United States)

    Yu, Minfeng; Zuo, Jinrong; Gu, Hao; Guo, Minliang; Yin, Yuelan


    The major extracellular protein p60 of Listeria monocytogenes (Lm-p60) is an autolysin that can hydrolyze the peptidoglycan of bacterial cell wall and has been shown to be required for L. monocytogenes virulence. The predicted three-dimensional structure of Lm-p60 showed that Lm-p60 could be split into two independent structural domains at the amino acid residue 270. Conserved motif analysis showed that V30, D207, S395, and H444 are the key amino acid residues of the corresponding motifs. However, not only the actual functions of these two domains but also the catalytic properties of Lm-p60 are unclear. We try to express recombinant Lm-p60 and identify the functions of two domains by residue substitution (V30A, D207A, S395A, and H444A) and peptide truncation. The C-terminal domain was identified as catalytic element and N-terminal domain as substrate recognition and binding element. Either N-terminal domain truncation or C-terminal domain truncation presents corresponding biological activity. The catalytic activity of Lm-p60 with a malfunctioned substrate-binding domain was decreased, while the substrate binding was not affected by a mulfunctioned catalytic domain. With turbidimetric method, we determined the optimal conditions for the bacteriolytic activity of Lm-p60 against Micrococcus lysodeikficus. The assay for the effect of Lm-p60 on the bacteriolytic activity of lysozyme revealed that the combined use of Lm-p60 protein with lysozyme showed a strong synergistic effect on the bacteriolytic activity. PMID:26363556

  9. Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase (United States)

    Swinglel, Mark; Honkanel, Richard; Ciszak, Ewa


    Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

  10. Conserved tryptophan in the core domain of transglutaminase is essential for catalytic activity


    Murthy, S. N. Prasanna; Iismaa, Siiri; Begg, Gillian; Freymann, Douglas M.; Graham, Robert M.; Lorand, Laszlo


    Transglutaminase 2 (TG2) is a distinctive member of the family of Ca2+-dependent enzymes recognized mostly by their abilities to catalyze the posttranslational crosslinking of proteins. TG2 uniquely binds and hydrolyzes GTP; binding GTP inhibits its crosslinking activity but allows it to function in signal transduction (hence the Gh designation). The core domain of TG2 (residues 139–471, rat) comprises the papain-like catalytic triad and the GTP-binding domain (residues 159–173) and contains ...

  11. The non-catalytic domains of Drosophila katanin regulate its abundance and microtubule-disassembly activity.

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    Kyle D Grode

    Full Text Available Microtubule severing is a biochemical reaction that generates an internal break in a microtubule and regulation of microtubule severing is critical for cellular processes such as ciliogenesis, morphogenesis, and meiosis and mitosis. Katanin is a conserved heterodimeric ATPase that severs and disassembles microtubules, but the molecular determinants for regulation of microtubule severing by katanin remain poorly defined. Here we show that the non-catalytic domains of Drosophila katanin regulate its abundance and activity in living cells. Our data indicate that the microtubule-interacting and trafficking (MIT domain and adjacent linker region of the Drosophila katanin catalytic subunit Kat60 cooperate to regulate microtubule severing in two distinct ways. First, the MIT domain and linker region of Kat60 decrease its abundance by enhancing its proteasome-dependent degradation. The Drosophila katanin regulatory subunit Kat80, which is required to stabilize Kat60 in cells, conversely reduces the proteasome-dependent degradation of Kat60. Second, the MIT domain and linker region of Kat60 augment its microtubule-disassembly activity by enhancing its association with microtubules. On the basis of our data, we propose that the non-catalytic domains of Drosophila katanin serve as the principal sites of integration of regulatory inputs, thereby controlling its ability to sever and disassemble microtubules.

  12. Structure of the catalytic domain of Plasmodium falciparum ARF GTPase-activating protein (ARFGAP)

    Energy Technology Data Exchange (ETDEWEB)

    Cook, William J.; Senkovich, Olga; Chattopadhyay, Debasish (UAB)


    The crystal structure of the catalytic domain of the ADP ribosylation factor GTPase-activating protein (ARFGAP) from Plasmodium falciparum has been determined and refined to 2.4 {angstrom} resolution. Multiwavelength anomalous diffraction (MAD) data were collected utilizing the Zn{sup 2+} ion bound at the zinc-finger domain and were used to solve the structure. The overall structure of the domain is similar to those of mammalian ARFGAPs. However, several amino-acid residues in the area where GAP interacts with ARF1 differ in P. falciparum ARFGAP. Moreover, a number of residues that form the dimer interface in the crystal structure are unique in P. falciparum ARFGAP.

  13. Different in vivo functions of the two catalytic domains of angiotensin converting enzyme (ACE)


    Bernstein, Kenneth E.; Shen, Xiao Z.; Gonzalez-Villalobos, Romer A.; Billet, Sandrine; Okwan-Duodu, Derick; Ong, Frank S.; Fuchs, Sebastien


    Angiotensin converting enzyme (ACE) can cleave angiotensin I, bradykinin, neurotensin and many other peptide substrates in vitro. In part, this is due to the structure of ACE, a protein composed of two independent catalytic domains. Until very recently, little was known regarding the specific in vivo role of each ACE domain, and they were commonly regarded as equivalent. This is not true, as shown by mouse models with a genetic inactivation of either the ACE N- or C-domains. In vivo, most ang...

  14. Catalytic properties of ADAM12 and its domain deletion mutants

    DEFF Research Database (Denmark)

    Jacobsen, Jonas; Visse, Robert; Sørensen, Hans Peter; Enghild, Jan J; Brew, Keith; Wewer, Ulla M; Nagase, Hideaki


    affinity (9-44 nM). However, TIMP-1 is a much weaker inhibitor. N-TIMP-3 variants that lack MMP inhibitory activity but retained the ability to inhibit ADAM17/TACE failed to inhibit ADAM12. These results indicate unique enzymatic properties of ADAM12 among the members of the ADAM family of......Human ADAM12 (a disintegrin and metalloproteinase) is a multidomain zinc metalloproteinase expressed at high levels during development and in human tumors. ADAM12 exists as two splice variants: a classical type 1 membrane-anchored form (ADAM12-L) and a secreted splice variant (ADAM12-S) consisting...... active on this substrate. It was also observed that NaCl inhibits ADAM12. Among the tissue inhibitors of metalloproteinases (TIMP) examined, the N-terminal domain of TIMP-3 (N-TIMP-3) inhibits ADAM12-S and ADAM12-PC with low nanomolar Ki(app) values while TIMP-2 inhibits them with a slightly lower...

  15. Biochemical properties and catalytic domain structure of the CcmH protein from Escherichia coli. (United States)

    Zheng, Xue-Ming; Hong, Jing; Li, Hai-Yin; Lin, Dong-Hai; Hu, Hong-Yu


    In the Gram-negative bacterium of Escherichia coli, eight genes organized as a ccm operon (ccmABCDEFGH) are involved in the maturation of c-type cytochromes. The proteins encoded by the last three genes ccmFGH are believed to form a lyase complex functioning in the reduction of apocytochrome c and haem attachment. Among them, CcmH is a membrane-associated protein; its N-terminus is a catalytic domain with the active CXXC motif and the C-terminus is predicted as a TPR-like domain with unknown function. By using SCAM (scanning cysteine accessibility mutagenesis) and Gaussia luciferase fusion assays, we provide experimental evidence for the entire topological structure of E. coli CcmH. The mature CcmH is a periplasm-resident oxidoreductase anchored to the inner membrane by two transmembrane segments. Both N- and C-terminal domains are located and function in the periplasmic compartment. Moreover, the N-terminal domain forms a monomer in solution, while the C-terminal domain is a compact fold with helical structures. The NMR solution structure of the catalytic domain in reduced form exhibits mainly a three-helix bundle, providing further information for the redox mechanism. The redox potential suggests that CcmH exhibits a strong reductase that may function in the last step of reduction of apocytochrome c for haem attachment. PMID:22789558

  16. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase

    International Nuclear Information System (INIS)

    The catalytic domain of human Dus2-like enzyme was purified and crystallized, and data were collected to 1.9 Å resolution. Dihydrouridine synthases catalyse the reduction of uridine to dihydrouridine in the D-loop and variable loop of tRNA. The human dihydrouridine synthase HsDus2L has been implicated in the development of pulmonary carcinogenesis. Here, the purification, crystallization and preliminary X-ray characterization of the HsDus2L catalytic domain are reported. The crystals belonged to space group P21 and contained a single molecule of HsDus2L in the asymmetric unit. A complete data set was collected to 1.9 Å resolution using synchrotron radiation

  17. Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, Alexander I.; Rogals, Monique J.; De, Soumya [Cornell University, Department of Molecular Biology and Genetics (United States); Lu, Kun Ping [Cancer Biology Program and Biology of Aging Program, Beth Israel Deaconess Medical Center, Harvard Medical School (United States); Kovrigin, Evgenii L. [Marquette University, Chemistry Department (United States); Nicholson, Linda K., E-mail: [Cornell University, Department of Molecular Biology and Genetics (United States)


    The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer, k{sub cat}{sup cis} and apparent Michaelis constants, K{sub M}{sup App}. By contrast, NMR lineshape analysis is a powerful tool for determining microscopic rates and populations of each state in a complex binding scheme. The isolated catalytic domain of Pin1 was employed as a first step towards elucidating the reaction scheme of the full-length enzyme. A 24-residue phosphopeptide derived from the amyloid precurser protein intracellular domain (AICD) phosphorylated at Thr668 served as a biologically-relevant Pin1 substrate. Specific {sup 13}C labeling at the Pin1-targeted proline residue provided multiple reporters sensitive to individual isomer binding and on-enzyme catalysis. We have performed titration experiments and employed lineshape analysis of phosphopeptide {sup 13}C-{sup 1}H constant time HSQC spectra to determine k{sub cat}{sup cis}, k{sub cat}{sup trans}, K{sub D}{sup cis}, and K{sub D}{sup trans} for the catalytic domain of Pin1 acting on this AICD substrate. The on-enzyme equilibrium value of [E{center_dot}trans]/[E{center_dot}cis] = 3.9 suggests that the catalytic domain of Pin1 is optimized to operate on this substrate near equilibrium in the cellular context. This highlights the power of lineshape analysis for determining the microscopic parameters of enzyme catalysis, and demonstrates the feasibility of future studies of Pin1-PPIase mutants to gain insights on the catalytic mechanism of this important enzyme.

  18. Crystallization and preliminary crystallographic study of a trypsin-resistant catalytic domain of human calcineurin

    International Nuclear Information System (INIS)

    A trypsin-resistant catalytic domain of human calcineurin α (A subunit, residues 20–347) was crystallized in space group P21212. An X-ray diffraction data set was collected to 2.87 Å resolution and the structure was solved by molecular replacement. Calcineurin, a Ca2+/calmodulin-dependent serine/threonine protein phosphatase, plays a key role in a number of cellular pathways, including T-cell activation, and is an important molecular target of the immunosuppressive drugs cyclosporin A and FK506. To understand the structural basis underlying the activation of calcineurin by calmodulin, X-ray crystallography was employed to solve the three-dimensional structure of the free calcineurin catalytic domain (residues 20–347 of the A subunit). To accomplish this, a bacterially expressed glutathione S-transferase (GST) fusion protein of the human calcineurin catalytic domain was first purified by GST-affinity chromatography. After limited digestion by trypsin, the catalytic domain (Cncat) was purified using anion-exchange and size-exclusion chromatography. Crystallization of Cncat was achieved by the hanging-drop vapour-diffusion method at pH 6.5 using PEG 6000 as precipitant. The diffraction results showed that the Cncat crystal belonged to the orthorhombic space group P21212, with unit-cell parameters a = 161.6, b = 87.4, c = 112.0 Å. There are four Cncat molecules in the asymmetric unit, with 49.5% solvent content. An X-ray diffraction data set was collected to 2.87 Å resolution and a clear molecular-replacement solution was obtained. The active site of Cncat is open to the solvent channels in the crystal packing

  19. Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis

    International Nuclear Information System (INIS)

    The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer, kcatcis and apparent Michaelis constants, KMApp. By contrast, NMR lineshape analysis is a powerful tool for determining microscopic rates and populations of each state in a complex binding scheme. The isolated catalytic domain of Pin1 was employed as a first step towards elucidating the reaction scheme of the full-length enzyme. A 24-residue phosphopeptide derived from the amyloid precurser protein intracellular domain (AICD) phosphorylated at Thr668 served as a biologically-relevant Pin1 substrate. Specific 13C labeling at the Pin1-targeted proline residue provided multiple reporters sensitive to individual isomer binding and on-enzyme catalysis. We have performed titration experiments and employed lineshape analysis of phosphopeptide 13C–1H constant time HSQC spectra to determine kcatcis, kcattrans, KDcis, and KDtrans for the catalytic domain of Pin1 acting on this AICD substrate. The on-enzyme equilibrium value of [E·trans]/[E·cis] = 3.9 suggests that the catalytic domain of Pin1 is optimized to operate on this substrate near equilibrium in the cellular context. This highlights the power of lineshape analysis for determining the microscopic parameters of enzyme catalysis, and demonstrates the feasibility of future studies of Pin1-PPIase mutants to gain insights on the catalytic mechanism of this important enzyme.

  20. X-ray Structure of Gelatinase A Catalytic Domain Complexed with a Hydroxamate Inhibitor


    Dhanaraj, Venugopal; Williams, Mark G.; Ye, Qi-Zhuang; Molina, Franck; Linda L. Johnson; Ortwine, Daniel F.; Pavlovsky, Alexander; Rubin, J. Ron; Skeean, Richard W.; White, Andy D.; Humblet, Christine; Hupe, Donald J.; Tom L Blundell


    Gelatinase A is a key enzyme in the family of matrix metalloproteinases (matrixins) that are involved in the degradation of the extracellular matrix. As this process is an integral part of tumour cell metastasis and angiogenesis, gelatinase is an important target for therapeutic intervention. The X-ray crystal structure of the gelatinase A catalytic domain (GaCD) complexed with batimastat (BB94), a hydroxamate inhibitor, shows an active site with a large S1' specificity pocket. The structure ...

  1. Comparison of Properties of Tumor Necrosis Factor-α Converting Enzyme (TACE) and Some Matrix Metalloproteases (MMPs) in Catalytic Domains

    Institute of Scientific and Technical Information of China (English)


    The crystal structural data of TACE, MMP-1, MMP-2, MMP-3 and MMP-9 were obtained from PDB database, and then their catalytic domains' properties including conformation, molecular surface hydrophobicity and electrostatic potential were analyzed and compared by using Insight Ⅱ molecular modeling software. It was found that the conformation and molecular surface hydrophobicity of catalytic domains of TACE and MMPs were not obviously different, but the molecular surface electrostatic potential of catalytic domain of TACE and MMPs had obvious differences.The findings are helpful in the Rational Drug Design of TACE selective inhibitor.

  2. Expression and purification of correctly processed, active human TACE catalytic domain in Saccharomyces cerevisiae. (United States)

    Clarke, H R; Wolfson, M F; Rauch, C T; Castner, B J; Huang, C P; Gerhart, M J; Johnson, R S; Cerretti, D P; Paxton, R J; Price, V L; Black, R A


    Human tumor necrosis factor-alpha (TNF alpha) converting enzyme (TACE) releases soluble TNF alpha from cells. It is a member of the adamalysin family of metalloproteases. A truncated form of TACE cDNA was expressed in Saccharomyces cerevisiae and purified to homogeneity in order to study TACE structure and function. Recombinant TACE was expressed as a preproprotein including the pro- and catalytic (PROCAT) domains fused to the yeast alpha-factor leader. A C-terminal immunoreactive FLAG peptide was added for Western blot detection and anti-FLAG antibody column purification. We constructed two glycosylation mutant PROCAT TACE isoforms to facilitate purification. A PROCAT isoform, mutated to eliminate two N-linked glycosylation sites, was buffer exchanged and purified to homogeneity by ion exchange chromatography and an anti-FLAG antibody affinity step. N-terminal sequence analysis showed that the mutant preproprotein was processed in yeast at the furin protease cleavage site and yielded an active catalytic domain which has TNF alpha peptide-specific protease activity. Mass spectrometry of the purified catalytic domain showed that removal of both N-linked sites results in a homogeneous sized polypeptide lacking further posttranslational modifications. PMID:9631522

  3. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry (United States)

    Yu, Deyang; Peng, Ying; Ayaz-Guner, Serife; Gregorich, Zachery R.; Ge, Ying


    AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that is essential in regulating energy metabolism in all eukaryotic cells. It is a heterotrimeric protein complex composed of a catalytic subunit (α) and two regulatory subunits (β and γ). C-terminal truncation of AMPKα at residue 312 yielded a protein that is active upon phosphorylation of Thr172 in the absence of β and γ subunits, which is refered to as the AMPK catalytic domain and commonly used to substitute for the AMPK heterotrimeric complex in in vitro kinase assays. However, a comprehensive characterization of the AMPK catalytic domain is lacking. Herein, we expressed a His-tagged human AMPK catalytic domin (denoted as AMPKΔ) in E. coli, comprehensively characterized AMPKΔ in its basal state and after in vitro phosphorylation using top-down mass spectrometry (MS), and assessed how phosphorylation of AMPKΔ affects its activity. Unexpectedly, we found that bacterially-expressed AMPKΔ was basally phosphorylated and localized the phosphorylation site to the His-tag. We found that AMPKΔ had noticeable basal activity and was capable of phosphorylating itself and its substrates without activating phosphorylation at Thr172. Moreover, our data suggested that Thr172 is the only site phosphorylated by its upstream kinase, liver kinase B1, and that this phosphorylation dramatically increases the kinase activity of AMPKΔ. Importantly, we demonstrated that top-down MS in conjunction with in vitro phosphorylation assay is a powerful approach for monitoring phosphorylation reaction and determining sequential order of phosphorylation events in kinase-substrate systems.

  4. The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase

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    Marletta Michael A


    Full Text Available Abstract Background Soluble guanylate cyclases generate cyclic GMP when bound to nitric oxide, thereby linking nitric oxide levels to the control of processes such as vascular homeostasis and neurotransmission. The guanylate cyclase catalytic module, for which no structure has been determined at present, is a class III nucleotide cyclase domain that is also found in mammalian membrane-bound guanylate and adenylate cyclases. Results We have determined the crystal structure of the catalytic domain of a soluble guanylate cyclase from the green algae Chlamydomonas reinhardtii at 2.55 Å resolution, and show that it is a dimeric molecule. Conclusion Comparison of the structure of the guanylate cyclase domain with the known structures of adenylate cyclases confirms the close similarity in architecture between these two enzymes, as expected from their sequence similarity. The comparison also suggests that the crystallized guanylate cyclase is in an inactive conformation, and the structure provides indications as to how activation might occur. We demonstrate that the two active sites in the dimer exhibit positive cooperativity, with a Hill coefficient of ~1.5. Positive cooperativity has also been observed in the homodimeric mammalian membrane-bound guanylate cyclases. The structure described here provides a reliable model for functional analysis of mammalian guanylate cyclases, which are closely related in sequence.

  5. Direct time-domain techniques for transient radiation and scattering

    International Nuclear Information System (INIS)

    A tutorial introduction to transient electromagnetics, focusing on direct time-domain techniques, is presented. Physical, mathematical, numerical, and experimental aspects of time-domain methods, with emphasis on wire objects excited as antennas or scatters are examined. Numerous computed examples illustrate the characteristics of direct time-domain procedures, especially where they may offer advantages over procedures in the more familiar frequency domain. These advantages include greater solution efficiency for many types of problems, the ability to handle nonlinearities, improved physical insight and interpretability, availability of wide-band information from a single calculation, and the possibility of isolating interactions among various parts of an object using time-range gating

  6. Expression, purification and enzymatic characterization of the catalytic domains of human tryptophan hydroxylase isoforms

    DEFF Research Database (Denmark)

    Windahl, Michael Skovbo; Boesen, Jane; Karlsen, Pernille Efferbach; Christensen, Hans Erik Mølager

    Tryptophan hydroxylase exists in two isoforms: Isoform 1 catalyses the first and rate-limiting step in the synthesis of serotonin in the peripheral parts of the body while isoform 2 catalyses this step in the brain. The catalytic domains of human tryptophan hydroxylase 1 and 2 have been expressed......, purified and the kinetic properties have been studied and are compared. Substrate inhibition by tryptophan is observed for isoform 1 but not for isoform 2. Large differences are observed in the K m,tetrahydrobiopterin values for the two isoforms, being >10 times larger for isoform 1 compared to isoform 2....

  7. Optimized bacterial expression and purification of the c-Src catalytic domain for solution NMR studies

    International Nuclear Information System (INIS)

    Progression of a host of human cancers is associated with elevated levels of expression and catalytic activity of the Src family of tyrosine kinases (SFKs), making them key therapeutic targets. Even with the availability of multiple crystal structures of active and inactive forms of the SFK catalytic domain (CD), a complete understanding of its catalytic regulation is unavailable. Also unavailable are atomic or near-atomic resolution information about their interactions, often weak or transient, with regulating phosphatases and downstream targets. Solution NMR, the biophysical method best suited to tackle this problem, was previously hindered by difficulties in bacterial expression and purification of sufficient quantities of soluble, properly folded protein for economically viable labeling with NMR-active isotopes. Through a choice of optimal constructs, co-expression with chaperones and optimization of the purification protocol, we have achieved the ability to bacterially produce large quantities of the isotopically-labeled CD of c-Src, the prototypical SFK, and of its activating Tyr-phosphorylated form. All constructs produce excellent spectra allowing solution NMR studies of this family in an efficient manner

  8. Identification of residues in the heme domain of soluble guanylyl cyclase that are important for basal and stimulated catalytic activity.

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    Padmamalini Baskaran

    Full Text Available Nitric oxide signals through activation of soluble guanylyl cyclase (sGC, a heme-containing heterodimer. NO binds to the heme domain located in the N-terminal part of the β subunit of sGC resulting in increased production of cGMP in the catalytic domain located at the C-terminal part of sGC. Little is known about the mechanism by which the NO signaling is propagated from the receptor domain (heme domain to the effector domain (catalytic domain, in particular events subsequent to the breakage of the bond between the heme iron and Histidine 105 (H105 of the β subunit. Our modeling of the heme-binding domain as well as previous homologous heme domain structures in different states point to two regions that could be critical for propagation of the NO activation signal. Structure-based mutational analysis of these regions revealed that residues T110 and R116 in the αF helix-β1 strand, and residues I41 and R40 in the αB-αC loop mediate propagation of activation between the heme domain and the catalytic domain. Biochemical analysis of these heme mutants allows refinement of the map of the residues that are critical for heme stability and propagation of the NO/YC-1 activation signal in sGC.

  9. Assay and Inhibition of the Purified Catalytic Domain of Diacylglycerol Lipase Beta. (United States)

    Singh, Praveen K; Markwick, Rachel; Lu, Leanne; Howell, Fiona V; Williams, Gareth; Doherty, Patrick


    The diacylglycerol lipases (DAGLα and DAGLβ) hydrolyze DAG to generate 2-arachidonoylglycerol (2-AG), the principal endocannabinoid and main precursor of arachidonic acid (AA). The DAGLs make distinct tissue specific contributions toward 2-AG and AA levels, and therefore, selective modulators for these enzymes could play crucial roles toward harnessing their therapeutic potential. Relatively high-throughput assays have recently been reported for DAGLα and have proven useful toward the characterization of inhibitors of this enzyme. Similar assays are also warranted for DAGLβ which was the aim of this study. We first adapted previously reported DAGLα membrane assays (using PNPB and DiFMUO as substrates) to measure recombinant DAGLβ activity in membranes. In contrast to results with DAGLα, both substrates provided a relatively limited signal window for measuring DAGLβ activity, however, an improved window was obtained when employing a third commercially available substrate, EnzChek. In order to further improve on the assay parameters, we successfully purified the glutathione S-transferase (GST) tagged catalytic domain of DAGLβ. Activity of the enzyme was confirmed using EnzChek as well as two DAGL inhibitors (THL and OMDM-188). The purified DAGLβ catalytic domain assay described here provides the basis for a relatively clean and convenient assay with the potential to be adapted for high-throughput drug discovery efforts. PMID:27115711

  10. Structure of the third catalytic domain of the protein disulfide isomerase ERp46

    International Nuclear Information System (INIS)

    The structure of the third catalytic domain of the human protein disulfide isomerase ERp46 has been determined to 2.0 Å resolution. Protein disulfide isomerases are responsible for catalyzing the proper oxidation and isomerization of disulfide bonds of newly synthesized proteins in the endoplasmic reticulum. Here, the crystal structure of the third catalytic domain of protein disulfide isomerase ERp46 (also known as protein disulfide isomerase A5 and TXNDC5) was determined to 2.0 Å resolution. The structure shows a typical thioredoxin-like fold, but also identifies regions of high structural variability. In particular, the loop between helix α2 and strand β3 adopts strikingly different conformations among the five chains of the asymmetric unit. Cys381 and Cys388 form a structural disulfide and its absence in one of the molecules leads to dramatic conformational changes. The tryptophan residue Trp349 of this molecule inserts into the cavity formed by helices α1 and α3 of a neighbouring molecule, potentially mimicking the interactions of ERp46 with misfolded substrates

  11. The Arabidopsis thaliana proteome harbors undiscovered multi-domain molecules with functional guanylyl cyclase catalytic centers

    KAUST Repository

    Wong, Aloysius Tze


    Background: Second messengers link external cues to complex physiological responses. One such messenger, 3\\',5\\'-cyclic guanosine monophosphate (cGMP), has been shown to play a key role in many physiological responses in plants. However, in higher plants, guanylyl cyclases (GCs), enzymes that generate cGMP from guanosine-5\\'-triphosphate (GTP) have remained elusive until recently. GC search motifs constructed from the alignment of known GCs catalytic centers form vertebrates and lower eukaryotes have led to the identification of a number of plant GCs that have been characterized in vitro and in vivo.Presentation of the hypothesis.Recently characterized GCs in Arabidopsis thaliana contributed to the development of search parameters that can identify novel candidate GCs in plants. We hypothesize that there are still a substantial number (> 40) of multi-domain molecules with potentially functional GC catalytic centers in plants that remain to be discovered and characterized. Testing the hypothesis. The hypothesis can be tested, firstly, by computational methods constructing 3D models of selected GC candidates using available crystal structures as templates. Homology modeling must include substrate docking that can provide support for the structural feasibility of the GC catalytic centers in those candidates. Secondly, recombinant peptides containing the GC domain need to be tested in in vitro GC assays such as the enzyme-linked immune-sorbent assay (ELISA) and/or in mass spectrometry based cGMP assays. In addition, quantification of in vivo cGMP transients with fluorescent cGMP-reporter assays in wild-type or selected mutants will help to elucidate the biological role of novel GCs.Implications of the hypothesis.If it turns out that plants do harbor a large number of functional GC domains as part of multi-domain enzymes, then major new insights will be gained into the complex signal transduction pathways that link cGMP to fundamental processes such as ion transport

  12. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. (United States)

    Van Roey, Patrick; Meehan, Lisa; Kowalski, Joseph C; Belfort, Marlene; Derbyshire, Victoria


    I-TevI, a member of the GIY-YIG family of homing endonucleases, consists of an N-terminal catalytic domain and a C-terminal DNA-binding domain joined by a flexible linker. The GIY-YIG motif is in the N-terminal domain of I-TevI, which corresponds to a phylogenetically widespread catalytic cartridge that is often associated with mobile genetic elements. The crystal structure of the catalytic domain of I-TevI, the first of any GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. Similarities in the three-dimensional arrangement of the catalytically important residues and the cation-binding site with those of the His-Cys box endonuclease I-PpoI suggest the possibility of mechanistic relationships among these different families of homing endonucleases despite completely different folds. PMID:12379841

  13. Direct observation of closure domain wall mediated spin waves

    International Nuclear Information System (INIS)

    The generation and guiding of spin waves from and by magnetic domain walls are demonstrated. The spin waves radiate from pinned and oscillating magnetic closure domain walls and propagate linearly along a narrow path formed by the surrounding 180° asymmetric Bloch domain walls. The propagating spin wave modes are directly visualized by time-resolved magneto-optical Kerr microscopy with picosecond temporal resolution. A linear relationship between excitation frequency, wavelength, and number of spin waves per domain exists. Independent of the field excitation frequency, a constant phase velocity of spin waves propagation is obtained. Spin waves characteristics can be tuned by varying the magnetic domain dynamics, allowing for variable spin wave characteristics with magnetic field characteristics and histories

  14. Structure of the catalytic domain of the hepatitis C virus NS2-3 protease

    Energy Technology Data Exchange (ETDEWEB)

    Lorenz,I.; Marcotrigiano, J.; Dentzer, T.; Rice, C.


    Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes two proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at four downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 Angstroms resolution. The structure reveals a dimeric cysteine protease with two composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the two active sites, predicting an inactive post-cleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design.

  15. Conformational selection in the recognition of phosphorylated substrates by the catalytic domain of human Pin1. (United States)

    Velazquez, Hector A; Hamelberg, Donald


    Post-translational phosphorylation and the related conformational changes in signaling proteins are responsible for regulating a wide range of subcellular processes. Human Pin1 is central to many of these cell signaling pathways in normal and aberrant subcellular processes, catalyzing cis-trans isomerization of the peptide ω-bond in phosphorylated serine/threonine-proline motifs in many proteins. Pin1 has therefore been identified as a possible drug target in many diseases, including cancer and Alzheimer's. The effects of phosphorylation on Pin1 substrates, and the atomistic basis for Pin1 recognition and catalysis, are not well understood. Here, we determine the conformational consequences of phosphorylation on Pin1 substrate analogues and the mechanism of recognition by the catalytic domain of Pin1 using all-atom molecular dynamics simulations. We show that phosphorylation induces backbone conformational changes on the peptide substrate analogues. We also show that Pin1 recognizes specific conformations of its substrate by conformational selection. Furthermore, dynamical correlated motions in the free Pin1 enzyme are present in the enzyme of the enzyme-substrate complex when the substrate is in the transition state configuration, suggesting that these motions play significant roles during catalytic turnover. These results provide a detailed atomistic picture of the mechanism of Pin1 recognition that can be exploited for drug design purposes and further our understanding of the synergistic complexities of post-translational phosphorylation and cis-trans isomerization. PMID:21967280

  16. NMR Structure and Dynamics of the Resuscitation Promoting Factor RpfC Catalytic Domain.

    Directory of Open Access Journals (Sweden)

    Vincenzo Maione

    Full Text Available Mycobacterium tuberculosis latent infection is maintained for years with no clinical symptoms and no adverse effects for the host. The mechanism through which dormant M. tuberculosis resuscitates and enters the cell cycle leading to tuberculosis is attracting much interest. The RPF family of proteins has been found to be responsible for bacteria resuscitation and normal proliferation. This family of proteins in M. tuberculosis is composed by five homologues (named RpfA-E and understanding their conformational, structural and functional peculiarities is crucial to the design of therapeutic strategies.Therefore, we report the structural and dynamics characterization of the catalytic domain of RpfC from M. tubercolosis by combining Nuclear Magnetic Resonance, Circular Dichroism and Molecular Dynamics data. We also show how the formation of a disulfide bridge, highly conserved among the homologues, is likely to modulate the shape of the RpfC hydrophobic catalytic cleft. This might result in a protein function regulation via a "conformational editing" through a disulfide bond formation.

  17. Direct formulation of the supersonic acoustic intensity in space domain

    DEFF Research Database (Denmark)

    Fernandez Grande, Efren; Jacobsen, Finn; Leclre, Quentin


    This paper proposes and examines a direct formulation in space domain of the so-called supersonic acoustic intensity. This quantity differs from the usual (active) intensity by excluding the circulating energy in the near-field of the source, providing a map of the acoustic energy that is radiated...... into the far field. To date, its calculation has been formulated in the wave number domain, filtering out the evanescent waves outside the radiation circle and reconstructing the acoustic field with only the propagating waves. In this study, the supersonic intensity is calculated directly in space...

  18. Crystallization and Preliminary X-ray Diffraction Analysis of the Glucuronoyl Esterase Catalytic Domain from Hypocrea jecorina (United States)

    The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was over-expressed, purified, and crystallized by sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. Crystals had space group P212121 and X-ray diffraction data were...

  19. Catalytic properties of two Rhizopus oryzae 99-880 glucoamylase enzymes without starch binding domains expressed in Pichia pastoris (United States)

    Catalytic properties of the two glucoamylases, AmyC and AmyD, without starch binding domains from Rhizopus oryzae strain 99-880 were heterologously expressed and purified to homogeneity. AmyC and AmyD demonstrate pH optima of 5.5 and 6.0, respectively, nearly 1 unit higher than most fungal glucoamy...

  20. Direct conversion of wood to methane by catalytic hydrothermal gasification

    Energy Technology Data Exchange (ETDEWEB)

    Kohler, C.; Schneebeli, J.; Binkert, P.; Biollaz, S.; Stucki, S


    Green production of substitute natural gas (SNG) from wood by a catalytic hydrothermal process was studied in a laboratory batch reactor suitable for high feed concentrations (10-30 wt%) at 350-460{sup o}C and 27-33 MPa. Raney Nickel was much more active than Ni/a-Al{sub 2}O{sub 3} at the conditions studied. A maximum methane yield of 0.24 g CH{sub 4}/g wood was obtained, corresponding to 67% of the theoretical maximum of 0.36 g CH{sub 4}/g wood. The carbon gasification was limited to 80% in our equipment due to accumulation of phenols and other aromatics in the condenser. At supercritical conditions the remaining liquid phase was always tar-free, colorless and contained less than 1 wt% of the feed carbon. An economic analysis for a 20 MWth SNG plant (calculated thermal process efficiency 85%) located in Switzerland yielded SNG production costs of 10 USD/GJ. Almost half of the SNG cost is made up by the feedstock cost. (author)

  1. Activities of human RRP6 and structure of the human RRP6 catalytic domain

    Energy Technology Data Exchange (ETDEWEB)

    Januszyk, Kurt; Liu, Quansheng; Lima, Christopher D. (SKI)


    The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-to-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known as PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to catalyze 3'-to-5' exoribonuclease activity on a variety of nuclear transcripts including ribosomal RNA subunits, RNA that has been poly-adenylated by TRAMP, as well as other nuclear RNA transcripts destined for processing and/or destruction. To characterize human RRP6, we expressed the full-length enzyme as well as truncation mutants that retain catalytic activity, compared their activities to analogous constructs for Saccharomyces cerevisiae Rrp6, and determined the X-ray structure of a human construct containing the exoribonuclease and HRDC domains that retains catalytic activity. Structural data show that the human active site is more exposed when compared to the yeast structure, and biochemical data suggest that this feature may play a role in the ability of human RRP6 to productively engage and degrade structured RNA substrates more effectively than the analogous budding yeast enzyme.

  2. Crystal Structure of the Catalytic Domain of Drosophila [beta]1,4-Galactosyltransferase-7

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Boopathy; Qasba, Pradman K. (NIH)


    The {beta}1,4-galactosyltransferase-7 ({beta}4Gal-T7) enzyme, one of seven members of the {beta}4Gal-T family, transfers in the presence of manganese Gal from UDP-Gal to an acceptor sugar (xylose) that is attached to a side chain hydroxyl group of Ser/Thr residues of proteoglycan proteins. It exhibits the least protein sequence similarity with the other family members, including the well studied family member {beta}4Gal-T1, which, in the presence of manganese, transfers Gal from UDP-Gal to GlcNAc. We report here the crystal structure of the catalytic domain of {beta}4Gal-T7 from Drosophila in the presence of manganese and UDP at 1.81 {angstrom} resolution. In the crystal structure, a new manganese ion-binding motif (HXH) has been observed. Superposition of the crystal structures of {beta}4Gal-T7 and {beta}4Gal-T1 shows that the catalytic pocket and the substrate-binding sites in these proteins are similar. Compared with GlcNAc, xylose has a hydroxyl group (instead of an N-acetyl group) at C2 and lacks the CH{sub 2}OH group at C5; thus, these protein structures show significant differences in their acceptor-binding site. Modeling of xylose in the acceptor-binding site of the {beta}4Gal-T7 crystal structure shows that the aromatic side chain of Tyr{sup 177} interacts strongly with the C5 atom of xylose, causing steric hindrance to any additional group at C5. Because Drosophila Cd7 has a 73% protein sequence similarity to human Cd7, the present crystal structure offers a structure-based explanation for the mutations in human Cd7 that have been linked to Ehlers-Danlos syndrome.

  3. Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation (United States)

    Lira-Navarrete, Erandi; de Las Rivas, Matilde; Compañón, Ismael; Pallarés, María Carmen; Kong, Yun; Iglesias-Fernández, Javier; Bernardes, Gonçalo J. L.; Peregrina, Jesús M.; Rovira, Carme; Bernadó, Pau; Bruscolini, Pierpaolo; Clausen, Henrik; Lostao, Anabel; Corzana, Francisco; Hurtado-Guerrero, Ramon


    Protein O-glycosylation is controlled by polypeptide GalNAc-transferases (GalNAc-Ts) that uniquely feature both a catalytic and lectin domain. The underlying molecular basis of how the lectin domains of GalNAc-Ts contribute to glycopeptide specificity and catalysis remains unclear. Here we present the first crystal structures of complexes of GalNAc-T2 with glycopeptides that together with enhanced sampling molecular dynamics simulations demonstrate a cooperative mechanism by which the lectin domain enables free acceptor sites binding of glycopeptides into the catalytic domain. Atomic force microscopy and small-angle X-ray scattering experiments further reveal a dynamic conformational landscape of GalNAc-T2 and a prominent role of compact structures that are both required for efficient catalysis. Our model indicates that the activity profile of GalNAc-T2 is dictated by conformational heterogeneity and relies on a flexible linker located between the catalytic and the lectin domains. Our results also shed light on how GalNAc-Ts generate dense decoration of proteins with O-glycans.

  4. Structure of the catalytic domain of the Tannerella forsythia matrix metallopeptidase karilysin in complex with a tetrapeptidic inhibitor

    DEFF Research Database (Denmark)

    Guevara, Tibisay; Ksiazek, Miroslaw; Skottrup, Peter Durand;


    Karilysin is the only metallopeptidase identified as a virulence factor in the odontopathogen Tannerella forsythia owing to its deleterious effect on the host immune response during bacterial infection. The very close structural and sequence-based similarity of its catalytic domain (Kly18...... to the primed side of the active-site cleft in a substrate-like manner. The catalytic zinc ion is clamped by the α-amino group and the carbonyl O atom of the serine, thus distantly mimicking the general manner of binding of hydroxamate inhibitors to metallopeptidases and contributing, together with three zinc...

  5. Cloning and expression of catalytic domain of Abl protein tyrosine kinase gene in E. coli

    Institute of Scientific and Technical Information of China (English)


    Protein tyrosine kinases (PTKs) regulate cell proliferation, differentiation and are involved in signal transduction. Uncontrolled signaling from receptor tyrosine kinases to intracellular tyrosine kinases can lead to inflamma tory responses and diseases such as cancer and atherosclerosis. Thus, inhibitors that block the activity of tyrosine kinases or the signaling pathways of PTKs activation could be assumed as the potential candidate for drug development. On this assumption, we cloned and expressed the Abl PTK gene in E. coli, and purified the PTK, which was used to screen the PTK inhibitors from the extracts of Chinese herbs. The catalytic domain sequence of PTK gene was amplified by PCR us ing the cDNA of abl from Abelson murine leukemia virus as template. The amplified fragment was then cloned into the GST-tagged expression vector pGEX2T. The recombinant plasmid was transformed into host cell E. coli DH5α and was induced to express PTK protein. The expression of the protein was detected using SDS-PAGE. The result showed that a specific protein was induced to express after 12 min induction, and reached peak level about 40% of the host total pro tein after 4 h induction. The molecular weight of the fusion protein was about 58 kD. The purified GST-PTK fusion pro tein presented higher activity for tyrosine phosphorylation.

  6. Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Shandilya, Shivender M.D.; Nalam, Madhavi N.L.; Nalivaika, Ellen A.; Gross, Phillip J.; Valesano, Johnathan C.; Shindo, Keisuke; Li, Ming; Munson, Mary; Royer, William E.; Harjes, Elena; Kono, Takahide; Matsuo, Hiroshi; Harris, Reuben S.; Somasundaran, Mohan; Schiffer, Celia A. (UMASS, MED); (UMM)


    APOBEC3G is a DNA cytidine deaminase that has antiviral activity against HIV-1 and other pathogenic viruses. In this study the crystal structure of the catalytically active C-terminal domain was determined to 2.25 {angstrom}. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second {beta} strand and a lengthening of the second {alpha} helix. Oligomerization is postulated to be critical for the function of APOBEC3G. In this structure, four extensive intermolecular interfaces are observed, suggesting potential models for APOBEC3G oligomerization. The structural and functional significance of these interfaces was probed by solution NMR and disruptive variants were designed and tested for DNA deaminase and anti-HIV activities. The variant designed to disrupt the most extensive interface lost both activities. NMR solution data provides evidence that another interface, which coordinates a novel zinc site, also exists. Thus, the observed crystallographic interfaces of APOBEC3G may be important for both oligomerization and function.

  7. Cloning, expression, purification, and characterization of the catalytic domain of sika deer MMP-13. (United States)

    Zhang, Xueliang; Wang, Jiawen; Liu, Meichen; Wang, Siming; Zhang, Hui; Zhao, Yu


    Matrix metalloproteinase 13 is one of three mammalian collagenases that are capable of initiating the degradation of interstitial collagens during wound healing. Herein, we report for the first time the molecular cloning of the catalytic domain (CD) of sika deer MMP-13, followed by protein expression in Escherichia coli and purification by affinity chromatography. The final yield was approximately 90.4 mg per liter of growth culture with a purity of 91.6%. The mass recovery during the purification and renaturation were 70.2% and 81.5%, respectively. Using gelatin zymography and a degradation assay, we found that the refolded sika deer MMP-13 (CD) could digest gelatin. The optimal pH and temperature for the enzyme bioactivity was 8.0 and 37 °C, respectively. The Km value for the enzyme-catalyzed digestion of gelatin was 136+/-8 μg/mL, and the Vmax was 4.12 × 10(3) U/μg. sdMMP13 (CD) was able to completely degrade collagen II and gelatin, and partially degrade fibronectin. The sdMMP-13 (CD) activity was significantly inhibited by several chemicals including 1, 10-phenanthroline, EDTA, Fe(2+), Cu(2+), and Mn(2+). PMID:27338011

  8. Biochemical and spectroscopic characterization of the catalytic domain of MMP16 (cdMMP16). (United States)

    Meng, Fan; Yang, Hao; Aitha, Mahesh; George, Sam; Tierney, David L; Crowder, Michael W


    Membrane-bound matrix metalloproteinase 16 (MMP16/MT3-MMP) is considered a drug target due to its role(s) in disease processes such as cancer and inflammation. Biochemical characterization of MMP16 is critical for developing new generation MMP inhibitors (MMPi), which exhibit high efficacies and selectivities. Herein, a modified over-expression and purification protocol was used to prepare the catalytic domain of MMP16 (cdMMP16). The resulting recombinant enzyme exhibited steady-state kinetic constants of K m = 10.6 ± 0.7 μM and k cat = 1.14 ± 0.02 s(-1), when using FS-6 as substrate, and the enzyme bound 1.8 ± 0.1 eq of Zn(II). The enzymatic activity of cdMMP16 is salt concentration-dependent, and cdMMP16 exhibits autoproteolytic activity under certain conditions, which may be related to an in vivo regulatory mechanism of MMP16 and of other membrane-type MMPs (MT-MMPs). Co(II)-substituted analogs (Co2- and ZnCo) of cdMMP16 were prepared and characterized using several spectroscopic techniques, such as UV-Vis, (1)H NMR, and EXAFS spectroscopies. A well-characterized cdMMP16 is now available for future inhibitor screening efforts. PMID:27229514

  9. The Role of Catalytic Substrate Morphology on the Shape and Domain Size of Two-Dimensional Boron Nitride Sheets (United States)

    Griep, Mark; Tay, Roland; Tumlin, Travis; Teo, Edwin; Mallick, Govind; Karna, Shashi


    Two-dimensional (2D) nanomaterials, including graphene and boron nitride (BN), has been of intense interest in recent years due to their exceptional electronic, thermal, and mechanical properties. Tailoring these novel properties to their maximum potential requires precise control of the atomic layer growth process. In recent years, catalytic growth of 2-D nanomaterials using chemical vapor deposition (CVD) process has emerged as an attractive approach due to their low-cost, scalalibility, and ability totransfer the grown materials on various substrates. In this approach, The the morphology and purity of the catalytic surface plays a critical role on the shape, size, and growth kintectics of the 2D nanomaterial. In this work, we present the results of our systematic studies of the role of catalytic surface morphology on the shape and domain size of CVD grown hexagonal boron nitride (hBN) films. The present work clearly demonstrates that that the presence of surface roghness in the form of ridges leads to a preferential growth of small-domain triangular BN sheets. A 10 to 100-fold reduction in the surfcae roughness leads to increased domain BN triangles, eventually transitioning to large-domain hexagonal shaped hBN sheets.

  10. A Wideband Direct Data Domain Genetic Algorithm Beamforming

    Directory of Open Access Journals (Sweden)

    H. M. Elkamchouchi


    Full Text Available In this paper, a wideband direct data-domain genetic algorithm beamforming is presented. Received wideband signals are decomposed to a set of narrow sub-bands using fast Fourier transform. Each sub-band is transformed to a reference frequency using the steering vector transformation. So, narrowband approaches could be used for any of these sub-bands. Hence, the direct data-domain genetic algorithm beamforming can be used to form a single ‘hybrid’ beam pattern with sufficiently deep nulls in order to separate and reconstruct frequency components of the signal of interest efficiently. The proposed approach avoids most of drawbacks of already-existing statistical and gradient-based approaches since formation of a covariance matrix is not needed, and a genetic algorithm is used to solve the beamforming problem.

  11. Catalytic polymeric electrodes for direct borohydride fuel cells (United States)

    Bayatsarmadi, Bita; Peters, Alice; Talemi, Pejman


    The direct borohydride fuel cell (DBFC) is a new class of fuel cells that produces non-toxic by-products and has a potential for a high voltage and high energy density. A major challenge in developing efficient DBFCs is the development of an efficient, stable, and economic catalyst for the oxidation of borohydride. In this paper, we report the use of conducting polymer Poly(3,4-ethylenedioxythiophene) (PEDOT) as electrocatalysts in DBFC. PEDOT electrodes prepared by vacuum phase polymerization exhibited electrocatalytic behavior towards oxidation of borohydride and reduction of hydrogen peroxide. Spectroscopic analysis of samples showed that PEDOT can act as an interface for electron transfer from borohydride ions. Comparing the polarization curves of DBFCs with PEDOT coated on graphite electrodes and cells with bare graphite electrodes, demonstrated higher voltage, maximum power density, and stability.

  12. Purification, crystallization and preliminary crystallographic analysis of the catalytic domain of the extracellular cellulase CBHI from Trichoderma harzianum

    International Nuclear Information System (INIS)

    The catalytic domain of CHBI was purified from a cellular extract of T. harzianum. Diffraction-quality crystals were obtained and a native X-ray data set was collected using a synchrotron source. The filamentous fungus Trichoderma harzianum has a considerable cellulolytic activity that is mediated by a complex of enzymes which are essential for the hydrolysis of microcrystalline cellulose. These enzymes were produced by the induction of T. harzianum with microcrystalline cellulose (Avicel) under submerged fermentation in a bioreactor. The catalytic core domain (CCD) of cellobiohydrolase I (CBHI) was purified from the extracellular extracts and submitted to robotic crystallization. Diffraction-quality CBHI CCD crystals were grown and an X-ray diffraction data set was collected under cryogenic conditions using a synchrotron-radiation source

  13. Prediction of a common beta-propeller catalytic domain for fructosyltransferases of different origin and substrate specificity.


    Pons, T.; L. Hernández; Batista, F. R.; Chinea, G.


    The three-dimensional (3D) structure of fructan biosynthetic enzymes is still unknown. Here, we have explored folding similarities between reported microbial and plant enzymes that catalyze transfructosylation reactions. A sequence-structure compatibility search using TOPITS, SDP, 3D-PSSM, and SAM-T98 programs identified a beta-propeller fold with scores above the confidence threshold that indicate a structurally conserved catalytic domain in fructosyltransferases (FTFs) of diverse origin and...

  14. The Type II Pullulanase of Thermococcus hydrothermalis: Molecular Characterization of the Gene and Expression of the Catalytic Domain


    Erra-Pujada, Marta; Debeire, Philippe; Duchiron, Francis; O’Donohue, Michael J.


    The gene encoding a hyperthermostable type II pullulanase produced by Thermococcus hydrothermalis (Th-Apu) has been isolated. Analysis of a total of 5.2 kb of genomic DNA has revealed the presence of three open reading frames, one of which (apuA) encodes the pullulanase. This enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. In addition to a typical N-terminal signal peptide, Th-Apu possesses a catalytic domain, a domain bearing S-layer homology-like motifs...

  15. Study on Application of Bi-directional Combination Technology Integrating Residue Hydrotreating with Catalytic Cracking RICP

    Institute of Scientific and Technical Information of China (English)

    Niu Chuanfeng; Gao Yongcan; Dai Lishun; Li Dadong


    After analysing the disadvantages of the traditional residue hydrotreating-catalytic cracking combination process, RIPP has proposed a bi-directional combination technology integrating residue hydrotreating with catalytic cracking called RICP which does not further recycles the FCC heavy cycle oil (HCO) inside the FCC unit and delivers HCO to the residue hydrotreating unit as a diluting oil for the residue that is concurrently subjected to hydrotreating prior to being used as the FCC feed oil. The RICP technology can stimulate residue hydrotreating reactions through utilization of HCO along with an increased yield of FCC light distillate, resulting in enhanced petroleum utilization and economic benefits of the refinery.

  16. Over-expression and refolding of isotopically labeled recombinant catalytic domain of human macrophage elastase (MMP-12) for NMR studies. (United States)

    Zheng, Xunhai; Ou, Li; Tong, Xiaotian; Zhu, Jing; Wu, Houming


    Human macrophage elastase (MMP-12) plays an important role in inflammatory processes and is involved in a number of physiological or pathological situations, such as conversion of plasminogen into angiostatin, allergic airway inflammation, vascular remodeling or alteration, as well as emphysema, and has been justified as a novel drug target. Here, we report the over-expression in Escherichia coil, purification and refolding of MMP-12 catalytic domain for NMR studies. The primary sequence of expressed protein was identified by means of MALDI-TOF MS, and was confirmed by the MALDI-TOF MS data of trypsin-digested peptides. A significantly optimized protocol has been worked out to prepare 15N and/or 13C-labeled MMP-12 catalytic domain, and the yield of the purified protein is estimated to 10-12 mg from 0.5L of M9 minimal media. Finally, the 15N-1H HSQC spectrum of uniformly 15N-labeled MMP-12 catalytic domain indicates the presence of well-ordered and properly folded protein in a monomeric form. PMID:17601747

  17. Sequence-Specific Assignment and Secondary Structure of the Catalytic Domain of Protein from Ubiquitination Pathway

    International Nuclear Information System (INIS)

    Ubiquitination is a post-translational protein modification which plays an important role in a wide variety of cellular processes including cell cycle, DNA repair and cell apoptosis. It is well known, that the ubiquitination requires sequential activity of three enzymes with different functions: activation, conjugation and ligation. Unfortunately, the three-dimensional structures of all three proteins responsible for these processes are not available at present and the process of proteins ubiquitination still is not understood in detail. In our communication, we present first, preliminary NMR data for the sequence-specific assignments for 112 amino acid residues long domain of one of the proteins from the ubiquitination pathway. The NMR samples were prepared by dissolving 1 mm either 15N-labeled or 15N, 13C-double labeled protein in 90%/10% H2O/D2O, 50 mm TRIS buffer, and 50 mm NaCl. The ph was adjusted to 6.5 (uncorrected value). All NMR measurements were performed on the Varian Unity+ 500 NMR spectrometer (11.7 T) equipped with three channels, Performa II PFG unit and 5 mm 1H, 13C, 15N-triple resonance pro behead. The 1H, 15N, and 13C backbone resonances were assigned by standard methods using 3D heteronuclear HNCACB, CBCA(CO)NH, HNCA, HN(CO)CA, HNCO, (HCA)CO(CA)NH NMR spectra collected at 303 K. The aliphatic 1H and 13C resonances were assigned on the basis of C(CO)NH, HBHA(CO)NH, and H(CO)NH experiments. After finishing of assignment procedure, solution of secondary structure in studied protein has been performed. The exact position of the α-helices and β-strands were solved on base analysis of cross-peaks between HN and Hα protons in 3D 15N-edited NOESY-HSQC spectrum, 3JNHα coupling constants evaluated from 3D HNHA experiment, and chemical shifts of backbone nuclei (TALOS software). Obtained results will be used in future for solution of three-dimensional structure of catalytic domain with high resolution by means NMR methods. (author)

  18. Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain


    Zhen Fang; Juan Zhang; Guocheng Du; Jian Chen


    The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic e...

  19. Dual-Bed Catalytic System for Direct Conversion of Methane to Liquid Hydrocarbons

    Institute of Scientific and Technical Information of China (English)

    N.A.S.Amin; Sriraj Ammasi


    A dual-bed catalytic system is proposed for the direct conversion of methane to liquid hydrocarbons. In this system, methane is converted in the first stage to oxidative coupling of methane (OCM) products by selective catalytic oxidation with oxygen over La-supported MgO catalyst. The second bed, comprising of the HZSM-5 zeolite catalyst, is used for the oligomerization of OCM light hydrocarbon products to liquid hydrocarbons. The effects of temperature (650-800 ℃), methane to oxygen ratio (4-10), and SiO2/Al2O3 ratio of the HZSM-5 zeolite catalyst on the process are studied. At higher reaction temperatures, there is considerable dealumination of HZSM-5, and thus its catalytic performance is reduced. The acidity of HZSM-5 in the second bed is responsible for the oligomerization reaction that leads to the formation of liquid hydrocarbons. The activities of the oligomerization sites were unequivocally affected by the SiO2/Al2O3 ratio. The relation between the acidity and the activity of HZSM-5 is studied by means of TPD-NH3 techniques. The rise in oxygen concentration is not beneficial for the C5+ selectivity, where the combustion reaction of intermediate hydrocarbon products that leads to the formation of carbon oxide (CO+CO2) products is more dominant than the oligomerization reaction. The dual-bed catalytic system is highly potential for directly converting methane to liquid fuels.

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

    Directory of Open Access Journals (Sweden)

    Yu Wei-Hsuan


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

  1. Direct Data Domain STAP using Sparse Representation of Clutter Spectrum

    CERN Document Server

    Sun, Ke; Wang, Yongliang; Wang, Xiqin


    Space-time adaptive processing (STAP) is an effective tool for detecting a moving target in the airborne radar system. Due to the fast-changing clutter scenario and/or non side-looking configuration, the stationarity of the training data is destroyed such that the statistical-based methods suffer performance degradation. Direct data domain (D3) methods avoid non-stationary training data and can effectively suppress the clutter within the test cell. However, this benefit comes at the cost of a reduced system degree of freedom (DOF), which results in performance loss. In this paper, by exploiting the intrinsic sparsity of the spectral distribution, a new direct data domain approach using sparse representation (D3SR) is proposed, which seeks to estimate the high-resolution space-time spectrum with only the test cell. The simulation of both side-looking and non side-looking cases has illustrated the effectiveness of the D3SR spectrum estimation using focal underdetermined system solution (FOCUSS) and norm minimiz...

  2. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

    Energy Technology Data Exchange (ETDEWEB)

    Holden, Lauren G.; Prochnow, Courtney; Chang, Y. Paul; Bransteitter, Ronda; Chelico, Linda; Sen, Udayaditya; Stevens, Raymond C.; Goodman, Myron F.; Chen, Xiaojiang S. (USC); (Scripps)


    The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded {beta}-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2. A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.

  3. Domain III function of Mu transposase analysed by directed placement of subunits within the transpososome

    Indian Academy of Sciences (India)

    Susana Mariconda; Soon-Young Namgoong; Ki-Hoon Yoon; Hong Jiang; Rasika M Harshey


    Assembly of the functional tetrameric form of Mu transposase (MuA protein) at the two att ends of Mu depends on interaction of MuA with multiple att and enhancer sites on supercoiled DNA, and is stimulated by MuB protein. The N-terminal domain I of MuA harbours distinct regions for interaction with the att ends and enhancer; the C-terminal domain III contains separate regions essential for tetramer assembly and interaction with MuB protein (III and III, respectively). Although the central domain II (the ‘DDE’ domain) of MuA harbours the known catalytic DDE residues, a 26 amino acid peptide within III also has a non-specific DNA binding and nuclease activity which has been implicated in catalysis. One model proposes that active sites for Mu transposition are assembled by sharing structural/catalytic residues between domains II and III present on separate MuA monomers within the MuA tetramer. We have used substrates with altered att sites and mixtures of MuA proteins with either wild-type or altered att DNA binding specificities, to create tetrameric arrangements wherein specific MuA subunits are nonfunctional in II, III or III domains. From the ability of these oriented tetramers to carry out DNA cleavage and strand transfer we conclude that domain III or III function is not unique to a specific subunit within the tetramer, indicative of a structural rather than a catalytic function for domain III in Mu transposition.

  4. The properties of catalytically-inactivated Trichoderma reesei cellobiohydrolase I: Role of the cellulose binding domain

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Donner, T.R.; Affholter, K.A. [Oak Ridge National Lab., TN (United States)


    Cellobiohydrolase I (CBH I) was purified from a crude cellulase by preparative isoelectric focusing. Treatment of CBH I with 1-ethyl-3-3(3-dimethylaminopropyl)-carbodiimide (EDC) resulted in its catalytic inactivation but did not abolish its ability to be absorbed to microcrystalline cellulose (Avicel). CBH I thus modified possessed a pI of between 8.5 and 9.3 and decreased tryptophan fluorescence compared to native CBH I. A comparison of the effect of native and modified CBH I on the morphology of crystalline cotton cellulose fibers was made using scanning electron microscopy.

  5. Goal Directed Model Inversion: Learning Within Domain Constraints (United States)

    Colombano, Silvano P.; Compton, Michael; Raghavan, Bharathi; Lum, Henry, Jr. (Technical Monitor)


    Goal Directed Model Inversion (GDMI) is an algorithm designed to generalize supervised learning to the case where target outputs are not available to the learning system. The output of the learning system becomes the input to some external device or transformation, and only the output of this device or transformation can be compared to a desired target. The fundamental driving mechanism of GDMI is to learn from success. Given that a wrong outcome is achieved, one notes that the action that produced that outcome "would have been right if the outcome had been the desired one." The algorithm makes use of these intermediate "successes" to achieve the final goal. A unique and potentially very important feature of this algorithm is the ability to modify the output of the learning module to force upon it a desired syntactic structure. This differs from ordinary supervised learning in the following way: in supervised learning the exact desired output pattern must be provided. In GDMI instead, it is possible to require simply that the output obey certain rules, i.e., that it "make sense" in some way determined by the knowledge domain. The exact pattern that will achieve the desired outcome is then found by the system. The ability to impose rules while allowing the system to search for its own answers in the context of neural networks is potentially a major breakthrough in two ways: 1) it may allow the construction of networks that can incorporate immediately some important knowledge, i.e. would not need to learn everything from scratch as normally required at present, and 2) learning and searching would be limited to the areas where it is necessary, thus facilitating and speeding up the process. These points are illustrated with examples from robotic path planning and parametric design.

