WorldWideScience

Sample records for catalytic core domain

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

    OpenAIRE

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

    2002-01-01

    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 ...

  2. 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.

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

    Science.gov (United States)

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

    2011-01-01

    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

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

    OpenAIRE

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

    1999-01-01

    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.

  5. Core-size-dependent catalytic properties of bimetallic Au/Ag core-shell nanoparticles.

    Science.gov (United States)

    Haldar, Krishna Kanta; Kundu, Simanta; Patra, Amitava

    2014-12-24

    Bimetallic core-shell nanoparticles have recently emerged as a new class of functional materials because of their potential applications in catalysis, surface enhanced Raman scattering (SERS) substrate and photonics etc. Here, we have synthesized Au/Ag bimetallic core-shell nanoparticles with varying the core diameter. The red-shifting of the both plasmonic peaks of Ag and Au confirms the core-shell structure of the nanoparticles. Transmission electron microscopy (TEM) analysis, line scan EDS measurement and UV-vis study confirm the formation of core-shell nanoparticles. We have examined the catalytic activity of these core-shell nanostructures in the reaction between 4-nitrophenol (4-NP) and NaBH4 to form 4-aminophenol (4-AP) and the efficiency of the catalytic reaction is found to be increased with increasing the core size of Au/Ag core-shell nanocrystals. The catalytic efficiency varies from 41.8 to 96.5% with varying core size from 10 to 100 nm of Au/Ag core-shell nanoparticles, and the Au100/Ag bimetallic core-shell nanoparticle is found to be 12-fold more active than that of the pure Au nanoparticles with 100 nm diameter. Thus, the catalytic properties of the metal nanoparticles are significantly enhanced because of the Au/Ag core-shell structure, and the rate is dependent on the size of the core of the nanoparticles. PMID:25456348

  6. Solution Conformation and Dynamics of the HIV-1 Integrase Core Domain*

    OpenAIRE

    Fitzkee, Nicholas C.; Masse, James E.; Shen, Yang; Davies, David R.; Bax, Ad

    2010-01-01

    The human immunodeficiency virus type 1 (HIV-1) integrase (IN) is a critical enzyme involved in infection. It catalyzes two reactions to integrate the viral cDNA into the host genome, 3′ processing and strand transfer, but the dynamic behavior of the active site during catalysis of these two processes remains poorly characterized. NMR spectroscopy can reveal important structural details about enzyme mechanisms, but to date the IN catalytic core domain has proven resistant to such an analysis....

  7. Evolutionary cores of domain co-occurrence networks

    Directory of Open Access Journals (Sweden)

    Almaas Eivind

    2005-03-01

    Full Text Available Abstract Background The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of these systems are scale-free while at the same time modular, resulting in a hierarchical architecture. The structure of the protein domain network, where individual domains correspond to nodes and their co-occurrences in a protein are interpreted as links, also falls into this category, suggesting that domains involved in the maintenance of increasingly developed, multicellular organisms accumulate links. Here, we take the next step by studying link based properties of the protein domain co-occurrence networks of the eukaryotes S. cerevisiae, C. elegans, D. melanogaster, M. musculus and H. sapiens. Results We construct the protein domain co-occurrence networks from the PFAM database and analyze them by applying a k-core decomposition method that isolates the globally central (highly connected domains in the central cores from the locally central (highly connected domains in the peripheral cores protein domains through an iterative peeling process. Furthermore, we compare the subnetworks thus obtained to the physical domain interaction network of S. cerevisiae. We find that the innermost cores of the domain co-occurrence networks gradually grow with increasing degree of evolutionary development in going from single cellular to multicellular eukaryotes. The comparison of the cores across all the organisms under consideration uncovers patterns of domain combinations that are predominately involved in protein functions such as cell-cell contacts and signal transduction. Analyzing a weighted interaction network of PFAM domains of Yeast, we find that domains having only a few partners frequently interact with these, while the converse is true for domains with a multitude of partners. Combining domain co-occurrence and interaction information, we observe

  8. Ribosomal small subunit domains radiate from a central core

    Science.gov (United States)

    Gulen, Burak; Petrov, Anton S.; Okafor, C. Denise; Vander Wood, Drew; O'Neill, Eric B.; Hud, Nicholas V.; Williams, Loren Dean

    2016-02-01

    The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2‧OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.

  9. 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

  10. Establishing a core domain set to measure rheumatoid arthritis flares

    DEFF Research Database (Denmark)

    Bykerk, Vivian P; Lie, Elisabeth; Bartlett, Susan J;

    2014-01-01

    OBJECTIVE: The OMERACT Rheumatoid Arthritis (RA) Flare Group (FG) is developing a data-driven, patient-inclusive, consensus-based RA flare definition for use in clinical trials, longterm observational studies, and clinical practice. At OMERACT 11, we sought endorsement of a proposed core domain set...

  11. 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....

  12. Time domain computational modeling of viscothermal acoustic propagation in catalytic converter substrates with porous walls

    Science.gov (United States)

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

    2005-08-01

    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.

  13. 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)

    2011-08-29

    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.

  14. 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

  15. Domain function dissection and catalytic properties of Listeria monocytogenes p60 protein with bacteriolytic activity.

    Science.gov (United States)

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

    2015-12-01

    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

  16. Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

    Science.gov (United States)

    Swinglel, Mark; Honkanel, Richard; Ciszak, Ewa

    2003-01-01

    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.

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

    OpenAIRE

    Wall Michael E; Ming Dengming; Sanbonmatsu Kevin Y

    2007-01-01

    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...

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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)

    2012-03-26

    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.

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

    OpenAIRE

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

    2010-01-01

    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...

  1. 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

    2008-01-01

    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...

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

    Directory of Open Access Journals (Sweden)

    Wall Michael E

    2007-11-01

    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.

  3. (Gold core) at (ceria shell) nanostructures for plasmon-enhanced catalytic reactions under visible light

    KAUST Repository

    Wang, Jianfang

    2014-08-26

    Driving catalytic reactions with sunlight is an excellent example of sustainable chemistry. A prerequisite of solar-driven catalytic reactions is the development of photocatalysts with high solar-harvesting efficiencies and catalytic activities. Herein, we describe a general approach for uniformly coating ceria on monometallic and bimetallic nanocrystals through heterogeneous nucleation and growth. The method allows for control of the shape, size, and type of the metal core as well as the thickness of the ceria shell. The plasmon shifts of the Au@CeO2 nanostructures resulting from the switching between Ce(IV) and Ce(III) are observed. The selective oxidation of benzyl alcohol to benzaldehyde, one of the fundamental reactions for organic synthesis, performed under both broad-band and monochromatic light, demonstrates the visible-light-driven catalytic activity and reveals the synergistic effect on the enhanced catalysis of the Au@CeO2 nanostructures. © 2014 American Chemical Society.

  4. Dealloying-based facile synthesis and highly catalytic properties of Au core/porous shell nanoparticles

    Science.gov (United States)

    Kim, Minho; Ko, Sung Min; Nam, Jwa-Min

    2016-06-01

    Porous nanostructures exhibit excellent catalytic properties due to high surface-to-volume ratio, good surface reactivity and various structural features, but controlling the distribution, size, shape and density of pores and structural features of these particles is highly challenging. Herein, we report a tunable dealloying-based facile synthetic strategy to form highly porous Au core/porous shell nanoparticles (CPS NPs) in high yield by selectively dissolving Ag atoms from Au/Au-Ag core/alloy shell NPs. The CPS NPs exhibit a very short induction time, high conversion rate constant, low activation energy and high turnover frequency due to their catalytically active porous shells containing networked thin ligaments, surface defects, ultra-high porosity and photothermal properties. The CPS NPs are more catalytic Au NPs than other reported Au nanostructures, and the strategy and results open avenues in porous nanostructures and nanocatalysts.Porous nanostructures exhibit excellent catalytic properties due to high surface-to-volume ratio, good surface reactivity and various structural features, but controlling the distribution, size, shape and density of pores and structural features of these particles is highly challenging. Herein, we report a tunable dealloying-based facile synthetic strategy to form highly porous Au core/porous shell nanoparticles (CPS NPs) in high yield by selectively dissolving Ag atoms from Au/Au-Ag core/alloy shell NPs. The CPS NPs exhibit a very short induction time, high conversion rate constant, low activation energy and high turnover frequency due to their catalytically active porous shells containing networked thin ligaments, surface defects, ultra-high porosity and photothermal properties. The CPS NPs are more catalytic Au NPs than other reported Au nanostructures, and the strategy and results open avenues in porous nanostructures and nanocatalysts. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01321j

  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.

    Science.gov (United States)

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

    1997-09-15

    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. Biochemical properties and catalytic domain structure of the CcmH protein from Escherichia coli.

    Science.gov (United States)

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

    2012-12-01

    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

  7. Synthesis of mesoporous silica hollow nanospheres with multiple gold cores and catalytic activity.

    Science.gov (United States)

    Chen, Junchen; Xue, Zhaoteng; Feng, Shanshan; Tu, Bo; Zhao, Dongyuan

    2014-09-01

    The core-shell Au@resorcinol-formaldehyde (RF) nanospheres with multiple cores have been successfully synthesized by a modified Stöber method. After coating mesoporous silica and the calcination, the Au@meso-SiO2 hollow nanospheres with multiple gold cores can be obtained, which have a high surface area (∼537 m(2)/g) and uniform pore size (∼2.5 nm). The Au@meso-SiO2 hollow nanospheres can be used as a catalyst for the reduction of 4-nitrophenol by NaBH4 into 4-aminophenol, and exhibit excellent catalytic performance. PMID:24935190

  8. 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

  9. Feasibility and Domain Validation of Rheumatoid Arthritis (RA) Flare Core Domain Set

    DEFF Research Database (Denmark)

    Bartlett, Susan J; Bykerk, Vivian P; Cooksey, Roxanne;

    2015-01-01

    OBJECTIVE: The Outcome Measures in Rheumatology (OMERACT) Rheumatoid Arthritis (RA) Flare Group was established to develop an approach to identify and measure RA flares. An overview of our OMERACT 2014 plenary is provided. METHODS: Feasibility and validity of flare domains endorsed at OMERACT 11...... (2012) were described based on initial data from 3 international studies collected using a common set of questions specific to RA flare. Mean flare frequency, severity, and duration data were presented, and domain scores were compared by flare status to examine known-groups validity. Breakout groups...... 2 other trials, with similar results. Breakout groups debated specific measurement issues. CONCLUSION: These data contribute initial evidence of feasibility and content validation of the OMERACT RA Flare Core Domain Set. Our research agenda for OMERACT 2016 includes establishing duration...

  10. 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: lkn2@cornell.edu [Cornell University, Department of Molecular Biology and Genetics (United States)

    2011-09-15

    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.

  11. 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

  12. 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.

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

    OpenAIRE

    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

    1999-01-01

    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 ...

  14. 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)

    2006-01-01

    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.

  15. Expression and purification of correctly processed, active human TACE catalytic domain in Saccharomyces cerevisiae.

    Science.gov (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

    1998-06-01

    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

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

    Directory of Open Access Journals (Sweden)

    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

  17. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues.

    Directory of Open Access Journals (Sweden)

    Hideaki Ando

    Full Text Available Phosphatidylinositol phosphate kinases (PIPKs are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5P2, a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα and type IIα (PIPKIIα in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3- cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5P2.

  18. [Molecular engineering of cellulase catalytic domain based on glycoside hydrolase family].

    Science.gov (United States)

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

    2013-04-01

    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

  19. Functional Role of Histidine in the Conserved His-x-Asp Motif in the Catalytic Core of Protein Kinases

    OpenAIRE

    Lun Zhang; Jian-Chuan Wang; Li Hou; Peng-Rong Cao; Li Wu; Qian-Sen Zhang; Huai-Yu Yang; Yi Zang; Jian-Ping Ding; Jia Li

    2015-01-01

    The His-x-Asp (HxD) motif is one of the most conserved structural components of the catalytic core of protein kinases; however, the functional role of the conserved histidine is unclear. Here we report that replacement of the HxD-histidine with Arginine or Phenylalanine in Aurora A abolishes both the catalytic activity and auto-phosphorylation, whereas the Histidine-to-tyrosine impairs the catalytic activity without affecting its auto-phosphorylation. Comparisons of the crystal structures of ...

  20. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry

    Science.gov (United States)

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

    2016-02-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Marletta Michael A

    2008-10-01

    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.

  2. 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....

  3. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Assay and Inhibition of the Purified Catalytic Domain of Diacylglycerol Lipase Beta.

    Science.gov (United States)

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

    2016-05-17

    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

  6. 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

  7. Two optical bistability domains in composites of metal nanoparticles with nonlinear dielectric core

    Energy Technology Data Exchange (ETDEWEB)

    Shewamare, Sisay, E-mail: sisayshewa20@yahoo.com [Department of Physics, Addis Ababa University, P.O. Box 1176, Addis Ababa (Ethiopia); Mal' nev, V.N., E-mail: vadimnmalnev@yahoo.com [Department of Physics, Addis Ababa University, P.O. Box 1176, Addis Ababa (Ethiopia)

    2012-12-15

    It is shown that the local field in metal spherical particles with a dielectric core in an external varying electric field has two maxima at two different frequencies. The second maximum becomes more important with an increment in the metal fraction. Due to the nonlinear dielectric function of the core, the composite of these inclusions may have two optically induced bistability domains at different frequencies. At rather high metal fraction, two bistability domains merge and form one entire bistability domain. The parameters of these domains are studied numerically. The paper focuses on the second bistability domain, which has not been discussed in the literature so far. This domain exists in a comparatively narrow frequency range and its onset fields are lower than those of the first bistability domain. The lowest bistability onset fields are obtained in the entire domain. This peculiarity of the optical induced bistability in the metal composite with small dielectric cores can be attractive for possible applications.

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

    KAUST Repository

    Wong, Aloysius Tze

    2013-07-08

    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

  9. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.

    Science.gov (United States)

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

    2002-11-01

    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

  10. 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.

    2006-01-01

    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.

  11. Conformational selection in the recognition of phosphorylated substrates by the catalytic domain of human Pin1.

    Science.gov (United States)

    Velazquez, Hector A; Hamelberg, Donald

    2011-11-01

    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

  12. 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.

  13. Modeling expert knowledge in the mediation domain: a mediation core ontology

    OpenAIRE

    Poblet, Marta; Casanovas, Pompeu

    2009-01-01

    In this paper we introduce the Mediation Core Ontology (MCO), and the steps taken in order to model the expert knowledge on the mediation domain. MCO is created from scratch by eliciting practical knowledge from mediation experts to identify the basic working concepts of the domain. MCO offers initial support towards knowledge acquisition and reasoning and, in later steps, will serve as a general basis for the development of different mediation domain and sub-domain ontologies to be used by ...

  14. Crystallization and Preliminary X-ray Diffraction Analysis of the Glucuronoyl Esterase Catalytic Domain from Hypocrea jecorina

    Science.gov (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...

  15. Catalytic properties of two Rhizopus oryzae 99-880 glucoamylase enzymes without starch binding domains expressed in Pichia pastoris

    Science.gov (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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-11-03

    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.

  17. Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation

    Science.gov (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

    2015-05-01

    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.

  18. Identifying core domains to assess flare in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Bartlett, Susan J; Hewlett, Sarah; Bingham, Clifton O;

    2012-01-01

    For rheumatoid arthritis (RA), there is no consensus on how to define and assess flare. Variability in flare definitions impairs understanding of findings across studies and limits ability to pool results. The OMERACT RA Flare Group sought to identify domains to define RA flares from patient and...

  19. Open Core Protocol (OCP) Clock Domain Crossing Interfaces

    DEFF Research Database (Denmark)

    Herlev, Mathias; Poulsen, Christian Keis; Sparsø, Jens

    2014-01-01

    The open core protocol (OCP) is an openly licensed configurable and scalable interface protocol for on-chip subsystem communications. The protocol defines read and write transactions from a master towards a slave across a point-to-point connection and the protocol assumes a single common clock. T...

  20. 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;

    2013-01-01

    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...

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

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    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.

  2. 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)

    2010-02-11

    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.

  3. Cloning, expression, purification, and characterization of the catalytic domain of sika deer MMP-13.

    Science.gov (United States)

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

    2016-11-01

    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

  4. Biochemical and spectroscopic characterization of the catalytic domain of MMP16 (cdMMP16).

    Science.gov (United States)

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

    2016-07-01

    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

  5. A Novel Approach to Predict Core Residues on Cancer-Related DNA-Binding Domains

    OpenAIRE

    Ka-Chun Wong

    2016-01-01

    Protein–DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the ...

  6. The Role of Catalytic Substrate Morphology on the Shape and Domain Size of Two-Dimensional Boron Nitride Sheets

    Science.gov (United States)

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

    2014-03-01

    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.

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

    OpenAIRE

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

    2000-01-01

    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...

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

    OpenAIRE

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

    1999-01-01

    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...

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

    Science.gov (United States)

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

    2007-12-01

    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

  10. 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)

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

    OpenAIRE

    Zhen Fang; Juan Zhang; Guocheng Du; Jian Chen

    2016-01-01

    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...

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

    Directory of Open Access Journals (Sweden)

    Yu Wei-Hsuan

    2012-05-01

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

  13. 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)

    2009-04-07

    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.

  14. Development of a Draft Core Set of Domains for Measuring Shared Decision Making in Osteoarthritis

    DEFF Research Database (Denmark)

    Toupin-April, Karine; Barton, Jennifer; Fraenkel, Liana;

    2015-01-01

    OBJECTIVE: Despite the importance of shared decision making for delivering patient-centered care in rheumatology, there is no consensus on how to measure its process and outcomes. The aim of this Outcome Measures in Rheumatology (OMERACT) working group is to determine the core set of domains for ...

  15. Direct observation of Σ7 domain boundary core structure in magnetic skyrmion lattice

    Science.gov (United States)

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

    2016-01-01

    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

  16. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis.

    Science.gov (United States)

    Boudvillain, M; Pyle, A M

    1998-12-01

    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

  17. 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)

    1993-12-31

    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.

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

    OpenAIRE

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

    2009-01-01

    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...

  19. Harmonic Domain Modelling of Transformer Core Nonlinearities Using the DIgSILENT PowerFactory Software

    DEFF Research Database (Denmark)

    Bak, Claus Leth; Bak-Jensen, Birgitte; Wiechowski, Wojciech

    2008-01-01

    This paper demonstrates the results of implementation and verification of an already existing algorithm that allows for calculating saturation characteristics of singlephase power transformers. The algorithm was described for the first time in 1993. Now this algorithm has been implemented using the...... DIgSILENT Programming Language (DPL) as an external script in the harmonic domain calculations of a power system analysis tool PowerFactory [10]. The algorithm is verified by harmonic measurements on a single-phase power transformer. A theoretical analysis of the core nonlinearities phenomena in...

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

    Directory of Open Access Journals (Sweden)

    Hye-Lim Kim

    2013-01-01

    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

  1. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.

    Science.gov (United States)

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

    1999-05-15

    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

  2. The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

    Science.gov (United States)

    De la Fuente, Ildefonso M.; Cortes, Jesus M.; Perez-Pinilla, Martin B.; Ruiz-Rodriguez, Vicente; Veguillas, Juan

    2011-01-01

    Background Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of enzymatic reactions which are always active under all environmental conditions, while the rest of catalytic processes are only intermittently active. The reactions of the metabolic core are essential for biomass formation and to assure optimal metabolic performance. The on-off catalytic reactions and the metabolic core are essential elements of a Systemic Metabolic Structure which seems to be a key feature common to all cellular organisms. Methodology/Principal Findings In order to investigate the functional importance of the metabolic core we have studied different catalytic patterns of a dissipative metabolic network under different external conditions. The emerging biochemical data have been analysed using information-based dynamic tools, such as Pearson's correlation and Transfer Entropy (which measures effective functionality). Our results show that a functional structure of effective connectivity emerges which is dynamical and characterized by significant variations of bio-molecular information flows. Conclusions/Significance We have quantified essential aspects of the metabolic core functionality. The always active enzymatic reactions form a hub –with a high degree of effective connectivity- exhibiting a wide range of functional information values being able to act either as a source or as a sink of bio-molecular causal interactions. Likewise, we have found that the metabolic core is an essential part of an emergent functional structure characterized by catalytic modules and metabolic switches which allow critical transitions in enzymatic activity. Both, the metabolic core and the catalytic switches in which also intermittently-active enzymes are involved seem to be fundamental elements in the self-regulation of the Systemic

  3. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.

    Science.gov (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

    2014-10-01

    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

  4. Immunotherapy using algal-produced Ara h 1 core domain suppresses peanut allergy in mice.

    Science.gov (United States)

    Gregory, James A; Shepley-McTaggart, Ariel; Umpierrez, Michelle; Hurlburt, Barry K; Maleki, Soheila J; Sampson, Hugh A; Mayfield, Stephen P; Berin, M Cecilia

    2016-07-01

    Peanut allergy is an IgE-mediated adverse reaction to a subset of proteins found in peanuts. Immunotherapy aims to desensitize allergic patients through repeated and escalating exposures for several months to years using extracts or flours. The complex mix of proteins and variability between preparations complicates immunotherapy studies. Moreover, peanut immunotherapy is associated with frequent negative side effects and patients are often at risk of allergic reactions once immunotherapy is discontinued. Allergen-specific approaches using recombinant proteins are an attractive alternative because they allow more precise dosing and the opportunity to engineer proteins with improved safety profiles. We tested whether Ara h 1 and Ara h 2, two major peanut allergens, could be produced using chloroplast of the unicellular eukaryotic alga, Chlamydomonas reinhardtii. C. reinhardtii is novel host for producing allergens that is genetically tractable, inexpensive and easy to grow, and is able to produce more complex proteins than bacterial hosts. Compared to the native proteins, algal-produced Ara h 1 core domain and Ara h 2 have a reduced affinity for IgE from peanut-allergic patients. We further found that immunotherapy using algal-produced Ara h 1 core domain confers protection from peanut-induced anaphylaxis in a murine model of peanut allergy. PMID:26801740

  5. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.

    Science.gov (United States)

    Sükösd, Zsuzsanna; Andersen, Ebbe S; Seemann, Stefan E; Jensen, Mads Krogh; Hansen, Mathias; Gorodkin, Jan; Kjems, Jørgen

    2015-12-01

    A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus. PMID:26476446

  6. A conserved tyrosine in the neck of a fungal kinesin regulates the catalytic motor core

    OpenAIRE

    Schäfer, Friederike; Deluca, Dominga; Majdic, Ulrike; Kirchner, Joachim; Schliwa, Manfred; Moroder, Luis; Woehlke, Günther

    2003-01-01

    The neck domain of fungal conventional kinesins displays characteristic properties which are reflected in a specific sequence pattern. The exchange of the strictly conserved Tyr 362, not present in animals, into Lys, Cys or Phe leads to a failure to dimerize. The destabilizing effect is confirmed by a lower coiled-coil propensity of mutant peptides. Whereas the Phe substitution has only a structural effect, the Lys and Cys replacements lead to dramatic kinetic changes. The steady state ATPase...

  7. Structural and catalytic properties of a novel vanadium containing solid core mesoporous silica shell catalysts for gas phase oxidation reaction

    Indian Academy of Sciences (India)

    N Venkatathri; Vijayamohanan K Pillai; A Rajini; M Nooka Raju; I A K Reddy

    2013-01-01

    A novel vanadium containing solid core mesoporous silica shell catalyst was synthesized with different Si/V ratios by sol-gel method under neutral conditions. The synthesized materials were characterized by various techniques and gas phase diphenyl methane oxidation reaction. The mesoporosity combined with microporosity are formed by incorporation of octadecyltrichloro silane and triethylamine in the catalyst and it was found out from E-DAX and BET—surface area analysis. The material was found to be nanocrystalline. Vanadium is present as V4+ species in as-synthesized samples and convert to V5+ on calcination. Most of the vanadium is present in tetrahedral or square pyramidal environment. Incorporation of vanadium in silica framework was confirmed by 29Si MAS NMR analysis. Among the various vanadium containing solid core mesoporous silica shell catalysts, the Si/V =100 ratio exhibited maximum efficiency towards diphenyl methane to benzophenone gas phase reaction. The optimum condition required for maximum conversion and selectivity was found out from the catalytic studies.

  8. 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

  9. 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.

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

    Science.gov (United States)

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

    2009-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    Eirini Trompouki

    2009-05-01

    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.

  12. Data for ion and seed dependent fibril assembly of a spidroin core domain

    Directory of Open Access Journals (Sweden)

    Martin Humenik

    2015-09-01

    Full Text Available This data article includes size exclusion chromatography data of soluble eADF4(C16, an engineered spider silk variant based on the core domain sequence of the natural dragline silk protein ADF4 of Araneus diadematus, in combination with light scattering; the protein is monomeric before assembly. The assembled mature fibrils were visualized by transmission electron microscopy (TEM and atomic force microscopy (AFM. Sonicated fibrils were used as seeds to by-pass the nucleation lag phase in eADF4(C16 assembly. We also provide data on the sedimentation kinetics of spider silk in the presence of different NaCl concentrations revealing very slow protein aggregation in comparison to the fast assembly triggered by phosphate ions published previously [1]. Experiments in the Data article represent supporting material for our work published recently [1], which described the assembly mechanism of recombinant eADF4(C16 fibrils.

  13. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    DEFF Research Database (Denmark)

    Sukosd, Zsuzsanna; Andersen, Ebbe S.; Seemann, Stefan E.;

    2015-01-01

    A distance constrained secondary structural model of the approximate to 10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which...... integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the...... structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite...