  6. Direct Catalytic Asymmetric Mannich-Type Reaction of α- and β-Fluorinated Amides. (United States)

    Brewitz, Lennart; Arteaga, Fernando Arteaga; Yin, Liang; Alagiri, Kaliyamoorthy; Kumagai, Naoya; Shibasaki, Masakatsu


    The last two decades have witnessed the emergence of direct enolization protocols providing atom-economical and operationally simple methods to use enolates for stereoselective C-C bond-forming reactions, eliminating the inherent drawback of the preformation of enolates using stoichiometric amounts of reagents. In its infancy, direct enolization relied heavily on the intrinsic acidity of the latent enolates, and the reaction scope was limited to readily enolizable ketones and aldehydes. Recent advances in this field enabled the exploitation of carboxylic acid derivatives for direct enolization, offering expeditious access to synthetically versatile chiral building blocks. Despite the growing demand for enantioenriched fluorine-containing small molecules, α- and β-fluorinated carbonyl compounds have been neglected in direct enolization chemistry because of the competing and dominating defluorination pathway. Herein we present a comprehensive study on direct and highly stereoselective Mannich-type reactions of α- and β-fluorine-functionalized 7-azaindoline amides that rely on a soft Lewis acid/hard Brønsted base cooperative catalytic system to guarantee an efficient enolization while suppressing undesired defluorination. This protocol contributes to provide a series of fluorinated analogs of enantioenriched β-amino acids for medicinal chemistry. PMID:26652911

  7. Solar reforming of methane in a direct absorption catalytic reactor on a parabolic dish

    Energy Technology Data Exchange (ETDEWEB)

    Muir, J.F.; Hogan, R.E. Jr.; Skocypec, R.D. (Sandia National Labs., Albuquerque, NM (USA)); Buck, R. (Deutsche Forschungsanstalt fuer Luft- und Raumfahrt e.V. (DLR), Stuttgart (Germany, F.R.). Inst. fuer Technische Thermodynamik)


    The concept of solar driven chemical reactions in a commercial-scale volumetric receiver/reactor on a parabolic concentrator was successfully demonstrated in the CAtalytically Enhanced Solar Absorption Receiver (CAESAR) test. Solar reforming of methane (CH{sub 4}) with carbon dioxide (CO{sub 2}) was achieved in a 64-cm diameter direct absorption reactor on a parabolic dish capable of 150 kW solar power. The reactor was a catalytic volumetric absorber consisting of a multi-layered, porous alumina foam disk coated with rhodium (Rh) catalyst. The system was operated during both steady-state and solar transient (cloud passage) conditions. The total solar power absorbed reached values up to 97 kW and the maximum methane conversion was 70%. Receiver thermal efficiencies ranged up to 85% and chemical efficiencies peaked at 54%. The absorber performed satisfactorily in promoting the reforming reaction during the tests without carbon formation. However, problems of cracking and degradation of the porous matrix, nonuniform dispersion of the Rh through the absorber, and catalyst deactivation due to sintering and possible encapsulation, must be resolved to achieve long-term operation and eventual commercialization. 17 refs., 11 figs., 1 tab.

  8. Truncation of the Catalytic Domain of the Cylindromatosis Tumor Suppressor Impairs Lung Maturation1


    Trompouki, Eirini; Tsagaratou, Ageliki; Kosmidis, Stylianos K; Dollé, Pascal; Qian, Jun; Dimitris L. Kontoyiannis; Cardoso, Wellington V.; Mosialos, George


    Cyld encodes a 956-amino acid deubiquitinating enzyme (CYLD), which is a negative regulator of nuclear factor κB and mitogen-activated protein kinase pathways. Mutations that truncate and inactivate the carboxyl-terminal deubiquitinating domain of CYLD underlie the development of skin appendage tumors in humans, whereas down-regulation of Cyld expression has been associated with the development of various types of human malignancies including lung cancer. To establish an animal model of human...

  9. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. (United States)

    Kowalski, J C; Belfort, M; Stapleton, M A; Holpert, M; Dansereau, J T; Pietrokovski, S; Baxter, S M; Derbyshire, V


    I-TevI is a member of the GIY-YIG family of homing endonucleases. It is folded into two structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding domain, separated by a flexible linker. In this study we have used genetic analyses, computational sequence analysis andNMR spectroscopy to define the configuration of theN-terminal domain and its relationship to the flexible linker. The catalytic domain is an alpha/beta structure contained within the first 92 amino acids of the 245-amino acid protein followed by an unstructured linker. Remarkably, this structured domain corresponds precisely to the GIY-YIG module defined by sequence comparisons of 57 proteins including more than 30 newly reported members of the family. Although much of the unstructured linker is not essential for activity, residues 93-116 are required, raising the possibility that this region may adopt an alternate conformation upon DNA binding. Two invariant residues of the GIY-YIG module, Arg27 and Glu75, located in alpha-helices, have properties of catalytic residues. Furthermore, the GIY-YIG sequence elements for which the module is named form part of a three-stranded antiparallel beta-sheet that is important for I-TevI structure and function. PMID:10219084

  10. Direct Comparison of Electrochemical and Spectrochemical Kinetics for Catalytic Oxygen Reduction

    Energy Technology Data Exchange (ETDEWEB)

    Wasylenko, Derek J.; Rodriguez, Carlos; Pegis, Michael L.; Mayer, James M.


    We describe here a direct comparison of electrochemical and spectrochemical experiments to determine rates and selectivity of oxygen reduction catalyzed by iron 5,10,15,20-meso-tetraphenylporphyrin chloride. Strong agreement was found between the two methods suggesting the same mechanism is occurring under both conditions, with the same overall third order rate constant kcat = (1.1 ± 0.1) × 106 M-2 s-1. This report provides a rare example of characterization of a redox catalytic process by two common but very different methods. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

  11. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2. (United States)

    Qiu, Wei; Lam, Robert; Voytyuk, Oleksandr; Romanov, Vladimir; Gordon, Roni; Gebremeskel, Simon; Vodsedalek, Jakub; Thompson, Christine; Beletskaya, Irina; Battaile, Kevin P; Pai, Emil F; Rottapel, Robert; Chirgadze, Nickolay Y


    The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated β-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, the high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors. PMID:25286857

  12. MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function

    Directory of Open Access Journals (Sweden)

    Hofmann Kay


    Full Text Available Abstract Background Three macromolecular assemblages, the lid complex of the proteasome, the COP9-Signalosome (CSN and the eIF3 complex, all consist of multiple proteins harboring MPN and PCI domains. Up to now, no specific function for any of these proteins has been defined, nor has the importance of these motifs been elucidated. In particular Rpn11, a lid subunit, serves as the paradigm for MPN-containing proteins as it is highly conserved and important for proteasome function. Results We have identified a sequence motif, termed the MPN+ motif, which is highly conserved in a subset of MPN domain proteins such as Rpn11 and Csn5/Jab1, but is not present outside of this subfamily. The MPN+ motif consists of five polar residues that resemble the active site residues of hydrolytic enzyme classes, particularly that of metalloproteases. By using site-directed mutagenesis, we show that the MPN+ residues are important for the function of Rpn11, while a highly conserved Cys residue outside of the MPN+ motif is not essential. Single amino acid substitutions in MPN+ residues all show similar phenotypes, including slow growth, sensitivity to temperature and amino acid analogs, and general proteasome-dependent proteolysis defects. Conclusions The MPN+ motif is abundant in certain MPN-domain proteins, including newly identified proteins of eukaryotes, bacteria and archaea thought to act outside of the traditional large PCI/MPN complexes. The putative catalytic nature of the MPN+ motif makes it a good candidate for a pivotal enzymatic function, possibly a proteasome-associated deubiquitinating activity and a CSN-associated Nedd8/Rub1-removing activity.

  13. PtRu-WO3 nanostructured electrode for highly catalytic activity in direct methanol fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Sung, Y.-E.; Park, K.-W. [Kwangju Institute of Science and Technology, Kwangju (Korea, Republic of). Dept. of Materials Science and Engineering


    Direct methanol fuel cells possess high energy density and low operating temperatures, and could prove of great interest in applications such as thin film fuel cells. The authors described how they designed and fabricated a novel electrode structure consisting of two phases of platinum, ruthenium (Pt, Ru) and tungsten-oxide (WOx), for use in thin film fuel cells. They used a co-sputtering system with a Pt and Ru metal and a tungsten oxide target. The substrates used for analysis by transmission electron microscopy (TEM) was copper (Cu) grids. Analysis of the crystallinity was performed using X-ray diffraction (XRD). The I-V characteristic curves for the electro-oxidation of methanol fuel were examined using three electrode electrochemical systems consisting of working (deposited electrodes), counter (Pt gauze), and reference (silver/silver-chlorine) electrodes at 25 degrees Celsius, to evaluate the performance of the electrodes. The results obtained suggest that the crystallinity of the PtRu alloy in the oxide is excellent. Superior catalytic activity (higher current density) was displayed by the PtRu alloy electrode, compared to that of pure Pt. Among all the electrodes, the PtRu-WO3 nanostructured alloy electrode displayed the highest electro-oxidation current density. By achieving an increased active surface area by nanophases and an improved catalytic activity of the alloy structure in nanostructured electrodes, it is possible to obtain highly efficient cell performance. The nanostructured electrode displayed higher methanol oxidation current compared to conventional alloy catalysts. 4 refs., 2 figs.

  14. Formation of domain reversal by direct irradiation with femtosecond laser in lithium niobate

    Institute of Scientific and Technical Information of China (English)

    Haisheng Zhu; Xianfeng Chen; Hongyun Chen; Xuewei Deng


    We propose that domain inversion can be directly induced by femtceecond laser both theoretically and experimentally, which opens a path to achieve three-dimensional (3D) nonlinear crystal with a period in sub-micron-scale. A simulation of domain inversion is modeled by considering the temporal distribution of femtosecond pulses. The calculation results clarify that the domain inversions can happen within or after the interaction with the laser pulse, and the response time of domain inversion is in the picosecond level depending on the intensity and the materials. The domain reversal windows of lithium niobate by femtosecond laser are observed which agrees with theoretical predictions qualitatively.

  15. A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation

    International Nuclear Information System (INIS)

    A 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKα2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function

  16. Motile properties of the bi-directional kinesin-5 Cin8 are affected by phosphorylation in its motor domain (United States)

    Shapira, Ofer; Gheber, Larisa


    The Saccharomyces cerevisiae kinesin-5 Cin8 performs essential mitotic functions in spindle assembly and anaphase B spindle elongation. Recent work has shown that Cin8 is a bi-directional motor which moves towards the minus-end of microtubules (MTs) under high ionic strength (IS) conditions and changes directionality in low IS conditions and when bound between anti-parallel microtubules. Previous work from our laboratory has also indicated that Cin8 is differentially phosphorylated during late anaphase at cyclin-dependent kinase 1 (Cdk1)-specific sites located in its motor domain. In vivo, such phosphorylation causes Cin8 detachment from spindles and reduces the spindle elongation rate, while maintaining proper spindle morphology. To study the effect of phosphorylation on Cin8 motor function, we examined in vitro motile properties of wild type Cin8, as well as its phosphorylation using phospho-deficient and phospho-mimic variants, in a single molecule fluorescence motility assay. Analysis was performed on whole cell extracts and on purified Cin8 samples. We found that addition of negative charges in the phospho-mimic mutant weakened the MT-motor interaction, increased motor velocity and promoted minus-end-directed motility. These results indicate that phosphorylation in the catalytic domain of Cin8 regulates its motor function. PMID:27216310

  17. Rescue of HIV-1 release by targeting widely divergent NEDD4-type ubiquitin ligases and isolated catalytic HECT domains to Gag.

    Directory of Open Access Journals (Sweden)

    Eric R Weiss

    Full Text Available Retroviruses engage the ESCRT pathway through late assembly (L domains in Gag to promote virus release. HIV-1 uses a PTAP motif as its primary L domain, which interacts with the ESCRT-I component Tsg101. In contrast, certain other retroviruses primarily use PPxY-type L domains, which constitute ligands for NEDD4-type ubiquitin ligases. Surprisingly, although HIV-1 Gag lacks PPxY motifs, the release of HIV-1 L domain mutants is potently enhanced by ectopic NEDD4-2s, a native isoform with a naturally truncated C2 domain that appears to account for the residual titer of L domain-defective HIV-1. The reason for the unique potency of the NEDD4-2s isoform has remained unclear. We now show that the naturally truncated C2 domain of NEDD4-2s functions as an autonomous Gag-targeting module that can be functionally replaced by the unrelated Gag-binding protein cyclophilin A (CypA. The residual C2 domain of NEDD4-2s was sufficient to transfer the ability to stimulate HIV-1 budding to other NEDD4 family members, including the yeast homologue Rsp5, and even to isolated catalytic HECT domains. The isolated catalytic domain of NEDD4-2s also efficiently promoted HIV-1 budding when targeted to Gag via CypA. We conclude that the regions typically required for substrate recognition by HECT ubiquitin ligases are all dispensable to stimulate HIV-1 release, implying that the relevant target for ubiquitination is Gag itself or can be recognized by divergent isolated HECT domains. However, the mere ability to ubiquitinate Gag was not sufficient to stimulate HIV-1 budding. Rather, our results indicate that the synthesis of K63-linked ubiquitin chains is critical for ubiquitin ligase-mediated virus release.

  18. Truncation of the Catalytic Domain of the Cylindromatosis Tumor Suppressor Impairs Lung Maturation1 (United States)

    Trompouki, Eirini; Tsagaratou, Ageliki; Kosmidis, Stylianos K; Dollé, Pascal; Qian, Jun; Kontoyiannis, Dimitris L; Cardoso, Wellington V; Mosialos, George


    Cyld encodes a 956-amino acid deubiquitinating enzyme (CYLD), which is a negative regulator of nuclear factor κB and mitogen-activated protein kinase pathways. Mutations that truncate and inactivate the carboxyl-terminal deubiquitinating domain of CYLD underlie the development of skin appendage tumors in humans, whereas down-regulation of Cyld expression has been associated with the development of various types of human malignancies including lung cancer. To establish an animal model of human CYLD inactivation and characterize the biological role of CYLD in vivo, we generated mice carrying a homozygous deletion of Cyld exon 9 (CyldΔ9/Δ9 mice) using a conditional approach. Deletion of exon 9 would cause a carboxyl-terminal truncation of CYLD and inactivation of its deubiquitinating activity. In accordance with previous studies, fibroblasts from CyldΔ9/Δ9 embryos had hyperactive nuclear factor κB and c-Jun kinase pathways compared with control fibroblasts. CyldΔ9/Δ9 newborn mice were smaller than wild-type littermates with a short and kinky tail and nomajor developmental defects. However, CyldΔ9/Δ9 mice died shortly after birth from apparent respiratory dysfunction. Histological examination of E18.5 CyldΔ9/Δ9 lungs demonstrated an immature phenotype characterized by hyperplasic mesenchyme but apparently normal epithelial, smooth muscle. and endothelial structures. Our study identifies an important role of CYLD in lung maturation, which may underlie the development of many cases of lung cancer. PMID:19412431

  19. Truncation of the Catalytic Domain of the Cylindromatosis Tumor Suppressor Impairs Lung Maturation

    Directory of Open Access Journals (Sweden)

    Eirini Trompouki


    Full Text Available Cyld encodes a 956-amino acid deubiquitinating enzyme (CYLD, which is a negative regulator of nuclear factor κB and mitogen-activated protein kinase pathways. Mutations that truncate and inactivate the carboxyl-terminal deubiquitinating domain of CYLD underlie the development of skin appendage tumors in humans, whereas down-regulation of Cyld expression has been associated with the development of various types of human malignancies including lung cancer. To establish an animal model of human CYLD inactivation and characterize the biological role of CYLD in vivo, we generated mice carrying a homozygous deletion of Cyld exon 9 (CyldΔ9/Δ9 mice using a conditional approach. Deletion of exon 9 would cause a carboxyl-terminal truncation of CYLD and inactivation of its deubiquitinating activity. In accordance with previous studies, fibroblasts from CyldΔ9/Δ9 embryos had hyperactive nuclear factor κB and c-Jun kinase pathways compared with control fibroblasts. CyldΔ9/Δ9 newborn mice were smaller than wild-type littermates with a short and kinky tail and nomajor developmental defects. However, CyldΔ9/Δ9 mice died shortly after birth from apparent respiratory dysfunction. Histological examination of E18.5 CyldΔ9/Δ9 lungs demonstrated an immature phenotype characterized by hyperplasic mesenchyme but apparently normal epithelial, smooth muscle. and endothelial structures. Our study identifies an important role of CYLD in lung maturation, which may underlie the development of many cases of lung cancer.

  20. Fusion proteins comprising the catalytic domain of mutansucrase and a starch-binding domain can after the morphology of amylose-free potato starch granules during biosynthesis


    Nazarian, F.; Kok-Jacon, G.A.; Vincken, J.P.; Q. JI; Suurs, L.C.J.M.; Visser, R.G.F.


    It has been shown previously that mutan can be co-synthesized with starch when a truncated mutansucrase (GtfICAT) is directed to potato tuber amyloplasts. The mutan seemed to adhere to the isolated starch granules, but it was not incorporated in the starch granules. In this study, GtfICAT was fused to the N- or C-terminus of a starch-binding domain (SBD). These constructs were introduced into two genetically different potato backgrounds (cv. Kardal and amf), in order to bring GtfICAT in more ...

  1. Direct observation of lipid domains in free standing bilayers: from simple to complex lipid mixtures

    DEFF Research Database (Denmark)

    Bagatolli, Luis A


    The direct observation of temperature-dependent lipid phase equilibria, using two-photon excitation fluorescence microscopy on giant unilamellar vesicles (GUVs) composed of different lipid mixtures, provides novel information about the physical characteristics of lipid domain coexistence. Physical......-dimethylamino-naphthalene (LAURDAN) under the two-photon excitation fluorescence microscopy will be particularly addressed, especially, the possibility to obtain information about the phase-state of different lipid domains directly from the fluorescent images. Udgivelsesdato: 2003-Jan...

  2. Direct Synthesis, Characterization and Catalytic Performance of Iron-Containing SBA-15 for Phenol Degradation

    Institute of Scientific and Technical Information of China (English)

    XIE Huan-ling; XU Wen-guo


    An iron-containing SBA-15(Fe-SBA-15) has been synthesized via one-pot hydrothermal method under weak acidic conditions. A series of characterizations show nanocomposite materials of iron particles supported over mesostructured materials. The catalytic activity of these iron-containing SBA-15 materials has been tested for the heterogeneous Fenton degradation of phenolic aqueous solutions. The catalytic performance has been monitored in terms of phenol conversion, whereas the catalytic stability was evaluated by catalyst recycle. The influence of concentration of hydrogen peroxide, catalyst loading, catalyst prepared with different Fe/Si molar ratios in the gel and pH values of the solution on phenol conversion has been studied. Achieving a good catalytic performance accompanied with a noteworthy stability, Fe-SBA-15 materials prepared by this method are shown as the successful catalyst for degradation of phenolic aqueous solutions by Fenton process.

  3. Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain. (United States)

    Fang, Zhen; Zhang, Juan; Du, Guocheng; Chen, Jian


    The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s(-1) mM(-1). The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD. PMID:27298079

  4. Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain (United States)

    Fang, Zhen; Zhang, Juan; Du, Guocheng; Chen, Jian


    The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s−1 mM−1. The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD. PMID:27298079

  5. The catalytic subunit of Dictyostelium cAMP-dependent protein kinase -- role of the N-terminal domain and of the C-terminal residues in catalytic activity and stability. (United States)

    Etchebehere, L C; Van Bemmelen, M X; Anjard, C; Traincard, F; Assemat, K; Reymond, C; Véron, M


    The C subunit of Dictyostelium cAMP-dependent protein kinase (PKA) is unusually large (73 kDa) due to the presence of 330 amino acids N-terminal to the conserved catalytic core. The sequence following the core, including a C-terminal -Phe-Xaa-Xaa-Phe-COOH motif, is highly conserved. We have characterized the catalytic activity and stability of C subunits mutated in sequences outside the catalytic core and we have analyzed their ability to interact with the R subunit and with the heat-stable protein-kinase inhibitor PKI. Mutants carrying deletions in the N-terminal domain displayed little difference in their kinetic properties and retained their capacity to be inhibited by R subunit and by PKI. In contrast, the mutation of one or both of the phenylalanine residues in the C-terminal motif resulted in a decrease of catalytic activity and stability of the proteins. Inhibition by the R subunit or by PKI were however unaffected. Sequence-comparison analysis of other protein kinases revealed that a -Phe-Xaa-Xaa-Phe- motif is present in many Ser/Thr protein kinases, although its location at the very end of the polypeptide is a particular feature of the PKA family. We propose that the presence of this motif may serve to identify isoforms of protein kinases. PMID:9342234

  6. Directional and polarimetric effects in the optical domain (United States)

    Vanderbilt, V. C.; Leroy, M.


    Papers focused on land surface, atmospheric, and ocean properties are reported. Specific comments pertaining to polarization, models and inversion, and measurements, are given. Recommendations are: continued research into the application potential of the BRDF (Bidirectional Reflectance Distribution Function) and polarization properties of ground surface and atmospheric targets; three dimensional models, which account for the statistical behavior of remotely sensed data, should be extended and inverted in order to support analysis of data potentially covering rolling terrain such that pixels represent heterogeneous mixtures of surface cover types and project ground footprints with sizes between 10 to 6 km, the ground pixel sizes of planned future sensors; available reflectance models should be further validated by means of multi dimensional (directional, spectral, temporal) field data and existing models should be intercompared in more depth to evaluate their performance and limitations; existing methods for model inversion should be validated in more depth in order to quantify the practical limitations and the expected accuracy of the parameters retrieved and new approaches should be developed based upon apriori knowledge of plant canopy development and spectral BRDF properties; there is a need to establish a protocol of validation and intercomparison of the indices and compositing techniques which have been proposed during these last years.

  7. Direct observation of electron dynamics in the attosecond domain. (United States)

    Föhlisch, A; Feulner, P; Hennies, F; Fink, A; Menzel, D; Sanchez-Portal, D; Echenique, P M; Wurth, W


    Dynamical processes are commonly investigated using laser pump-probe experiments, with a pump pulse exciting the system of interest and a second probe pulse tracking its temporal evolution as a function of the delay between the pulses. Because the time resolution attainable in such experiments depends on the temporal definition of the laser pulses, pulse compression to 200 attoseconds (1 as = 10(-18) s) is a promising recent development. These ultrafast pulses have been fully characterized, and used to directly measure light waves and electronic relaxation in free atoms. But attosecond pulses can only be realized in the extreme ultraviolet and X-ray regime; in contrast, the optical laser pulses typically used for experiments on complex systems last several femtoseconds (1 fs = 10(-15) s). Here we monitor the dynamics of ultrafast electron transfer--a process important in photo- and electrochemistry and used in solid-state solar cells, molecular electronics and single-electron devices--on attosecond timescales using core-hole spectroscopy. We push the method, which uses the lifetime of a core electron hole as an internal reference clock for following dynamic processes, into the attosecond regime by focusing on short-lived holes with initial and final states in the same electronic shell. This allows us to show that electron transfer from an adsorbed sulphur atom to a ruthenium surface proceeds in about 320 as. PMID:16034414

  8. Direct Observation of Field and Temperature Induced Domain Replication in Dipolar Coupled Perpendicular Anisotropy Films

    Energy Technology Data Exchange (ETDEWEB)

    Hauet, T.; Gunther, C.M.; Pfau, B.; Eisebitt, S.; Fischer, P.; Rick, R. L.; Thiele, J.-U.; Hellwig, O.; Schabes, M.E.


    Dipolar interactions in a soft/Pd/hard [CoNi/Pd]{sub 30}/Pd/[Co/Pd]{sub 20} multilayer system, where a thick Pd layer between two ferromagnetic units prevents direct exchange coupling, are directly revealed by combining magnetometry and state-of-the-art layer resolving soft x-ray imaging techniques with sub-100-nm spatial resolution. The domains forming in the soft layer during external magnetic field reversal are found to match the domains previously trapped in the hard layer. The low Curie temperature of the soft layer allows varying its intrinsic parameters via temperature and thus studying the competition with dipolar fields due to the domains in the hard layer. Micromagnetic simulations elucidate the role of [CoNi/Pd] magnetization, exchange, and anisotropy in the duplication process. Finally, thermally driven domain replication in remanence during temperature cycling is demonstrated.

  9. Changes in Protein Domains outside the Catalytic Site of the Bacteriophage Qβ Replicase Reduce the Mutagenic Effect of 5-Azacytidine (United States)

    Cabanillas, Laura; Sanjuán, Rafael


    ABSTRACT The high genetic heterogeneity and great adaptability of RNA viruses are ultimately caused by the low replication fidelity of their polymerases. However, single amino acid substitutions that modify replication fidelity can evolve in response to mutagenic treatments with nucleoside analogues. Here, we investigated how two independent mutants of the bacteriophage Qβ replicase (Thr210Ala and Tyr410His) reduce sensitivity to the nucleoside analogue 5-azacytidine (AZC). Despite being located outside the catalytic site, both mutants reduced the mutation frequency in the presence of the drug. However, they did not modify the type of AZC-induced substitutions, which was mediated mainly by ambiguous base pairing of the analogue with purines. Furthermore, the Thr210Ala and Tyr410His substitutions had little or no effect on replication fidelity in untreated viruses. Also, both substitutions were costly in the absence of AZC or when the action of the drug was suppressed by adding an excess of natural pyrimidines (uridine or cytosine). Overall, the phenotypic properties of these two mutants were highly convergent, despite the mutations being located in different domains of the Qβ replicase. This suggests that treatment with a given nucleoside analogue tends to select for a unique functional response in the viral replicase. IMPORTANCE In the last years, artificial increase of the replication error rate has been proposed as an antiviral therapy. In this study, we investigated the mechanisms by which two substitutions in the Qβ replicase confer partial resistance to the mutagenic nucleoside analogue AZC. As opposed to previous work with animal viruses, where different mutations selected sequentially conferred nucleoside analogue resistance through different mechanisms, our results suggest that there are few or no alternative AZC resistance phenotypes in Qβ. Also, despite resistance mutations being highly costly in the absence of the drug, there was no sequential


    Energy Technology Data Exchange (ETDEWEB)

    Robert S. Weber


    Arthur D. Little, Inc., together with its commercialization partner, Engelhard Corporation, and its university partner Tufts, investigated a single-step process for direct, catalytic reduction of sulfur dioxide from regenerable flue gas desulfurization processes to the more valuable elemental sulfur by-product. This development built on recently demonstrated SO{sub 2}-reduction catalyst performance at Tufts University on a DOE-sponsored program and is, in principle, applicable to processing of regenerator off-gases from all regenerable SO{sub 2}-control processes. In this program, laboratory-scale catalyst optimization work at Tufts was combined with supported catalyst formulation work at Engelhard, bench-scale supported catalyst testing at Arthur D. Little and market assessments, also by Arthur D. Little. Objectives included identification and performance evaluation of a catalyst which is robust and flexible with regard to choice of reducing gas. The catalyst formulation was improved significantly over the course of this work owing to the identification of a number of underlying phenomena that tended to reduce catalyst selectivity. The most promising catalysts discovered in the bench-scale tests at Tufts were transformed into monolith-supported catalysts at Engelhard. These catalyst samples were tested at larger scale at Arthur D. Little, where the laboratory-scale results were confirmed, namely that the catalysts do effectively reduce sulfur dioxide to elemental sulfur when operated under appropriate levels of conversion and in conditions that do not contain too much water or hydrogen. Ways to overcome those limitations were suggested by the laboratory results. Nonetheless, at the end of Phase I, the catalysts did not exhibit the very stringent levels of activity or selectivity that would have permitted ready scale-up to pilot or commercial operation. Therefore, we chose not to pursue Phase II of this work which would have included further bench-scale testing

  11. Direct observation of doping incorporation pathways in self-catalytic GaMnAs nanowires

    DEFF Research Database (Denmark)

    Kasama, Takeshi; Thuvander, M.; Siusys, A.;


    Doping mechanisms of Mn in GaAs nanowires (NWs) that have been grown self-catalytically at 600 degrees C by molecular beam epitaxy (MBE) are investigated using advanced electron microscopy techniques and atom probe tomography, Mn is found to be incorporated primarily in the form of non-magnetic t...

  12. Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers. (United States)

    Woźniak-Celmer, E; Ołdziej, S; Ciarkowski, J


    The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature strongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pseudo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility

  13. Engineering of a novel hybrid enzyme: an anti-inflammatory drug target with triple catalytic activities directly converting arachidonic acid into the inflammatory prostaglandin E2 (United States)

    Ruan, Ke-He; Cervantes, Vanessa; So, Shui-Ping


    Cyclooxygenase isoform-2 (COX-2) and microsomal prostaglandin E2 synthase-1 (mPGES-1) are inducible enzymes that become up-regulated in inflammation and some cancers. It has been demonstrated that their coupling reaction of converting arachidonic acid (AA) into prostaglandin (PG) E2 (PGE2) is responsible for inflammation and cancers. Understanding their coupling reactions at the molecular and cellular levels is a key step toward uncovering the pathological processes in inflammation. In this paper, we describe a structure-based enzyme engineering which produced a novel hybrid enzyme that mimics the coupling reactions of the inducible COX-2 and mPGES-1 in the native ER membrane. Based on the hypothesized membrane topologies and structures, the C-terminus of COX-2 was linked to the N-terminus of mPGES-1 through a transmembrane linker to form a hybrid enzyme, COX-2-10aa-mPGES-1. The engineered hybrid enzyme expressed in HEK293 cells exhibited strong triple-catalytic functions in the continuous conversion of AA into PGG2 (catalytic-step 1), PGH2 (catalytic-step 2) and PGE2 (catalytic-step 3), a pro-inflammatory mediator. In addition, the hybrid enzyme was also able to directly convert dihomo-gamma-linolenic acid (DGLA) into PGG1, PGH1 and then PGE1 (an anti-inflammatory mediator). The hybrid enzyme retained similar Kd and Vmax values to that of the parent enzymes, suggesting that the configuration between COX-2 and mPGES-1 (through the transmembrane domain) could mimic the native conformation and membrane topologies of COX-2 and mPGES-1 in the cells. The results indicated that the quick coupling reaction between the native COX-2 and mPGES-1 (in converting AA into PGE2) occurred in a way so that both enzymes are localized near each other in a face-to-face orientation, where the COX-2 C-terminus faces the mPGES-1 N-terminus in the ER membrane. The COX-2-10aa-mPGES-1 hybrid enzyme engineering may be a novel approach in creating inflammation cell and animal models, which

  14. Effect of mutating the regulatory phosphoserine and conserved threonine on the activity of the expressed catalytic domain of Acanthamoeba myosin I heavy chain kinase


    Szczepanowska, Joanna; Ramachandran, Umamaheswari; Herring, Christopher J.; Gruschus, James M.; Qin, Jun; Korn, Edward D.; Brzeska, Hanna


    Phosphorylation of Ser-627 is both necessary and sufficient for full activity of the expressed 35-kDa catalytic domain of myosin I heavy chain kinase (MIHCK). Ser-627 lies in the variable loop between highly conserved residues DFG and APE at a position at which a phosphorylated Ser/Thr also occurs in many other Ser/Thr protein kinases. The variable loop of MIHCK contains two other hydroxyamino acids: Thr-631, which is conserved in almost all Ser/Thr kinases, and Thr-632, which is not conserve...

  15. The Relative Influence of Different Domains of Social Connectedness on Self-Directed Violence in Adolescence (United States)

    Kaminski, Jennifer W.; Puddy, Richard W.; Hall, Diane M.; Cashman, Sandra Y.; Crosby, Alexander E.; Ortega, LaVonne A. G.


    Previous research has linked greater social connectedness with a lowered risk of self-directed violence among adolescents. However, few studies have analyzed the comparative strength of different domains of connectedness (e.g., family, peers and school) to determine where limited resources might best be focused. Data to address that gap were taken…

  16. Structure of the catalytic domain of the human mitochondrial Lon protease: Proposed relation of oligomer formation and activity

    Czech Academy of Sciences Publication Activity Database

    García-Nafría, J.; Ondrovičová, G.; Blagova, E.; Levdikov, V. M.; Bauer, J. A.; Suzuki, C. K.; Kutejová, Eva; Wilkinson, A. J.; Wilson, K. S.


    Roč. 19, č. 5 (2010), s. 987-999. ISSN 0961-8368 Institutional research plan: CEZ:AV0Z50200510 Keywords : ATP-dependent protease * Lon protease * catalytic dyad Subject RIV: CE - Biochemistry Impact factor: 2.741, year: 2010

  17. Direct observation of Σ7 domain boundary core structure in magnetic skyrmion lattice (United States)

    Matsumoto, Takao; So, Yeong-Gi; Kohno, Yuji; Sawada, Hidetaka; Ikuhara, Yuichi; Shibata, Naoya


    Skyrmions are topologically protected nanoscale magnetic spin entities in helical magnets. They behave like particles and tend to form hexagonal close-packed lattices, like atoms, as their stable structure. Domain boundaries in skyrmion lattices are considered to be important as they affect the dynamic properties of magnetic skyrmions. However, little is known about the fine structure of such skyrmion domain boundaries. We use differential phase contrast scanning transmission electron microscopy to directly visualize skyrmion domain boundaries in FeGe1−xSix induced by the influence of an “edge” of a crystal grain. Similar to hexagonal close-packed atomic lattices, we find the formation of skyrmion “Σ7” domain boundary, whose orientation relationship is predicted by the coincidence site lattice theory to be geometrically stable. On the contrary, the skyrmion domain boundary core structure shows a very different structure relaxation mode. Individual skyrmions can flexibly change their size and shape to accommodate local coordination changes and free volumes formed at the domain boundary cores. Although atomic rearrangement is a common structural relaxation mode in crystalline grain boundaries, skyrmions show very unique and thus different responses to such local lattice disorders. PMID:26933690

  18. Direct catalytic transformation of carbohydrates into 5-ethoxymethylfurfural with acid–base bifunctional hybrid nanospheres

    International Nuclear Information System (INIS)

    Graphical abstract: Catalytic conversion of carbohydrates into HMF and EMF in ethanol/DMSO with acid–base bifunctional hybrid nanospheres prepared from self-assembly of corresponding basic amino acids and HPA. - Highlights: • Acid–base bifunctional nanospheres were efficient for production of EMF from sugars. • Synthesis of EMF in a high yield of 76.6% was realized from fructose. • Fructose based biopolymers could also be converted into EMF with good yields. • Ethyl glucopyranoside was produced in good yields from glucose in ethanol. - Abstract: A series of acid–base bifunctional hybrid nanospheres prepared from the self-assembly of basic amino acids and phosphotungstic acid (HPA) with different molar ratios were employed as efficient and recyclable catalysts for synthesis of liquid biofuel 5-ethoxymethylfurfural (EMF) from various carbohydrates. A high EMF yield of 76.6%, 58.5%, 42.4%, and 36.5% could be achieved, when fructose, inulin, sorbose, and sucrose were used as starting materials, respectively. Although, the acid–base bifunctional nanocatalysts were inert for synthesis of EMF from glucose based carbohydrates, ethyl glucopyranoside in good yields could be obtained from glucose in ethanol. Moreover, the nanocatalyst functionalized with acid and basic sites was able to be reused several times with no significant loss in catalytic activity

  19. Catalysis looks to the future. Panel on new directions in catalytic science and technology

    Energy Technology Data Exchange (ETDEWEB)


    Catalysts play a vital role in providing society with fuels, commodity and fine chemicals, pharmaceuticals, and means for protecting the environment. To be useful, a good catalyst must have a high turnover frequency (activity), produce the right kind of product (selectivity), and have a long life (durability), all at an acceptable cost. Research in the field of catalysis provides the tools and understanding required to facilitate and accelerate the development of improved catalysts and to open opportunities for the discovery of new catalytic processes. The aim of this report is to identify the research opportunities and challenges for catalysis in the coming decades and to detail the resources necessary to ensure steady progress. Chapter 2 discusses opportunities for developing new catalysts to meet the demands of the chemical and fuel industries, and the increasing role of catalysis in environmental protection. The intellectual challenges for advancing the frontiers of catalytic science are outlined in Chapter 3. The human and institutional resources available in the US for carrying out research on catalysis are summarized in Chapter 4. The findings and recommendations of the panel for industry, academe, the national laboratories, and the federal government are presented in Chapter 5.

  20. Testing the Higgs sector directly in the non-relativistic domain

    CERN Document Server

    Zhang, Zhentao


    Directly measuring the Higgs self-coupling is of great importance for testing the Brout-Englert-Higgs mechanism in the Standard Model. As a scattering that contains the direct information from the Higgs self-coupling, we investigate the process $\\mu^-\\mu^+\\rightarrow HH$ in the threshold region. We calculate the one-loop corrections to the cross section and consider the non-perturbative contribution from the Higgs self-interactions in the final state. It is found that the scattering in the non-relativistic domain could be an especial process to testing the Higgs sector directly.

  1. Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins

    Directory of Open Access Journals (Sweden)

    Koskela Harri


    Full Text Available Abstract Background Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains resistant to numerous antibiotics has created a need for new antimicrobial agents and novel drug targets. S. aureus PrsA is a membrane associated extra-cytoplasmic lipoprotein which contains a parvulin-type peptidyl-prolyl cis-trans isomerase domain. PrsA is known to act as an essential folding factor for secreted proteins in Gram-positive bacteria and thus it is a potential target for antimicrobial drugs against S. aureus. Results We have solved a high-resolution solution structure of the parvulin-type peptidyl-prolyl cis-trans isomerase domain of S. aureus PrsA (PrsA-PPIase. The results of substrate peptide titrations pinpoint the active site and demonstrate the substrate preference of the enzyme. With detailed NMR spectroscopic investigation of the orientation and tautomeric state of the active site histidines we are able to give further insight into the structure of the catalytic site. NMR relaxation analysis gives information on the dynamic behaviour of PrsA-PPIase. Conclusion Detailed structural description of the S. aureus PrsA-PPIase lays the foundation for structure-based design of enzyme inhibitors. The structure resembles hPin1-type parvulins both structurally and regarding substrate preference. Even though a wealth of structural data is available on parvulins, the catalytic mechanism has yet to be resolved. The structure of S. aureus PrsA-PPIase and our findings on the role of the conserved active site histidines help in designing further experiments to solve the detailed catalytic mechanism.

  2. Direction of arrival estimation using array model in time-frequency domain

    Institute of Scientific and Technical Information of China (English)

    LIU Yun; LI Zhishun


    Time-frequency analysis is combined with array processing to develop a direction of arrival (DOA) estimation method. The array data model is constructed in time-frequency domain by cross time-frequency distribution between the output of a reference sensor and those of two symmetric sub-arrays. Accordingly a subspace method is presented based on the average of two sub-arrays' time-frequency data vector model instead of the conventional array model, to estimate DOAs of multiple signals. Because the array data is processed both in spatial domain and 2-D time-frequency domain, the proposed method has an ability to select the signal of interesting, and is suitable for non-stationary signal. Additionally, the method is robust to noise and holds an advantage of low computational load. Simulations are conducted to verify the efficiency of the method and comparision is made with other methods.

  3. The SH3 domain, but not the catalytic domain, is required for phospholipase C-γ1 to mediate epidermal growth factor-induced mitogenesis


    Xie, Zhongjian; Chen, Ying; Pennypacker, Sally D.; Zhou, Zhiguang; PENG, DAN


    Phospholipase C-γ1 (PLC-γ1) is a multiple-domain protein and plays an important role in epidermal growth factor (EGF)-induced cell mitogenesis, but the underlying mechanism is unclear. We have previously demonstrated that PLC-γ1 is required for EGF-induced mitogenesis of squamous cell carcinoma (SCC) cells, but the mitogenic function of PLC-γ1 is independent of its lipase activity. Earlier studies suggest that the Src homology 3 (SH3) domain of PLC-γ1 possesses mitogenic activity. In the pres...

  4. Memory for serial order across domains: An overview of the literature and directions for future research. (United States)

    Hurlstone, Mark J; Hitch, Graham J; Baddeley, Alan D


    From vocabulary learning to imitating sequences of motor actions, the ability to plan, represent, and recall a novel sequence of items in the correct order is fundamental for many verbal and nonverbal higher level cognitive activities. Here we review phenomena of serial order documented across the verbal, visual, and spatial short-term memory domains and interpret them with reference to the principles of serial order and ancillary assumptions instantiated in contemporary computational theories of memory for serial order. We propose that functional similarities across domains buttress the notion that verbal, visual, and spatial sequences are planned and controlled by a competitive queuing (CQ) mechanism in which items are simultaneously active in parallel and the strongest item is chosen for output. Within the verbal short-term memory CQ system, evidence suggests that serial order is represented via a primacy gradient, position marking, response suppression, and cumulative matching. Evidence further indicates that output interference operates during recall and that item similarity effects manifest during both serial order encoding and retrieval. By contrast, the principles underlying the representation of serial order in the visual and spatial CQ systems are unclear, largely because the relevant studies have yet to be performed. In the spatial domain, there is some evidence for a primacy gradient and position marking, whereas in the visual domain there is no direct evidence for either of the principles of serial order. We conclude by proposing some directions for future research designed to bridge this and other theoretical gaps in the literature. PMID:24079725

  5. Aminopeptidase N is directly sorted to the apical domain in MDCK cells

    DEFF Research Database (Denmark)

    Wessels, H P; Hansen, Gert Helge; Fuhrer, C; Look, A T; Sjöström, H; Norén, Ove; Spiess, M

    In different epithelial cell types, integral membrane proteins appear to follow different sorting pathways to the apical surface. In hepatocytes, several apical proteins were shown to be transported there indirectly via the basolateral membrane, whereas in MDCK cells a direct sorting pathway from...... the trans-Golgi-network to the apical membrane has been demonstrated. However, different proteins had been studied in these cells. To compare the sorting of a single protein in both systems, we have expressed aminopeptidase N, which already had been shown to be sorted indirectly in hepatocytes, in...... transfected MDCK cells. As expected, it was predominantly localized to the apical domain of the plasma membrane. By monitoring the appearance of newly synthesized aminopeptidase N at the apical and basolateral surface, it was found to be directly sorted to the apical domain in MDCK cells, indicating that the...

  6. MMP-12 Catalytic Domain Recognizes Triple Helical Peptide Models of Collagen V with Exosites and High Activity*S⃞


    Bhaskaran, Rajagopalan; Palmier, Mark O.; Lauer-Fields, Janelle L.; Fields, Gregg B.; Van Doren, Steven R.


    Matrix metalloproteinase (MMP)-12 (or metalloelastase) efficiently hydrolyzed the gelatinase-selective α1(V)436-447 fluorescent triple helical peptide (THP) when the substrate was submicromolar. The sequence of this THP was derived from collagen V, a component of collagen I fibrils. The hemopexin domains of MMP-12 and -9 each increased kcat/Km toward this substrate by decreasing Km, just as the hemopexin domain of MMP-1 enhances its triple helical peptidase activit...

  7. Advanced byproduct recovery: Direct catalytic reduction of sulfur dioxide to elemental sulfur. Quarterly report, April 1--June 30, 1997

    Energy Technology Data Exchange (ETDEWEB)



    The team of Arthur D. Little, Tufts University and Engelhard Corporation are conducting Phase 1 of a four and a half year, two-phase effort to develop and scale-up an advanced byproduct recovery technology that is a direct, single-stage, catalytic process for converting sulfur dioxide to elemental sulfur. This catalytic process reduces SO{sub 2} over a fluorite-type oxide (such as ceria and zirconia). The catalytic activity can be significantly promoted by active transition metals, such as copper. More than 95% elemental sulfur yield, corresponding to almost complete sulfur dioxide conversion, was obtained over a Cu-Ce-O oxide catalyst as part of an on-going DOE-sponsored, University Coal Research Program. This type of mixed metal oxide catalyst has stable activity, high selectivity for sulfur production, and is resistant to water and carbon dioxide poisoning. Tests with CO and CH{sub 4} reducing gases indicate that the catalyst has the potential for flexibility with regard to the composition of the reducing gas, making it attractive for utility use. The performance of the catalyst is consistently good over a range of SO{sub 2} inlet concentration (0.1 to 10%) indicating its flexibility in treating SO{sub 2} tail gases as well as high concentration streams. The principal objective of the Phase 1 program is to identify and evaluate the performance of a catalyst which is robust and flexible with regard to choice of reducing gas. In order to achieve this goal, the authors have planned a structured program including: Market/process/cost/evaluation; Lab-scale catalyst preparation/optimization studies; Lab-scale, bulk/supported catalyst kinetic studies; Bench-scale catalyst/process studies; and Utility review. Progress is reported from all three organizations.

  8. A direct solver with O(N) complexity for integral equations on one-dimensional domains


    Gillman, Adrianna; Young, Patrick; Martinsson, Per-Gunnar


    An algorithm for the direct inversion of the linear systems arising from Nystrom discretization of integral equations on one-dimensional domains is described. The method typically has O(N) complexity when applied to boundary integral equations (BIEs) in the plane with non-oscillatory kernels such as those associated with the Laplace and Stokes' equations. The scaling coefficient suppressed by the "big-O" notation depends logarithmically on the requested accuracy. The method can also be applie...

  9. Crystallization and preliminary X-ray diffraction studies of the catalytic domain of a novel chitinase, a member of GH family 23, from the moderately thermophilic bacterium Ralstonia sp. A-471

    International Nuclear Information System (INIS)

    The catalytic domain of a novel chitinase, which is a member of GH family 23, from the moderately thermophilic bacterium Ralstonia sp. A-471 was crystallized and diffraction data were collected to 1.85 Å resolution. Chitinase from the moderately thermophilic bacterium Ralstonia sp. A-471 (Ra-ChiC) is divided into two domains: a chitin-binding domain (residues 36–80) and a catalytic domain (residues 103–252). Although the catalytic domain of Ra-ChiC has homology to goose-type lysozyme, Ra-ChiC does not show lysozyme activity but does show chitinase activity. The catalytic domain with part of an interdomain loop (Ra-ChiC89–252) was crystallized under several different conditions using polyethylene glycol as a precipitant. The crystals diffracted to 1.85 Å resolution and belonged to space group P6122 or P6522, with unit-cell parameters a = b = 100, c = 243 Å. The calculated Matthews coefficient was approximately 3.2, 2.4 or 1.9 Å3 Da−1 assuming the presence of three, four or five Ra-ChiC89–252 molecules in the asymmetric unit, respectively

  10. Invoking Direct Exciton-Plasmon Interactions by Catalytic Ag Deposition on Au Nanoparticles: Photoelectrochemical Bioanalysis with High Efficiency. (United States)

    Ma, Zheng-Yuan; Xu, Fei; Qin, Yu; Zhao, Wei-Wei; Xu, Jing-Juan; Chen, Hong-Yuan


    In this work, direct exciton-plasmon interactions (EPI) between CdS quantum dots (QDs) and Ag nanoparticles (NPs) were invoked ingeniously by catalytic Ag deposition on Au NPs for the stimulation of high efficient damping effect toward the excitonic responses in CdS QDs, on the basis of which a novel photoelectrochemical (PEC) bioanalytical format was achieved for sensitive microRNA detection. Specifically, upon the configurational change from the hairpin probe DNA to the "Y"-shaped ternary conjugate consisting of the original probe DNA, assistant DNA, and the target microRNA, the alkaline phosphatase (ALP) catalytic chemistry would then trigger the transition of the interparticle interplay from the CdS QDs-Au NPs to the CdS QDs-Ag NPs systems for the microRNA detection due to the dependence of the photocurrent quenching on the target concentration. This work not only provided a unique method for EPI generation among the PEC nanosystems but also offered a versatile and general protocol for future PEC bioanalysis development. PMID:27023112

  11. Direct observation of doping incorporation pathways in self-catalytic GaMnAs nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Kasama, T., E-mail:; Yazdi, S. [Center for Electron Nanoscopy, Technical University of Denmark, DK-2800 Kongens Lyngby (Denmark); Thuvander, M. [Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg (Sweden); Siusys, A. [Institute of Physics, Polish Academy of Sciences, al. Lotników 32/46, PL-02-668 Warszawa (Poland); Gontard, L. C. [Instituto de Ciencia de Materiales de Sevilla (CSIC-US), C/Américo Vespucio 49, 41092 Seville (Spain); Kovács, A.; Duchamp, M.; Dunin-Borkowski, R. E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Gustafsson, A. [Solid State Physics and the Nanometer Structure Consortium, Lund University, P.O. Box 118, SE-221 00 Lund (Sweden); Sadowski, J. [Institute of Physics, Polish Academy of Sciences, al. Lotników 32/46, PL-02-668 Warszawa (Poland); MAX-IV Laboratory, Lund University, P.O. Box 118, SE-221 00 Lund (Sweden)


    Doping mechanisms of Mn in GaAs nanowires (NWs) that have been grown self-catalytically at 600 °C by molecular beam epitaxy (MBE) are investigated using advanced electron microscopy techniques and atom probe tomography. Mn is found to be incorporated primarily in the form of non-magnetic tetragonal Ga{sub 0.82}Mn{sub 0.18} nanocrystals in Ga catalyst droplets at the ends of the NWs, while trace amounts of Mn (22 ± 4 at. ppm) are also distributed randomly in the NW bodies without forming clusters or precipitates. The nanocrystals are likely to form after switching off the reaction in the MBE chamber, since they are partially embedded in neck regions of the NWs. The Ga{sub 0.82}Mn{sub 0.18} nanocrystals and the low Mn concentration in the NW bodies are insufficient to induce a ferromagnetic phase transition, suggesting that it is difficult to have high Mn contents in GaAs even in 1-D NW growth via the vapor-liquid-solid process.

  12. Obtaining a mutant of Bacillus amyloliquefaciens xylanase A with improved catalytic activity by directed evolution. (United States)

    Xu, Xin; Liu, Ming-Qi; Huo, Wen-Kang; Dai, Xian-Jun


    This study aimed to obtain xylanase exhibiting improved enzyme properties to satisfy the requirements for industrial applications. The baxA gene encoding Bacillus amyloliquefaciens xylanase A was mutated by error-prone touchdown PCR. The mutant, pCbaxA50, was screened from the mutant library by using the 96-well plate high-throughput screening method. Sequence alignment revealed the identical mutation point S138T in xylanase (reBaxA50) produced by the pCbaxA50. The specific activity of the purified reBaxA50 was 9.38U/mg, which was 3.5 times higher than that of its parent expressed in Escherichia coli BL21 (DE3), named reBaxA. The optimum temperature of reBaxA and reBaxA50 were 55°C and 50°C, respectively. The optimum pH of reBaxA and reBaxA50 were pH 6 and pH 5, respectively. Moreover, reBaxA50 was more stable than reBaxA under thermal and extreme pH treatment. The half-life at 60°C and apparent melting temperature of reBaxA50 were 9.74min and 89.15°C, respectively. High-performance liquid chromatography showed that reBaxA50 released xylooligosaccharides from oat spelt, birchwood, and beechwood xylans, with xylotriose as the major product; beechwood xylan was also the most thoroughly hydrolyzed. This study demonstrated that the S138T mutation possibly improved the catalytic activity and thermostability of reBaxA50. PMID:26992794

  13. Fine tuning of the catalytic activity of colicin e7 nuclease domain by systematic n-terminal mutations

    DEFF Research Database (Denmark)

    Németh, Eszter; Körtvélyesi, Tamás; Thulstrup, Peter W.; Christensen, Hans Erik Mølager; Kožíšek, Milan; Nagata, Kyosuke; Czene, Aniko; Gyurcsik, Béla


    The nuclease domain of colicin E7 (NColE7) promotes the nonspecific cleavage of nucleic acids at its C-terminal HNH motif. Interestingly, the deletion of four N-terminal residues (446–449NColE75KRNK) resulted in complete loss of the enzyme activity. R447A mutation was reported to decrease the nuc...


    Institute of Scientific and Technical Information of China (English)


    Objective. To investigate the expression of telomerase gene hTRT mRNA in HeLa cells and to obtain hTRT pro-tein for futher study. Methods. The gene for encoding hTRT catalytic domain was cloned based on RT-PCR amplification from HeLa cells and sequenced. The cloned hTRTcDNA was in-frame inserted into His-tag fusion expression vector pEK318. The His-tag hTRT fusion proteins were purified by Ni-NTA chromatography and stained by westerm blotting. Results. An approximately 620bp fragment was generated and cloned into pBluescript SK + between Sail and BamHI sites. DNA sequencing showed the isolated fragment was consistem to those reported. SDS-PAGE present that a 17kDa protein was expressed stably in E. coli JM109 harboring pEKTRTM4 containing 6 × His-tag and hTRT 150aa, and the expression level of the protein was about 26% of the total bacterial proteins, while the expression of pEKTRT containing 6 × His-tag and hTRT 243aa was only detectable as 27 kDa band in western blotting. Both of fu-sion proteins were purified by Ni-NTA chromatography and showed single band( > 95% purifity) in Coomassie Bril-liant staining. Westem-blotting confirmed that two proteins could be recognized by the Ni-NTA AP conjugate. Conclusions. The hTRT catalytic domain was highly conserved. The expressed hTRT protein contained recogniz-able His-tag, telomerase-specific and strong antigenic epitops, which may be convenient for further investigation.

  15. Direct numerical simulation of turbulent heat transfer in a fluid-porous domain

    International Nuclear Information System (INIS)

    Turbulent heat transfer in a channel partially filled by a porous medium is investigated using a direct numerical simulation of an incompressible flow. The porous medium consists of a three-dimensional Cartesian grid of cubes, which has a relatively high permeability. The energy equation is not solved in the cubes. Three different heating configurations are studied. The simulation is performed for a bulk Reynolds number Reb = 5500 and a Prandtl number Pr = 0.1. The turbulent flow quantities are compared with the results of Breugem and Boersma ['Direct numerical simulations of turbulent flow over a permeable wall using a direct and a continuum approach,' Phys. Fluids 17, 025103 (2005)] to validate the numerical approach and macroscopic turbulent quantities are analyzed. Regarding the temperature fields, original results are obtained. The temperature fields show an enhanced turbulent heat transfer just above the porous region compared to the solid top wall, which can be related to the large vortical structures that develop in this region. Furthermore, these large structures induce pressure waves inside the porous domain which are responsible of large temperature fluctuations deep inside the porous region where the flow is laminar. Finally, macroscopic turbulent quantities are computed to get reference results for the development of macroscopic turbulent heat transfer models in fluid-porous domain. (authors)

  16. Catalytic Enhancement of Carbon Black and Coal-Fueled Hybrid Direct Carbon Fuel Cells

    DEFF Research Database (Denmark)

    Deleebeeck, Lisa; Ippolito, Davide; Kammer Hansen, Kent


    Hybrid direct carbon fuel cells (HDCFCs) consisting of a solid carbon (carbon black)-molten carbonate ((62–38 wt% Li-K)2CO3) mixtures in the anode chamber of an anode-supported solid oxide fuel cell type full-cell are tested for their electrochemical performance between 700 and 800°C. Performance...

  17. Isolation of an Active Catalytic Core of Streptococcus downei MFe28 GTF-I Glucosyltransferase


    Monchois, Vincent; Arguello-Morales, Martha; Russell, Roy R. B.


    Truncated variants of GTF-I from Streptococcus downei MFe28 were purified by means of a histidine tag. Sequential deletions showed that the C-terminal domain was not directly involved in the catalytic process but was required for primer activation. A fully active catalytic core of only 100 kDa was isolated.



    Maria Gonta; Gheorghe Duca; Vera Matveevici; Larisa Mocanu


    Advanced oxidation methods of organic compounds lead to their partial mineralization and increase of the adsorption process efficiency on the surface of oxidized activated carbon. We have studied the oxidation process using model solutions containing mixture of dye direct brown (DB), ethylene glycol (EGL) and sodium lauryl sulfate (SLS) under the action of Fenton reagent, in the presence and absence of UV irradiation or under the action of electric current (in the electrochemical cell). The s...

  19. Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics. (United States)

    Bujnicki, J M; Rotkiewicz, P; Kolinski, A; Rychlewski, L


    Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain (CD) of the I-TevI homing endonuclease, a representative of the GIY-YIG superfamily of homing endonucleases. The secondary structure of the I-TevI CD has been determined using NMR spectroscopy, but computational sequence analysis failed to detect any protein of known tertiary structure related to the GIY-YIG nucleases (Kowalski et al., Nucleic Acids Res., 1999, 27, 2115-2125). To provide further insight into the structure-function relationships of all GIY-YIG superfamily members, including the recently described subfamily of type II restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9-11), we incorporated the experimentally determined and predicted secondary and tertiary restraints in a reduced (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available experimental data to be put into a structural context and suggests that the GIY-YIG domain may dimerize in order to bring together the conserved residues of the active site. PMID:11739889

  20. Easy moment direction and antiferromagnetic domain wall motion in Mn2Au (United States)

    Barthem, Vitoria M. T. S.; Colin, Claire V.; Haettel, Richard; Dufeu, Didier; Givord, Dominique


    The interest of giving active functions to antiferromagnetic (AFM) materials in spintronics devices has been realized recently. Mn2Au is a high-Néel temperature antiferromagnet with large Mn moment, lying in plane of the tetragonal structure. To determine the direction of the moments in Mn2Au, an original approach is demonstrated, which should be generic to planar AFM materials. It involves the rotation of the granular sample around an axis perpendicular to the applied magnetic field. The family of easy moment directions is . For grains prevented from rotating, the dominant magnetization process is AFM domain wall motion. Textured Mn2Au nanoelements could be introduced in spintronics devices, in which the Mn moments would be switched under modest external excitation.

  1. Directional Molecular Transportation Based on a Catalytic Stopper-Leaving Rotaxane System. (United States)

    Meng, Zheng; Xiang, Jun-Feng; Chen, Chuan-Feng


    Ratchet mechanism has proved to be a key principle in designing molecular motors and machines that exploit random thermal fluctuations for directional motion with energy input. To integrate ratchet mechanism into artificial systems, precise molecular design is a prerequisite to control the pathway of relative motion between their subcomponents, which is still a formidable challenge. Herein, we report a straightforward method to control the transportation barrier of a macrocycle by selectively detaching one of the two stoppers using a novel DBU-catalyzed stopper-leaving reaction in a rotaxane system. The macrocycle was first allowed to thread onto a semidumbbell axle from the open end and subsequently thermodynamically captured into a nonsymmetrical rotaxane. Then, it was driven energetically uphill until it reached a kinetically trapped state by destroying its interaction with ammonium site, and was finally quantitatively released from the other end when the corresponding stopper barrier was removed. Although the directional transportation at the present system was achieved by discrete chemical reactions for the sake of higher transportation efficiency, it represents a new molecular transportation model by the strategy of using stopper-leavable rotaxane. PMID:27078221

  2. Directed evolution of Mycobacterium tuberculosis β-lactamase reveals gatekeeper residue that regulates antibiotic resistance and catalytic efficiency.

    Directory of Open Access Journals (Sweden)

    Christian Feiler

    Full Text Available Directed evolution can be a powerful tool for revealing the mutational pathways that lead to more resistant bacterial strains. In this study, we focused on the bacterium Mycobacterium tuberculosis, which is resistant to members of the β-lactam class of antibiotics and thus continues to pose a major public health threat. Resistance of this organism is the result of a chromosomally encoded, extended spectrum class A β-lactamase, BlaC, that is constitutively produced. Here, combinatorial enzyme libraries were selected on ampicillin to identify mutations that increased resistance of bacteria to β-lactams. After just a single round of mutagenesis and selection, BlaC mutants were evolved that conferred 5-fold greater antibiotic resistance to cells and enhanced the catalytic efficiency of BlaC by 3-fold compared to the wild-type enzyme. All isolated mutants carried a mutation at position 105 (e.g., I105F that appears to widen access to the active site by 3.6 Å while also stabilizing the reorganized topology. In light of these findings, we propose that I105 is a 'gatekeeper' residue of the active site that regulates substrate hydrolysis by BlaC. Moreover, our results suggest that directed evolution can provide insight into the development of highly drug resistant microorganisms.

  3. Green synthesis of silver nanoparticles using Terminalia cuneata and its catalytic action in reduction of direct yellow-12 dye (United States)

    Edison, Thomas Nesakumar Jebakumar Immanuel; Lee, Yong Rok; Sethuraman, Mathur Gopalakrishnan


    Facile green synthesis of silver nanoparticles (AgNPs) using aqueous bark extract of Terminalia cuneata has been reported in this article. The effects of concentration of the extract, reaction time and pH were studied by UV-Vis spectroscopy. Appearance of yellow color with λmax around ~ 420 nm suggested the formation of AgNPs. The stable AgNPs were further characterized by Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), dynamic light scattering (DLS) with zeta potential and high resolution transmission electron microscopy (HR-TEM) with energy dispersive X-ray spectroscopy (EDS) analysis. The synthesized AgNPs were in the size range of 25-50 nm with a distorted spherical shape identified from HR-TEM analysis. The catalytic activity of AgNPs on the reduction of direct yellow-12 using NaBH4 was analyzed using a UV-Vis spectrophotometer. This study showed the efficacy of biogenic AgNPs in catalyzing the reduction of direct yellow-12.

  4. Domains of quality of life of people with profound multiple disabilities : The perspective of parents and direct support staff

    NARCIS (Netherlands)

    Petry, K; Maes, B; Vlaskamp, C


    Background This study considered the general validity of the basic domains of quality of life that appear in theoretical models, in relation to people with profound multiple disabilities. The authors examined how parents and direct support staff operationalized these basic domains for people with pr

  5. Direct conversion of methane to aromatics in a catalytic co-ionic membrane reactor. (United States)

    Morejudo, S H; Zanón, R; Escolástico, S; Yuste-Tirados, I; Malerød-Fjeld, H; Vestre, P K; Coors, W G; Martínez, A; Norby, T; Serra, J M; Kjølseth, C


    Nonoxidative methane dehydroaromatization (MDA: 6CH4 ↔ C6H6 + 9H2) using shape-selective Mo/zeolite catalysts is a key technology for exploitation of stranded natural gas reserves by direct conversion into transportable liquids. However, this reaction faces two major issues: The one-pass conversion is limited by thermodynamics, and the catalyst deactivates quickly through kinetically favored formation of coke. We show that integration of an electrochemical BaZrO3-based membrane exhibiting both proton and oxide ion conductivity into an MDA reactor gives rise to high aromatic yields and improved catalyst stability. These effects originate from the simultaneous extraction of hydrogen and distributed injection of oxide ions along the reactor length. Further, we demonstrate that the electrochemical co-ionic membrane reactor enables high carbon efficiencies (up to 80%) that improve the technoeconomic process viability. PMID:27493179

  6. Direct Production of 5-Hydroxymethylfurfural via Catalytic Conversion of Simple and Complex Sugars over Phosphated TiO2. (United States)

    Atanda, Luqman; Shrotri, Abhijit; Mukundan, Swathi; Ma, Qing; Konarova, Muxina; Beltramini, Jorge


    A water-THF biphasic system containing N-methyl-2-pyrrolidone (NMP) was found to enable the efficient synthesis of 5-hydroxymethylfurfural (HMF) from a variety of sugars (simple to complex) using phosphated TiO2 as a catalyst. Fructose and glucose were selectively converted to HMF resulting in 98 % and 90 % yield, respectively, at 175 °C. Cellobiose and sucrose also gave rise to high HMF yields of 94 % and 98 %, respectively, at 180 °C. Other sugar variants such as starch (potato and rice) and cellulose were also investigated. The yields of HMF from starch (80-85 %) were high, whereas cellulose resulted in a modest yield of 33 %. Direct transformation of cellulose to HMF in significant yield (86 %) was assisted by mechanocatalytic depolymerization-ball milling of acid-impregnated cellulose. This effectively reduced cellulose crystallinity and particle size, forming soluble cello-oligomers; this is responsible for the enhanced substrate-catalytic sites contact and subsequent rate of HMF formation. During catalyst recyclability, P-TiO2 was observed to be reusable for four cycles without any loss in activity. We also investigated the conversion of the cello-oligomers to HMF in a continuous flow reactor. Good HMF yield (53 %) was achieved using a water-methyl isobutyl ketone+NMP biphasic system. PMID:26238933

  7. Polarography study of catalytic electroreduction of indium (3) hydroxocompleX and direct electroreduction of indium (3) aquo-ions

    International Nuclear Information System (INIS)

    The kinetics and mechanism of In3+ aquoions discharge on the mercury cathode both in he catalysis by OH- ions and in the direct electroreduction of In3+ aquo-ions are polarographically investigated. In a non-compleXing (NaClO4) background electrolyte at pH3+ aquo-ion discharge, catalized by OH- ions (first wave), is due to the following electrode reactions: In(H2O)63++H2O reversible In(OH)(H2O)52++H3O+. In(OH)(H2O)52 slowly → In(OH)(Hsub(2)O)sub(4)(Hsub(2)O)sub(ads)sup(2+) + H2O In(OH)(Hsub(2)O)sub(4)(Hsub(2)O)sub(ads)sup(2+) reversible In(Hg)+OH- +4H2O + Hsub(2)Osub(ads). The study of a parallel discharge of In3+ second wave aquo-ions enabled to determine the kinetic parameters of this process (K0=4.0x10-12 cm/s, ap 0.84,1 mole/l NaClO4) withaut a distorting effect of the catalytic discharge of the In(3) hydrocomplex

  8. Copper directs ATP7B to the apical domain of hepatic cells via basolateral endosomes. (United States)

    Nyasae, Lydia K; Schell, Michael J; Hubbard, Ann L


    Physiologic Cu levels regulate the intracellular location of the Cu ATPase ATP7B. Here, we determined the routes of Cu-directed trafficking of endogenous ATP7B in the polarized hepatic cell line WIF-B and in the liver in vivo. Copper (10 µm) caused ATP7B to exit the trans-Golgi network (TGN) in vesicles, which trafficked via large basolateral endosomes to the apical domain within 1 h. Although perturbants of luminal acidification had little effect on the TGN localization of ATP7B in low Cu, they blocked delivery to the apical membrane in elevated Cu. If the vesicular proton-pump inhibitor bafilomycin-A1 (Baf) was present with Cu, ATP7B still exited the TGN, but accumulated in large endosomes located near the coverslip, in the basolateral region. Baf washout restored ATP7B trafficking to the apical domain. If ATP7B was staged apically in high Cu, Baf addition promoted the accumulation of ATP7B in subapical endosomes, indicating a blockade of apical recycling, with concomitant loss of ATP7B at the apical membrane. The retrograde pathway to the TGN, induced by Cu removal, was far less affected by Baf than the anterograde (Cu-stimulated) case. Overall, loss of acidification-impaired Cu-regulated trafficking of ATP7B at two main sites: (i) sorting and exit from large basolateral endosomes and (ii) recycling via endosomes near the apical membrane. PMID:25243755

  9. Direct imaging of the structural domains in the iron pnictides AFe2As2 (A=Ca, Sr, Ba)

    International Nuclear Information System (INIS)

    The parent compounds of recently discovered iron-arsenide superconductors, AFe2As2 with alkaline earth A=Ca,Sr,Ba, undergo simultaneous structural and magnetic phase transitions at a temperature TSM. Using a combination of polarized light microscopy and spatially resolved high-energy synchrotron x-ray diffraction we show that the orthorhombic distortion leads to the formation of 45o-type structural domains in all parent compounds. Domains penetrate through the sample thickness in the c direction and are not affected by crystal imperfections such as growth terraces. The domains form regular stripe patterns in the plane with a characteristic dimension of 10--50 μm. The direction of the stripes is fixed with respect to the tetragonal (100) and (010) directions but can change by 90o on thermal cycling through the transition. This domain pattern may have profound implications for intrinsic disorder and anisotropy of iron arsenides.

  10. Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity. (United States)

    Murashko, Oleg N; Kaberdin, Vladimir R; Lin-Chao, Sue


    RNase E plays an essential role in RNA processing and decay and tethers to the cytoplasmic membrane in Escherichia coli; however, the function of this membrane-protein interaction has remained unclear. Here, we establish a mechanistic role for the RNase E-membrane interaction. The reconstituted highly conserved N-terminal fragment of RNase E (NRne, residues 1-499) binds specifically to anionic phospholipids through electrostatic interactions. The membrane-binding specificity of NRne was confirmed using circular dichroism difference spectroscopy; the dissociation constant (K(d)) for NRne binding to anionic liposomes was 298 nM. E. coli RNase G and RNase E/G homologs from phylogenetically distant Aquifex aeolicus, Haemophilus influenzae Rd, and Synechocystis sp. were found to be membrane-binding proteins. Electrostatic potentials of NRne and its homologs were found to be conserved, highly positive, and spread over a large surface area encompassing four putative membrane-binding regions identified in the "large" domain (amino acids 1-400, consisting of the RNase H, S1, 5'-sensor, and DNase I subdomains) of E. coli NRne. In vitro cleavage assay using liposome-free and liposome-bound NRne and RNA substrates BR13 and GGG-RNAI showed that NRne membrane binding altered its enzymatic activity. Circular dichroism spectroscopy showed no obvious thermotropic structural changes in membrane-bound NRne between 10 and 60 °C, and membrane-bound NRne retained its normal cleavage activity after cooling. Thus, NRne membrane binding induced changes in secondary protein structure and enzymatic activation by stabilizing the protein-folding state and increasing its binding affinity for its substrate. Our results demonstrate that RNase E-membrane interaction enhances the rate of RNA processing and decay. PMID:22509045

  11. Distributive Processing by the Iron(II)/α-Ketoglutarate-Dependent Catalytic Domains of the TET Enzymes Is Consistent with Epigenetic Roles for Oxidized 5-Methylcytosine Bases. (United States)

    Tamanaha, Esta; Guan, Shengxi; Marks, Katherine; Saleh, Lana


    The ten-eleven translocation (TET) proteins catalyze oxidation of 5-methylcytosine ((5m)C) residues in nucleic acids to 5-hydroxymethylcytosine ((5hm)C), 5-formylcytosine ((5f)C), and 5-carboxycytosine ((5ca)C). These nucleotide bases have been implicated as intermediates on the path to active demethylation, but recent reports have suggested that they might have specific regulatory roles in their own right. In this study, we present kinetic evidence showing that the catalytic domains (CDs) of TET2 and TET1 from mouse and their homologue from Naegleria gruberi, the full-length protein NgTET1, are distributive in both chemical and physical senses, as they carry out successive oxidations of a single (5m)C and multiple (5m)C residues along a polymethylated DNA substrate. We present data showing that the enzyme neither retains (5hm)C/(5f)C intermediates of preceding oxidations nor slides along a DNA substrate (without releasing it) to process an adjacent (5m)C residue. These findings contradict a recent report by Crawford et al. ( J. Am. Chem. Soc. 2016 , 138 , 730 ) claiming that oxidation of (5m)C by CD of mouse TET2 is chemically processive (iterative). We further elaborate that this distributive mechanism is maintained for TETs in two evolutionarily distant homologues and posit that this mode of function allows the introduction of (5m)C forms as epigenetic markers along the DNA. PMID:27362828

  12. CDKL5 gene status in female patients with epilepsy and Rett-like features: two new mutations in the catalytic domain

    Directory of Open Access Journals (Sweden)

    Maortua Hiart


    Full Text Available Abstract Background Mutations in the cyclin-dependent kinase-like 5 gene (CDKL5 located in the Xp22 region have been shown to cause a subset of atypical Rett syndrome with infantile spasms or early seizures starting in the first postnatal months. Methods We performed mutation screening of CDKL5 in 60 female patients who had been identified as negative for the methyl CpG-binding protein 2 gene (MECP2 mutations, but who had current or past epilepsy, regardless of the age of onset, type, and severity. All the exons in the CDKL5 gene and their neighbouring sequences were examined, and CDKL5 rearrangements were studied by multiplex ligation-dependent probe amplification (MLPA. Results Six previously unidentified DNA changes were detected, two of which were disease-causing mutations in the catalytic domain: a frameshift mutation (c.509_510insGT; p.Glu170GlyfsX36 and a complete deletion of exon 10. Both were found in patients with seizures that started in the first month of life. Conclusions This study demonstrated the importance of CDKL5 mutations as etiological factors in neurodevelopmental disorders, and indicated that a thorough analysis of the CDKL5 gene sequence and its rearrangements should be considered in females with Rett syndrome-like phenotypes, severe encephalopathy and epilepsy with onset before 5 months of age. This study also confirmed the usefulness of MLPA as a diagnostic screening method for use in clinical practice.

  13. Crystal structure of the N-acetyltransferase domain of human N-acetyl-L-glutamate synthase in complex with N-acetyl-L-glutamate provides insights into its catalytic and regulatory mechanisms.

    Directory of Open Access Journals (Sweden)

    Gengxiang Zhao

    Full Text Available N-acetylglutamate synthase (NAGS catalyzes the conversion of AcCoA and L-glutamate to CoA and N-acetyl-L-glutamate (NAG, an obligate cofactor for carbamyl phosphate synthetase I (CPSI in the urea cycle. NAGS deficiency results in elevated levels of plasma ammonia which is neurotoxic. We report herein the first crystal structure of human NAGS, that of the catalytic N-acetyltransferase (hNAT domain with N-acetyl-L-glutamate bound at 2.1 Å resolution. Functional studies indicate that the hNAT domain retains catalytic activity in the absence of the amino acid kinase (AAK domain. Instead, the major functions of the AAK domain appear to be providing a binding site for the allosteric activator, L-arginine, and an N-terminal proline-rich motif that is likely to function in signal transduction to CPS1. Crystalline hNAT forms a dimer similar to the NAT-NAT dimers that form in crystals of bifunctional N-acetylglutamate synthase/kinase (NAGS/K from Maricaulis maris and also exists as a dimer in solution. The structure of the NAG binding site, in combination with mutagenesis studies, provide insights into the catalytic mechanism. We also show that native NAGS from human and mouse exists in tetrameric form, similar to those of bifunctional NAGS/K.

  14. Crystal structure of the N-acetyltransferase domain of human N-acetyl-L-glutamate synthase in complex with N-acetyl-L-glutamate provides insights into its catalytic and regulatory mechanisms. (United States)

    Zhao, Gengxiang; Jin, Zhongmin; Allewell, Norma M; Tuchman, Mendel; Shi, Dashuang


    N-acetylglutamate synthase (NAGS) catalyzes the conversion of AcCoA and L-glutamate to CoA and N-acetyl-L-glutamate (NAG), an obligate cofactor for carbamyl phosphate synthetase I (CPSI) in the urea cycle. NAGS deficiency results in elevated levels of plasma ammonia which is neurotoxic. We report herein the first crystal structure of human NAGS, that of the catalytic N-acetyltransferase (hNAT) domain with N-acetyl-L-glutamate bound at 2.1 Å resolution. Functional studies indicate that the hNAT domain retains catalytic activity in the absence of the amino acid kinase (AAK) domain. Instead, the major functions of the AAK domain appear to be providing a binding site for the allosteric activator, L-arginine, and an N-terminal proline-rich motif that is likely to function in signal transduction to CPS1. Crystalline hNAT forms a dimer similar to the NAT-NAT dimers that form in crystals of bifunctional N-acetylglutamate synthase/kinase (NAGS/K) from Maricaulis maris and also exists as a dimer in solution. The structure of the NAG binding site, in combination with mutagenesis studies, provide insights into the catalytic mechanism. We also show that native NAGS from human and mouse exists in tetrameric form, similar to those of bifunctional NAGS/K. PMID:23894642

  15. Direct catalytic conversion of methane and light hydrocarbon gases. Final report, October 1, 1986--July 31, 1989

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, R.B. Jr.; Posin, B.M.; Chan, Yee-Wai


    This project explored conversion of methane to useful products by two techniques that do not involve oxidative coupling. The first approach was direct catalytic dehydrocoupling of methane to give hydrocarbons and hydrogen. The second approach was oxidation of methane to methanol by using heterogenized versions of catalysts that were developed as homogeneous models of cytochrome-P450, an enzyme that actively hydroxylates hydrocarbons by using molecular oxygen. Two possibilities exist for dehydrocoupling of methane to higher hydrocarbons: The first, oxidative coupling to ethane/ethylene and water, is the subject of intense current interest. Nonoxidative coupling to higher hydrocarbons and hydrogen is endothermic, but in the absence of coke formation the theoretical thermodynamic equilibrium yield of hydrocarbons varies from 25% at 827{degrees}C to 65% at 1100{degrees}C (at atmospheric pressure). In this project we synthesized novel, highly dispersed metal catalysts by attaching metal clusters to inorganic supports. The second approach mimics microbial metabolism of methane to produce methanol. The methane mono-oxygenase enzyme responsible for the oxidation of methane to methanol in biological systems has exceptional selectivity and very good rates. Enzyme mimics are systems that function as the enzymes do but overcome the problems of slow rates and poor stability. Most of that effort has focused on mimics of cytochrome P-450, which is a very active selective oxidation enzyme and has a metalloporphyrin at the active site. The interest in nonporphyrin mimics coincides with the interest in methane mono-oxygenase, whose active site has been identified as a {mu}-oxo dinuclear iron complex.We employed mimics of cytochrome P-450, heterogenized to provide additional stability. The oxidation of methane with molecular oxygen was investigated in a fixed-bed, down-flow reactor with various anchored metal phthalocyanines (PC) and porphyrins (TPP) as the catalysts.

  16. Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains. (United States)

    Ishikawa, Fumihiro; Miyamoto, Kengo; Konno, Sho; Kasai, Shota; Kakeya, Hideaki


    A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique

  17. Crystallization and preliminary X-ray characterization of a catalytic and ATP-binding domain of a putative PhoR histidine kinase from the γ-radioresistant bacterium Deinococcus radiodurans

    International Nuclear Information System (INIS)

    The expression, purification and crystallization of a catalytic and ATP-binding domain of PhoR histidine kinase from D. radiodurans is described. The gene product of histidine kinase DR2244 (putative phoR) encoded by Deinococcus radiodurans has been suggested to be involved in the PhoR–PhoB two-component regulatory system. This two-component signalling system is activated upon phosphate starvation in several bacteria, including D. radiodurans. Single crystals were obtained from a recombinant preparation of the catalytic/ATP-binding (CA) domain of D. radiodurans PhoR (79–224) overexpressed in Escherichia coli. The crystals belonged to space group P212121, with unit-cell parameters a = 46.9, b = 81.8, c = 204.6 Å. The crystals contained six molecules in the asymmetric unit. Diffraction data were collected to 2.4 Å resolution on beamline ID23-2 of the European Synchrotron Radiation Facility

  18. Toward antibody-directed "abzyme" prodrug therapy, ADAPT: carbamate prodrug activation by a catalytic antibody and its in vitro application to human tumor cell killing.


    Wentworth, P; Datta, A.; Blakey, D; Boyle, T; Partridge, L. J.; Blackburn, G M


    Antibody-directed enzyme prodrug therapy, ADEPT, is a recent approach to targeted cancer chemotherapy intended to diminish the nonspecific toxicity associated with many commonly used chemotherapeutic agents. Most ADEPT systems incorporate a bacterial enzyme, and thus their potential is reduced because of the immunogenicity of that component of the conjugate. This limitation can be circumvented by the use of a catalytic antibody, which can be "humanized," in place of the bacterial enzyme catal...

  19. A direct solver with O(N) complexity for integral equations on one-dimensional domains

    CERN Document Server

    Gillman, Adrianna; Martinsson, Per-Gunnar


    An algorithm for the direct inversion of the linear systems arising from Nystrom discretization of integral equations on one-dimensional domains is described. The method typically has O(N) complexity when applied to boundary integral equations (BIEs) in the plane with non-oscillatory kernels such as those associated with the Laplace and Stokes' equations. The scaling coefficient suppressed by the "big-O" notation depends logarithmically on the requested accuracy. The method can also be applied to BIEs with oscillatory kernels such as those associated with the Helmholtz and Maxwell equations; it is efficient at long and intermediate wave-lengths, but will eventually become prohibitively slow as the wave-length decreases. To achieve linear complexity, rank deficiencies in the off-diagonal blocks of the coefficient matrix are exploited. The technique is conceptually related to the H and H^2 matrix arithmetic of Hackbusch and co-workers, and is closely related to previous work on Hierarchically Semi-Separable mat...

  20. Assignments and structure determination of the catalytic domain of human fibroblast collagenase using 3D double and triple resonance NMR spectroscopy

    International Nuclear Information System (INIS)

    We report here the backbone 1HN, 15N, 13Cα, 13CO, and 1Hα NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13Cα, and 13CO resonances) were used to establish sequential connections. The connections using 13Cα resonances were obtained from HNCOCA and HNCA experiments; 13CO connections were obtained from HNCO and HNCACO experiments. The sequential proton assignment pathway was established from a 3D(1H/15N) NOESY-HSQC experiment. Amino acid typing was accomplished using 13C and 15N chemical shifts, specific labeling of 15N-Leu, and spin pattern recognition from DQF-COSY. The secondary structure was determined by analyzing the 3D (1H/15N) NOESY-HSQC. A preliminary NMR structure calculation of HFC was found to be in agreement with recent X-ray structures of human fibroblast collagenase and human neutrophil collagenase as well as similar to recent NMR structures of a highly homologous protein, stromelysin. All three helices were located; a five-stranded β-sheet (four parallel strands, one antiparallel strand) was also determined. β-Sheet regions were identified by cross-strand dαN and dNN connections and by strong intraresidue dαN correlations, and were corroborated by observing slow amide proton exchange. Chemical shift changes in a selectively 15N-labeled sample suggest that substantial structural changes occur in the active site cleft on the binding of an inhibitor

  1. A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly.

    Directory of Open Access Journals (Sweden)

    Allison Ballandras

    Full Text Available Integrase (IN is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained on the catalytic core domain (CCD of the avian Rous and Sarcoma Virus strain Schmidt-Ruppin A (RSV-A and on the CCD of HIV-1 IN. A ribonuclease-H like motif was revealed as well as a dimeric interface stabilized by two pairs of α-helices (α1/α5, α5/α1. These structural features have been validated in other structures of IN CCDs. We have determined the crystal structure of the Rous-associated virus type-1 (RAV-1 IN CCD to 1.8 Å resolution. RAV-1 IN shows a standard activity for integration and its CCD differs in sequence from that of RSV-A by a single accessible residue in position 182 (substitution A182T. Surprisingly, the CCD of RAV-1 IN associates itself with an unexpected dimeric interface characterized by three pairs of α-helices (α3/α5, α1/α1, α5/α3. A182 is not involved in this novel interface, which results from a rigid body rearrangement of the protein at its α1, α3, α5 surface. A new basic groove that is suitable for single-stranded nucleic acid binding is observed at the surface of the dimer. We have subsequently determined the structure of the mutant A182T of RAV-1 IN CCD and obtained a RSV-A IN CCD-like structure with two pairs of buried α-helices at the interface. Our results suggest that the CCD of avian INs can dimerize in more than one state. Such flexibility can further explain the multifunctionality of retroviral INs, which beside integration of dsDNA are implicated in different steps of the retroviral cycle in presence of viral ssRNA.

  2. A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly. (United States)

    Ballandras, Allison; Moreau, Karen; Robert, Xavier; Confort, Marie-Pierre; Merceron, Romain; Haser, Richard; Ronfort, Corinne; Gouet, Patrice


    Integrase (IN) is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV) inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained on the catalytic core domain (CCD) of the avian Rous and Sarcoma Virus strain Schmidt-Ruppin A (RSV-A) and on the CCD of HIV-1 IN. A ribonuclease-H like motif was revealed as well as a dimeric interface stabilized by two pairs of α-helices (α1/α5, α5/α1). These structural features have been validated in other structures of IN CCDs. We have determined the crystal structure of the Rous-associated virus type-1 (RAV-1) IN CCD to 1.8 Å resolution. RAV-1 IN shows a standard activity for integration and its CCD differs in sequence from that of RSV-A by a single accessible residue in position 182 (substitution A182T). Surprisingly, the CCD of RAV-1 IN associates itself with an unexpected dimeric interface characterized by three pairs of α-helices (α3/α5, α1/α1, α5/α3). A182 is not involved in this novel interface, which results from a rigid body rearrangement of the protein at its α1, α3, α5 surface. A new basic groove that is suitable for single-stranded nucleic acid binding is observed at the surface of the dimer. We have subsequently determined the structure of the mutant A182T of RAV-1 IN CCD and obtained a RSV-A IN CCD-like structure with two pairs of buried α-helices at the interface. Our results suggest that the CCD of avian INs can dimerize in more than one state. Such flexibility can further explain the multifunctionality of retroviral INs, which beside integration of dsDNA are implicated in different steps of the retroviral cycle in presence of viral ssRNA. PMID:21857987

  3. Properties and catalytic activities of MICAL1, the flavoenzyme involved in cytoskeleton dynamics, and modulation by its CH, LIM and C-terminal domains. (United States)

    Vitali, Teresa; Maffioli, Elisa; Tedeschi, Gabriella; Vanoni, Maria A


    MICAL1 is a cytoplasmic 119 kDa protein participating in cytoskeleton dynamics through the NADPH-dependent oxidase and F-actin depolymerizing activities of its N-terminal flavoprotein domain, which is followed by calponin homology (CH), LIM domains and a C-terminal region with Pro-, Glu-rich and coiled-coil motifs. MICAL1 and truncated forms lacking the C-terminal, LIM and/or CH regions have been produced and characterized. The CH, LIM and C-terminal regions cause an increase of Km,NADPH exhibited by the NADPH oxidase activity of the flavoprotein domain, paralleling changes in the overall protein charge. The C-terminus also determines a ∼ 10-fold decrease of kcat, revealing its role in establishing an inactive/active conformational equilibrium, which is at the heart of the regulation of MICAL1 in cells. F-actin lowers Km,NADPH (10-50 μM) and increases kcat (10-25 s(-1)) to similar values for all MICAL forms. The apparent Km,actin of MICAL1 is ∼ 10-fold higher than that of the other forms (3-5 μM), reflecting the fact that F-actin binds to the flavoprotein domain in the MICAL's active conformation and stabilizes it. Analyses of the reaction in the presence of F-actin indicate that actin depolymerization is mediated by H2O2 produced by the NADPH oxidase reaction, rather than due to direct hydroxylation of actin methionine residues. PMID:26845023

  4. Direct writing of ferroelectric domains on strontium barium niobate crystals using focused ultraviolet laser light

    Energy Technology Data Exchange (ETDEWEB)

    Boes, Andreas; Crasto, Tristan; Steigerwald, Hendrik; Mitchell, Arnan [School of Electrical and Computer Engineering and ARC Center for Ultra-High Bandwidth Devices for Optical Systems (CUDOS), RMIT University, Melbourne, Victoria 3001 (Australia); Wade, Scott [Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, Victoria 3122 (Australia); Frohnhaus, Jakob; Soergel, Elisabeth [Institute of Physics, University of Bonn, Wegelerstr. 8, 53115 Bonn (Germany)


    We report ferroelectric domain inversion in strontium barium niobate (SBN) single crystals by irradiating the surface locally with a strongly focused ultraviolet (UV) laser beam. The generated domains are investigated using piezoresponse force microscopy. We propose a simple model that allows predicting the domain width as a function of the irradiation intensity, which indeed applies for both SBN and LiNbO{sub 3}. Evidently, though fundamentally different, the domain structure of both SBN and LiNbO{sub 3} can be engineered through similar UV irradiation.

  5. The Effect of a Three-Way Catalytic Converter on Particulate Matter from a Gasoline Direct-Injection Engine During Cold-Start


    Whelan, Ian; Timoney, David; Smith, William; et al


    This work investigates the effect of a three-way catalytic converter and sampling dilution ratio on nano-scale exhaust particulate matter emissions from a gasoline direct-injection engine during cold-start and warm-up transients. Experimental results are presented from a four cylinder in-line, four stroke, wall-guided direct-injection, turbo-charged and inter-cooled 1.6 litre gasoline engine. A fast-response particulate spectrometer for exhaust nano-particle measurement up to 1000 nm was util...

  6. Quantum fluctuations in planar domain wall space-times: A possible origin of primordial preferred direction

    International Nuclear Information System (INIS)

    We study the gravitational effects of a planar domain wall on quantum fluctuations of a massless scalar field during inflation. By obtaining an exact solution of the scalar field equation in de-Sitter space, we show that the gravitational effects of the domain wall break the rotational invariance of the primordial power spectrum without affecting the translational invariance. The strength of rotational violation is determined by one dimensionless parameter β, which is a function of two physical parameters, the domain wall surface tension σ and cosmological constant Λ. In the limit of small β, the leading effect of rotational violation of the primordial power spectrum is scale-invariant.

  7. Functional Role of Tia1/Pub1 and Sup35 Prion Domains: Directing Protein Synthesis Machinery to the Tubulin Cytoskeleton


    Li, Xiang; Joseph B. Rayman; Kandel, Eric R.; Derkatch, Irina L.


    Tia1/Pub1 is a stress granule component carrying a Q/N-rich prion domain. We provide direct evidence that Tia1 forms a prion in yeast. Moreover, Tia1/Pub1 acts co-operatively with release factor Sup35/eRF3 to establish a two-protein self-propagating state. This two-protein prion driven by the Q/N-rich prion domains of Sup35 and Tia1/Pub1 can be visualized as distinctive line structures along tubulin cytoskeleton. Furthermore, we find that tubulin-associated complex containing Pub1 and Sup35 o...

  8. Directly created electrostatic micro-domains on hydroxyapatite: probing with a Kelvin Force probe and a protein

    CERN Document Server

    Plecenik, Tomas; Gregor, Maros; Truchly, Martin; Lang, Sidney; Gandhi, Abbasi; Zahoran, Miroslav; Laffir, Fathima; Soulimane, Tewfik; Vargova, Melinda; Plesch, Gustav; Kus, Peter; Plecenik, Andrej; Tofail, S A M; 10.1007/s10856-011-4498-x


    Micro-domains of modified surface potential (SP) were created on hydroxyapatite (HAp) films by direct patterning by midenergy focused electron beam, typically available as a microprobe of Scanning Electron Microscopes. The SP distribution of these patterns has been studied on sub-micrometer scale by the Kelvin Probe Force Microscopy method as well as lysozyme adsorption. Since the lysozyme is positively charged at physiological pH, it allows us to track positively and negatively charged areas of the SP patterns. Distribution of the adsorbed proteins over the domains was in good agreement with the observed SP patterns.

  9. Directly catalytic upgrading bio-oil vapor produced by prairie cordgrass pyrolysis over Ni/HZSM-5 using a two stage reactor

    Directory of Open Access Journals (Sweden)

    Shouyun Cheng


    Full Text Available Catalytic cracking is one of the most promising processes for thermochemical conversion of biomass to advanced biofuels in recent years. However, current effectiveness of catalysts and conversion efficiency still remain challenges. An investigation of directly catalytic upgrading bio-oil vapors produced in prairie cordgrass (PCG pyrolysis over Ni/HZSM-5 and HZSM-5 in a two stage packed-bed reactor was carried out. The Ni/HZSM-5 catalyst was synthesized using an impregnation method. Fresh and used catalysts were characterized by BET and XRD. The effects of catalysts on pyrolysis products yields and quality were examined. Both catalysts improved bio-oil product distribution compared to non-catalytic treatment. When PCG pyrolysis vapor was treated with absence of catalyst, the produced bio-oils contained higher alcohols (10.97% and furans (10.14%. In contrast, the bio-oils contained the second highest hydrocarbons (34.97%)and the highest phenols (46.97% when PCG pyrolysis vapor was treated with Ni/HZSM-5. Bio-oils containing less ketones and aldehydes were produced by both Ni/HZSM-5 and HZSM-5, but no ketones were found in Ni/HZSM-5 treatment compared to HZSM-5 (2.94%. The pyrolysis gas compositions were also affected by the presenting of HZSM-5 or Ni/HZSM-5 during the catalytic upgrading process. However, higher heating values and elemental compositions (C, H and N of bio-chars produced in all treatments had no significant difference.


    Starch-lipid composites, prepared by excess steam jet-cooking aqueous mixtures of starch and lipid, are used in various applications for which their performance can depend upon accurate quantitation of lipid contained within these composites. A rapid and non-destructive method based on time-domain ...

  11. Directly created electrostatic micro-domains on hydroxyapatite: probing with a Kelvin Force probe and a protein


    Plecenik, Tomas; Robin, Sylvain; Gregor, Maros; Truchly, Martin; Lang, Sidney; Gandhi, Abbasi; Zahoran, Miroslav; Laffir, Fathima; Soulimane, Tewfik; Vargova, Melinda; Plesch, Gustav; Kus, Peter; Plecenik, Andrej; Tofail, S. A. M.


    Micro-domains of modified surface potential (SP) were created on hydroxyapatite (HAp) films by direct patterning by midenergy focused electron beam, typically available as a microprobe of Scanning Electron Microscopes. The SP distribution of these patterns has been studied on sub-micrometer scale by the Kelvin Probe Force Microscopy method as well as lysozyme adsorption. Since the lysozyme is positively charged at physiological pH, it allows us to track positively and negatively charged areas...

  12. Crystal Structure of the N-Acetyltransferase Domain of Human N-Acetyl-L-Glutamate Synthase in Complex with N-Acetyl-L-Glutamate Provides Insights into Its Catalytic and Regulatory Mechanisms


    Zhao, Gengxiang; Jin, Zhongmin; Allewell, Norma M.; Tuchman, Mendel; Shi, Dashuang


    N-acetylglutamate synthase (NAGS) catalyzes the conversion of AcCoA and L-glutamate to CoA and N-acetyl-L-glutamate (NAG), an obligate cofactor for carbamyl phosphate synthetase I (CPSI) in the urea cycle. NAGS deficiency results in elevated levels of plasma ammonia which is neurotoxic. We report herein the first crystal structure of human NAGS, that of the catalytic N-acetyltransferase (hNAT) domain with N-acetyl-L-glutamate bound at 2.1 Å resolution. Functional studies indicate that the hNA...

  13. The metavinculin tail domain directs constitutive interactions with raver1 and vinculin RNA


    Lee, Jun Hyuck; Rangarajan, Erumbi S.; Vonrhein, Clemens; Bricogne, Gerard; Izard, Tina


    Vinculin is a key regulator of the attachment of the actin cytoskeleton to the cell membrane at cellular adhesion sites that is crucial for processes like cell motility and migration, development, survival, and wound healing. Vinculin loss results in embryonic lethality, cardiovascular diseases, and cancer. Its tail domain, Vt, is crucial for vinculin activation and focal adhesion turnover and binds to the actin cytoskeleton and acidic phospholipids upon which it unfurls. The RNA binding prot...

  14. Direct photoaffinity labeling by nucleotides of the apparent catalytic site on the heavy chains of smooth muscle and Acanthamoeba myosins

    International Nuclear Information System (INIS)

    The heavy chains of Acanthamoeba myosins, IA, IB and II, turkey gizzard myosin, and rabbit skeletal muscle myosin subfragment-1 were specifically labeled by radioactive ATP, ADP, and UTP, each of which is a substrate or product of myosin ATPase activity, when irradiated with uv light at 00C. With UTP, as much as 0.45 mol/mol of Acanthamoeba myosin IA heavy chain and 1 mol/mol of turkey gizzard myosin heavy chain was incorporated. Evidence that the ligands were associated with the catalytic site included the observations that reaction occurred only with nucleotides that are substrates or products of the ATPase activity; that the reaction was blocked by pyrophosphate which is an inhibitor of the ATPase activity; that ATP was bound as ADP; and that label was probably restricted to a single peptide following limited subtilisin proteolysis of labeled Acanthamoeba myosin IA heavy chain and extensive cleavage with CNBr and trypsin of labeled turkey gizzard myosin heavy chain

  15. Functional Role of Tia1/Pub1 and Sup35 Prion Domains: Directing Protein Synthesis Machinery to the Tubulin Cytoskeleton (United States)

    Li, Xiang; Rayman, Joseph B.; Kandel, Eric R; Derkatch, Irina L.


    SUMMARY Tia1/Pub1 is a stress granule component carrying a Q/N-rich prion domain. We provide direct evidence that Tia1 forms a prion in yeast. Moreover, Tia1/Pub1 acts co-operatively with release factor Sup35/eRF3 to establish a two-protein self-propagating state. This two-protein prion driven by the Q/N-rich prion domains of Sup35 and Tia1/Pub1 can be visualized as distinctive line structures along tubulin cytoskeleton. Furthermore, we find that tubulin-associated complex containing Pub1 and Sup35 oligomers normally exists in yeast, and its assembly depends on prion domains of Pub1 and Sup35. This Sup35/Pub1 complex, which also contains TUB1 mRNA and components of translation machinery, is important for the integrity of the tubulin cytoskeleton: PUB1 disruption and Sup35 depletion from the complex lead to cytoskeletal defects. We propose that the complex is implicated in protein synthesis at the site of microtubule assembly. Thus our study identifies the role for prion domains in the assembly of multi-protein complexes. PMID:24981173

  16. Direct measurement of super-paramagnetic fluctuations in mono-domain Fe particles

    Energy Technology Data Exchange (ETDEWEB)

    Casalta, H.; Schleger, P.; Ehlers, G.; Farago, B. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); Bellouard, C. [Lab. Metal Physique, Nancy (France); Hennion, M.; Mirebeau, I. [Laboratoire Leon Brillouin (LLB) - Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France); Dormann, J.L. [LMO, Versailles (France); Kelsch, M.; Linde, M.; Philip, F. [Max-Planck-Institut fuer Metallforschung, Stuttgart (Germany)


    By combining measurements on two spin-echo spectrometers IN15, we have measured the super-parametric relaxation of nano-scale, magnetic mono-domain iron particles over a very wide time range (0.01 to 160 nsec). Taking into account the effect of particle size distribution, we fit the line-shape of the intermediate scattering function and determine the temperature T and Q dependence of the longitudinal super-spin relaxation time. It is found that below 40 K, inter-particle correlations affect the longitudinal super-spin fluctuations. (authors) 6 refs., 2 figs.

  17. Direct measurement of super-paramagnetic fluctuations in mono-domain Fe particles

    International Nuclear Information System (INIS)

    By combining measurements on two spin-echo spectrometers IN15, we have measured the super-parametric relaxation of nano-scale, magnetic mono-domain iron particles over a very wide time range (0.01 to 160 nsec). Taking into account the effect of particle size distribution, we fit the line-shape of the intermediate scattering function and determine the temperature T and Q dependence of the longitudinal super-spin relaxation time. It is found that below 40 K, inter-particle correlations affect the longitudinal super-spin fluctuations. (authors)

  18. Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of the catalytic domain of a hyperthermostable endo-1,4-β-d-mannanase from Thermotoga petrophila RKU-1

    International Nuclear Information System (INIS)

    The catalytic domain of a hyperthermostable endo-1,4-β-d-mannanase from T. petrophila RKU-1 has been cloned, overexpressed in E. coli cells, purified and crystallized in two distinct crystalline forms by the sitting-drop vapour-diffusion method. Endo-1,4-β-d-mannanases play key roles in seed germination and fruit ripening and have recently received much attention owing to their potential applications in the food, detergent and kraft pulp industries. In order to delineate their structural determinants for specificity and stability, X-ray crystallographic investigations combined with detailed functional studies are being performed. In this work, crystals of the catalytic domain of a hyperthermostable endo-1,4-β-d-mannanase from Thermotoga petrophila RKU-1 were obtained from three different conditions, resulting in two crystalline forms. Crystals from conditions with phosphate or citrate salts as precipitant (CryP) belonged to space group P212121, with unit-cell parameters a = 58.76, b = 87.99, c = 97.34 Å, while a crystal from a condition with ethanol as precipitant (CryE) belonged to space group I212121, with unit-cell parameters a = 91.03, b = 89.97, c = 97.89 Å. CryP and CryE diffracted to resolutions of 1.40 and 1.45 Å, respectively

  19. Directional effects consideration to improve out-doors emissivity retrieval in the 3-13 mum domain. (United States)

    Kanani, Keyvan; Poutier, Laurent; Nerry, Françoise; Stoll, Marc-Philippe


    This work analyses and solves for issues encountered when retrieving surface emissivity in LWIR (750 to 1250 cm(-1)) and MWIR (2000 to 3500 cm(-1)) bands under outdoor conditions. The Spectral Smoothness method, which takes advantage of high spectral resolution measurements to solve for temperature emissivity separation, and which has already proven its efficiency in the LWIR domain, was applied in an experimental campaign to assess its ability to operate both in the LWIR and MWIR domains. In the MWIR band, directional behaviour of surface emissivity is shown to be a source of systematic errors in the retrieved emissivity and a new method, called SmaC (SMoothness And Continuity), corrects for this error by providing quantitative estimates on the deviation of the surface from Lambertian behavior. PMID:19547618

  20. Real-Time Nearfield Acoustic Holography: Implementation of the Direct and Inverse Impulse Responses in the Time-Wavenumber Domain

    CERN Document Server

    Thomas, Jean-Hugh; Paillasseur, Sébastien; Pascal, Jean-Claude


    The aim of the study is to demonstrate that some methods are more relevant for implementing the Real-Time Nearfield Acoustic Holography than others. First by focusing on the forward propagation problem, different approaches are compared to build the impulse response to be used. One of them in particular is computed by an inverse Fourier transform applied to the theoretical transfer function for propagation in the frequency-wavenumber domain. Others are obtained by directly sampling an analytical impulse response in the time-wavenumber domain or by additional low-pass filtering. To estimate the performance of each impulse response, a simulation test involving several monopoles excited by non stationary signals is presented and some features are proposed to assess the accuracy of the temporal signals resulting from reconstruction processing on a forward plane. Then several inverse impulse responses used to solve the inverse problem, which consists in back propagating the acoustic signals acquired by the microph...

  1. Direct visualization of the thermomagnetic behavior of pseudo-single-domain magnetite particles. (United States)

    Almeida, Trevor P; Muxworthy, Adrian R; Kovács, András; Williams, Wyn; Brown, Paul D; Dunin-Borkowski, Rafal E


    The study of the paleomagnetic signal recorded by rocks allows scientists to understand Earth's past magnetic field and the formation of the geodynamo. The magnetic recording fidelity of this signal is dependent on the magnetic domain state it adopts. The most prevalent example found in nature is the pseudo-single-domain (PSD) structure, yet its recording fidelity is poorly understood. Here, the thermoremanent behavior of PSD magnetite (Fe3O4) particles, which dominate the magnetic signatures of many rock lithologies, is investigated using electron holography. This study provides spatially resolved magnetic information from individual Fe3O4 grains as a function of temperature, which has been previously inaccessible. A small exemplar Fe3O4 grain (~150 nm) exhibits dynamic movement of its magnetic vortex structure above 400°C, recovering its original state upon cooling, whereas a larger exemplar Fe3O4 grain (~250 nm) is shown to retain its vortex state on heating to 550°C, close to the Curie temperature of 580°C. Hence, we demonstrate that Fe3O4 grains containing vortex structures are indeed reliable recorders of paleodirectional and paleointensity information, and the presence of PSD magnetic signals does not preclude the successful recovery of paleomagnetic signals. PMID:27152353

  2. Site-directed mutants of human RECQ1 reveal functional importance of the zinc binding domain. (United States)

    Sami, Furqan; Gary, Ronald K; Fang, Yayin; Sharma, Sudha


    RecQ helicases are a highly conserved family of ATP-dependent DNA-unwinding enzymes with key roles in DNA replication and repair in all kingdoms of life. The RECQ1 gene encodes the most abundant RecQ homolog in humans. We engineered full-length RECQ1 harboring point mutations in the zinc-binding motif (amino acids 419-480) within the conserved RecQ-specific-C-terminal (RQC) domain known to be critical for diverse biochemical and cellular functions of RecQ helicases. Wild-type RECQ1 contains a zinc ion. Substitution of three of the four conserved cysteine residues that coordinate zinc severely impaired the ATPase and DNA unwinding activities but retained DNA binding and single strand DNA annealing activities. Furthermore, alteration of these residues attenuated zinc binding and significantly changed the overall conformation of full-length RECQ1 protein. In contrast, substitution of cysteine residue at position 471 resulted in a wild-type like RECQ1 protein. Differential contribution of the conserved cysteine residues to the structure and functions of the RECQ1 protein is also inferred by homology modeling. Overall, our results indicate that the zinc binding motif in the RQC domain of RECQ1 is a key structural element that is essential for the structure-functions of RECQ1. Given the recent association of RECQ1 mutations with breast cancer, these results will contribute to understanding the molecular basis of RECQ1 functions in cancer etiology. PMID:27248010

  3. Direct visualization of the thermomagnetic behavior of pseudo–single-domain magnetite particles (United States)

    Almeida, Trevor P.; Muxworthy, Adrian R.; Kovács, András; Williams, Wyn; Brown, Paul D.; Dunin-Borkowski, Rafal E.


    The study of the paleomagnetic signal recorded by rocks allows scientists to understand Earth’s past magnetic field and the formation of the geodynamo. The magnetic recording fidelity of this signal is dependent on the magnetic domain state it adopts. The most prevalent example found in nature is the pseudo–single-domain (PSD) structure, yet its recording fidelity is poorly understood. Here, the thermoremanent behavior of PSD magnetite (Fe3O4) particles, which dominate the magnetic signatures of many rock lithologies, is investigated using electron holography. This study provides spatially resolved magnetic information from individual Fe3O4 grains as a function of temperature, which has been previously inaccessible. A small exemplar Fe3O4 grain (~150 nm) exhibits dynamic movement of its magnetic vortex structure above 400°C, recovering its original state upon cooling, whereas a larger exemplar Fe3O4 grain (~250 nm) is shown to retain its vortex state on heating to 550°C, close to the Curie temperature of 580°C. Hence, we demonstrate that Fe3O4 grains containing vortex structures are indeed reliable recorders of paleodirectional and paleointensity information, and the presence of PSD magnetic signals does not preclude the successful recovery of paleomagnetic signals. PMID:27152353

  4. Direct observation of ferrimagnetic/ferroelastic domain interactions in magnetite below the Verwey transition

    DEFF Research Database (Denmark)

    Kasama, Takeshi; Church, Nathan S.; Feinberg, Joshua M.; Dunin-Borkowski, Rafal E.; Harrison, Richard J.

    The magnetic behaviour of magnetite at low temperatures is dominated by its transformation to a monoclinic crystal structure that is simultaneously ferrimagnetic, ferroelastic and ferroelectric below similar to 125 K (the Verwey transition). Here we use electron microscopy to reveal the relations......The magnetic behaviour of magnetite at low temperatures is dominated by its transformation to a monoclinic crystal structure that is simultaneously ferrimagnetic, ferroelastic and ferroelectric below similar to 125 K (the Verwey transition). Here we use electron microscopy to reveal the...... relationship between ferrimagnetic and ferroelastic domain structures in monoclinic magnetite. We present dynamic observations of magnetite during heating and cooling across the Verwey transition, revealing a diversity of unexpected interaction phenomena between crystallographic twins and magnetic domain walls....... This study provides a new understanding of the low-temperature magnetic properties of magnetite that will affect a broad range of rock magnetic studies, from the interpretation of magnetic remanence in terrestrial rocks and sediments to the search for biogenic magnetite in extraterrestrial materials....

  5. Direct Time-domain Observation of Conformational Relaxation in Gas-phase Cold Collisions


    Drayna, Garrett K.; Hallas, Christian; Wang, Kenneth; Domingos, Sérgio R.; Eibenberger, Sandra; Doyle, John M.; Patterson, David


    Cooling molecules in the gas phase is important for precision spectroscopy, cold molecule physics, and physical chemistry. Measurements of conformational relaxation cross sections shed important light on potential energy surfaces and energy flow within a molecule. However, gas-phase conformational cooling has not been previously observed directly. In this work, we directly observe conformational dynamics of 1,2-propanediol in cold (6K) collisions with atomic helium using microwave spectroscop...

  6. Catalytic Coanda combustion

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, J.D.; Smith, A.G.; Kopmels, M.


    A catalytic reaction is enhanced by the use of the Coanda effect to maximise contact between reactant and catalyst. A device utilising this principle comprises a Coanda surface which directs the flow of fuel from a slot to form a primary jet which entrains the surrounding ambient air and forms a combustible mixture for reaction on a catalytic surface. The Coanda surface may have an internal or external nozzle which may be axi-symmetric or two-dimensional. (author)

  7. Direct 'in situ', low VOC, high yielding, CO2 expanded phase catalytic chain transfer polymerisation: towards scale-up. (United States)

    Adlington, Kevin; Green, Anthony; Wang, Wenxin; Howdle, Steven M; Irvine, Derek J


    The successful application of catalytic chain transfer polymerisation (CCTP) by adopting an 'in situ' catalyst preparation methodology in several polymerisation media is described. More specifically, this study is focused on reporting the development of 'in situ' CCTP within a CO(2) expanded phase polymerisation process, which achieved high yields of polymer whilst minimising both VOC footprint and CO(2) compression costs. The 'in situ' method is shown to be effective in controlling polymerisations conducted in both conventional solvents and bulk under inert atmosphere, delivering molecular weight reductions and a Cs value of appropriate similar magnitude to those achieved by the benchmark, commercially sourced CoPhBF catalyst. The 'in situ' effect has been achieved with equal efficiency when both using catalysts with different axial ligands and where the complex is required to undergo a facile ligand dissociation in order to create the required catalyst necessary to achieve CCTP control. Furthermore, both catalysts are shown to effectively control polymerisations in a CO(2) expanded phase process, in which a small amount of compressed CO(2) is introduced to reduce the viscosity of the reaction mixture, allowing for easy heat transfer and good catalyst diffusion during reaction. In this way, yield limitations imposed to avoid the Trommsdorff effect required in bulk processing and the need for post precipitation have been successfully overcome. Both of these factors further improve the sustainability of such a polymerisation process. However, the 'in situ', high pressure expanded phase environment was observed to retard the ligand dissociation required for catalyst activation. PMID:23085824

  8. A maximum likelihood direction of arrival estimation method for open-sphere microphone arrays in the spherical harmonic domain. (United States)

    Hu, Yuxiang; Lu, Jing; Qiu, Xiaojun


    Open-sphere microphone arrays are preferred over rigid-sphere arrays when minimal interaction between array and the measured sound field is required. However, open-sphere arrays suffer from poor robustness at null frequencies of the spherical Bessel function. This letter proposes a maximum likelihood method for direction of arrival estimation in the spherical harmonic domain, which avoids the division of the spherical Bessel function and can be used at arbitrary frequencies. Furthermore, the method can be easily extended to wideband implementation. Simulation and experiment results demonstrate the superiority of the proposed method over the commonly used methods in open-sphere configurations. PMID:26328695

  9. Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity. (United States)

    Axarli, Irine; Muleta, Abdi W; Vlachakis, Dimitrios; Kossida, Sophia; Kotzia, Georgia; Maltezos, Anastasios; Dhavala, Prathusha; Papageorgiou, Anastassios C; Labrou, Nikolaos E


    A library of Tau class GSTs (glutathione transferases) was constructed by DNA shuffling using the DNA encoding the Glycine max GSTs GmGSTU2-2, GmGSTU4-4 and GmGSTU10-10. The parental GSTs are >88% identical at the sequence level; however, their specificity varies towards different substrates. The DNA library contained chimaeric structures of alternated segments of the parental sequences and point mutations. Chimaeric GST sequences were expressed in Escherichia coli and their enzymatic activities towards CDNB (1-chloro-2,4-dinitrobenzene) and the herbicide fluorodifen (4-nitrophenyl α,α,α-trifluoro-2-nitro-p-tolyl ether) were determined. A chimaeric clone (Sh14) with enhanced CDNB- and fluorodifen-detoxifying activities, and unusual co-operative kinetics towards CDNB and fluorodifen, but not towards GSH, was identified. The structure of Sh14 was determined at 1.75 Å (1 Å=0.1 nm) resolution in complex with S-(p-nitrobenzyl)-glutathione. Analysis of the Sh14 structure showed that a W114C point mutation is responsible for the altered kinetic properties. This was confirmed by the kinetic properties of the Sh14 C114W mutant. It is suggested that the replacement of the bulky tryptophan residue by a smaller amino acid (cysteine) results in conformational changes of the active-site cavity, leading to enhanced catalytic activity of Sh14. Moreover, the structural changes allow the strengthening of the two salt bridges between Glu(66) and Lys(104) at the dimer interface that triggers an allosteric effect and the communication between the hydrophobic sites. PMID:26637269

  10. Direct observation of deterministic domain wall trajectory in magnetic network structures (United States)

    Sethi, P.; Murapaka, C.; Goolaup, S.; Chen, Y. J.; Leong, S. H.; Lew, W. S.


    Controlling the domain wall (DW) trajectory in magnetic network structures is crucial for spin-based device related applications. The understanding of DW dynamics in network structures is also important for study of fundamental properties like observation of magnetic monopoles at room temperature in artificial spin ice lattice. The trajectory of DW in magnetic network structures has been shown to be chirality dependent. However, the DW chirality periodically oscillates as it propagates a distance longer than its fidelity length due to Walker breakdown phenomenon. This leads to a stochastic behavior in the DW propagation through the network structure. In this study, we show that the DW trajectory can be deterministically controlled in the magnetic network structures irrespective of its chirality by introducing a potential barrier. The DW propagation in the network structure is governed by the geometrically induced potential barrier and pinning strength against the propagation. This technique can be extended for controlling the trajectory of magnetic charge carriers in an artificial spin ice lattice.

  11. A Multiple-Labeling Strategy for Nonribosomal Peptide Synthetases Using Active-Site-Directed Proteomic Probes for Adenylation Domains. (United States)

    Ishikawa, Fumihiro; Suzuki, Takehiro; Dohmae, Naoshi; Kakeya, Hideaki


    Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple-labeling technique with active-site-directed probes for adenylation domains. When applied to gramicidin S-producing and -nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high-resolution identification of low-abundance active NRPS enzymes in native proteomic environments. PMID:26467472

  12. A high-order public domain code for direct numerical simulations of turbulent combustion

    CERN Document Server

    Babkovskaia, N; Brandenburg, A


    A high-order scheme for direct numerical simulations of turbulent combustion is discussed. Its implementation in the massively parallel and publicly available Pencil Code is validated with the focus on hydrogen combustion. Ignition delay times (0D) and laminar flame velocities (1D) are calculated and compared with results from the commercially available Chemkin code. The scheme is verified to be fifth order in space. Upon doubling the resolution, a 32-fold increase in the accuracy of the flame front is demonstrated. Finally, also turbulent and spherical flame front velocities are calculated and the implementation of the non-reflecting so-called Navier-Stokes Characteristic Boundary Condition is validated in all three directions.

  13. Direct Machine Translation System from Punjabi to Hindi for Newspapers headlines Domain


    Sumita Rani; Dr. Vijay Luxmi


    Machine Translation System is an important area in Natural Language Processing. The Direct MT system is based upon the utilization of syntactic and vocabulary similarities between more or few related natural languages. The relation between two or more languages is based upon their common parent language. The similarity between Punjabi and Hindi languages is due to their parent language Sanskrit. Punjabi and Hindi are closely related languages with lots of similarities in syntax and vocabulary...

  14. Direct Time-Domain-Based Approach for Study of Space-Vector Pulsewidth Modulation

    DEFF Research Database (Denmark)

    Oleschuk, V.; Blaabjerg, Frede; Stankovic, A.M.

    Direct time-do main-based approach, which is characterized by the simplicity and clarity, is proposed for the study and design of space-vector based methods of pulsewidth modulation (PWM) for standard voltage source inverters for adjustable speed motor drives. This approach is based on the detailed...... consideration of switching state sequences of three-phase inverter (with the corresponding duty-cycles), which are integrated characteristics of space vector PWM schemes and versions. It also permits providing of synchronization of output voltage waveforms and improvement of computational effectiveness of...

  15. A high-order public domain code for direct numerical simulations of turbulent combustion (United States)

    Babkovskaia, N.; Haugen, N. E. L.; Brandenburg, A.


    A high-order scheme for direct numerical simulations of turbulent combustion is discussed. Its implementation in the massively parallel and publicly available PENCIL CODE is validated with the focus on hydrogen combustion. This is the first open source DNS code with detailed chemistry available. An attempt has been made to present, for the first time, the full set of evolution and auxiliary equations required for a complete description of single phase non-isothermal fluid dynamics with detailed chemical reactions. Ignition delay times (0D) and laminar flame velocities (1D) are calculated and compared with results from the commercially available Chemkin code. The scheme is verified to be fifth order in space. Upon doubling the resolution, a 32-fold increase in the accuracy of the flame front is demonstrated. Finally, also turbulent and spherical flame front velocities are calculated and the implementation of the non-reflecting so-called Navier-Stokes Characteristic Boundary Condition is validated in all three directions.