  14. 3D whole core fine mesh multigroup diffusion calculations by domain decomposition through alternate dissections

    International Nuclear Information System (INIS)

    The fine mesh diffusion formulation is extended to deal with multigroup 3-D problems in rectangular geometries. The formulation includes interface discontinuity factors per cell type, pre-calculated from transport solutions. The iterative scheme, aiming to an efficient parallel implementation in memory distributed multi-processors, is based on domain decomposition in the 4 possible sets of 4 neighbor quarters of assemblies. The alternate dissections achieve convergence to the exact boundary conditions, while attenuating high frequency noise. Whole core convergence is accelerated in the long wavelength effects by a consistent high-order analytical nodal solution performed by the ANDES solver. A neutronics - thermal-hydraulics iterative scheme is also developed to compute best estimate results, by coupling at the detailed cell-subchannel scale the COBAYA3 code with several TH subchannel codes. The numerical performance and convergence rates are verified by computing pin-cell scale solutions for the OECD/NEA/USNRC PWR MOX/UO2 Core Transient Benchmark in 8 energy groups and heterogeneous assemblies. The cell-subchannel scale neutronics and thermal-hydraulics coupling, allows the verification of the effects of the detailed TH feedbacks on cross-sections and, thus, on fuel pin powers, calculated here for a 3D color-set of two different fuel types of the previous benchmark, using COBAYA3 and COBRA-3C. (authors)

  15. Generation of a Maize B Centromere Minimal Map Containing the Central Core Domain.

    Science.gov (United States)

    Ellis, Nathanael A; Douglas, Ryan N; Jackson, Caroline E; Birchler, James A; Dawe, R Kelly

    2015-12-01

    The maize B centromere has been used as a model for centromere epigenetics and as the basis for building artificial chromosomes. However, there are no sequence resources for this important centromere. Here we used transposon display for the centromere-specific retroelement CRM2 to identify a collection of 40 sequence tags that flank CRM2 insertion points on the B chromosome. These were confirmed to lie within the centromere by assaying deletion breakpoints from centromere misdivision derivatives (intracentromere breakages caused by centromere fission). Markers were grouped together on the basis of their association with other markers in the misdivision series and assembled into a pseudocontig containing 10.1 kb of sequence. To identify sequences that interact directly with centromere proteins, we carried out chromatin immunoprecipitation using antibodies to centromeric histone H3 (CENH3), a defining feature of functional centromeric sequences. The CENH3 chromatin immunoprecipitation map was interpreted relative to the known transmission rates of centromere misdivision derivatives to identify a centromere core domain spanning 33 markers. A subset of seven markers was mapped in additional B centromere misdivision derivatives with the use of unique primer pairs. A derivative previously shown to have no canonical centromere sequences (Telo3-3) lacks these core markers. Our results provide a molecular map of the B chromosome centromere and identify key sequences within the map that interact directly with centromeric histone H3. PMID:26511496

  16. Quanty for core level spectroscopy - excitons, resonances and band excitations in time and frequency domain

    Science.gov (United States)

    Haverkort, Maurits W.

    2016-05-01

    Depending on the material and edge under consideration, core level spectra manifest themselves as local excitons with multiplets, edge singularities, resonances, or the local projected density of states. Both extremes, i.e., local excitons and non-interacting delocalized excitations are theoretically well under control. Describing the intermediate regime, where local many body interactions and band-formation are equally important is a challenge. Here we discuss how Quanty, a versatile quantum many body script language, can be used to calculate a variety of different core level spectroscopy types on solids and molecules, both in the frequency as well as the time domain. The flexible nature of Quanty allows one to choose different approximations for different edges and materials. For example, using a newly developed method merging ideas from density renormalization group and quantum chemistry [1-3], Quanty can calculate excitons, resonances and band-excitations in x-ray absorption, photoemission, x-ray emission, fluorescence yield, non-resonant inelastic x-ray scattering, resonant inelastic x-ray scattering and many more spectroscopy types. Quanty can be obtained from: http://www.quanty.org.

  17. Non-catalytic site HIV-1 integrase inhibitors disrupt core maturation and induce a reverse transcription block in target cells.

    Directory of Open Access Journals (Sweden)

    Mini Balakrishnan

    Full Text Available HIV-1 integrase (IN is the target for two classes of antiretrovirals: i the integrase strand-transfer inhibitors (INSTIs and ii the non-catalytic site integrase inhibitors (NCINIs. NCINIs bind at the IN dimer interface and are thought to interfere primarily with viral DNA (vDNA integration in the target cell by blocking IN-vDNA assembly as well as the IN-LEDGF/p75 interaction. Herein we show that treatment of virus-producing cells, but not of mature virions or target cells, drives NCINI antiviral potency. NCINIs target an essential late-stage event in HIV replication that is insensitive to LEDGF levels in the producer cells. Virus particles produced in the presence of NCINIs displayed normal Gag-Pol processing and endogenous reverse transcriptase activity, but were defective at initiating vDNA synthesis following entry into the target cell. NCINI-resistant virus carrying a T174I mutation in the IN dimer interface was less sensitive to the compound-induced late-stage effects, including the reverse transcription block. Wild-type, but not T174I virus, produced in the presence of NCINIs exhibited striking defects in core morphology and an increased level of IN oligomers that was not observed upon treatment of mature cell-free particles. Collectively, these results reveal that NCINIs act through a novel mechanism that is unrelated to the previously observed inhibition of IN activity or IN-LEDGF interaction, and instead involves the disruption of an IN function during HIV-1 core maturation and assembly.

  18. Non-catalytic site HIV-1 integrase inhibitors disrupt core maturation and induce a reverse transcription block in target cells.

    Science.gov (United States)

    Balakrishnan, Mini; Yant, Stephen R; Tsai, Luong; O'Sullivan, Christopher; Bam, Rujuta A; Tsai, Angela; Niedziela-Majka, Anita; Stray, Kirsten M; Sakowicz, Roman; Cihlar, Tomas

    2013-01-01

    HIV-1 integrase (IN) is the target for two classes of antiretrovirals: i) the integrase strand-transfer inhibitors (INSTIs) and ii) the non-catalytic site integrase inhibitors (NCINIs). NCINIs bind at the IN dimer interface and are thought to interfere primarily with viral DNA (vDNA) integration in the target cell by blocking IN-vDNA assembly as well as the IN-LEDGF/p75 interaction. Herein we show that treatment of virus-producing cells, but not of mature virions or target cells, drives NCINI antiviral potency. NCINIs target an essential late-stage event in HIV replication that is insensitive to LEDGF levels in the producer cells. Virus particles produced in the presence of NCINIs displayed normal Gag-Pol processing and endogenous reverse transcriptase activity, but were defective at initiating vDNA synthesis following entry into the target cell. NCINI-resistant virus carrying a T174I mutation in the IN dimer interface was less sensitive to the compound-induced late-stage effects, including the reverse transcription block. Wild-type, but not T174I virus, produced in the presence of NCINIs exhibited striking defects in core morphology and an increased level of IN oligomers that was not observed upon treatment of mature cell-free particles. Collectively, these results reveal that NCINIs act through a novel mechanism that is unrelated to the previously observed inhibition of IN activity or IN-LEDGF interaction, and instead involves the disruption of an IN function during HIV-1 core maturation and assembly. PMID:24040198

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

    Science.gov (United States)

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

    2016-01-01

    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

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

    Science.gov (United States)

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

    2016-01-01

    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

  1. Functional analysis of the catalytic subunit of Dictyostelium PKA in vivo.

    Science.gov (United States)

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

    1998-03-01

    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

  2. Changes in Protein Domains outside the Catalytic Site of the Bacteriophage Qβ Replicase Reduce the Mutagenic Effect of 5-Azacytidine

    Science.gov (United States)

    Cabanillas, Laura; Sanjuán, Rafael

    2014-01-01

    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

  3. Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.

    Science.gov (United States)

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

    2001-01-01

    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

  4. Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

    Energy Technology Data Exchange (ETDEWEB)

    Wallentine, Brad D.; Wang, Ying; Tretyachenko-Ladokhina, Vira; Tan, Martha; Senear, Donald F. [University of California, Irvine, Irvine, CA 92697 (United States); Luecke, Hartmut, E-mail: hudel@uci.edu [University of California, Irvine, Irvine, CA 92697 (United States); University of California, Irvine, Irvine, CA 92697 (United States); University of California, Irvine, Irvine, CA 92697 (United States); University of California, Irvine, Irvine, CA 92697 (United States); Universidad del Pais Vasco, 48940 Leioa (Spain)

    2013-10-01

    X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53. To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutation substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol{sup −1} (15.1 kJ mol{sup −1}). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the

  5. Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

    International Nuclear Information System (INIS)

    X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53. To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutation substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol−1 (15.1 kJ mol−1). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the β-sandwich scaffold. On the

  6. Facile synthesis of near-monodisperse Ag-Ni core-shell nanoparticles and their application for catalytic generation of hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Guo Huizhang; Chen Yuanzhi; Chen Xiaozhen; Wen Ruitao; Yue Guanghui; Peng Dongliang, E-mail: yuanzhi@xmu.edu.cn, E-mail: dlpeng@xmu.edu.cn [Department of Materials Science and Engineering, College of Materials, Xiamen University, Xiamen 361005 (China)

    2011-05-13

    Magnetically recyclable Ag-Ni core-shell nanoparticles have been fabricated via a simple one-pot synthetic route using oleylamine both as solvent and reducing agent and triphenylphosphine as a surfactant. As characterized by transmission electron microscopy (TEM), the as-synthesized Ag-Ni core-shell nanoparticles exhibit a very narrow size distribution with a typical size of 14.9 {+-} 1.2 nm and a tunable shell thickness. UV-vis absorption spectroscopy study shows that the formation of a Ni shell on Ag core can damp the surface plasmon resonance (SPR) of the Ag core and lead to a red-shifted SPR absorption peak. Magnetic measurement indicates that all the as-synthesized Ag-Ni core-shell nanoparticles are superparamagnetic at room temperature, and their blocking temperatures can be controlled by modulating the shell thickness. The as-synthesized Ag-Ni core-shell nanoparticles exhibit excellent catalytic properties for the generation of H{sub 2} from dehydrogenation of sodium borohydride in aqueous solutions. The hydrogen generation rate of Ag-Ni core-shell nanoparticles is found to be much higher than that of Ag and Ni nanoparticles of a similar size, and the calculated activation energy for hydrogen generation is lower than that of many bimetallic catalysts. The strategy employed here can also be extended to other noble-magnetic metal systems.

  7. Facile synthesis of near-monodisperse Ag-Ni core-shell nanoparticles and their application for catalytic generation of hydrogen

    International Nuclear Information System (INIS)

    Magnetically recyclable Ag-Ni core-shell nanoparticles have been fabricated via a simple one-pot synthetic route using oleylamine both as solvent and reducing agent and triphenylphosphine as a surfactant. As characterized by transmission electron microscopy (TEM), the as-synthesized Ag-Ni core-shell nanoparticles exhibit a very narrow size distribution with a typical size of 14.9 ± 1.2 nm and a tunable shell thickness. UV-vis absorption spectroscopy study shows that the formation of a Ni shell on Ag core can damp the surface plasmon resonance (SPR) of the Ag core and lead to a red-shifted SPR absorption peak. Magnetic measurement indicates that all the as-synthesized Ag-Ni core-shell nanoparticles are superparamagnetic at room temperature, and their blocking temperatures can be controlled by modulating the shell thickness. The as-synthesized Ag-Ni core-shell nanoparticles exhibit excellent catalytic properties for the generation of H2 from dehydrogenation of sodium borohydride in aqueous solutions. The hydrogen generation rate of Ag-Ni core-shell nanoparticles is found to be much higher than that of Ag and Ni nanoparticles of a similar size, and the calculated activation energy for hydrogen generation is lower than that of many bimetallic catalysts. The strategy employed here can also be extended to other noble-magnetic metal systems.

  8. Fabrication of Core-Shell Structural SiO2@H3[PM12O40] Material and Its Catalytic Activity

    Directory of Open Access Journals (Sweden)

    Xin Yang

    2014-01-01

    Full Text Available Through a natural tree grain template and sol-gel technology, the heterogeneous catalytic materials based on polyoxometalate compounds H3[PM12O40] encapsulating SiO2: SiO2@H3[PM12O40] (SiO2@PM12, M = W, Mo with core-shell structure had been prepared. The structure and morphology of the core-shell microspheres were characterized by the XRD, IR spectroscopy, UV-Vis absorbance, and SEM. These microsphere materials can be used as heterogeneous catalysts with high activity and stability for catalytic wet air oxidation of pollutant dyes safranine T (ST at room condition. The results show that the catalysts have excellent catalytic activity in treatment of wastewater containing 10 mg/L ST, and 94% of color can be removed within 60 min. Under different cycling runs, it is shown that the catalysts are stable under such operating conditions and the leaching tests show negligible leaching effect owing to the lesser dissolution.

  9. Synthesis of Hβ (core)/SAPO-11 (shell) Composite Molecular Sieve and its Catalytic Performances in the Methylation of Naphthalene with Methanol

    International Nuclear Information System (INIS)

    Hβ (core)/SAPO-11 (shell) composite molecular sieve was synthesized by the hydrothermal method in order to combine the advantages of Hβ and SAPO-11 for the methylation of naphthalene with methanol. For comparison, the mechanical mixture was prepared through the blending of Hβ and SAPO-11. The physicochemical properties of Hβ, SAPO-11, the composite and the mechanical mixture were characterized by various characterization methods. The characterization results indicated that Hβ/SAPO-11 composite molecular sieve exhibited a core-shell structure, with the Hβ phase as the core and the SAPO-11 phase as the shell. The pore diameter of the composite was between that of Hβ and SAPO-11. The composite had fewer acid sites than Hβ and mechanical mixture while more acid sites than SAPO-11. The experimental results indicated that the composite exhibited high catalytic performances for the methylation of naphthalene with methanol

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

    OpenAIRE

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

    1998-01-01

    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...

  11. Magnetic Co@g-C3N4 Core-Shells on rGO Sheets for Momentum Transfer with Catalytic Activity toward Continuous-Flow Hydrogen Generation.

    Science.gov (United States)

    Duan, Shasha; Han, Guosheng; Su, Yongheng; Zhang, Xiaoyu; Liu, Yanyan; Wu, Xianli; Li, Baojun

    2016-06-28

    Magnetic core-shell structures provide abundant opportunities for the construction of multifunctional composites. In this article, magnetic core-shells were fabricated with Co nanoparticles (NPs) as cores and g-C3N4 as shells. In the fabrication process, the Co@g-C3N4 core-shells were anchored onto the rGO nanosheets to form a Co@g-C3N4-rGO composite (CNG-I). For hydrogen generation from the hydrolysis of NaBH4 or NH3BH3, the Co NP cores act as catalytic active sites. The g-C3N4 shells protect Co NPs cores from aggregating or growing. The connection between Co NPs and rGO was strengthened by the g-C3N4 shells to prevent them from leaching or flowing away. The g-C3N4 shells also work as a cocatalyst for hydrogen generation. The magnetism of Co NPs and the shape of rGO nanosheets achieve effective momentum transfer in the external magnetic field. In the batch reactor, a higher catalytic activity was obtained for CNG-I in self-stirring mode than in magneton stirring mode. In the continuous-flow process, stable hydrogen generation was carried out with CNG-I being fixed and propelled by the external magnetic field. The separation film is unnecessary because of magnetic momentum transfer. This idea of the composite design and magnetic momentum transfer will be useful for the development of both hydrogen generation and multifunctional composite materials. PMID:27276187

  12. Domain Walls and Anchoring Transitions Mimicking Nematic Biaxiality in the Oxadiazole Bent-Core Liquid Crystal C7

    OpenAIRE

    Kim, Young-Ki; Cukrov, Greta; Xiang, Jie; Shin, Sung-Tae; Lavrentovich, Oleg D.

    2015-01-01

    We investigate the origin of secondary disclinations that were recently described as a new evidence of a biaxial nematic phase in an oxadiazole bent-core thermotropic liquid crystal C7. With an assortment of optical techniques such as polarizing optical microscopy, LC PolScope, and fluorescence confocal polarizing microscopy, we demonstrate that the secondary disclinations represent non-singular domain walls formed in an uniaxial nematic during the surface anchoring transition, in which surfa...

  13. 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

  14. High-resolution structure of an α-spectrin SH3-domain mutant with a redesigned hydrophobic core

    International Nuclear Information System (INIS)

    The structure of an α-spectrin SH3-domain mutant with a stabilized hydrophobic core and distal loop has been solved at 1 Å resolution. The α-spectrin SH3 domain (Spc-SH3) is a small modular domain which has been broadly used as a model protein in folding studies and these studies have sometimes been supported by structural information obtained from the coordinates of Spc-SH3 mutants. The structure of B5/D48G, a multiple mutant designed to improve the hydrophobic core and as a consequence the protein stability, has been solved at 1 Å resolution. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 24.79, b = 37.23, c = 62.95 Å. This mutant also bears a D48G substitution in the distal loop and this mutation has also been reported to increase the stability of the protein by itself. The structure of the B5/D48G mutant shows a highly packed hydrophobic core and a more ordered distal loop compared with previous Spc-SH3 structures

  15. 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.

    2010-01-01

    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

  16. 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

    2009-03-01

    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.

  17. Exploring the 49-kDa subunit as part of the catalytic core of complex I (NADH:ubiquinone oxidoreductase) from Yarrowia lipolytica

    OpenAIRE

    Grgic, Ljuban

    2004-01-01

    Ligands of Iron-Sulphur Cluster N2: In this work the ubiquinone reducing catalytic core of NADH:ubiquinone oxidoreductase (complex I) from Y. lipolytica was studied by a series of point mutations replacing conserved histidines or arginines in the 49-kDa subunit. Although the missing 4th ligand of cluster N2 could not be found in the 49-kDa subunit of complex I, it was clearly demonstrated that iron-sulphur cluster N2 resides directly on the interface between the PSST and 49-kDa subunits. The ...

  18. Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change

    OpenAIRE

    Borda, Emily J.; Markley, John C.; Sigurdsson, Snorri Th.

    2003-01-01

    We have characterized a novel Zn2+-catalyzed cleavage site between nucleotides C3 and U4 in the catalytic core of the hammerhead ribozyme. In contrast to previously described divalent metal-ion-dependent cleavage of RNA, U4 cleavage is only observed in the presence of Zn2+. This new cleavage site has an unusual pH dependence, in that U4 cleavage products are only observed above pH 7.9 and reach a maximum yield at about pH 8.5. These data, together with the fact that no metal ion-binding site ...

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

    OpenAIRE

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

    2010-01-01

    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...

  20. New experimental treatments of core social domain in Autism Spectrum Disorders

    OpenAIRE

    Roberto eCanitano

    2014-01-01

    Current therapeutics in Autism Spectrum Disorders (ASD) only treat the associated symptoms, without addressing core social dysfunctions. A paradigm shift in research of the pathogenesis of ASD, its synaptic abnormalities and altered signaling in multiple dynamic systems, have led to new experimental treatments for treating the core social abnormalities of ASD. NMDA antagonists, especially memantine, have been introduced in clinical trials addressing glutamatergic transmission in children a...

  1. New Experimental Treatments for Core Social Domain in Autism Spectrum Disorders

    OpenAIRE

    Canitano, Roberto

    2014-01-01

    Current therapeutics in autism spectrum disorders (ASD) only treat the associated symptoms, without addressing core social dysfunctions. A paradigm shift in research of the pathogenesis of ASD, its synaptic abnormalities and altered signaling in multiple dynamic systems, have led to new experimental treatments for treating the core social abnormalities of ASD. NMDA antagonists, especially memantine, have been introduced in clinical trials addressing glutamatergic transmission in children and ...

  2. Hepatitis B Virus Core Protein Phosphorylation Sites Affect Capsid Stability and Transient Exposure of the C-terminal Domain.

    Science.gov (United States)

    Selzer, Lisa; Kant, Ravi; Wang, Joseph C-Y; Bothner, Brian; Zlotnick, Adam

    2015-11-20

    Hepatitis B virus core protein has 183 amino acids divided into an assembly domain and an arginine-rich C-terminal domain (CTD) that regulates essential functions including genome packaging, reverse transcription, and intracellular trafficking. Here, we investigated the CTD in empty hepatitis B virus (HBV) T=4 capsids. We examined wild-type core protein (Cp183-WT) and a mutant core protein (Cp183-EEE), in which three CTD serines are replaced with glutamate to mimic phosphorylated protein. We found that Cp183-WT capsids were less stable than Cp183-EEE capsids. When we tested CTD sensitivity to trypsin, we detected two different populations of CTDs differentiated by their rate of trypsin cleavage. Interestingly, CTDs from Cp183-EEE capsids exhibited a much slower rate of proteolytic cleavage when compared with CTDs of Cp183-WT capsids. Cryo-electron microscopy studies of trypsin-digested capsids show that CTDs at five-fold symmetry vertices are most protected. We hypothesize that electrostatic interactions between glutamates and arginines in Cp183-EEE, particularly at five-fold, increase capsid stability and reduce CTD exposure. Our studies show that quasi-equivalent CTDs exhibit different rates of exposure and thus might perform distinct functions during the hepatitis B virus lifecycle. Our results demonstrate a structural role for CTD phosphorylation and indicate crosstalk between CTDs within a capsid particle. PMID:26405031

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

    OpenAIRE

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

    2008-01-01

    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...

  4. 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

  5. Quantitative analysis of the interaction between the envelope protein domains and the core protein of human hepatitis B virus

    International Nuclear Information System (INIS)

    Interaction between preformed nucleocapsids and viral envelope proteins is critical for the assembly of virus particles in infected cells. The pre-S1 and pre-S2 and cytosolic regions of the human hepatitis B virus envelope protein had been implicated in the interaction with the core protein of nucleocapsids. The binding affinities of specific subdomains of the envelope protein to the core protein were quantitatively measured by both ELISA and BIAcore assay. While a marginal binding was detected with the pre-S1 or pre-S2, the core protein showed high affinities to pre-S with apparent dissociation constants (KDapp) of 7.3 ± 0.9 and 8.2 ± 0.4 μM by ELISA and BIAcore assay, respectively. The circular dichroism analysis suggested that conformational change occurs in pre-S through interaction with core protein. These results substantiate the importance of specific envelope domains in virion assembly, and demonstrate that the interaction between viral proteins can be quantitatively measured in vitro

  6. Antigenic determinants and functional domains in core antigen and e antigen from hepatitis B virus

    International Nuclear Information System (INIS)

    The precore/core gene of hepatitis B virus directs the synthesis of two polypeptides, the 21-kilodalton subunit (p21c) forming the viral nucleocapsid (serologically defined as core antigen [HBcAg]) and a secreted processed protein (p17e, serologically defined as HBe antigen [HBeAg]). Although most of their primary amino acid sequences are identical, HBcAg and HBeAg display different antigenic properties that are widely used in hepatitis B virus diagnosis. To locate and to characterize the corresponding determinants, segments of the core gene were expressed in Escherichia coli and probed with a panel of polyclonal or monoclonal antibodies in radioimmunoassays or enzyme-linked immunosorbent assays, Western blots, and competition assays. Three distinct major determinants were characterized. It is postulated that HBcAg and HBeAg share common basic three-dimensional structure exposing the common linear determinant HBe1 but that they differ in the presentation of two conformational determinants that are either introduced (HBc) or masked (HBe2) in the assembled core. The simultaneous presentation of HBe1 and HBc, two distinctly different antigenic determinants with overlapping amino acid sequences, is interpreted to indicate the presence of slightly differently folded, stable conformational states of p21c in the hepatitis virus nucleocapsid

  7. 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

    2014-01-01

    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...

  8. 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

    OpenAIRE

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

    2007-01-01

    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 ...

  9. 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

    2003-01-01

    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....

  10. MOLECULAR CLONING OF hTRT CATALYTIC DOMAIN FROM HeLa CELLS AND ITS EXPRESSION IN E. Coli AND PURIFICATION

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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.

  11. Harmonic Domain Modelling of Transformer Core Nonlinearities Using the DIgSILENT PowerFactory Software

    OpenAIRE

    Bak, Claus Leth; Bak-Jensen, Birgitte; Wiechowski, Wojciech

    2008-01-01

    This paper demonstrates the results of implementation and verification of an already existing algorithm that allows for calculating saturation characteristics of singlephase power transformers. The algorithm was described for the first time in 1993. Now this algorithm has been implemented using the DIgSILENT Programming Language (DPL) as an external script in the harmonic domain calculations of a power system analysis tool PowerFactory [10]. The algorithm is verified by harmonic measurements ...

  12. Identifying flares in rheumatoid arthritis: reliability and construct validation of the OMERACT RA Flare Core Domain Set

    Science.gov (United States)

    Bykerk, Vivian P; Bingham, Clifton O; Choy, Ernest H; Lin, Daming; Alten, Rieke; Christensen, Robin; Furst, Daniel E; Hewlett, Sarah; Leong, Amye; March, Lyn; Woodworth, Thasia; Boire, Gilles; Haraoui, Boulos; Hitchon, Carol; Jamal, Shahin; Keystone, Edward C; Pope, Janet; Tin, Diane; Thorne, J Carter

    2016-01-01

    Objective To evaluate the reliability of concurrent flare identification using 3 methods (patient, rheumatologist and Disease Activity Score (DAS)28 criteria), and construct validity of candidate items representing the Outcome Measures in Rheumatology Clinical Trials (OMERACT) RA Flare Core Domain Set. Methods Candidate flare questions and legacy measures were administered at consecutive visits to Canadian Early Arthritis Cohort (CATCH) patients between November 2011 and November 2014. The American College of Rheumatology (ACR) core set indicators were recorded. Concordance to identify flares was assessed using the agreement coefficient. Construct validity of flare questions was examined: convergent (Spearman's r); discriminant (mean differences between flaring/non-flaring patients); and consequential (proportions with prior treatment reductions and intended therapeutic change postflare). Results The 849 patients were 75% female, 81% white, 42% were in remission/low disease activity (R/LDA), and 16–32% were flaring at the second visit. Agreement of flare status was low–strong (κ's 0.17–0.88) and inversely related to RA disease activity level. Flare domains correlated highly (r's≥0.70) with each other, patient global (r's≥0.66) and corresponding measures (r's 0.49–0.92); and moderately highly with MD and patient-reported joint counts (r's 0.29–0.62). When MD/patients agreed the patient was flaring, mean flare domain between-group differences were 2.1–3.0; 36% had treatment reductions prior to flare, with escalation planned in 61%. Conclusions Flares are common in rheumatoid arthritis (RA) and are often preceded by treatment reductions. Patient/MD/DAS agreement of flare status is highest in patients worsening from R/LDA. OMERACT RA flare questions can discriminate between patients with/without flare and have strong evidence of construct and consequential validity. Ongoing work will identify optimal scoring and cut points to identify RA flares. PMID

  13. Expression divergence of the AGL6 MADS domain transcription factor lineage after a core eudicot duplication suggests functional diversification

    Directory of Open Access Journals (Sweden)

    Melzer Siegbert

    2010-07-01

    Full Text Available Abstract Background Because of their known role as transcriptional regulators of key plant developmental processes, the diversification of MADS-box gene function is thought to be a major driving force in the developmental evolution of plants. Yet the function of some MADS-box gene subfamilies has remained elusive thus far. One such lineage, AGL6, has now been functionally characterized in three angiosperm species, but a phylogenetic framework for comparison of AGL6 gene function is currently missing. Results Based on phylogenetic analyses of newly isolated and EST-based sequences, we describe the duplication history of the AGL6 subfamily in angiosperms. Our analyses provide support for four ancient duplications in the evolution of the AGL6 lineage: one at the base of core eudicots resulting in euAGL6 and AGL6-like gene clades, one during basal angiosperm diversification and two in monocot evolution. To investigate whether the spatial domains in which AGL6 genes function have diverged after duplication, we use quantitative Real Time PCR. We show that the core eudicot AGL6-like clade acquired expression in vegetative tissues, while its paralog euAGL6 remains predominantly confined to reproductive tissues. Conclusions These and previous data lead us to propose that the AGL6 lineage in core eudicots, in addition to functions related to the expression in reproductive structures, may have acquired a function in developmental transitions of vegetative shoots.

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

    Science.gov (United States)

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

    2001-10-01

    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

  15. Synthesis and Catalytic Activity of a Two-core Ruthenium Carbene Complex: a Unique Catalyst for Ring Closing Metathesis Reaction

    Institute of Scientific and Technical Information of China (English)

    SHAO Ming-bo; WANG Jian-hui

    2011-01-01

    The reaction of a ruthenium carbide complex RuCl2(C:)(PCy3)2 with [H(Et2O)x]+[BF4]- at a molar ratio of 1:2 produced a two-core ruthenium carbene complex,{[RuCl(=HPCy3)(PCy3)]2(μ-Cl)3}+[BF4]-,in the form of a yellow-green crystalline solid in a yield of 94%.This two-core ruthenium complex is a selective catalyst for ring closing metathesis of unsubstituted terminal dienes.More importantly,no isomerized byproduct was observed for N-substrates when the two-core ruthenium complex was used as the catalyst at an elevated temperature(137 ℃),indicating that the complex is a chemo-selective catalyst for ring closing metathesis reactions.

  16. Plasmonic enhancement of the optical absorption and catalytic efficiency of BiVO₄ photoanodes decorated with Ag@SiO₂ core-shell nanoparticles.

    Science.gov (United States)

    Abdi, Fatwa F; Dabirian, Ali; Dam, Bernard; van de Krol, Roel

    2014-08-01

    Recent progress in the development of bismuth vanadate (BiVO4) photoanodes has firmly established it as a promising material for solar water splitting applications. Performance limitations due to intrinsically poor catalytic activity and slow electron transport have been successfully addressed through the application of water oxidation co-catalysts and novel doping strategies. The next bottleneck to tackle is the modest optical absorption in BiVO4, particularly close to its absorption edge of 2.4 eV. Here, we explore the modification of the BiVO4 surface with Ag@SiO2 core-shell plasmonic nanoparticles. A photocurrent enhancement by a factor of ~2.5 is found under 1 sun illumination (AM1.5). We show that this enhancement consists of two contributions: optical absorption and catalysis. The optical absorption enhancement is induced by the excitation of localized surface plasmon resonances in the Ag nanoparticles, and agrees well with our full-field electromagnetic simulations. Far-field effects (scattering) are found to be dominant, with a smaller contribution from near-field plasmonic enhancement. In addition, a significant catalytic enhancement is observed, which is tentatively attributed to the electrocatalytic activity of the Ag@SiO2 nanoparticles. PMID:24942363

  17. New experimental treatments of core social domain in Autism Spectrum Disorders

    Directory of Open Access Journals (Sweden)

    Roberto eCanitano

    2014-06-01

    Full Text Available Current therapeutics in Autism Spectrum Disorders (ASD only treat the associated symptoms, without addressing core social dysfunctions. A paradigm shift in research of the pathogenesis of ASD, its synaptic abnormalities and altered signaling in multiple dynamic systems, have led to new experimental treatments for treating the core social abnormalities of ASD. NMDA antagonists, especially memantine, have been introduced in clinical trials addressing glutamatergic transmission in children and adolescents with ASD. GABAergic signaling has been targeted in trials using the GABAB receptor agonist arbaclofen for ASD patients with promising results. Oxytocin has been recognized as implicated in social development and affiliative behaviours. Preliminary findings from clinical trials using oxytocin in children with ASD show encouraging improvements in social cognition, but larger studies are needed. In two of the single gene disorders associated with ASD, Insulin Growth Factor (IGF-1 is a new treatment that has been tested in Rett Syndrome and Phelan-McDermid Syndrome (Chromosome 22 deletion syndrome. IGF-1 has been demonstrated to reverse the reduction in the number of excitatory synapses and the density of neurons that characterize these conditions in animal studies and it is being introduced as an experimental treatment..As a novel approach to verify treatment efficacy,neural processing modifications were recently evaluated by fMRI after a Pivotal Response Training (PRT intervention. Another study of neural changes in response to treatment examined variations in EEG signaling in patientsafter an Early Start Denver Model (ESDM intervention.

  18. Dissociation of Bak α1 helix from the core and latch domains is required for apoptosis.

    Science.gov (United States)

    Alsop, Amber E; Fennell, Stephanie C; Bartolo, Ray C; Tan, Iris K L; Dewson, Grant; Kluck, Ruth M

    2015-01-01

    During apoptosis, Bak permeabilizes mitochondria after undergoing major conformational changes, including poorly defined N-terminal changes. Here, we characterize those changes using 11 antibodies that were epitope mapped using peptide arrays and mutagenesis. After Bak activation by Bid, epitopes throughout the α1 helix are exposed indicating complete dissociation of α1 from α2 in the core and from α6-α8 in the latch. Moreover, disulfide tethering of α1 to α2 or α6 blocks cytochrome c release, suggesting that α1 dissociation is required for further conformational changes during apoptosis. Assaying epitope exposure when α1 is tethered shows that Bid triggers α2 movement, followed by α1 dissociation. However, α2 reaches its final position only after α1 dissociates from the latch. Thus, α1 dissociation is a key step in unfolding Bak into three major components, the N terminus, the core (α2-α5) and the latch (α6-α8). PMID:25880232

  19. 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

    2002-09-01

    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.

  20. CORE

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Hundebøll, Martin;

    2013-01-01

    different flows. Instead of maintaining these approaches separate, we propose a protocol (CORE) that brings together these coding mechanisms. Our protocol uses random linear network coding (RLNC) for intra- session coding but allows nodes in the network to setup inter- session coding regions where flows...... increase the benefits of XORing by exploiting the underlying RLNC structure of individual flows. This goes beyond providing additional reliability to each individual session and beyond exploiting coding opportunistically. Our numerical results show that CORE outperforms both forwarding and COPE......-like schemes in general. More importantly, we show gains of up to 4 fold over COPE-like schemes in terms of transmissions per packet in one of the investigated topologies....

  1. Photochemical synthesis of bimetallic Au-Ag nanoparticles with "core-shell" type structure by seed mediated catalytic growth

    Institute of Scientific and Technical Information of China (English)

    DONG Shou-an; TANG Chun

    2005-01-01

    The colloidal Au core/Ag shell structure composite nanoparticles were synthesized in PEG-acetone solution by photochemical route. The monodispersed Au nanoparticles with average diameter of 3.9 nm were used as growth seeds. The optical property of colloids and the sizes of composite nanoparticles were characterized when the molar ratio of Au to Ag ranges from 4 : 1 to 1 : 4. The results show that a composite nanoparticle structure similar to strawberry shape is formed at the molar ratio of Au to Ag from 4 : 1 to 1 : 1; the composite nanoparticles consisting of a core of Au and shell of Ag were generated at the 1: 4 molar ratio, having a striking feature of forming interconnected network structure.

  2. Immobilization of metalloporphyrins on CeO2@SiO2 with a core-shell structure prepared via microemulsion method for catalytic oxidation of ethylbenzene

    Institute of Scientific and Technical Information of China (English)

    沈丹华; 吉琳韬; 付玲玲; 董旭龙; 刘志刚; 刘强; 刘世明

    2015-01-01

    CeO2@SiO2 core−shell nanoparticles were prepared by microemulsion method, and metalloporphyrins were immobilized on the CeO2@SiO2 core−shell nanoparticles surface via amide bond. The supported metalloporphyrin catalysts were characterized by N2 adsorption−desorption isotherm (BET), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), ultraviolet and visible spectroscopy (UV-Vis), and Fourier transform infrared spectroscopy (FT-IR). The results show that the morphology of CeO2@SiO2 nanoparticles is core−shell microspheres with about 30 nm in diameter, and metalloporphyrins are immobilized on the CeO2@SiO2 core−shell nanoparticles via amide bond. Especially, the core−shell structure contains multi CeO2 core and thin SiO2 shell, which may benefit the synergistic effect between the CeO2 core and the porphyrin anchored on the very thin SiO2 shell. As a result, this supported metalloporphyrin catalysts present comparably high catalytic activity and stability for oxidation of ethylbenzene with molecular oxygen, namely, ethylbenzene conversion remains around 12% with identical selectivity of about 80%for acetophenone even after six-times reuse of the catalyst.

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

    KAUST Repository

    Liu, Chenggang

    2012-04-03

    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.

  4. Insight into the Catalytic Mechanism of Bimetallic Platinum-Copper Core-Shell Nanostructures for Nonaqueous Oxygen Evolution Reactions.

    Science.gov (United States)

    Ma, Lu; Luo, Xiangyi; Kropf, A Jeremy; Wen, Jianguo; Wang, Xiaoping; Lee, Sungsik; Myers, Deborah J; Miller, Dean; Wu, Tianpin; Lu, Jun; Amine, Khalil

    2016-01-13

    The oxygen evolution reaction (OER) plays a critical role in multiple energy conversion and storage applications. However, its sluggish kinetics usually results in large voltage polarization and unnecessary energy loss. Therefore, designing efficient catalysts that could facilitate this process has become an emerging topic. Here, we present a unique Pt-Cu core-shell nanostructure for catalyzing the nonaqueous OER. The catalysts were systematically investigated with comprehensive spectroscopic techniques, and applied in nonaqueous Li-O2 electrochemical cells, which exhibited dramatically reduced charging overpotential (OER catalysts. PMID:26709945

  5. Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity.

    Science.gov (United States)

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

    2012-05-01

    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

  6. Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site

    Energy Technology Data Exchange (ETDEWEB)

    Wielens, Jerome; Headey, Stephen J.; Jeevarajah, Dharshini; Rhodes, David I.; Deadman, John; Chalmers, David K.; Scanlon, Martin J.; Parker, Michael W. (SVIMR-A); (Avea); (Monash IPS)

    2010-04-19

    HIV integrase (IN) is an essential enzyme in HIV replication and an important target for drug design. IN has been shown to interact with a number of cellular and viral proteins during the integration process. Disruption of these important interactions could provide a mechanism for allosteric inhibition of IN. We present the highest resolution crystal structure of the IN core domain to date. We also present a crystal structure of the IN core domain in complex with sucrose which is bound at the dimer interface in a region that has previously been reported to bind integrase inhibitors.

  7. Selective catalytic reduction of NO over Fe-ZSM-5: mechanistic insights by operando HERFD-XANES and valence-to-core X-ray emission spectroscopy.

    Science.gov (United States)

    Boubnov, Alexey; Carvalho, Hudson W P; Doronkin, Dmitry E; Günter, Tobias; Gallo, Erik; Atkins, Andrew J; Jacob, Christoph R; Grunwaldt, Jan-Dierk

    2014-09-17

    An in-depth understanding of the active site requires advanced operando techniques and the preparation of defined catalysts. We elucidate here the mechanism of the selective catalytic reduction of NO by NH3 (NH3-SCR) over a Fe-ZSM-5 zeolite catalyst. 1.3 wt % Fe-ZSM-5 with low nuclearity Fe sites was synthesized, tested in the SCR reaction and characterized by UV-vis, X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) spectroscopy. Next, this defined Fe-zeolite catalyst was studied by complementary high-energy-resolution fluorescence-detected XANES (HERFD-XANES) and valence-to-core X-ray emission spectroscopy (V2C XES) under different model in situ and realistic working (operando) conditions identical to the catalyst test bench including the presence of water vapor. HERFD-XANES uncovered that the coordination (between 4 and 5), geometry (tetrahedral, partly 5-fold), and oxidation state of the Fe centers (reduced in NH3, partly in SCR mixture, slight reduction in NO) strongly changed. V2C XES supported by DFT calculations provided important insight into the chemical nature of the species adsorbed on Fe sites. The unique combination of techniques applied under realistic reaction conditions and the corresponding catalytic data unraveled the adsorption of ammonia via oxygen on the iron site. The derived reaction model supports a mechanism where adsorbed NOx reacts with ammonia coordinated to the Fe(3+) site yielding Fe(2+) whose reoxidation is slow. PMID:25105343

  8. 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.

    Science.gov (United States)

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

    2016-08-01

    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

  9. 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

    2012-08-01

    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.

  10. 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.

  11. 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.

    Science.gov (United States)

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

    2013-01-01

    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

  12. Chimeric Hepatitis B core antigen virus-like particles displaying the envelope domain III of dengue virus type 2

    Directory of Open Access Journals (Sweden)

    Arora Upasana

    2012-07-01

    Full Text Available Abstract Background Dengue is a global public health problem for which no drug or vaccine is available. Currently, there is increasing interest in developing non-replicating dengue vaccines based on a discrete antigenic domain of the major structural protein of dengue viruses (DENVs, known as envelope domain III (EDIII. The use of bio-nanoparticles consisting of recombinant viral structural polypeptides, better known as virus-like particles (VLPs, has emerged as a potential platform technology for vaccine development. This work explores the feasibility of developing nanoparticles based on E. coli-expressed recombinant Hepatitis B virus core antigen (HBcAg designed to display EDIII moiety of DENV on the surface. Findings We designed a synthetic gene construct encoding HBcAg containing an EDIII insert in its c/e1 loop. The fusion antigen HBcAg-EDIII-2 was expressed in E. coli, purified to near homogeneity using Ni+2 affinity chromatography and demonstrated to assemble into discrete 35–40 nm VLPs by electron microscopy. Competitive ELISA analyses showed that the EDIII-2 moieties of the VLPs are accessible to anti-EDIII-2-specific monoclonal and polyclonal antibodies, suggesting that they are surface-displayed. The VLPs were highly immunogenic eliciting high titer anti-EDIII-2 antibodies that were able to recognize, bind and neutralize infectious DENV based on ELISA, immunofluorescence and virus-neutralization assays. Conclusion This work demonstrates that HBcAg-derived nanoparticles can serve as a useful platform for the display of DENV EDIII. The EDIII-displaying nanoparticles may have potential applications in diagnostics/vaccines for dengue.

  13. 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

  14. Hamming distance geometry of a protein conformational space. Application to the clustering of a 4 ns molecular dynamics trajectory of the HIV-1 integrase catalytic core

    CERN Document Server

    Laboulais, C; Le Bret, M; Gabarro-Arpa, J; Laboulais, Cyril; Ouali, Mohammed; Bret, Marc Le; Gabarro-Arpa, Jacques

    2001-01-01

    Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space in two halves. Thus, the information encoded in the binary sequences is also used to characterize the regions of conformational space visited by the system. We apply this distance and their associated geometric structures, to the clustering and analysis of conformations sampled during a 4 ns molecular dynamics simulation of the HIV-1 integrase catalytic core. The cluster analysis of the simulation shows a division of the trajectory into two segments of 2.6 and 1.4 ns length, which are qualitatively different: the data points to the fact that equilibration is only reached at the end of the first segment. Some length of the paper is devoted to compare the Hamming distance to the r.m.s. deviation measure. Th...

  15. 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

  16. Difference in fibril core stability between two tau four-repeat domain proteins: a hydrogen-deuterium exchange coupled to mass spectrometry study.

    Science.gov (United States)

    Ramachandran, Gayathri; Udgaonkar, Jayant B

    2013-12-10

    One of the signatures of Alzheimer's disease and tauopathies is fibrillization of the microtubule-associated protein tau. The purpose of this study was to compare the high-resolution structure of fibrils formed by two different tau four-repeat domain constructs, tau4RD and tauK18, using hydrogen-deuterium exchange coupled to mass spectrometry as a tool. While the two fibrils are found to be constructed on similar structural principles, the tauK18 fibril has a slightly more stable core. This difference in fibril core stability appears to be reflective of the mechanistic differences in the aggregation pathways of the two proteins. PMID:24256615

  17. Identification of a novel antimicrobial peptide from human hepatitis B virus core protein arginine-rich domain (ARD.

    Directory of Open Access Journals (Sweden)

    Heng-Li Chen

    Full Text Available The rise of multidrug-resistant (MDR pathogens causes an increasing challenge to public health. Antimicrobial peptides are considered a possible solution to this problem. HBV core protein (HBc contains an arginine-rich domain (ARD at its C-terminus, which consists of 16 arginine residues separated into four clusters (ARD I to IV. In this study, we demonstrated that the peptide containing the full-length ARD I-IV (HBc147-183 has a broad-spectrum antimicrobial activity at micro-molar concentrations, including some MDR and colistin (polymyxin E-resistant Acinetobacter baumannii. Furthermore, confocal fluorescence microscopy and SYTOX Green uptake assay indicated that this peptide killed Gram-negative and Gram-positive bacteria by membrane permeabilization or DNA binding. In addition, peptide ARD II-IV (HBc153-176 and ARD I-III (HBc147-167 were found to be necessary and sufficient for the activity against P. aeruginosa and K. peumoniae. The antimicrobial activity of HBc ARD peptides can be attenuated by the addition of LPS. HBc ARD peptide was shown to be capable of direct binding to the Lipid A of lipopolysaccharide (LPS in several in vitro binding assays. Peptide ARD I-IV (HBc147-183 had no detectable cytotoxicity in various tissue culture systems and a mouse animal model. In the mouse model by intraperitoneal (i.p. inoculation with Staphylococcus aureus, timely treatment by i.p. injection with ARD peptide resulted in 100-fold reduction of bacteria load in blood, liver and spleen, as well as 100% protection of inoculated animals from death. If peptide was injected when bacterial load in the blood reached its peak, the protection rate dropped to 40%. Similar results were observed in K. peumoniae using an IVIS imaging system. The finding of anti-microbial HBc ARD is discussed in the context of commensal gut microbiota, development of intrahepatic anti-viral immunity and establishment of chronic infection with HBV. Our current results suggested that

  18. Preparation of Ag{sub core}/Au{sub shell} bimetallic nanoparticles from physical mixtures of Au clusters and Ag ions under dark conditions and their catalytic activity for aerobic glucose oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Haijun, E-mail: zhanghaijun@wust.edu.cn [College of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei Province 430081 (China); Toshima, Naoki; Takasaki, Kanako [Department of Applied Chemistry, Tokyo University of Science Yamaguchi, SanyoOnoda-shi, Yamaguchi 756-0884 (Japan); Okumura, Mitsutaka [Department of Chemistry, Graduate School of Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043 (Japan)

    2014-02-15

    Graphical abstract: The synthesis, characterization and catalytic activities for glucose oxidation of AgAu bimetallic nanoparticles (BNPs) with size of less than 2 nm are reported. The catalytic activity of Ag{sub 10}Au{sub 90} BNPs was about two times higher than that of Au NPs, even the BNPs have a larger particle size than that of Au NPs. -- Highlights: • Ag{sub core}/Au{sub shell} BNPs with size of less than 2.0 nm were prepared. • No any reducing reagents and lights were used for the preparation of the BNPs. • The catalytic activity of the BNPs is about two times higher than that of Au NPs. -- Abstract: AgAu bimetallic nanoparticles (BNPs), one of the most extensively studied bimetallic systems in the literatures, could have various structures and compositions depending on their preparation conditions. In the present work, catalytically highly active PVP-protected Ag{sub core}/Au{sub shell} BNPs of about 2.5 nm in diameter were fabricated from physical mixtures of aqueous dispersions of Au nanoparticles and Ag{sup +} ions under dark conditions without using any reducing agents. The prepared Ag{sub core}/Au{sub shell} BNP colloidal catalysts, which possessed a high activity for aerobic glucose oxidation, were characterized by Ultraviolet–visible spectrophotometry (UV–Vis), Inductive coupled plasma emission spectrometer (ICP), Transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS) and Energy disperse spectroscopy (EDS) in High-resolution scanning transmission electron microscopy (HR-STEM). The highest activity (11,360 mol-glucose h{sup −1} mol-metal{sup −1}) was observed for the BNPs with the Ag/Au atomic ratio of 1/9, the TOF value of which is about two times higher than that of Au nanoparticles with the particle size of 1.3 nm. The enhanced catalytic activity of the prepared Ag{sub core}/Au{sub shell} BNPs compared to Au NPs can be ascribed to the presence of negatively charged Au atoms resulted from electron donations

  19. 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

    OpenAIRE

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

    2013-01-01

    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...

  20. 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

  1. SWIFT: Using task-based parallelism, fully asynchronous communication, and graph partition-based domain decomposition for strong scaling on more than 100,000 cores

    CERN Document Server

    Schaller, Matthieu; Chalk, Aidan B G; Draper, Peter W

    2016-01-01

    We present a new open-source cosmological code, called SWIFT, designed to solve the equations of hydrodynamics using a particle-based approach (Smooth Particle Hydrodynamics) on hybrid shared/distributed-memory architectures. SWIFT was designed from the bottom up to provide excellent strong scaling on both commodity clusters (Tier-2 systems) and Top100-supercomputers (Tier-0 systems), without relying on architecture-specific features or specialized accelerator hardware. This performance is due to three main computational approaches: (1) Task-based parallelism for shared-memory parallelism, which provides fine-grained load balancing and thus strong scaling on large numbers of cores. (2) Graph-based domain decomposition, which uses the task graph to decompose the simulation domain such that the work, as opposed to just the data, as is the case with most partitioning schemes, is equally distributed across all nodes. (3) Fully dynamic and asynchronous communication, in which communication is modelled as just anot...

  2. Crystallization and preliminary crystallographic studies of Mycobacterium tuberculosis DNA gyrase B C-terminal domain, part of the enzyme reaction core

    International Nuclear Information System (INIS)

    The crystallization of DNA gyrase B C-terminal domain is described. DNA gyrase subunit B C-terminal domain (GyrB-CTD) is a functional module of DNA gyrase which participates in forming the core of DNA gyrase and plays critical roles in G-segment binding and T-segment loading and passage. Here, the purification, crystallization and preliminary X-ray crystallographic studies of GyrB-CTD from Mycobacterium tuberculosis H37Rv are reported. Diffraction data were collected from crystals of native GyrB-CTD and its selenomethionine derivative to resolutions of 2.8 and 3.0 Å, respectively. These crystals belonged to space group P212121 with similar unit-cell parameters. The native protein crystals had unit-cell parameters a = 52.831, b = 52.763, c = 192.579 Å

  3. cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs

    DEFF Research Database (Denmark)

    Wu, R R; Couchman, J R

    1997-01-01

    Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain chondroitin sulfate, and a core protein, bamacan, has been partially characterized. We have now...... obtained cDNA clones encoding the entire bamacan core protein of Mr = 138 kD, which reveal a five domain, head-rod-tail configuration. The head and tail are potentially globular, while the central large rod probably forms coiled-coil structures, with one large central and several very short interruptions....... This molecular architecture is novel for an extracellular matrix molecule, but it resembles that of a group of intracellular proteins, including some proposed to stabilize the mitotic chromosome scaffold. We have previously proposed a similar stabilizing role for bamacan in the basement membrane matrix...

  4. 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)

    2012-08-15

    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.)

  5. A Low Affinity Ground State Conformation for the Dynein Microtubule Binding Domain*

    OpenAIRE

    McNaughton, Lynn; Tikhonenko, Irina; Banavali, Nilesh K.; LeMaster, David M.; Koonce, Michael P.

    2010-01-01

    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...

  6. Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRζ fragments

    International Nuclear Information System (INIS)

    P212121 crystals of SIV Nef core domain bound to a peptide fragment of the T-cell receptor ζ subunit exhibited noncrystallographic symmetry and nearly perfect pseudo-merohedral twinning simulating tetragonal symmetry. For a different peptide fragment, nontwinned tetragonal crystals were observed but diffracted to lower resolution. The structure was determined after assignment of the top molecular-replacement solutions to various twin or NCS domains followed by refinement under the appropriate twin law. HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling ζ subunit of the T-cell receptor (TCRζ). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCRζ fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCRζ polypeptide (Leu51–Asp93) was determined to 3.7 Å resolution (Rwork = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCRζ polypeptide (Ala63–Arg80) was determined to 2.05 Å resolution (Rwork = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P212121. The reduction in crystal space-group symmetry induced by the truncated TCRζ polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, −l) and a and b unit-cell parameters that were nearly identical predisposed the P212121 crystal form to pseudo-merohedral twinning

  7. 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

    2011-11-01

    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.

  8. Protein kinase domain of twitchin has protein kinase activity and an autoinhibitory region.

    Science.gov (United States)

    Lei, J; Tang, X; Chambers, T C; Pohl, J; Benian, G M

    1994-08-19

    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

  9. The Rho Termination Factor of Clostridium botulinum contains a Prion-Like Domain with a highly Amyloidogenic Core

    Directory of Open Access Journals (Sweden)

    Irantzu ePallares

    2016-01-01

    Full Text Available Prion-like proteins can switch between a soluble intrinsically disordered conformation and a highly ordered amyloid assembly. This conformational promiscuity is encoded in specific sequence regions, known as prion domains (PrDs. Prions are best known as the causative factors of neurological diseases in mammals. However, bioinformatics analyses reveal that proteins bearing PrDs are present in all kingdoms of life, including bacteria, thus supporting the idea that they serve conserved beneficial cellular functions. Despite the proportion of predicted prion-like proteins in bacterial proteomes is generally low, pathogenic species seem to have a higher prionic load, suggesting that these malleable proteins may favor pathogenic traits. In the present work, we performed a stringent computational analysis of the Clostridium botulinum pathogen proteome in the search for prion-like proteins. A total of 54 candidates were predicted for this anaerobic bacterium, including the transcription termination Rho factor. This RNA-binding protein has been shown to play a crucial role in bacterial adaptation to changing environments. We show here that the predicted disordered PrD domain of this RNA-binding protein contains an inner, highly polar, asparagine-rich short sequence able to spontaneously self-assemble into amyloid-like structures, bearing thus the potential to induce a Rho factor conformational switch that might rewire gene expression in response to environmental conditions.

  10. The Rho Termination Factor of Clostridium botulinum Contains a Prion-Like Domain with a Highly Amyloidogenic Core

    Science.gov (United States)

    Pallarès, Irantzu; Iglesias, Valentin; Ventura, Salvador

    2016-01-01

    Prion-like proteins can switch between a soluble intrinsically disordered conformation and a highly ordered amyloid assembly. This conformational promiscuity is encoded in specific sequence regions, known as prion domains (PrDs). Prions are best known as the causative factors of neurological diseases in mammals. However, bioinformatics analyses reveal that proteins bearing PrDs are present in all kingdoms of life, including bacteria, thus supporting the idea that they serve conserved beneficial cellular functions. Despite the proportion of predicted prion-like proteins in bacterial proteomes is generally low, pathogenic species seem to have a higher prionic load, suggesting that these malleable proteins may favor pathogenic traits. In the present work, we performed a stringent computational analysis of the Clostridium botulinum pathogen proteome in the search for prion-like proteins. A total of 54 candidates were predicted for this anaerobic bacterium, including the transcription termination Rho factor. This RNA-binding protein has been shown to play a crucial role in bacterial adaptation to changing environments. We show here that the predicted disordered PrD domain of this RNA-binding protein contains an inner, highly polar, asparagine-rich short sequence able to spontaneously self-assemble into amyloid-like structures, bearing thus the potential to induce a Rho factor conformational switch that might rewire gene expression in response to environmental conditions. PMID:26779170

  11. Theoretical studies on the interactions of XIAP-BIR3 domain with bicyclic and tricyclic core monovalent Smac mimetics.