  16. Direct Time-Domain Observation of Conformational Relaxation in Gas-Phase Cold Collisions. (United States)

    Drayna, Garrett K; Hallas, Christian; Wang, Kenneth; Domingos, Sergio R; Eibenberger, Sandra; Doyle, John M; Patterson, David


    Cooling molecules in the gas phase is important for precision spectroscopy, cold molecule physics, and physical chemistry. Measurements of conformational relaxation cross sections shed important light on potential energy surfaces and energy flow within a molecule. However, gas-phase conformational cooling has not been previously observed directly. In this work, we directly observe conformational dynamics of 1,2-propanediol in cold (6 K) collisions with atomic helium using microwave spectroscopy and buffer-gas cooling. Precise knowledge and control of the collisional environment in the buffer-gas allows us to measure the absolute collision cross-section for conformational relaxation. Several conformers of 1,2-propanediol are investigated and found to have relaxation cross-sections with He ranging from σ=4.7(3.0)×10(-18)  cm(2) to σ>5×10(-16)  cm(2) . Our method is applicable to a broad class of molecules and could be used to provide information about the potential energy surfaces of previously uninvestigated molecules. PMID:26992036

  17. Direct Time-domain Observation of Conformational Relaxation in Gas-phase Cold Collisions

    CERN Document Server

    Drayna, Garrett K; Wang, Kenneth; Domingos, Sergio R; Eibengerber, Sandra; Doyle, John M; Patterson, David


    Cooling molecules in the gas phase is important for precision spectroscopy, cold molecule physics, and physical chemistry. Measurements of conformational relaxation cross sections shed important light on potential energy surfaces and energy flow within a molecule. However, gas-phase conformational cooling has not been previously observed directly. In this work, we directly observe conformational dynamics of 1,2-propanediol in cold (6K) collisions with atomic helium using microwave spectroscopy and buffer-gas cooling. Precise knowledge and control of the collisional environment in the buffer-gas allows us to measure the absolute collision cross-section for conformational relaxation. Several conformers of 1,2-propanediol are investigated and found to have relaxation cross-sections with He ranging from $\\sigma=4.7(3.0)\\times10^{-18}\\:\\mathrm{cm}^{2}$ to $\\sigma>5\\times10^{-16}\\:\\mathrm{cm}^{2}$. Our method is applicable to a broad class of molecules and could be used to provide information about the potential en...

  18. Inhibition of Melanization by a Parasitoid Serine Protease Homolog Venom Protein Requires Both the Clip and the Non-Catalytic Protease-Like Domains

    Directory of Open Access Journals (Sweden)

    Sassan Asgari


    Full Text Available Endoparasitoid wasps inject a variety of components into their host hemocoel at oviposition to facilitate successful development of their progeny. Among these are venom proteins which have been shown to play crucial roles in host regulation. A serine protease homolog (SPH-like venom protein from Cotesia rubecula was previously shown to inhibit melanization in the host hemolymph by blocking activation of prophenoloxidase to phenoloxidase, a key enzyme in melanin formation. Similar to other SPHs, Vn50 consists of a clip and a protease-like (SPL domain. Protein modeling demonstrated that Vn50 has a very similar structure to known SPHs and functional analysis of Vn50 domains expressed in insect cells indicated that neither of the domains on its own has an inhibitory effect on melanization.

  19. Direct visualization of lipid domains in human skin stratum corneum's lipid membranes

    DEFF Research Database (Denmark)

    Plasencia, I; Norlen, Lars; Bagatolli, Luis


    iii), whether pH has a direct effect on the lipid matrix phase behavior. In this work the lateral structure of membranes composed of lipids extracted from human skin stratum corneum was studied in a broad temperature range (10 degrees C-90 degrees C) using different techniques such as differential...... scanning calorimetry, fluorescence spectroscopy, and two-photon excitation and laser scanning confocal fluorescence microscopy. Here we show that hydrated bilayers of human skin stratum corneum lipids express a giant sponge-like morphology with dimensions corresponding to the global three......The main function of skin is to serve as a physical barrier between the body and the environment. This barrier capacity is in turn a function of the physical state and structural organization of the stratum corneum extracellular lipid matrix. This lipid matrix is essentially composed of very long...

  20. Directed Evolution of Mycobacterium tuberculosis β-Lactamase Reveals Gatekeeper Residue That Regulates Antibiotic Resistance and Catalytic Efficiency


    Feiler, Christian; Fisher, Adam C.; Boock, Jason T.; Marrichi, Matthew J.; Wright, Lori; Schmidpeter, Philipp A. M.; Blankenfeldt, Wulf; Pavelka, Martin; DeLisa, Matthew P.


    Directed evolution can be a powerful tool for revealing the mutational pathways that lead to more resistant bacterial strains. In this study, we focused on the bacterium Mycobacterium tuberculosis, which is resistant to members of the β-lactam class of antibiotics and thus continues to pose a major public health threat. Resistance of this organism is the result of a chromosomally encoded, extended spectrum class A β-lactamase, BlaC, that is constitutively produced. Here, combinatorial enzyme ...

  1. PNA-mediated modulation and redirection of Her-2 pre-mRNA splicing: specific skipping of erbB-2 exon 19 coding for the ATP catalytic domain

    DEFF Research Database (Denmark)

    Pankratova, Stanislava; Nielsen, Birgit N; Shiraishi, Takehiko;


    The Her-2 receptor coded for by the proto-oncogenic erbB-2 gene is a clinically validated target for treatment of a significant genetic subclass of breast cancers, and Her-2 is also overexpressed or mutated in a range of other cancers. In an approach to exploit antisense mediated splicing...... oligomers that specifically induce skipping of exon 19 as this exon is coding for the ATP catalytic domain of Her-2, and if expressed such truncated version of the Her-2 protein should be functionally inactive in a dominant negative fashion. Therefore, antisense compounds having efficient erbB-2 exon 19...... skipping activity could be very interesting in terms of drug discovery. In the present study we identified PNA oligomers having such activity in SK-BR-3 and HeLa cancer cells in culture....

  2. Crystallization and preliminary crystallographic analysis of the catalytic domain of human flap endonuclease 1 in complex with a nicked DNA product: use of a DPCS kit for efficient protein–DNA complex crystallization

    International Nuclear Information System (INIS)

    Human flap endonuclease 1 complexed with nicked DNA has been crystallized. A diffraction data set was collected to a resolution of 2.75 Å. Flap endonuclease 1 (FEN1) is a structure-specific nuclease that removes the RNA/DNA primer associated with Okazaki fragments in DNA replication. Here, crystals of the complex between the catalytic domain of human FEN1 and a DNA product have been obtained. For efficient crystallization screening, a DNA–protein complex crystallization screening (DPCS) kit was designed based on commercial crystallization kits. The crystal was found to belong to space group P21, with unit-cell parameters a = 61.0, b = 101.3, c = 106.4 Å, β = 106.4°. The asymmetric unit is predicted to contain two complexes in the crystallographic asymmetric unit. A diffraction data set was collected to a resolution of 2.75 Å

  3. The Lectin Domain of the Polypeptide GalNAc Transferase Family of Glycosyltransferases (ppGalNAc Ts) Acts as a Switch Directing Glycopeptide Substrate Glycosylation in an N- or C-terminal Direction, Further Controlling Mucin Type O-Glycosylation

    DEFF Research Database (Denmark)

    Gerken, Thomas A; Revoredo, Leslie; Thome, Joseph J C; Tabak, Lawrence A; Vester-Christensen, Malene Bech; Clausen, Henrik; Gahlay, Gagandeep K; Jarvis, Donald L; Johnson, Roy W; Moniz, Heather A; Moremen, Kelley


    Mucin type O-glycosylation is initiated by a large family of polypeptide GalNAc transferases (ppGalNAc Ts) that add α-GalNAc to the Ser and Thr residues of peptides. Of the 20 human isoforms, all but one are composed of two globular domains linked by a short flexible linker: a catalytic domain an...

  4. The C-terminal domain of human grp94 protects the catalytic subunit of protein kinase CK2 (CK2alpha) against thermal aggregation. Role of disulfide bonds

    DEFF Research Database (Denmark)

    Roher, N; Miró, F; Boldyreff, B; Llorens, F; Plana, M; Issinger, O G; Itarte, E


    The C-terminal domain (residues 518-803) of the 94 kDa glucose regulated protein (grp94) was expressed in Escherichia coli as a fusion protein with a His6-N-terminal tag (grp94-CT). This truncated form of grp94 formed dimers and oligomers that could be dissociated into monomers by treatment with...

  5. Directed Self-assembly of Block Copolymer with Sub-15 nm Domain Spacing Using Nanoimprinted Photoresist Templates (United States)

    Sun, Zhiwei; Chen, Zhenbin; Zhang, Wenxu; Coughlin, E. Bryan; Xiao, Shuaigang; Russell, Thomas

    There has been increasing interest in preparing block copolymer thin films with ultra-small domain spacings for use as etching masks for ultra-high resolution nanolithography. One method to prepare block copolymer materials with small feature sizes is salt doping, increasing the Flory-Huggins interaction and allowing microphase separation to be maintained at lower molecular weights. Lamellae-forming P2VP- b-PS- b-P2VP block copolymer with various molecular weight was synthesized using RAFT polymerization with a dual functional chain transfer agent. Copper (II) Chloride or Gold (III) chloride was found to be selectively associated with P2VP block and increase the unfavorable interactions between PS and P2VP blocks, driving the disordered block copolymer into the ordered state. A 14 nm lamellar spacing of P2VP- b-PS- b-P2VP thin film was prepared using copper (II) Chloride doping after acetone vapor annealing on neutral brushes. Metallic nano-wire arrays were prepared after selective infiltration of platinum salt into the P2VP domain and oxygen plasma treatment. The directed self-assembly of salt doped P2VP- b-PS- b-P2VP triblock copolymer having long-rang lateral order on nanoimprinted photoresist templates with shallow trenches was also studied.

  6. Variable domain I of nematode CLEs directs post-translational targeting of CLE peptides to the extracellular space. (United States)

    Wang, Jianying; Joshi, Sneha; Korkin, Dmitry; Mitchum, Melissa G


    Effector proteins expressed in the esophageal gland cells of cyst nematodes are delivered into plant cells through a hollow, protrusible stylet. Although evidence indicates that effector proteins function in the cytoplasm of the syncytium, technical constraints have made it difficult to directly determine where nematode effector proteins are initially delivered: cytoplasm, extracellular space, or both. Recently, we demonstrated that soybean cyst nematode CLE (HgCLE) propeptides are delivered to the cytoplasm of syncytial cells. Genetic and biochemical analyses indicate that the variable domain (VD) sequence is then required for targeting cytoplasmically delivered nematode CLEs to the apoplast where they function as ligand mimics of endogenous plant CLE peptides. The fact that nematode CLEs are targeted through the gland cell secretory pathway and delivered as mature propeptides into plant cells makes it impossible for these proteins to be subsequently delivered to the extracellular space via co-translational translocation through the endoplasmic reticulum (ER) secretory pathway of the host cell. However, when expressed in transgenic plants, if the mature nematode CLE propeptide harbored a functional cryptic signal peptide, it could possibly traffic to the apoplast through the ER secretory pathway by co-translational translocation. Here, we present evidence that VDI, the N-terminal sequence of the variable domain of HgCLE2, is sufficient for trafficking CLE peptides to the apoplast and that trafficking is indeed through an alternative pathway other than co-translational translocation. PMID:21150256

  7. An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues.

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    Full Text Available The aspiration to mimic and accelerate natural evolution has fueled interest in directed evolution experiments, which endow or enhance functionality in enzymes. Barring a few de novo approaches, most methods take a template protein having the desired activity, known active site residues and structure, and proceed to select a target protein which has a pre-existing scaffold congruent to the template motif. Previously, we have established a computational method (CLASP based on spatial and electrostatic properties to detect active sites, and a method to quantify promiscuity in proteins. We exploit the prospect of promiscuous active sites to serve as the starting point for directed evolution and present a method to select a target protein which possesses a significant partial match with the template scaffold (DECAAF. A library of partial motifs, constructed from the active site residues of the template protein, is used to rank a set of target proteins based on maximal significant matches with the partial motifs, and cull out the best candidate from the reduced set as the target protein. Considering the scenario where this 'incubator' protein lacks activity, we identify mutations in the target protein that will mirror the template motif by superimposing the target and template protein based on the partial match. Using this superimposition technique, we analyzed the less than expected gain of activity achieved by an attempt to induce β-lactamase activity in a penicillin binding protein (PBP (PBP-A from T. elongatus, and attributed this to steric hindrance from neighboring residues. We also propose mutations in PBP-5 from E. coli, which does not have similar steric constraints. The flow details have been worked out in an example which aims to select a substitute protein for human neutrophil elastase, preferably related to grapevines, in a chimeric anti-microbial enzyme which bolsters the innate immune defense system of grapevines.

  8. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during MicroRNA biogenesis

    KAUST Repository

    Liu, Chenggang


    Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher Kcat and lower Km values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates. © 2012 American Society of Plant Biologists.

  9. Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site. (United States)

    Derbyshire, V; Kowalski, J C; Dansereau, J T; Hauer, C R; Belfort, M


    I-TevI, the T4 td intron-encoded endonuclease, catalyzes the first step in intron homing by making a double-strand break in the intronless allele within a sequence designated the homing site. The 28 kDa enzyme, which interacts with the homing site over a span of 37 bp, binds as a monomer, contacting two domains of the substrate. In this study, limited proteolysis experiments indicate that I-TevI consists of two domains that behave as discrete physical entities as judged by a number of functional and structural criteria. Overexpression clones for each domain were constructed and the proteins were purified. The carboxy-terminal domain has DNA-binding activity coincident with the primary binding region of the homing site and binds with the same affinity as the full-length enzyme. The isolated amino-terminal domain, contains the conserved GIY-YIG motif, consistent with its being the catalytic domain. Furthermore, site-directed mutagenesis of a conserved arginine residue within the extended motif rendered the full-length protein catalytically inactive, although DNA-binding was maintained. This is the first evidence that the GIY-YIG motif is important for catalytic activity. An enzyme with an N-terminal catalytic domain and a C-terminal DNA-binding domain connected by a flexible linker is in accord with the bipartite structure of the homing site. PMID:9048944

  10. Direct catalytic conversion of methane and light hydrocarbon gases. Quarterly report No. 8, July 16--September 30, 1988

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, R.B. Jr.; Posin, B.M.; Chan, Yee Wai


    The goal of this research is to develop catalysts that directly convert methane and light hydrocarbons to intermediates that later can be converted to either liquid fuels or value-added chemicals, as economics dictate. During this reporting period, we investigated the behavior of some of our catalysts under working conditions using diffuse reflectance fourier transform infrared spectroscopy (DRIFT). Two catalysts (FeRu{sub 3} and Ru{sub 4} on magnesia) were examined under nitrogen, and the Ru{sub 4}/MgO system was examined under a methane/argon mixture. We synthesized ruthenium clusters supported on carbon as catalysts for methane reforming and new phthalocyanines to be used as catalyst precursors for oxidizing methane to methanol. The Ru{sub 4} and FeRu{sub 3} complexes supported on magnesia exhibited very different behavior in the DRIFT cell when heated under nitrogen. The FeRu{sub 3}/MgO system was completely decarbonylated by 400{degrees}C, while spectrum of the Ru{sub 4} system displayed carbonyl peaks until the temperature rose to over 600{degrees}C. The ru{sub 4}/MgO system behaved almost identically under methane/argon as it did under nitrogen in the carbonyl region. In the C-H region of the spectrum (2800-3100 cm{sup {minus}1}), peaks were observed under methane but not under nitrogen. The intensity of these peaks did not vary with temperature. We synthesized new catalysts by supporting the Ru{sub 4} and Ru{sub 6} clusters on carbon. Both acidic zeolites (Type Y or 5A) and basic magnesia (MgO) have been observed to react with hydrocarbons at high temperatures; these reactions generally lead to coking, then deactivation of the catalyst contained on these supports. We expect carbon to be a truly inert support.

  11. A first case of congenital TTP on the African continent due to a new homozygous mutation in the catalytic domain of ADAMTS13. (United States)

    Meyer, Sara C; Jeddi, Ramzi; Meddeb, Balkis; Gouider, Emna; Lämmle, Bernhard; Kremer Hovinga, Johanna A


    Hereditary thrombotic thrombocytopenic purpura (TTP) is a rare disorder characterized by occlusive microvascular thrombosis, consumptive thrombocytopenia, and microangiopathic hemolytic anemia. Homozygous or compound heterozygous mutations in the ADAMTS13 gene result in a congenital severe ADAMTS13 deficiency and subsequent accumulation of ultra-large von Willebrand factor multimers, which tend to form platelet thrombi in the microcirculation. We report a first case of congenital TTP on the African continent with a new, homozygous mutation in the metalloprotease domain of ADAMTS13. An initially oligo-symptomatic presentation was followed by acute exacerbation with ischemic stroke and acute renal failure highlighting the severity of this syndrome. PMID:18443791

  12. Statistical characteristic in time-domain of direct current corona-generated audible noise from conductor in corona cage (United States)

    Li, Xuebao; Cui, Xiang; Lu, Tiebing; Ma, Wenzuo; Bian, Xingming; Wang, Donglai; Hiziroglu, Huseyin


    The corona-generated audible noise (AN) has become one of decisive factors in the design of high voltage direct current (HVDC) transmission lines. The AN from transmission lines can be attributed to sound pressure pulses which are generated by the multiple corona sources formed on the conductor, i.e., transmission lines. In this paper, a detailed time-domain characteristics of the sound pressure pulses, which are generated by the DC corona discharges formed over the surfaces of a stranded conductors, are investigated systematically in a laboratory settings using a corona cage structure. The amplitude of sound pressure pulse and its time intervals are extracted by observing a direct correlation between corona current pulses and corona-generated sound pressure pulses. Based on the statistical characteristics, a stochastic model is presented for simulating the sound pressure pulses due to DC corona discharges occurring on conductors. The proposed stochastic model is validated by comparing the calculated and measured A-weighted sound pressure level (SPL). The proposed model is then used to analyze the influence of the pulse amplitudes and pulse rate on the SPL. Furthermore, a mathematical relationship is found between the SPL and conductor diameter, electric field, and radial distance.

  13. Direct Observation of Correlated Interdomain Motion in Alcohol Dehydrogenase


    Biehl, R.; Hoffmann, B.; Monkenbusch, M.; Falus, P.; Préost, S.; Merkel, R.; Richter, D.


    Interdomain motions in proteins are essential to enable or promote biochemical function. Neutron spinecho spectroscopy is used to directly observe the domain dynamics of the protein alcohol dehydrogenase. The collective motion of domains as revealed by their coherent form factor relates to the cleft opening dynamics between the binding and the catalytic domains enabling binding and release of the functional important cofactor. The cleft opening mode hardens as a result of an overall stiffenin...

  14. Effect of ethanol-diesel blend fuels on emission and particle size distribution in a common-rail direct injection diesel engine with warm-up catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hwanam [Graduate School of Mechanical Engineering, Chonnam National University, Gwangju 500-757 (Korea); Choi, Byungchul [Graduate School of Mechanical Engineering, Chonnam National University, Gwangju 500-757 (Korea); School of Mechanical Systems Engineering, Chonnam National University, Gwangju 500-757 (Korea)


    In this study, the exhaust gas from a common-rail direct injection diesel engine was investigated both upstream and downstream warm-up catalytic converters (WCC). Three different types of ultra-low sulfur fuels (ethanol-diesel blend, ethanol-diesel blend with cetane improver and pure diesel) were tested in this study. The objective of the work was to study the engine performance and the formation of THC (total hydro carbon), CO (carbon monoxide), NO{sub x} (nitrogen oxides), smoke and PM (particulate matters) when using these fuels. THC and CO emissions of the ethanol-diesel blend fuels were slightly increased, and about 50-80% mean conversion efficiencies of THC and CO on catalysts were achieved in the ECE R49 13-mode cycle. Smoke was decreased by more than 42% in the entire ECE 13-mode cycles. From the measurement of scanning mobility particle sizer (SMPS) for the particle size range of 10-385 nm, the total number and total mass of the PM of the ethanol-diesel blend fuels were decreased by about 11.7-15% and 19.2-26.9%, respectively. (author)

  15. Evolution of random catalytic networks

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, S.M. [Santa Fe Inst., NM (United States); Reidys, C.M. [Santa Fe Inst., NM (United States)]|[Los Alamos National Lab., NM (United States)


    In this paper the authors investigate the evolution of populations of sequences on a random catalytic network. Sequences are mapped into structures, between which are catalytic interactions that determine their instantaneous fitness. The catalytic network is constructed as a random directed graph. They prove that at certain parameter values, the probability of some relevant subgraphs of this graph, for example cycles without outgoing edges, is maximized. Populations evolving under point mutations realize a comparatively small induced subgraph of the complete catalytic network. They present results which show that populations reliably discover and persist on directed cycles in the catalytic graph, though these may be lost because of stochastic effects, and study the effect of population size on this behavior.

  16. Direct observations of ferromagnetic and antiferromagnetic domains in Pt/Co/Cr2O3/Pt perpendicular exchange biased film

    Directory of Open Access Journals (Sweden)

    Yu Shiratsuchi


    Full Text Available By using focused soft X-rays, magnetic domain imaging based on X-ray magnetic circular dichroism (XMCD measurements was performed on a Pt/Co/Cr2O3/Pt film that exhibits both perpendicular magnetic anisotropy and perpendicular exchange anisotropy. In the AC-demagnetized state, spatial distributions of the XMCD corresponding to the magnetic domains were clearly observed. In particular, ferromagnetic and antiferromagnetic magnetic domains were separately observed by tuning the photon energy to either the ferromagnetic Co L3 edge or the antiferromagnetic Cr L3 edge. The ferromagnetic domain pattern is similar to the ones previously reported for Co/Pt multilayers, and the ferromagnetic and antiferromagnetic domains are spatially coupled. The magnetization curve measured after cooling the sample, while maintaining the demagnetized state, exhibited positive and negative exchange biases simultaneously, which suggests that the exchange bias is determined on a domain-by-domain basis.

  17. Frequency domain near-infrared multiwavelength imager design using high-speed, direct analog-to-digital conversion (United States)

    Zimmermann, Bernhard B.; Fang, Qianqian; Boas, David A.; Carp, Stefan A.


    Frequency domain near-infrared spectroscopy (FD-NIRS) has proven to be a reliable method for quantification of tissue absolute optical properties. We present a full-sampling direct analog-to-digital conversion FD-NIR imager. While we developed this instrument with a focus on high-speed optical breast tomographic imaging, the proposed design is suitable for a wide-range of biophotonic applications where fast, accurate quantification of absolute optical properties is needed. Simultaneous dual wavelength operation at 685 and 830 nm is achieved by concurrent 67.5 and 75 MHz frequency modulation of each laser source, respectively, followed by digitization using a high-speed (180 MS/s) 16-bit A/D converter and hybrid FPGA-assisted demodulation. The instrument supports 25 source locations and features 20 concurrently operating detectors. The noise floor of the instrument was measured at Titration experiments consisting of 200 different absorption and scattering values were conducted to demonstrate accurate optical property quantification over the entire range of physiologically expected values.


    Institute of Scientific and Technical Information of China (English)

    Shao Wei; Qian Zuping; Yuan Feng


    A robust phase-only Direct Data Domain Least Squares (D3LS) algorithm based on generalized Rayleigh quotient optimization using hybrid Genetic Algorithm (GA) is presented in this letter. The optimization efficiency and computational speed are improved via the hybrid GA composed of standard GA and Nelder-Mead simplex algorithms. First, the objective function, with a form of generalized Rayleigh quotient, is derived via the standard D3LS algorithm. It is then taken as a fitness function and the unknown phases of all adaptive weights are taken as decision variables.Then, the nonlinear optimization is performed via the hybrid GA to obtain the optimized solution of phase-only adaptive weights. As a phase-only adaptive algorithm, the proposed algorithm is simpler than conventional algorithms when it comes to hardware implementation. Moreover, it processes only a single snapshot data as opposed to forming sample covariance matrix and operating matrix inversion. Simulation results show that the proposed algorithm has a good signal recovery and interferences nulling performance, which are superior to that of the phase-only D3LS algorithm based on standard GA.

  19. Purification and Characterization of the Catalytic Domain of Protein Tyrosine Phosphatase SHP-1 and the Preparation of Anti-△SHP-1 Antibodies

    Institute of Scientific and Technical Information of China (English)

    LI Wan-nan; ZHUANG Yan; LI He; SUN Ying; FU Yao; WU Xiao-xia; ZHAO Zhi-zhuang; FU Xue-qi


    This study is focused on the expression of an SH2 domain-truncated form of protein tyrosine phosphatase SHP-1(designated △SHP-1) and the preparation of its polyelonal antibodies.A cDNA fragment encoding △SHP-1 was amplified by PCR and then cloned into the pT7 expression vector.The recombinant pT7-△SHP-1 plasmid was used to transform Rosetta(DE3) E.coll cells.△SHP-1 was distributed in the exclusion body of E.coll cell extracts and was purified through a two-column chromatographic procedure.The purified enzyme exhibited an expected molecular weight on SDS-gels and HPLC gel filtration columns.It possesses robust tyrosine phosphatase activity and shows typical enzymatic characteristics of classic tyrosine phosphatases.To generate polyclonal anti-△SHP-1 antibodies,purified recombinant △SHP-1 was used to immunize a rabbit.The resultant anti-serum was subjected to purification on △SHP-1 antigen affinity chromatography.The purified polyclonal antibody displayed a high sensitivity and specificity toward △SHP-1.This study thus provides the essential materials for further investigating the biological function and pathological implication of SHP-1 and screening the inhibitors and activators of the enzyme for therapeutic drug development.

  20. Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals

    DEFF Research Database (Denmark)

    Janeček, Štefan; Svensson, Birte; MacGregor, E. Ann


    kinase SNF1 complex, and an adaptor–regulator related to the SNF1/AMPK family, AKINβγ. CBM20s and CBM48s of amylolytic enzymes occur predominantly in the microbial world, whereas the non-amylolytic proteins containing these modules are mostly of plant and animal origin. Comparison of amino acid sequences......Starch-binding domains (SBDs) comprise distinct protein modules that bind starch, glycogen or related carbohydrates and have been classified into different families of carbohydrate-binding modules (CBMs). The present review focuses on SBDs of CBM20 and CBM48 found in amylolytic enzymes from several...... glycoside hydrolase (GH) families GH13, GH14, GH15, GH31, GH57 and GH77, as well as in a number of regulatory enzymes, e.g., phosphoglucan, water dikinase-3, genethonin-1, laforin, starch-excess protein-4, the β-subunit of AMP-activated protein kinase and its homologues from sucrose non-fermenting-1 protein...

  1. Cyclin H binding to the RARα activation function (AF)-2 domain directs phosphorylation of the AF-1 domain by cyclin-dependent kinase 7


    Bour, Gaétan; Gaillard, Emilie; Bruck, Nathalie; Lalevée, Sébastien; Plassat, Jean-Luc; Busso, Didier; Samama, Jean-Pierre; Rochette-Egly, Cécile


    The transcriptional activity of nuclear retinoic acid receptors (RARs), which act as RAR/retinoid X receptor (RXR) heterodimers, depends on two activation functions, AF-1 and AF-2, which are targets for phosphorylations and synergize for the activation of retinoic acid target genes. The N-terminal AF-1 domain of RARα is phosphorylated at S77 by the cyclin-dependent kinase (cdk)-activating kinase (CAK) subcomplex (cdk7/cyclin H/MAT1) of the general transcription factor TFIIH. Here, we show tha...

  2. The E2-25K ubiquitin-associated (UBA) domain aids in polyubiquitin chain synthesis and linkage specificity

    International Nuclear Information System (INIS)

    Research highlights: → We examine the role of a ubiquitin-associated (UBA) domain in an E2 enzyme. → The E2-25K UBA domain directs polyubiquitin chain linkage specificity. → The E2-25K UBA domain regulates length of polyubiquitin chains synthesized. -- Abstract: E2-25K is an ubiquitin-conjugating enzyme with the ability to synthesize Lys48-linked polyubiquitin chains. E2-25K and its homologs represent the only known E2 enzymes which contain a C-terminal ubiquitin-associated (UBA) domain as well as the conserved catalytic ubiquitin-conjugating (UBC) domain. As an additional non-covalent binding surface for ubiquitin, the UBA domain must provide some functional specialization. We mapped the protein-protein interface involved in the E2-25K UBA/ubiquitin complex by solution nuclear magnetic resonance (NMR) spectroscopy and subsequently modeled the structure of the complex. Domain-domain interactions between the E2-25K catalytic UBC domain and the UBA domain do not induce significant structural changes in the UBA domain or alter the affinity of the UBA domain for ubiquitin. We determined that one of the roles of the C-terminal UBA domain, in the context of E2-25K, is to increase processivity in Lys48-linked polyubiquitin chain synthesis, possibly through increased binding to the ubiquitinated substrate. Additionally, we see evidence that the UBA domain directs specificity in polyubiquitin chain linkage.

  3. Catalytic Combustion of Gasified Waste

    Energy Technology Data Exchange (ETDEWEB)

    Kusar, Henrik


    This thesis concerns catalytic combustion for gas turbine application using a low heating-value (LHV) gas, derived from gasified waste. The main research in catalytic combustion focuses on methane as fuel, but an increasing interest is directed towards catalytic combustion of LHV fuels. This thesis shows that it is possible to catalytically combust a LHV gas and to oxidize fuel-bound nitrogen (NH{sub 3}) directly into N{sub 2} without forming NO{sub x} The first part of the thesis gives a background to the system. It defines waste, shortly describes gasification and more thoroughly catalytic combustion. The second part of the present thesis, paper I, concerns the development and testing of potential catalysts for catalytic combustion of LHV gases. The objective of this work was to investigate the possibility to use a stable metal oxide instead of noble metals as ignition catalyst and at the same time reduce the formation of NO{sub x} In paper II pilot-scale tests were carried out to prove the potential of catalytic combustion using real gasified waste and to compare with the results obtained in laboratory scale using a synthetic gas simulating gasified waste. In paper III, selective catalytic oxidation for decreasing the NO{sub x} formation from fuel-bound nitrogen was examined using two different approaches: fuel-lean and fuel-rich conditions. Finally, the last part of the thesis deals with deactivation of catalysts. The various deactivation processes which may affect high-temperature catalytic combustion are reviewed in paper IV. In paper V the poisoning effect of low amounts of sulfur was studied; various metal oxides as well as supported palladium and platinum catalysts were used as catalysts for combustion of a synthetic gas. In conclusion, with the results obtained in this thesis it would be possible to compose a working catalytic system for gas turbine application using a LHV gas.

  4. Metal-free phthalocyanine (H2Pc molecule adsorbed on the Au(111 surface: formation of a wide domain along a single lattice direction

    Directory of Open Access Journals (Sweden)

    Tadahiro Komeda, Hironari Isshiki and Jie Liu


    Full Text Available Using low-temperature scanning tunneling microscopy (STM, we observed the bonding configuration of the metal-free phthalocyanine (H2Pc molecule adsorbed on the Au(111 surface. A local lattice formation started from a quasi-square lattice aligned to the close-packed directions of the Au(111 surface. Although we expected the lattice alignment to be equally distributed along the three crystallographically equivalent directions, the domain aligned normal to the ridge of the herringbone structure was missing in the STM images. We attribute this effect to the uniaxial contraction of the reconstructed Au(111 surface that can account for the formation of a large lattice domain along a single crystallographical direction.

  5. An α-Helical Extension of the ELMO1 Pleckstrin Homology Domain Mediates Direct Interaction to DOCK180 and Is Critical in Rac Signaling


    Komander, David; Patel, Manishha; Laurin, Mélanie; Fradet, Nadine; Pelletier, Ariane; Barford, David; Côté, Jean-François


    The mammalian DOCK180 protein belongs to an evolutionarily conserved protein family, which together with ELMO proteins, is essential for activation of Rac GTPase-dependent biological processes. Here, we have analyzed the DOCK180-ELMO1 interaction, and map direct interaction interfaces to the N-terminal 200 amino acids of DOCK180, and to the C-terminal 200 amino acids of ELMO1, comprising the ELMO1 PH domain. Structural and biochemical analysis of this PH domain reveals that it is incapable of...

  6. A semi-alternating direction method for a 2-D fractional FitzHugh-Nagumo monodomain model on an approximate irregular domain (United States)

    Liu, F.; Zhuang, P.; Turner, I.; Anh, V.; Burrage, K.


    A FitzHugh-Nagumo monodomain model has been used to describe the propagation of the electrical potential in heterogeneous cardiac tissue. In this paper, we consider a two-dimensional fractional FitzHugh-Nagumo monodomain model on an irregular domain. The model consists of a coupled Riesz space fractional nonlinear reaction-diffusion model and an ordinary differential equation, describing the ionic fluxes as a function of the membrane potential. Second, we use a decoupling technique and focus on solving the Riesz space fractional nonlinear reaction-diffusion model. A novel spatially second-order accurate semi-implicit alternating direction method (SIADM) for this model on an approximate irregular domain is proposed. Third, stability and convergence of the SIADM are proved. Finally, some numerical examples are given to support our theoretical analysis and these numerical techniques are employed to simulate a two-dimensional fractional FitzHugh-Nagumo model on both an approximate circular and an approximate irregular domain.

  7. APPL proteins FRET at the BAR: direct observation of APPL1 and APPL2 BAR domain-mediated interactions on cell membranes using FRET microscopy.

    Directory of Open Access Journals (Sweden)

    Heidi J Chial

    Full Text Available BACKGROUND: Human APPL1 and APPL2 are homologous RAB5 effectors whose binding partners include a diverse set of transmembrane receptors, signaling proteins, and phosphoinositides. APPL proteins associate dynamically with endosomal membranes and are proposed to function in endosome-mediated signaling pathways linking the cell surface to the cell nucleus. APPL proteins contain an N-terminal Bin/Amphiphysin/Rvs (BAR domain, a central pleckstrin homology (PH domain, and a C-terminal phosphotyrosine binding (PTB domain. Previous structural and biochemical studies have shown that the APPL BAR domains mediate homotypic and heterotypic APPL-APPL interactions and that the APPL1 BAR domain forms crescent-shaped dimers. Although previous studies have shown that APPL minimal BAR domains associate with curved cell membranes, direct interaction between APPL BAR domains on cell membranes in vivo has not been reported. METHODOLOGY: Herein, we used a laser-scanning confocal microscope equipped with a spectral detector to carry out fluorescence resonance energy transfer (FRET experiments with cyan fluorescent protein/yellow fluorescent protein (CFP/YFP FRET donor/acceptor pairs to examine interactions between APPL minimal BAR domains at the subcellular level. This comprehensive approach enabled us to evaluate FRET levels in a single cell using three methods: sensitized emission, standard acceptor photobleaching, and sequential acceptor photobleaching. We also analyzed emission spectra to address an outstanding controversy regarding the use of CFP donor/YFP acceptor pairs in FRET acceptor photobleaching experiments, based on reports that photobleaching of YFP converts it into a CFP-like species. CONCLUSIONS: All three methods consistently showed significant FRET between APPL minimal BAR domain FRET pairs, indicating that they interact directly in a homotypic (i.e., APPL1-APPL1 and APPL2-APPL2 and heterotypic (i.e., APPL1-APPL2 manner on curved cell membranes

  8. The PDZ domain of the guanine nucleotide exchange factor PDZGEF directs binding to phosphatidic acid during brush border formation.

    Directory of Open Access Journals (Sweden)

    Sarah V Consonni

    Full Text Available PDZGEF is a guanine nucleotide exchange factor for the small G protein Rap. It was recently found that PDZGEF contributes to establishment of intestinal epithelial polarity downstream of the kinase Lkb1. By binding to phosphatidic acid enriched at the apical membrane, PDZGEF locally activates Rap2a resulting in induction of brush border formation via a pathway that includes the polarity players TNIK, Mst4 and Ezrin. Here we show that the PDZ domain of PDZGEF is essential and sufficient for targeting PDZGEF to the apical membrane of polarized intestinal epithelial cells. Inhibition of PLD and consequently production of phosphatidic acid inhibitis targeting of PDZGEF to the plasma membrane. Furthermore, localization requires specific positively charged residues within the PDZ domain. We conclude that local accumulation of PDZGEF at the apical membrane during establishment of epithelial polarity is mediated by electrostatic interactions between positively charged side chains in the PDZ domain and negatively charged phosphatidic acid.

  9. Structural Evidence for Direct Interactions Between the BRCT Domains of Human BRCA1 and a Phospho-Peptide from Human ACC1

    Energy Technology Data Exchange (ETDEWEB)

    Shen,Y.; Tong, L.


    The tandem BRCA1 C-terminal (BRCT) domains are phospho-serine/threonine recognition modules essential for the function of BRCA1. Recent studies suggest that acetyl-CoA carboxylase 1 (ACC1), an enzyme with crucial roles in de novo fatty acid biosynthesis and lipogenesis and essential for cancer cell survival, may be a novel binding partner for BRCA1, through interactions with its BRCT domains. We report here the crystal structure at 3.2 Angstroms resolution of human BRCA1 BRCT domains in complex with a phospho-peptide from human ACC1 (p-ACC1 peptide, with the sequence 1258-DSPPQ-pS-PTFPEAGH-1271), which provides molecular evidence for direct interactions between BRCA1 and ACC1. The p-ACC1 peptide is bound in an extended conformation, located in a groove between the tandem BRCT domains. There are recognizable and significant structural differences to the binding modes of two other phospho-peptides to these domains, from BACH1 and CtIP, even though they share a conserved pSer-Pro-(Thr/Val)-Phe motif. Our studies establish a framework for understanding the regulation of lipid biosynthesis by BRCA1 through its inhibition of ACC1 activity, which could be a novel tumor suppressor function of BRCA1.

  10. On the Structural Context and Identification of Enzyme Catalytic Residues


    Yu-Tung Chien; Shao-Wei Huang


    Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The...

  11. Catalytically inactive lipoprotein lipase expression in muscle of transgenic mice increases very low density lipoprotein uptake: Direct evidence that lipoprotein lipase bridging occurs in vivo


    Merkel, Martin; Kako, Yuko; Radner, Herbert; Cho, Irene S.; Ramasamy, Ravi; Brunzell, John D.; Goldberg, Ira J.; Breslow, Jan L.


    Lipoprotein lipase (LPL) is the central enzyme in plasma triglyceride hydrolysis. In vitro studies have shown that LPL also can enhance lipoprotein uptake into cells via pathways that are independent of catalytic activity but require LPL as a molecular bridge between lipoproteins and proteoglycans or receptors. To investigate whether this bridging function occurs in vivo, two transgenic mouse lines were established expressing a muscle creatine kinase promoter-driven human LPL (hLPL) minigene ...

  12. Activation of p115-RhoGEF Requires Direct Association of G[alpha subscript 13] and the Dbl Homology Domain

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Zhe; Guo, Liang; Hadas, Jana; Gutowski, Stephen; Sprang, Stephen R.; Sternweis, Paul C. (IIT); (UTSMC); (Montana)


    RGS-containing RhoGEFs (RGS-RhoGEFs) represent a direct link between the G{sub 12} class of heterotrimeric G proteins and the monomeric GTPases. In addition to the canonical Dbl homology (DH) and pleckstrin homology domains that carry out the guanine nucleotide exchange factor (GEF) activity toward RhoA, these RhoGEFs also possess RGS homology (RH) domains that interact with activated {alpha} subunits of G{sub 12} and G{sub 13}. Although the GEF activity of p115-RhoGEF (p115), an RGS-RhoGEF, can be stimulated by G{alpha}{sub 13}, the exact mechanism of the stimulation has remained unclear. Using combined studies with small angle x-ray scattering, biochemistry, and mutagenesis, we identify an additional binding site for activated G{alpha}{sub 13} in the DH domain of p115. Small angle x-ray scattering reveals that the helical domain of G{alpha}{sub 13} docks onto the DH domain, opposite to the surface of DH that binds RhoA. Mutation of a single tryptophan residue in the {alpha}3b helix of DH reduces binding to activated G{alpha}{sub 13} and ablates the stimulation of p115 by G{alpha}{sub 13}. Complementary mutations at the predicted DH-binding site in the {alpha}B-{alpha}C loop of the helical domain of G{alpha}{sub 13} also affect stimulation of p115 by G{alpha}{sub 13}. Although the GAP activity of p115 is not required for stimulation by G{alpha}{sub 13}, two hydrophobic motifs in RH outside of the consensus RGS box are critical for this process. Therefore, the binding of G{alpha}{sub 13} to the RH domain facilitates direct association of G{alpha}{sub 13} to the DH domain to regulate its exchange activity. This study provides new insight into the mechanism of regulation of the RGS-RhoGEF and broadens our understanding of G protein signaling.

  13. Directed evolution of the forkhead-associated domain to generate anti-phosphospecific reagents by phage-display


    Pershad, Kritika; Wypisniak, Karolina; Kay, Brian K.


    While affinity reagents are valuable tools for monitoring protein phosphorylation and studying signaling events in cells, generating them through immunization of animals with phosphopeptides is expensive, laborious and time consuming. An attractive alternative is to use protein evolution techniques and isolate new anti-phosphopeptide binding specificities from a library of variants of a phosphopeptide-binding domain. To explore this strategy, we attempted to display on the surface of bacterio...

  14. A novel epidermal growth factor receptor variant lacking multiple domains directly activates transcription and is overexpressed in tumors


    Piccione, EC; Lieu, TJ; Gentile, CF; Williams, TR; Connolly, AJ; Godwin, AK; Koong, AC; Wong, AJ


    The epidermal growth factor receptor (EGFR) is essential to multiple physiological and neoplastic processes via signaling by its tyrosine kinase domain and subsequent activation of transcription factors. EGFR overexpression and alteration, including point mutations and structural variants, contribute to oncogenesis in many tumor types. In this study, we identified an in-frame splice variant of the EGFR called mini-LEEK (mLEEK) that is more broadly expressed than the EGFR and is overexpressed ...

  15. An alpha-helical extension of the ELMO1 pleckstrin homology domain mediates direct interaction to DOCK180 and is critical in Rac signaling. (United States)

    Komander, David; Patel, Manishha; Laurin, Mélanie; Fradet, Nadine; Pelletier, Ariane; Barford, David; Côté, Jean-François


    The mammalian DOCK180 protein belongs to an evolutionarily conserved protein family, which together with ELMO proteins, is essential for activation of Rac GTPase-dependent biological processes. Here, we have analyzed the DOCK180-ELMO1 interaction, and map direct interaction interfaces to the N-terminal 200 amino acids of DOCK180, and to the C-terminal 200 amino acids of ELMO1, comprising the ELMO1 PH domain. Structural and biochemical analysis of this PH domain reveals that it is incapable of phospholipid binding, but instead structurally resembles FERM domains. Moreover, the structure revealed an N-terminal amphiphatic alpha-helix, and point mutants of invariant hydrophobic residues in this helix disrupt ELMO1-DOCK180 complex formation. A secondary interaction between ELMO1 and DOCK180 is conferred by the DOCK180 SH3 domain and proline-rich motifs at the ELMO1 C-terminus. Mutation of both DOCK180-interaction sites on ELMO1 is required to disrupt the DOCK180-ELMO1 complex. Significantly, although this does not affect DOCK180 GEF activity toward Rac in vivo, Rac signaling is impaired, implying additional roles for ELMO in mediating intracellular Rac signaling. PMID:18768751

  16. Cloning, expression, and purification of human cyclophilin in Escherichia coli and assessment of the catalytic role of cysteines by site-directed mutagenesis

    International Nuclear Information System (INIS)

    The cDNA encoding human cyclophilin from the Jurkat T-cell lymphoma line has been cloned by the expression cassette polymerase chain reaction and sequenced, and an expression vector has been constructed under control of the tac promoter for efficient expression in Escherichia coli. Active cyclophilin is produced at up to 40% of soluble cell protein, facilitating a one-column purification to homogeneity. Wild-type cyclophilin was characterized for binding of the potent immunosuppressant agent cyclosporin A by tryptophan fluorescence enhancement and for inhibition of cyclophilin's peptidyl-proly cis-trans isomerase (rotamase) activity. With N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as the substrate, recombinant human cyclophilin has a high catalytic efficiency. To test the prior suggestion that a cysteine residue may be essential for catalysis and immunosuppressant binding, the four cysteines at positions 52, 62, 115, and 161 were mutated individually to alanine and the purified mutant proteins were shown to retain full affinity for cyclosporin A and equivalent catalytic efficiency as a rotamase. Clearly the cysteines play no essential role in catalysis or cyclosporin A binding. These results rule out the recently proposed mechanism. Involving the formation of tetrahedral hemithioorthoamide. Whereas mechanisms that embody other tetrahedral intermediates may be operative, an alternative mechanism is considered that involves distortion of bound substrate with a twisted (90 degree) peptidyl-prolyl amide bond

  17. Effect of induced shielding current transmission in longitudinal direction on levitation force of melt grown single-domain YBa2Cu3O7- x cylindrical superconductor (United States)

    Yang, Wanmin; Zhou, Lian; Feng, Yong; Zhang, Pingxiang; Nicolsky, R.; de Andrade, R.


    A novel layer deletion method is used to experimentally investigate the effect of induced shielding current transmission (ISCT) in the longitudinal direction on the levitation force of a single-domain YBa2Cu3O7-x (YBCO) cylindrical superconductor (ϕ30×7 mm). In the experiment the sample was gradually sliced into two equal sheets, at the middle height along a diameter with 5 mm every step. The experimental results show that the levitation force is closely related with the ISCT in the longitudinal direction. Any layer deletion, even a small piece of layer deletion can reduce the levitation force of the sample. After the whole layer was deleted the levitation force can diminish about 50%. It is also found that the levitation force is directly proportional to the effective factor of surface area, which is equal to the top surface area divided by the total surface area parallel to the top surface of the sample.

  18. Effect of induced shielding current transmission in longitudinal direction on levitation force of melt grown single-domain YBa2Cu3O7-x cylindrical superconductor

    Institute of Scientific and Technical Information of China (English)

    YANG; Wanmin; ZHOU; Lian; FENG; Yong; ZHANG; Pingxiang; R.


    A novel layer deletion method is used to experimentally investigate the effect of induced shielding current transmission (ISCT) in the longitudinal direction on the levitation force of a single-domain YBa2Cu3O7-x (YBCO) cylindrical superconductor (φ30x7 mm). In the experiment the sample was gradually sliced into two equal sheets, at the middle height along a diameter with 5 mm every step. The experimental results show that the levitation force is closely related with the ISCT in the longitudinal direction. Any layer deletion, even a small piece of layer deletion can reduce the levitation force of the sample. After the whole layer was deleted the levitation force can diminish about 50%. It is also found that the levitation force is directly proportional to the effective factor of surface area, which is equal to the top surface area divided by the total surface area parallel to the top surface of the sample.

  19. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Directory of Open Access Journals (Sweden)

    Etchells J Peter


    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  20. Apo-states of calmodulin and CaBP1 control CaV1 voltage-gated calcium channel function through direct competition for the IQ domain (United States)

    Findeisen, Felix; Rumpf, Christine; Minor, Daniel L.


    In neurons, binding of calmodulin (CaM) or calcium-binding protein 1 (CaBP1) to the CaV1 (L-type) voltage-gated calcium channel IQ domain endows the channel with diametrically opposed properties. CaM causes calcium-dependent inactivation (CDI) and limits calcium entry, whereas CaBP1 blocks CDI and allows sustained calcium influx. Here, we combine isothermal titration calorimetry (ITC) with cell-based functional measurements and mathematical modeling to show that these calcium sensors behave in a competitive manner that is explained quantitatively by their apo-state binding affinities for the IQ domain. This competition can be completely blocked by covalent tethering of CaM to the channel. Further, we show that Ca2+/CaM has a sub-picomolar affinity for the IQ domain that is achieved without drastic alteration of calcium binding properties. The observation that the apo-forms of CaM and CaBP1 compete with each other demonstrates a simple mechanism for direct modulation of CaV1 function and suggests a means by which excitable cells may dynamically tune CaV activity. PMID:23811053

  1. Convergence analysis of a class of massively parallel direction splitting algorithms for the Navier-Stokes equations in simple domains

    KAUST Repository

    Guermond, Jean-Luc


    We provide a convergence analysis for a new fractional timestepping technique for the incompressible Navier-Stokes equations based on direction splitting. This new technique is of linear complexity, unconditionally stable and convergent, and suitable for massive parallelization. © 2012 American Mathematical Society.

  2. Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis. (United States)

    Heimer, Brandon W; Tam, Brooke E; Sikes, Hadley D


    Methyl-binding domain (MBD) family proteins specifically bind double-stranded, methylated DNA which makes them useful for DNA methylation analysis. We displayed three of the core members MBD1, MBD2 and MBD4 on the surface of Saccharomyces cerevisiae cells. Using the yeast display platform, we determined the equilibrium dissociation constant of human MBD2 (hMBD2) to be 5.9 ± 1.3 nM for binding to singly methylated DNA. The measured affinity for DNA with two methylated sites varied with the distance between the sites. We further used the yeast display platform to evolve the hMBD2 protein for improved binding affinity. Affecting five amino acid substitutions doubled the affinity of the wild-type protein to 3.1 ± 1.0 nM. The most prevalent of these mutations, K161R, occurs away from the DNA-binding site and bridges the N- and C-termini of the protein by forming a new hydrogen bond. The F208Y and L170R mutations added new non-covalent interactions with the bound DNA strand. We finally concatenated the high-affinity MBD variant and expressed it in Escherichia coli as a green fluorescent protein fusion. Concatenating the protein from 1× to 3× improved binding 6-fold for an interfacial binding application. PMID:26384511

  3. Loss of sialic acid binding domain redirects protein σ1 to enhance M cell-directed vaccination.

    Directory of Open Access Journals (Sweden)

    Dagmara Zlotkowska

    Full Text Available Ovalbumin (OVA genetically fused to protein sigma 1 (pσ1 results in tolerance to both OVA and pσ1. Pσ1 binds in a multi-step fashion, involving both protein- and carbohydrate-based receptors. To assess the relative pσ1 components responsible for inducing tolerance and the importance of its sialic binding domain (SABD for immunization, modified OVA-pσ1, termed OVA-pσ1(short, was deleted of its SABD, but with its M cell targeting moiety intact, and was found to be immunostimulatory and enhanced CD4(+ and CD8(+ T cell proliferation. When used to nasally immunize mice given with and without cholera toxin (CT adjuvant, elevated SIgA and serum IgG responses were induced, and OVA-pσ1(s was more efficient for immunization than native OVA+CT. The immune antibodies (Abs were derived from elevated Ab-forming cells in the upper respiratory tissues and submaxillary glands and were supported by mixed Th cell responses. Thus, these studies show that pσ1(s can be fused to vaccines to effectively elicit improved SIgA responses.

  4. HIV-1 Nef Selectively Activates Src Family Kinases Hck, Lyn, and c-Src through Direct SH3 Domain Interaction*


    Trible, Ronald P.; Emert-Sedlak, Lori; Smithgall, Thomas E


    Nef is an HIV-1 virulence factor that promotes viral pathogenicity by altering host cell signaling pathways. Nef binds several members of the Src kinase family, and these interactions have been implicated in the pathogenesis of HIV/AIDS. However, the direct effect of Nef interaction on Src family kinase (SFK) regulation and activity has not been systematically addressed. We explored this issue using Saccharomyces cerevisiae, a well defined model system for the study of SFK regulation. Previou...

  5. An Experimental Study on the Fast Light Off of Catalytic Converter in a Gasoline Direct Injection Engine%直喷汽油机催化器快速起燃的试验研究

    Institute of Scientific and Technical Information of China (English)

    于秀敏; 董伟; 嵇全喜


    针对EA888直喷汽油机建立了试验台架及试验测控系统,通过试验研究了过量空气系数和两次喷射比例对催化器起燃特性的影响规律.试验结果表明,采用微稀的混合气有利于催化器的快速起燃,采用两次喷射有助于推迟点火,提高排气温度,缩短催化器起燃时间.%A test bench and its control system are established for EA888 direct injection gasoline engine, and an experimental study is conducted on the rule of the effects of excess air coefficient and the fuel proportion ratio in two-stage fuel injection on the light-off characteristics of catalytic converter. The results show that a slight-lean mixture is conducive to the rapid light off of catalytic converter, and two-stage injection helps delay ignition, raise exhaust temperature and shorten the light-off time of catalyst.

  6. Prospective isolation of mesenchymal stem cells from human bone marrow using novel antibodies directed against Sushi domain containing 2. (United States)

    Sivasubramaniyan, Kavitha; Harichandan, Abhishek; Schumann, Susanne; Sobiesiak, Malgorzata; Lengerke, Claudia; Maurer, Andreas; Kalbacher, Hubert; Bühring, Hans-Jörg


    Several strategies have been developed to facilitate the prospective isolation of bone marrow-derived mesenchymal stem/stromal cells (BM-MSCs) based on the selective expression or absence of surface markers. Recently, we described the monoclonal antibodies W3D5 and W5C5, which selectively react with BM-MSCs, but not with hematopoietic cells. Both antibodies showed an identical reactivity pattern, indicating that they may recognize the same molecule. To identify the cognate antigen, cultured MSCs were sorted for cells expressing either very high levels of W5C5/W3D5 antigen or for cells which were negative for this antigen. Further processing of these cells for microarray analysis revealed a 20-fold enrichment of the type 1 integral membrane protein Sushi domain containing 2 (SUSD2) in the in W5C5(+) subset. To confirm the identity of the W5C5/W3D5 antigen to SUSD2, HEK293 cells were transfected with the full-length coding sequence of human SUSD2 followed by reactivity analysis of W5C5 and W3D5 antibodies with the transfected line. Flow cytometric analysis showed that both antibodies selectively recognized HEK293/huSUSD2 cells, but not the parental cell line. In line with this, SUSD2 siRNA treatment of SUSD2(+) WERI-RB-1 retinoblastoma cells reduced the expression levels of W3D5 and W5C5 antigens to ~39% and 37%, respectively. Finally, FACSorting and colony assays revealed that only SUSD2(+), but not SUSD2(-) BM cells give rise to colony-forming units-fibroblasts and are able to differentiate into osteoblasts, adipocytes, and chondrocytes. In conclusion, we identified SUSD2 as a novel and specific marker for the prospective isolation of BM-MSCs. PMID:23406305

  7. Human small cell lung cancer NYH cells selected for resistance to the bisdioxopiperazine topoisomerase II catalytic inhibitor ICRF-187 demonstrate a functional R162Q mutation in the Walker A consensus ATP binding domain of the alpha isoform

    DEFF Research Database (Denmark)

    Wessel, I; Jensen, L H; Jensen, P B;


    Bisdioxopiperazine drugs such as ICRF-187 are catalytic inhibitors of DNA topoisomerase II, with at least two effects on the enzyme: namely, locking it in a closed-clamp form and inhibiting its ATPase activity. This is in contrast to topoisomerase II poisons as etoposide and amsacrine (m-AMSA), w...

  8. Direct observation of low-temperature catalytic decomposition of H{sub 3}BO{sub 3} shell in core/shell Ni/H{sub 3}BO{sub 3} nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, X.F. [Dalian University of Technology, School of Materials Science and Engineering, Dalian, Liaoning (China); Industrial Materials Institute, National Research Council of Canada, Boucherville, Quebec (Canada); Guan, P.F. [Tohoku University, World Premier International Research Center, Advanced Institute for Materials Research, Sendai (Japan); Dong, X.L. [Dalian University of Technology, School of Materials Science and Engineering, Dalian, Liaoning (China)


    Decomposition of H{sub 3}BO{sub 3} to B{sub 2}O{sub 3} in core/shell Ni/H{sub 3}BO{sub 3} nanoparticles was in situ recorded by transmission electron microscope as the irradiation time. The direct observation provides compelling evidence of the synergetic effect of the Ni core and the H{sub 3}BO{sub 3} shell, revealing the catalytic mechanisms of metal nanostructures that induce the decomposition at 124 C, lower than the bulk counterpart at 300 C. This phenomenon can be theoretically explained by considering the weakening of B-O bond at the Ni-H{sub 3}BO{sub 3} interface, and has important implications in understanding the lubricant behavior of H{sub 3}BO{sub 3} in frictional wear. (orig.)

  9. ADAR proteins: structure and catalytic mechanism. (United States)

    Goodman, Rena A; Macbeth, Mark R; Beal, Peter A


    Since the discovery of the adenosine deaminase (ADA) acting on RNA (ADAR) family of proteins in 1988 (Bass and Weintraub, Cell 55:1089-1098, 1988) (Wagner et al. Proc Natl Acad Sci U S A 86:2647-2651, 1989), we have learned much about their structure and catalytic mechanism. However, much about these enzymes is still unknown, particularly regarding the selective recognition and processing of specific adenosines within substrate RNAs. While a crystal structure of the catalytic domain of human ADAR2 has been solved, we still lack structural data for an ADAR catalytic domain bound to RNA, and we lack any structural data for other ADARs. However, by analyzing the structural data that is available along with similarities to other deaminases, mutagenesis and other biochemical experiments, we have been able to advance the understanding of how these fascinating enzymes function. PMID:21769729

  10. The ETS domain transcription factor ELK1 directs a critical component of growth signaling by the androgen receptor in prostate cancer cells. (United States)

    Patki, Mugdha; Chari, Venkatesh; Sivakumaran, Suneethi; Gonit, Mesfin; Trumbly, Robert; Ratnam, Manohar


    The androgen receptor (AR) is essential for diverse aspects of prostate development and function. Molecular mechanisms by which prostate cancer (PC) cells redirect AR signaling to genes that primarily support growth are unclear. A systematic search for critical AR-tethering proteins led to ELK1, an ETS transcription factor of the ternary complex factor subfamily. Although genetically redundant, ELK1 was obligatory for AR-dependent growth and clonogenic survival in both hormone-dependent PC and castration-recurrent PC cells but not for AR-negative cell growth. AR required ELK1 to up-regulate a major subset of its target genes that was strongly and primarily enriched for cell growth functions. AR functioned as a coactivator of ELK1 by association through its A/B domain, bypassing the classical mechanism of ELK1 activation by phosphorylation and without inducing ternary complex target genes. The ELK1-AR synergy per se was ligand-independent, although it required ligand for nuclear localization of AR as targeting the AR A/B domain to the nucleus recapitulated the action of hormone; accordingly, Casodex was a poor antagonist of the synergy. ELK3, the closest substitute for ELK1 in structure/function and genome recognition, did not interact with AR. ELK1 thus directs selective and sustained gene induction that is a substantial and critical component of growth signaling by AR in PC cells. The ELK1-AR interaction offers a functionally tumor-selective drug target. PMID:23426362

  11. ATM Localization and Heterochromatin Repair Depend on Direct Interaction of the 53BP1-BRCT2 Domain with γH2AX

    Directory of Open Access Journals (Sweden)

    Robert A. Baldock


    Full Text Available 53BP1 plays multiple roles in mammalian DNA damage repair, mediating pathway choice and facilitating DNA double-strand break repair in heterochromatin. Although it possesses a C-terminal BRCT2 domain, commonly involved in phospho-peptide binding in other proteins, initial recruitment of 53BP1 to sites of DNA damage depends on interaction with histone post-translational modifications—H4K20me2 and H2AK13/K15ub—downstream of the early γH2AX phosphorylation mark of DNA damage. We now show that, contrary to current models, the 53BP1-BRCT2 domain binds γH2AX directly, providing a third post-translational mark regulating 53BP1 function. We find that the interaction of 53BP1 with γH2AX is required for sustaining the 53BP1-dependent focal concentration of activated ATM that facilitates repair of DNA double-strand breaks in heterochromatin in G1.