    Science.gov (United States)

    Ling, Baoping; Dong, Lihua; Zhang, Rui; Wang, Zhiguo; Liu, Yongjun; Liu, Chengbu

    2010-11-01

    X-linked IAP can bind caspase-9 and inhibit its activity. Mitochondrial protein Smac/DIABLO can also interact with XIAP and relieve the inhibition on caspase-9 to induce apoptosis. A series of artificial Smac mimetics have been used to mimic the Smac N-terminal tetrapeptide AVPI to bind to XIAP-BIR3, but these structural diverse mimetics exhibited distinct binding affinities. To get an insight into the binding nature and optimize the structures, molecular docking and dynamics simulations were used to study the binding of XIAP-BIR3 with three groups of Smac mimetics. The docking results reveal that these Smac mimetics anchored on the surface groove of XIAP-BIR3 and superimposed well with AVPI. The modifications on the seven-membered ring of bicyclic core segment do not strengthen the binding affinity, while a benzyl introduced to the five-membered ring is favorable to the binding. Molecular dynamics simulations on three typical systems show that these complexes are very stable. Hydrogen bonds between the bicyclic core segment and Thr308 play critical roles in maintaining the stability of complex. The binding free energies calculated by MM_PBSA method are consistent with the experimental results. PMID:20980180

  12. 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;

    2010-01-01

    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....

  13. 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

  14. 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

    2001-01-01

    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...

  15. The pro region required for folding of carboxypeptidase Y is a partially folded domain with little regular structural core

    DEFF Research Database (Denmark)

    Sørensen, P; Winther, Jakob R.; Kaarsholm, N C; Poulsen, F M

    1993-01-01

    pro region is a partially folded protein domain under the conditions where it is functional. It is characterized by a relatively high content of secondary structural elements but a very low content of defined tertiary structure. Although these characteristics are reminiscent of the compact denatured...... states that have been identified as intermediates in protein folding ("molten globules"), the pro region exhibits only very weak binding of the hydrophobic probe 1-anilino-8-naphthalenesulfonate, and it is resistant toward complete thermal unfolding. Altogether the data indicate an extremely flexible......The pro region of carboxypeptidase Y (CPY) from yeast is necessary for the correct folding of the enzyme [Winther, J. R., & Sørensen P. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 9330-9334]. Using fluorescence, circular dichroism, and heteronuclear NMR analyses, it is demonstrated that the isolated...

  16. Properties and catalytic activities of MICAL1, the flavoenzyme involved in cytoskeleton dynamics, and modulation by its CH, LIM and C-terminal domains.

    Science.gov (United States)

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

    2016-03-01

    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

  17. A truncated fragment of Ov-ASP-1 consisting of the core pathogenesis-related-1 (PR-1) domain maintains adjuvanticity as the full-length protein.

    Science.gov (United States)

    Guo, Jingjing; Yang, Yi; Xiao, Wenjun; Sun, Weilai; Yu, Hong; Du, Lanying; Lustigman, Sara; Jiang, Shibo; Kou, Zhihua; Zhou, Yusen

    2015-04-15

    The Onchocerca volvulus activation-associated secreted protein-1 (Ov-ASP-1) has good adjuvanticity for a variety of antigens and vaccines, probably due to its ability activate antigen-processing cells (APCs). However, the functional domain of Ov-ASP-1 as an adjuvant is not clearly defined. Based on the structural prediction of this protein family, we constructed a 16-kDa recombinant protein of Ov-ASP-1 that contains only the core pathogenesis-related-1 (PR-1) domain (residues 10-153), designated ASPPR. We found that ASPPR exhibits adjuvanticity similar to that of the full-length Ov-ASP-1 (residues 10-220) for various antigens, including ovalbumin (OVA), HBsAg protein antigen, and the HIV peptide 5 (Pep5) antigen, but it is more suitable for vaccine design in ASPPR-antigen fusion proteins, and more stable in PBS than Ov-ASP-1 stored at -70 °C. These results suggest that ASPPR might be the functional region of Ov-ASP-1 as an adjuvant, and therefore could be developed as an adjuvant for human use. PMID:25736195

  18. Connective tissue disease related interstitial lung diseases and idiopathic pulmonary fibrosis: provisional core sets of domains and instruments for use in clinical trials

    Science.gov (United States)

    Saketkoo, Lesley Ann; Mittoo, Shikha; Huscher, Dörte; Khanna, Dinesh; Dellaripa, Paul F; Distler, Oliver; Flaherty, Kevin R; Frankel, Sid; Oddis, Chester V; Denton, Christopher P; Fischer, Aryeh; Kowal-Bielecka, Otylia M; LeSage, Daphne; Merkel, Peter A; Phillips, Kristine; Pittrow, David; Swigris, Jeffrey; Antoniou, Katerina; Baughman, Robert P; Castelino, Flavia V; Christmann, Romy B; Christopher-Stine, Lisa; Collard, Harold R; Cottin, Vincent; Danoff, Sonye; Highland, Kristin B; Hummers, Laura; Shah, Ami A; Kim, Dong Soon; Lynch, David A; Miller, Frederick W; Proudman, Susanna M; Richeldi, Luca; Ryu, Jay H; Sandorfi, Nora; Sarver, Catherine; Wells, Athol U; Strand, Vibeke; Matteson, Eric L; Brown, Kevin K; Seibold, James R

    2014-01-01

    Rationale Clinical trial design in interstitial lung diseases (ILDs) has been hampered by lack of consensus on appropriate outcome measures for reliably assessing treatment response. In the setting of connective tissue diseases (CTDs), some measures of ILD disease activity and severity may be confounded by non-pulmonary comorbidities. Methods The Connective Tissue Disease associated Interstitial Lung Disease (CTD-ILD) working group of Outcome Measures in Rheumatology—a non-profit international organisation dedicated to consensus methodology in identification of outcome measures—conducted a series of investigations which included a Delphi process including >248 ILD medical experts as well as patient focus groups culminating in a nominal group panel of ILD experts and patients. The goal was to define and develop a consensus on the status of outcome measure candidates for use in randomised controlled trials in CTD-ILD and idiopathic pulmonary fibrosis (IPF). Results A core set comprising specific measures in the domains of lung physiology, lung imaging, survival, dyspnoea, cough and health-related quality of life is proposed as appropriate for consideration for use in a hypothetical 1-year multicentre clinical trial for either CTD-ILD or IPF. As many widely used instruments were found to lack full validation, an agenda for future research is proposed. Conclusion Identification of consensus preliminary domains and instruments to measure them was attained and is a major advance anticipated to facilitate multicentre RCTs in the field. PMID:24368713

  19. A first case of congenital TTP on the African continent due to a new homozygous mutation in the catalytic domain of ADAMTS13.

    Science.gov (United States)

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

    2008-08-01

    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

  20. Outer domains of integrase within retroviral intasomes are dispensible for catalysis of DNA integration.

    Science.gov (United States)

    Li, Min; Lin, Shiqiang; Craigie, Robert

    2016-02-01

    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

  1. DFT study of Fe-Ni core-shell nanoparticles: Stability, catalytic activity, and interaction with carbon atom for single-walled carbon nanotube growth

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Zhimin; Wang, Qiang, E-mail: wangqiang@njtech.edu.cn; Shan, Xiaoye; Zhu, Hongjun, E-mail: zhuhj@njtech.edu.cn [Department of Applied Chemistry, College of Science, Nanjing Tech University, Nanjing 211816 (China); Li, Wei-qi [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); Chen, Guang-hui [Department of Chemistry, Shantou University, Shantou, Guangdong 515063 (China)

    2015-02-21

    Metal catalysts play an important role in the nucleation and growth of single-walled carbon nanotubes (SWCNTs). It is essential for probing the nucleation and growth mechanism of SWCNTs to fundamentally understand the properties of the metal catalysts and their interaction with carbon species. In this study, we systematically studied the stability of 13- and 55-atom Fe and Fe-Ni core-shell particles as well as these particles interaction with the carbon atoms using the density functional theory calculations. Icosahedral 13- and 55-atom Fe-Ni core-shell bimetallic particles have higher stability than the corresponding monometallic Fe and Ni particles. Opposite charge transfer (or distribution) in these particles leads to the Fe surface-shell displays a positive charge, while the Ni surface-shell exhibits a negative charge. The opposite charge transfer would induce different chemical activities. Compared with the monometallic Fe and Ni particles, the core-shell bimetallic particles have weaker interaction with C atoms. More importantly, C atoms only prefer staying on the surface of the bimetallic particles. In contrast, C atoms prefer locating into the subsurface of the monometallic particles, which is more likely to form stable metal carbides. The difference of the mono- and bimetallic particles on this issue may result in different nucleation and growth mechanism of SWCNTs. Our findings provide useful insights for the design of bimetallic catalysts and a better understanding nucleation and growth mechanism of SWCNTs.

  2. DFT study of Fe-Ni core-shell nanoparticles: Stability, catalytic activity, and interaction with carbon atom for single-walled carbon nanotube growth

    International Nuclear Information System (INIS)

    Metal catalysts play an important role in the nucleation and growth of single-walled carbon nanotubes (SWCNTs). It is essential for probing the nucleation and growth mechanism of SWCNTs to fundamentally understand the properties of the metal catalysts and their interaction with carbon species. In this study, we systematically studied the stability of 13- and 55-atom Fe and Fe-Ni core-shell particles as well as these particles interaction with the carbon atoms using the density functional theory calculations. Icosahedral 13- and 55-atom Fe-Ni core-shell bimetallic particles have higher stability than the corresponding monometallic Fe and Ni particles. Opposite charge transfer (or distribution) in these particles leads to the Fe surface-shell displays a positive charge, while the Ni surface-shell exhibits a negative charge. The opposite charge transfer would induce different chemical activities. Compared with the monometallic Fe and Ni particles, the core-shell bimetallic particles have weaker interaction with C atoms. More importantly, C atoms only prefer staying on the surface of the bimetallic particles. In contrast, C atoms prefer locating into the subsurface of the monometallic particles, which is more likely to form stable metal carbides. The difference of the mono- and bimetallic particles on this issue may result in different nucleation and growth mechanism of SWCNTs. Our findings provide useful insights for the design of bimetallic catalysts and a better understanding nucleation and growth mechanism of SWCNTs

  3. Amperometric glucose sensor based on enhanced catalytic reduction of oxygen using glucose oxidase adsorbed onto core-shell Fe3O4-silica-Au magnetic nanoparticles

    International Nuclear Information System (INIS)

    Monodisperse Fe3O4 magnetic nanoparticles (NPs) were prepared under facile solvothermal conditions and successively functionalized with silica and Au to form core/shell Fe3O4-silica-Au NPs. Furthermore, the samples were used as matrix to construct a glucose sensor based on glucose oxidase (GOD). The immobilized GOD retained its bioactivity with high protein load of 3.92 × 10−9 mol·cm−2, and exhibited a surface-controlled quasi-reversible redox reaction, with a fast heterogeneous electron transfer rate of 7.98 ± 0.6 s−1. The glucose biosensor showed a broad linear range up to 3.97 mM with high sensitivity of 62.45 μA·mM−1 cm−2 and fast response (less than 5 s). - Graphical abstract: Core-shell structured Fe3O4-silica-Au nanoparticles were prepared and used as matrix to construct an amperometric glucose sensor based on glucose oxidase, which showed broad linear range, high sensitivity, and fast response. Highlights: ► Synthesis of monodispersed Fe3O4 nanoparticles. ► Fabrication of core/shell Fe3O4-silica-Au nanoparticles. ► Construction of a novel glucose sensor with wide linear range, high sensitivity and fast response.

  4. The crystal structure of the core domain of a cellulose induced protein (Cip1 from Hypocrea jecorina, at 1.5 A resolution.

    Directory of Open Access Journals (Sweden)

    Frida Jacobson

    Full Text Available In an effort to characterise the whole transcriptome of the fungus Hypocrea jecorina, cDNA clones of this fungus were identified that encode for previously unknown proteins that are likely to function in biomass degradation. One of these newly identified proteins, found to be co-regulated with the major H. jecorina cellulases, is a protein that was denoted Cellulose induced protein 1 (Cip1. This protein consists of a glycoside hydrolase family 1 carbohydrate binding module connected via a linker region to a domain with yet unknown function. After cloning and expression of Cip1 in H. jecorina, the protein was purified and biochemically characterised with the aim of determining a potential enzymatic activity for the novel protein. No hydrolytic activity against any of the tested plant cell wall components was found. The proteolytic core domain of Cip1 was then crystallised, and the three-dimensional structure of this was determined to 1.5 Å resolution utilising sulphur single-wavelength anomalous dispersion phasing (sulphor-SAD. A calcium ion binding site was identified in a sequence conserved region of Cip1 and is also seen in other proteins with the same general fold as Cip1, such as many carbohydrate binding modules. The presence of this ion was found to have a structural role. The Cip1 structure was analysed and a structural homology search was performed to identify structurally related proteins. The two published structures with highest overall structural similarity to Cip1 found were two poly-lyases: CsGL, a glucuronan lyase from H. jecorina and vAL-1, an alginate lyase from the Chlorella virus. This indicates that Cip1 may be a lyase. However, initial trials did not detect significant lyase activity for Cip1. Cip1 is the first structure to be solved of the 23 currently known Cip1 sequential homologs (with a sequence identity cut-off of 25%, including both bacterial and fungal members.

  5. Metallic Sn spheres and SnO2@C core-shells by anaerobic and aerobic catalytic ethanol and CO oxidation reactions over SnO2 nanoparticles

    OpenAIRE

    Won Joo Kim; Sung Woo Lee; Youngku Sohn

    2015-01-01

    SnO2 has been studied intensely for applications to sensors, Li-ion batteries and solar cells. Despite this, comparatively little attention has been paid to the changes in morphology and crystal phase that occur on the metal oxide surface during chemical reactions. This paper reports anaerobic and aerobic ethanol and CO oxidation reactions over SnO2 nanoparticles (NPs), as well as the subsequent changes in the nature of the NPs. Uniform SnO2@C core-shells (10 nm) were formed by an aerobic eth...

  6. 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

    2008-01-01

    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.

  7. 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

    2011-01-01

    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...

  8. A facile approach to fabrication of novel CeO{sub 2}-TiO{sub 2} core-shell nanocomposite leads to excellent UV-shielding ability and lower catalytic activity

    Energy Technology Data Exchange (ETDEWEB)

    Bahadur, Newaz Mohammed, E-mail: nmbahadur@yahoo.com [Utsunomiya University, Laboratory of Powder Technology, Graduate School of Engineering, Venture Business Laboratry (Japan); Kurayama, Fumio [Utsunomiya University, Center for Optical Research and Education (Japan); Furusawa, Takeshi; Sato, Masahide [Utsunomiya University, Department of Advanced Interdisciplinary Sciences (Japan); Siddiquey, Iqbal Ahmed [Utsunomiya University, Laboratory of Powder Technology, Graduate School of Engineering, Venture Business Laboratry (Japan); Hossain, Md. Mufazzal [University of Dhaka, Department of Chemistry (Bangladesh); Suzuki, Noboru [Utsunomiya University, Laboratory of Powder Technology, Graduate School of Engineering, Venture Business Laboratry (Japan)

    2013-01-15

    This study reports the development of a fast and facile route for the synthesis of novel CeO{sub 2}-TiO{sub 2} core-shell nanocomposite particles using microwave (MW) irradiation of the mixture of commercial CeO{sub 2}, titanium-tetra-n-butoxide (TBOT) and aqueous ammonia. Solutions of TBOT in ethanol and ammonia were mixed with dispersed CeO{sub 2} nanoparticles in ethanol, and the mixture was rapidly MW irradiated at 70 Degree-Sign C for 2 min. The resulting nanocomposite particles were characterized in terms of phase, shell thickness, composition, surface charge, morphology, and chemical state of the elements by XRD, TEM, XPS, SEM, Zeta potential analyzer, XRF, and FT-IR. Conventional methods of the synthesis of CeO{sub 2}-TiO{sub 2} nanocomposite require a long time, and TiO{sub 2} is rarely found as a coated material. In contrast, the MW method was able to synthesize CeO{sub 2}-TiO{sub 2} core-shell nanocompsite particles within a very short time. CeO{sub 2}-TiO{sub 2} nanocomposite particles were fairly unaggregated with an average titania layer thickness of 2-5 nm. The obtained nanocomposites retained the crystalline cubic phase of CeO{sub 2}, and the phase of coated TiO{sub 2} was amorphous. The catalytic activities of uncoated and TiO{sub 2}-coated CeO{sub 2} nanoparticles for the oxidation of organic compounds were evaluated by the degradation study of methylene blue in air atmosphere at 403 K. The enhanced UV-shielding ability and visible transparency of the nanocomposite obtained by UV visible spectroscopic measurements suggested that the core-shell material has novel characteristics for using as a sunscreen material.

  9. Metallic Sn spheres and SnO2@C core-shells by anaerobic and aerobic catalytic ethanol and CO oxidation reactions over SnO2 nanoparticles

    Science.gov (United States)

    Kim, Won Joo; Lee, Sung Woo; Sohn, Youngku

    2015-08-01

    SnO2 has been studied intensely for applications to sensors, Li-ion batteries and solar cells. Despite this, comparatively little attention has been paid to the changes in morphology and crystal phase that occur on the metal oxide surface during chemical reactions. This paper reports anaerobic and aerobic ethanol and CO oxidation reactions over SnO2 nanoparticles (NPs), as well as the subsequent changes in the nature of the NPs. Uniform SnO2@C core-shells (10 nm) were formed by an aerobic ethanol oxidation reaction over SnO2 NPs. On the other hand, metallic Sn spheres were produced by an anaerobic ethanol oxidation reaction at 450 °C, which is significantly lower than that (1200 °C) used in industrial Sn production. Anaerobic and aerobic CO oxidation reactions were also examined. The novelty of the methods for the production of metallic Sn and SnO2@C core-shells including other anaerobic and aerobic reactions will contribute significantly to Sn and SnO2-based applications.

  10. Enhancement of cytotoxic T lymphocyte activity by dendritic cells loaded with Tat-protein transduction domain-fused hepatitis B virus core antigen

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The protein transduction domain (PTD) of human immuno-deficiency virus-1-Tat protein has a unique potency to pen-etrate the cellular membranes. To synthesize the sequence of Tat-PTD and hepatitis B virus core antigen (HBcAg), we spliced these sequences and linked a fusion gene into the pMAL-c2x vector. The fusion proteins were purified by affin-ity chromatography and pulsed with bone marrow -derived den-dritic cells (DCs), and the transduction of recombinant pro-tein was detected by immunofluorescence antibody assay.Results showed that recombinant PTD-HBcAg could pen-etrate into DC cytoplasm while recombinant HBcAg was de-tected on the surface of cells. The percentage of DC surface molecules, such as CD80, CD86 and major histocompatibii-ity complex Ⅱ, and production of cytokine (IL-12pT0) induced by recombinant PTD-HBcAg were significantly higher than those induced by recombinant HBcAg or tumor necrosis fac-tor-α. DCs treated with PTD-HBcAg induced T cells to dif-ferentiate into specific cytotoxic T lymphocytes (CTLs) and enhanced the CTL killing response. In conclusion, the ex-pressed and purified PTD-HBcAg fusion protein could pen-etrate into cells through the plasma membrane, promote DC maturation, and enhance T cells response to generate HBcAg-specific CTLs efficiently.

  11. Vanadium complexes having [VO]2+, [VO]3+ and [VO2]+ cores with hydrazones of 2,6-diformyl-4-methylphenol: synthesis, characterization, reactivity, and catalytic potential.

    Science.gov (United States)

    Maurya, Mannar R; Haldar, Chanchal; Kumar, Amit; Kuznetsov, Maxim L; Avecilla, Fernando; Costa Pessoa, João

    2013-09-01

    The Schiff bases H3dfmp(L)2 obtained by the condensation of 2,6-diformyl-4-methylphenol and hydrazones [L = isonicotinoylhydrazide (inh), nicotinoylhydrazide (nah) and benzoylhydrazide (bhz)] are prepared and characterized. By reaction of [V(IV)O(acac)2] and the H3dfmp(L)2 in methanol the V(IV)O-complexes [V(IV)O{Hdfmp(inh)2}(H2O)] (1), [V(IV)O{Hdfmp(nah)2}(H2O)] (2) and [V(IV)O{Hdfmp(bhz)2}(H2O)] (3) were obtained. Upon their aerial oxidation in methanol [V(V)O(OMe)(MeOH){Hdfmp(inh)2}] (4), [V(V)O(OMe)(MeOH){Hdfmp(nah)2}] (5) and [V(V)O(OMe)(MeOH){Hdfmp(bhz)2}] (6) were isolated. In the presence of KOH, oxidation of 1-3 results in the formation of [V(V)O2{H2dfmp(inh)2}]n·5H2O (7), K[V(V)O2{Hdfmp(nah)2}] (8) and K[V(V)O2{Hdfmp(bhz)2}] (9). All compounds are characterized in the solid state and in solution, namely by spectroscopic techniques (IR, UV-Vis, EPR, (1)H, (13)C and (51)V NMR), and DFT is also used to calculate the V(IV) hyperfine coupling constants of V(IV)-compounds and (51)V NMR chemical shifts of several V(V)-species and assign them to those formed in solution. Single crystal X-ray analysis of [V(V)O(OMe)(MeOH){Hdfmp(bhz)2}] (6) and [V(V)O2{H2dfmp(inh)2}]n·5H2O (7) confirm the coordination of the ligand in the dianionic (ONO(2-)) enolate tautomeric form, one of the hydrazide moieties remaining non-coordinated. In the case of 7 the free N(pyridine) atom of the inh moiety coordinates to the other vanadium center yielding a polynuclear complex in the solid state. It is also demonstrated that the V(V)O2-complexes are catalyst precursors in the oxidative bromination of styrene by H2O2, therefore acting as functional models of vanadium dependent haloperoxidases. Plausible intermediates involved in the catalytic process are established by UV-Vis, (51)V NMR and DFT studies. PMID:23680862

  12. Bifunctional catalytic electrode

    Science.gov (United States)

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

    2005-01-01

    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.

  13. Functional interactions of the AF-2 activation domain core region of the human androgen receptor with the amino-terminal domain and with the transcriptional coactivator TIF2 (transcriptional intermediary factor2)

    OpenAIRE

    Berrevoets, Cor; P. Doesburg; Steketee, Karine; Trapman, Jan; Brinkmann, Albert

    1998-01-01

    textabstractPrevious studies in yeast and mammalian cells showed a functional interaction between the amino-terminal domain and the carboxy-terminal, ligand-binding domain (LBD) of the human androgen receptor (AR). In the present study, the AR subdomains involved in this in vivo interaction were determined in more detail. Cotransfection experiments in Chinese hamster ovary (CHO) cells and two-hybrid experiments in yeast revealed that two regions in the NH2-terminal domain are involved in the ...

  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)

    2008-08-11

    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.

    Science.gov (United States)

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

    2008-07-01

    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. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

    International Nuclear Information System (INIS)

    The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional regulation, protein–protein interaction, RNA binding or metal-ion sensing. Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2-DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23-SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63-THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63-THEAC and Q2LQ23-SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2-DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63-THEAC and Q2LQ23-SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63-THEAC and Q2LQ23-SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63-THEAC, but is absent from the NTD of Q2LQ23-SYNAS. Second, whereas the structure of the CTD of Q2LQ23-SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure

  17. NlpC/P60 domain-containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan.

    Science.gov (United States)

    Bannantine, John P; Lingle, Cari K; Adam, Philip R; Ramyar, Kasra X; McWhorter, William J; Stabel, Judith R; Picking, William D; Geisbrecht, Brian V

    2016-04-01

    A subset of proteins containing NlpC/P60 domains are bacterial peptidoglycan hydrolases that cleave noncanonical peptide linkages and contribute to cell wall remodeling as well as cell separation during late stages of division. Some of these proteins have been shown to cleave peptidoglycan in Mycobacterium tuberculosis and play a role in Mycobacterium marinum virulence of zebra fish; however, there are still significant knowledge gaps concerning the molecular function of these proteins in Mycobacterium avium subspecies paratuberculosis (MAP). The MAP genome sequence encodes five NlpC/P60 domain-containing proteins. We describe atomic resolution crystal structures of two such MAP proteins, MAP_1272c and MAP_1204. These crystal structures, combined with functional assays to measure peptidoglycan cleavage activity, led to the observation that MAP_1272c does not have a functional catalytic core for peptidoglycan hydrolysis. Furthermore, the structure and sequence of MAP_1272c demonstrate that the catalytic residues normally required for hydrolysis are absent, and the protein does not bind peptidoglycan as efficiently as MAP_1204. While the NlpC/P60 catalytic triad is present in MAP_1204, changing the catalytic cysteine-155 residue to a serine significantly diminished catalytic activity, but did not affect binding to peptidoglycan. Collectively, these findings suggest a broader functional repertoire for NlpC/P60 domain-containing proteins than simply hydrolases. PMID:26799947

  18. Molecular determinants of interactions between the N-terminal domain and the transmembrane core that modulate hERG K+ channel gating.

    Directory of Open Access Journals (Sweden)

    Jorge Fernández-Trillo

    Full Text Available A conserved eag domain in the cytoplasmic amino terminus of the human ether-a-go-go-related gene (hERG potassium channel is critical for its slow deactivation gating. Introduction of gene fragments encoding the eag domain are able to restore normal deactivation properties of channels from which most of the amino terminus has been deleted, and also those lacking exclusively the eag domain or carrying a single point mutation in the initial residues of the N-terminus. Deactivation slowing in the presence of the recombinant domain is not observed with channels carrying a specific Y542C point mutation in the S4-S5 linker. On the other hand, mutations in some initial positions of the recombinant fragment also impair its ability to restore normal deactivation. Fluorescence resonance energy transfer (FRET analysis of fluorophore-tagged proteins under total internal reflection fluorescence (TIRF conditions revealed a substantial level of FRET between the introduced N-terminal eag fragments and the eag domain-deleted channels expressed at the membrane, but not between the recombinant eag domain and full-length channels with an intact amino terminus. The FRET signals were also minimized when the recombinant eag fragments carried single point mutations in the initial portion of their amino end, and when Y542C mutated channels were used. These data suggest that the restoration of normal deactivation gating by the N-terminal recombinant eag fragment is an intrinsic effect of this domain directed by the interaction of its N-terminal segment with the gating machinery, likely at the level of the S4-S5 linker.

  19. Structural rearrangements of a polyketide synthase module during its catalytic cycle.

    Science.gov (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

    2014-06-26

    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

  20. 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;

    1999-01-01

    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...