  12. ATM Localization and Heterochromatin Repair Depend on Direct Interaction of the 53BP1-BRCT2 Domain with γH2AX. (United States)

    Baldock, Robert A; Day, Matthew; Wilkinson, Oliver J; Cloney, Ross; Jeggo, Penelope A; Oliver, Antony W; Watts, Felicity Z; Pearl, Laurence H


    53BP1 plays multiple roles in mammalian DNA damage repair, mediating pathway choice and facilitating DNA double-strand break repair in heterochromatin. Although it possesses a C-terminal BRCT2 domain, commonly involved in phospho-peptide binding in other proteins, initial recruitment of 53BP1 to sites of DNA damage depends on interaction with histone post-translational modifications--H4K20me2 and H2AK13/K15ub--downstream of the early γH2AX phosphorylation mark of DNA damage. We now show that, contrary to current models, the 53BP1-BRCT2 domain binds γH2AX directly, providing a third post-translational mark regulating 53BP1 function. We find that the interaction of 53BP1 with γH2AX is required for sustaining the 53BP1-dependent focal concentration of activated ATM that facilitates repair of DNA double-strand breaks in heterochromatin in G1. PMID:26628370

  13. Direct visualization of chemical and thermo-remanent magnetization of pseudo-single-domain magnetite grains and the implications for reliable paleomagentic signal acquisition (United States)

    Almeida, T.; Muxworthy, A. R.; Kasama, T.; Williams, W.; Kovács, A.; Dunin-Borkowski, R.; Hansen, T. W.


    In order to reliably interpret paleomagnetic measurements, the mechanisms of chemical remanent magnetization (CRM) and thermoremanent magnetization (TRM) must be fully understood. Currently, most models of CRM and TRM processes only exist for the smallest, uniformly magnetized grains, termed single domain (SD). However, the magnetic signal from rocks is often dominated by slightly larger grains containing non-uniform magnetization states, termed pseudo-SD (PSD) grains. Magnetite (Fe3O4) is the most magnetic naturally occurring mineral on Earth, carrying the dominant magnetic signature in rocks and providing a critical tool in paleomagnetism. The oxidation of Fe3O4 to other iron oxides, such as maghemite (γ-Fe2O3) and hematite (α-Fe2O3), is of particular interest as it influences the preservation of remanence of the Earth's magnetic field by Fe3O4. Further, TRM in Fe3O4 grains is acquired in the direction of the ambient geomagnetic field as they cool below their Curie temperature (TC) of ~ 580 ˚C. The latest transmission electron microscopy (TEM) techniques like electron holography and environmental TEM (ETEM) allows for the imaging of magnetization in nano-scale minerals during in situ heating under vacuum and controlled atmospheres. In the present study, synthetic Fe3O4 particles in the PSD size range (CRM was visualized using electron holography, in the form of reconstructed magnetic induction maps, where the oxidized grains exhibited a loss of overall remanence and change in remanent direction. The thermomagnetic behavior of Fe3O4 particles in the PSD size range is also investigated using off-axis electron holography. Magnetic induction maps, which are recorded during in situ heating up to above the TC, reveal the PSD nature of several Fe3O4 grains by visualizing their vortex domain states. The vortex states in small Fe3O4 grains (Fig. 1a & b) are shown to rotate or collapse into a single-domain state close to its unblocking temperature (Fig. 1c), rather than

  14. Analysis of the Staphylococcus aureus DgkB Structure Reveals a Common Catalytic Mechanism for the Soluble Diacylglycerol Kinases

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Darcie J.; Jerga, Agoston; Rock, Charles O.; White, Stephen W. (SJCH)


    Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg{sup 2+} site and an associated Asp{center_dot}water{center_dot}Mg{sup 2+} network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp{center_dot}water{center_dot}Mg{sup 2+} network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB.

  15. Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases. (United States)

    Miller, Darcie J; Jerga, Agoston; Rock, Charles O; White, Stephen W


    Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg2+ site and an associated Asp*water*Mg2+ network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp*water*Mg2+ network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB. PMID:18611377

  16. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut


    politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...... theoretical constructs that can explain language choice which were supposed to be a more powerful explanatory tool than more obvious (and observable) parameters like topic, place (setting) and interlocutor. In the meantime, at least in Scandinavia, the term ‘domain’ has been taken up in the debate among...

  17. An MHC-I cytoplasmic domain/HIV-1 Nef fusion protein binds directly to the mu subunit of the AP-1 endosomal coat complex.

    Directory of Open Access Journals (Sweden)

    Rajendra Kumar Singh

    Full Text Available BACKGROUND: The down-regulation of the major histocompatibility complex class I (MHC-I from the surface of infected cells by the Nef proteins of primate immunodeficiency viruses likely contributes to pathogenesis by providing evasion of cell-mediated immunity. HIV-1 Nef-induced down-regulation involves endosomal trafficking and a cooperative interaction between the cytoplasmic domain (CD of MHC-I, Nef, and the clathrin adaptor protein complex-1 (AP-1. The CD of MHC-I contains a key tyrosine within the sequence YSQA that is required for down-regulation by Nef, but this sequence does not conform to the canonical AP-binding tyrosine-based motif Yxxphi, which mediates binding to the medium (micro subunits of AP complexes. We previously proposed that Nef allows the MHC-I CD to bind the mu subunit of AP-1 (micro1 as if it contained a Yxxphimotif. METHODS AND FINDINGS: Here, we show that a direct interaction between the MHC-I CD/Nef and micro1 plays a primary role in the down-regulation of MHC-I: GST pulldown assays using recombinant proteins indicated that most of the MHC-I CD and Nef residues that are required for the down-regulation in human cells contribute to direct interactions with a truncated version of micro1. Specifically, the tyrosine residue of the YSQA sequence in the MHC-I CD as well as Nef residues E62-65 and P78 each contributed to the interaction between MHC-I CD/Nef and micro1 in vitro, whereas Nef M20 had little to no role. Conversely, residues F172/D174 and V392/L395 of the binding pocket on micro1 for Yxxphi motifs were required for a robust interaction. CONCLUSIONS: These data indicate that the MHC-I cytoplasmic domain, Nef, and the C-terminal two thirds of the mu subunit of AP-1 are sufficient to constitute a biologically relevant interaction. The data also reveal an unexpected role for a hydrophobic pocket in micro1 for interaction with MHC-I CD/Nef.

  18. Direct coal liquefaction using iron-titanium hydride as a hydrogen distribution and catalytic material. Yearly report No. 1, September 1, 1984-August 31, 1985

    Energy Technology Data Exchange (ETDEWEB)

    Smith, J.E. Jr.


    During this year the experimental apparatus was completed after substantial delays by the manufacturer and eight direct coal liquefaction experiments were accomplished. These experiments have produced conversion and selectivity data on samples of Utah coal slurried in tetralin and catalyzed using iron-titanium hydride. Hydrogen loading of the alloy, catalyst particle size, catalyst concentration, coal particle size, operating temperatures for alloy addition and liquefaction without the catalysts present, have all been studied during these experiments. Conversions as high as 61% DAF in 30 min have been recorded at 500/sup 0/F and 500 psia. Product selectivities favor the oil fraction during the initial phase of the reaction, but as the reaction proceeds the heavier fractions are observed to increase at the expense of the oil fraction. We are currently working on a kinetic model in an effort to predict these results. Additionally, proton NMR, fractional distillation, and chromatographic analyses are currently being performed on the recovered product. We have completed the study of Utah coal and are moving on to samples of Kentucky and Alabama coals after a minor modification of the experimental apparatus is completed. Equipment manufacture, delivery, and installation delays, totaling over 6 months, greatly reduced the time available for research, making a 6 month no cost extension necessary. The extended time will permit completion of the proposed research tasks. 10 figs., 8 tabs.

  19. RNA-Free and Ribonucleoprotein-Associated Influenza Virus Polymerases Directly Bind the Serine-5-Phosphorylated Carboxyl-Terminal Domain of Host RNA Polymerase II (United States)

    Martínez-Alonso, Mónica; Hengrung, Narin


    ABSTRACT Influenza viruses subvert the transcriptional machinery of their hosts to synthesize their own viral mRNA. Ongoing transcription by cellular RNA polymerase II (Pol II) is required for viral mRNA synthesis. By a process known as cap snatching, the virus steals short 5′ capped RNA fragments from host capped RNAs and uses them to prime viral transcription. An interaction between the influenza A virus RNA polymerase and the C-terminal domain (CTD) of the large subunit of Pol II has been established, but the molecular details of this interaction remain unknown. We show here that the influenza virus ribonucleoprotein (vRNP) complex binds to the CTD of transcriptionally engaged Pol II. Furthermore, we provide evidence that the viral polymerase binds directly to the serine-5-phosphorylated form of the Pol II CTD, both in the presence and in the absence of viral RNA, and show that this interaction is conserved in evolutionarily distant influenza viruses. We propose a model in which direct binding of the viral RNA polymerase in the context of vRNPs to Pol II early in infection facilitates cap snatching, while we suggest that binding of free viral polymerase to Pol II late in infection may trigger Pol II degradation. IMPORTANCE Influenza viruses cause yearly epidemics and occasional pandemics that pose a threat to human health, as well as represent a large economic burden to health care systems globally. Existing vaccines are not always effective, as they may not exactly match the circulating viruses. Furthermore, there are a limited number of antivirals available, and development of resistance to these is a concern. New measures to combat influenza are needed, but before they can be developed, it is necessary to better understand the molecular interactions between influenza viruses and their host cells. By providing further insights into the molecular details of how influenza viruses hijack the host transcriptional machinery, we aim to uncover novel targets for

  20. Catalytic cracking process (United States)

    Lokhandwala, Kaaeid A.; Baker, Richard W.


    Processes and apparatus for providing improved catalytic cracking, specifically improved recovery of olefins, LPG or hydrogen from catalytic crackers. The improvement is achieved by passing part of the wet gas stream across membranes selective in favor of light hydrocarbons over hydrogen.

  1. Catalytic distillation structure (United States)

    Smith, Jr., Lawrence A.


    Catalytic distillation structure for use in reaction distillation columns, a providing reaction sites and distillation structure and consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and being present with the catalyst component in an amount such that the catalytic distillation structure consist of at least 10 volume % open space.

  2. Advances in Study on Catalysts for Phenol Synthesis via Catalytic Hydroxylation of Benzene in China

    Institute of Scientific and Technical Information of China (English)

    Zheng Zhaohui


    Synthesis of phenol via direct hydroxylation of benzene as a typical reaction of atomic economy has attracted extensive attention worldwide and has also become an actively investigated domain in China. This article refers to the recent domestic advances in study on phenol synthesis via hydroxylation of benzene from the viewpoint of catalysts, and considers the TS-1/H2O2 and FeZSM-5/N2O catalytic systems to be promising ones with good prospects for commercialization along with some suggestions on future research work.

  3. Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9. (United States)

    Omanakuttan, Athira; Nambiar, Jyotsna; Harris, Rodney M; Bose, Chinchu; Pandurangan, Nanjan; Varghese, Rebu K; Kumar, Geetha B; Tainer, John A; Banerji, Asoke; Perry, J Jefferson P; Nair, Bipin G


    Cashew nut shell liquid (CNSL) has been used in traditional medicine for the treatment of a wide variety of pathophysiological conditions. To further define the mechanism of CNSL action, we investigated the effect of cashew nut shell extract (CNSE) on two matrix metalloproteinases, MMP-2/gelatinase A and MMP-9/gelatinase B, which are known to have critical roles in several disease states. We observed that the major constituent of CNSE, anacardic acid, markedly inhibited the gelatinase activity of 3T3-L1 cells. Our gelatin zymography studies on these two secreted gelatinases, present in the conditioned media from 3T3-L1 cells, established that anacardic acid directly inhibited the catalytic activities of both MMP-2 and MMP-9. Our docking studies suggested that anacardic acid binds into the MMP-2/9 active site, with the carboxylate group of anacardic acid chelating the catalytic zinc ion and forming a hydrogen bond to a key catalytic glutamate side chain and the C15 aliphatic group being accommodated within the relatively large S1' pocket of these gelatinases. In agreement with the docking results, our fluorescence-based studies on the recombinant MMP-2 catalytic core domain demonstrated that anacardic acid directly inhibits substrate peptide cleavage in a dose-dependent manner, with an IC₅₀ of 11.11 μM. In addition, our gelatinase zymography and fluorescence data confirmed that the cardol-cardanol mixture, salicylic acid, and aspirin, all of which lack key functional groups present in anacardic acid, are much weaker MMP-2/MMP-9 inhibitors. Our results provide the first evidence for inhibition of gelatinase catalytic activity by anacardic acid, providing a novel template for drug discovery and a molecular mechanism potentially involved in CNSL therapeutic action. PMID:22745359

  4. γ-Aminobutyric Acid Type A (GABAA) Receptor Subunits Play a Direct Structural Role in Synaptic Contact Formation via Their N-terminal Extracellular Domains. (United States)

    Brown, Laura E; Nicholson, Martin W; Arama, Jessica E; Mercer, Audrey; Thomson, Alex M; Jovanovic, Jasmina N


    The establishment of cell-cell contacts between presynaptic GABAergic neurons and their postsynaptic targets initiates the process of GABAergic synapse formation. GABAA receptors (GABAARs), the main postsynaptic receptors for GABA, have been recently demonstrated to act as synaptogenic proteins that can single-handedly induce the formation and functional maturation of inhibitory synapses. To establish how the subunit composition of GABAARs influences their ability to induce synaptogenesis, a co-culture model system incorporating GABAergic medium spiny neurons and the HEK293 cells, stably expressing different combinations of receptor subunits, was developed. Analyses of HEK293 cell innervation by medium spiny neuron axons using immunocytochemistry, activity-dependent labeling, and electrophysiology have indicated that the γ2 subunit is required for the formation of active synapses and that its effects are influenced by the type of α/β subunits incorporated into the functional receptor. To further characterize this process, the large N-terminal extracellular domains (ECDs) of α1, α2, β2, and γ2 subunits were purified using the baculovirus/Sf9 cell system. When these proteins were applied to the co-cultures of MSNs and α1/β2/γ2-expressing HEK293 cells, the α1, β2, or γ2 ECD each caused a significant reduction in contact formation, in contrast to the α2 ECD, which had no effect. Together, our experiments indicate that the structural role of GABAARs in synaptic contact formation is determined by their subunit composition, with the N-terminal ECDs of each of the subunits directly participating in interactions between the presynaptic and postsynaptic elements, suggesting the these interactions are multivalent and specific. PMID:27129275

  5. The heptahelical domain of GABAB2 is activated directly by CGP7930, a positive allosteric modulator of the GABA(B) receptor


    Binet, Virginie; Brajon, Carole; Le Corre, Laurent; Acher, Francine; Pin, Jean-Philippe; Prézeau, Laurent


    International audience The gamma-aminobutyric acid, type B (GABA(B)) receptor is well recognized as being composed of two subunits, GABA(B1) and GABA(B2). Both subunits share structural homology with other class-III G-protein-coupled receptors. They are composed of two main domains: a heptahelical domain (HD) typical of all G-protein-coupled receptors and a large extracellular domain (ECD). Although GABA(B1) binds GABA, GABA(B2) is required for GABA(B1) to reach the cell surface. However, ...

  6. Studies of Catalytic Model Systems

    DEFF Research Database (Denmark)

    Holse, Christian

    the Cu/ZnO nanoparticles is highly relevant to industrial methanol synthesis for which the direct interaction of Cu and ZnO nanocrystals synergistically boost the catalytic activity. The dynamical behavior of the nanoparticles under reducing and oxidizing environments were studied by means of ex situ...... observed by XPS as the nanoparticles are reduced. The Cu/ZnO nanoparticles are tested on a  µ-reactor platform and prove to be active towards methanol synthesis, making it an excellent model system for further investigations into activity depended morphology changes....

  7. Catalytic Synthesis Lactobionic Acid

    Directory of Open Access Journals (Sweden)

    V.G. Borodina


    Full Text Available Gold nanoparticles are obtained, characterized and deposited on the carrier. Conducted catalytic synthesis of lactobionic acid from lactose. Received lactobionic acid identify on the IR spectrum.

  8. Catalytic distillation process (United States)

    Smith, Jr., Lawrence A.


    A method for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C.sub.4 feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.

  9. Catalytic ignition of light hydrocarbons

    Institute of Scientific and Technical Information of China (English)

    K. L. Hohn; C.-C. Huang; C. Cao


    Catalytic ignition refers to phenomenon where sufficient energy is released from a catalytic reaction to maintain further reaction without additional extemai heating. This phenomenon is important in the development of catalytic combustion and catalytic partial oxidation processes, both of which have received extensive attention in recent years. In addition, catalytic ignition studies provide experimental data which can be used to test theoretical hydrocarbon oxidation models. For these reasons, catalytic ignition has been frequently studied. This review summarizes the experimental methods used to study catalytic ignition of light hydrocarbons and describes the experimental and theoretical results obtained related to catalytic ignition. The role of catalyst metal, fuel and fuel concentration, and catalyst state in catalytic ignition are examined, and some conclusions are drawn on the mechanism of catalytic ignition.

  10. Domain Engineering (United States)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  11. Toward Facilitative Mentoring and Catalytic Interventions (United States)

    Smith, Melissa K.; Lewis, Marilyn


    In TESOL teacher mentoring, giving advice can be conceptualized as a continuum, ranging from directive to facilitative feedback. The goal, over time, is to lead toward the facilitative end of the continuum and specifically to catalytic interventions that encourage self-reflection and autonomous learning. This study begins by examining research on…

  12. Catalytic coherence transformations (United States)

    Bu, Kaifeng; Singh, Uttam; Wu, Junde


    Catalytic coherence transformations allow the otherwise impossible state transformations using only incoherent operations with the aid of an auxiliary system with finite coherence that is not being consumed in any way. Here we find the necessary and sufficient conditions for the deterministic and stochastic catalytic coherence transformations between a pair of pure quantum states. In particular, we show that the simultaneous decrease of a family of Rényi entropies of the diagonal parts of the states under consideration is a necessary and sufficient condition for the deterministic catalytic coherence transformations. Similarly, for stochastic catalytic coherence transformations we find the necessary and sufficient conditions for achieving a higher optimal probability of conversion. We thus completely characterize the coherence transformations among pure quantum states under incoherent operations. We give numerous examples to elaborate our results. We also explore the possibility of the same system acting as a catalyst for itself and find that indeed self-catalysis is possible. Further, for the cases where no catalytic coherence transformation is possible we provide entanglement-assisted coherence transformations and find the necessary and sufficient conditions for such transformations.

  13. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei; Hu, Pingping; Chen, Jianmin; Liu, Xi; Tang, Xingfu


    Atomically dispersed noble-metal catalysts with highly dense active sites are promising materials with which to maximise metal efficiency and to enhance catalytic performance; however, their fabrication remains challenging because metal atoms are prone to sintering, especially at a high metal...... loading. A dynamic process of formation of isolated metal atom catalytic sites on the surface of the support, which was achieved starting from silver nanoparticles by using a thermal surface-mediated diffusion method, was observed directly by using in situ electron microscopy and in situ synchrotron X......-ray diffraction. A combination of electron microscopy images with X-ray absorption spectra demonstrated that the silver atoms were anchored on five-fold oxygen-terminated cavities on the surface of the support to form highly dense isolated metal active sites, leading to excellent reactivity in catalytic oxidation...

  14. Importance of a flexible hinge near the motor domain in kinesin-driven motility.


    Grummt, M; Woehlke, G; Henningsen, U; Fuchs, S; Schleicher, M.; Schliwa, M


    Conventional kinesin is a molecular motor consisting of an N-terminal catalytic motor domain, an extended stalk and a small globular C-terminus. Whereas the structure and function of the catalytic motor domain has been investigated, little is known about the function of domains outside the globular head. A short coiled-coil region adjacent to the motor domain, termed the neck, is known to be important for dimerization and may be required for kinesin processivity. We now provide evidence that ...

  15. A non-stationary model for catalytic converters with cylindrical geometry


    Hoernel, J. -D.


    We prove some existence and uniqueness results and some qualitative properties for the solution of a system modelling the catalytic conversion in a cylinder. This model couples parabolic partial differential equations posed in a cylindrical domain and on its boundary.

  16. Direct Labeling of Polyphosphate at the Ultrastructural Level in Saccharomyces cerevisiae by Using the Affinity of the Polyphosphate Binding Domain of Escherichia coli Exopolyphosphatase


    Saito, Katsuharu; Ohtomo, Ryo; Kuga-Uetake, Yukari; Aono, Toshihiro; Saito, Masanori


    Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate and has many biological functions in prokaryotic and eukaryotic organisms. To investigate polyP localization, we developed a novel technique using the affinity of the recombinant polyphosphate binding domain (PPBD) of Escherichia coli exopolyphosphatase to polyP. An epitope-tagged PPBD was expressed and purified from E. coli. Equilibrium binding assay of PPBD revealed its high affinity for long-chain polyP and its weak affi...

  17. Catalytic methanol dissociation

    International Nuclear Information System (INIS)

    Results of the methanol dissociation study on copper/potassium catalyst with alumina support at various temperatures are presented. The following gaseous and liquid products at. The catalytic methanol dissociation is obtained: hydrogen, carbon monoxide, carbon dioxide, methane, and dimethyl ether. Formation rates of these products are discussed. Activation energies of corresponding reactions are calculated

  18. Catalytic Phosphination and Arsination

    Institute of Scientific and Technical Information of China (English)

    Kwong Fuk Yee; Chan Kin Shing


    The catalytic, user-friendly phosphination and arsination of aryl halides and triflates by triphenylphosphine and triphenylarsine using palladium catalysts have provided a facile synthesis of functionalized aryl phosphines and arsines in neutral media. Modification of the cynaoarisne yielded optically active N, As ligands which will be screened in various asymmetric catalysis.

  19. Monolithic catalytic igniters (United States)

    La Ferla, R.; Tuffias, R. H.; Jang, Q.


    Catalytic igniters offer the potential for excellent reliability and simplicity for use with the diergolic bipropellant oxygen/hydrogen as well as with the monopropellant hydrazine. State-of-the-art catalyst beds - noble metal/granular pellet carriers - currently used in hydrazine engines are limited by carrier stability, which limits the hot-fire temperature, and by poor thermal response due to the large thermal mass. Moreover, questions remain with regard to longevity and reliability of these catalysts. In this work, Ultramet investigated the feasibility of fabricating monolithic catalyst beds that overcome the limitations of current catalytic igniters via a combination of chemical vapor deposition (CVD) iridium coatings and chemical vapor infiltration (CVI) refractory ceramic foams. It was found that under all flow conditions and O2:H2 mass ratios tested, a high surface area monolithic bed outperformed a Shell 405 bed. Additionally, it was found that monolithic catalytic igniters, specifically porous ceramic foams fabricated by CVD/CVI processing, can be fabricated whose catalytic performance is better than Shell 405 and with significantly lower flow restriction, from materials that can operate at 2000 C or higher.

  20. Catalytic conversion of light alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Lyons, J.E.


    The second Quarterly Report of 1992 on the Catalytic Conversion of Light Alkanes reviews the work done between April 1, 1992 and June 31, 1992 on the Cooperative Agreement. The mission of this work is to devise a new catalyst which can be used in a simple economic process to convert the light alkanes in natural gas to oxygenate products that can either be used as clean-burning, high octane liquid fuels, as fuel components or as precursors to liquid hydrocarbon uwspomdon fuel. During the past quarter we have continued to design, prepare, characterize and test novel catalysts for the mild selective reaction of light hydrocarbons with air or oxygen to produce alcohols directly. These catalysts are designed to form active metal oxo (MO) species and to be uniquely active for the homolytic cleavage of the carbon-hydrogen bonds in light alkanes producing intermediates which can form alcohols. We continue to investigate three molecular environments for the active catalytic species that we are trying to generate: electron-deficient macrocycles (PHASE I), polyoxometallates (PHASE II), and regular oxidic lattices including zeolites and related structures as well as other molecular surface structures having metal oxo groups (PHASE I).

  1. Life and death of a single catalytic cracking particle

    NARCIS (Netherlands)

    Meirer, Florian; Kalirai, Samanbir; Morris, Darius; Soparawalla, Santosh; Liu, Yijin; Mesu, Gerbrand; Andrews, Joy C; Weckhuysen, Bert M


    Fluid catalytic cracking (FCC) particles account for 40 to 45% of worldwide gasoline production. The hierarchical complex particle pore structure allows access of long-chain feedstock molecules into active catalyst domains where they are cracked into smaller, more valuable hydrocarbon products (for

  2. pH-dependent electron transfer reaction and direct bioelectrocatalysis of the quinohemoprotein pyranose dehydrogenase. (United States)

    Takeda, Kouta; Matsumura, Hirotoshi; Ishida, Takuya; Yoshida, Makoto; Igarashi, Kiyohiko; Samejima, Masahiro; Ohno, Hiroyuki; Nakamura, Nobuhumi


    A pyranose dehydrogenase from Coprinopsis cinerea (CcPDH) is an extracellular quinohemoeprotein, which consists a b-type cytochrome domain, a pyrroloquinoline-quinone (PQQ) domain, and a family 1-type carbohydrate-binding module. The electron transfer reaction of CcPDH was studied using some electron acceptors and a carbon electrode at various pH levels. Phenazine methosulfate (PMS) reacted directly at the PQQ domain, whereas cytochrome c (cyt c) reacted via the cytochrome domain of intact CcPDH. Thus, electrons are transferred from reduced PQQ in the catalytic domain of CcPDH to heme b in the N-terminal cytochrome domain, which acts as a built-in mediator and transfers electron to a heterogenous electron transfer protein. The optimal pH values of the PMS reduction (pH 6.5) and the cyt c reduction (pH 8.5) differ. The catalytic currents for the oxidation of l-fucose were observed within a range of pH 4.5 to 11. Bioelectrocatalysis of CcPDH based on direct electron transfer demonstrated that the pH profile of the biocatalytic current was similar to the reduction activity of cyt c characters. PMID:27338639

  3. Direct interaction of the kringle domain of urokinase-type plasminogen activator (uPA) and integrin alpha v beta 3 induces signal transduction and enhances plasminogen activation. (United States)

    Tarui, Takehiko; Akakura, Nobuaki; Majumdar, Mousumi; Andronicos, Nicholas; Takagi, Junichi; Mazar, Andrew P; Bdeir, Khalil; Kuo, Alice; Yarovoi, Serge V; Cines, Douglas B; Takada, Yoshikazu


    It has been questioned whether there are receptors for urokinase-type plasminogen activator (uPA) that facilitate plasminogen activation other than the high affinity uPA receptor (uPAR/CD87) since studies of uPAR knockout mice did not support a major role of uPAR in plasminogen activation. uPA also promotes cell adhesion, chemotaxis, and proliferation besides plasminogen activation. These uPA-induced signaling events are not mediated by uPAR, but mediated by unidentified, lower-affinity receptors for the uPA kringle. We found that uPA binds specifically to integrin alpha v beta 3 on CHO cells depleted of uPAR. The binding of uPA to alpha v beta 3 required the uPA kringle domain. The isolated uPA kringle domain binds specifically to purified, recombinant soluble, and cell surface alpha v beta 3, and other integrins (alpha 4 beta 1 and alpha 9 beta 1), and induced migration of CHO cells in an alpha v beta 3-dependent manner. The binding of the uPA kringle to alpha v beta 3 and uPA kringle-induced alpha v beta 3-dependent cell migration were blocked by homologous plasminogen kringles 1-3 or 1-4 (angiostatin), a known integrin antagonist. We studied whether the binding of uPA to integrin alpha v beta 3 through the kringle domain plays a role in plasminogen activation. On CHO cell depleted of uPAR, uPA enhanced plasminogen activation in a kringle and alpha v beta 3-dependent manner. Endothelial cells bound to and migrated on uPA and uPA kringle in an alpha v beta 3-dependent manner. These results suggest that uPA binding to integrins through the kringle domain plays an important role in both plasminogen activation and uPA-induced intracellular signaling. The uPA kringle-integrin interaction may represent a novel therapeutic target for cancer, inflammation, and vascular remodeling. PMID:16525582

  4. Functional implications of C-terminus of TBX5 with high homology to C-terminal domain of yeast DNA-directed RNA polymerase Ⅱ largest subunit

    Institute of Scientific and Technical Information of China (English)

    ZHOU Zhu-ren; GONG Li-guo; GENG Wen-qing; QIU Guang-rong; SUN Kai-lai


    @@ TBX5, as a member of the T-box-containing transcription factor family, encodes a protein of 518 amino acids and is expressed in the embryonic heart and developing limb tissues.1 The coding region of TBX5 cDNA is 1.5 kb with eight exons including the N-terminal portion, the DNA binding domain and C-terminal region. We reported that the abnormality in transcription level of the TbX5 gene might be the mechanism underlying human simple congenital heart disease in the absence of TBX5 mutations.

  5. Relationship between structure and catalytic performance of dealuminated Y zeolites

    International Nuclear Information System (INIS)

    Dealuminated Y zeolites which have been prepared by hydrothermal and chemical treatments show differences in catalytic performance when tested fresh; however, these differences disappear after the zeolites have been steamed. The catalytic behavior of fresh and steamed zeolites is directly related to zeolite structural and chemical characteristics. Such characteristics determine the strength and density of acid sites for catalytic cracking. Dealuminated zeolites were characterized using x-ray diffraction, porosimetry, solid-state NMR and elemental analysis. Hexadecane cracking was used as a probe reaction to determine catalytic properties. Cracking activity was found to be proportional to total aluminum content in the zeolite. Product selectivity was dependent on unit cell size, presence of extra framework alumina and spatial distribution of active sites. The results from this study elucidate the role that zeolite structure plays in determining catalytic performance

  6. The catalytic residues of Tn3 resolvase


    Olorunniji, F.J.; Stark, W M


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

  7. Catalytic thermal barrier coatings (United States)

    Kulkarni, Anand A.; Campbell, Christian X.; Subramanian, Ramesh


    A catalyst element (30) for high temperature applications such as a gas turbine engine. The catalyst element includes a metal substrate such as a tube (32) having a layer of ceramic thermal barrier coating material (34) disposed on the substrate for thermally insulating the metal substrate from a high temperature fuel/air mixture. The ceramic thermal barrier coating material is formed of a crystal structure populated with base elements but with selected sites of the crystal structure being populated by substitute ions selected to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a higher rate than would the base compound without the ionic substitutions. Precious metal crystallites may be disposed within the crystal structure to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a lower light-off temperature than would the ceramic thermal barrier coating material without the precious metal crystallites.

  8. Functional analysis of the catalytic subunit of Dictyostelium PKA in vivo. (United States)

    Dammann, H; Traincard, F; Anjard, C; van Bemmelen, M X; Reymond, C; Véron, M


    The catalytic subunit of the cAMP-dependent protein kinase (PKA) from Dictyostelium discoideum contains several domains, including an unusually long N-terminal extension preceding a highly conserved catalytic core. We transformed the aggregationless PkaC-null strain with several deletion constructs of both domains. Strains transformed with genes expressing catalytically-inactive polypeptides could not rescue development. Cotransformation with constructs encoding the N-terminal extension and the catalytic core, both unable to rescue development by themselves, yielded transformants able to proceed to late development. A 27-amino acid long hydrophobic region, immediately upstream of the catalytic core, was found indispensable for PKA function. A putative role of this sequence in the acquisition of the active conformation of the protein is discussed. PMID:9533959

  9. A single residue mutation abolishes attachment of the CBM26 starch-binding domain from Lactobacillus amylovorus alpha-amylase. (United States)

    Rodríguez-Sanoja, Romina; Oviedo, N; Escalante, L; Ruiz, B; Sánchez, S


    Starch is degraded by amylases that frequently have a modular structure composed of a catalytic domain and at least one non-catalytic domain that is involved in polysaccharide binding. The C-terminal domain from the Lactobacillus amylovorus alpha-amylase has an unusual architecture composed of five tandem starch-binding domains (SBDs). These domains belong to family 26 in the carbohydrate-binding modules (CBM) classification. It has been reported that members of this family have only one site for starch binding, where aromatic amino acids perform the binding function. In SBDs, fold similarities are better conserved than sequences; nevertheless, it is possible to identify in CBM26 members at least two aromatic residues highly conserved. We attempt to explain polysaccharide recognition for the L. amylovorus alpha-amylase SBD through site-directed mutagenesis of aromatic amino acids. Three amino acids were identified as essential for binding, two tyrosines and one tryptophan. Y18L and Y20L mutations were found to decrease the SBD binding capacity, but unexpectedly, the mutation at W32L led to a total loss of affinity, either with linear or ramified substrates. The critical role of Trp 32 in substrate binding confirms the presence of just one binding site in each alpha-amylase SBD. PMID:19052787

  10. Domain motions of Argonaute, the catalytic engine of RNA interference


    Wall Michael E; Ming Dengming; Sanbonmatsu Kevin Y


    Abstract Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quant...

  11. Domain motions of Argonaute, the catalytic engine of RNA interference

    Directory of Open Access Journals (Sweden)

    Wall Michael E


    Full Text Available Abstract Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. Results The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes – an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Conclusion Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

  12. Catalytic Oxidation of Methane into Methanol over Copper-Exchanged Zeolites with Oxygen at Low Temperature


    Narsimhan, Karthik; Iyoki, Kenta; Dinh, Kimberly; Román-Leshkov, Yuriy


    The direct catalytic conversion of methane to liquid oxygenated compounds, such as methanol or dimethyl ether, at low temperature using molecular oxygen is a grand challenge in C–H activation that has never been met with synthetic, heterogeneous catalysts. We report the first demonstration of direct, catalytic oxidation of methane into methanol with molecular oxygen over copper-exchanged zeolites at low reaction temperatures (483–498 K). Reaction kinetics studies show sustained catalytic acti...

  13. The Impact of Participative and Directive Leadership on Teachers' Performance: The Intervening Effects of Job Structuring, Decision Domain, and Leader-Member Exchange (United States)

    Somech, Anit; Wenderow, Maayan


    Purpose: The contingency model theory suggests that the effects of a leadership style cannot be studied without explicit attention to the given situation. Accordingly, the authors propose a model that allows them to examine simultaneously the relative impact of participative leadership and directive leadership on teachers' performance through the…

  14. Protein domain organisation: adding order

    Directory of Open Access Journals (Sweden)

    Kummerfeld Sarah K


    Full Text Available Abstract Background Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. Results We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Conclusion Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected

  15. Catalytic reforming process

    Energy Technology Data Exchange (ETDEWEB)

    Absil, R.P.; Huss, A. Jr.; McHale, W.D.; Partridge, R.D.


    This patent describes a catalytic reforming process which comprises contacting a naphtha range feed with a low acidity extrudate comprising an intermediate and/or a large pore acidic zeolite bound with a low acidity refractory oxide under reforming conditions to provide a reaction product of increased aromatic content, the extrudate having been prepared with at least an extrusion-facilitating amount of a low acidity refractory oxide in colloidal form and containing at least one metal species selected from the platinum group metals.

  16. Oscillatory Behavior during the Catalytic Partial Oxidation of Methane: Following Dynamic Structural Changes of Palladium Using the QEXAFS Technique

    DEFF Research Database (Denmark)

    Stoetzel, Jan; Frahm, Ronald; Kimmerle, Bertram;


    Pd/Al2O3 catalysts oscillate between ignition and extinction of the catalytic partial oxidation of methane when they are exposed to a 2:1 reaction mixture of methane and oxygen. The oscillations of the catalytic performance and the structure of Pd/Al2O3 catalysts in a fixed-bed reactor were...... combination of total oxidation and reforming in the catalytic capillary reactor was observed. This change in catalytic performance was directly linked to changes in the oxidation state of the Pd/Al2O3 catalysts at different positions along the catalytic reactor. During the ignition of the catalytic partial...

  17. Domain crossing

    DEFF Research Database (Denmark)

    Schraefel, M. C.; Rouncefield, Mark; Kellogg, Wendy; Ackerman, Mark; Marsden, Gary; Bødker, Susanne; Wyche, Susan; Reddy, Madhu

    In CSCW, how much do we need to know about another domain/culture before we observe, intersect and intervene with designs. What optimally would that other culture need to know about us? Is this a “how long is a piece of string” question, or an inquiry where we can consider a variety of contexts a...

  18. Novel Catalytic Membrane Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Stuart Nemser, PhD


    There are many industrial catalytic organic reversible reactions with amines or alcohols that have water as one of the products. Many of these reactions are homogeneously catalyzed. In all cases removal of water facilitates the reaction and produces more of the desired chemical product. By shifting the reaction to right we produce more chemical product with little or no additional capital investment. Many of these reactions can also relate to bioprocesses. Given the large number of water-organic compound separations achievable and the ability of the Compact Membrane Systems, Inc. (CMS) perfluoro membranes to withstand these harsh operating conditions, this is an ideal demonstration system for the water-of-reaction removal using a membrane reactor. Enhanced reaction synthesis is consistent with the DOE objective to lower the energy intensity of U.S. industry 25% by 2017 in accord with the Energy Policy Act of 2005 and to improve the United States manufacturing competitiveness. The objective of this program is to develop the platform technology for enhancing homogeneous catalytic chemical syntheses.

  19. A novel ammonia-assisted method for the direct synthesis of Mn3O4 nanoparticles at room temperature and their catalytic activity during the rapid degradation of azo dyes (United States)

    Mansournia, Mohammadreza; Azizi, Fatemeh; Rakhshan, Narges


    In this study, we prepared trimanganese tetroxide nanoparticles from MnCl2 solution in an ammonia atmosphere using a new surfactant-free method at room temperature. We analyzed and characterized the effects of different processing conditions, such as the concentrations of manganese and the ammonia source, as well as the reaction time, on the structure, purity, and morphology of the products using powder X-ray diffraction (XRD), scanning electron microscopy, and Fourier transformation infrared spectroscopy (FTIR) techniques. The XRD and FTIR analyses confirmed that the prepared products comprised single phase Mn3O4. At room temperature, the paramagnetic characteristics were also verified by vibrating sample magnetometry. Furthermore, we tested the catalytic activity of the nanoparticles during the degradation of methyl orange and Congo red, which are organic pollutants. Our experiments demonstrated the rapid color removal and reduction in the chemical oxygen demand (>70% and >50% within 10 min, respectively) using aqueous solutions of azo dyes.

  20. Identification of a direct interaction between residue 19 in the helical portion of calcitonin and the amino-terminal domain of the calcitonin receptor from photoaffinity cross-linking and mutational studies

    International Nuclear Information System (INIS)

    Full text: Calcitonins (CTs) are 32 amino acid hormones with both peripheral and central actions mediated via specific cell surface receptors, which belong to the superfamily of class II G-protein coupled receptors. Chimeric receptor and mutational data suggested that the helical portion (residues 8-22) of salmon CT (sCT) is important for high affinity binding to the amino-terminal extracellular domain of the human CT receptor (hCTR). In this study, we have developed photoactive sCT analogues [Arg11,18, Bpa19]sCT and [Arg11, 18, Bpa19]sCT(8-32) that incorporate a photolabile Bpa (p-benzoyl-L-phenylalanine) into position 19 of the helical domain of the ligand and used this to determine a specific receptor fragment proximate to it. These analogues saturably bound to the CTR with high affinity (IC50 = 3 nM) which was similar to that of the natural sCT and its antagonist (IC50 = 2 nM and 20 nM, respectively). Upon photolysis, radioiodinated 125I-[Arg11,18, Bpa19]sCT and 125I-[Arg11,18, Bpa19]sCT(8-32) efficiently and specifically cross-linked to hCTR stably expressed in baby hamster kidney cells (Hollexl cells, ∼ 800,000 receptors per cell), generating a single radiolabeled band of ∼ 72-kDa on SDS/PAGE autoradiography. To identify the 'contact domain' within CTR involved in binding of 125I-[Arg11, 18, Bpa19]sCT and 125I-[Arg11,18, Bpa19]sCT(8-32), the radiolabeled band containing the ligand-receptor conjugate was subjected to chemical and enzymatic cleavage. Cyanogen bromide cleavage of the native receptor yielded a radiolabeled fragment of apparent Mr ∼ 31-kDa that shifted to Mr ∼ 14 kDa after deglycosylation. This receptor domain corresponded to amino acids 59-134 of the hCTR, located at the amino-terminal extracellular region of the receptor. These results provide the first direct demonstration of a contact domain between calcitonin and its receptor, and will contribute towards the modelling of CT-CTR interface. Copyright (2001) Australasian Society of

  1. Mutations in the catalytic core or the C-terminus of murine leukemia virus (MLV) integrase disrupt virion infectivity and exert diverse effects on reverse transcription

    International Nuclear Information System (INIS)

    Understanding of the structures and functions of the retroviral integrase (IN), a key enzyme in the viral replication cycle, is essential for developing antiretroviral treatments and facilitating the development of safer gene therapy vehicles. Thus, four MLV IN-mutants were constructed in the context of a retroviral vector system, harbouring either a substitution in the catalytic centre, deletions in the C-terminus, or combinations of both modifications. IN-mutants were tested for their performance in different stages of the viral replication cycle: RNA-packaging; RT-activity; transient and stable infection efficiency; dynamics of reverse transcription and nuclear entry. All mutant vectors packaged viral RNA with wild-type efficiencies and displayed only slight reductions in RT-activity. Deletion of either the IN C-terminus alone, or in addition to part of the catalytic domain exerted contrasting effects on intracellular viral DNA levels, implying that IN influences reverse transcription in more than one direction

  2. Bifunctional catalytic electrode (United States)

    Cisar, Alan (Inventor); Murphy, Oliver J. (Inventor); Clarke, Eric (Inventor)


    The present invention relates to an oxygen electrode for a unitized regenerative hydrogen-oxygen fuel cell and the unitized regenerative fuel cell having the oxygen electrode. The oxygen electrode contains components electrocatalytically active for the evolution of oxygen from water and the reduction of oxygen to water, and has a structure that supports the flow of both water and gases between the catalytically active surface and a flow field or electrode chamber for bulk flow of the fluids. The electrode has an electrocatalyst layer and a diffusion backing layer interspersed with hydrophilic and hydrophobic regions. The diffusion backing layer consists of a metal core having gas diffusion structures bonded to the metal core.

  3. Multi-domain CGFS-type glutaredoxin Grx4 regulates iron homeostasis via direct interaction with a repressor Fep1 in fission yeast

    International Nuclear Information System (INIS)

    Research highlights: → Monothiol glutaredoxin Grx4 allows Fep1-mediated de-repression of iron uptake genes at low iron. → Grx4 directly interacts with Fep1 in vivo and in vitro. → The Cys172 in the CGFS motif of Grx4 is necessary for cell proliferation and iron regulation. → The Cys172 of Grx4 is required for normal interaction with Fep1. -- Abstract: The fission yeast Schizosaccharomyces pombe contains two CGFS-type monothiol glutaredoxins, Grx4 and Grx5, which are localized primarily in the nucleus and mitochondria, respectively. We observed involvement of Grx4 in regulating iron-responsive gene expression, which is modulated by a repressor Fep1. Lack of Grx4 caused defects not only in growth but also in the expression of both iron-uptake and iron-utilizing genes regardless of iron availability. In order to unravel how Grx4 is involved in Fep1-mediated regulation, interaction between them was investigated. Co-immunoprecipitation and bimolecular fluorescence complementation (BiFC) revealed that Grx4 physically interacts with Fep1 in vivo. BiFC revealed localized nuclear dots produced by interaction of Grx4 with Fep1. Mutation of cysteine-172 in the CGFS motif to serine (C172S) produced effects similarly observed under Grx4 depletion, such as the loss of iron-dependent gene regulation and the absence of nuclear dots in BiFC analysis. These results suggest that the ability of Grx4 to bind iron, most likely Fe-S cofactor, could be critical in interacting with and modulating the activity of Fep1.

  4. Direct Observation of Magnetic Field Induced Ferroelectric Domain Evolution in Self-Assembled Quasi (0-3) BiFeO3-CoFe2O4 Thin Films. (United States)

    Li, Linglong; Lu, Lu; Zhang, Dawei; Su, Ran; Yang, Guang; Zhai, Junyi; Yang, Yaodong


    Strain-mediated magnetoelectric (ME) coupling effect is expected in self-assembly heterostructures engineered by ferroelectric and ferromagnetic materials, contributing to the enhanced overall magnetoelectric effect. Microstructures as well as the connectivity configuration are considered to play a significant role in achieving efficient magnetoelectric properties. Different from the conventional (1-3) and (2-2) type composite films, we fabricate BiFeO3-CoFe2O4 (BFO-CFO) composite thin films with a novel quasi (0-3) type connectivity via a dual-target pulsed laser deposition process. The self-assembly growth mechanism has been studied, which demonstrates that the perovskite (BFO) matrix segments the connectivity of spinel (CFO) resulting in a quasi (0-3) composite. Direct observation of ferroelectric domain wall motion under external magnetic fields proves a strong magnetoelectric coupling effect in these (0-3) thin films. Our preliminary findings reveal the promising application potential of this new structure as multiferroic domain wall devices. PMID:26698906

  5. Catalytic and glycan-binding abilities of ppGalNAc-T2 are regulated by acetylation

    DEFF Research Database (Denmark)

    Zlocowski, Natacha; Sendra, Victor G; Lorenz, Virginia; Villarreal, Marcos A; Jorge, Alberto; Núñez, Yolanda; Bennett, Eric P; Clausen, Henrik; Nores, Gustavo A; Irazoqui, Fernando J


    ); the first five are located in the catalytic domain. Specific glycosyltransferase activity of ppGalNAc-T2 was reduced 95% by acetylation. The last two amino acids, K521 and S529, are located in the lectin domain, and their acetylation results in alteration of the carbohydrate-binding ability of pp...... activity (catalytic capacity and glycan-binding ability) of ppGalNAc-T2 is regulated by acetylation....

  6. Life and death of a single catalytic cracking particle. (United States)

    Meirer, Florian; Kalirai, Sam; Morris, Darius; Soparawalla, Santosh; Liu, Yijin; Mesu, Gerbrand; Andrews, Joy C; Weckhuysen, Bert M


    Fluid catalytic cracking (FCC) particles account for 40 to 45% of worldwide gasoline production. The hierarchical complex particle pore structure allows access of long-chain feedstock molecules into active catalyst domains where they are cracked into smaller, more valuable hydrocarbon products (for example, gasoline). In this process, metal deposition and intrusion is a major cause for irreversible catalyst deactivation and shifts in product distribution. We used x-ray nanotomography of industrial FCC particles at differing degrees of deactivation to quantify changes in single-particle macroporosity and pore connectivity, correlated to iron and nickel deposition. Our study reveals that these metals are incorporated almost exclusively in near-surface regions, severely limiting macropore accessibility as metal concentrations increase. Because macropore channels are "highways" of the pore network, blocking them prevents feedstock molecules from reaching the catalytically active domains. Consequently, metal deposition reduces conversion with time on stream because the internal pore volume, although itself unobstructed, becomes largely inaccessible. PMID:26601160

  7. Unsteady catalytic processes and sorption-catalytic technologies

    International Nuclear Information System (INIS)

    Catalytic processes that occur under conditions of the targeted unsteady state of the catalyst are considered. The highest efficiency of catalytic processes was found to be ensured by a controlled combination of thermal non-stationarity and unsteady composition of the catalyst surface. The processes based on this principle are analysed, in particular, catalytic selective reduction of nitrogen oxides, deep oxidation of volatile organic impurities, production of sulfur by the Claus process and by hydrogen sulfide decomposition, oxidation of sulfur dioxide, methane steam reforming and anaerobic combustion, selective oxidation of hydrocarbons, etc.

  8. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune


    remote access via IP-based devices such as smartphones. The Trusted Domain platform fits existing legacy technologies by managing their interoperability and access controls, and it seeks to avoid the security issues of relying on third-party servers outside the home. It is a distributed system that......In the digital age of home automation and with the proliferation of mobile Internet access, the intelligent home and its devices should be accessible at any time from anywhere. There are many challenges such as security, privacy, ease of configuration, incompatible legacy devices, a wealth of...

  9. Catalytic production of biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Theilgaard Madsen, A.


    The focus of this thesis is the catalytic production of diesel from biomass, especially emphasising catalytic conversion of waste vegetable oils and fats. In chapter 1 an introduction to biofuels and a review on different catalytic methods for diesel production from biomass is given. Two of these methods have been used industrially for a number of years already, namely the transesterification (and esterification) of oils and fats with methanol to form fatty acid methyl esters (FAME), and the hydrodeoxygenation (HDO) of fats and oils to form straight-chain alkanes. Other possible routes to diesel include upgrading and deoxygenation of pyrolysis oils or aqueous sludge wastes, condensations and reductions of sugars in aqueous phase (aqueous-phase reforming, APR) for monofunctional hydrocarbons, and gasification of any type of biomass followed by Fischer-Tropsch-synthesis for alkane biofuels. These methods have not yet been industrialised, but may be more promising due to the larger abundance of their potential feedstocks, especially waste feedstocks. Chapter 2 deals with formation of FAME from waste fats and oils. A range of acidic catalysts were tested in a model fat mixture of methanol, lauric acid and trioctanoin. Sulphonic acid-functionalised ionic liquids showed extremely fast convertion of lauric acid to methyl laurate, and trioctanoate was converted to methyl octanoate within 24 h. A catalyst based on a sulphonated carbon-matrix made by pyrolysing (or carbonising) carbohydrates, so-called sulphonated pyrolysed sucrose (SPS), was optimised further. No systematic dependency on pyrolysis and sulphonation conditions could be obtained, however, with respect to esterification activity, but high activity was obtained in the model fat mixture. SPS impregnated on opel-cell Al{sub 2}O{sub 3} and microporous SiO{sub 2} (ISPS) was much less active in the esterification than the original SPS powder due to low loading and thereby low number of strongly acidic sites on the

  10. Molecular dynamics characterization of five pathogenic factor X mutants associated with decreased catalytic activity

    KAUST Repository

    Abdel-Azeim, Safwat


    Factor X (FX) is one of the major players in the blood coagulation cascade. Upon activation to FXa, it converts prothrombin to thrombin, which in turn converts fibrinogen into fibrin (blood clots). FXa deficiency causes hemostasis defects, such as intracranial bleeding, hemathrosis, and gastrointestinal blood loss. Herein, we have analyzed a pool of pathogenic mutations, located in the FXa catalytic domain and directly associated with defects in enzyme catalytic activity. Using chymotrypsinogen numbering, they correspond to D102N, T135M, V160A, G184S, and G197D. Molecular dynamics simulations were performed for 1.68 μs on the wild-type and mutated forms of FXa. Overall, our analysis shows that four of the five mutants considered, D102N, T135M, V160A, and G184S, have rigidities higher than those of the wild type, in terms of both overall protein motion and, specifically, subpocket S4 flexibility, while S1 is rather insensitive to the mutation. This acquired rigidity can clearly impact the substrate recognition of the mutants.

  11. Aluminosilicate nanoparticles for catalytic hydrocarbon cracking. (United States)

    Liu, Yu; Pinnavaia, Thomas J


    Aluminosilicate nanoparticles containing 9.0-20 nm mesopores were prepared through the use of protozeolitic nanoclusters as the inorganic precursor and starch as a porogen. The calcined, porogen-free composition containing 2 mol % aluminum exhibited the porosity, hydrothermal stability, and acidity needed for the cracking of very large hydrocarbons. In fact, the hydrothermal stability of the nanoparticles to pure steam at 800 degrees C, along with the cumene cracking activity, surpassed the analogous performance properties of ultrastable Y zeolite, the main catalyst component of commercial cracking catalysts. The remarkable hydrothermal stability and catalytic reactivity of the new nanoparticles are attributable to a unique combination of two factors, the presence of protozeolitic nanoclusters in the pore walls and the unprecedented pore wall thickness (7-15 nm). In addition, the excellent catalytic longevity of the nanoparticles is most likely facilitated by the small domain size of the nanoparticles that greatly improves access to the acid sites on the pore walls and minimizes the diffusion length of coke precursors out of the pores. PMID:12603109

  12. CO2催化转化为高附加值燃料:现状、挑战及其未来方向%Catalytic conversion of CO2 to value added fuels:Current status, challenges, and future directions

    Institute of Scientific and Technical Information of China (English)

    Jingjie Wu; Xiao-Dong Zhou


    The electrochemical reduction of CO2 into liquid fuels especially coupling with the intermittent renewable electricity offers a promising means of storing electricity in chemical form, which reduc‐es the dependence on fossil fuels and mitigates the negative impact of anthropogenic CO2 emissions on the planet. Although converting CO2 to fuels is not in itself a new concept, the field has not sub‐stantially advanced in the last 30 years primarily because of the challenge of discovery of structural electrocatalysts and the development of membrane architectures for efficient collection of reactants and separation of products. This overview summarizes recent advances in catalytic conversion of CO2 and presents the challenges and future directions in producing value‐added fuels.

  13. Catalytic mechanisms of direct pyrrole synthesis via dehydrogenative coupling mediated by PNP-Ir or PNN-Ru pincer complexes: Crucial role of proton-transfer shuttles in the PNP-Ir system

    KAUST Repository

    Qu, Shuanglin


    Kempe et al. and Milstein et al. have recently advanced the dehydrogenative coupling methodology to synthesize pyrroles from secondary alcohols (e.g., 3) and β-amino alcohols (e.g., 4), using PNP-Ir (1) and PNN-Ru (2) pincer complexes, respectively. We herein present a DFT study to characterize the catalytic mechanism of these reactions. After precatalyst activation to give active 1A/2A, the transformation proceeds via four stages: 1A/2A-catalyzed alcohol (3) dehydrogenation to give ketone (11), base-facilitated C-N coupling of 11 and 4 to form an imine-alcohol intermediate (18), base-promoted cyclization of 18, and catalyst regeneration via H2 release from 1R/2R. For alcohol dehydrogenations, the bifunctional double hydrogen-transfer pathway is more favorable than that via β-hydride elimination. Generally, proton-transfer (H-transfer) shuttles facilitate various H-transfer processes in both systems. Notwithstanding, H-transfer shuttles play a much more crucial role in the PNP-Ir system than in the PNN-Ru system. Without H-transfer shuttles, the key barriers up to 45.9 kcal/mol in PNP-Ir system are too high to be accessible, while the corresponding barriers (<32.0 kcal/mol) in PNN-Ru system are not unreachable. Another significant difference between the two systems is that the addition of alcohol to 1A giving an alkoxo complex is endergonic by 8.1 kcal/mol, whereas the addition to 2A is exergonic by 8.9 kcal/mol. The thermodynamic difference could be the main reason for PNP-Ir system requiring lower catalyst loading than the PNN-Ru system. We discuss how the differences are resulted in terms of electronic and geometric structures of the catalysts and how to use the features in catalyst development. © 2014 American Chemical Society.

  14. Allosteric inhibition of Aurora-A kinase by a synthetic vNAR domain. (United States)

    Burgess, Selena G; Oleksy, Arkadiusz; Cavazza, Tommaso; Richards, Mark W; Vernos, Isabelle; Matthews, David; Bayliss, Richard


    The vast majority of clinically approved protein kinase inhibitors target the ATP-binding pocket directly. Consequently, many inhibitors have broad selectivity profiles and most have significant off-target effects. Allosteric inhibitors are generally more selective, but are difficult to identify because allosteric binding sites are often unknown or poorly characterized. Aurora-A is activated through binding of TPX2 to an allosteric site on the kinase catalytic domain, and this knowledge could be exploited to generate an inhibitor. Here, we generated an allosteric inhibitor of Aurora-A kinase based on a synthetic, vNAR single domain scaffold, vNAR-D01. Biochemical studies and a crystal structure of the Aurora-A/vNAR-D01 complex show that the vNAR domain overlaps with the TPX2 binding site. In contrast with the binding of TPX2, which stabilizes an active conformation of the kinase, binding of the vNAR domain stabilizes an inactive conformation, in which the αC-helix is distorted, the canonical Lys-Glu salt bridge is broken and the regulatory (R-) spine is disrupted by an additional hydrophobic side chain from the activation loop. These studies illustrate how single domain antibodies can be used to characterize the regulatory mechanisms of kinases and provide a rational basis for structure-guided design of allosteric Aurora-A kinase inhibitors. PMID:27411893

  15. Detection of a novel mutation in the SRC homology domain 2 (SH2) of Bruton`s tyrosine kinase and direct female carrier evaluation in a family with x-linked agammaglobulinemia

    Energy Technology Data Exchange (ETDEWEB)

    Schuster, V.; Seidenspinner, S.; Wolfgang Kreth, H. [Univ. of Wuerzburg (Germany)


    X-linked agammaglobulinemia (XLA) is an inherited immunodeficiency disease with a block in differentiation from pre-B to B cells resulting in a selective defect in the humoral immune response. Affected males have very low concentrations of serum immunoglobulins leading predominantly to recurrent bacterial infections beginning at age 6 to 18 months. The gene responsible for XLA was identified recently to encode a cytoplasmatic tyrosine kinase (Bruton`s tyrosine kinase, BTK). We have analyzed the BTK gene in a large family in which two brothers presented with the severe phenotype of XLA. Genomic DNA of affected boys and from healthy relatives was amplified by PCR with primers specific for the putative promoter region and for all 19 exons, including flanking intron boundaries, and subsequently screened for mutations using single strand conformation polymorphism (SSCP) analysis. Altered single strand band patterns were found using primers specific for exon 10, 15, and 18. Direct cycle-sequencing of these BTK segments detected two known polymorphisms in intron 14 and in exon 18. Sequencing of exon 10 from two boys with XLA demonstrated a novel point mutation in the SH2 domain of BTK. Direct identification of healthy female carriers in three generations was performed by amplification mutagenesis using PCR with a modified first primer. This method can easily be applied also to prenatal diagnosis. 25 refs., 3 figs.

  16. Immigration process in catalytic medium

    Institute of Scientific and Technical Information of China (English)


    The longtime behavior of the immigration process associated with a catalytic super-Brownian motion is studied. A large number law is proved in dimension d≤3 and a central limit theorem is proved for dimension d=3.

  17. Catalytic DNA with phosphatase activity


    Chandrasekar, Jagadeeswaran; Silverman, Scott K.


    Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been identified by in vitro selection for various catalytic activities. Expanding the limits of DNA catalysis is an important fundamental objective and may facilitate practical utility of catalysts that can be obtained from entirely unbiased (random) sequence populations. In this study, we show that DNA can catalyze Zn2+-dependent phosphomonoester hydrolysis of tyrosine and serine side chains (i.e., exhibit phosphatase ac...

  18. Texture of lipid bilayer domains

    DEFF Research Database (Denmark)

    Jensen, Uffe Bernchou; Brewer, Jonathan R.; Midtiby, Henrik Skov; Ipsen, John Hjort; Bagatolli, Luis; Simonsen, Adam Cohen


    We investigate the texture of gel (g) domains in binary lipid membranes composed of the phospholipids DPPC and DOPC. Lateral organization of lipid bilayer membranes is a topic of fundamental and biological importance. Whereas questions related to size and composition of fluid membrane domain are...... chains. By imaging the intensity variations as a function of the polarization angle, we map the lateral variations of the lipid tilt within domains. Results reveal that gel domains are composed of subdomains with different lipid tilt directions. We have applied a Fourier decomposition method as a...... which correlates with the phase state of the membrane. This is quantified by the generalized polarization (GP) function, and we demonstrate that a GP analysis can be performed on supported membranes. The results show that although the gel domains have heterogeneous texture, the membrane phase state does...