  1. Recommended Patient-Reported Core Set of Symptoms and Quality-of-Life Domains to Measure in Ovarian Cancer Treatment Trials

    OpenAIRE

    Donovan, Kristine A.; Donovan, Heidi S.; Cella, David; Gaines, Martha E.; Penson, Richard T.; Plaxe, Steven C.; von Gruenigen, Vivian E.; Bruner, Deborah Watkins; Reeve, Bryce B.; Wenzel, Lari

    2014-01-01

    There is no consensus as to what symptoms or quality-of-life (QOL) domains should be measured as patient-reported outcomes (PROs) in ovarian cancer clinical trials. A panel of experts convened by the National Cancer Institute reviewed studies published between January 2000 and August 2011. The results were included in and combined with an expert consensus-building process to identify the most salient PROs for ovarian cancer clinical trials. We identified a set of PROs specific to ovarian canc...

  2. ADAR proteins: structure and catalytic mechanism.

    Science.gov (United States)

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

    2012-01-01

    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

  3. Recommended patient-reported core set of symptoms and quality-of-life domains to measure in ovarian cancer treatment trials.

    Science.gov (United States)

    Donovan, Kristine A; Donovan, Heidi S; Cella, David; Gaines, Martha E; Penson, Richard T; Plaxe, Steven C; von Gruenigen, Vivian E; Bruner, Deborah Watkins; Reeve, Bryce B; Wenzel, Lari

    2014-07-01

    There is no consensus as to what symptoms or quality-of-life (QOL) domains should be measured as patient-reported outcomes (PROs) in ovarian cancer clinical trials. A panel of experts convened by the National Cancer Institute reviewed studies published between January 2000 and August 2011. The results were included in and combined with an expert consensus-building process to identify the most salient PROs for ovarian cancer clinical trials. We identified a set of PROs specific to ovarian cancer: abdominal pain, bloating, cramping, fear of recurrence/disease progression, indigestion, sexual dysfunction, vomiting, weight gain, and weight loss. Additional PROs identified in parallel with a group charged with identifying the most important PROs across cancer types were anorexia, cognitive problems, constipation, diarrhea, dyspnea, fatigue, nausea, neuropathy, pain, and insomnia. Physical and emotional domains were considered to be the most salient domains of QOL. Findings of the review and consensus process provide good support for use of these ovarian cancer-specific PROs in ovarian cancer clinical trials. PMID:25006190

  4. Bonding Quandary in the [Cu3S2](3+) Core: Insights from the Analysis of Domain Averaged Fermi Holes and the Local Spin

    Czech Academy of Sciences Publication Activity Database

    Ponec, Robert; Ramos-Córdoba, E.; Salvador, P.

    2013-01-01

    Roč. 117, č. 9 (2013), s. 1975-1982. ISSN 1089-5639 R&D Projects: GA ČR GA203/09/0118 Grant ostatní: SMCT(ES) MAT2008-04834; SMCT(ES) CTQ2011-23441/BQU; SFPU(ES) AP2008-01231 Institutional support: RVO:67985858 Keywords : Cu3S2 core * dafh analysis * bonding quandary Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.775, year: 2013

  5. The conserved core domain of the human TATA binding protein is sufficient to assemble the multisubunit RNA polymerase I-specific transcription factor SL1.

    OpenAIRE

    Rudloff, U; Eberhard, D; Grummt, I

    1994-01-01

    The human ribosomal RNA polymerase (Pol) I promoter selectivity factor SL1 is a complex consisting of the TATA binding protein (TBP) and three TBP-associated factors (TAFs). We have investigated which elements of TBP are involved in the assembly of Pol I-specific TBP-TAF complexes by comparing SL1 isolated from two human cell lines, one expressing epitope-tagged full-length TBP and another expressing a deletion of nearly the entire N-terminal domain (e delta NTBP). We have immunopurified epit...

  6. Recognition of the Xenopus ribosomal core promoter by the transcription factor xUBF involves multiple HMG box domains and leads to an xUBF interdomain interaction.

    OpenAIRE

    Leblanc, B.; Read, C.; Moss, T

    1993-01-01

    The interaction of the ribosomal transcription factor xUBF with the RNA polymerase I core promoter of Xenopus laevis has been studied both at the DNA and protein levels. It is shown that a single xUBF-DNA complex forms over the 40S initiation site (+1) and involves at least the DNA sequences between -20 and +60 bp. DNA sequences upstream of +10 and downstream of +18 are each sufficient to direct complex formation independently. HMG box 1 of xUBF independently recognizes the sequences -20 to -...

  7. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    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...

  8. Functional role of the additional domains in inulosucrase (IslA from Leuconostoc citreum CW28

    Directory of Open Access Journals (Sweden)

    Munguia Agustin

    2008-01-01

    Full Text Available Abstract Background Inulosucrase (IslA from Leuconostoc citreum CW28 belongs to a new subfamily of multidomain fructosyltransferases (FTFs, containing additional domains from glucosyltransferases. It is not known what the function of the additional domains in this subfamily is. Results Through construction of truncated versions we demonstrate that the acquired regions are involved in anchoring IslA to the cell wall; they also confer stability to the enzyme, generating a larger structure that affects its kinetic properties and reaction specificity, particularly the hydrolysis and transglycosylase ratio. The accessibility of larger molecules such as EDTA to the catalytic domain (where a Ca2+ binding site is located is also affected as demonstrated by the requirement of 100 times higher EDTA concentrations to inactivate IslA with respect to the smallest truncated form. Conclusion The C-terminal domain may have been acquired to anchor inulosucrase to the cell surface. Furthermore, the acquired domains in IslA interact with the catalytic core resulting in a new conformation that renders the enzyme more stable and switch the specificity from a hydrolytic to a transglycosylase mechanism. Based on these results, chimeric constructions may become a strategy to stabilize and modulate biocatalysts based on FTF activity.

  9. Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9.

    Science.gov (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

    2012-10-01

    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

  10. Real-Time Spectroscopic Monitoring of the Synthesis of Core and Core/Shell Upconversion Nanocrystals and Finite-Difference Time Domain Modeling of the Interaction Between Light and Spherical Microwell Arrays

    Science.gov (United States)

    Suter, John

    Nanocrystalline beta-NaYF4:17% Yb3+, 3% Er 3+ has significant potential for applications in a wide variety of fields including solar technologies, security printing, and biological imaging and sensing. In order to increase the potential of these nanocrystals for these applications, we have developed a method for the real-time, in situ, spectroscopic monitoring of nanocrystal growth and shell-addition. In situ real-time monitoring of upconversion emission is applied to study the reaction mechanism for the synthesis of beta-NaYF 4:17% Yb3+, 3% Er3++ nanoparticles in oleic acid and octadecene via the heat-up method. Transmission electron microscopy is used to correlate the spectroscopic signature of the reaction mixture with its composition. The power of real-time spectroscopic monitoring to precisely time the duration of the various stages of the reaction, and to accurately identify the transitions between those stages, including the completion of the reaction, is demonstrated. Real-time spectroscopic monitoring is used to study the effect of increasing the oleic acid concentration on the duration of these stages as well as the size and shape of resulting nanocrystals. The use of real-time spectroscopic monitoring to study shell-addition, specifically, the addition of an un-doped NaYF4 shell, is also discussed. Patterned gold surfaces are known to enhance the upconversion efficiency of lanthanide based upconversion materials, such as nanocrystalline beta-NaYF 4:17% Yb3+, 3% Er3+. Here, spherical microwell arrays are shown to provide up to a 40x enhancement of upconversion emission from beta-NaYF4:17% Yb3+, 3% Er 3+ nanocrystals. Finite-Difference Time-Domain (FDTD) is a method to solve, numerically, the Maxwell equations across a 3D simulation grid and has been used to simulate the interaction of light with a variety of materials, including metal surfaces and particles. FDTD simulations is used to investigate the nature of the enhancement from the patterned gold

  11. Aspartoacylase catalytic deficiency as the cause of Canavan disease: a structural perspective.

    Science.gov (United States)

    Wijayasinghe, Yasanandana S; Pavlovsky, Alexander G; Viola, Ronald E

    2014-08-01

    Canavan disease (CD) is a fatal, childhood neurological disorder caused by mutations in the ASPA gene, leading to catalytic deficiencies in the aspartoacylase (ASPA) enzyme and impaired N-acetyl-l-aspartic acid metabolism in the brain. To study the possible structural defects triggered by these mutations, four ASPA missense mutations associated with different disease severities have been structurally characterized. These mutant enzymes each have overall structures similar to that of the native ASPA enzyme, but with varying degrees of alterations that offer explanations for the respective loss of catalytic activity. The K213E mutant, a nonconservative mutant associated with a mild disease phenotype, has minimal structural differences compared to the native enzyme. In contrast, the loss of van der Waals contacts in the F295S mutant and the loss of hydrophobic and hydrogen bonding interactions in the Y231C mutant lead to a local collapse of the hydrophobic core structure in the carboxyl-terminal domain, contributing to a decrease in protein stability. The structure of the E285A mutant, the most common clinical mutant, reveals that the loss of hydrogen bonding interactions with the carboxylate side chain of Glu285 disturbs the active site architecture, leading to altered substrate binding and lower catalytic activity. Our improved understanding of the nature of these structural defects provides a basis for the development of treatment therapies for CD. PMID:25003821

  12. Catalytic cracking process

    Science.gov (United States)

    Lokhandwala, Kaaeid A.; Baker, Richard W.

    2001-01-01

    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.

  13. Catalytic distillation structure

    Science.gov (United States)

    Smith, Jr., Lawrence A.

    1984-01-01

    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.

  14. Catalytic Synthesis Lactobionic Acid

    Directory of Open Access Journals (Sweden)

    V.G. Borodina

    2014-07-01

    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.

  15. Catalytic distillation process

    Science.gov (United States)

    Smith, Jr., Lawrence A.

    1982-01-01

    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.

  16. Catalytic Coanda combustion

    Energy Technology Data Exchange (ETDEWEB)

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

    1992-09-16

    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)

  17. Catalytic ignition of light hydrocarbons

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

    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.

  18. Iterative type I polyketide synthases for enediyne core biosynthesis.

    Science.gov (United States)

    Horsman, Geoffrey P; Van Lanen, Steven G; Shen, Ben

    2009-01-01

    Enediyne natural products are extremely potent antitumor antibiotics with a remarkable core structure consisting of two acetylenic groups conjugated to a double bond within either a 9- or 10-membered ring. Biosynthesis of this fascinating scaffold is catalyzed in part by an unusual iterative type I polyketide synthase, PKSE, that is shared among all enediyne biosynthetic pathways whose gene clusters have been sequenced to date. The PKSE is unusual in two main respects: (1) it contains an acyl carrier protein (ACP) domain with no sequence homology to any known proteins, and (2) it is self-phosphopantetheinylated by an integrated phosphopantetheinyl transferase (PPTase) domain. The unusual domain architecture and biochemistry of the PKSE hold promise both for the rapid identification of new enediyne natural products and for obtaining fundamental catalytic insights into enediyne biosynthesis. This chapter describes methods for rapid PCR-based classification of conserved enediyne biosynthetic genes, heterologous production of 9-membered PKSE proteins and isolation of the resulting polyene product, and in vitro characterization of the PKSE ACP domain. PMID:19362637

  19. Domain Engineering

    Science.gov (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.

  20. Over-expression of the catalytic core of mitochondrial DNA (mtDNA) polymerase in the nervous system of Drosophila melanogaster reduces median life span by inducing mtDNA depletion

    Science.gov (United States)

    Martínez-Azorín, Francisco; Calleja, Manuel; Hernández-Sierra, Rosana; Farr, Carol L.; Kaguni, Laurie S.; Garesse, Rafael

    2016-01-01

    DNA polymerase γ (pol γ) is the sole DNA polymerase devoted to mitochondrial DNA (mtDNA) replication. We have characterized the molecular and physiological effects of over-expression of the catalytic subunit of pol γ, pol γ-α, in the nervous system of Drosophila melanogaster using the upstream activation sequence (UAS)/yeast transcriptional activator by binding to UAS (GAL4) system. Tissue-specific over-expression of pol γ-α was confirmed by immunoblot analysis, whereas the very low levels of endogenous protein are undetectable in UAS or GAL4 control lines. The transgenic flies over-expressing pol γ-α in the nervous system showed a moderate increase in pupal lethality, and a significant decrease in the median life span of adult flies. Moreover, these flies displayed a decrease in the rate of synthesis of mtDNA, which is accompanied by a significant mtDNA depletion, and a corresponding decrease in the levels of mitochondrial transcription factor A (mtTFA). Biochemical analysis showed an oxidative phosphorylation (OXPHOS) defect in transgenic flies, which were more susceptible to oxidative stress. Although we did not detect apoptosis in the nervous system of adult transgenic flies, brains of larvae over-expressing pol γ-α showed evidence of increased cell death that correlates with the observed phenotypes. Our data establish an animal model that mimics some of the features of human mtDNA depletion syndromes. PMID:17999718

  1. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in...

  2. Amperometric glucose sensor based on enhanced catalytic reduction of oxygen using glucose oxidase adsorbed onto core-shell Fe{sub 3}O{sub 4}-silica-Au magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Wang Aijun [College of Geography and Environmental Science, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004 (China); Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007 (China); Li Yongfang [College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003 (China); Li Zhonghua [Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007 (China); Feng Jiuju, E-mail: jjfengnju@gmail.com [College of Geography and Environmental Science, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004 (China); Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007 (China); Sun Yanli [Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007 (China); Chen Jianrong [College of Geography and Environmental Science, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004 (China)

    2012-08-01

    Monodisperse Fe{sub 3}O{sub 4} magnetic nanoparticles (NPs) were prepared under facile solvothermal conditions and successively functionalized with silica and Au to form core/shell Fe{sub 3}O{sub 4}-silica-Au NPs. Furthermore, the samples were used as matrix to construct a glucose sensor based on glucose oxidase (GOD). The immobilized GOD retained its bioactivity with high protein load of 3.92 Multiplication-Sign 10{sup -9} mol{center_dot}cm{sup -2}, and exhibited a surface-controlled quasi-reversible redox reaction, with a fast heterogeneous electron transfer rate of 7.98 {+-} 0.6 s{sup -1}. The glucose biosensor showed a broad linear range up to 3.97 mM with high sensitivity of 62.45 {mu}A{center_dot}mM{sup -1} cm{sup -2} and fast response (less than 5 s). - Graphical abstract: Core-shell structured Fe{sub 3}O{sub 4}-silica-Au nanoparticles were prepared and used as matrix to construct an amperometric glucose sensor based on glucose oxidase, which showed broad linear range, high sensitivity, and fast response. Highlights: Black-Right-Pointing-Pointer Synthesis of monodispersed Fe{sub 3}O{sub 4} nanoparticles. Black-Right-Pointing-Pointer Fabrication of core/shell Fe{sub 3}O{sub 4}-silica-Au nanoparticles. Black-Right-Pointing-Pointer Construction of a novel glucose sensor with wide linear range, high sensitivity and fast response.

  3. The influence of core materials and mix on the performance of a 100 kVA three phase transformer core

    Energy Technology Data Exchange (ETDEWEB)

    Snell, David E-mail: dave.snell@cogent-power.com; Coombs, Alan

    2003-01-01

    Various grades of grain-oriented electrical steel, and the effect of mixing domain refined and non-domain refined materials in the same three phase transformer core have been assessed using a developed computer-based test system. Ball unit domain refined material and non-domain refined material can be successfully mixed in the same core, without degrading performance.

  4. Catalytic coherence transformations

    Science.gov (United States)

    Bu, Kaifeng; Singh, Uttam; Wu, Junde

    2016-04-01

    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.

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

    OpenAIRE

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

    1998-01-01

    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 ...

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

    OpenAIRE

    Hoernel, J. -D.

    2006-01-01

    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.

  7. 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

  8. Catalytic Phosphination and Arsination

    Institute of Scientific and Technical Information of China (English)

    Kwong Fuk Yee; Chan Kin Shing

    2004-01-01

    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.

  9. Monolithic catalytic igniters

    Science.gov (United States)

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

    1993-01-01

    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.

  10. 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

    2015-01-01

    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

  11. Ice cores

    DEFF Research Database (Denmark)

    Svensson, Anders

    Ice cores from Antarctica, from Greenland, and from a number of smaller glaciers around the world yield a wealth of information on past climates and environments. Ice cores offer unique records on past temperatures, atmospheric composition (including greenhouse gases), volcanism, solar activity......, dustiness, and biomass burning, among others. In Antarctica, ice cores extend back more than 800,000 years before present (Jouzel et al. 2007), whereas. Greenland ice cores cover the last 130,000 years...

  12. The catalytic residues of Tn3 resolvase

    OpenAIRE

    Olorunniji, F.J.; Stark, W M

    2009-01-01

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

  13. Catalytic asymmetric formal synthesis of beraprost

    Science.gov (United States)

    Kobayashi, Yusuke; Kuramoto, Ryuta

    2015-01-01

    Summary The first catalytic asymmetric synthesis of the key intermediate for beraprost has been achieved through an enantioselective intramolecular oxa-Michael reaction of an α,β-unsaturated amide mediated by a newly developed benzothiadiazine catalyst. The Weinreb amide moiety and bromo substituent of the Michael adduct were utilized for the C–C bond formations to construct the scaffold. All four contiguous stereocenters of the tricyclic core were controlled via Rh-catalyzed stereoselective C–H insertion and the subsequent reduction from the convex face. PMID:26734111

  14. Catalytic thermal barrier coatings

    Science.gov (United States)

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

    2009-06-02

    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.

  15. Molecular models of human P-glycoprotein in two different catalytic states

    Directory of Open Access Journals (Sweden)

    Tulkens Paul M

    2009-01-01

    Full Text Available Abstract Background P-glycoprotein belongs to the family of ATP-binding cassette proteins which hydrolyze ATP to catalyse the translocation of their substrates through membranes. This protein extrudes a large range of components out of cells, especially therapeutic agents causing a phenomenon known as multidrug resistance. Because of its clinical interest, its activity and transport function have been largely characterized by various biochemical studies. In the absence of a high-resolution structure of P-glycoprotein, homology modeling is a useful tool to help interpretation of experimental data and potentially guide experimental studies. Results We present here three-dimensional models of two different catalytic states of P-glycoprotein that were developed based on the crystal structures of two bacterial multidrug transporters. Our models are supported by a large body of biochemical data. Measured inter-residue distances correlate well with distances derived from cross-linking data. The nucleotide-free model features a large cavity detected in the protein core into which ligands of different size were successfully docked. The locations of docked ligands compare favorably with those suggested by drug binding site mutants. Conclusion Our models can interpret the effects of several mutants in the nucleotide-binding domains (NBDs, within the transmembrane domains (TMDs or at the NBD:TMD interface. The docking results suggest that the protein has multiple binding sites in agreement with experimental evidence. The nucleotide-bound models are exploited to propose different pathways of signal transmission upon ATP binding/hydrolysis which could lead to the elaboration of conformational changes needed for substrate translocation. We identified a cluster of aromatic residues located at the interface between the NBD and the TMD in opposite halves of the molecule which may contribute to this signal transmission. Our models may characterize different steps

  16. Qualification of a passive catalytic module for hydrogen mitigation

    International Nuclear Information System (INIS)

    The advantage of passive catalytic modules for hydrogen mitigation during core-melt accidents, as compared with active devices like forced-flow recombiners or ignitors, is given by the high reliability of operation and the elimination of potentially violent combustion events. An important step in the qualification of a passive catalytic module system is the determination of the total required capacity and its distribution at various locations in the containment. Experiments and analytic modeling work were performed to qualify the installation of a system of catalytic modules for a large dry pressurized water reactor (PWR) containment. The operational capacity of a prototype catalytic module was determined experimentally, and a corresponding model correlation was developed and integrated into the GOTHIC containment code. This modified code was validated against experimental data. As an application, predictions of the effects, resulting from backfitting a large, dry PWR containment with 50 catalytic modules, were done using the modified code. The catalytic modules keep the hydrogen concentrations below a level of 10% where violent deflagrations could be expected. Local higher concentrations near the release location are inert due to associated low oxygen and high steam concentrations. A proper distribution of the modules in the containment guarantees full mixing of the atmosphere due to natural convective currents

  17. Catalytic reforming process

    Energy Technology Data Exchange (ETDEWEB)

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

    1989-06-13

    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.

  18. 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...

  19. Novel Catalytic Membrane Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Stuart Nemser, PhD

    2010-10-01

    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.

  20. Papain digestion of crude Trichoderma reesei cellulase: Purification and properties of cellobiohydrolase I and II core proteins

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Brown, J.P.; Evans, B.R.; Affholter, K.A.

    1992-01-01

    Papain digestion of a crude Trichoderma reesei cellulose preparation followed by gel filtration on a Superdex column resulted in the separation of cellobiohydrolase (CBH) I and II core proteins (cp). They were further purified to apparent homogeneity by chromatofocusing. N-terminal protein sequencing of the CBH II cp preparation confirmed its identity. A comparison of the catalytic activity and cellulose-binding ability of these core proteins was made. The major differences between them were the findings that CBH II cp possessed a sixfold higher specific activity toward p-nitrophenylcellobioside than the native CBH II preparation and still bound to microcrystalline cellulose, unlike CBH I cp. Neither CBH I cp nor CBH II cp had activity toward carboxymethylcellulose, but both were able to hydrolyze barley b-glucan. These data suggest that removal of the cellulose-binding domain and hinge region from CBH I and II have different effects on their properties.

  1. Papain digestion of crude Trichoderma reesei cellulase: Purification and properties of cellobiohydrolase I and II core proteins

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Brown, J.P.; Evans, B.R.; Affholter, K.A.

    1992-12-01

    Papain digestion of a crude Trichoderma reesei cellulose preparation followed by gel filtration on a Superdex column resulted in the separation of cellobiohydrolase (CBH) I and II core proteins (cp). They were further purified to apparent homogeneity by chromatofocusing. N-terminal protein sequencing of the CBH II cp preparation confirmed its identity. A comparison of the catalytic activity and cellulose-binding ability of these core proteins was made. The major differences between them were the findings that CBH II cp possessed a sixfold higher specific activity toward p-nitrophenylcellobioside than the native CBH II preparation and still bound to microcrystalline cellulose, unlike CBH I cp. Neither CBH I cp nor CBH II cp had activity toward carboxymethylcellulose, but both were able to hydrolyze barley b-glucan. These data suggest that removal of the cellulose-binding domain and hinge region from CBH I and II have different effects on their properties.

  2. Ice Cores

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Records of past temperature, precipitation, atmospheric trace gases, and other aspects of climate and environment derived from ice cores drilled on glaciers and ice...

  3. 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)

    1997-06-01

    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.

  4. Catalytic Combustion of Gasified Waste

    Energy Technology Data Exchange (ETDEWEB)

    Kusar, Henrik

    2003-09-01

    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.

  5. rSac3,a novel Sac domain phosphoinositide phosphatase,promotes neurite outgrowth in PC12 cells

    Institute of Scientific and Technical Information of China (English)

    Yiyuan Yuan; Xiang Gao; Ning Guo; Hui Zhang; Zhiqin Xie; Meilei Jin; Baoming Li; Lei yu; Naihe Jing

    2007-01-01

    Sac domain-containing proteins belong to a newly identified family of phosphoinositide phosphatases(the PIPPase family).Despite well-characterized enzymatic activity,the biological functions of this mammalian Sac domain PIPPase family remain largely unknown.We identified a novel Sac domain-containing protein,rat Sac3(rSac3),which iS widely expressed in various tissues and localized to the endoplasmic reticulum,Golgi complex and recycling endosomes.rSac3 displays PIPPase activity with PI(3)P,PI(4)P and PI(3,5)P2 as substrates in vitro,and a mutation in the catalytic core of the Sac domain abolishes its enzymatic activity.The expression of rSac3 iS upregulated during nerve growth factor (NGF)-stimulated PC12 cell neuronal differentiation,and overexpression of this protein promotes neurite outgrowth in PC12 cells.Conversely,inhibition of rSac3 expression by antisense oligonucleotides reduces neurite outgrowth of NGFstimulated PC12 cells,and the active site mutation of rSac3 eliminates its neurite-outgrowth-promoting activity.These results indicate that rSac3 promotes neurite outgrowth in differentiating neurons through its PIPPase activity,suggesting that Sac domain PIPPase proteins may participate in forward membrane trafficking from the endoplasmic reticulum and Golgi complex to the plasma membrane,and may function as regulators of this crucial process of neuronal cell growth and differentiation.

  6. 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

    2011-01-01

    ); 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....

  7. Life and death of a single catalytic cracking particle.

    Science.gov (United States)

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

    2015-04-01

    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

  8. 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.

  9. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    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...

  10. Catalytic production of biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Theilgaard Madsen, A.

    2011-07-01

    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

  11. Single-chain folding of polymers for catalytic systems in water.

    Science.gov (United States)

    Terashima, Takaya; Mes, Tristan; De Greef, Tom F A; Gillissen, Martijn A J; Besenius, Pol; Palmans, Anja R A; Meijer, E W

    2011-04-01

    Enzymes are a source of inspiration for chemists attempting to create versatile synthetic catalysts. In order to arrive at a polymeric chain carrying catalytic units separated spatially, it is a prerequisite to fold these polymers in water into well-defined compartmentalized architectures thus creating a catalytic core. Herein, we report the synthesis, physical properties, and catalytic activity of a water-soluble segmented terpolymer in which a helical structure in the apolar core is created around a ruthenium-based catalyst. The supramolecular chirality of this catalytic system is the result of the self-assembly of benzene-1,3,5-tricarboxamide side chains, while the catalyst arises from the sequential ruthenium-catalyzed living radical polymerization of the different monomers followed by ligand exchange. The polymers exhibit a two-state folding process and show transfer hydrogenation in water. PMID:21405022

  12. Core transfer

    Science.gov (United States)

    Good news for all petroleum geoscientists, mining and environmental scientists, university researchers, and the like: Shell Oil Company has deeded its Midland core and sample repository to the Bureau of Economic Geology (BEG) at the University of Texas at Austin. The Midland repository includes more than 1 million linear meters of slab, whole core, and prepared cuttings. Data comprising one of the largest U.S. core collections—the geologic samples from wells drilled in Texas and 39 other states—are now public data and will be incorporated into the existing BEG database. Both Shell and the University of Texas at Austin are affiliated with the American Geological Institute, which assisted in arranging the transfer as part of its goal to establish a National Geoscience Data Repository System at regional centers across the United States.

  13. Core strengthening.

    Science.gov (United States)

    Arendt, Elizabeth A

    2007-01-01

    Several recent studies have evaluated interventional techniques designed to reduce the risk of serious knee injuries, particularly noncontact anterior cruciate ligament injuries in female athletes. Maintenance of rotational control of the limb underneath the pelvis, especially in response to cutting and jumping activities, is a common goal in many training programs. Rotational control of the limb underneath the pelvis is mediated by a complex set of factors including the strength of the trunk muscles and the relationship between the core muscles. It is important to examine the interrelationship between lower extremity function and core stability. PMID:17472321

  14. Core BPEL

    DEFF Research Database (Denmark)

    Hallwyl, Tim; Højsgaard, Espen

    The Web Services Business Process Execution Language (WS-BPEL) is a language for expressing business process behaviour based on web services. The language is intentionally not minimal but provides a rich set of constructs, allows omission of constructs by relying on defaults, and supports language...... extensions. Combined with the fact that the language definition does not provide a formal semantics, it is an arduous task to work formally with the language (e.g. to give an implementation). In this paper we identify a core subset of the language, called Core BPEL, which has fewer and simpler constructs...