  19. DENN Domain Proteins: Regulators of Rab GTPases*


    Marat, Andrea L.; Dokainish, Hatem; McPherson, Peter S


    The DENN domain is a common, evolutionarily ancient, and conserved protein module, yet it has gone largely unstudied; until recently, little was known regarding its functional roles. New studies reveal that various DENN domains interact directly with members of the Rab family of small GTPases and that DENN domains function enzymatically as Rab-specific guanine nucleotide exchange factors. Thus, DENN domain proteins appear to be generalized regulators of Rab function. Study of these proteins w...

  20. Reverse flow catalytic membrane reactors for energy efficient syngas production


    Smit, Joris


    To improve the recuperative heat exchange, a Reverse Flow Catalytic Membrane Reactor (RFCMR) with porous membranes is proposed in this thesis, in which very efficient heat exchange between the feed and product streams is achieved by using the reverse flow concept (i.e. periodic alternation of the flow direction of the gas through a fixed catalyst bed).

  1. Using advanced electron microscopy for the characterization of catalytic materials (United States)

    Pyrz, William D.

    -corrected electron microscopy was used to systematically examine, atomic column by atomic column, the effect of elemental substitution on the long-range crystalline order, atomic coordinates, and site occupancies of the various formulations such that trends could be developed linking these properties to catalytic yields. To accomplish this task, an algorithm was developed that enabled the direct extraction of atomic coordinates and site occupancies from high-angle annular dark-field (HAADF) images to within 1% and 15% uncertainty, respectively. Furthermore, this general method could be applied to various crystalline systems and may dramatically improve the quality of initial structural models used in Rietveld refinements. Improvement in the quality of starting models may increase the structural and chemical complexity of inorganic structures that can be solved by using "powder methods" alone. In addition to the development of these trends, HAADF analyses also revealed the presence of coherent compositional miscibility gaps, rotational twin domains, and structural intergrowths in the complex Mo-V-M-O oxide system. Other catalytic systems that are addressed in this dissertation include Pd, Ag, and bimetallic Pd-Ag catalysts for the selective hydrogenation of acetylene in excess ethylene, alkali and alkaline earth promoted Ru catalysts for the production of clean hydrogen through the decomposition of ammonia, the production of Pt nanoparticles using dendrimer templates, and Pt-Re bimetallic catalysts for the conversion of glycerol to hydrocarbons and syn gas. In each of these studies, electron microscopy was used as a complimentary tool to synthetic and reaction studies to better understand interactions between the nanoparticles and the support/template, to determine the effect of adding various promoters, or to understand the nanoscale structural and chemical changes associated with the formation of bimetallic nanoparticles. A final area addressed in this dissertation is the

  2. Computer simulations suggest direct and stable tip to tip interaction between the outer membrane channel TolC and the isolated docking domain of the multidrug RND efflux transporter AcrB. (United States)

    Schmidt, Thomas H; Raunest, Martin; Fischer, Nadine; Reith, Dirk; Kandt, Christian


    One way by which bacteria achieve antibiotics resistance is preventing drug access to its target molecule for example through an overproduction of multi-drug efflux pumps of the resistance nodulation division (RND) protein super family of which AcrAB-TolC in Escherichia coli is a prominent example. Although representing one of the best studied efflux systems, the question of how AcrB and TolC interact is still unclear as the available experimental data suggest that either both proteins interact in a tip to tip manner or do not interact at all but are instead connected by a hexamer of AcrA molecules. Addressing the question of TolC-AcrB interaction, we performed a series of 100 ns - 1 µs-molecular dynamics simulations of membrane-embedded TolC in presence of the isolated AcrB docking domain (AcrBDD). In 5/6 simulations we observe direct TolC-AcrBDD interaction that is only stable on the simulated time scale when both proteins engage in a tip to tip manner. At the same time we find TolC opening and closing freely on extracellular side while remaining closed at the inner periplasmic bottleneck region, suggesting that either the simulated time is too short or additional components are required to unlock TolC. PMID:27045078


    Institute of Scientific and Technical Information of China (English)

    丁一慧; 黄伟; 晋萍; 谢克昌


    The selective conversion of methane to more useful target products such as acetic acid would be far more attractive. The classical utilization and recent research for methane conversion to acetic acid by both the indirect route involved multi-step process through syngas stage and the direct one avoided syngas production were reviewed in this paper. Technology comparison and results analysis of the indirect route with the direct one, and of homogeneous catalyst systems with heterogeneous ones employed in oxidative carbonylation or carboxylation of methane to synthesize acetic acid directly led to such a suggestion as follows. That is, an environmentally benign route to direct synthesis of acetic acid from inexpensive feedstocks methane and carbon dioxide, in particular, using solid, heterogeneous catalysts at low temperature has its remarkable significance in view of energy, environment and economy. The further research will enrich the theory and practice of green C1 chemistry and performance of thermodynamically unfavo-rable reactions.%对甲烷经合成气路线间接制乙酸的现状及在温和条件下直接转化制乙酸的研究进展作了述评.通过对间接与直接路线的比较,以及在直接路线中,甲烷低温氧化羰化和直接羧化制乙酸均相与非均相催化体系的分析,指出了CH4-CO2低温直接合成乙酸在工艺过程上的显著优势,尤其是采用非均相催化体系.该工艺为乙酸合成和CH4与CO2的绿色化学利用开辟了新途径,其研究将会丰富C1化学化工的理论与实践,并为实现热力学不利反应提供实验方法和理论依据.

  4. Metallocene Catalytic Insertion Polymerization of 1-Silene to Polycarbosilanes (United States)

    Tian, Yuelong; Ge, Min; Zhang, Weigang; Lv, Xiaoxu; Yu, Shouquan


    Metallocene of zirconium were used as a catalyst for an insertion polymerization of 1-methylsilene directly into pre-ceramic precursor polyzirconocenecarbosilane (PZCS) during dechlorination of dichlorodimethylesilane by sodium, which exhibits high catalytic effectiveness with the maximum conversion ratio of polycarbosilane up to 91%. The average molecular weights of polymers synthesized are less than 1400, all with very narrow polymolecularities. The mechanism of catalytic polymerization was assumed to be similar to a coordination insertion polymerization of 1-olefins by metallocenes. The obtained PZCS show high ceramic yields with formation of composite ceramics of ZrC-SiC, which are novel polymeric precursors of ultra-high temperature ceramic (UHTC) fiber and composite.


    Energy Technology Data Exchange (ETDEWEB)



    This project was directed at an investigation of catalytic NO{sub x} reduction on carbonaceous supports at low temperatures. The experimental work was conducted primarily in a packed bed reactor/gas flow system that was constructed for this work. The analytical techniques employed were mass spectrometry, NO{sub x} chemiluminescence, and gas chromatography. The experimental plan was focused on steady-state reactivity experiments, followed by temperature programmed desorption (TPD) of surface intermediates, and also selected temperature-programmed reaction (TPR) experiments. Both uncatalyzed and catalyzed (potassium-promoted) phenolic resin char, were investigated as well as the catalytic effect of additional CO in the gas phase.

  6. Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation (United States)

    Gone, Swapna; Alfonso-Prieto, Mercedes; Paudyal, Samridhdi; Nicholson, Allen W.


    Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double-helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions. Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4–fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester.

  7. Catalytic activity of Au nanoparticles

    DEFF Research Database (Denmark)

    Larsen, Britt Hvolbæk; Janssens, Ton V.W.; Clausen, Bjerne;


    Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change with par......Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change...... with particle size. We find that the fraction of low-coordinated Au atoms scales approximately with the catalytic activity, suggesting that atoms on the corners and edges of Au nanoparticles are the active sites. This effect is explained using density functional calculations....

  8. Catalytic distillation water recovery subsystem (United States)

    Budininkas, P.; Rasouli, F.


    An integrated engineering breadboard subsystem for the recovery of potable water from untreated urine based on the vapor phase catalytic ammonia removal was designed, fabricated and tested. Unlike other evaporative methods, this process catalytically oxidizes ammonia and volatile hydrocarbons vaporizing with water to innocuous products; therefore, no pretreatment of urine is required. Since the subsystem is fabricated from commercially available components, its volume, weight and power requirements are not optimized; however, it is suitable for zero-g operation. The testing program consists of parametric tests, one month of daily tests and a continuous test of 168 hours duration. The recovered water is clear, odorless, low in ammonia and organic carbon, and requires only an adjustment of its pH to meet potable water standards. The obtained data indicate that the vapor phase catalytic ammonia removal process, if further developed, would also be competitive with other water recovery systems in weight, volume and power requirements.

  9. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    Vivek V Ranade


    Catalytic reactions are ubiquitous in chemical and allied industries. A homogeneous or heterogeneous catalyst which provides an alternative route of reaction with lower activation energy and better control on selectivity can make substantial impact on process viability and economics. Extensive studies have been conducted to establish sound basis for design and engineering of reactors for practising such catalytic reactions and for realizing improvements in reactor performance. In this article, application of recent (and not so recent) developments in engineering reactors for catalytic reactions is discussed. Some examples where performance enhancement was realized by catalyst design, appropriate choice of reactor, better injection and dispersion strategies and recent advances in process intensification/ multifunctional reactors are discussed to illustrate the approach.

  10. Chemically-Modified Cellulose Paper as a Microstructured Catalytic Reactor

    Directory of Open Access Journals (Sweden)

    Hirotaka Koga


    Full Text Available We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.

  11. Genetic identification of essential indels and domains in carbamoyl phosphate synthetase II of Toxoplasma gondii. (United States)

    Fox, Barbara A; Ristuccia, Jessica G; Bzik, David J


    New treatments need to be developed for the significant human diseases of toxoplasmosis and malaria to circumvent problems with current treatments and drug resistance. Apicomplexan parasites causing these lethal diseases are deficient in pyrimidine salvage, suggesting that selective inhibition of de novo pyrimidine biosynthesis can lead to a severe loss of uridine 5'-monophosphate (UMP) and thymidine 5'-monophosphate (dTMP) pools, thereby inhibiting parasite RNA and DNA synthesis. Disruption of Toxoplasma gondii carbamoyl phosphate synthetase II (CPSII) induces a severe uracil auxotrophy with no detectable parasite replication in vitro and complete attenuation of virulence in mice. Here we show that a CPSII cDNA minigene efficiently complements the uracil auxotrophy of CPSII-deficient mutants, restoring parasite growth and virulence. Our complementation assays reveal that engineered mutations within, or proximal to, the catalytic triad of the N-terminal glutamine amidotransferase (GATase) domain inactivate the complementation activity of T. gondii CPSII and demonstrate a critical dependence on the apicomplexan CPSII GATase domain in vivo. Surprisingly, indels present within the T. gondii CPSII GATase domain as well as the C-terminal allosteric regulatory domain are found to be essential. In addition, several mutations directed at residues implicated in allosteric regulation in Escherichia coli CPS either abolish or markedly suppress complementation and further define the functional importance of the allosteric regulatory region. Collectively, these findings identify novel features of T. gondii CPSII as potential parasite-selective targets for drug development. PMID:18992249

  12. Catalytic conversion of biomass to fuels. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Garten, R. L.; Ushiba, K. K.; Cooper, M.; Mahawili, I.


    This report presents an assessment and perspective concerning the application of catalytic technologies to the thermochemical conversion of biomass resources to fuels. The major objectives of the study are: to provide a systematic assessment of the role of catalysis in the direct thermochemical conversion of biomass into gaseous and liquid fuels; to establish the relationship between potential biomass conversion processes and catalytic processes currently under development in other areas, with particular emphasis on coal conversion processes; and to identify promising catalytic systems which could be utilized to reduce the overall costs of fuels production from biomass materials. The report is divided into five major parts which address the above objectives. In Part III the physical and chemical properties of biomass and coal are compared, and the implications for catalytic conversion processes are discussed. With respect to chemical properties, biomass is shown to have significant advantages over coal in catalytic conversion processes because of its uniformly high H/C ratio and low concentrations of potential catalyst poisons. The physical properties of biomass can vary widely, however, and preprocessing by grinding is difficult and costly. Conversion technologies that require little preprocessing and accept a wide range of feed geometries, densities, and particle sizes appear desirable. Part IV provides a comprehensive review of existing and emerging thermochemical conversion technologies for biomass and coal. The underlying science and technology for gasification and liquefaction processes are presented.

  13. First crystal structure and catalytic mechanism of a bacterial glucuronosyltransferase

    International Nuclear Information System (INIS)

    Xanthomonas campestris GumK (β-1,2-glucuronosyltransferase) is a membrane associated protein involved in the biosynthesis of xanthan, an exo polysaccharide crucial for this bacterium's phyto pathogenicity. Xanthan is also used in many important industrial applications. The x-ray crystal structure of apo-GumK was solved at 1.9 A resolution. The enzyme has two well defined Rossmann domains with a catalytic cleft between them. Recently, the crystal structure of GumK complexed with the donor substrate was also solved. We identified a number of catalytically important residues, including Asp157, which serves as the general base in the transfer reaction. The biological and structural data reported here shed light on the molecular basis for donor and acceptor selectivity in glucuronosyltransferases. (author)

  14. Role of the NC-Loop in Catalytic Activity and Stability in Lipase from Fervidobacterium changbaicum


    Li, Binchun; Yang, Guangyu; Wu, Lie; Feng, Yan


    Flexible NC-loops between the catalytic domain and the cap domain of the α/β hydrolase fold enzymes show remarkable diversity in length, sequence, and configuration. Recent investigations have suggested that the NC-loop might be involved in catalysis and substrate recognition in many enzymes from the α/β hydrolase fold superfamily. To foster a deep understanding of its role in catalysis, stability, and divergent evolution, we here systemically investigated the function of the NC-loop (residue...

  15. Hydrophobic catalysts for liquid phase catalytic exchange: a review of preparation methods and influencing factors of catalytic activities

    International Nuclear Information System (INIS)

    Liquid phase catalytic exchange (LPCE) between liquid water and gaseous hydro- gen has been developed for various applications, such as tritium recovery, water upgrade and heavy-water production. Good wetproofing properties of the hydrophobic catalysts can make the reaction to proceed smoothly. In this article, the preparation methods of the hydrophobic catalysts and the factors affecting the catalytic activities are reviewed. In particular, progress on the hydrophobic Pt/C/inert carrier catalysts is introduced, including the selection of inert carrier and active metal carrier, and the preparation methods of carbon- supported Pt based catalysts. Basic research activities on controllable fabrication of hydro- phobic catalysts are discussed, including the LPCE reaction mechanism, and the relation between the microstructure of active metal and the catalytic activity, etc. Finally, questions remaining to be answered and future directions in the field of hydrophobic catalysts are discussed. (authors)

  16. Catalytic properties of niobium compounds

    International Nuclear Information System (INIS)

    The catalytic activity and selectivity of niobium compounds including oxides, salts, organometallic compounds and others are outlined. The application of these compounds as catalysts to diversified reactions is reported. The nature and action of niobium catalysts are characteristic and sometimes anomalous, suggesting the necessity of basic research and the potential use as catalysts for important processes in the chemical industry. (Author)

  17. Reaction engineering in direct coal liquefaction (United States)

    Shah, Y. T.

    Processes for direct coal liquefaction by solvent extraction are considered along with the structure and properties of coal and the mechanism of coal liquefaction, heteroatom removal during liquefaction, kinetic models for donor-solvent coal liquefaction, the design of coal liquefaction reactors, and the refining of coal liquids. Attention is given to the catalytic hydrogenation of coal in the presence of a solvent, the origin and character of coal, laboratory reactors for rate measurements, reaction networks based on lumped fractions, free-radical reaction models, reactor types, the compatibility of coal-derived liquids and petroleum fuels, the stability of coal liquids, thermal cracking, catalytic hydrotreating, catalytic cracking, and catalytic reforming.

  18. Ultrasound assisted co-precipitation of nanostructured CuO-ZnO-Al2O3 over HZSM-5: effect of precursor and irradiation power on nanocatalyst properties and catalytic performance for direct syngas to DME. (United States)

    Allahyari, Somaiyeh; Haghighi, Mohammad; Ebadi, Amanollah; Hosseinzadeh, Shahin


    Nanostructured CuO-ZnO-Al2O3/HZSM-5 was synthesized from nitrate and acetate precursors using ultrasound assisted co-precipitation method under different irradiation powers. The CuO-ZnO-Al2O3/HZSM-5 nanocatalysts were characterized using XRD, FESEM, BET, FTIR and EDX Dot-mapping analyses. The results indicated precursor type and irradiation power have significant influences on phase structure, morphology, surface area and functional groups. It was observed that the acetate formulated CuO-ZnO-Al2O3/HZSM-5 nanocatalyst have smaller CuO crystals with better dispersion and stronger interaction between components in comparison to nitrate based nanocatalysts. Ultrasound assisted co-precipitation synthesis method resulted in nanocatalyst with more uniform morphology compared to conventional method and increasing irradiation power yields smaller particles with better dispersion and higher surface area. Additionally the crystallinity of CuO is lower at high irradiation powers leading to stronger interaction between metal oxides. The nanocatalysts performance were tested at 200-300 °C, 10-40 bar and space velocity of 18,000-36,000 cm(3)/g h with the inlet gas composition of H2/CO = 2/1 in a stainless steel autoclave reactor. The acetate based nanocatalysts irradiated with higher levels of power exhibited better reactivity in terms of CO conversion and DME yield. While there is an optimal temperature for CO conversion and DME yield in direct synthesis of DME, CO conversion and DME yield both increase with the pressure increase. Furthermore ultrasound assisted co-precipitation method yields more stable CuO-ZnO-Al2O3/HZSM-5 nanocatalyst while conventional precipitated nanocatalyst lost their activity ca. 18% and 58% in terms of CO conversion and DME yield respectively in 24 h time on stream test. PMID:24409466

  19. Carbon nanofibers: a versatile catalytic support

    Directory of Open Access Journals (Sweden)

    Nelize Maria de Almeida Coelho


    Full Text Available The aim of this article is present an overview of the promising results obtained while using carbon nanofibers based composites as catalyst support for different practical applications: hydrazine decomposition, styrene synthesis, direct oxidation of H2S into elementary sulfur and as fuel-cell electrodes. We have also discussed some prospects of the use of these new materials in total combustion of methane and in ammonia decomposition. The macroscopic carbon nanofibers based composites were prepared by the CVD method (Carbon Vapor Deposition employing a gaseous mixture of hydrogen and ethane. The results showed a high catalytic activity and selectivity in comparison to the traditional catalysts employed in these reactions. The fact was attributed, mainly, to the morphology and the high external surface of the catalyst support.

  20. Fuel Flexible, Low Emission Catalytic Combustor for Opportunity Fuel Applications

    Energy Technology Data Exchange (ETDEWEB)

    Eteman, Shahrokh


    Limited fuel resources, increasing energy demand and stringent emission regulations are drivers to evaluate process off-gases or process waste streams as fuels for power generation. Often these process waste streams have low energy content and/or highly reactive components. Operability of low energy content fuels in gas turbines leads to issues such as unstable and incomplete combustion. On the other hand, fuels containing higher-order hydrocarbons lead to flashback and auto-ignition issues. Due to above reasons, these fuels cannot be used directly without modifications or efficiency penalties in gas turbine engines. To enable the use of these wide variety of fuels in gas turbine engines a rich catalytic lean burn (RCL®) combustion system was developed and tested in a subscale high pressure (10 atm.) rig. The RCL® injector provided stability and extended turndown to low Btu fuels due to catalytic pre-reaction. Previous work has shown promise with fuels such as blast furnace gas (BFG) with LHV of 85 Btu/ft3 successfully combusted. This program extends on this work by further modifying the combustor to achieve greater catalytic stability enhancement. Fuels containing low energy content such as weak natural gas with a Lower Heating Value (LHV) of 6.5 MJ/m3 (180 Btu/ft3 to natural gas fuels containing higher hydrocarbon (e.g ethane) with LHV of 37.6 MJ/m3 (1010 Btu/ft3) were demonstrated with improved combustion stability; an extended turndown (defined as the difference between catalytic and non-catalytic lean blow out) of greater than 250oF was achieved with CO and NOx emissions lower than 5 ppm corrected to 15% O2. In addition, for highly reactive fuels the catalytic region preferentially pre-reacted the higher order hydrocarbons with no events of flashback or auto-ignition allowing a stable and safe operation with low NOx and CO emissions.

  1. Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4

    DEFF Research Database (Denmark)

    McDonough, Michael A.; Kadirvelraj, Renuka; Harris, Pernille;


    Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamno galacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from...... Aspergillus aculeatus has been determined to 1.5 Angstrom resolution representing the first known structure from polysaccharide lyase family 4 and of an enzyme with this catalytic specificity. The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows...... structural homology to non-catalytic domains from other carbohydrate active enzymes....

  2. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan


    Domains are considered to be the building blocks of protein structures. A protein can contain a single domain or multiple domains, each one typically associated with a specific function. The combination of domains determines the function of the protein, its subcellular localization and the interacti

  3. Imaging Ferroelectric Domains and Domain Walls Using Charge Gradient Microscopy: Role of Screening Charges. (United States)

    Tong, Sheng; Jung, Il Woong; Choi, Yoon-Young; Hong, Seungbum; Roelofs, Andreas


    Advanced scanning probe microscopies (SPMs) open up the possibilities of the next-generation ferroic devices that utilize both domains and domain walls as active elements. However, current SPMs lack the capability of dynamically monitoring the motion of domains and domain walls in conjunction with the transport of the screening charges that lower the total electrostatic energy of both domains and domain walls. Charge gradient microscopy (CGM) is a strong candidate to overcome these shortcomings because it can map domains and domain walls at high speed and mechanically remove the screening charges. Yet the underlying mechanism of the CGM signals is not fully understood due to the complexity of the electrostatic interactions. Here, we designed a semiconductor-metal CGM tip, which can separate and quantify the ferroelectric domain and domain wall signals by simply changing its scanning direction. Our investigation reveals that the domain wall signals are due to the spatial change of polarization charges, while the domain signals are due to continuous removal and supply of screening charges at the CGM tip. In addition, we observed asymmetric CGM domain currents from the up and down domains, which are originated from the different debonding energies and the amount of the screening charges on positive and negative bound charges. We believe that our findings can help design CGM with high spatial resolution and lead to breakthroughs in information storage and energy-harvesting devices. PMID:26751281

  4. Catalytic Fast Pyrolysis: A Review

    Directory of Open Access Journals (Sweden)

    Theodore Dickerson


    Full Text Available Catalytic pyrolysis is a promising thermochemical conversion route for lignocellulosic biomass that produces chemicals and fuels compatible with current, petrochemical infrastructure. Catalytic modifications to pyrolysis bio-oils are geared towards the elimination and substitution of oxygen and oxygen-containing functionalities in addition to increasing the hydrogen to carbon ratio of the final products. Recent progress has focused on both hydrodeoxygenation and hydrogenation of bio-oil using a variety of metal catalysts and the production of aromatics from bio-oil using cracking zeolites. Research is currently focused on developing multi-functional catalysts used in situ that benefit from the advantages of both hydrodeoxygenation and zeolite cracking. Development of robust, highly selective catalysts will help achieve the goal of producing drop-in fuels and petrochemical commodities from wood and other lignocellulosic biomass streams. The current paper will examine these developments by means of a review of existing literature.

  5. Combined catalytic converter and afterburner

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.


    This patent describes the combined use of a catalytic converter and afterburner. An afterburner chamber and a catalyst matrix are disposed in series within a casing. A combustible premixed charge is ignited in the afterburner chamber before it enters the catalyst matrix. This invention overcomes the problem encountered in previous designs of some of the premixed charge passing unreacted through the device unless a very long afterburner chamber is used. (UK)

  6. Investigations for designing catalytic recombiners

    International Nuclear Information System (INIS)

    In case of a severe accident in pressurised water reactors (PWR) a high amount of hydrogen up to about 20,000 m3 might be generated and released into the containments. The mixture consisting of hydrogen and oxygen may either burn or detonate, if ignited. In case of detonation the generated shock wave may endanger the components of the plant or the plant itself. Consequently, effective removal of hydrogen is required. The fact that hydrogen and oxygen react exo-thermally on catalytically acting surfaces already at low temperatures generating steam and heat is made use of in catalytic recombiners. They consist of substrates coated with catalyst (mainly platinum or palladium) which are arranged inside a casing. Being passively acting measures, recombiners do not need any additional energy supply. Experimental investigations on catalytic hydrogen recombination are conducted at FZJ (Forschungszentrum Juelich) using three test facilities. The results yield insight in the development potential of contemporary recombiner systems as well as of innovative systems. Detailed investigations on a recombiner section show strong temperature gradients over the surface of a catalytically coated sample. Dependent on the flow velocity, ignition temperature may be reached at the leading edge already at an inlet hydrogen concentration of about 5 vol.-%. The thermal strain of the substrate leads to considerable detachment of catalyst particles probably causing unintended ignition of the flammable mixture. Temperature peaks can be prevented effectively by leaving the first part of the plate uncoated. In order to avoid overheating of the catalyst elements of a recombiner even at high hydrogen concentrations a modular system of porous substrates is proposed. The metallic substrates are coated with platinum at low catalyst densities thus limiting the activity of the single specimen. A modular arrangement of these elements provides high recombination rates over a large hydrogen concentration

  7. Structures composing protein domains

    Czech Academy of Sciences Publication Activity Database

    Kubrycht, J.; Sigler, Karel; Souček, P.; Hudeček, J.


    Roč. 95, č. 8 (2013), s. 1511-1524. ISSN 0300-9084 Institutional support: RVO:61388971 Keywords : Catalytic * Disordered * Fold Subject RIV: EE - Microbiology, Virology Impact factor: 3.123, year: 2013

  8. Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP

    Institute of Scientific and Technical Information of China (English)

    Qin Yu; Liyan Hu; Qing Yao; Yongqun Zhu; Na Dong; Da-Cheng Wang; Feng Shao


    Rab GTPases are emerging targets of diverse bacterial pathogens.Here,we perform biochemical and structural analyses of LepB,a Rab GTPase-activating protein (GAP) effector from Legionellapneumophila.We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors.Exhaustive mutation analyses identify Arg444 as the arginine finger,but no catalytically essential glutamine residues.Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AIF3 support the catalytic role of Arg444,and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs.Glu449,structurally equivalent to TBC RabGAP glutamine finger in apo-LepB,undergoes a drastic movement upon Rab1 binding,which induces Rab1 Gin70 side-chain flipping towards GDP-AIF3 through a strong ionic interaction.This conformationally rearranged Gln70 acts as the catalytic cis-glutamine,therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB.Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs,particularly those from bacterial pathogens.

  9. Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular α-Amylase Enzyme System with FNIII and CBM25 Domains. (United States)

    Valk, Vincent; Eeuwema, Wieger; Sarian, Fean D; van der Kaaij, Rachel M; Dijkhuizen, Lubbert


    The bacterium Microbacterium aurum strain B8.A, originally isolated from a potato plant wastewater facility, is able to degrade different types of starch granules. Here we report the characterization of an unusually large, multidomain M. aurum B8.A α-amylase enzyme (MaAmyA). MaAmyA is a 1,417-amino-acid (aa) protein with a predicted molecular mass of 148 kDa. Sequence analysis of MaAmyA showed that its catalytic core is a family GH13_32 α-amylase with the typical ABC domain structure, followed by a fibronectin (FNIII) domain, two carbohydrate binding modules (CBM25), and another three FNIII domains. Recombinant expression and purification yielded an enzyme with the ability to degrade wheat and potato starch granules by introducing pores. Characterization of various truncated mutants of MaAmyA revealed a direct relationship between the presence of CBM25 domains and the ability of MaAmyA to form pores in starch granules, while the FNIII domains most likely function as stable linkers. At the C terminus, MaAmyA carries a 300-aa domain which is uniquely associated with large multidomain amylases; its function remains to be elucidated. We concluded that M. aurum B8.A employs a multidomain enzyme system to initiate degradation of starch granules via pore formation. PMID:26187958

  10. Structured materials for catalytic and sensing applications (United States)

    Hokenek, Selma

    The optical and chemical properties of the materials used in catalytic and sensing applications directly determine the characteristics of the resultant catalyst or sensor. It is well known that a catalyst needs to have high activity, selectivity, and stability to be viable in an industrial setting. The hydrogenation activity of palladium catalysts is known to be excellent, but the industrial applications are limited by the cost of obtaining catalyst in amounts large enough to make their use economical. As a result, alloying palladium with a cheaper, more widely available metal while maintaining the high catalytic activity seen in monometallic catalysts is, therefore, an attractive option. Similarly, the optical properties of nanoscale materials used for sensing must be attuned to their application. By adjusting the shape and composition of nanoparticles used in such applications, very fine changes can be made to the frequency of light that they absorb most efficiently. The design, synthesis, and characterization of (i) size controlled monometallic palladium nanoparticles for catalytic applications, (ii) nickel-palladium bimetallic nanoparticles and (iii) silver-palladium nanoparticles with applications in drug detection and biosensing through surface plasmon resonance, respectively, will be discussed. The composition, size, and shape of the nanoparticles formed were controlled through the use of wet chemistry techniques. After synthesis, the nanoparticles were analyzed using physical and chemical characterization techniques such as X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM), and Scanning Transmission Electron Microscopy- Energy-Dispersive Spectrometry (STEM-EDX). The Pd and Ni-Pd nanoparticles were then supported on silica for catalytic testing using mass spectrometry. The optical properties of the Ag-Pd nanoparticles in suspension were further investigated using ultraviolet-visible spectrometry (UV-Vis). Monometallic palladium particles have

  11. Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer

    Energy Technology Data Exchange (ETDEWEB)

    Kaspera, Ruediger; Sahele, Tariku; Lakatos, Kyle [Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610 (United States); Totah, Rheem A., E-mail: [Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610 (United States)


    Highlights: Black-Right-Pointing-Pointer Cytochrome P450BM-3 reduced aldehydes to alcohols efficiently (k{sub cat} {approx} 25 min{sup -1}). Black-Right-Pointing-Pointer Reduction is a direct hydride transfer from R-NADP{sup 2}H to the carbonyl moiety. Black-Right-Pointing-Pointer P450 domain variants enhance reduction through potential allosteric/redox interactions. Black-Right-Pointing-Pointer Novel reaction will have implications for metabolism of xenobiotics. -- Abstract: Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k{sub cat} of {approx}25 min{sup -1} was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. The reduction was caused by a direct hydride transfer from preferentially R-NADP{sup 2}H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP{sup 2}H but not D{sub 2}O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.

  12. Structural domains in NADPH: Protochlorophyllide oxidoreductases involved in catalysis and substrate binding. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Timko, Michael P.


    Until recently little direct information was available about specific structural determinants within the light-dependent NADPH: protochlorophyllide oxidoreductases (PORs) required for substrate and cofactor binding, catalytic activity, and thylakoid membrane localization. Based on our previous DOE-funded studies, during the past year we brought to fruition a number of ongoing experiments, initiated several new avenues of investigations, and overall have made considerable progress towards establishing the basic structural parameters governing POR function. Our studies to date have defined residues and domains involved in substrate and cofactor binding and catalysis, and elaborated on the mechanism for membrane localization of POR in developing plastids. Our results and their significance, as well as our work in progress, are detailed.

  13. The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1

    Energy Technology Data Exchange (ETDEWEB)

    Syeda, Farisa; Fagan, Rebecca L.; Wean, Matthew; Avvakumov, George V.; Walker, John R.; Xue, Sheng; Dhe-Paganon, Sirano; Brenner, Charles (Iowa); (Toronto)


    Dnmt1 (DNA methyltransferase 1) is the principal enzyme responsible for maintenance of cytosine methylation at CpG dinucleotides in the mammalian genome. The N-terminal replication focus targeting sequence (RFTS) domain of Dnmt1 has been implicated in subcellular localization, protein association, and catalytic function. However, progress in understanding its function has been limited by the lack of assays for and a structure of this domain. Here, we show that the naked DNA- and polynucleosome-binding activities of Dnmt1 are inhibited by the RFTS domain, which functions by virtue of binding the catalytic domain to the exclusion of DNA. Kinetic analysis with a fluorogenic DNA substrate established the RFTS domain as a 600-fold inhibitor of Dnmt1 enzymatic activity. The crystal structure of the RFTS domain reveals a novel fold and supports a mechanism in which an RFTS-targeted Dnmt1-binding protein, such as Uhrf1, may activate Dnmt1 for DNA binding.

  14. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. (United States)

    Handley, Lindsey D; Treuheit, Nicholas A; Venkatesh, Varun J; Komives, Elizabeth A


    Human α-thrombin is a serine protease with dual functions. Thrombin acts as a procoagulant, cleaving fibrinogen to make the fibrin clot, but when bound to thrombomodulin (TM), it acts as an anticoagulant, cleaving protein C. A minimal TM fragment consisting of the fourth, fifth, and most of the sixth EGF-like domain (TM456m) that has been prepared has much improved solubility, thrombin binding capacity, and anticoagulant activity versus those of previous TM456 constructs. In this work, we compare backbone amide exchange of human α-thrombin in three states: apo, D-Phe-Pro-Arg-chloromethylketone (PPACK)-bound, and TM456m-bound. Beyond causing a decreased level of amide exchange at their binding sites, TM and PPACK both cause a decreased level of amide exchange in other regions including the γ-loop and the adjacent N-terminus of the heavy chain. The decreased level of amide exchange in the N-terminus of the heavy chain is consistent with the historic model of activation of serine proteases, which involves insertion of this region into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of thrombin, hydrogen-deuterium exchange mass spectrometry results suggest that the conformation of apo-thrombin does not yet have the N-terminus of the heavy chain properly inserted for optimal catalytic activity, and that binding of TM allosterically promotes the catalytically active conformation. PMID:26468766

  15. Production of filamentous carbon and H{sub 2} by solarthermal catalytic cracking of CH{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Kirillov, V.; Kuvshinov, G. [Boreskov Inst. of Catalysis (Russian Federation); Reller, A. [Hamburg Univ., Hamburg (Germany); Steinfeld, A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)


    The catalytic thermal decomposition of methane has been experimentally studied using high-temperature solar process heat. Nickel catalyst particles, fluidized in methane, were directly irradiated at the PSI solar furnace. Carbon deposition consisted of randomly interlaced filaments that grew as fibers and hollow nanotubes (of approx. 30 nm diameter) originating at each catalytic particle. (author) 4 figs., 7 refs.

  16. Trends in catalytic NO decomposition over transition metal surfaces

    DEFF Research Database (Denmark)

    Falsig, Hanne; Bligaard, Thomas; Rass-Hansen, Jeppe;


    The formation of NOx from combustion of fossil and renewable fuels continues to be a dominant environmental issue. We take one step towards rationalizing trends in catalytic activity of transition metal catalysts for NO decomposition by combining microkinetic modelling with density functional...... theory calculations. We show specifically why the key problem in using transition metal surfaces to catalyze direct NO decomposition is their significant relative overbinding of atomic oxygen compared to atomic nitrogen....

  17. Coordinated DNA dynamics during the human telomerase catalytic cycle


    Joseph W. Parks; Stone, Michael D.


    The human telomerase reverse transcriptase (hTERT) utilizes a template within the integral RNA subunit (hTR) to direct extension of telomeres. Telomerase exhibits repeat addition processivity (RAP) and must therefore translocate the nascent DNA product into a new RNA:DNA hybrid register to prime each round of telomere repeat synthesis. Here we use single-molecule FRET and nuclease protection assays to monitor telomere DNA structure and dynamics during the telomerase catalytic cycle. DNA trans...

  18. Tumor-directed lymphocyte-activating cytokines: refolding-based preparation of recombinant human interleukin-12 and an antibody variable domain-fused protein by additive-introduced stepwise dialysis

    International Nuclear Information System (INIS)

    Integration of lymphocyte-activating cytokines (e.g., interleukin-12: IL-12) to tumor cells offers promise for cancer immunotherapy, but the preparation of such heterodimeric proteins by refolding is difficult because of subunit instability. We achieved the refolding of Escherichia coli-expressed human IL-12 by a stepwise dialysis method, preventing the formation of insoluble aggregates by adding a redox reagent and an aggregation suppressor. We also constructed a tumor-specific IL-12 protein, each subunit of which was fused with one chain of variable domain fragment (Fv) of anticarcinoembryonic antigen (CEA) antibody T84.66 (aCEA-IL12). Fusion of IL-12 with Fv greatly increased the yield of functional heterodimer. Several assays have indicated that the Fv domain and IL-12 domain of the fused protein had cognate biological activities, and it enhanced the cytotoxicity of T-LAK cells for the cancer cell line

  19. Adapting Mathematical Domain Reasoners

    CERN Document Server

    Heeren, Bastiaan


    Mathematical learning environments help students in mastering mathematical knowledge. Mature environments typically offer thousands of interactive exercises. Providing feedback to students solving interactive exercises requires domain reasoners for doing the exercise-specific calculations. Since a domain reasoner has to solve an exercise in the same way a student should solve it, the structure of domain reasoners should follow the layered structure of the mathematical domains. Furthermore, learners, teachers, and environment builders have different requirements for adapting domain reasoners, such as providing more details, disallowing or enforcing certain solutions, and combining multiple mathematical domains in a new domain. In previous work we have shown how domain reasoners for solving interactive exercises can be expressed in terms of rewrite strategies, rewrite rules, and views. This paper shows how users can adapt and configure such domain reasoners to their own needs. This is achieved by enabling users...

  20. Building new catalytic sensors with plasma nanostructuring of metals

    International Nuclear Information System (INIS)

    Today, plasma nanostructuring of materials plays important role in improvement of different sensors including catalytic, by expanding the limits of operation in various directions. Herein a review of catalytic sensors based on metal-oxide layer for measuring the concentration of atom radicals of parent molecules is presented. Catalytic sensors are small pieces of suitable materials allowing for in-situ determination of the atom concentration. Oxygen atoms are detected using materials that form oxide films with moderate or high binding energy such as nickel and niobium oxides. Best sensitivity for oxygen atoms is obtained using catalytic sensors with nanostructured surface, more precisely metal-oxide nanowire surfaces. In any case, the sensing capacity depends on the probability for heterogeneous surface recombination of atoms to stable molecules. The sensors measure the atom densities in a broad range from roughly 1013 to 1016 cm-3, i.e. the ranges commonly found in material processing. Whereas new nanostructured surfaces expand the measurement detection range as well as add very interesting features to sensors, such as capacity to overcome radical overloads and temperature stresses. Several examples of application are presented and discussed. (author)

  1. Pair interaction of catalytically active colloids: from assembly to escape (United States)

    Sharifi-Mood, Nima; Mozaffari, Ali; Córdova-Figueroa, Ubaldo M.


    The dynamics and pair trajectory of two self-propelled colloids are reported. The autonomous motions of the colloids are due to a catalytic chemical reaction taking place asymmetrically on their surfaces that generates a concentration gradient of interactive solutes around the particles and actuate particle propulsion. We consider two spherical particles with symmetric catalytic caps extending over the local polar angles $\\theta^1_{cap}$ and $\\theta^2_{cap}$ from the centers of active sectors in an otherwise quiescent fluid. A combined analytical-numerical technique was developed to solve the coupled mass transfer equation and the hydrodynamics in the Stokes flow regime. The ensuing pair trajectory of the colloids is controlled by the reacting coverages $\\theta^j_{cap}$ and their initial relative orientation with respect to each other. Our analysis indicates two possible scenarios for pair trajectories of catalytic self-propelled particles: either the particles approach, come into contact and assemble or they interact and move away from each other (escape). For arbitrary motions of the colloids, it is found that the direction of particle rotations is the key factor in determining the escape or assembly scenario. Based on the analysis, a phase diagram is sketched for the pair trajectory of the catalytically active particles as a function of active coverages and their initial relative orientations. We believe this study has important implications in elucidation of collective behaviors of auotophoretically self-propelled colloids.

  2. Structural basis for catalytically restrictive dynamics of a high-energy enzyme state (United States)

    Kovermann, Michael; Ådén, Jörgen; Grundström, Christin; Elisabeth Sauer-Eriksson, A.; Sauer, Uwe H.; Wolf-Watz, Magnus


    An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or `invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power--a key aspect in rational design of enzymes catalysing novel reactions.

  3. Domain walls at finite temperature

    International Nuclear Information System (INIS)

    It is suggested that the phase transition of lambda phi 4 theory as a function of temperature coincides with the spontaneous appearance of domain walls. Based on one-loop calculations, T sub(c) = 4M/√ lambda is estimated as the temperature for these domains to because energetically favored, to be compared with T sub(c) = 4.9M/√ lambda from effective potential calculations (which are performed directly in the broken phase). Domain walls, as well as other Types of fluctuations, disorder the system above T sub(c), leading to =0. The critical exponent for the specific heat above T sub(c) is computed; and α=2/3 + 0 (√ lambda) is obtained. (Author)

  4. Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes

    Directory of Open Access Journals (Sweden)

    Rybarczyk-Mydłowska Katarzyna


    Full Text Available Abstract Background Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5 cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed. Results Single nematodes were used to obtain (partial genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C. Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns. Conclusions All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root

  5. The All-DQ-Domain EMTP


    Gibson H.M. Sianipar


    This paper presents an improvement to dq-domain method of calculating electromagnetic transients. The proposed methodology works on dq-domain model for all components of the power system and during all time iterations. This is a new direction distinct from the old one where the network is invariably modeled in phase-domain. By modeling the network in dq-domain there is no more problem of interfacing machine to network as usually met in the existing method as machine is modeled invariably in ...

  6. The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf

    Directory of Open Access Journals (Sweden)

    Geldner Niko


    Full Text Available Abstract Background Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs that stimulate the exchange of the tightly bound GDP nucleotide by GTP. The catalytic domain responsible for nucleotide exchange is in general associated with non-catalytic domains that define the spatio-temporal conditions of activation. In the case of small G proteins of the Arf subfamily, which are major regulators of membrane trafficking, GEFs form a heterogeneous family whose only common characteristic is the well-characterized Sec7 catalytic domain. In contrast, the function of non-catalytic domains and how they regulate/cooperate with the catalytic domain is essentially unknown. Results Based on Sec7-containing sequences from fully-annotated eukaryotic genomes, including our annotation of these sequences from Paramecium, we have investigated the domain architecture of large ArfGEFs of the BIG and GBF subfamilies, which are involved in Golgi traffic. Multiple sequence alignments combined with the analysis of predicted secondary structures, non-structured regions and splicing patterns, identifies five novel non-catalytic structural domains which are common to both subfamilies, revealing that they share a conserved modular organization. We also report a novel ArfGEF subfamily with a domain organization so far unique to alveolates, which we name TBS (TBC-Sec7. Conclusion Our analysis unifies the BIG and GBF subfamilies into a higher order subfamily, which, together with their being the only subfamilies common to all eukaryotes, suggests that they descend from a common ancestor from which species-specific ArfGEFs have subsequently evolved. Our identification of a conserved modular architecture provides a background for future functional investigation of non-catalytic domains.

  7. Functional domain walls in multiferroics (United States)

    Meier, Dennis


    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics.

  8. Regulation of Escherichia coli RelA Requires Oligomerization of the C-Terminal Domain


    Gropp, Michal; Strausz, Yael; Gross, Miriam; Glaser, Gad


    The E. coli RelA protein is a ribosome-dependent (p)ppGpp synthetase that is activated in response to amino acid starvation. RelA can be dissected both functionally and physically into two domains: The N-terminal domain (NTD) (amino acids [aa] 1 to 455) contains the catalytic domain of RelA, and the C-terminal domain (CTD) (aa 455 to 744) is involved in regulating RelA activity. We used mutational analysis to localize sites important for RelA activity and control in these two domains. We inse...

  9. Kinetics of heterogeneous catalytic reactions

    CERN Document Server

    Boudart, Michel


    This book is a critical account of the principles of the kinetics of heterogeneous catalytic reactions in the light of recent developments in surface science and catalysis science. Originally published in 1984. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase acc

  10. Molecular catalytic coal liquid conversion

    Energy Technology Data Exchange (ETDEWEB)

    Stock, L.M.; Yang, Shiyong [Univ. of Chicago, IL (United States)


    This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under very mild conditions. Accomplishments and conclusions are discussed.

  11. Catalytic Spectrophotometric Determination of Chromium


    STOYANOVA, Angelina Miltcheva


    The catalytic effect of chromium(III) and chromium(VI) on the oxidation of sulfanilic acid by hydrogen peroxide was studied. The reaction was followed spectrophotometrically by measuring the absorbance of the reaction product at 360 nm. Under the optimum conditions 2 calibration graphs (for chromium(III) up to 100 ng mL-1, and for chromium(VI) up to 200 ng mL-1) were obtained, using the ``fixed time'' method with detection limits of 4.9 ng mL-1 and 3.8 ng mL-1, respectively...

  12. Catalytic Combustion of Ethyl Acetate


    ÖZÇELİK, Tuğba GÜRMEN; ATALAY, Süheyda; ALPAY, Erden


    The catalytic combustion of ethyl acetate over prepared metal oxide catalysts was investigated. CeO, Co2O3, Mn2O3, Cr2O3, and CeO-Co2O3 catalysts were prepared on monolith supports and they were tested. Before conducting the catalyst experiments, we searched for the homogeneous gas phase combustion reaction of ethyl acetate. According to the homogeneous phase experimental results, 45% of ethyl acetate was converted at the maximum reactor temperature tested (350 °C). All the prepare...

  13. Estimating the temperature of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.


    A method is described for estimating the temperature in a catalytic converter used in the exhaust system of an internal combustion engine. Pressure sensors monitor the flow resistance across the catalytic converter to provide an indication of the temperature inside. This feedback system allows heating devices to be switched off and thus avoid overheating, while maintaining the catalytic converter's efficiency by assuring that it does not operate below its light off temperature. (UK)

  14. Estimating the temperature of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.


    A method of estimating the temperature of a catalytic converter used in the exhaust system of an internal combustion engine is described. Heated exhaust gas oxygen (HEGO) sensors are placed upstream and downstream of the catalytic converter. The temperature of the catalytic converter shortly after start-up is measured by monitoring the resistance of the HEGO sensor's heating element. The downstream sensor is used for mixture control and to double check results of the upstream sensor. (UK)

  15. Catalytic Oxidation of Methane into Methanol over Copper-Exchanged Zeolites with Oxygen at Low Temperature. (United States)

    Narsimhan, Karthik; Iyoki, Kenta; Dinh, Kimberly; Román-Leshkov, Yuriy


    The direct catalytic conversion of methane to liquid oxygenated compounds, such as methanol or dimethyl ether, at low temperature using molecular oxygen is a grand challenge in C-H activation that has never been met with synthetic, heterogeneous catalysts. We report the first demonstration of direct, catalytic oxidation of methane into methanol with molecular oxygen over copper-exchanged zeolites at low reaction temperatures (483-498 K). Reaction kinetics studies show sustained catalytic activity and high selectivity for a variety of commercially available zeolite topologies under mild conditions (e.g., 483 K and atmospheric pressure). Transient and steady state measurements with isotopically labeled molecules confirm catalytic turnover. The catalytic rates and apparent activation energies are affected by the zeolite topology, with caged-based zeolites (e.g., Cu-SSZ-13) showing the highest rates. Although the reaction rates are low, the discovery of catalytic sites in copper-exchanged zeolites will accelerate the development of strategies to directly oxidize methane into methanol under mild conditions. PMID:27413787

  16. Nanostructured Catalytic Reactors for Air Purification Project (United States)

    National Aeronautics and Space Administration — This SBIR Phase II project proposes the development of lightweight compact nanostructured catalytic reactors for air purification from toxic gaseous organic...

  17. Nanostructured Catalytic Reactors for Air Purification Project (United States)

    National Aeronautics and Space Administration — This SBIR Phase I project proposes the development of lightweight compact nanostructured catalytic reactors for air purification from toxic gaseous organic...

  18. Catalytic Ignition and Upstream Reaction Propagation in a Platinum Tube (United States)

    Struk, P. M.; Dietrich, D. L.; Mellish, B. P.; Miller, F. J.; T'ien, J. S.


    A challenge for catalytic combustion in monolithic reactors at elevated temperatures is the start-up or "light-off" from a cold initial condition. In this work, we demonstrate a concept called "back-end catalytic ignition that potentially can be utilized in the light-off of catalytic monoliths. An external downstream flame or Joule heating raises the temperature of a small portion of the catalyst near the outlet initiating a localized catalytic reaction that propagates upstream heating the entire channel. This work uses a transient numerical model to demonstrate "back-end" ignition within a single channel which can characterize the overall performance of a monolith. The paper presents comparisons to an experiment using a single non-adiabatic channel but the concept can be extended to the adiabatic monolith case. In the model, the time scales associated with solid heat-up are typically several orders of magnitude larger than the gas-phase and chemical kinetic time-scales. Therefore, the model assumes a quasi-steady gas-phase with respect to a transient solid. The gas phase is one-dimensional. Appropriate correlations, however, account for heat and mass transfer in a direction perpendicular to the flow. The thermally-thin solid includes axial conduction. The gas phase, however, does not include axial conduction due to the high Peclet number flows. The model includes both detailed gas-phase and catalytic surface reactions. The experiment utilizes a pure platinum circular channel oriented horizontally though which a CO/O2 mixture (equivalence ratios ranging from 0.6 to 0.9) flows at 2 m/s.

  19. Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms


    Barchiesi, Julieta; Hedin, Nicolás; Gomez-Casati, Diego F.; Miguel A Ballicora; Busi, María V.


    Background Starch-binding domains are key modules present in several enzymes involved in polysaccharide metabolism. These non-catalytic modules have already been described as essential for starch-binding and the catalytic activity of starch synthase III from the higher plant Arabidopsis thaliana. In Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, there are three SSIII isoforms, known as Ostta SSIII-A, SSIII-B and SSIII-C. Results In this work, using in silico and in...

  20. Catalytic converters in the fireplace

    International Nuclear Information System (INIS)

    In addition to selecting the appropriate means of heating and using dry fuel, the amount of harmful emissions contained by flue gases produced by fireplaces can be reduced by technical means. One such option is to use an oxidising catalytic converter. Tests at TTS Institute's Heating Studies Experimental Station have focused on two such converters (dense and coarse) mounted in light-weight iron heating stoves. The ability of the dense catalytic converter to oxidise carbon monoxide gases proved to be good. The concentration of carbon monoxide in the flue gases was reduced by as much as 90 %. Measurements conducted by VTT (Technical Research Centre of Finland) showed that the conversion of other gases, e.g. of methane, was good. The exhaust resistance caused by the dense converter was so great as to necessitate the mounting of a fluegas evacuation fan in the chimney for the purpose of creating sufficient draught. When relying on natural draught, the dense converter requires a chimney of at least 7 metres and a by-pass connection while the fire is being lit. In addition, the converter will have to be constructed to be less dense and this will mean that it's capability to oxidise non-combusted gases will be reduced. The coarse converter did not impair the draught but it's oxidising property was insufficient. With the tests over, the converter was not observed to have become blocked up by impurities

  1. Catalytic reforming feed characterisation technique

    Energy Technology Data Exchange (ETDEWEB)

    Larraz Mora, R.; Arvelo Alvarez, R. [Univ. of La Laguna, Chemical Engineering Dept., La Laguna (Spain)


    The catalytic reforming of naphtha is one of the major refinery processes, designed to increase the octane number of naphtha or to produce aromatics. The naphtha used as catalytic reformer feedstock usually contains a mixture of paraffins, naphthenes, and aromatics in the carbon number range C{sub 6} to C{sub 10}. The detailed chemical composition of the feed is necessary to predict the aromatics and hydrogen production as well as the operation severity. The analysis of feed naphtha is usually reported in terms of its ASTM distillation curve and API or specific gravity. Since reforming reactions are described in terms of lumped chemical species (paraffins, naphthenes and aromatics), a feed characterisation technique should be useful in order to predict reforming operating conditions and detect feed quality changes. Unfortunately online analyzer applications as cromatography or recently introduced naphtha NMR [1] are scarce in most of refineries. This work proposes an algorithmic characterisation method focusing on its main steps description. The method could help on the subjects previously described, finally a calculation example is shown. (orig.)

  2. Field induced domain switching as the origin of anomalous lattice strain along non-polar direction in rhombohedral BiScO{sub 3}-PbTiO{sub 3} close to the morphotropic phase boundary

    Energy Technology Data Exchange (ETDEWEB)

    Lalitha, K. V.; Ranjan, Rajeev, E-mail: [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012 (India); Fancher, Chris M.; Jones, Jacob L. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695 (United States)


    The lattice strain and domain switching behavior of xBiScO{sub 3}–(1-x)PbTiO{sub 3} (x = 0.40) was investigated as a function of cyclic field and grain orientation by in situ X-ray diffraction during application of electric fields. The electric field induced 200 lattice strain was measured to be five times larger than the 111 lattice strain in pseudorhombohedral xBiScO{sub 3}–(1-x)PbTiO{sub 3} (x = 0.40). It is shown that the anomalous 200 lattice strain is not an intrinsic phenomenon, but arises primarily due to stress associated with the reorientation of the 111 domains in dense polycrystalline ceramic.

  3. Field induced domain switching as the origin of anomalous lattice strain along non-polar direction in rhombohedral BiScO3-PbTiO3 close to the morphotropic phase boundary

    International Nuclear Information System (INIS)

    The lattice strain and domain switching behavior of xBiScO3–(1-x)PbTiO3 (x = 0.40) was investigated as a function of cyclic field and grain orientation by in situ X-ray diffraction during application of electric fields. The electric field induced 200 lattice strain was measured to be five times larger than the 111 lattice strain in pseudorhombohedral xBiScO3–(1-x)PbTiO3 (x = 0.40). It is shown that the anomalous 200 lattice strain is not an intrinsic phenomenon, but arises primarily due to stress associated with the reorientation of the 111 domains in dense polycrystalline ceramic

  4. Contrasting intra- and extracellular distribution of catalytic ferrous iron in ovalbumin-induced peritonitis. (United States)

    Ito, Fumiya; Nishiyama, Takahiro; Shi, Lei; Mori, Masahiko; Hirayama, Tasuku; Nagasawa, Hideko; Yasui, Hiroyuki; Toyokuni, Shinya


    Iron is an essential nutrient for every type of life on earth. However, excess iron is cytotoxic and can lead to an increased cancer risk in humans. Catalytic ferrous iron [Fe(II)] is an initiator of the Fenton reaction, which causes oxidative stress by generating hydroxyl radicals. Recently, it became possible to localize catalytic Fe(II) in situ with a turn-on fluorescent probe, RhoNox-1. Here, we screened each organ/cell of rats to globally evaluate the distribution of catalytic Fe(II) and found that eosinophils showed the highest abundance. In various cells, lysosomes were the major organelle, sharing ∼40-80% of RhoNox-1 fluorescence. We then used an ovalbumin-induced allergic peritonitis model to study the dynamics of catalytic Fe(II). Peritoneal lavage revealed that the total iron contents per cell were significantly decreased, whereas an increase in the number of inflammatory cells (macrophages, neutrophils, eosinophils and lymphocytes) resulted in an increased total iron content of the peritoneal inflammatory cells. Notably, macrophages, eosinophils and neutrophils exhibited significantly increased catalytic Fe(II) with increased DMT1 expression and decreased ferritin expression, though catalytic Fe(II) was significantly decreased in the peritoneal lavage fluid. In conclusion, catalytic Fe(II) in situ more directly reflects cellular activity and the accompanying pathology than total iron does. PMID:27262439

  5. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. (United States)

    Xiong, Zi-Jian; Huang, Jingjing; Poda, Gennady; Pomès, Régis; Privé, Gilbert G


    Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30Å from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction. PMID:27349982

  6. Neutralization of botulinum neurotoxin by a human monoclonal antibody specific for the catalytic light chain.

    Directory of Open Access Journals (Sweden)

    Sharad P Adekar

    Full Text Available BACKGROUND: Botulinum neurotoxins (BoNT are a family of category A select bioterror agents and the most potent biological toxins known. Cloned antibody therapeutics hold considerable promise as BoNT therapeutics, but the therapeutic utility of antibodies that bind the BoNT light chain domain (LC, a metalloprotease that functions in the cytosol of cholinergic neurons, has not been thoroughly explored. METHODS AND FINDINGS: We used an optimized hybridoma method to clone a fully human antibody specific for the LC of serotype A BoNT (BoNT/A. The 4LCA antibody demonstrated potent in vivo neutralization when administered alone and collaborated with an antibody specific for the HC. In Neuro-2a neuroblastoma cells, the 4LCA antibody prevented the cleavage of the BoNT/A proteolytic target, SNAP-25. Unlike an antibody specific for the HC, the 4LCA antibody did not block entry of BoNT/A into cultured cells. Instead, it was taken up into synaptic vesicles along with BoNT/A. The 4LCA antibody also directly inhibited BoNT/A catalytic activity in vitro. CONCLUSIONS: An antibody specific for the BoNT/A LC can potently inhibit BoNT/A in vivo and in vitro, using mechanisms not previously associated with BoNT-neutralizing antibodies. Antibodies specific for BoNT LC may be valuable components of an antibody antidote for BoNT exposure.

  7. SERCA mutant E309Q binds two Ca ions but adopts a catalytically incompetent conformation

    DEFF Research Database (Denmark)

    Clausen, Johannes D.; Bublitz, Maike; Arnou, Bertrand; Montigny, Cédric; Jaxel, Christine; Møller, Jesper Vuust; Nissen, Poul; Andersen, Jens Peter; le Maire, Marc


    The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) couples ATP hydrolysis to transport of Ca2+. This directed energy transfer requires cross-talk between the two Ca2+ sites and the phosphorylation site over 50 Å distance. We have addressed the mechano-structural basis for this intramolecular...... signal by analysing the structure and the functional properties of SERCA mutant E309Q. Glu309 contributes to Ca2+ coordination at site II, and a consensus has been that E309Q only binds Ca2+ at site I. The crystal structure of E309Q in the presence of Ca2+ and an ATP analogue, however, reveals two...... occupied Ca2+ sites of a non-catalytic Ca2E1 state. Ca2+ is bound with micromolar affinity by both Ca2+ sites in E309Q, but without cooperativity. The Ca2+-bound mutant does phosphorylate from ATP, but at a very low maximal rate. Phosphorylation depends on the correct positioning of the A-domain, requiring...

  8. Ultraviolet laser deposition of graphene thin films without catalytic layers

    KAUST Repository

    Sarath Kumar, S. R.


    In this letter, the formation of nanostructured graphene by ultraviolet laser ablation of a highly ordered pyrolytic graphite target under optimized conditions is demonstrated, without a catalytic layer, and a model for the growth process is proposed. Previously, graphene film deposition by low-energy laser (2.3 eV) was explained by photo-thermal models, which implied that graphene films cannot be deposited by laser energies higher than the C-C bond energy in highly ordered pyrolytic graphite (3.7 eV). Here, we show that nanostructured graphene films can in fact be deposited using ultraviolet laser (5 eV) directly over different substrates, without a catalytic layer. The formation of graphene is explained by bond-breaking assisted by photoelectronic excitation leading to formation of carbon clusters at the target and annealing out of defects at the substrate.