  15. Aluminosilicate nanoparticles for catalytic hydrocarbon cracking.

    Science.gov (United States)

    Liu, Yu; Pinnavaia, Thomas J

    2003-03-01

    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

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

    Science.gov (United States)

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

    2015-10-01

    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

  17. Soluble organic nanotubes for catalytic systems

    Science.gov (United States)

    Xiong, Linfeng; Yang, Kunran; Zhang, Hui; Liao, Xiaojuan; Huang, Kun

    2016-03-01

    In this paper, we report a novel method for constructing a soluble organic nanotube supported catalyst system based on single-molecule templating of core-shell bottlebrush copolymers. Various organic or metal catalysts, such as sodium prop-2-yne-1-sulfonate (SPS), 1-(2-(prop-2-yn-1-yloxy)ethyl)-1H-imidazole (PEI) and Pd(OAc)2 were anchored onto the tube walls to functionalize the organic nanotubes via copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Depending on the ‘confined effect’ and the accessible cavity microenvironments of tubular structures, the organic nanotube catalysts showed high catalytic efficiency and site-isolation features. We believe that the soluble organic nanotubes will be very useful for the development of high performance catalyst systems due to their high stability of support, facile functionalization and attractive textural properties.

  18. Immigration process in catalytic medium

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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.

  19. Catalytic DNA with phosphatase activity

    OpenAIRE

    Chandrasekar, Jagadeeswaran; Silverman, Scott K.

    2013-01-01

    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...

  20. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the RNA polymerase domain of primase from Streptococcus mutans strain UA159

    International Nuclear Information System (INIS)

    The RNA polymerase domain of primase from S. mutans strain UA159 was cloned, overexpressed, purified and crystallized. X-ray diffraction data were collected to a resolution of 1.60 Å. Primase is the enzyme that synthesizes RNA primers on single-stranded DNA during normal DNA replication. In this study, the catalytic core domain of primase from Streptococcus mutans UA159 was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 1.60 Å resolution using a synchrotron-radiation source. The crystal belonged to space group P41 or P43, with unit-cell parameters a = b = 52.63, c = 110.31 Å. The asymmetric unit is likely to contain one molecule, with a corresponding VM of 1.77 Å3 Da−1 and a solvent content of 30.7%

  1. Identification of Residues in the C-terminal Domain of HIV-1 Integrase That Mediate Binding to the Transportin-SR2 Protein*

    Science.gov (United States)

    De Houwer, Stephanie; Demeulemeester, Jonas; Thys, Wannes; Taltynov, Oliver; Zmajkovicova, Katarina; Christ, Frauke; Debyser, Zeger

    2012-01-01

    Transportin-SR2 (TRN-SR2 and TNPO3) is a cellular cofactor of HIV replication that has been implicated in the nuclear import of HIV. TRN-SR2 was originally identified in a yeast two-hybrid screen as an interaction partner of HIV integrase (IN) and in two independent siRNA screens as a cofactor of viral replication. We have now studied the interaction of TRN-SR2 and HIV IN in molecular detail and identified the TRN-SR2 interacting regions of IN. A weak interaction with the catalytic core domain (CCD) and a strong interaction with the C-terminal domain (CTD) of IN were detected. By dissecting the catalytic core domain (CCD) of IN into short structural fragments, we identified a peptide (INIP1, amino acids 170EHLKTAVQMAVFIHNFKRKGGI191) retaining the ability to interact with TRN-SR2. By dissecting the C-terminal domain (CTD) of IN, we could identify two interacting peptides (amino acids 214QKQITKIQNFRVYYR228 and 262RRKVKIIRDYGK273) that come together in the CTD tertiary structure to form an exposed antiparallel β-sheet. Through site-specific mutagenesis, we defined the following sets of amino acids in IN as important for the interaction with TRN-SR2: Phe-185/Lys-186/Arg-187/Lys-188 in the CCD and Arg-262/Arg-263/Lys-264 and Lys-266/Arg-269 in the CTD. An HIV-1 strain carrying K266A/R269A in IN was replication-defective due to a block in reverse transcription, confounding the study of nuclear import. Insight into the IN/TRN-SR2 interaction interface is necessary to guide drug discovery efforts targeting the nuclear entry step of replication. PMID:22872638

  2. Frequency domain nonlinear optics

    Science.gov (United States)

    Legare, Francois

    2016-05-01

    The universal dilemma of gain narrowing occurring in fs amplifiers prevents ultra-high power lasers from delivering few-cycle pulses. This problem is overcome by a new amplification concept: Frequency domain Optical Parametric Amplification - FOPA. It enables simultaneous up-scaling of peak power and amplified spectral bandwidth and can be performed at any wavelength range of conventional amplification schemes, however, with the capability to amplify single cycles of light. The key idea for amplification of octave-spanning spectra without loss of spectral bandwidth is to amplify the broad spectrum ``slice by slice'' in the frequency domain, i.e. in the Fourier plane of a 4f-setup. The striking advantages of this scheme, are its capability to amplify (more than) one octave of bandwidth without shorting the corresponding pulse duration. This is because ultrabroadband phase matching is not defined by the properties of the nonlinear crystal employed but the number of crystals employed. In the same manner, to increase the output energy one simply has to increase the spectral extension in the Fourier plane and to add one more crystal. Thus, increasing pulse energy and shortening its duration accompany each other. A proof of principle experiment was carried out at ALLS on the sub-two cycle IR beam line and yielded record breaking performance in the field of few-cycle IR lasers. 100 μJ two-cycle pulses from a hollow core fibre compression setup were amplified to 1.43mJ without distorting spatial or temporal properties. Pulse duration at the input of FOPA and after FOPA remains the same. Recently, we have started upgrading this system to be pumped by 250 mJ to reach 40 mJ two-cycle IR few-cycle pulses and latest results will be presented at the conference. Furthermore, the extension of the concept of FOPA to other nonlinear optical processes will be discussed. Frequency domain nonlinear optics.

  3. Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation

    Science.gov (United States)

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

    2016-05-01

    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.

  4. Catalytic activity of Au nanoparticles

    DEFF Research Database (Denmark)

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

    2007-01-01

    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....

  5. Catalytic distillation water recovery subsystem

    Science.gov (United States)

    Budininkas, P.; Rasouli, F.

    1985-01-01

    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.

  6. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    Vivek V Ranade

    2014-03-01

    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.

  7. Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site.

    Science.gov (United States)

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

    1997-02-01

    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

  8. Insights into function of PSI domains from structure of the Met receptor PSI domain

    International Nuclear Information System (INIS)

    PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel β-sheet and two α-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor

  9. 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)

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

    OpenAIRE

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

    2012-01-01

    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...

  11. 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)

  12. Structural models of vanadate-dependent haloperoxidases, their reactivity, immobilization on polymer support and catalytic activities

    Indian Academy of Sciences (India)

    Mannar R Maurya

    2011-03-01

    The design of structural and functional models of enzymes vanadate-dependent haloperoxidases (VHPO) and the isolation and/or generation of species having {VO(H2O)}, {VO2}, {VO(OH)} and {VO(O2)} cores, proposed as intermediate(s) during catalytic action, in solution have been studied. Catalytic potential of these complexes have been tested for oxo-transfer as well as oxidative bromination and sulfide oxidation reactions. Some of the oxidovanadium(IV) and dioxidovanadium(V) complexes have been immobilized on polymer support in order to improve their recycle ability during catalytic activities and turn over number. The formulations of the polymer-anchored complexes are based on the respective neat complexes and conclusions drawn from the various characterization studies. These catalysts have successfully been used for all catalytic reactions mentioned above. These catalysts are stable and recyclable.

  13. Domain structure of circular and ring magnets

    International Nuclear Information System (INIS)

    We present the results of a study of the domain structure and the magnetization reversal processes in arrays of circular and ring magnets, obtained by magnetic force microscopy and magnetization measurements. The particles, with outer diameter 0.55 and 2.2 μm, were made of Permalloy films of thickness 24 and 66 nm. In the circular elements two domain configurations were observed: a vortex structure with perpendicular magnetization at the core and a 'bud' state. In the ring elements the domain structure was found to depend on the ring width: a flux closed state was formed in wide rings and the 'onion' state was observed in narrow rings

  14. The Catalytic Enantioselective Total Synthesis of (+)‐Liphagal

    DEFF Research Database (Denmark)

    Day, Joshua J.; McFadden, Ryan M.; Virgil, Scott C.;

    2011-01-01

    Ring a ding: The first catalytic enantioselective total synthesis of the meroterpenoid natural product (+)-liphagal is disclosed. The approach showcases a variety of technology including enantioselective enolate alkylation, a photochemical alkyne-alkene [2+2] reaction, microwaveassisted metal...... establish the trans homodecalin system found in the natural product...... catalysis, and an intramolecular aryne capture cyclization reaction. Pivotal to the successful completion of the synthesis was a sequence involving ring expansion from a [6-5-4] tricycle to a [6-7] bicyclic core followed by stereoselective hydrogenation of a sterically occluded tri-substituted olefin to...

  15. 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;

    2004-01-01

    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....

  16. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan

    2008-01-01

    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

  17. 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)

    2013-09-25

    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.

  18. Catalytic Fast Pyrolysis: A Review

    Directory of Open Access Journals (Sweden)

    Theodore Dickerson

    2013-01-01

    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.

  19. Combined catalytic converter and afterburner

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-11-30

    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)

  20. 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

  1. Structures composing protein domains

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

    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

  2. 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

    2013-01-01

    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.

  3. On simultaneous s-cores/t-cores

    OpenAIRE

    Aukerman, D; Kane, B.; Sze, L

    2009-01-01

    In this paper, the authors investigate the question of when a partition of n∈N is an s-core and also a t-core when s and t are not relatively prime. A characterization of all such s/t-cores is given, as well as a generating function dependent upon the polynomial generating functions for s/t-cores when s and t are relatively prime. Furthermore, characterizations and generating functions are given for s/t-cores which are self-conjugate and also for (e,r)/(e′,r)-cores.

  4. 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)

    2015-11-30

    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.

  5. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin.

    Science.gov (United States)

    Handley, Lindsey D; Treuheit, Nicholas A; Venkatesh, Varun J; Komives, Elizabeth A

    2015-11-01

    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

  6. Dual-core antiresonant hollow core fibers.

    Science.gov (United States)

    Liu, Xuesong; Fan, Zhongwei; Shi, Zhaohui; Ma, Yunfeng; Yu, Jin; Zhang, Jing

    2016-07-25

    In this work, dual-core antiresonant hollow core fibers (AR-HCFs) are numerically demonstrated, based on our knowledge, for the first time. Two fiber structures are proposed. One is a composite of two single-core nested nodeless AR-HCFs, exhibiting low confinement loss and a circular mode profile in each core. The other has a relatively simple structure, with a whole elliptical outer jacket, presenting a uniform and wide transmission band. The modal couplings of the dual-core AR-HCFs rely on a unique mechanism that transfers power through the air. The core separation and the gap between the two cores influence the modal coupling strength. With proper designs, both of the dual-core fibers can have low phase birefringence and short modal coupling lengths of several centimeters. PMID:27464191

  7. Adapting Mathematical Domain Reasoners

    CERN Document Server

    Heeren, Bastiaan

    2010-01-01

    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...

  8. Mining e-Learning Domain Concept Map from Academic Articles

    Science.gov (United States)

    Chen, Nian-Shing; Kinshuk; Wei, Chun-Wang; Chen, Hong-Jhe

    2008-01-01

    Recent researches have demonstrated the importance of concept map and its versatile applications especially in e-Learning. For example, while designing adaptive learning materials, designers need to refer to the concept map of a subject domain. Moreover, concept maps can show the whole picture and core knowledge about a subject domain. Research…

  9. The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf

    Directory of Open Access Journals (Sweden)

    Geldner Niko

    2005-02-01

    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.

  10. Enantioselective Synthesis of the 5-6-7 Carbocyclic Core of the Gagunin Diterpenoids

    OpenAIRE

    Shibuya, Grant M.; Enquist, John A.; Stoltz, Brian M.

    2013-01-01

    A catalytic enantioselective double allylic alkylation reaction has been employed in the synthesis of the core of the gagunin diterpenoids. Enantioenriched material was advanced in 11 steps to afford the core of the highly oxygenated target, which includes two all-carbon quaternary stereocenters.

  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. Regulation of Escherichia coli RelA Requires Oligomerization of the C-Terminal Domain

    OpenAIRE

    Gropp, Michal; Strausz, Yael; Gross, Miriam; Glaser, Gad

    2001-01-01

    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...

  13. Kinetics of heterogeneous catalytic reactions

    CERN Document Server

    Boudart, Michel

    2014-01-01

    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

  14. Molecular catalytic coal liquid conversion

    Energy Technology Data Exchange (ETDEWEB)

    Stock, L.M.; Yang, Shiyong [Univ. of Chicago, IL (United States)

    1995-12-31

    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.

  15. 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....

  16. Catalytic Spectrophotometric Determination of Chromium

    OpenAIRE

    STOYANOVA, Angelina Miltcheva

    2005-01-01

    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...

  17. Catalytic Combustion of Ethyl Acetate

    OpenAIRE

    ÖZÇELİK, Tuğba GÜRMEN; ATALAY, Süheyda; ALPAY, Erden

    2007-01-01

    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...

  18. Emergency core cooling device

    International Nuclear Information System (INIS)

    The present invention provides an emergency core cooling device without using a reactor core spray device, in which the reactor core of a BWR type reactor is cooled effectively and certainly by flooding of the reactor core. That is, the emergency core cooling device comprises a high pressure core water injection system as an emergency core cooling system (ECCS) for cooling the inside of the reactor core upon loss of coolants accident (LOCA). By means of the high pressure core water injection system, water is injected from a condensate storage vessel or a suppression pool to the inside of the reactor core shroud upon LOCA. Accordingly, the reactor core is cooled effectively by reactor core flooding. In this device, cooling water can be injected to the inside of the reactor core shroud by means of the high pressure core injection system upon LOCA in which the coolants are discharged from the outside of the reactor core shroud. On the other hand, upon LOCA in which the coolants are discharged from the inside of the reactor core shroud, the cooling water can be supplied to the reactor core by means of a cooling system upon reactor isolation which injects water to the outside of the reactor core or a low pressure water injection system. (I.S.)

  19. Estimating the temperature of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-11-02

    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)

  20. Estimating the temperature of a catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Ma, T.T.-H.

    1994-11-02

    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)

  1. A Dublin Core Application Profile in the Agricultural Domain

    OpenAIRE

    Onyancha, Irene; Keizer, Johannes; Katz, Stephen

    2001-01-01

    This report outlines a proposed metadata framework for resource discovery of agricultural resources, and in particular to describe information resources in agricultural sciences. The overall work is the result of a collaborative effort between a number of partners in the agricultural community and the Library and Documentation Systems Division of FAO. The endeavour is formally referred to as the "Agricultural Metadata Standards Initiative" (Agstandards). It is based upon the elements and qual...

  2. The human core exosome interacts with differentially localized processive RNases

    DEFF Research Database (Denmark)

    Tomecki, Rafal; Kristiansen, Maiken Søndergaard; Lykke-Andersen, Søren;

    2010-01-01

    The eukaryotic RNA exosome is a ribonucleolytic complex involved in RNA processing and turnover. It consists of a nine-subunit catalytically inert core that serves a structural function and participates in substrate recognition. Best defined in Saccharomyces cerevisiae, enzymatic activity comes...... from the associated subunits Dis3p (Rrp44p) and Rrp6p. The former is a nuclear and cytoplasmic RNase II/R-like enzyme, which possesses both processive exo- and endonuclease activities, whereas the latter is a distributive RNase D-like nuclear exonuclease. Although the exosome core is highly conserved......, identity and arrangements of its catalytic subunits in different vertebrates remain elusive. Here, we demonstrate the association of two different Dis3p homologs--hDIS3 and hDIS3L--with the human exosome core. Interestingly, these factors display markedly different intracellular localizations: hDIS3...

  3. Nanostructured Catalytic Reactors for Air Purification Project

    Data.gov (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...

  4. Nanostructured Catalytic Reactors for Air Purification Project

    Data.gov (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...

  5. Thermally Stable Nanocatalyst for High Temperature Reactions: Pt-Mesoporous Silica Core-Shell Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Joo, Sang Hoon; Park, J.Y.; Tsung, C.-K.; Yamada, Y.; Yang, P.; Somorjai, G.A.

    2008-10-25

    Recent advances in colloidal synthesis enabled the precise control of size, shape and composition of catalytic metal nanoparticles, allowing their use as model catalysts for systematic investigations of the atomic-scale properties affecting catalytic activity and selectivity. The organic capping agents stabilizing colloidal nanoparticles, however, often limit their application in high-temperature catalytic reactions. Here we report the design of a high-temperature stable model catalytic system that consists of Pt metal core coated with a mesoporous silica shell (Pt{at}mSiO{sub 2}). While inorganic silica shells encaged the Pt cores up to 750 C in air, the mesopores directly accessible to Pt cores made the Pt{at}mSiO{sub 2} nanoparticles as catalytically active as bare Pt metal for ethylene hydrogenation and CO oxidation. The high thermal stability of Pt{at}mSiO{sub 2} nanoparticles permitted high-temperature CO oxidation studies, including ignition behavior, which was not possible for bare Pt nanoparticles because of their deformation or aggregation. The results suggest that the Pt{at}mSiO{sub 2} nanoparticles are excellent nanocatalytic systems for high-temperature catalytic reactions or surface chemical processes, and the design concept employed in the Pt{at}mSiO{sub 2} core-shell catalyst can be extended to other metal-metal oxide compositions.

  6. Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms

    OpenAIRE

    Barchiesi, Julieta; Hedin, Nicolás; Gomez-Casati, Diego F.; Miguel A Ballicora; Busi, María V.

    2015-01-01

    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...

  7. Catalytic conversion of light alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Lyons, J.E.

    1992-06-30

    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).

  8. 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

  9. 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)

    2002-09-01

    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.)

  10. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.

    Science.gov (United States)

    Xiong, Zi-Jian; Huang, Jingjing; Poda, Gennady; Pomès, Régis; Privé, Gilbert G

    2016-07-31

    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

  11. General Music and the Common Core: A Brief Discussion

    Science.gov (United States)

    Cardany, Audrey Berger

    2013-01-01

    The Common Core Standards and the wide-spread state adoption have implications for music teachers. Alignment with English language arts Common Core Standards is discussed, with examples provided for elementary general music experiences. The author notes the challenge of retaining focus on the music domain while meeting the expectations of the…

  12. Core-shell palladium nanoparticle@metal-organic frameworks as multifunctional catalysts for cascade reactions.

    Science.gov (United States)

    Zhao, Meiting; Deng, Ke; He, Liangcan; Liu, Yong; Li, Guodong; Zhao, Huijun; Tang, Zhiyong

    2014-02-01

    Uniform core-shell Pd@IRMOF-3 nanostructures, where single Pd nanoparticle core is surrounded by amino-functionalized IRMOF-3 shell, are prepared by a facile mixed solvothermal method. When used as multifunctional catalysts, the Pd@IRMOF-3 nanocomposites exhibit high activity, enhanced selectivity, and excellent stability in the cascade reaction. Both experimental evidence and theoretical calculations reveal that the high catalytic performance of Pd@IRMOF-3 nanocomposites originates from their unique core-shell structures. PMID:24437922

  13. Clojure for domain-specific languages

    CERN Document Server

    Kelker, Ryan D

    2013-01-01

    An example-oriented approach to develop custom domain-specific languages.If you've already developed a few Clojure applications and wish to expand your knowledge on Clojure or domain-specific languages in general, then this book is for you. If you're an absolute Clojure beginner, then you may only find the detailed examples of the core Clojure components of value. If you've developed DSLs in other languages, this Lisp and Java-based book might surprise you with the power of Clojure.

  14. Skyrmions from Instantons inside Domain Walls

    CERN Document Server

    Eto, M; Ohashi, K; Tong, D; Eto, Minoru; Nitta, Muneto; Ohashi, Keisuke; Tong, David

    2005-01-01

    Some years ago, Atiyah and Manton described a method to construct approximate Skyrmion solutions from Yang-Mills instantons. Here we present a dynamical realization of this construction using domain walls in a five-dimensional gauge theory. The non-abelian gauge symmetry is broken in each vacuum but restored in the core of the domain wall, allowing instantons to nestle inside the wall. We show that the worldvolume dynamics of the wall is given by the Skyrme model, including the four-derivative term, and the instantons appear as Skyrmions.

  15. Structural Basis for the Catalytic Activity of Human Serine/Threonine Protein Phosphatase-5

    Science.gov (United States)

    Swingle, M. R.; Honkanen, R.; Ciszak, E. M.

    2004-01-01

    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.

  16. Structural Basis for the Catalytic Activity of Human SER/THR Protein Phosphatase-5

    Science.gov (United States)

    Swingle, M. R.; Honkanen, R.; Ciszak, E.

    2004-01-01

    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.

  17. Modelling of procecces in catalytic recombiners

    International Nuclear Information System (INIS)

    In order to achieve a high degree of safety in nuclear power plants and prevent possible accident scenarios, their consequences are calculated and analysed with numeric codes. One of the most important part of nuclear safety research of hazardous incidents are development and validation of these numeric models, which are implemented into accident codes. The severe hydrogen release during a core meltdown is one of the considered scenario of performed accident analyses. One of the most important measure for the elimination of the hydrogen is catalytic recombiners. Converting the hydrogen with the atmospheric oxygen to water vapor in an exothermic reaction will prevent possible detonation of the hydrogen/air atmosphere. Within the dissertation the recombiner simulation REKO-DIREKT was developed and validated by an extensive experimental database. The performance of recombiners with regard to the conversion of the hydrogen and the temperature development is modelled. The REKO-DIREKT program is unique and has made significant revolution in research of hydrogen safety. For the first time it has been possible to show the performance of the recombiner so great in detail by using REKO-DIREKT. In the future engineers of nuclear power plants will have opportunity to have precise forecasts about the process of the possible accidents with hydrogen release. Also with presence of water vapor or with oxygen depletion which are included in the model. The major discussion of the hydrogen ignition at hot catalyst steel plates can be evaluated in the future with REKO-DIREKT more reliably than the existing used models. (orig.)

  18. Acoustics of automotive catalytic converter assemblies

    Science.gov (United States)

    Dickey, Nolan S.; Selamet, Ahmet; Parks, Steve J.; Tallio, Kevin V.; Miazgowicz, Keith D.; Radavich, Paul M.

    2003-10-01

    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.

  19. Understanding catalytic biomass conversion through data mining

    NARCIS (Netherlands)

    E.J. Ras; B. McKay; G. Rothenberg

    2010-01-01

    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

  20. Silver nanocluster catalytic microreactors for water purification

    Science.gov (United States)

    Da Silva, B.; Habibi, M.; Ognier, S.; Schelcher, G.; Mostafavi-Amjad, J.; Khalesifard, H. R. M.; Tatoulian, M.; Bonn, D.

    2016-07-01

    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.

  1. Selective catalytic oxidation of ammonia

    Energy Technology Data Exchange (ETDEWEB)

    Leppaelahti, J.; Koljonen, T. [VTT Energy, Espoo (Finland)

    1996-12-31

    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.)

  2. 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

  3. Catalytic Graphitization of Phenolic Resin

    Institute of Scientific and Technical Information of China (English)

    Mu Zhao; Huaihe Song

    2011-01-01

    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.

  4. Reducing catalytic converter pressure loss

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-06-01

    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.

  5. Non-catalytic recuperative reformer

    Energy Technology Data Exchange (ETDEWEB)

    Khinkis, Mark J.; Kozlov, Aleksandr P.; Kurek, Harry

    2015-12-22

    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.

  6. Fluctuations in catalytic surface reactions

    CERN Document Server

    Imbihl, R

    2003-01-01

    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...

  7. Catalytic, enantioselective, vinylogous aldol reactions.

    Science.gov (United States)

    Denmark, Scott E; Heemstra, John R; Beutner, Gregory L

    2005-07-25

    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

  8. Electrochemical promotion of catalytic reactions

    Science.gov (United States)

    Imbihl, R.

    2010-05-01

    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.

  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. Catalytic converter with thermoelectric generator

    Energy Technology Data Exchange (ETDEWEB)

    Parise, R.J.

    1998-07-01

    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.

  11. The evolution of catalytic function

    Science.gov (United States)

    Maurel, Marie-Christine; Ricard, Jacques

    2006-03-01

    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.

  12. 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.

  13. Academic Rigor: The Core of the Core

    Science.gov (United States)

    Brunner, Judy

    2013-01-01

    Some educators see the Common Core State Standards as reason for stress, most recognize the positive possibilities associated with them and are willing to make the professional commitment to implementing them so that academic rigor for all students will increase. But business leaders, parents, and the authors of the Common Core are not the only…

  14. SUC-CORE: SUC 2.0 Annotated with NP Coreference

    OpenAIRE

    Nilsson Björkenstam, Kristina; Byström, Emil

    2012-01-01

    SUC-CORE is a subset of Stockholm Umeå Corpus 2.0 and Swedish Treebank, annotated with noun phrase coreference. While most coreference annotated corpora consist of texts of similar types within related domains, SUC-CORE consists of both informative and imaginative prose and covers a wide range of literary genres and domains.

  15. 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)

  16. 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

    2004-12-01

    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

  17. Frustratingly Easy Domain Adaptation

    CERN Document Server

    Daumé, Hal

    2009-01-01

    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.

  18. CULTURAL DOMAINS: TRANSLATION PROBLEMS

    OpenAIRE

    Isabel Negro Alousque

    2009-01-01

    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...

  19. Visualizing latent domain knowledge

    OpenAIRE

    Chen, C.; Kuljis, J; Paul, RJ

    2001-01-01

    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...

  20. Electric-field-driven dynamics of magnetic domain walls in magnetic nanowires patterned on ferroelectric domains

    Science.gov (United States)

    Van de Wiele, Ben; Leliaert, Jonathan; Franke, Kévin J. A.; van Dijken, Sebastiaan

    2016-03-01

    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.

  1. Extracting the Cores of Implicit Communities

    Institute of Scientific and Technical Information of China (English)

    YANG Nan; LIN Songxiang; GAO Qiang

    2007-01-01

    In this paper, we improve the trawling and point out some communities missed by trawling. We use the DBG (Dense Bipartite Graph) to identify a structure of a potential community instead of CBG (Complete Bipartite Graph). Based on DBG, we proposed a new method based on edge removal to extract cores from a web graph. Moreover, we improve the crawler to save only potential pages as fans of a core and save a lot of disk storage space. To evaluate the set of cores whether or not belong to a community, the statistics of term frequency is used. In the paper,the dataset of experiment were crawled under domain ".cn". The result show that the our algorithm works properly and some new cores can be found by our method.

  2. A non-stationary problem coupling PDEs and ODEs modelizing an automotive catalytic converter

    OpenAIRE

    Hoernel, J. -D.

    2005-01-01

    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.

  3. Structure-based identification of catalytic residues.

    Science.gov (United States)

    Yahalom, Ran; Reshef, Dan; Wiener, Ayana; Frankel, Sagiv; Kalisman, Nir; Lerner, Boaz; Keasar, Chen

    2011-06-01

    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 http://www.cs.bgu.ac.il/∼meshi/functionPrediction. PMID:21491495

  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)

    2004-04-01

    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.

    2016-03-29

    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. Topological Domain Theory

    OpenAIRE

    Battenfeld, Ingo

    2008-01-01

    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.

  8. Modeling Protein Domain Function

    Science.gov (United States)

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    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…

  9. Domain Walls on Singularities

    CERN Document Server

    Halyo, Edi

    2009-01-01

    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.

  10. Co-Cu Nanoparticles: Synthesis by Galvanic Replacement and Phase Rearrangement during Catalytic Activation.

    Science.gov (United States)

    Nafria, Raquel; Genç, Aziz; Ibáñez, Maria; Arbiol, Jordi; Ramírez de la Piscina, Pilar; Homs, Narcís; Cabot, Andreu

    2016-03-01

    The control of the phase distribution in multicomponent nanomaterials is critical to optimize their catalytic performance. In this direction, while impressive advances have been achieved in the past decade in the synthesis of multicomponent nanoparticles and nanocomposites, element rearrangement during catalyst activation has been frequently overseen. Here, we present a facile galvanic replacement-based procedure to synthesize Co@Cu nanoparticles with narrow size and composition distributions. We further characterize their phase arrangement before and after catalytic activation. When oxidized at 350 °C in air to remove organics, Co@Cu core-shell nanostructures oxidize to polycrystalline CuO-Co3O4 nanoparticles with randomly distributed CuO and Co3O4 crystallites. During a posterior reduction treatment in H2 atmosphere, Cu precipitates in a metallic core and Co migrates to the nanoparticle surface to form Cu@Co core-shell nanostructures. The catalytic behavior of such Cu@Co nanoparticles supported on mesoporous silica was further analyzed toward CO2 hydrogenation in real working conditions. PMID:26878153

  11. Sub-nanometer dimensions control of core/shell nanoparticles prepared by atomic layer deposition

    International Nuclear Information System (INIS)

    Bimetallic core/shell nanoparticles (NPs) are the subject of intense research due to their unique electronic, optical and catalytic properties. Accurate and independent control over the dimensions of both core and shell would allow for unprecedented catalytic performance. Here, we demonstrate that both core and shell dimensions of Pd/Pt core/shell nanoparticles (NPs) supported on Al2O3 substrates can be controlled at the sub-nanometer level by using a novel strategy based on atomic layer deposition (ALD). From the results it is derived that the main conditions for accurate dimension control of these core/shell NPs are: (i) a difference in surface energy between the deposited core metal and the substrate to obtain island growth; (ii) a process yielding linear growth of the NP cores with ALD cycles to obtain monodispersed NPs with a narrow size distribution; (iii) a selective ALD process for the shell metal yielding a linearly increasing thickness to obtain controllable shell growth exclusively on the cores. For Pd/Pt core/shell NPs it is found that a minimum core diameter of 1 nm exists above which the NP cores are able to catalytically dissociate the precursor molecules for shell growth. In addition, initial studies on the stability of these core/shell NPs have been carried out, and it has been demonstrated that core/shell NPs can be deposited by ALD on high aspect ratio substrates such as nanowire arrays. These achievements show therefore that ALD has significant potential for the preparation of tuneable heterogeneous catalyst systems. (paper)

  12. Copper on activated carbon for catalytic wet air oxidation

    Directory of Open Access Journals (Sweden)

    Nora Dolores Martínez

    2009-03-01

    Full Text Available Textile industry is an important source of water contamination. Some of the organic contaminants cannot be eliminated by nature in a reasonable period. Heterogeneous catalytic wet air oxidation is one of the most effective methods to purify wastewater with organic contaminants. In this work, catalysts based on copper supported on activated carbon were synthesized. The activated carbons were obtained from industrial wastes (apricot core and grape stalk of San Juan, Argentina. These were impregnated with a copper salt and thermically treated in an inert atmosphere. Analysis of specific surface, pore volume, p zc, acidity, basicity and XRD patterns were made in order to characterize the catalysts. The catalytic activity was tested in the oxidation of methylene blue (MB and polyvinyl alcohol (PVA in aqueous phase with pure oxygen. Reaction tests were carried out in a Parr batch reactor at different temperatures, with a 0.2 MPa partial pressure of oxygen. The amount of unconverted organics was measured by spectrophotometry. Higher temperatures were necessary for the degradation of PVA compared to those for methylene blue.

  13. 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.

    2016-05-29

    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.

  14. Halogen Chemistry on Catalytic Surfaces.

    Science.gov (United States)

    Moser, Maximilian; Pérez-Ramírez, Javier

    2016-01-01

    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

  15. Vacuum-insulated catalytic converter

    Energy Technology Data Exchange (ETDEWEB)

    Benson, David K. (Golden, CO)

    2001-01-01

    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.

  16. Structure-guided Mutational Analysis of the Nucleotidyltransferase Domain of Escherichia coli DNA Ligase (LigA)*

    OpenAIRE

    Wang, Li Kai; Zhu, Hui; Shuman, Stewart

    2009-01-01

    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...

  17. Phosphorylation of the Kinase Homology Domain Is Essential for Activation of the A-Type Natriuretic Peptide Receptor

    OpenAIRE

    Potter, Lincoln R.; Hunter, Tony

    1998-01-01

    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...

  18. Catalytic models developed through social work

    DEFF Research Database (Denmark)

    Jensen, Mogens

    2015-01-01

    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....

  19. Catalytic converters as a source of platinum

    Directory of Open Access Journals (Sweden)

    A. Fornalczyk

    2011-10-01

    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.

  20. WW or WoW: the WW domains in a union of bliss.

    Science.gov (United States)

    Sudol, Marius; Recinos, Claudia C; Abraczinskas, Jennifer; Humbert, Jasper; Farooq, Amjad

    2005-12-01

    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

  1. Banded transformer cores

    Science.gov (United States)

    Mclyman, C. W. T. (Inventor)

    1974-01-01

    A banded transformer core formed by positioning a pair of mated, similar core halves on a supporting pedestal. The core halves are encircled with a strap, selectively applying tension whereby a compressive force is applied to the core edge for reducing the innate air gap. A dc magnetic field is employed in supporting the core halves during initial phases of the banding operation, while an ac magnetic field subsequently is employed for detecting dimension changes occurring in the air gaps as tension is applied to the strap.

  2. 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

  3. Characterization of Aqueous Peroxomolybdates with Catalytic Applicability

    OpenAIRE

    Taube, Fabian

    2003-01-01

    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 ...

  4. MOBILE COMPLEX FOR CATALYTIC THERMAL WASTE TREATMENT

    OpenAIRE

    Vedi V.E.; Rovenskii A.I.

    2012-01-01

    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. MOBILE COMPLEX FOR CATALYTIC THERMAL WASTE TREATMENT

    Directory of Open Access Journals (Sweden)

    Vedi V.E.

    2012-12-01

    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.

  6. Temperature Modulation of a Catalytic Gas Sensor

    OpenAIRE

    Eike Brauns; Eva Morsbach; Sebastian Kunz; Marcus Baeumer; Walter Lang

    2014-01-01

    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...

  7. Catalytic ammonia oxidation to nitrogen (I) oxide

    OpenAIRE

    MASALITINA NATALIYA YUREVNA; SAVENKOV ANATOLIY SERGEEVICH

    2015-01-01

    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.

  8. Feature-Level Domain Adaptation

    OpenAIRE

    Kouw, Wouter M.; Krijthe, Jesse H.; Loog, Marco; van der Maaten, Laurens J. P.

    2015-01-01

    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...

  9. 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

    2007-01-01

    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.

  10. 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

  11. 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...

  12. Cage-bell Pt-Pd nanostructures with enhanced catalytic properties and superior methanol tolerance for oxygen reduction reaction

    Science.gov (United States)

    Chen, Dong; Ye, Feng; Liu, Hui; Yang, Jun

    2016-04-01

    Precisely tailoring the structure and fully making use of the components of nanoparticles are effective to enhance their catalytic performance for a given reaction. We herein demonstrate the design of cage-bell structured Pt-Pd nanoparticles, where a Pd shell is deliberately selected to enhance the catalytic property and methanol tolerance of Pt for oxygen reduction reaction. This strategy starts with the synthesis of core-shell Pt@Ag nanoparticles, followed by galvanic replacement reaction between the Ag shell and Pd2+ ions to form core-shell-shell Pt@Ag@Ag-Pd nanoparticles with a Pt core and double shells composed of Ag at inner and alloy Ag-Pd at outer, respectively. Then, the core-shell-shell templates are agitated with saturated NaCl solution to eliminate the Ag component from the double shells, leading to the formation of bimetallic Pt-Pd nanoparticles with a cage-bell structure, defined as a movable Pt core enclosed by a porous Pd shell, which show enhanced catalytic activity for oxygen reduction compared with that of the Pt seeds due to the additional catalysis from Pd shell. In addition, owing to the different diffusion behavior of methanol and oxygen molecules in the porous Pd shell, the Pt-Pd cage-bell nanostructures also exhibit superior methanol tolerant property in catalyzing the oxygen reduction.

  13. 磺酸官能化的磁性核壳结构的纳米材料用于果糖脱水制备5-羟甲基糠醛%Nanocoating of magnetic cores with sulfonic acid functionalized shells for the catalytic dehydration of fructose to 5-hydroxymethylfurfural

    Institute of Scientific and Technical Information of China (English)

    张晓辰; 王敏; 王业红; 张超峰; 张哲; 王峰; 徐杰

    2014-01-01

    通过反相微乳液法制备了以Fe3O4为核,磺酸官能化的硅基材料为壳层的磁性酸性催化剂.首先制备纳米Fe3O4磁核,然后涂层包覆苯基修饰的纳米级硅层,最后进行苯基磺化修饰,制得固体酸催化剂Fe3O4@Si/Ph-SO3H.在果糖脱水制备5-羟甲基糠醛反应中,该催化剂表现出较好的催化活性,优于传统催化剂A-15,且与均相无机酸催化活性相当.当采用二甲基亚砜作溶剂,在110 oC下反应3 h,果糖转化率达到99%,5-羟甲基糠醛收率为82%.另外,该催化剂经磁法回收后可多次重复使用.%A magnetically recyclable acid catalyst composed of an Fe3O4 core and sulfonic acid functionalized silica shell has been prepared using the reverse microemulsion method. The Fe3O4 core was coated with a phenyl modified silica shell nanolayer, and the phenyl groups were subsequently sulfonated to generate a solid sulfonic acid catalyst. The resulting acid catalyst showed higher activity than the conventional A-15 catalyst and comparable activity to several homogeneous sulfonic acid catalysts for the dehydration of fructose to 5-hydroxymethylfurfural (HMF). This process gave a fructose conversion of 99%with an HMF yield of 82%following 3 h in dimethylsulfoxide at 110 °C. Fur-thermore, the catalyst could be magnetically separated and recycled several times without losing its activity.

  14. Catalytic and surface oxidation processes on transition metal surfaces

    OpenAIRE

    Jaatinen, Sampsa

    2007-01-01

    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. ...

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

    OpenAIRE

    Yu-Tung Chien; Shao-Wei Huang

    2013-01-01

    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...

  16. Visualizing Knowledge Domains.

    Science.gov (United States)

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    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;…

  17. Conserved Domain Database (CDD)

    Data.gov (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.

  18. QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme.

    Science.gov (United States)

    Mu, Xia; Zhang, Chunchun; Xu, Dingguo

    2016-06-01

    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

  19. K-core inflation

    OpenAIRE

    Wolman, Alexander L.

    2011-01-01

    K-core inflation is a new class of underlying inflation measures. The two most popular measures of underlying inflation are core inflation and trimmed mean inflation. The former removes fixed categories of goods and services (food and energy) from the inflation calculation, and the latter removes fixed percentiles of the weighted distribution of price changes. In contrast, k-core inflation specifies a size of relative price change to be removed from the inflation calculation. Thus, the catego...

  20. 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

  1. Structure of the Tribolium castaneum Telomerase Catalytic Subunit TERT

    Energy Technology Data Exchange (ETDEWEB)

    Gillis,A.; Schuller, A.; Skordalakes, E.

    2008-01-01

    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.

  2. A novel liquid system of catalytic hydrogenation

    Institute of Scientific and Technical Information of China (English)

    LI; XiaoNian; XIANG; YiZhi

    2007-01-01

    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.

  3. Spherical core-shell magnetic particles constructed by main-chain palladium N-heterocyclic carbenes

    Science.gov (United States)

    Zhao, Huaixia; Li, Liuyi; Wang, Jinyun; Wang, Ruihu

    2015-02-01

    The encapsulation of the functional species on magnetic core is a facile approach for the synthesis of core-shell magnetic materials, and surface encapsulating matrices play crucial roles in regulating their properties and applications. In this study, two core-shell palladium N-heterocyclic carbene (NHC) particles (Fe3O4@PNP1 and Fe3O4@PNP2) were prepared by a one-pot reaction of semi-rigid tripodal imidazolium salts and palladium acetate in the presence of magnetite nanoparticles. The magnetite nanoparticles are encapsulated inside the main-chain palladium, which act as cores. The conjugated effects of triphenyltriazine and triphenylbenzene in the imidazolium salts have important influence on their physical properties and catalytic performances. Fe3O4@PNP2 shows better recyclability than Fe3O4@PNP1. Unexpectedly, Pd(ii) is well maintained after six consecutive catalytic runs in Fe3O4@PNP2, and Pd(0) and Pd(ii) coexist in Fe3O4@PNP1 under the same conditions; moreover, the morphologies of these spherical core-shell particles show no significant variation after six consecutive catalytic runs.The encapsulation of the functional species on magnetic core is a facile approach for the synthesis of core-shell magnetic materials, and surface encapsulating matrices play crucial roles in regulating their properties and applications. In this study, two core-shell palladium N-heterocyclic carbene (NHC) particles (Fe3O4@PNP1 and Fe3O4@PNP2) were prepared by a one-pot reaction of semi-rigid tripodal imidazolium salts and palladium acetate in the presence of magnetite nanoparticles. The magnetite nanoparticles are encapsulated inside the main-chain palladium, which act as cores. The conjugated effects of triphenyltriazine and triphenylbenzene in the imidazolium salts have important influence on their physical properties and catalytic performances. Fe3O4@PNP2 shows better recyclability than Fe3O4@PNP1. Unexpectedly, Pd(ii) is well maintained after six consecutive catalytic runs in

  4. Effective particle magnetic moment of multi-core particles

    Energy Technology Data Exchange (ETDEWEB)

    Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian [Acreo Swedish ICT AB, Arvid Hedvalls backe 4, SE-411 33 Göteborg (Sweden); Wetterskog, Erik; Svedlindh, Peter [Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala (Sweden); Lak, Aidin; Ludwig, Frank [Institute of Electrical Measurement and Fundamental Electrical Engineering, TU Braunschweig, D‐38106 Braunschweig Germany (Germany); IJzendoorn, Leo J. van [Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven (Netherlands); Westphal, Fritz; Grüttner, Cordula [Micromod Partikeltechnologie GmbH, D ‐18119 Rostock (Germany); Gehrke, Nicole [nanoPET Pharma GmbH, D ‐10115 Berlin Germany (Germany); Gustafsson, Stefan; Olsson, Eva [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg (Sweden); Johansson, Christer, E-mail: christer.johansson@acreo.se [Acreo Swedish ICT AB, Arvid Hedvalls backe 4, SE-411 33 Göteborg (Sweden)

    2015-04-15

    In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems – BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm – and one single-core particle system – SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm.

  5. Effective particle magnetic moment of multi-core particles

    Science.gov (United States)

    Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian; Wetterskog, Erik; Svedlindh, Peter; Lak, Aidin; Ludwig, Frank; van IJzendoorn, Leo J.; Westphal, Fritz; Grüttner, Cordula; Gehrke, Nicole; Gustafsson, Stefan; Olsson, Eva; Johansson, Christer

    2015-04-01

    In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems - BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm - and one single-core particle system - SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm.

  6. 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)

    2009-07-06

    Escherichia coli glycogen synthase (EcGS, EC 2.4.1.21) 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

  7. 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

    2015-01-01

    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...

  8. Catalytic microreactors for portable power generation

    Energy Technology Data Exchange (ETDEWEB)

    Karagiannidis, Symeon [Paul Scherer Institute, Villigen (Switzerland)

    2011-07-01

    ''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.)

  9. Catalytic nanoarchitectonics for environmentally compatible energy generation

    Directory of Open Access Journals (Sweden)

    Hideki Abe

    2016-01-01

    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.

  10. Use catalytic combustion for LHV gases

    Energy Technology Data Exchange (ETDEWEB)

    Tucci, E.R.

    1982-03-01

    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.

  11. Xylan-Degrading Catalytic Flagellar Nanorods.

    Science.gov (United States)

    Klein, Ágnes; Szabó, Veronika; Kovács, Mátyás; Patkó, Dániel; Tóth, Balázs; Vonderviszt, Ferenc

    2015-09-01

    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

  12. Flow parameters of IC engine catalytic converters

    Energy Technology Data Exchange (ETDEWEB)

    Zmudka, Z.; Postrzednik, S. [Silesian Univ. of Tech., Gliwice (Poland)

    2007-07-01

    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.)

  13. Electro Catalytic Oxidation (ECO) Operation

    Energy Technology Data Exchange (ETDEWEB)

    Morgan Jones

    2011-03-31

    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

  14. 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)

    2015-07-28

    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.

  15. 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...

  16. Core Skills in Action.

    Science.gov (United States)

    Further Education Unit, London (England).

    This bulletin provides an update on current developments in core skills in further education. Section 1 contains information about the Further Education Unit's (FEU's) Core Skills Post-16 project, in which colleges are testing principles that underpin all good quality learning programs. Important findings and examples are outlined under the five…

  17. 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;

    2006-01-01

    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...

  18. 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: ingemar@ifm.liu.se

    2008-03-15

    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.

  19. Thermal and catalytic pyrolysis of plastic waste

    Directory of Open Access Journals (Sweden)

    Débora Almeida

    2016-02-01

    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.

  20. Catalytic Enantioselective Functionalization of Unactivated Terminal Alkenes.

    Science.gov (United States)

    Coombs, John R; Morken, James P

    2016-02-01

    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

  1. 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)

    2012-07-01

    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.)

  2. Heterogeneous Catalytic Ozonization of Sulfosalicylic Acid

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    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.

  3. Large domain graphene

    OpenAIRE

    Li, Xuesong; Magnuson, Carl W.; Venugopal, Archana; Vogel, Eric M.; Rodney S. Ruoff; Colombo, Luigi

    2010-01-01

    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...

  4. Engineered magnetic domain textures in exchange bias bilayer systems

    Science.gov (United States)

    Gaul, Alexander; Hankemeier, Sebastian; Holzinger, Dennis; Müglich, Nicolas David; Staeck, Philipp; Frömter, Robert; Oepen, Hans Peter; Ehresmann, Arno

    2016-07-01

    A magnetic domain texture has been deterministically engineered in a topographically flat exchange-biased (EB) thin film system. The texture consists of long-range periodically arranged unit cells of four individual domains, characterized by individual anisotropies, individual geometry, and with non-collinear remanent magnetizations. The texture has been engineered by a sequence of light-ion bombardment induced magnetic patterning of the EB layer system. The magnetic texture's in-plane spatial magnetization distribution and the corresponding domain walls have been characterized by scanning electron microscopy with polarization analysis (SEMPA). The influence of magnetic stray fields emerging from neighboring domain walls and the influence of the different anisotropies of the adjacent domains on the Néel type domain wall core's magnetization rotation sense and widths were investigated. It is shown that the usual energy degeneracy of clockwise and counterclockwise rotating magnetization through the walls is revoked, suppressing Bloch lines along the domain wall. Estimates of the domain wall widths for different domain configurations based on material parameters determined by vibrating sample magnetometry were quantitatively compared to the SEMPA data.

  5. Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

    Directory of Open Access Journals (Sweden)

    Serrano Luis

    2008-10-01

    Full Text Available Abstract Background Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Results Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located in the phosphopeptide and specificity binding sites and a number of residues at the other side of the domain near the linkers that connect the SH2 domain to the SH3 and kinase domains. We find that for this particular domain, communication is affected by a series of contiguous residues that connect distal sites by crossing the core of the SH2 domain. Conclusion As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road, next to the existing attempts at sequence level, to predict long-range interactions within protein structures.

  6. Diastereomeric liquid crystal domains at the mesoscale

    Science.gov (United States)

    Chen, Dong; Tuchband, Michael R.; Horanyi, Balazs; Korblova, Eva; Walba, David M.; Glaser, Matthew A.; Maclennan, Joseph E.; Clark, Noel A.

    2015-08-01

    In many technologies used to achieve separation of enantiomers, chiral selectors are designed to display differential affinity for the two enantiomers of a chiral compound. Such complexes are diastereomeric, differing in structure and free energy for the two enantiomers and enabling chiral discrimination. Here we present evidence for strong diastereomeric interaction effects at the mesoscale, manifested in chiral liquid crystal guest materials confined in a chiral, nanoporous network of semi-crystalline helical nanofilaments. The nanoporous host is itself an assembly of achiral, bent-core liquid crystal molecules that phase-separate into a conglomerate of 100 micron-scale, helical nanofilament domains that differ in structure only in the handedness of their homogeneous chirality. With the inclusion of a homochiral guest liquid crystal, these enantiomeric domains become diastereomeric, exhibiting unexpected and markedly different mesoscale structures and orientation transitions producing optical effects in which chirality has a dominant role.

  7. Modules, Theories, or Islands of Expertise? Domain Specificity in Socialization

    Science.gov (United States)

    Gelman, Susan A.

    2010-01-01

    The domain-specific approach to socialization processes presented by J. E. Grusec and M. Davidov (this issue) provides a compelling framework for integrating and interpreting a large and disparate body of research findings, and it generates a wealth of testable new hypotheses. At the same time, it introduces core theoretical questions regarding…

  8. Bosonic interactions with a domain wall

    CERN Document Server

    Morris, J R

    2016-01-01

    We consider here the interaction of scalar bosons with a topological domain wall. Not only is there a continuum of scattering states, but there is also an interesting "quasi-discretuum" of positive energy bosonic bound states, describing bosons entrapped within the wall's core. The full spectrum of the scattering and bound state energies and eigenstates is obtainable from a Schr\\"odinger-type of equation with a P\\"oschl-Teller potential. We also consider the presence of a boson gas within the wall and high energy boson emission.

  9. DOMAIN ONTOLOGY DEVELOPMENT FOR COMMUNICABLE DISEASES

    Directory of Open Access Journals (Sweden)

    Iti Mathur

    2013-02-01

    Full Text Available Web has become the very first resource to search for any kind of information. With the emergence of semantic web, our search queries have started generating more informed results. Ontologies are at the core of any semantic web application. They help in rapid development of distributed systems by providing information on the fly. This key feature of distribution and sharing of information has made ontologies as a new knowledge representation mechanism. A mechanism which is strongly backed by a sound inference system. In this paper, we shall discuss the development, verification and validation of an ontology in a health domain.

  10. Structure of the ATP Synthase Catalytic Complex (F1) from Escherichia coli in an Autoinhibited conformation

    Energy Technology Data Exchange (ETDEWEB)

    G Cingolani; T Duncan

    2011-12-31

    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.

  11. Atomic Pseudo-Valuation Domains

    CERN Document Server

    Stines, Elijah

    2012-01-01

    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.

  12. Domain: Labour market

    NARCIS (Netherlands)

    Oude Mulders, J.; Wadensjö, E.; Hasselhorn, H.M.; Apt, W.

    2015-01-01

    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

  13. Skyrmions and domain walls

    OpenAIRE

    Piette, B.; Zakrzewski, W. J.

    1997-01-01

    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.

  14. Fuzzy Bases of Fuzzy Domains

    OpenAIRE

    Sanping Rao; Qingguo Li

    2013-01-01

    This paper is an attempt to develop quantitative domain theory over frames. Firstly, we propose the notion of a fuzzy basis, and several equivalent characterizations of fuzzy bases are obtained. Furthermore, the concept of a fuzzy algebraic domain is introduced, and a relationship between fuzzy algebraic domains and fuzzy domains is discussed from the viewpoint of fuzzy basis. We finally give an application of fuzzy bases, where the image of a fuzzy domain can be preserved under some special ...

  15. Atomic Pseudo-Valuation Domains

    OpenAIRE

    Stines, Elijah

    2012-01-01

    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, ...

  16. Cross-Domain Sparse Coding

    OpenAIRE

    Wang, Jim Jing-Yan

    2013-01-01

    Sparse coding has shown its power as an effective data representation method. However, up to now, all the sparse coding approaches are limited within the single domain learning problem. In this paper, we extend the sparse coding to cross domain learning problem, which tries to learn from a source domain to a target domain with significant different distribution. We impose the Maximum Mean Discrepancy (MMD) criterion to reduce the cross-domain distribution difference of sparse codes, and also ...

  17. CoRE Kernels

    OpenAIRE

    Li, Ping

    2014-01-01

    The term "CoRE kernel" stands for correlation-resemblance kernel. In many applications (e.g., vision), the data are often high-dimensional, sparse, and non-binary. We propose two types of (nonlinear) CoRE kernels for non-binary sparse data and demonstrate the effectiveness of the new kernels through a classification experiment. CoRE kernels are simple with no tuning parameters. However, training nonlinear kernel SVM can be (very) costly in time and memory and may not be suitable for truly lar...

  18. IGCSE core mathematics

    CERN Document Server

    Wall, Terry

    2013-01-01

    Give your core level students the support and framework they require to get their best grades with this book dedicated to the core level content of the revised syllabus and written specifically to ensure a more appropriate pace. This title has been written for Core content of the revised Cambridge IGCSE Mathematics (0580) syllabus for first teaching from 2013. ? Gives students the practice they require to deepen their understanding through plenty of practice questions. ? Consolidates learning with unique digital resources on the CD, included free with every book. We are working with Cambridge

  19. Structural Basis for the Catalytic Activity of Human Serine/Threonine Protein Phosphatase type 5 (PP5)

    Science.gov (United States)

    Swingle, Mark R.; Ciszak, Ewa M.; Honkanen, Richard E.