  9. Guiding catalytically active particles with chemically patterned surfaces

    CERN Document Server

    Uspal, W E; Dietrich, S; Tasinkevych, M


    Catalytically active Janus particles suspended in solution create gradients in the chemical composition of the solution along their surfaces, as well as along any nearby container walls. The former leads to self-phoresis, while the latter gives rise to chemi-osmosis, providing an additional contribution to self-motility. Chemi-osmosis strongly depends on the molecular interactions between the diffusing chemical species and the wall. We show analytically, using an approximate "point-particle" approach, that by chemically patterning a planar substrate one can direct the motion of Janus particles: the induced chemi-osmotic flows can cause particles to either "dock" at the chemical step between the two materials, or to follow a chemical stripe. These theoretical predictions are confirmed by full numerical calculations. Generically, docking occurs for particles which tend to move away from their catalytic caps, while stripe-following occurs in the opposite case. Our analysis reveals the physical mechanisms governi...

  10. Heterogeneous Photo catalytic Degradation of Hazardous Waste in Aqueous Suspension

    International Nuclear Information System (INIS)

    The photo catalytic degradation of hazardous waste like chlorinated paraffin compound (1,12-Dichlorodoecane Ded) was investigated in different aquatic media using GC-MSD. The direct photolysis of Ded in HPLC water was considered to be negligible (k = 0.0020+-0.0007h-1). An acceleration of the photodegradation rate was occurred in presence of different TiO2 catalyst systems. Molecular oxygen was found to play a vital role in the degradation process. Anatase TiO2 was proved to be the most efficient one (k=0.7670+-0.0876h-1), while the rate constant of the rutile TiO2 was calculated to be 0.2780+-0.0342h-1. Improvement of photo catalytic efficiency of rutile TiO2 was achieved by addition of Fe+2 giving a rate constant =0.6710+-0.0786h-1

  11. Structural Basis for the Catalytic Activity of Human Serine/Threonine Protein Phosphatase-5 (United States)

    Swingle, M. R.; Honkanen, R.; Ciszak, E. M.


    Serinehhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth and cellular responses to stress. Here we report the crystal structure of the PP5 catalytic domain (PP5c) at a resolution of 1.6 A. From this structure we resolved the mechanism for PP5-mediated hydrolysis of phosphoprotein substrates, which requires the precise positioning of two metal ions within a con served Aspn-271-M(sub 1):M(sub 2)-W(sup 1)-His-427-His-304-Asp-274 catalytic motif. The structure of PPSc provides a structural basis for explaining the exceptional catalytic proficiency of protein phosphatases, which are among the most powerful known catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of the PP5c should also aid development of type-specific inhibitors.

  12. Structural Basis for the Catalytic Activity of Human SER/THR Protein Phosphatase-5 (United States)

    Swingle, M. R.; Honkanen, R.; Ciszak, E.


    Serinekhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth. Here we report the 1.6 Angstrom resolution crystal structure of PP5 catalytic domain with metal and phosphate ions in the active site. The structure reveals a mechanism for PPS-mediated catalysis that requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1),-M(sub 2)-His(sup 427)-W(sup 2)-His(sup 304)-Asp(sup 274) catalytic motif, and provides a structural basis for the exceptional catalytic proficiency of protein phosphatases placing them among the most powerful catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of PP5 should aid development of specific inhibitors.

  13. Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum.

    Directory of Open Access Journals (Sweden)

    Binchun Li

    Full Text Available Flexible NC-loops between the catalytic domain and the cap domain of the α/β hydrolase fold enzymes show remarkable diversity in length, sequence, and configuration. Recent investigations have suggested that the NC-loop might be involved in catalysis and substrate recognition in many enzymes from the α/β hydrolase fold superfamily. To foster a deep understanding of its role in catalysis, stability, and divergent evolution, we here systemically investigated the function of the NC-loop (residues 131-151 in a lipase (FClip1 from thermophilic bacterium Fervidobacterium changbaicum by loop deletion, alanine-scanning mutagenesis and site-directed mutagenesis. We found that the upper part of the NC-loop (residues 131-138 was of great importance to enzyme catalysis. Single substitutions in this region could fine-tune the activity of FClip1 as much as 41-fold, and any deletions from this region rendered the enzyme completely inactive. The lower part of the NC-loop (residues 139-151 was capable of enduring extensive deletions without loss of activity. The shortened mutants in this region were found to show both improved activity and increased stability simultaneously. We therefore speculated that the NC-loop, especially the lower part, would be a perfect target for enzyme engineering to optimize the enzymatic properties, and might present a hot zone for the divergent evolution of α/β hydrolases. Our findings may provide an opportunity for better understanding of the mechanism of divergent evolution in the α/β hydrolase fold superfamily, and may also guide the design of novel biocatalysts for industrial applications.

  14. Acoustics of automotive catalytic converter assemblies (United States)

    Dickey, Nolan S.; Selamet, Ahmet; Parks, Steve J.; Tallio, Kevin V.; Miazgowicz, Keith D.; Radavich, Paul M.


    In an automotive exhaust system, the purpose of the catalytic converter is to reduce pollutant emissions. However, catalytic converters also affect the engine and exhaust system breathing characteristics; they increase backpressure, affect exhaust system acoustic characteristics, and contribute to exhaust manifold tuning. Thus, radiated sound models should include catalytic converters since they can affect both the source characteristics and the exhaust system acoustic behavior. A typical catalytic converter assembly employs a ceramic substrate to carry the catalytically active noble metals. The substrate has numerous parallel tubes and is mounted in a housing with swelling mat or wire mesh around its periphery. Seals at the ends of the substrate can be used to help force flow through the substrate and/or protect the mat material. Typically, catalytic converter studies only consider sound propagation in the small capillary tubes of the substrate. Investigations of the acoustic characteristics of entire catalytic converter assemblies (housing, substrate, seals, and mat) do not appear to be available. This work experimentally investigates the acoustic behavior of catalytic converter assemblies and the contributions of the separate components to sound attenuation. Experimental findings are interpreted with respect to available techniques for modeling sound propagation in ceramic substrates.

  15. Understanding catalytic biomass conversion through data mining

    NARCIS (Netherlands)

    E.J. Ras; B. McKay; G. Rothenberg


    Catalytic conversion of biomass is a key challenge that we chemists face in the twenty-first century. Worldwide, research is conducted into obtaining bulk chemicals, polymers and fuels. Our project centres on glucose valorisation via furfural derivatives using catalytic hydrogenation. We present her

  16. Silver nanocluster catalytic microreactors for water purification (United States)

    Da Silva, B.; Habibi, M.; Ognier, S.; Schelcher, G.; Mostafavi-Amjad, J.; Khalesifard, H. R. M.; Tatoulian, M.; Bonn, D.


    A new method for the elaboration of a novel type of catalytic microsystem with a high specific area catalyst is developed. A silver nanocluster catalytic microreactor was elaborated by doping a soda-lime glass with a silver salt. By applying a high power laser beam to the glass, silver nanoclusters are obtained at one of the surfaces which were characterized by BET measurements and AFM. A microfluidic chip was obtained by sealing the silver coated glass with a NOA 81 microchannel. The catalytic activity of the silver nanoclusters was then tested for the efficiency of water purification by using catalytic ozonation to oxidize an organic pollutant. The silver nanoclusters were found to be very stable in the microreactor and efficiently oxidized the pollutant, in spite of the very short residence times in the microchannel. This opens the way to study catalytic reactions in microchannels without the need of introducing the catalyst as a powder or manufacturing complex packed bed microreactors.

  17. Esterification of glycerol from biodiesel production to glycerol carbonate in non-catalytic supercritical dimethyl carbonate. (United States)

    Ilham, Zul; Saka, Shiro


    Conversion of glycerol from biodiesel production to glycerol carbonate was studied by esterification with dimethyl carbonate in a non-catalytic supercritical condition. It was found that in a non-catalytic supercritical condition, glycerol at higher purity gave higher yield of glycerol carbonate at 98 wt% after reaction at 300 °C/20-40 MPa/15 min. The yield of glycerol carbonate was observed to increase with molar ratio, temperature, pressure and time until a certain equilibrium limit. The existence of impurities such as water and remnants of alkaline catalyst in crude glycerol will direct the reaction to produce glycidol. Although impurities might not be desirable, the non-catalytic supercritical dimethyl carbonate could be an alternative method for conversion of glycerol from biodiesel production to value-added glycerol carbonate.Graphical abstractPlausible reaction scheme for conversion of glycerol to glycerol carbonate in non-catalytic supercritical dimethyl carbonate. PMID:27386367

  18. Catalytic converter applications for two stroke, spark-ignited marine engines

    Energy Technology Data Exchange (ETDEWEB)

    Fujimoto, Hiroaki; Isogawa, Atsushi; Matsumoto, Naoto


    When catalytic converters are used for cleansing of exhaust gas from two-stroke marine engines, new issues must be brought up in combination with prior technology. Therefore, a study was made of V6, 2600cc engine having a large volume of hydrocarbon emissions with respect to three issues: (1) To what degree seawater effects catalytic converter performance and possible countermeasures; (2) Effects attained on cleansing level and catalyst temperature; (3) Finding abatement levels for catalyst deterioration and exhaust emission output in the marine mode. It was found that physical adsorption was a significant factor in catalytic degradation resulting from direct contact with seawater. The cleansing levels obtained when a marine engine is equipped with a catalyst converter were found by clarifying the extent of effects of catalyst volume, performance and temperature. The reduction obtained in exhaust emission allowing for a deterioration factor, is shown in a catalytic converter heated to the maximum temperature of 960 C.

  19. Selective catalytic burning of graphene by SiOx layer depletion. (United States)

    Lee, Kyoung-Jae; Ihm, Kyuwook; Kumar, Yogesh; Baik, Jaeyoon; Yang, Mihyun; Shin, Hyun-Joon; Kang, Tai-Hee; Chung, Sukmin; Hong, Byung Hee


    We report catalytic decomposition of few-layer graphene on an Au/SiOx/Si surface wherein oxygen is supplied by dissociation of the native SiOx layer at a relatively low temperature of 400 °C. The detailed chemical evolution of the graphene covered SiOx/Si surface with and without gold during the catalytic process is investigated using a spatially resolved photoelectron emission method. The oxygen atoms from the native SiOx layer activate the gold-mediated catalytic decomposition of the entire graphene layer, resulting in the formation of direct contact between the Au and the Si substrate. The notably low contact resistivity found in this system suggests that the catalytic depletion of a SiOx layer could realize a new way to micromanufacture high-quality electrical contact. PMID:24316816

  20. Selective catalytic oxidation of ammonia

    Energy Technology Data Exchange (ETDEWEB)

    Leppaelahti, J.; Koljonen, T. [VTT Energy, Espoo (Finland)


    In the combustion of fossil fuels, the principal source of nitrogen oxides is nitrogen bound in the fuel structure. In gasification, a large part of fuel nitrogen forms NH{sub 3}, which may form nitrogen oxides during gas combustion. If NH{sub 3} and other nitrogen species could be removed from hot gas, the NO emission could be considerably reduced. However, relatively little attention has been paid to finding new means of removing nitrogen compounds from the hot gasification gas. The possibility of selectively oxidizing NH{sub 3} to N{sub 2} in the hot gasification has been studied at VTT Energy. The largest NH{sub 3} reductions have been achieved by catalytic oxidation on aluminium oxides. (author) (4 refs.)

  1. Catalytic hydrogenation of carbon monoxide

    International Nuclear Information System (INIS)

    Focus of this project is on developing new approaches for hydrogenation of carbon monoxide to produce organic oxygenates at mild conditions. The strategies to accomplish CO reduction are based on favorable thermodynamics manifested by rhodium macrocycles for producing a series of intermediates implicated in the catalytic hydrogenation of CO. Metalloformyl complexes from reactions of H2 and CO, and CO reductive coupling to form metallo α-diketone species provide alternate routes to organic oxygenates that utilize these species as intermediates. Thermodynamic and kinetic-mechanistic studies are used in guiding the design of new metallospecies to improve the thermodynamic and kinetic factors for individual steps in the overall process. Electronic and steric effects associated with the ligand arrays along with the influences of the reaction medium provide the chemical tools for tuning these factors. Non-macrocyclic ligand complexes that emulate the favorable thermodynamic features associated with rhodium macrocycles, but that also manifest improved reaction kinetics are promising candidates for future development

  2. Catalytic Graphitization of Phenolic Resin

    Institute of Scientific and Technical Information of China (English)

    Mu Zhao; Huaihe Song


    The catalytic graphitization of thermal plastic phenolic-formaldehyde resin with the aid of ferric nitrate (FN) was studied in detail. The morphologies and structural features of the products including onion-like carbon nanoparticles and bamboo-shaped carbon nanotubes were investigated by transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction and Raman spectroscopy measurements. It was found that with the changes of loading content of FN and residence time at 1000℃, the products exhibited various morphologies. The TEM images showed that bamboo-shaped carbon nanotube consisted of tens of bamboo sticks and onion-like carbon nanoparticle was made up of quasi-spherically concentrically closed carbon nanocages.

  3. Reducing catalytic converter pressure loss

    Energy Technology Data Exchange (ETDEWEB)



    This article examines why approximately 30--40% of total exhaust-system pressure loss occurs in the catalytic converter and what can be done to reduce pressure loss. High exhaust-system backpressure is of concern in the design of power trains for passenger cars and trucks because it penalizes fuel economy and limits peak power. Pressure losses occur due to fluid shear and turning during turbulent flow in the converter headers and in entry separation and developing laminar-flow boundary layers within the substrate flow passages. Some of the loss mechanisms are coupled. For example, losses in the inlet header are influenced by the presence of the flow resistance of a downstream substrate. Conversely, the flow maldistribution and pressure loss of the substrate(s) depend on the design of the inlet header.

  4. Non-catalytic recuperative reformer

    Energy Technology Data Exchange (ETDEWEB)

    Khinkis, Mark J.; Kozlov, Aleksandr P.; Kurek, Harry


    A non-catalytic recuperative reformer has a flue gas flow path for conducting hot flue gas from a thermal process and a reforming mixture flow path for conducting a reforming mixture. At least a portion of the reforming mixture flow path is embedded in the flue gas flow path to permit heat transfer from the hot flue gas to the reforming mixture. The reforming mixture flow path contains substantially no material commonly used as a catalyst for reforming hydrocarbon fuel (e.g., nickel oxide, platinum group elements or rhenium), but instead the reforming mixture is reformed into a higher calorific fuel via reactions due to the heat transfer and residence time. In a preferred embodiment, extended surfaces of metal material such as stainless steel or metal alloy that are high in nickel content are included within at least a portion of the reforming mixture flow path.

  5. Fluctuations in catalytic surface reactions

    CERN Document Server

    Imbihl, R


    The internal reaction-induced fluctuations which occur in catalytic CO oxidation on a Pt field emitter tip have been studied using field electron microscopy (FEM) as a spatially resolving method. The structurally heterogeneous Pt tip consists of facets of different orientations with nanoscale dimensions. The FEM resolution of roughly 2 nm corresponds to a few hundred reacting adsorbed particles whose variations in the density are imaged as brightness fluctuations. In the bistable range of the reaction one finds fluctuation-induced transitions between the two stable branches of the reaction kinetics. The fluctuations exhibit a behaviour similar to that of an equilibrium phase transition, i.e. the amplitude diverges upon approaching the bifurcation point terminating the bistable range of the reaction. Simulations with a hybrid Monte Carlo/mean-field model reproduce the experimental observations. Fluctuations on different facets are typically uncorrelated but within a single facet a high degree of spatial cohere...

  6. Catalytic, enantioselective, vinylogous aldol reactions. (United States)

    Denmark, Scott E; Heemstra, John R; Beutner, Gregory L


    In 1935, R. C. Fuson formulated the principle of vinylogy to explain how the influence of a functional group may be felt at a distant point in the molecule when this position is connected by conjugated double-bond linkages to the group. In polar reactions, this concept allows the extension of the electrophilic or nucleophilic character of a functional group through the pi system of a carbon-carbon double bond. This vinylogous extension has been applied to the aldol reaction by employing "extended" dienol ethers derived from gamma-enolizable alpha,beta-unsaturated carbonyl compounds. Since 1994, several methods for the catalytic, enantioselective, vinylogous aldol reaction have appeared, with which varying degrees of regio- (site), enantio-, and diastereoselectivity can be attained. In this Review, the current scope and limitations of this transformation, as well as its application in natural product synthesis, are discussed. PMID:15940727

  7. Electrochemical promotion of catalytic reactions (United States)

    Imbihl, R.


    The electrochemical promotion of heterogeneously catalyzed reactions (EPOC) became feasible through the use of porous metal electrodes interfaced to a solid electrolyte. With the O 2- conducting yttrium stabilized zirconia (YSZ), the Na + conducting β″-Al 2O 3 (β-alumina), and several other types of solid electrolytes the EPOC effect has been demonstrated for about 100 reaction systems in studies conducted mainly in the mbar range. Surface science investigations showed that the physical basis for the EPOC effect lies in the electrochemically induced spillover of oxygen and alkali metal, respectively, onto the surface of the metal electrodes. For the catalytic promotion effect general concepts and mechanistic schemes were proposed but these concepts and schemes are largely speculative. Applying surface analytical tools to EPOC systems the proposed mechanistic schemes can be verified or invalidated. This report summarizes the progress which has been achieved in the mechanistic understanding of the EPOC effect.

  8. Chimeric Plant Calcium/Calmodulin-Dependent Protein Kinase Gene with a Neural Visinin-Like Calcium-Binding Domain (United States)

    Patil, Shameekumar; Takezawa, D.; Poovaiah, B. W.


    Calcium, a universal second messenger, regulates diverse cellular processes in eukaryotes. Ca-2(+) and Ca-2(+)/calmodulin-regulated protein phosphorylation play a pivotal role in amplifying and diversifying the action of Ca-2(+)- mediated signals. A chimeric Ca-2(+)/calmodulin-dependent protein kinase (CCaMK) gene with a visinin-like Ca-2(+)- binding domain was cloned and characterized from lily. The cDNA clone contains an open reading frame coding for a protein of 520 amino acids. The predicted structure of CCaMK contains a catalytic domain followed by two regulatory domains, a calmodulin-binding domain and a visinin-like Ca-2(+)-binding domain. The amino-terminal region of CCaMK contains all 11 conserved subdomains characteristic of serine/threonine protein kinases. The calmodulin-binding region of CCaMK has high homology (79%) to alpha subunit of mammalian Ca-2(+)/calmodulin-dependent protein kinase. The calmodulin-binding region is fused to a neural visinin-like domain that contains three Ca-2(+)-binding EF-hand motifs and a biotin-binding site. The Escherichia coli-expressed protein (approx. 56 kDa) binds calmodulin in a Ca-2(+)-dependent manner. Furthermore, Ca-45-binding assays revealed that CCaMK directly binds Ca-2(+). The CCaMK gene is preferentially expressed in developing anthers. Southern blot analysis revealed that CCaMK is encoded by a single gene. The structural features of the gene suggest that it has multiple regulatory controls and could play a unique role in Ca-2(+) signaling in plants.

  9. Diamagnetic (Condon) domains

    International Nuclear Information System (INIS)

    This paper is the first systematic review of experimental research on diamagnetic (aka Condon) domains that form in nonmagnetic metals at low temperatures due to the development of Landau levels. A variety of methods were used to study the domains. Muon spectroscopy studies showed such domains to be present in all metals studied, pointing to the universal nature of the phenomenon. For silver, the domain structure size as measured by Hall microsensors turned out to be an order of magnitude larger than expected. In beryllium, it was found that domains do not come to the surface but rather remain in the bulk of the crystal. The magnetostriction of beryllium during domain formation is measured. It is shown that magnetization current in a domain wall is entirely caused by the charge density gradient in the wall, due to the lattice being deformed oppositely in neighboring domains. It is observed for the first time that the de Haas-van Alphen effect exhibits hysteresis at the transition to the domain state, and this fact was used for the experimental determination of the phase diagrams for the domain states of silver and beryllium. (reviews of topical problems)

  10. Development and test of a new catalytic converter for natural gas fuelled engine

    Indian Academy of Sciences (India)

    M A Kalam; H H Masjuki; M Redzuan; T M I Mahlia; M A Fuad; M Mohibah; K H Halim; A Ishak; M Khair; A Shahrir; A Yusoff


    This paper presents characteristics of a new catalytic converter (catco) to be used for natural gas fuelled engine. The catco were developed based on catalyst materials consisting of metal oxides such as titanium dioxide (TiO2) and cobalt oxide (CoO) with wire mesh substrate. Both of the catalyst materials (such as TiO2 and CoO) are inexpensive in comparison with conventional catalysts (noble metals) such as palladium or platinum. In addition, the noble metals such as platinum group metals are now identified as human health risk due to their rapid emissions in the environment from various resources like conventional catalytic converter, jewelers and other medical usages. It can be mentioned that the TiO2/CoO based catalytic converter and a new natural gas engine such as compressed natural gas (CNG) direct injection (DI) engine were developed under a research collaboration program. The original engine manufacture catalytic conveter (OEM catco) was tested for comparison purposes. The OEM catco was based on noble metal catalyst with honeycomb ceramic substrate. It is experimentally found that the conversion efficiencies of TiO2/CoO based catalytic converter are 93%, 89% and 82% for NOx, CO and HC emissions respectively. It is calculated that the TiO2/CoO based catalytic converter reduces 24%, 41% and 40% higher NOx, CO and HC emissions in comparison to OEM catco respectively. The objective of this paper is to develop a low-cost three way catalytic converter to be used with the newly developed CNG-DI engine. Detailed review on catalytic converter, low-cost catalytic converter development characteristics and CNGDI engine test results have been presented with discussions.

  11. Catalytic converter with thermoelectric generator

    Energy Technology Data Exchange (ETDEWEB)

    Parise, R.J.


    The unique design of an electrically heated catalyst (EHC) and the inclusion of an ECO valve in the exhaust of an internal combustion engine will meet the strict new emission requirements, especially at vehicle cold start, adopted by several states in this country as well as in Europe and Japan. The catalytic converter (CC) has been a most useful tool in pollution abatement for the automobile. But the emission requirements are becoming more stringent and, along with other improvements, the CC must be improved to meet these new standards. Coupled with the ECO valve, the EHC can meet these new emission limits. In an internal combustion engine vehicle (ICEV), approximately 80% of the energy consumed leaves the vehicle as waste heat: out the tail pipe, through the radiator, or convected/radiated off the engine. Included with the waste heat out the tail pipe are the products of combustion which must meet strict emission requirements. The design of a new CC is presented here. This is an automobile CC that has the capability of producing electrical power and reducing the quantity of emissions at vehicle cold start, the Thermoelectric Catalytic Power Generator. The CC utilizes the energy of the exothermic reactions that take place in the catalysis substrate to produce electrical energy with a thermoelectric generator. On vehicle cold start, the thermoelectric generator is used as a heat pump to heat the catalyst substrate to reduce the time to catalyst light-off. Thus an electrically heated catalyst (EHC) will be used to augment the abatement of tail pipe emissions. Included with the EHC in the exhaust stream of the automobile is the ECO valve. This valve restricts the flow of pollutants out the tail pipe of the vehicle for a specified amount of time until the EHC comes up to operating temperature. Then the ECO valve opens and allows the full exhaust, now treated by the EHC, to leave the vehicle.

  12. The evolution of catalytic function (United States)

    Maurel, Marie-Christine; Ricard, Jacques


    It is very likely that the main driving force of enzyme evolution is the requirement to improve catalytic and regulatory efficiency which results from the intrinsic performance as well as from the spatial and functional organization of enzymes in living cells. Kinetic co-operativity may occur in simple monomeric proteins if they display “slow” conformational transitions, at the cost of catalytic efficiency. Oligomeric enzymes on the other hand can be both efficient and co-operative. We speculate that the main reason for the emergence of co-operative oligomeric enzymes is the need for catalysts that are both cooperative and efficient. As it is not useful for an enzyme to respond to a change of substrate concentration in a complex kinetic way, the emergence of symmetry has its probable origin in a requirement for “functional simplicity”. In a living cell, enzyme are associated with other macromolecules and membranes. The fine tuning of their activity may also be reached through mutations of the microenvironment. Our hypothesis is that these mutations are related to the vectorial transport of molecules, to achieve the hysteresis loops of enzyme reactions generated by the coupling of reaction and diffusion, through the co-operativity brought about by electric interactions between a charged substrate and a membrane, and last but not least, through oscillations. As the physical origins of these effects are very simple and do not require complex molecular devices, it is very likely that the functional advantage generated by the spatial and functional organization of enzyme molecules within the cell have appeared in prebiotic catalysis or very early during the primeval stages of biological evolution. We shall began this paper by presenting the nature of the probable earliest catalysts in the RNA world.

  13. Structure and function of C-terminal catalytic region of pasteurella multocida toxin

    International Nuclear Information System (INIS)

    Pasteurella multocida toxin (PMT) is one of virulence factors responsible for the pathogenesis in some Pasteurellosis. We determined the crystal structure of the C-terminal region of PMT (C-PMT), which carries an intracellularly active moiety. The overall structure of C-PMT displays three different domains designated C1, C2 and C3. We found in the C3 domain the Cys-His-Asp catalytic triad that is organized only when the Cys is released from a disulfide bond. The steric alignment of the triad corresponded well to that of papain or other enzymes carrying the Cys-His-Asp triad. Our results demonstrate that PMT is an enzymatic toxin carrying the cysteine-protease like catalytic triad, which is organized only under reducing conditions. (author)

  14. Revolutionary systems for catalytic combustion and diesel catalytic particulate traps.

    Energy Technology Data Exchange (ETDEWEB)

    Stuecker, John Nicholas; Witze, Peter O.; Ferrizz, Robert Matthew; Cesarano, Joseph, III; Miller, James Edward


    This report is a summary of an LDRD project completed for the development of materials and structures conducive to advancing the state of the art for catalyst supports and diesel particulate traps. An ancillary development for bio-medical bone scaffolding was also realized. Traditionally, a low-pressure drop catalyst support, such as a ceramic honeycomb monolith, is used for catalytic reactions that require high flow rates of gases at high-temperatures. A drawback to the traditional honeycomb monoliths under these operating conditions is poor mass transfer to the catalyst surface in the straight-through channels. ''Robocasting'' is a unique process developed at Sandia National Laboratories that can be used to manufacture ceramic monoliths with alternative 3-dimensional geometries, providing tortuous pathways to increase mass transfer while maintaining low-pressure drops. These alternative 3-dimensional geometries may also provide a foundation for the development of self-regenerating supports capable of trapping and combusting soot particles from a diesel engine exhaust stream. This report describes the structures developed and characterizes the improved catalytic performance that can result. The results show that, relative to honeycomb monolith supports, considerable improvement in mass transfer efficiency is observed for robocast samples synthesized using an FCC-like geometry of alternating rods. Also, there is clearly a trade-off between enhanced mass transfer and increased pressure drop, which can be optimized depending on the particular demands of a given application. Practical applications include the combustion of natural gas for power generation, production of syngas, and hydrogen reforming reactions. The robocast lattice structures also show practicality for diesel particulate trapping. Preliminary results for trapping efficiency are reported as well as the development of electrically resistive lattices that can regenerate the structure

  15. Frustratingly Easy Domain Adaptation

    CERN Document Server

    Daumé, Hal


    We describe an approach to domain adaptation that is appropriate exactly in the case when one has enough ``target'' data to do slightly better than just using only ``source'' data. Our approach is incredibly simple, easy to implement as a preprocessing step (10 lines of Perl!) and outperforms state-of-the-art approaches on a range of datasets. Moreover, it is trivially extended to a multi-domain adaptation problem, where one has data from a variety of different domains.



    Isabel Negro Alousque


    Much of the lexis of a language has a cultural referent and is thus specific to a speech community. The meaning of culturally marked words is often difficult to grasp without some cultural knowledge and poses translation problems, particularly when the words are associated with cultural domains (Nida, 2001). In the present paper we focus on the French cultural domain of cooking. After outlining the elements of the domain, we analyse the difficulties in translating the lexical units from the d...

  17. Visualizing latent domain knowledge


    Chen, C.; Kuljis, J; Paul, RJ


    Knowledge discovery and data mining commonly rely on finding salient patterns of association from a vast amount of data. Traditional citation analysis of scientific literature draws insights from strong citation patterns. Latent domain knowledge, in contrast to the mainstream domain knowledge, often consists of highly relevant but relatively infrequently cited scientific works. Visualizing latent domain knowledge presents a significant challenge to knowledge discovery and quantitative studies...

  18. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. (United States)

    Boudvillain, M; Pyle, A M


    Group II introns are self-splicing RNA molecules that are of considerable interest as ribozymes, mobile genetic elements and examples of folded RNA. Although these introns are among the most common ribozymes, little is known about the chemical and structural determinants for their reactivity. By using nucleotide analog interference mapping (NAIM), it has been possible to identify the nucleotide functional groups (Rp phosphoryls, 2'-hydroxyls, guanosine exocyclic amines, adenosine N7 and N6) that are most important for composing the catalytic core of the intron. The majority of interference effects occur in clusters located within the two catalytically essential Domains 1 and 5 (D1 and D5). Collectively, the NAIM results indicate that key tetraloop-receptor interactions display a specific chemical signature, that the epsilon-epsilon' interaction includes an elaborate array of additional features and that one of the most important core structures is an uncharacterized three-way junction in D1. By combining NAIM with site-directed mutagenesis, a new tertiary interaction, kappa-kappa', was identified between this region and the most catalytically important section of D5, adjacent to the AGC triad in stem 1. Together with the known zeta-zeta' interaction, kappa-kappa' anchors D5 firmly into the D1 scaffold, thereby presenting chemically essential D5 functionalities for participation in catalysis. PMID:9843513

  19. A non-stationary problem coupling PDEs and ODEs modelizing an automotive catalytic converter


    Hoernel, J. -D.


    In this paper we prove the existence and uniqueness of the solution of a non-stationary problem that modelizes the behaviour of the concentrations and the temperature of gases going through a cylindrical passage of an automotive catalytic converter. This problem couples parabolic partial differential equations in a domain with one parabolic partial differential equation and some ordinary differential equations on a part of its boundary.

  20. Quasiparticles near domain walls in hexagonal superconductors (United States)

    Mukherjee, S. P.; Samokhin, K. V.


    We calculate the energy spectrum of quasiparticles trapped by a domain wall separating different time-reversal symmetry-breaking ground states in a hexagonal superconductor, such as UPt3. The bound-state energy is found to be strongly dependent on the gap symmetry, the domain-wall orientation, the quasiparticle's direction of semiclassical propagation, and the phase difference between the domains. We calculate the corresponding density of states and show how one can use its prominent features, in particular, the zero-energy singularity, to distinguish between different pairing symmetries.

  1. Structure-based identification of catalytic residues. (United States)

    Yahalom, Ran; Reshef, Dan; Wiener, Ayana; Frankel, Sagiv; Kalisman, Nir; Lerner, Boaz; Keasar, Chen


    The identification of catalytic residues is an essential step in functional characterization of enzymes. We present a purely structural approach to this problem, which is motivated by the difficulty of evolution-based methods to annotate structural genomics targets that have few or no homologs in the databases. Our approach combines a state-of-the-art support vector machine (SVM) classifier with novel structural features that augment structural clues by spatial averaging and Z scoring. Special attention is paid to the class imbalance problem that stems from the overwhelming number of non-catalytic residues in enzymes compared to catalytic residues. This problem is tackled by: (1) optimizing the classifier to maximize a performance criterion that considers both Type I and Type II errors in the classification of catalytic and non-catalytic residues; (2) under-sampling non-catalytic residues before SVM training; and (3) during SVM training, penalizing errors in learning catalytic residues more than errors in learning non-catalytic residues. Tested on four enzyme datasets, one specifically designed by us to mimic the structural genomics scenario and three previously evaluated datasets, our structure-based classifier is never inferior to similar structure-based classifiers and comparable to classifiers that use both structural and evolutionary features. In addition to the evaluation of the performance of catalytic residue identification, we also present detailed case studies on three proteins. This analysis suggests that many false positive predictions may correspond to binding sites and other functional residues. A web server that implements the method, our own-designed database, and the source code of the programs are publicly available at∼meshi/functionPrediction. PMID:21491495

  2. Key parameters controlling the performance of catalytic motors (United States)

    Esplandiu, Maria J.; Afshar Farniya, Ali; Reguera, David


    The development of autonomous micro/nanomotors driven by self-generated chemical gradients is a topic of high interest given their potential impact in medicine and environmental remediation. Although impressive functionalities of these devices have been demonstrated, a detailed understanding of the propulsion mechanism is still lacking. In this work, we perform a comprehensive numerical analysis of the key parameters governing the actuation of bimetallic catalytic micropumps. We show that the fluid motion is driven by self-generated electro-osmosis where the electric field originates by a proton current rather than by a lateral charge asymmetry inside the double layer. Hence, the surface potential and the electric field are the key parameters for setting the pumping strength and directionality. The proton flux that generates the electric field stems from the proton gradient induced by the electrochemical reactions taken place at the pump. Surprisingly the electric field and consequently the fluid flow are mainly controlled by the ionic strength and not by the conductivity of the solution, as one could have expected. We have also analyzed the influence of the chemical fuel concentration, electrochemical reaction rates, and size of the metallic structures for an optimized pump performance. Our findings cast light on the complex chemomechanical actuation of catalytic motors and provide important clues for the search, design, and optimization of novel catalytic actuators.

  3. Key parameters controlling the performance of catalytic motors. (United States)

    Esplandiu, Maria J; Afshar Farniya, Ali; Reguera, David


    The development of autonomous micro/nanomotors driven by self-generated chemical gradients is a topic of high interest given their potential impact in medicine and environmental remediation. Although impressive functionalities of these devices have been demonstrated, a detailed understanding of the propulsion mechanism is still lacking. In this work, we perform a comprehensive numerical analysis of the key parameters governing the actuation of bimetallic catalytic micropumps. We show that the fluid motion is driven by self-generated electro-osmosis where the electric field originates by a proton current rather than by a lateral charge asymmetry inside the double layer. Hence, the surface potential and the electric field are the key parameters for setting the pumping strength and directionality. The proton flux that generates the electric field stems from the proton gradient induced by the electrochemical reactions taken place at the pump. Surprisingly the electric field and consequently the fluid flow are mainly controlled by the ionic strength and not by the conductivity of the solution, as one could have expected. We have also analyzed the influence of the chemical fuel concentration, electrochemical reaction rates, and size of the metallic structures for an optimized pump performance. Our findings cast light on the complex chemomechanical actuation of catalytic motors and provide important clues for the search, design, and optimization of novel catalytic actuators. PMID:27036470

  4. Development of Catalytic Cooking Plates

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, Anna-Karin; Silversand, Fredrik [CATATOR AB, Lund (Sweden); Tena, Emmanuel; Berger, Marc [Gaz de France (France)


    Gas catalytic combustion for gas stoves or cooking plates (closed catalytic burner system with ceramic plates) is a very promising technique in terms of ease of cleaning, power modulation and emissions. Previous investigations show that wire mesh catalysts, prepared and supplied by Catator AB (CAT), seem to be very well suited for such applications. Beside significantly reducing the NOx-emissions, these catalysts offer important advantages such as good design flexibility, low pressure drop and high heat transfer capacity, where the latter leads to a quick thermal response. Prior to this project, Gaz de France (GdF) made a series of measurements with CAT's wire mesh catalysts in their gas cooking plates and compared the measured performance with similar results obtained with theirs cordierite monolith catalysts. Compared to the monolith catalyst, the wire mesh catalyst was found to enable very promising results with respect to both emission levels (<10 mg NO{sub x} /kWh, <5 mg CO/kWh) and life-time (>8000 h vs. 700 h at 200 kW/m{sup 2}). It was however established that the radiation and hence, the thermal efficiency of the cooking plate, was significantly less than is usually measured in combination with the monolith (15 % vs. 32 %). It was believed that the latter could be improved by developing new burner designs based on CAT's wire mesh concept. As a consequence, a collaboration project between GdF, CAT and the Swedish Gas Technology AB was created. This study reports on the design, the construction and the evaluation of new catalytic burners, based on CAT's wire mesh catalysts, used for the combustion of natural gas in gas cooking stoves. The evaluation of the burners was performed with respect to key factors such as thermal efficiency, emission quality and pressure drop, etc, by the use of theoretical simulations and experimental tests. Impacts of parameters such as the the wire mesh number, the wire mesh structure (planar or folded), the

  5. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Directory of Open Access Journals (Sweden)

    Julien Robert-Paganin

    Full Text Available FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686: one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  6. Catalytic reaction in confined flow channel

    Energy Technology Data Exchange (ETDEWEB)

    Van Hassel, Bart A.


    A chemical reactor comprises a flow channel, a source, and a destination. The flow channel is configured to house at least one catalytic reaction converting at least a portion of a first nanofluid entering the channel into a second nanofluid exiting the channel. The flow channel includes at least one turbulating flow channel element disposed axially along at least a portion of the flow channel. A plurality of catalytic nanoparticles is dispersed in the first nanofluid and configured to catalytically react the at least one first chemical reactant into the at least one second chemical reaction product in the flow channel.

  7. A segmental labeling strategy for unambiguous determination of domain–domain interactions of large multi-domain proteins

    International Nuclear Information System (INIS)

    NMR structural determination of large multi-domain proteins is a challenging task due to significant spectral overlap with a particular difficulty in unambiguous identification of domain–domain interactions. Segmental labeling is a NMR strategy that allows for isotopically labeling one domain and leaves the other domain unlabeled. This significantly simplifies spectral overlaps and allows for quick identification of domain–domain interaction. Here, a novel segmental labeling strategy is presented for detection of inter-domain NOEs. To identify domain–domain interactions in human apolipoprotein E (apoE), a multi-domain, 299-residues α-helical protein, on-column expressed protein ligation was utilized to generate a segmental-labeled apoE samples in which the N-terminal (NT-) domain was 2H(99%)/15N-labeled whereas the C-terminal (CT-) domain was either 15N- or 15N/13C-labeled. 3-D 15N-edited NOESY spectra of these segmental-labeled apoE samples allow for direct observation of the inter-domain NOEs between the backbone amide protons of the NT-domain and the aliphatic protons of the CT-domain. This straightforward approach permits unambiguous identification of 78 inter-domain NOEs, enabling accurate definition of the relative positions of both the NT- and the CT-domains and determination of the NMR structure of apoE.

  8. Topological Domain Theory


    Battenfeld, Ingo


    This thesis presents Topological Domain Theory as a powerful and flexible framework for denotational semantics. Topological Domain Theory models a wide range of type constructions and can interpret many computational features. Furthermore, it has close connections to established frameworks for denotational semantics, as well as to well-studied mathematical theories, such as topology and computable analysis.

  9. Modeling Protein Domain Function (United States)

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth


    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  10. Domain Walls on Singularities

    CERN Document Server

    Halyo, Edi


    We describe domain walls that live on $A_2$ and $A_3$ singularities. The walls are BPS if the singularity is resolved and non--BPS if it is deformed and fibered. We show that these domain walls may interpolate between vacua that support monopoles and/or vortices.

  11. Hydrogen mitigation by catalytic recombiners and ignition during severe accidents

    International Nuclear Information System (INIS)

    A large amount of hydrogen is expected to be released within a large dry containment of a PWR shortly after the onset of a severe accident, leading to core melting. According to local gas concentrations, turbulence and structural configurations within the containment, the released hydrogen can reach the boundary of deflagration or under certain conditions cause local detonations threatening the containment integrity. During the last few years, several concepts of mitigation have been developed to limit the hydrogen concentrations and extensive efforts have been given to investigate the use of catalytic recombiners as well as the use of deliberate ignition within the contemplated framework of a 'Dual-concept'. Although the recent recommendation of the German Reactor Safety Commission (RSK) foresees the sole application of catalytic recombiners to remove hydrogen during severe accident, a review is planned within two years for the partial and directed additional application of early ignitions or post dilution of the atmosphere of the compartments in conjunction with the recombiners installed. This presentation will review the results of large number of experiments performed both in small scale and large scale to qualify the recombiners. It is also the subject of the presentation to address the requirements for proper and secure functioning of the catalyzers under the existing boundary conditions during the severe accidents. These requirements ask for measures, starting from the proper selection of catalysts, multi purposed catalytic devices and their protection against contamination during the standby condition as well as against aerosol deposition and surface poisoning during the propagation of an accident. A short review of the results to large scale experiments with the combined application of catalytic devices and igniters form also a part of this presentation. (author). 8 refs., 2 tabs., 7 figs

  12. Catalytic Chemistry on Oxide Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Asthagiri, Aravind; Dixon, David A.; Dohnalek, Zdenek; Kay, Bruce D.; Rodriquez, Jose A.; Rousseau, Roger J.; Stacchiola, Dario; Weaver, Jason F.


    Metal oxides represent one of the most important and widely employed materials in catalysis. Extreme variability of their chemistry provides a unique opportunity to tune their properties and to utilize them for the design of highly active and selective catalysts. For bulk oxides, this can be achieved by varying their stoichiometry, phase, exposed surface facets, defect, dopant densities and numerous other ways. Further, distinct properties from those of bulk oxides can be attained by restricting the oxide dimensionality and preparing them in the form of ultrathin films and nanoclusters as discussed throughout this book. In this chapter we focus on demonstrating such unique catalytic properties brought by the oxide nanoscaling. In the highlighted studies planar models are carefully designed to achieve minimal dispersion of structural motifs and to attain detailed mechanistic understanding of targeted chemical transformations. Detailed level of morphological and structural characterization necessary to achieve this goal is accomplished by employing both high-resolution imaging via scanning probe methods and ensemble-averaged surface sensitive spectroscopic methods. Three prototypical examples illustrating different properties of nanoscaled oxides in different classes of reactions are selected.

  13. Halogen Chemistry on Catalytic Surfaces. (United States)

    Moser, Maximilian; Pérez-Ramírez, Javier


    Halogens are key building blocks for the manufacture of high-value products such as chemicals, plastics, and pharmaceuticals. The catalytic oxidation of HCl and HBr is an attractive route to recover chlorine and bromine in order to ensure the sustainability of the production processes. Very few materials withstand the high corrosiveness and the strong exothermicity of the reactions and among them RuO2 and CeO2-based catalysts have been successfully applied in HCl oxidation. The search for efficient systems for HBr oxidation was initiated by extrapolating the results of HCl oxidation based on the chemical similarity of these reactions. Interestingly, despite its inactivity in HCl oxidation, TiO2 was found to be an outstanding HBr oxidation catalyst, which highlighted that the latter reaction is more complex than previously assumed. Herein, we discuss the results of recent comparative studies of HCl and HBr oxidation on both rutile-type (RuO2, IrO2, and TiO2) and ceria-based catalysts using a combination of advanced experimental and theoretical methods to provide deeper molecular-level understanding of the reactions. This knowledge aids the design of the next-generation catalysts for halogen recycling. PMID:27131113

  14. Vacuum-insulated catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Benson, David K. (Golden, CO)


    A catalytic converter has an inner canister that contains catalyst-coated substrates and an outer canister that encloses an annular, variable vacuum insulation chamber surrounding the inner canister. An annular tank containing phase-change material for heat storage and release is positioned in the variable vacuum insulation chamber a distance spaced part from the inner canister. A reversible hydrogen getter in the variable vacuum insulation chamber, preferably on a surface of the heat storage tank, releases hydrogen into the variable vacuum insulation chamber to conduct heat when the phase-change material is hot and absorbs the hydrogen to limit heat transfer to radiation when the phase-change material is cool. A porous zeolite trap in the inner canister absorbs and retains hydrocarbons from the exhaust gases when the catalyst-coated substrates and zeolite trap are cold and releases the hydrocarbons for reaction on the catalyst-coated substrate when the zeolite trap and catalyst-coated substrate get hot.

  15. Structure-guided Mutational Analysis of the Nucleotidyltransferase Domain of Escherichia coli DNA Ligase (LigA)*


    Wang, Li Kai; Zhu, Hui; Shuman, Stewart


    NAD+-dependent DNA ligases (LigA) are ubiquitous in bacteria, where they are essential for growth and present attractive targets for antimicrobial drug discovery. LigA has a distinctive modular structure in which a nucleotidyltransferase catalytic domain is flanked by an upstream NMN-binding module and by downstream OB-fold, zinc finger, helix-hairpin-helix, and BRCT domains. Here we conducted a structure-function analysis of the nucleotidyltransferase domain of Escher...

  16. Phosphorylation of the Kinase Homology Domain Is Essential for Activation of the A-Type Natriuretic Peptide Receptor


    Potter, Lincoln R.; Hunter, Tony


    Natriuretic peptide receptor A (NPR-A) is the biological receptor for atrial natriuretic peptide (ANP). Activation of the NPR-A guanylyl cyclase requires ANP binding to the extracellular domain and ATP binding to a putative site within its cytoplasmic region. The allosteric interaction of ATP with the intracellular kinase homology domain (KHD) is hypothesized to derepress the carboxyl-terminal guanylyl cyclase catalytic domain, resulting in the synthesis of the second messenger, cyclic GMP. H...

  17. Catalytic models developed through social work

    DEFF Research Database (Denmark)

    Jensen, Mogens


    The article develops the concept of catalytic processes in relation to social work with adolescents in an attempt to both reach a more nuanced understanding of social work and at the same time to develop the concept of catalytic processes in psychology. The social work is pedagogical treatment of...... adolescents placed in out-of-home care and is characterised using three situated cases as empirical data. Afterwards the concept of catalytic processes is briefly presented and then applied in an analysis of pedagogical treatment in the three cases. The result is a different conceptualisation of the social...... work with new possibilities of development of the work, but also suggestions for development of the concept of catalytic processes....

  18. Catalytic converters as a source of platinum

    Directory of Open Access Journals (Sweden)

    A. Fornalczyk


    Full Text Available The increase of Platinum Group Metals demand in automotive industry is connected with growing amount of cars equipped with the catalytic converters. The paper presents the review of available technologies during recycling process. The possibility of removing platinum from the used catalytic converters applying pyrometallurgical and hyrdometallurgical methods were also investigated. Metals such as Cu, Pb, Ca, Mg, Cd were used in the pyrometallurgical research (catalytic converter was melted with Cu, Pb and Ca or Mg and Cd vapours were blown through the whole carrier. In hydrometallurgical research catalytic converters was dissolved in aqua regia. Analysis of Pt contents in the carrier before and after the process was performed by means of atomic absorption spectroscopy. Obtained result were discussed.

  19. WW or WoW: the WW domains in a union of bliss. (United States)

    Sudol, Marius; Recinos, Claudia C; Abraczinskas, Jennifer; Humbert, Jasper; Farooq, Amjad


    WW domains are small protein modules that recognize proline-rich peptide motifs or phosphorylated-serine/threonine proline sites in cognate proteins. Within host proteins these modules are joined to other protein domains or to a variety of catalytic domains acting together as adaptors or targeting anchors of enzymes. An important aspect of signaling by WW domains is their ability to recognize their cognate ligands in tandem. Tandem WW domains not only act in a synergistic manner but also appear to chaperone the function of each other. In this review, we focus on structure, function, and mechanism of the tandem WW domains co-operativity as well as independent actions. We emphasize here the implications of tandem arrangement and cooperative function of the domains for signaling pathways. PMID:16393779

  20. A catalytic approach to estimate the redox potential of heme-peroxidases

    International Nuclear Information System (INIS)

    The redox potential of heme-peroxidases varies according to a combination of structural components within the active site and its vicinities. For each peroxidase, this redox potential imposes a thermodynamic threshold to the range of oxidizable substrates. However, the instability of enzymatic intermediates during the catalytic cycle precludes the use of direct voltammetry to measure the redox potential of most peroxidases. Here we describe a novel approach to estimate the redox potential of peroxidases, which directly depends on the catalytic performance of the activated enzyme. Selected p-substituted phenols are used as substrates for the estimations. The results obtained with this catalytic approach correlate well with the oxidative capacity predicted by the redox potential of the Fe(III)/Fe(II) couple

  1. Kinetic catalytic studies of scorpion's hemocyanin

    International Nuclear Information System (INIS)

    Hemocyanins are copper proteins which function as oxygen carriers in the haemolymph of Molluscs and Arthropods. They possess enzymatic properties: peroxidatic and catalatic activities, although they have neither iron nor porphyrin ring at the active site. The kinetics of the catalytic reaction is described. The reaction of superoxide anion with hemocyanin has been studied using pulse radiolysis at pH 9. The catalytic rate constant is 3.5 X 107 mol-1.l.s-1

  2. Characterization of Aqueous Peroxomolybdates with Catalytic Applicability


    Taube, Fabian


    Abstract This thesis is a summary of five papers, containing equilibrium and structure studies of aqueous molybdate and peroxomolybdate species. Some of the peroxomolybdate species have also been studied in terms of their dynamic and catalytic properties. The primary objective was to characterize species with potential catalytic activity, with emphasis on thebleach process of kraft pulp. For this, potentiometry, EXAFS and 17O, 31P, 1H and 95 Mo NMR have been used. The molybdate speciation in ...



    Vedi V.E.; Rovenskii A.I.


    The design and purpose of the basic units of the mobile waste processing complex “MPK” are described. Experimental data of catalytic purification of exhaust gases are presented. Experimental data on catalytic clearing of final gases of a designed mobile incinerator plant are shown. It is defined, that concentrating of parasitic bridging in waste gases of the complex are considerably smaller, rather than allowed by normative documents.


    Directory of Open Access Journals (Sweden)

    Vedi V.E.


    Full Text Available The design and purpose of the basic units of the mobile waste processing complex “MPK” are described. Experimental data of catalytic purification of exhaust gases are presented. Experimental data on catalytic clearing of final gases of a designed mobile incinerator plant are shown. It is defined, that concentrating of parasitic bridging in waste gases of the complex are considerably smaller, rather than allowed by normative documents.

  5. Temperature Modulation of a Catalytic Gas Sensor


    Eike Brauns; Eva Morsbach; Sebastian Kunz; Marcus Baeumer; Walter Lang


    The use of catalytic gas sensors usually offers low selectivity, only based on their different sensitivities for various gases due to their different heats of reaction. Furthermore, the identification of the gas present is not possible, which leads to possible misinterpretation of the sensor signals. The use of micro-machined catalytic gas sensors offers great advantages regarding the response time, which allows advanced analysis of the sensor response. By using temperature modulation, additi...

  6. Catalytic ammonia oxidation to nitrogen (I) oxide




    The process of synthesis of nitrous oxide by low-temperature catalytical oxidation of NH has been investigated for organic synthesis. The investigation has been carried out by the stage separation approach with NH oxidation occurring in several reaction zones, which characterized by different catalytic conditions. The selectivity for N₂O was 92–92,5 % at the ammonia conversion of 98–99.5 % in the optimal temperature range.

  7. Compiling Dictionaries Using Semantic Domains*

    Directory of Open Access Journals (Sweden)

    Ronald Moe


    Full Text Available

    Abstract: The task of providing dictionaries for all the world's languages is prodigious, re-quiring efficient techniques. The text corpus method cannot be used for minority languages lacking texts. To meet the need, the author has constructed a list of 1 600 semantic domains, which he has successfully used to collect words. In a workshop setting, a group of speakers can collect as many as 17 000 words in ten days. This method results in a classified word list that can be efficiently expanded into a full dictionary. The method works because the mental lexicon is a giant web or-ganized around key concepts. A semantic domain can be defined as an important concept together with the words directly related to it by lexical relations. A person can utilize the mental web to quickly jump from word to word within a domain. The author is developing a template for each domain to aid in collecting words and in de-scribing their semantics. Investigating semantics within the context of a domain yields many in-sights. The method permits the production of both alphabetically and semantically organized dic-tionaries. The list of domains is intended to be universal in scope and applicability. Perhaps due to universals of human experience and universals of linguistic competence, there are striking simi-larities in various lists of semantic domains developed for languages around the world. Using a standardized list of domains to classify multiple dictionaries opens up possibilities for cross-lin-guistic research into semantic and lexical universals.


    Opsomming: Samestelling van woordeboeke deur gebruikmaking van se-mantiese domeine. Die taak van die voorsiening van woordeboeke aan al die tale van die wêreld is geweldig en vereis doeltreffende tegnieke. Die

  8. Safe domain and elementary geometry

    CERN Document Server

    Richard, J M


    A classical problem of mechanics involves a projectile fired from a given point with a given velocity whose direction is varied. This results in a family of trajectories whose envelope defines the border of a 'safe' domain. In the simple cases of a constant force, harmonic potential and Kepler or Coulomb motion, the trajectories are conic curves whose envelope in a plane is another conic section which can be derived either by simple calculus or by geometrical considerations. The case of harmonic forces reveals a subtle property of the maximal sum of distances within an ellipse.

  9. Feature-Level Domain Adaptation


    Kouw, Wouter M.; Krijthe, Jesse H.; Loog, Marco; van der Maaten, Laurens J. P.


    Domain adaptation is the supervised learning setting in which the training and test data originate from different domains: the so-called source and target domains. In this paper, we propose and study a domain adaption approach, called feature-level domain adaptation (flda), that models the dependence between two domains by means of a feature-level transfer distribution. The domain adapted classifier is trained by minimizing the expected loss under this transfer distribution. Our empirical eva...

  10. Preparation and Catalytic Oxidation Activity on 2-mercaptoethanol of a Novel Catalytic Cellulose Fibres

    Institute of Scientific and Technical Information of China (English)

    YAO Yu-yuan; LI Ying-jie; CHEN Wen-xing; Lü Wang-yang; Lü Su-fang; XU Min-hong; LIU Fan


    Cobalt tetra(N-carbonylacylic) aminophthalocyanine was supported on cellulose fibres by graft reaction to obtain a novel polymer catalyst, catalytic cellulose fibres (CCF),and the optimal supporting conditions were pH = 6, 80℃,t = 120 min. The catalytic oxidation activity of CCF towards oxidation of 2-mereaptoethanol (MEA) in aqueous solution was investigated. The experimental results demonstrated that CCF had good catalytic oxidation activity on MEA at room temperature, causing no secondary pollution and remaining efficient for the repetitive tests with no obvious decrease of catalytic activity.

  11. Macrodomains: Structure, Function, Evolution, and Catalytic Activities. (United States)

    Rack, Johannes Gregor Matthias; Perina, Dragutin; Ahel, Ivan


    Recent developments indicate that macrodomains, an ancient and diverse protein domain family, are key players in the recognition, interpretation, and turnover of ADP-ribose (ADPr) signaling. Crucial to this is the ability of macrodomains to recognize ADPr either directly, in the form of a metabolic derivative, or as a modification covalently bound to proteins. Thus, macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. Their importance is further indicated by the fact that dysregulation or mutation of a macrodomain is associated with several diseases, including cancer, developmental defects, and neurodegeneration. In this review, we summarize the current insights into macrodomain evolution and how this evolution influenced their structural and functional diversification. We highlight some aspects of macrodomain roles in pathobiology as well as their emerging potential as therapeutic targets. PMID:26844395

  12. Low efficiency deasphalting and catalytic cracking

    International Nuclear Information System (INIS)

    This patent describes a process for converting an asphaltene and metals containing heavy hydrocarbon feed to lighter, more valuable products the metals comprising Ni and V. It comprises: demetallizing the feed by deasphalting the feed in a solvent deasphalting means operating at solvent deasphalting conditions including a solvent: feed volume ratio of about 1:1 to 4:1, using a solvent selected from the group of C4 to 400 degrees F. hydrocarbons and mixtures thereof; recovering from the solvent rich fraction a demetallized oil intermediate product, having a boiling range and containing at least 10 wt.% of the asphaltenes, and 5 to 30% of the Ni and V, and at least 10 wt.% of the solvent present in the solvent rich phase produced in the deasphalting means; catalytically cracking the demetallized oil intermediate product in a catalytic cracking means operating at catalytic cracking conditions to produce a catalytically cracked product vapor fraction having a lower boiling range than the boiling range of the demetallized oil intermediate product; and fractionating the catalytically cracked product in a fractionation means to produce catalytically cracked product fractions

  13. A Low Affinity Ground State Conformation for the Dynein Microtubule Binding Domain*


    McNaughton, Lynn; Tikhonenko, Irina; Banavali, Nilesh K.; LeMaster, David M.; Koonce, Michael P.


    Dynein interacts with microtubules through a dedicated binding domain that is dynamically controlled to achieve high or low affinity, depending on the state of nucleotide bound in a distant catalytic pocket. The active sites for microtubule binding and ATP hydrolysis communicate via conformational changes transduced through a ∼10-nm length antiparallel coiled-coil stalk, which connects the binding domain to the roughly 300-kDa motor core. Recently, an x-ray structure of the murine cytoplasmic...

  14. Outer domains of integrase within retroviral intasomes are dispensible for catalysis of DNA integration. (United States)

    Li, Min; Lin, Shiqiang; Craigie, Robert


    Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) comprising a pair of viral DNA ends synapsed by a tetramer of integrase. Current integrase inhibitors act on intasomes rather than free integrase protein. Structural and functional studies of intasomes are essential to understand their mechanism of action and how the virus can escape by mutation. To date, prototype foamy virus (PFV) is the only retrovirus for which high-resolution structures of intasomes have been determined. In the PFV intasome structure, only the core domains of the outer subunits are ordered; the N-terminal domain, C-terminal domain, and N-terminal extension domain are disordered. Are these "missing domains" required for function or are they dispensable? We have devised a strategy to assemble "hetero-intasomes" in which the outer domains are not present as a tool to assess the functional role of the missing domains for catalysis of integration. We find that the disordered domains of outer subunits are not required for intasome assembly or catalytic activity as catalytic core domains can substitute for the outer subunits in the case of both PFV and HIV-1 intasomes. PMID:26537415

  15. Domain-Specific Multimodeling

    DEFF Research Database (Denmark)

    Hessellund, Anders

    Enterprise systems are complex artifacts. They are hard to build, manage, understand, and evolve. Existing software development paradigms fail to properly address challenges such as system size, domain complexity, and software evolution when development is scaled to enterprise systems. We propose...... domain-specific multimodeling as a development paradigm to tackle these challenges in a language-oriented manner. The different concerns of a system are conceptually separated and made explicit as independent domain-specific languages. This approach increases productivity and quality by raising the...

  16. Distinct functional domains in nesprin-1α and nesprin-2β bind directly to emerin and both interactions are disrupted in X-linked Emery-Dreifuss muscular dystrophy

    International Nuclear Information System (INIS)

    Emerin and specific isoforms of nesprin-1 and -2 are nuclear membrane proteins which are binding partners in multi-protein complexes spanning the nuclear envelope. We report here the characterisation of the residues both in emerin and in nesprin-1α and -2β which are involved in their interaction and show that emerin requires nesprin-1 or -2 to retain it at the nuclear membrane. Using several protein-protein interaction methods, we show that residues 368 to 627 of nesprin-1α and residues 126 to 219 of nesprin-2β, which show high homology to one another, both mediate binding to emerin residues 140-176. This region has previously been implicated in binding to F-actin, β-catenin and lamin A/C suggesting that it is critical for emerin function. Confirmation that these protein domains interact in vivo was shown using GFP-dominant negative assays. Exogenous expression of either of these nesprin fragments in mouse myoblast C2C12 cells displaced endogenous emerin from the nuclear envelope and reduced the targeting of newly synthesised emerin. Furthermore, we are the first to report that emerin mutations which give rise to X-linked Emery-Dreifuss muscular dystrophy, disrupt binding to both nesprin-1α and -2β isoforms, further indicating a role of nesprins in the pathology of Emery-Dreifuss muscular dystrophy

  17. Structural requirements for assembly of dimeric IgA probed by site-directed mutagenesis of J chain and a cysteine residue of the alpha-chain CH2 domain. (United States)

    Krugmann, S; Pleass, R J; Atkin, J D; Woof, J M


    The structural features of J chain required for interaction with IgA in IgA dimer assembly were investigated by coexpression of wild-type and mutant forms of J chain with IgA1 in CHO cells. With wild-type J chain, a mixture of J chain-containing dimers and monomers was secreted. Substitution of Cys14 of J chain with Ser resulted in expression of only monomer IgA covalently associated with J chain. Similarly, mutation of Cys68 to Ser also resulted in expression predominantly of a monomer IgA-J chain species. These results suggest that Cys14 and Cys68 play critical roles in formation of J chain-containing IgA dimers, with each forming a disulfide bridge to an IgA monomer. Substitution of Asn48 with Ala, to prevent attachment of N-linked carbohydrate to J chain, also resulted in markedly reduced dimer assembly, suggesting a requirement for the sugar moiety in J chain function. We also mutated Cys311 on the C alpha2 domain of the IgA heavy chain to Ser. When coexpressed with wild-type J chain, this mutant was still capable of forming dimers, indicating that this residue was not involved in dimerization. Taken together, our results are consistent with an arrangement in which IgA monomers are linked end-to-end with J chain interposed. PMID:9200460

  18. Precipitation and calcination synthesis methods forming nano-sized platinum catalytic particles for methanol and hydrogen oxidation (United States)

    Naidoo, S.; Naidoo, Q.; Musil, E.; Linkov, V.; Vaivars, G.


    Under varying experimental conditions of calcination and precipitation reactions, different particle sizes and levels of platinum on carbon supported (Pt/C) catalysts were obtained. Rapid precipitation following a chemical reaction ensured formation of nano-sized catalytic particles using super-saturated concentrations under controlled conditions was a significant contribution in understanding the synthesis process and how it relates to an increased number of catalytic reaction sites ultimately providing superior electrochemical (EC) activity. These conditions influenced nucleation and growth rates of the catalytic particles. The super-saturation concentrations of the reactants in the reaction vessel played a direct role in producing the desired morphology of the crystallites.

  19. Activation of G Protein-Coupled Receptor Kinase 1 Involves Interactions between Its N-Terminal Region and Its Kinase Domain

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chih-chin; Orban, Tivadar; Jastrzebska, Beata; Palczewski, Krzysztof; Tesmer, John J.G. (Case Western); (Michigan)


    G protein-coupled receptor kinases (GRKs) phosphorylate activated G protein-coupled receptors (GPCRs) to initiate receptor desensitization. In addition to the canonical phosphoacceptor site of the kinase domain, activated receptors bind to a distinct docking site that confers higher affinity and activates GRKs allosterically. Recent mutagenesis and structural studies support a model in which receptor docking activates a GRK by stabilizing the interaction of its 20-amino acid N-terminal region with the kinase domain. This interaction in turn stabilizes a closed, more active conformation of the enzyme. To investigate the importance of this interaction for the process of GRK activation, we first validated the functionality of the N-terminal region in rhodopsin kinase (GRK1) by site-directed mutagenesis and then introduced a disulfide bond to cross-link the N-terminal region of GRK1 with its specific binding site on the kinase domain. Characterization of the kinetic and biophysical properties of the cross-linked protein showed that disulfide bond formation greatly enhances the catalytic efficiency of the peptide phosphorylation, but receptor-dependent phosphorylation, Meta II stabilization, and inhibition of transducin activation were unaffected. These data indicate that the interaction of the N-terminal region with the kinase domain is important for GRK activation but does not dictate the affinity of GRKs for activated receptors.

  20. Catalytic and surface oxidation processes on transition metal surfaces


    Jaatinen, Sampsa


    Transition metals are technologically important catalytic materials. The transition metal catalysts are used for example in petroleum and fertilizer industry. In the car industry the catalytic materials are used in the catalytic converters. Because of the industrial importance the catalytic metals have been widely studied throughout the past decades. Nonetheless, the oxidation mechanisms of small molecules and the effect of alloying to catalytic properties of metals are not fully understood. ...

  1. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)


    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  2. A new and unexpected domain-domain interaction in the AraC protein. (United States)

    Cole, Stephanie Dirla; Schleif, Robert


    An interaction between the dimerization domains and DNA binding domains of the dimeric AraC protein has previously been shown to facilitate repression of the Escherichia coli araBAD operon by AraC in the absence of arabinose. A new interaction between the domains of AraC in the presence of arabinose is reported here, the regulatory consequences of which are unknown. Evidence for the interaction is the following: the dissociation rate of arabinose-bound AraC from half-site DNA is considerably faster than that of free DNA binding domain, and the affinity of the dimerization domains for arabinose is increased when half-site DNA is bound. In addition, an increase in the fluorescence intensity of tryptophan residues located in the arabinose-bound dimerization domain is observed upon binding of half-site DNA to the DNA binding domains. Direct physical evidence of the new domain-domain interaction is demonstrated by chemical crosslinking and NMR experiments. PMID:22383259

  3. Low energy electron imaging of domains and domain walls in magnesium-doped lithium niobate (United States)

    Nataf, G. F.; Grysan, P.; Guennou, M.; Kreisel, J.; Martinotti, D.; Rountree, C. L.; Mathieu, C.; Barrett, N.


    The understanding of domain structures, specifically domain walls, currently attracts a significant attention in the field of (multi)-ferroic materials. In this article, we analyze contrast formation in full field electron microscopy applied to domains and domain walls in the uniaxial ferroelectric lithium niobate, which presents a large 3.8 eV band gap and for which conductive domain walls have been reported. We show that the transition from Mirror Electron Microscopy (MEM – electrons reflected) to Low Energy Electron Microscopy (LEEM – electrons backscattered) gives rise to a robust contrast between domains with upwards (Pup) and downwards (Pdown) polarization, and provides a measure of the difference in surface potential between the domains. We demonstrate that out-of-focus conditions of imaging produce contrast inversion, due to image distortion induced by charged surfaces, and also carry information on the polarization direction in the domains. Finally, we show that the intensity profile at domain walls provides experimental evidence for a local stray, lateral electric field. PMID:27608605

  4. Low energy electron imaging of domains and domain walls in magnesium-doped lithium niobate. (United States)

    Nataf, G F; Grysan, P; Guennou, M; Kreisel, J; Martinotti, D; Rountree, C L; Mathieu, C; Barrett, N


    The understanding of domain structures, specifically domain walls, currently attracts a significant attention in the field of (multi)-ferroic materials. In this article, we analyze contrast formation in full field electron microscopy applied to domains and domain walls in the uniaxial ferroelectric lithium niobate, which presents a large 3.8 eV band gap and for which conductive domain walls have been reported. We show that the transition from Mirror Electron Microscopy (MEM - electrons reflected) to Low Energy Electron Microscopy (LEEM - electrons backscattered) gives rise to a robust contrast between domains with upwards (Pup) and downwards (Pdown) polarization, and provides a measure of the difference in surface potential between the domains. We demonstrate that out-of-focus conditions of imaging produce contrast inversion, due to image distortion induced by charged surfaces, and also carry information on the polarization direction in the domains. Finally, we show that the intensity profile at domain walls provides experimental evidence for a local stray, lateral electric field. PMID:27608605

  5. Visualizing Knowledge Domains. (United States)

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.


    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  6. Conserved Domain Database (CDD) (United States)

    U.S. Department of Health & Human Services — CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.

  7. Flexible time domain averaging technique (United States)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng


    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  8. Aconitase: its source of catalytic protons

    International Nuclear Information System (INIS)

    An ordinary isotope partition experiment was performed to determine the rate of dissociation of the proton from the donor site for the hydration of cis-aconitate. Aconitase in [3H] water was efficiently diluted into well-mixed solutions of cis-aconitate. Citrate and isocitrate that were formed within 2 s were more heavily labeled than could be explained by consideration of an isotope effect in the processing of one proton per enzyme equivalent. Control experiments indicate that mixing was much more rapid than catalytic turnover, ruling out incompletely diluted [3H] water as a significant isotope source. Therefore, it appears that significantly more than one enzyme-bound tritium atom (protons) must have been used in the course of the multiple turnover of the enzyme after the dilution was complete. Isotope incorporation reached values in excess of four proton equivalent as a limit with simple Michaelis dependence on cis-aconitate. From the half-saturation concentration value for trapping, 0.15 mM, the t/sub 1/2/ for exchange of each of these protons with solvent appears to be ∼0.1 s at 00C. The large number of protons trapped seems to suggest the existence of a structurally stabilized pool of protons, or water, that communicates between the active site base and the medium in the hydration of cis-aconitate. The proton abstracted in the dehydration of [3H] citrate is transferred directly to undissociated cis-aconitate to form isocitrate without dilution, or cis-aconitate having dissociated, the tritium passes to the medium, presumably through the pool of bound protons indicated above. All of the citrate-derived protons can be found in isocitrate if cis-aconitate is added in sufficient concentration. Therefore, the abstracted proton dissociates slowly, if at all, from the enzyme in all intermediates except those from which cis-aconitate has dissociated

  9. QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme. (United States)

    Mu, Xia; Zhang, Chunchun; Xu, Dingguo


    Angiotensin-converting enzyme (ACE) converts angiotensin I to angiotensin II and degrades bradykinin and other vasoactive peptides. ACE inhibitors are used to treat diseases such as hypertension and heart failure. It is thus highly desirable to understand the catalytic mechanism of ACE, as this should facilitate the design of more powerful and selective ACE inhibitors. ACE exhibits two different active domains, the C-domain and the N-domain. In this work, we systematically investigated the inhibitor- and substrate-binding patterns in the N-domain of human ACE using a combined quantum mechanical and molecular mechanical approach. The hydrolysis of hippuryl-histidyl-leucine (HHL) as catalyzed by the N-domain of human somatic ACE was explored, and the effects of chloride ion on the overall reaction were also investigated. Two models, one with and one without a chloride ion at the first binding position, were then designed to examine the chloride dependence of inhibitor-substrate binding and the catalytic mechanism. Our calculations indicate that the hydrolysis reaction follows a stepwise general base/general acid catalysis path. The estimated mean free energy barrier height in the two models is about 15.6 kcal/mol, which agrees very well with the experimentally estimated value of 15.8 kcal/mol. Our simulations thus suggest that the N-domain is in a mixed form during ACE-catalyzed hydrolysis, with the single-chloride-ion and the double-chloride-ion forms existing simultaneously. Graphical Abstract Superposition of ACE C- and N- domains. PMID:27184002

  10. Catalytic partial oxidation of pyrolysis oils (United States)

    Rennard, David Carl


    details the catalytic partial oxidation of glycerol without preheat: droplets of glycerol are sprayed directly onto the top of the catalyst bed, where they react autothermally with contact times on the order of tau ≈ 30 ms. The reactive flash volatilization of glycerol results in equilibrium syngas production over Rh-Ce catalysts. In addition, water can be added to the liquid glycerol, resulting in true autothermal reforming. This highly efficient process can increase H2 yields and alter the H2 to CO ratio, allowing for flexibility in syngas quality depending on the purpose. Chapter 5 details the results of a time on stream experiment, in which optimal syngas conditions are chosen. Although conversion is 100% for 450 hours, these experiments demonstrate the deactivation of the catalyst over time. Deactivation is exhibited by decreases in H2 and CO 2 production accompanied by a steady increase in CO and temperature. These results are explained as a loss of water-gas shift equilibration. SEM images suggest catalyst sintering may play a role; EDS indicates the presence of impurities on the catalyst. In addition, the instability of quartz in the reactor is demonstrated by etching, resulting in a hole in the reactor tube at the end of the experiment. These results suggest prevaporization may be desirable in this application, and that quartz is not a suitable material for the reactive flash volatilization of oxygenated fuels. In Chapter 6, pyrolysis oil samples from three sources - poplar, pine, and hardwoods - are explored in the context of catalytic partial oxidation. Lessons derived from the tests with model compounds are applied to reactor design, resulting in the reactive flash vaporization of bio oils. Syngas is successfully produced, though deactivation due to coke and ash deposition keeps H2 below equlibrium. Coke formation is observed on the reactor walls, but is avoided between the fuel injection site and catalyst by increasing the proximity of these in the reactor

  11. Nanoscale domain switching behaviour in polycrystalline ferroelectric thin films

    International Nuclear Information System (INIS)

    We report on the nanoscale domain switching behaviour in polycrystalline tetragonal perovskite lead zirconate titanate (PZT) ferroelectric thin films investigated via piezoresponse force microscopy (PFM). Local domain structures were imaged as a function of varying biasing conditions and spatial location of the tip within 50-100 nm sized grains. Nanoscale piezoresponse images provided direct visual evidence of the complex interplay between electrical and mechanical fields in a polycrystalline system, which causes effects such as correlated switching between the grain of interest and neighbouring grains, ferroelastic domain switching, inhomogeneous piezostrain profiles and domain pinning on very minute length scales. Detailed investigations on mechanisms which induce such domain behaviour are presented

  12. Protein kinase domain of twitchin has protein kinase activity and an autoinhibitory region. (United States)

    Lei, J; Tang, X; Chambers, T C; Pohl, J; Benian, G M


    Twitchin is a 753-kDa polypeptide located in the muscle A-bands of the nematode, Caenorhabditis elegans. It consists of multiple copies of both fibronectin III and immunoglobulin C2 domains and, near the C terminus, a protein kinase domain with greatest homology to the catalytic domains of myosin light chain kinases. We have expressed and purified from Escherichia coli twitchin's protein kinase catalytic core and flanking sequences that do not include fibronectin III and immunoglobulin C2 domains. The protein was shown to phosphorylate a model substrate and to undergo autophosphorylation. The autophosphorylation occurs at a slow rate, attaining a maximum at 3 h with a stoichiometry of about 1.0 mol of phosphate/mol of protein, probably through an intramolecular mechanism. Sequence analysis of proteolytically derived phosphopeptides revealed that autophosphorylation occurred N-terminal to the catalytic core, predominantly at Thr-5910, with possible minor sites at Ser5912 and/or Ser-5913. This portion of twitchin (residues 5890-6268) was also phosphorylated in vitro by protein kinase C in the absence of calcium and phosphotidylserine, but not by cAMP-dependent protein kinase. By comparing the activities of three twitchin segments, the enzyme appears to be inhibited by the 60-amino acid residues lying just C-terminal to the kinase catalytic core. Thus, like a number of other protein kinases including myosin light chain kinases, the twitchin kinase appears to be autoregulated. PMID:8063727

  13. Thermo-Catalytic Methane Decomposition for Hydrogen Production: Effect of Palladium Promoter on Ni-based Catalysts


    Irene Lock Sow Mei; S.S.M. Lock; Dai-Viet N. Vo; Bawadi Abdullah


    Hydrogen production from the direct thermo-catalytic decomposition of methane is a promising alternative for clean fuel production. However, thermal decomposition of methane can hardly be of any practical and empirical interest in the industry unless highly efficient and effective catalysts, in terms of both catalytic activity and operational lifetime have been developed. In this study, the effect of palladium (Pd) as a promoter onto Ni supported on alumina catalyst has been investigated by u...

  14. Internal stress distribution for generating closure domains in laser-irradiated Fe–3%Si(110) steels

    International Nuclear Information System (INIS)

    Internal stress distribution for generating closure domains occurring in laser-irradiated Fe–3%Si(110) steels was investigated using high-energy X-ray analysis and domain theory based on the variational principle. The measured triaxial stresses inside the specimen were compressive and the stress in the rolling direction became more dominant than stresses in the other directions. The calculations based on the variational principle of magnetic energy for closure domains showed that the measured triaxial stresses made the closure domains more stable than the basic domain without closure domains. The experimental and calculation results reveal that the laser-introduced internal stresses result in the occurrence of the closure domains

  15. Internal stress distribution for generating closure domains in laser-irradiated Fe–3%Si(110) steels

    Energy Technology Data Exchange (ETDEWEB)

    Iwata, Keiji, E-mail: [Advanced Technology Research Laboratories, Nippon Steel and Sumitomo Metal Corporation, Futtsu, Chiba 293-8511 (Japan); Research Institute of Electrical Communication, Tohoku University, Aoba, Sendai 980-8577 (Japan); Imafuku, Muneyuki; Orihara, Hideto; Sakai, Yusuke; Ohya, Shin-Ichi [Department of Mechanical Systems Engineering, Tokyo City University, Tokyo, 158-0087 (Japan); Suzuki, Tamaki [Advanced Technology Research Laboratories, Nippon Steel and Sumitomo Metal Corporation, Futtsu, Chiba 293-8511 (Japan); Shobu, Takahisa [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Sayo, Hyogo 679-5148 (Japan); Akita, Koichi [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Naka, Ibaraki 319-1195 (Japan); Ishiyama, Kazushi [Research Institute of Electrical Communication, Tohoku University, Aoba, Sendai 980-8577 (Japan)


    Internal stress distribution for generating closure domains occurring in laser-irradiated Fe–3%Si(110) steels was investigated using high-energy X-ray analysis and domain theory based on the variational principle. The measured triaxial stresses inside the specimen were compressive and the stress in the rolling direction became more dominant than stresses in the other directions. The calculations based on the variational principle of magnetic energy for closure domains showed that the measured triaxial stresses made the closure domains more stable than the basic domain without closure domains. The experimental and calculation results reveal that the laser-introduced internal stresses result in the occurrence of the closure domains.

  16. Structural rearrangements of a polyketide synthase module during its catalytic cycle. (United States)

    Whicher, Jonathan R; Dutta, Somnath; Hansen, Douglas A; Hale, Wendi A; Chemler, Joseph A; Dosey, Annie M; Narayan, Alison R H; Håkansson, Kristina; Sherman, David H; Smith, Janet L; Skiniotis, Georgios


    The polyketide synthase (PKS) mega-enzyme assembly line uses a modular architecture to synthesize diverse and bioactive natural products that often constitute the core structures or complete chemical entities for many clinically approved therapeutic agents. The architecture of a full-length PKS module from the pikromycin pathway of Streptomyces venezuelae creates a reaction chamber for the intramodule acyl carrier protein (ACP) domain that carries building blocks and intermediates between acyltransferase, ketosynthase and ketoreductase active sites (see accompanying paper). Here we determine electron cryo-microscopy structures of a full-length pikromycin PKS module in three key biochemical states of its catalytic cycle. Each biochemical state was confirmed by bottom-up liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry. The ACP domain is differentially and precisely positioned after polyketide chain substrate loading on the active site of the ketosynthase, after extension to the β-keto intermediate, and after β-hydroxy product generation. The structures reveal the ACP dynamics for sequential interactions with catalytic domains within the reaction chamber, and for transferring the elongated and processed polyketide substrate to the next module in the PKS pathway. During the enzymatic cycle the ketoreductase domain undergoes dramatic conformational rearrangements that enable optimal positioning for reductive processing of the ACP-bound polyketide chain elongation intermediate. These findings have crucial implications for the design of functional PKS modules, and for the engineering of pathways to generate pharmacologically relevant molecules. PMID:24965656

  17. Crystal structure studies of NADP+ dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain

    International Nuclear Information System (INIS)

    Highlights: • We determined the structure of isocitrate dehydrogenase with citrate and cofactor. • The structure reveals a unique novel terminal domain involved in dimerization. • Clasp domain shows significant difference, and catalytic residues are conserved. • Oligomerization of the enzyme is quantized with subunit-subunit interactions. • Novel domain of this enzyme is classified as subfamily of the type IV. - Abstract: NADP+ dependent isocitrate dehydrogenase (IDH) is an enzyme catalyzing oxidative decarboxylation of isocitrate into oxalosuccinate (intermediate) and finally the product α-ketoglutarate. The crystal structure of Thermus thermophilus isocitrate dehydrogenase (TtIDH) ternary complex with citrate and cofactor NADP+ was determined using X-ray diffraction method to a resolution of 1.80 Å. The overall fold of this protein was resolved into large domain, small domain and a clasp domain. The monomeric structure reveals a novel terminal domain involved in dimerization, very unique and novel domain when compared to other IDH’s. And, small domain and clasp domain showing significant differences when compared to other IDH’s of the same sub-family. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDH’s. Also, helices/beta sheets are absent in the small domain, when compared to other IDH’s of the same sub family. The overall TtIDH structure exhibits closed conformation with catalytic triad residues, Tyr144-Asp248-Lys191 are conserved. Oligomerization of the protein is quantized using interface area and subunit–subunit interactions between protomers. Overall, the TtIDH structure with novel terminal domain may be categorized as a first structure of subfamily of type IV

  18. Structure of the Tribolium castaneum Telomerase Catalytic Subunit TERT

    Energy Technology Data Exchange (ETDEWEB)

    Gillis,A.; Schuller, A.; Skordalakes, E.


    A common hallmark of human cancers is the overexpression of telomerase, a ribonucleoprotein complex that is responsible for maintaining the length and integrity of chromosome ends. Telomere length deregulation and telomerase activation is an early, and perhaps necessary, step in cancer cell evolution. Here we present the high-resolution structure of the Tribolium castaneum catalytic subunit of telomerase, TERT. The protein consists of three highly conserved domains, organized into a ring-like structure that shares common features with retroviral reverse transcriptases, viral RNA polymerases and B-family DNA polymerases. Domain organization places motifs implicated in substrate binding and catalysis in the interior of the ring, which can accommodate seven to eight bases of double-stranded nucleic acid. Modelling of an RNA-DNA heteroduplex in the interior of this ring demonstrates a perfect fit between the protein and the nucleic acid substrate, and positions the 3'-end of the DNA primer at the active site of the enzyme, providing evidence for the formation of an active telomerase elongation complex.

  19. A novel liquid system of catalytic hydrogenation

    Institute of Scientific and Technical Information of China (English)

    LI; XiaoNian; XIANG; YiZhi


    On the basis that endothermic aqueous-phase reforming of oxygenated hydrocarbons for H2 production and exothermic liquid phase hydrogenation of organic compounds are carried out under extremely close conditions of temperature and pressure over the same type of catalyst, a novel liquid system of catalytic hydrogenation has been proposed, in which hydrogen produced from aqueous-phase reforming of oxygenated hydrocarbons is in situ used for liquid phase hydrogenation of organic compounds. The usage of active hydrogen generated from aqueous-phase reforming of oxygenated hydrocarbons for liquid catalytic hydrogenation of organic compounds could lead to increasing the selectivity to H2 in the aqueous-phase reforming due to the prompt removal of hydrogen on the active centers of the catalyst. Meanwhile, this novel liquid system of catalytic hydrogenation might be a potential method to improve the selectivity to the desired product in liquid phase catalytic hydrogenation of organic compounds. On the other hand, for this novel liquid system of catalytic hydrogenation, some special facilities for H2 generation, storage and transportation in traditional liquid phase hydrogenation industry process are yet not needed. Thus, it would simplify the working process of liquid phase hydrogenation and increase the energy usage and hydrogen productivity.

  20. Slow catalytic pyrolysis of rapeseed cake: Product yield and characterization of the pyrolysis liquid


    Smets, Koen; Roukaerts, A.; Czech, Jan; REGGERS, Guy; Schreurs, Sonja; Carleer, Robert; Yperman, Jan


    The performance of three catalysts during slow catalytic pyrolysis of rapeseed cake from 150 to 550 degrees C over a time period of 20 min followed by an isothermal period of 30 min at 550 degrees C was investigated. Na2CO3 was premixed with the rapeseed cake, while gamma-Al2O3 and HZSM-5 were tested without direct biomass contact. Catalytic experiments resulted in lower liquid and higher gas yields. The total amount of organic compounds in the pyrolysis liquid was considerably reduced by the...

  1. Advanced catalytic plasma exhaust clean-up process for ITER-EDA

    Energy Technology Data Exchange (ETDEWEB)

    Glugla, M. [Kernforschungszentrum Karlsruhe, Inst. fuer Radiochemie (Germany); Penzhorn, R.D. [Kernforschungszentrum Karlsruhe, Inst. fuer Radiochemie (Germany); Hermann, P. [Kernforschungszentrum Karlsruhe, Inst. fuer Radiochemie (Germany); Ache, H.J. [Kernforschungszentrum Karlsruhe, Inst. fuer Radiochemie (Germany)


    A new catalyst reactor (PERMCAT) has been developed to further improve the catalytic conversion / permeation based plasma exhaust clean-up process realized in the facility CAPRICE at the Tritium Laboratory Karlsruhe (TLK). The reactor directly combines a nickel catalyst with permeation tubes and removes residual amounts of tritium from tritiated species by isotopic swamping with hydrogen. Succesful integration of such a unit into the CAPRICE catalytic clean-up approach could lead to a fully continuous process and bring about a considerable reduction in non-recoverable tritium. (orig.).

  2. Advanced catalytic plasma exhaust clean-up process for ITER-EDA

    International Nuclear Information System (INIS)

    A new catalyst reactor (PERMCAT) has been developed to further improve the catalytic conversion / permeation based plasma exhaust clean-up process realized in the facility CAPRICE at the Tritium Laboratory Karlsruhe (TLK). The reactor directly combines a nickel catalyst with permeation tubes and removes residual amounts of tritium from tritiated species by isotopic swamping with hydrogen. Succesful integration of such a unit into the CAPRICE catalytic clean-up approach could lead to a fully continuous process and bring about a considerable reduction in non-recoverable tritium. (orig.)

  3. The Crystal Structures of the Open and Catalytically Competent Closed Conformation of Escherichia coli Glycogen Synthase

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, Fang; Jia, Xiaofei; Yep, Alejandra; Preiss, Jack; Geiger, James H.; (MSU)


    Escherichia coli glycogen synthase (EcGS, EC is a retaining glycosyltransferase (GT) that transfers glucose from adenosine diphosphate glucose to a glucan chain acceptor with retention of configuration at the anomeric carbon. EcGS belongs to the GT-B structural superfamily. Here we report several EcGS x-ray structures that together shed considerable light on the structure and function of these enzymes. The structure of the wild-type enzyme bound to ADP and glucose revealed a 15.2 degrees overall domain-domain closure and provided for the first time the structure of the catalytically active, closed conformation of a glycogen synthase. The main chain carbonyl group of His-161, Arg-300, and Lys-305 are suggested by the structure to act as critical catalytic residues in the transglycosylation. Glu-377, previously thought to be catalytic is found on the alpha-face of the glucose and plays an electrostatic role in the active site and as a glucose ring locator. This is also consistent with the structure of the EcGS(E377A)-ADP-HEPPSO complex where the glucose moiety is either absent or disordered in the active site

  4. Catalytic microreactors for portable power generation

    Energy Technology Data Exchange (ETDEWEB)

    Karagiannidis, Symeon [Paul Scherer Institute, Villigen (Switzerland)


    ''Catalytic Microreactors for Portable Power Generation'' addresses a problem of high relevance and increased complexity in energy technology. This thesis outlines an investigation into catalytic and gas-phase combustion characteristics in channel-flow, platinum-coated microreactors. The emphasis of the study is on microreactor/microturbine concepts for portable power generation and the fuels of interest are methane and propane. The author carefully describes numerical and experimental techniques, providing a new insight into the complex interactions between chemical kinetics and molecular transport processes, as well as giving the first detailed report of hetero-/homogeneous chemical reaction mechanisms for catalytic propane combustion. The outcome of this work will be widely applied to the industrial design of micro- and mesoscale combustors. (orig.)

  5. Catalytic nanoarchitectonics for environmentally compatible energy generation

    Directory of Open Access Journals (Sweden)

    Hideki Abe


    Full Text Available Environmentally compatible energy management is one of the biggest challenges of the 21st century. Low-temperature conversion of chemical to electrical energy is of particular importance to minimize the impact to the environment while sustaining the consumptive economy. In this review, we shed light on one of the most versatile energy-conversion technologies: heterogeneous catalysts. We establish the integrity of structural tailoring in heterogeneous catalysts at different scales in the context of an emerging paradigm in materials science: catalytic nanoarchitectonics. Fundamental backgrounds of energy-conversion catalysis are first provided together with a perspective through state-of-the-art energy-conversion catalysis including catalytic exhaust remediation, fuel-cell electrocatalysis and photosynthesis of solar fuels. Finally, the future evolution of catalytic nanoarchitectonics is overviewed: possible combinations of heterogeneous catalysts, organic molecules and even enzymes to realize reaction-selective, highly efficient and long-life energy conversion technologies which will meet the challenge we face.

  6. Use catalytic combustion for LHV gases

    Energy Technology Data Exchange (ETDEWEB)

    Tucci, E.R.


    This paper shows how low heating value (LHV) waste gases can be combusted to recover energy even when the gases won't burn in a normal manner. Significant energy and economic savings can result by adopting this process. Catalytic combustion is a heterogeneous surface-catalyzed air oxidation of fuel, gaseous or liquid, to generate thermal energy in a flameless mode. The catalytic combustion process is quite complex since it involves numerous catalytic surface and gas-phase chemical reactions. During low temperature surface-catalyzed combustion, as in start-up, the combustion stage is under kinetically controlled conditions. The discussion covers the following topics - combustor substrates; combustor washcoating and catalyzing; combustor operational modes (turbine or tabular modes); applications in coal gasification and in-situ gasification; waste process gases. 16 refs.

  7. Xylan-Degrading Catalytic Flagellar Nanorods. (United States)

    Klein, Ágnes; Szabó, Veronika; Kovács, Mátyás; Patkó, Dániel; Tóth, Balázs; Vonderviszt, Ferenc


    Flagellin, the main component of flagellar filaments, is a protein possessing polymerization ability. In this work, a novel fusion construct of xylanase A from B. subtilis and Salmonella flagellin was created which is applicable to build xylan-degrading catalytic nanorods of high stability. The FliC-XynA chimera when overexpressed in a flagellin deficient Salmonella host strain was secreted into the culture medium by the flagellum-specific export machinery allowing easy purification. Filamentous assemblies displaying high surface density of catalytic sites were produced by ammonium sulfate-induced polymerization. FliC-XynA nanorods were resistant to proteolytic degradation and preserved their enzymatic activity for a long period of time. Furnishing enzymes with self-assembling ability to build catalytic nanorods offers a promising alternative approach to enzyme immobilization onto nanostructured synthetic scaffolds. PMID:25966869

  8. Flow parameters of IC engine catalytic converters

    Energy Technology Data Exchange (ETDEWEB)

    Zmudka, Z.; Postrzednik, S. [Silesian Univ. of Tech., Gliwice (Poland)


    Conversion rate of harmful substances is the principal parameter of catalyst work in respect of ecology. However, resistance of exhaust gas flow through the catalytic converter is also essential problem, apart from its chemical efficiency because fitting the catalyst in exhaust system alters flow characteristic of this system significantly. Catalytic converter can be treated as local or linear resistance element of exhaust system. The first model, in which flow resistance generated by a catalyst is treated as local resistance, is more simplified. Resistance number of the converter was calculated using Darcy model. In the second case, exhaust gas flow resistance through catalyst is treated as linear resistance with energy dissipation (linear frictional resistance) distributed linearly along way of exhaust gas flow. Friction number for the tested converter was calculated and analysed. The problem has been illustrated by results of experimental researches of three-way catalytic converter installed in exhaust system of spark ignition engine and its basic analysis. (orig.)

  9. Electro Catalytic Oxidation (ECO) Operation

    Energy Technology Data Exchange (ETDEWEB)

    Morgan Jones


    The power industry in the United States is faced with meeting many new regulations to reduce a number of air pollutants including sulfur dioxide, nitrogen oxides, fine particulate matter, and mercury. With over 1,000 power plants in the US, this is a daunting task. In some cases, traditional pollution control technologies such as wet scrubbers and SCRs are not feasible. Powerspan's Electro-Catalytic Oxidation, or ECO{reg_sign} process combines four pollution control devices into a single integrated system that can be installed after a power plant's particulate control device. Besides achieving major reductions in emissions of sulfur dioxide (SO{sub 2}), nitrogen oxides (NOx), fine particulate matter (PM2.5) and mercury (Hg), ECO produces a highly marketable fertilizer, which can help offset the operating costs of the process system. Powerspan has been operating a 50-MW ECO commercial demonstration unit (CDU) at FirstEnergy Corp.'s R.E. Burger Plant near Shadyside, Ohio, since February 2004. In addition to the CDU, a test loop has been constructed beside the CDU to demonstrate higher NOx removal rates and test various scrubber packing types and wet ESP configurations. Furthermore, Powerspan has developed the ECO{reg_sign}{sub 2} technology, a regenerative process that uses a proprietary solvent to capture CO{sub 2} from flue gas. The CO{sub 2} capture takes place after the capture of NOx, SO{sub 2}, mercury, and fine particulate matter. Once the CO{sub 2} is captured, the proprietary solution is regenerated to release CO{sub 2} in a form that is ready for geological storage or beneficial use. Pilot scale testing of ECO{sub 2} began in early 2009 at FirstEnergy's Burger Plant. The ECO{sub 2} pilot unit is designed to process a 1-MW flue gas stream and produce 20 tons of CO{sub 2} per day, achieving a 90% CO{sub 2} capture rate. The ECO{sub 2} pilot program provided the opportunity to confirm process design and cost estimates, and prepare for large

  10. Axion domain wall baryogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Daido, Ryuji; Kitajima, Naoya [Department of Physics, Tohoku University,Sendai 980-8578 (Japan); Takahashi, Fuminobu [Department of Physics, Tohoku University,Sendai 980-8578 (Japan); Kavli IPMU, TODIAS, University of Tokyo,Kashiwa 277-8583 (Japan)


    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m≃10{sup 8}–10{sup 13} GeV and f≃10{sup 13}–10{sup 16} GeV. Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  11. Domain Theory for Concurrency

    DEFF Research Database (Denmark)

    Nygaard, Mikkel

    Concurrent computation can be given an abstract mathematical treatment very similar to that provided for sequential computation by domain theory and denotational semantics of Scott and Strachey. A simple domain theory for concurrency is presented. Based on a categorical model of linear logic and...... nondeterministic dataflow. The domain theory can be generalised to presheaf models, providing a more refined treatment of nondeterministic branching and supporting notions of bisimulation. The operational semantics for HOPLA is guided by the idea that derivations of transitions in the operational semantics should...... correspond to elements of the presheaf denotations. Similar guidelines lead to an operational semantics for the first-order fragment of Affine HOPLA. An extension of the operational semantics to the full language is based on a stable denotational semantics which associates to each computation the minimal...

  12. Electric-field-driven dynamics of magnetic domain walls in magnetic nanowires patterned on ferroelectric domains (United States)

    Van de Wiele, Ben; Leliaert, Jonathan; Franke, Kévin J. A.; van Dijken, Sebastiaan


    Strong coupling of magnetic domain walls onto straight ferroelastic boundaries of a ferroelectric layer enables full and reversible electric-field control of magnetic domain wall motion. In this paper, the dynamics of this new driving mechanism is analyzed using micromagnetic simulations. We show that transverse domain walls with a near-180° spin structure are stabilized in magnetic nanowires and that electric fields can move these walls with high velocities. Above a critical velocity, which depends on material parameters, nanowire geometry and the direction of domain wall motion, the magnetic domain walls depin abruptly from the ferroelastic boundaries. Depinning evolves either smoothly or via the emission and annihilation of a vortex or antivortex core (Walker breakdown). In both cases, the magnetic domain wall slows down after depinning in an oscillatory fashion and eventually comes to a halt. The simulations provide design rules for hybrid ferromagnetic-ferroelectric domain-wall-based devices and indicate that material disorder and structural imperfections only influence Walker-breakdown-like depinning at high domain wall velocities.

  13. Domain and domain walls NMR spectra in R Co2 intermetallic compounds

    International Nuclear Information System (INIS)

    NMR signals in ferromagnets originate from domains and domain walls. THe technique has the ability to distinguish signals originating from these two regions, through the selection of the radiofrequency (RF) power level applied to the sample. The dependence of the spin echo amplitude upon the RF field intensity can give information on magnetic properties such as domain walls mobility, distribution of local magnetic anisotropies, etc. NMR spectra obtained under different RF intensities allow the investigation of different regions of the samples. In this paper we have applied this technique to the study of the spin-echo amplitude and of the spectra of 59 Co in the series of the Laves phase intermetallic compounds R Co2, where R=Gd, Dy, Tb at 4.2 K, as a function of the RF Field. The results were analyzed according to a model which takes into account several features characteristic of ferromagnetic powdered samples. These include the distribution of the direction of the hyperfine fielding respect to the RF field, the variation of the enhancement factor within the domain-walls, the distribution of wall areas, etc. The analysis suggests that whereas in Tb Co2 the NMR signals come purely from domain walls, in Dy Co2 they come mainly from domains. Gd Co2 behaves as an intermediate case where there exists a mixture of contributions to the NMR signals. In this case we were able to observe and measure separately the NMR spectra of nuclei from domains and domain walls. (author)

  14. Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase. (United States)

    Manuel, Raymond C; Hitomi, Kenichi; Arvai, Andrew S; House, Paul G; Kurtz, Andrew J; Dodson, M L; McCullough, Amanda K; Tainer, John A; Lloyd, R Stephen


    The Escherichia coli adenine DNA glycosylase, MutY, plays an important role in the maintenance of genomic stability by catalyzing the removal of adenine opposite 8-oxo-7,8-dihydroguanine or guanine in duplex DNA. Although the x-ray crystal structure of the catalytic domain of MutY revealed a mechanism for catalysis of the glycosyl bond, it appeared that several opportunistically positioned lysine side chains could participate in a secondary beta-elimination reaction. In this investigation, it is established via site-directed mutagenesis and the determination of a 1.35-A structure of MutY in complex with adenine that the abasic site (apurinic/apyrimidinic) lyase activity is alternatively regulated by two lysines, Lys142 and Lys20. Analyses of the crystallographic structure also suggest a role for Glu161 in the apurinic/apyrimidinic lyase chemistry. The beta-elimination reaction is structurally and chemically uncoupled from the initial glycosyl bond scission, indicating that this reaction occurs as a consequence of active site plasticity and slow dissociation of the product complex. MutY with either the K142A or K20A mutation still catalyzes beta and beta-delta elimination reactions, and both mutants can be trapped as covalent enzyme-DNA intermediates by chemical reduction. The trapping was observed to occur both pre- and post-phosphodiester bond scission, establishing that both of these intermediates have significant half-lives. Thus, the final spectrum of DNA products generated reflects the outcome of a delicate balance of closely related equilibrium constants. PMID:15326180

  15. Revisiting the mechanism of the autoactivation of the complement protease C1r in the C1 complex: structure of the active catalytic region of C1r. (United States)

    Kardos, József; Harmat, Veronika; Palló, Anna; Barabás, Orsolya; Szilágyi, Katalin; Gráf, László; Náray-Szabó, Gábor; Goto, Yuji; Závodszky, Péter; Gál, Péter


    C1r is a modular serine protease which is the autoactivating component of the C1 complex of the classical pathway of the complement system. We have determined the first crystal structure of the entire active catalytic region of human C1r. This fragment contains the C-terminal serine protease (SP) domain and the preceding two complement control protein (CCP) modules. The activated CCP1-CCP2-SP fragment makes up a dimer in a head-to-tail fashion similarly to the previously characterized zymogen. The present structure shows an increased number of stabilizing interactions. Moreover, in the crystal lattice there is an enzyme-product relationship between the C1r molecules of neighboring dimers. This enzyme-product complex exhibits the crucial S1-P1 salt bridge between Asp631 and Arg446 residues, and intermolecular interaction between the CCP2 module and the SP domain. Based on these novel structural information we propose a new split-and-reassembly model for the autoactivation of the C1r. This model is consistent with experimental results that have not been explained adequately by previous models. It allows autoactivation of C1r without large-scale, directed movement of C1q arms. The model is concordant with the stability of the C1 complex during activation of the next complement components. PMID:17996945

  16. Domain architecture of protein-disulfide isomerase facilitates its dual role as an oxidase and an isomerase in Ero1p-mediated disulfide formation

    DEFF Research Database (Denmark)

    Kulp, M. S.; Frickel, E. M.; Ellgaard, Lars;


    reduction/rearrangement of non-native disulfides is poorly understood. We analyzed the role of individual PDI domains in disulfide bond formation in a reaction driven by their natural oxidant, Ero1p. We found that Ero1p oxidizes the isolated PDI catalytic thioredoxin domains, A and A' at the same rate. In...

  17. Cross-catalytic peptide nucleic acid (PNA) replication based on templated ligation

    DEFF Research Database (Denmark)

    Singhal, Abhishek; Nielsen, Peter E


    We report the first PNA self-replicating system based on template directed cross-catalytic ligation, a process analogous to biological replication. Using two template PNAs and four pentameric precursor PNAs, all four possible carbodiimide assisted amide ligation products were detected and...... identified by HPLC and MALDI-TOF analysis. We conclude that the two template complementary reaction products are generated via cross-catalysis, while the other two self-complementary (and in principle auto-catalytic) products are formed via intra-complex coupling between the two sets of complementary PNA...... precursors. Cross-catalytic product formation followed product inhibited kinetics, but approximately two replication rounds were observed. Analogous but less efficient replication was found for a similar tetrameric system. These results demonstrate that simpler nucleobase replication systems than natural...

  18. Application of hierarchical MFI zeolite for the catalytic pyrolysis of Japanese larch. (United States)

    Park, Kyu-Hong; Park, Hyun Ju; Kim, Jeongnam; Ryoo, Ryong; Jeon, Jong-Ki; Park, Junhong; Park, Young-Kwon


    The catalytic pyrolysis of Japanese larch was carried out over a hierarchical MFI zeolite (Meso MFI C16). The zeolite was synthesized using an amphiphilic organosilane as a mesopore-directing agent, and its catalytic activity was compared with that of the conventional HZSM-5 and the mesoporous material from HZSM-5 (MMZ(ZSM-5)). The effect of the hierarchical MFI zeolite on the product distribution and chemical composition of the bio-oil was also examined. The hierarchical MFI zeolite exhibited the highest activity in deoxygenation and aromatization during the catalytic pyrolysis of Japanese larch. In particular, it showed high selectivity for valuable aromatics, such as benzene, toluene, and xylenes (BTX), even though it decreased the organic fraction of bio-oil. Its higher mesoporosity resulted, however, in an increase in the coke amount and in undesirable products, such as polycyclic aromatic hydrocarbons (PAHs). PMID:20352861

  19. A catalytic surface for amyloid fibril formation

    Energy Technology Data Exchange (ETDEWEB)

    Hammarstroem, P; Ali, M M; Mishra, R; Tengvall, P; Lundstroem, I [Department of Physics, Biology and Chemistry, Linkoeping University, SE-581 83 Linkoeping (Sweden); Svensson, S [Astra Zeneca R and D, SE-151 85 Soedertaelje (Sweden)], E-mail:


    A hydrophobic surface incubated in a solution of protein molecules (insulin monomers) was made into a catalytic surface for amyloid fibril formation by repeatedly incubate, rinse and dry the surface. The present contribution describes how this unexpected transformation occurred and its relation to rapid fibrillation of insulin solutions in contact with the surface. A tentative model of the properties of the catalytic surface is given, corroborated by ellipsometric measurements of the thickness of the organic layer on the surface and by atomic force microscopy. The surfaces used were spontaneously oxidized silicon made hydrophobic through treatment in dichlorodimethylsilane.

  20. Thermal and catalytic pyrolysis of plastic waste

    Directory of Open Access Journals (Sweden)

    Débora Almeida


    Full Text Available Abstract The amount of plastic waste is growing every year and with that comes an environmental concern regarding this problem. Pyrolysis as a tertiary recycling process is presented as a solution. Pyrolysis can be thermal or catalytical and can be performed under different experimental conditions. These conditions affect the type and amount of product obtained. With the pyrolysis process, products can be obtained with high added value, such as fuel oils and feedstock for new products. Zeolites can be used as catalysts in catalytic pyrolysis and influence the final products obtained.

  1. Catalytic Enantioselective Functionalization of Unactivated Terminal Alkenes. (United States)

    Coombs, John R; Morken, James P


    Terminal alkenes are readily available functional groups which appear in α-olefins produced by the chemical industry, and they appear in the products of many contemporary synthetic reactions. While the organic transformations that apply to alkenes are amongst the most studied reactions in all of chemical synthesis, the number of reactions that apply to nonactivated terminal alkenes in a catalytic enantioselective fashion is small in number. This Minireview highlights the cases where stereocontrol in catalytic reactions of 1-alkenes is high enough to be useful for asymmetric synthesis. PMID:26764019

  2. Catalytic gasification of oil-shales

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, A.; Avakyan, T. [I.M. Gubkin Russian State Univ. of Oil and Gas, Moscow (Russian Federation); Strizhakova, Yu. [Samara State Univ. (Russian Federation)


    Nowadays, the problem of complex usage of solid fossil fuels as raw materials for obtaining of motor fuels and chemical products is becoming increasingly important. A one of possible solutions of the problem is their gasification with further processing of gaseous and liquid products. In this work we have investigated the process of thermal and catalytic gasification of Baltic and Kashpir oil-shales. We have shown that, as compared with non-catalytic process, using of nickel catalyst in the reaction increases the yield of gas, as well as hydrogen content in it, and decreases the amount of liquid products. (orig.)

  3. Heterogeneous Catalytic Ozonization of Sulfosalicylic Acid

    Institute of Scientific and Technical Information of China (English)


    This paper describes the potential of heterogeneous catalytic ozonization of sulfo-salicylic acid (SSal). It was found that catalytic ozonization in the presence of Mn-Zr-O (a modified manganese dioxide supported on silica gel) had significantly enhanced the removal rate (72%) of total organic carbon (TOC) compared with that of ozonization alone (19%). The efficient removal rate of TOC was probably due to increasing the adsorption ability of catalyst and accelerating decomposition of ozone to produce more powerful oxidants than ozone.

  4. Large domain graphene


    Li, Xuesong; Magnuson, Carl W.; Venugopal, Archana; Vogel, Eric M.; Rodney S. Ruoff; Colombo, Luigi


    Graphene growth by chemical vapor deposition has received a lot of attention recently owing to the ease with which large area films can be grown, but growth of large domain or equivalently large grain size has not been reported yet. In this brevia, we report on a CVD process that yields graphene with domains of hundreds of micrometers, by very low pressure CVD, less than 50 mTorr, and very low precursor flow rates using methane as the source of carbon on the inside of copper foil enclosures a...

  5. Bilayer thickness mismatch controls domain size in biomimetic membranes (United States)

    Heberle, Frederick A.; Petruzielo, Robin S.; Pan, Jianjun; Drazba, Paul; Kučerka, Norbert; Standaert, Robert F.; Feigenson, Gerald W.; Katsara, John


    In order to promote functionality, cells may alter the spatial organization of membrane lipids and proteins, including separation of liquid phases into distinct domains. In model membranes, domain size and morphology depend strongly on composition and temperature, but the physicochemical mechanisms controlling them are poorly understood. Theoretical work suggests a role for interfacial energy at domain boundaries, which may be driven in part by thickness mismatch between a domain and its surrounding bilayer. However, no direct evidence linking thickness mismatch to domain size in free-standing bilayers has been reported. We describe the use of Small Angle Neutron Scattering (SANS) to detect domains in simplified lipid-only models that mimic the composition of plasma membrane. We find that domain size is controlled by the degree of acyl chain unsaturation of low-melting temperature lipids, and that this size transition is correlated to changes in the thickness mismatch between coexisting liquid phases.

  6. Concept of the field-driven domain wall motion memory

    International Nuclear Information System (INIS)

    In this paper, the concept of field-driven domain wall motion memory is presented. It is confirmed that a domain is shifted with a carefully designed non-uniform field by micromagnetic simulations. The shift of a domain-a bit-can be established by the motion of two domain walls to the same direction and the same distance. In order to get a better understanding of the domain wall motion under the non-uniform transverse magnetic field, we investigate the motion of the transverse Neel-type domain wall by micromagnetic simulations and the collective coordinate approach. The validity of the equation of motion for the domain wall is confirmed by the micromagnetic simulations as functions of the gradient of the non-uniform field, the saturation magnetization, and the Gilbert damping parameter α

  7. Beamforming in Short Time Fractional Fourier Domain (FRFD

    Directory of Open Access Journals (Sweden)

    Mostafa Rahmani


    Full Text Available This study aims to generate a model for the problem of beamforming in fractional Fourier domain, through which a general solution for obtaining weighted beamforming in fractional Fourier domain for different criteria might be delivered. In order to generate this model, a description of fractional delay concept is presented, through which the string vector in fractional Fourier domain is calculated and a model for beamforming in fractional Fourier domain is generated which is similar to that used for obtaining weighted beamforming in time domain for narrow-band signals. To complement our solution, a method for obtaining the optimal fractional domain as well as direction of arrival in optimal fractional Fourier domain.

  8. Nonlinear analysis of sequence repeats of multi-domain proteins

    International Nuclear Information System (INIS)

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences

  9. Quantitative analysis of magnetic resonance time domain signals

    International Nuclear Information System (INIS)

    A magnetic resonance time domain signal is often made up of a limited number of exponentially decaying sinusoids plus white noise. Traditionally, quantitative analysis of the signal is carried out in the frequency domain, after applying FFT in conjunction with a time window. It is shown that quantitative analysis directly in the time domain is feasible, and in fact yields several advantages. Various methods are applied and compared. (Auth.)

  10. Domain Wall Mobility in Co-Based Amorphous Wire

    Directory of Open Access Journals (Sweden)

    Maria Kladivova


    Full Text Available Dynamics of the domain wall between opposite circularly magnetized domains in amorphous cylindrical sample with circular easy direction is theoretically studied. The wall is driven by DC current. Various mechanisms which influence the wall velocity were taken into account: current magnitude, deformation of the mowing wall, Hall effect, axially magnetized domain in the middle of the wire. Theoretical results obtained are in a good agreement with experiments on Cobased amorphous ferromagnetic wires.

  11. Greatly Enhancing Catalytic Activity of Graphene by Doping the Underlying Metal Substrate. (United States)

    Guo, Na; Xi, Yongjie; Liu, Shuanglong; Zhang, Chun


    Graphene-based solid-state catalysis represents a new direction in applications of graphene and has attracted a lot of interests recently. However, the difficulty in fine control and large-scale production of previously proposed graphene catalysts greatly limits their industrial applications. Here we present a novel way to enhance the catalytic activity of graphene, which is highly efficient yet easy to fabricate and control. By first-principles calculations, we show that when the underlying metal substrate is doped with impurities, the catalytic activity of the supported graphene can be drastically enhanced. Graphene supported on a Fe/Ni(111) surface is chosen as a model catalyst, and the chemical reaction of CO oxidation is used to probe the catalytic activity of graphene. When the underlying Fe/Ni(111) substrate is impurity free, the graphene is catalytically inactive. When a Zn atom is doped into the substrate, the catalytic activity of the supported graphene is greatly enhanced, and the reaction barrier of the catalyzed CO oxidation is reduced to less than 0.5 eV. Intriguing reaction mechanism of catalyzed CO oxidation is revealed. These studies suggest a new class of graphene-based catalysts and pave the way for future applications of graphene in solid-state catalysis. PMID:26156332

  12. Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Thoden, James B.; Reinhardt, Laurie A.; Cook, Paul D.; Menden, Patrick; Cleland, W.W.; Holden, Hazel M. (UW); (Mount Union); (UW-MED)


    N-Acetylperosamine is an unusual dideoxysugar found in the O-antigens of some Gram-negative bacteria, including the pathogenic Escherichia coli strain O157:H7. The last step in its biosynthesis is catalyzed by PerB, an N-acetyltransferase belonging to the left-handed {beta}-helix superfamily of proteins. Here we describe a combined structural and functional investigation of PerB from Caulobacter crescentus. For this study, three structures were determined to 1.0 {angstrom} resolution or better: the enzyme in complex with CoA and GDP-perosamine, the protein with bound CoA and GDP-N-acetylperosamine, and the enzyme containing a tetrahedral transition state mimic bound in the active site. Each subunit of the trimeric enzyme folds into two distinct regions. The N-terminal domain is globular and dominated by a six-stranded mainly parallel {beta}-sheet. It provides most of the interactions between the protein and GDP-perosamine. The C-terminal domain consists of a left-handed {beta}-helix, which has nearly seven turns. This region provides the scaffold for CoA binding. On the basis of these high-resolution structures, site-directed mutant proteins were constructed to test the roles of His 141 and Asp 142 in the catalytic mechanism. Kinetic data and pH-rate profiles are indicative of His 141 serving as a general base. In addition, the backbone amide group of Gly 159 provides an oxyanion hole for stabilization of the tetrahedral transition state. The pH-rate profiles are also consistent with the GDP-linked amino sugar substrate entering the active site in its unprotonated form. Finally, for this investigation, we show that PerB can accept GDP-3-deoxyperosamine as an alternative substrate, thus representing the production of a novel trideoxysugar.

  13. Structure of the ATP Synthase Catalytic Complex (F1) from Escherichia coli in an Autoinhibited conformation

    Energy Technology Data Exchange (ETDEWEB)

    G Cingolani; T Duncan


    ATP synthase is a membrane-bound rotary motor enzyme that is critical for cellular energy metabolism in all kingdoms of life. Despite conservation of its basic structure and function, autoinhibition by one of its rotary stalk subunits occurs in bacteria and chloroplasts but not in mitochondria. The crystal structure of the ATP synthase catalytic complex (F{sub 1}) from Escherichia coli described here reveals the structural basis for this inhibition. The C-terminal domain of subunit {var_epsilon} adopts a heretofore unknown, highly extended conformation that inserts deeply into the central cavity of the enzyme and engages both rotor and stator subunits in extensive contacts that are incompatible with functional rotation. As a result, the three catalytic subunits are stabilized in a set of conformations and rotational positions distinct from previous F{sub 1} structures.

  14. Atomic Pseudo-Valuation Domains

    CERN Document Server

    Stines, Elijah


    Pseudo-valuation domains have been studied since their introduction in 1978 by Hedstrom and Houston. Related objects, boundary valuation domains, were introduced by Maney in 2004. Here, it is shown that the class of atomic pseudo-valuation domains coincides with the class of boundary valuation domains. It is also shown that power series rings and generalized power series rings give examples of pseudo-valuation domains whose congruence lattices can be characterized. The paper also introduces, and makes use of, a sufficient condition on the group of divisibility of a domain to guarantee that it is a pseudo-valuation domain.

  15. Domain: Labour market

    NARCIS (Netherlands)

    Oude Mulders, J.; Wadensjö, E.; Hasselhorn, H.M.; Apt, W.


    This domain chapter is dedicated to summarize research on the effects of labour market contextual factors on labour market participation of older workers (aged 50+) and identify research gaps. While employment participation and the timing of (early) retirement is often modelled as an individual deci

  16. Skyrmions and domain walls


    Piette, B.; Zakrzewski, W. J.


    We study the 3+1 dimensional Skyrme model with a mass term different from the usual one. We show that this new model possesses domain walls solutions. We describe how, in the equivalent 2+1 dimensional model, the Skyrmion is absorbed by the wall.

  17. Key Feature of the Catalytic Cycle of TNF-α Converting Enzyme Involves Communication Between Distal Protein Sites and the Enzyme Catalytic Core

    International Nuclear Information System (INIS)

    Despite their key roles in many normal and pathological processes, the molecular details by which zinc-dependent proteases hydrolyze their physiological substrates remain elusive. Advanced theoretical analyses have suggested reaction models for which there is limited and controversial experimental evidence. Here we report the structure, chemistry and lifetime of transient metal-protein reaction intermediates evolving during the substrate turnover reaction of a metalloproteinase, the tumor necrosis factor-α converting enzyme (TACE). TACE controls multiple signal transduction pathways through the proteolytic release of the extracellular domain of a host of membrane-bound factors and receptors. Using stopped-flow x-ray spectroscopy methods together with transient kinetic analyses, we demonstrate that TACE's catalytic zinc ion undergoes dynamic charge transitions before substrate binding to the metal ion. This indicates previously undescribed communication pathways taking place between distal protein sites and the enzyme catalytic core. The observed charge transitions are synchronized with distinct phases in the reaction kinetics and changes in metal coordination chemistry mediated by the binding of the peptide substrate to the catalytic metal ion and product release. Here we report key local charge transitions critical for proteolysis as well as long sought evidence for the proposed reaction model of peptide hydrolysis. This study provides a general approach for gaining critical insights into the molecular basis of substrate recognition and turnover by zinc metalloproteinases that may be used for drug design

  18. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. (United States)

    Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen-Hsiang; Parks, Jerry M; Smith, Jeremy C; Weiss, Kevin L; Keen, David A; Blakeley, Matthew P; Louis, John M; Langan, Paul; Weber, Irene T; Kovalevsky, Andrey


    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level. PMID:26958828

  19. Catalytic processes during preferential oxidation of CO in H 2-rich streams over catalysts based on copper-ceria (United States)

    Gamarra, D.; Hornés, A.; Koppány, Zs.; Schay, Z.; Munuera, G.; Soria, J.; Martínez-Arias, A.

    Nanostructured catalysts based on combinations between oxidised copper and cerium entities prepared by two different methods (impregnation of ceria and coprecipitation of the two components within reverse microemulsions) have been examined with respect to their catalytic performance for preferential oxidation of CO in a H 2-rich stream (CO-PROX). Correlations between their catalytic and redox properties are established on the basis of parallel analyses of temperature programmed reduction results employing both H 2 and CO as reactants as well as by XPS. Although general catalytic trends can be directly correlated with the redox properties observed upon separate interactions with each of the two reductants (CO and H 2), the existence of interferences between both reductants must be considered to complete details for such activity/redox correlation. Differences in the nature of the active oxidised copper-cerium contacts present in each case determine the catalytic properties of these systems for the CO-PROX process.

  20. Faraday instability in deformable domains

    International Nuclear Information System (INIS)

    Hydrodynamical instabilities are usually studied either in bounded regions or free to grow in space. In this article we review the experimental results of an intermediate situation, in which an instability develops in deformable domains. The Faraday instability, which consists in the formation of surface waves on a liquid experiencing a vertical forcing, is triggered in floating liquid lenses playing the role of deformable domains. Faraday waves deform the lenses from the initial circular shape and the mutual adaptation of instability patterns with the lens boundary is observed. Two archetypes of behaviour have been found. In the first archetype a stable elongated shape is reached, the wave vector being parallel to the direction of elongation. In the second archetype the waves exceed the response of the lens border and no equilibrium shape is reached. The lens stretches and eventually breaks into fragments that have a complex dynamics. The difference between the two archetypes is explained by the competition between the radiation pressure the waves exert on the lens border and its response due to surface tension.