    2004-01-01

    Serine/threonine protein phosphatase-5 (PP5) is a member of the PPP-gene family of protein phosphatases that is widely expressed in mammalian tissues and is highly conserved among eukaryotes. PP5 associates with several proteins that affect signal transduction networks, including the glucocorticoid receptor (GR)-heat shock protein-90 (Hsp90)-heterocomplex, the CDC16 and CDC27 subunits of the anaphase-promoting complex, elF2alpha kinase, the A subunit of PP2A, the G12-alpha / G13-alpha subunits of heterotrimeric G proteins and DNA-PK. The catalytic domain of PP5 (PP5c) shares 35-45% sequence identity with the catalytic domains of other PPP-phosphatases, including protein phosphatase-1 (PP1), -2A (PP2A), -2B / calcineurin (PP2B), -4 (PP4), -6 (PP6), and -7 (PP7). Like PP1, PP2A and PP4, PP5 is also sensitive to inhibition by okadaic acid, microcystin, cantharidin, tautomycin, and calyculin A. Here we report the crystal structure of the PP5 catalytic domain (PP5c) at a resolution of 1.6 angstroms. From this structure we propose a mechanism for PP5-mediated hydrolysis of phosphoprotein substrates, which requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1):M(sub 2)-W(sup 1)-His(sup 304)-Asp(sup 274) catalytic motif. The structure of PP5c provides a possible 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.

  20. Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism

    Science.gov (United States)

    Torres, Idelisse Ortiz; Kuchenbecker, Kristopher M.; Nnadi, Chimno I.; Fletterick, Robert J.; Kelly, Mark J. S.; Fujimori, Danica Galonić

    2015-02-01

    The retinoblastoma binding protein KDM5A removes methyl marks from lysine 4 of histone H3 (H3K4). Misregulation of KDM5A contributes to the pathogenesis of lung and gastric cancers. In addition to its catalytic jumonji C domain, KDM5A contains three PHD reader domains, commonly recognized as chromatin recruitment modules. It is unknown whether any of these domains in KDM5A have functions beyond recruitment and whether they regulate the catalytic activity of the demethylase. Here using biochemical and nuclear magnetic resonance (NMR)-based structural studies, we show that the PHD1 preferentially recognizes unmethylated H3K4 histone tail, product of KDM5A-mediated demethylation of tri-methylated H3K4 (H3K4me3). Binding of unmodified H3 peptide to the PHD1 stimulates catalytic domain-mediated removal of methyl marks from H3K4me3 peptide and nucleosome substrates. This positive-feedback mechanism—enabled by the functional coupling between a reader and a catalytic domain in KDM5A—suggests a model for the spread of demethylation on chromatin.

  1. Toward a catalytic site in DNA

    DEFF Research Database (Denmark)

    Jakobsen, Ulla; Rohr, Katja; Vogel, Stefan

    2007-01-01

    A number of functionalized polyaza crown ether building blocks have been incorporated into DNA-conjugates as catalytic Cu(2+) binding sites. The effect of the DNA-conjugate catalyst on the stereochemical outcome of a Cu(2+)-catalyzed Diels-Alder reaction will be presented....

  2. SELECTIVE CATALYTIC REDUCTION MERCURY FIELD SAMPLING PROJECT

    Science.gov (United States)

    A lack of data still exists as to the effect of selective catalytic reduction (SCR), selective noncatalytic reduction (SNCR), and flue gas conditioning on the speciation and removal of mercury (Hg) at power plants. This project investigates the impact that SCR, SNCR, and flue gas...

  3. Toward Facilitative Mentoring and Catalytic Interventions

    Science.gov (United States)

    Smith, Melissa K.; Lewis, Marilyn

    2015-01-01

    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…

  4. Catalytic reaction dynamics in inhomogeneous networks.

    Science.gov (United States)

    Watanabe, Akitomo; Yakubo, Kousuke

    2014-05-01

    Biochemical reactions in a cell can be modeled by a catalytic reaction network (CRN). It has been reported that catalytic chain reactions occur intermittently in the CRN with a homogeneous random-graph topology and its avalanche-size distribution obeys a power law with the exponent 4/3 [A. Awazu and K. Kaneko, Phys. Rev. E 80, 010902(R) (2009)]. This fact indicates that the catalytic reaction dynamics in homogeneous CRNs exhibits self-organized criticality (SOC). Structures of actual CRNs are, however, known to be highly inhomogeneous. We study the influence of various types of inhomogeneities found in real-world metabolic networks on the universality class of SOC. Our numerical results clarify that SOC keeps its universality class even for networks possessing structural inhomogeneities such as the scale-free property, community structures, and degree correlations. In contrast, if the CRN has inhomogeneous catalytic functionality, the universality class of SOC depends on how widely distributed the number of reaction paths catalyzed by a single chemical species is. PMID:25353843

  5. Novel Metal Nanomaterials and Their Catalytic Applications.

    Science.gov (United States)

    Wang, Jiaqing; Gu, Hongwei

    2015-01-01

    In the rapidly developing areas of nanotechnology, nano-scale materials as heterogeneous catalysts in the synthesis of organic molecules have gotten more and more attention. In this review, we will summarize the synthesis of several new types of noble metal nanostructures (FePt@Cu nanowires, Pt@Fe₂O₃ nanowires and bimetallic Pt@Ir nanocomplexes; Pt-Au heterostructures, Au-Pt bimetallic nanocomplexes and Pt/Pd bimetallic nanodendrites; Au nanowires, CuO@Ag nanowires and a series of Pd nanocatalysts) and their new catalytic applications in our group, to establish heterogeneous catalytic system in "green" environments. Further study shows that these materials have a higher catalytic activity and selectivity than previously reported nanocrystal catalysts in organic reactions, or show a superior electro-catalytic activity for the oxidation of methanol. The whole process might have a great impact to resolve the energy crisis and the environmental crisis that were caused by traditional chemical engineering. Furthermore, we hope that this article will provide a reference point for the noble metal nanomaterials' development that leads to new opportunities in nanocatalysis. PMID:26393550

  6. Catalytic dehydrogenations of ethylbenzene to styrene

    NARCIS (Netherlands)

    Nederlof, C.

    2012-01-01

    This research work on the catalytic dehydrogenation of ethylbenzene (EB) to styrene (ST) had a primary goal of developing improved catalysts for dehydrogenation processes both in CO2 as well as with O2 that can compete with the conventional dehydrogenation process in steam. In order to achieve this

  7. Electrochemical Promotion of Catalytic Reactions Using

    DEFF Research Database (Denmark)

    Petrushina, Irina; Bjerrum, Niels; Cleemann, Lars Nilausen;

    2007-01-01

    This paper presents the results of a study on electrochemical promotion (EP) of catalytic reactions using Pt/C/polybenzimidazole(H3PO4)/Pt/C fuel cell performed by the Energy and Materials Science Group (Technical University of Denmark) during the last 6 years[1-4]. The development of our...

  8. Shungite carbon catalytic effect on coal treatment

    Energy Technology Data Exchange (ETDEWEB)

    Grigorieva, E.N.; Rozhkova, N.N. [Russian Academy of Sciences, Moscow (Russian Federation). Institute for High Temperature

    1999-07-01

    The catalytic ability of shungite carbon in reactions of coal organic matter models appeared to be due to its fullerene structure only. Transition metal sulphides present in shungite carbon are not active in the conditions of coal treatment. Shungite carbon was shown to exhibit an acceleration of thermolysis of coal and organic matter models, mainly dehydrogenation. 5 refs., 1 tabs.

  9. Catalytic oxidation of industrial organic solvent vapors.

    Science.gov (United States)

    Tzortzatou, Katerina; Grigoropoulou, Eleni

    2010-01-01

    In the present study the catalytic oxidation of an industrial organic solvent consisting predominantly of C-9 to C-10 paraffins and napthtenics and derived from low aromatic white spirit on CuO and Pt catalysts was investigated at ambient pressure and temperatures between 330 and 770 K. Catalysts were prepared in the laboratory and compared to commercial ones. Characterization was based on x-ray diffraction (XRD) analysis, x-ray fluorescence (XRF) analysis, scanning electron microscope (SEM) analysis and nitrogen adsorption data. The commercial platinum catalyst was proved highly efficient in the oxidation of the commercial solvent, necessitating lower temperatures for total oxidation. Catalyst loading in active component is clearly not of primordial importance, since its dispersion and crystallinity as well as the presence of other metallic compounds influence also the catalytic activity. In the case of copper catalysts studied, the different support (alumina) characteristics also would contribute to the difference in catalytic activity. Finally, the power law kinetics may successfully be used in order to explain the catalytic oxidation data of the organic solvent, where its constituents are modeled as a single carbon-containing compound. PMID:20390900

  10. Catalytic Converters Maintain Air Quality in Mines

    Science.gov (United States)

    2014-01-01

    At Langley Research Center, engineers developed a tin-oxide based washcoat to prevent oxygen buildup in carbon dioxide lasers used to detect wind shears. Airflow Catalyst Systems Inc. of Rochester, New York, licensed the technology and then adapted the washcoat for use as a catalytic converter to treat the exhaust from diesel mining equipment.

  11. Novel Metal Nanomaterials and Their Catalytic Applications

    Directory of Open Access Journals (Sweden)

    Jiaqing Wang

    2015-09-01

    Full Text Available In the rapidly developing areas of nanotechnology, nano-scale materials as heterogeneous catalysts in the synthesis of organic molecules have gotten more and more attention. In this review, we will summarize the synthesis of several new types of noble metal nanostructures (FePt@Cu nanowires, Pt@Fe2O3 nanowires and bimetallic Pt@Ir nanocomplexes; Pt-Au heterostructures, Au-Pt bimetallic nanocomplexes and Pt/Pd bimetallic nanodendrites; Au nanowires, CuO@Ag nanowires and a series of Pd nanocatalysts and their new catalytic applications in our group, to establish heterogeneous catalytic system in “green” environments. Further study shows that these materials have a higher catalytic activity and selectivity than previously reported nanocrystal catalysts in organic reactions, or show a superior electro-catalytic activity for the oxidation of methanol. The whole process might have a great impact to resolve the energy crisis and the environmental crisis that were caused by traditional chemical engineering. Furthermore, we hope that this article will provide a reference point for the noble metal nanomaterials’ development that leads to new opportunities in nanocatalysis.

  12. Performance characterization of a hydrogen catalytic heater.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Terry Alan; Kanouff, Michael P.

    2010-04-01

    This report describes the performance of a high efficiency, compact heater that uses the catalytic oxidation of hydrogen to provide heat to the GM Hydrogen Storage Demonstration System. The heater was designed to transfer up to 30 kW of heat from the catalytic reaction to a circulating heat transfer fluid. The fluid then transfers the heat to one or more of the four hydrogen storage modules that make up the Demonstration System to drive off the chemically bound hydrogen. The heater consists of three main parts: (1) the reactor, (2) the gas heat recuperator, and (3) oil and gas flow distribution manifolds. The reactor and recuperator are integrated, compact, finned-plate heat exchangers to maximize heat transfer efficiency and minimize mass and volume. Detailed, three-dimensional, multi-physics computational models were used to design and optimize the system. At full power the heater was able to catalytically combust a 10% hydrogen/air mixture flowing at over 80 cubic feet per minute and transfer 30 kW of heat to a 30 gallon per minute flow of oil over a temperature range from 100 C to 220 C. The total efficiency of the catalytic heater, defined as the heat transferred to the oil divided by the inlet hydrogen chemical energy, was characterized and methods for improvement were investigated.

  13. Exact Results for Kinetics of Catalytic Reactions

    OpenAIRE

    Frachebourg, L.; Krapivsky, P. L.

    1995-01-01

    The kinetics of an irreversible catalytic reaction on substrate of arbitrary dimension is examined. In the limit of infinitesimal reaction rate (reaction-controlled limit), we solve the dimer-dimer surface reaction model (or voter model) exactly in arbitrary dimension $D$. The density of reactive interfaces is found to exhibit a power law decay for $D

  14. Catalytic asymmetric synthesis of mycocerosic acid

    NARCIS (Netherlands)

    ter Horst, B.; Feringa, B.L.; J. Minnaard, A.

    2007-01-01

    The first catalytic asymmetric total synthesis of mycocerosic acid was achieved via the application of iterative enantioselective 1,4-addition reactions and allows for the efficient construction of 1,3-polymethyl arrays with full stereocontrol; further exemplified by the synthesis of tetramethyl-dec

  15. Electrochemical promotion of sulfur dioxide catalytic oxidation

    DEFF Research Database (Denmark)

    Petrushina, Irina; Bandur, Viktor; Cappeln, Frederik Vilhelm;

    2000-01-01

    The effect of electrochemical polarization on the catalytic SO2 oxidation in the molten V2O5-K2S2O7 system has been studied using a gold working electrode in the temperature range 400-460 degrees C. A similar experiment has been performed with the industrial catalyst VK-58. The aim of the present...

  16. Catalytic site interactions in yeast OMP synthase

    DEFF Research Database (Denmark)

    Hansen, Michael Riis; Barr, Eric W.; Jensen, Kaj Frank; Willemoës, Martin; Grubmeyer, Charles; Winther, Jakob R.

    2014-01-01

    45 (2006) 5330-5342]. This behavior was investigated in the yeast enzyme by mutations in the conserved catalytic loop and 5-phosphoribosyl-1-diphosphate (PRPP) binding motif. Although the reaction is mechanistically sequential, the wild-type (WT) enzyme shows parallel lines in double reciprocal...

  17. Catalytic treatment of diesel engines, NOx emissions

    International Nuclear Information System (INIS)

    Some aspects of the operation of diesel engines are revised together with the pollutant emissions they produce, as well as the available catalytic technologies for the treatment of diesel emissions. Furthermore the performance of a catalyst developed in the environmental catalysis group for NOx reduction using synthetic gas mixtures simulating the emissions from diesel engines is presented

  18. CFD Analysis of Core Bypass Phenomena

    International Nuclear Information System (INIS)

    The U.S. Department of Energy is exploring the potential for the VHTR which will be either of a prismatic or a pebble-bed type. One important design consideration for the reactor core of a prismatic VHTR is coolant bypass flow which occurs in the interstitial regions between fuel blocks. Such gaps are an inherent presence in the reactor core because of tolerances in manufacturing the blocks and the inexact nature of their installation. Furthermore, the geometry of the graphite blocks changes over the lifetime of the reactor because of thermal expansion and irradiation damage. The existence of the gaps induces a flow bias in the fuel blocks and results in unexpected increase of maximum fuel temperature. Traditionally, simplified methods such as flow network calculations employing experimental correlations are used to estimate flow and temperature distributions in the core design. However, the distribution of temperature in the fuel pins and graphite blocks as well as coolant outlet temperatures are strongly coupled with the local heat generation rate within fuel blocks which is not uniformly distributed in the core. Hence, it is crucial to establish mechanistic based methods which can be applied to the reactor core thermal hydraulic design and safety analysis. Computational Fluid Dynamics (CFD) codes, which have a capability of local physics based simulation, are widely used in various industrial fields. This study investigates core bypass flow phenomena with the assistance of commercial CFD codes and establishes a baseline for evaluation methods. A one-twelfth sector of the hexagonal block surface is modeled and extruded down to whole core length of 10.704m. The computational domain is divided vertically with an upper reflector, a fuel section and a lower reflector. Each side of the one-twelfth grid can be set as a symmetry boundary

  19. CFD Analysis of Core Bypass Phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Richard W. Johnson; Hiroyuki Sato; Richard R. Schultz

    2010-03-01

    The U.S. Department of Energy is exploring the potential for the VHTR which will be either of a prismatic or a pebble-bed type. One important design consideration for the reactor core of a prismatic VHTR is coolant bypass flow which occurs in the interstitial regions between fuel blocks. Such gaps are an inherent presence in the reactor core because of tolerances in manufacturing the blocks and the inexact nature of their installation. Furthermore, the geometry of the graphite blocks changes over the lifetime of the reactor because of thermal expansion and irradiation damage. The existence of the gaps induces a flow bias in the fuel blocks and results in unexpected increase of maximum fuel temperature. Traditionally, simplified methods such as flow network calculations employing experimental correlations are used to estimate flow and temperature distributions in the core design. However, the distribution of temperature in the fuel pins and graphite blocks as well as coolant outlet temperatures are strongly coupled with the local heat generation rate within fuel blocks which is not uniformly distributed in the core. Hence, it is crucial to establish mechanistic based methods which can be applied to the reactor core thermal hydraulic design and safety analysis. Computational Fluid Dynamics (CFD) codes, which have a capability of local physics based simulation, are widely used in various industrial fields. This study investigates core bypass flow phenomena with the assistance of commercial CFD codes and establishes a baseline for evaluation methods. A one-twelfth sector of the hexagonal block surface is modeled and extruded down to whole core length of 10.704m. The computational domain is divided vertically with an upper reflector, a fuel section and a lower reflector. Each side of the sector grid can be set as a symmetry boundary

  20. CFD Analysis of Core Bypass Phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Richard W. Johnson; Hiroyuki Sato; Richard R. Schultz

    2009-11-01

    The U.S. Department of Energy is exploring the potential for the VHTR which will be either of a prismatic or a pebble-bed type. One important design consideration for the reactor core of a prismatic VHTR is coolant bypass flow which occurs in the interstitial regions between fuel blocks. Such gaps are an inherent presence in the reactor core because of tolerances in manufacturing the blocks and the inexact nature of their installation. Furthermore, the geometry of the graphite blocks changes over the lifetime of the reactor because of thermal expansion and irradiation damage. The existence of the gaps induces a flow bias in the fuel blocks and results in unexpected increase of maximum fuel temperature. Traditionally, simplified methods such as flow network calculations employing experimental correlations are used to estimate flow and temperature distributions in the core design. However, the distribution of temperature in the fuel pins and graphite blocks as well as coolant outlet temperatures are strongly coupled with the local heat generation rate within fuel blocks which is not uniformly distributed in the core. Hence, it is crucial to establish mechanistic based methods which can be applied to the reactor core thermal hydraulic design and safety analysis. Computational Fluid Dynamics (CFD) codes, which have a capability of local physics based simulation, are widely used in various industrial fields. This study investigates core bypass flow phenomena with the assistance of commercial CFD codes and establishes a baseline for evaluation methods. A one-twelfth sector of the hexagonal block surface is modeled and extruded down to whole core length of 10.704m. The computational domain is divided vertically with an upper reflector, a fuel section and a lower reflector. Each side of the one-twelfth grid can be set as a symmetry boundary

  1. The influence of copper in dealloyed binary platinum–copper electrocatalysts on methanol electroxidation catalytic activities

    International Nuclear Information System (INIS)

    In this study, we prepared and characterized carbon paper-supported dealloyed binary Pt–Cu core–shell electrocatalysts (denoted as PtxCu(100−x)/CP) by cyclic co-electrodeposition and selective copper dealloying in an acidic medium, and we investigated the effect of the copper content in the samples on the catalytic activities toward methanol electroxidation reaction (MOR). X-ray photo-emission spectroscopy (XPS) and inductively coupled plasma atomic emission spectroscopy (ICP-AES) indicated that the structure of dealloyed binary Pt–Cu catalysts possessed a Pt-rich shell and a Cu rich core. X-ray absorption near edge spectroscopy (XANES) displayed that the oxidation states of Pt and Cu were zero and one, respectively, implying the formation of metallic Pt and Cu2O, respectively. X-ray diffraction spectroscopy (XRD) confirmed that Cu was inserted into a face-centered cubic Pt structure forming Pt–Cu alloys. Scanning electron microscopy (SEM) and transmission electron microscope (TEM) displayed a cubic shape of Pt/CP and a spherical shape of PtxCu(100−x)/CP with several hundred nanometer sizes of agglomeration that depended on the Cu content. Cyclic voltammetry, chronoamperometry, and electrochemical impedance spectroscopy were performed to confirm that the sample of Pt70Cu30/CP exhibited the best catalytic activities in terms of the specific current, current density, catalytic poisoning tolerance, and stability. - Graphical abstract: Display Omitted - Highlights: • Binary electrocatalysts of PtxCu(100−x)/CP were prepared by cyclic co-electrodeposition and selective copper dealloying. • The structures of PtxCu(100−x)/CP were a Pt rich shell and a Cu rich core. • The Pt70Cu30/CP was the excellent catalytic activity towards methanol electrooxidation and COads tolerance

  2. 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

    2000-12-01

    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.

  3. Isolation of key amino acid residues at the N-terminal end of the core region Streptococcus downei glucansucrase, GTF-I.

    Science.gov (United States)

    Monchois, V; Vignon, M; Russell, R R

    1999-11-01

    Related streptococcal and Leuconostoc mesenteroides glucansucrases are enzymes of medical and biotechnological interest. Molecular modelling has suggested that the catalytic domain contains a circularly permuted version of the (beta/alpha)8 barrel structure found in the amylase superfamily, and site-directed mutagenesis has identified critical amino acids in this region. In this study, sequential N-terminal truncations of Streptococcus downei GTF-I showed that key amino acids are also present in the first one-third of the core domain. Mutations were introduced at Trp-344, Glu-349 and His-355, residues that are conserved in all glucansucrases and lie within a region which is a target for inhibitory antibodies. W344L, E349L and H355V substitutions were assayed for their effect on mutan synthesis and also on oligosaccharide synthesis with various acceptors. It appeared that Trp-344 and His-355 are involved in the action mechanism of GTF-I; His-355 may also play a role in a binding subsite necessary for oligosaccharide and glucan elongation. PMID:10570812

  4. Assessing Core Competencies

    Science.gov (United States)

    Narayanan, M.

    2004-12-01

    Catherine Palomba and Trudy Banta offer the following definition of assessment, adapted from one provided by Marches in 1987. Assessment in the systematic collection, review, and use of information about educational programs undertaken for the purpose of improving student learning and development. (Palomba and Banta 1999). It is widely recognized that sophisticated computing technologies are becoming a key element in today's classroom instructional techniques. Regardless, the Professor must be held responsible for creating an instructional environment in which the technology actually supplements learning outcomes of the students. Almost all academic disciplines have found a niche for computer-based instruction in their respective professional domain. In many cases, it is viewed as an essential and integral part of the educational process. Educational institutions are committing substantial resources to the establishment of dedicated technology-based laboratories, so that they will be able to accommodate and fulfill students' desire to master certain of these specific skills. This type of technology-based instruction may raise some fundamental questions about the core competencies of the student learner. Some of the most important questions are : 1. Is the utilization of these fast high-powered computers and user-friendly software programs creating a totally non-challenging instructional environment for the student learner ? 2. Can technology itself all too easily overshadow the learning outcomes intended ? 3. Are the educational institutions simply training students how to use technology rather than educating them in the appropriate field ? 4. Are we still teaching content-driven courses and analysis oriented subject matter ? 5. Are these sophisticated modern era technologies contributing to a decline in the Critical Thinking Capabilities of the 21st century technology-savvy students ? The author tries to focus on technology as a tool and not on the technology

  5. Controlling core/shell Au/FePt nanoparticle electrocatalysis via changing the core size and shell thickness

    Science.gov (United States)

    Sun, Xiaolian; Li, Dongguo; Guo, Shaojun; Zhu, Wenlei; Sun, Shouheng

    2016-01-01

    Using a modified seed-mediated method, we synthesized core/shell Au/FePt nanoparticles (NPs) with Au sizes of 4, 7, and 9 nm and the FePt shell was controlled to have similar FePt compositions and 0.5, 1, and 2 nm thickness. We studied both core and shell effects on electrochemical and electrocatalytic properties of the Au/FePt NPs, and found that the Au core did change the redox chemistry of the FePt shell and promoted its electrochemical oxidation of methanol. The catalytic activity was dependent on the FePt thicknesses, but not much on the Au core sizes, and the 1 nm FePt shell was found to be the optimal thickness for catalyzing methanol oxidation in 0.1 M HClO4 + 0.1 M methanol, offering not only high activity (1.19 mA cm-2 at 0.5 V vs. Ag/AgCl), but also enhanced stability. Our studies demonstrate a general approach to the design and tuning of shell catalysis in the core/shell structure to achieve optimal catalysis for important electrochemical reactions.Using a modified seed-mediated method, we synthesized core/shell Au/FePt nanoparticles (NPs) with Au sizes of 4, 7, and 9 nm and the FePt shell was controlled to have similar FePt compositions and 0.5, 1, and 2 nm thickness. We studied both core and shell effects on electrochemical and electrocatalytic properties of the Au/FePt NPs, and found that the Au core did change the redox chemistry of the FePt shell and promoted its electrochemical oxidation of methanol. The catalytic activity was dependent on the FePt thicknesses, but not much on the Au core sizes, and the 1 nm FePt shell was found to be the optimal thickness for catalyzing methanol oxidation in 0.1 M HClO4 + 0.1 M methanol, offering not only high activity (1.19 mA cm-2 at 0.5 V vs. Ag/AgCl), but also enhanced stability. Our studies demonstrate a general approach to the design and tuning of shell catalysis in the core/shell structure to achieve optimal catalysis for important electrochemical reactions. Electronic supplementary information (ESI

  6. Geophysics: Earth's core problem

    Science.gov (United States)

    Dobson, David

    2016-06-01

    Measurements of the electrical resistance and thermal conductivity of iron at extreme pressures and temperatures cast fresh light on controversial numerical simulations of the properties of Earth's outer core. See Letters p.95 & 99

  7. iPSC Core

    Data.gov (United States)

    Federal Laboratory Consortium — The induced Pluripotent Stem Cells (iPSC) Core was created in 2011 to accelerate stem cell research in the NHLBI by providing investigators consultation, technical...

  8. Biospecimen Core Resource - TCGA

    Science.gov (United States)

    The Cancer Genome Atlas (TCGA) Biospecimen Core Resource centralized laboratory reviews and processes blood and tissue samples and their associated data using optimized standard operating procedures for the entire TCGA Research Network.

  9. PWR degraded core analysis

    International Nuclear Information System (INIS)

    A review is presented of the various phenomena involved in degraded core accidents and the ensuing transport of fission products from the fuel to the primary circuit and the containment. The dominant accident sequences found in the PWR risk studies published to date are briefly described. Then chapters deal with the following topics: the condition and behaviour of water reactor fuel during normal operation and at the commencement of degraded core accidents; the generation of hydrogen from the Zircaloy-steam and the steel-steam reactions; the way in which the core deforms and finally melts following loss of coolant; debris relocation analysis; containment integrity; fission product behaviour during a degraded core accident. (U.K.)

  10. Structure of the yeast Bre1 RING domain

    Science.gov (United States)

    Kumar, Pankaj; Wolberger, Cynthia

    2015-01-01

    Monoubiquitination of histone H2B at Lys123 in yeast plays a critical role in regulating transcription, mRNA export, DNA replication and the DNA damage response. The RING E3 ligase, Bre1, catalyzes monoubiquitination of H2B in concert with the E2 ubiquitin conjugating enzyme, Rad6. The crystal structure of a C-terminal fragment of Bre1 shows that the catalytic RING domain is preceded by an N-terminal helix that mediates coiled-coil interactions with a crystallographically related monomer. Homology modeling suggests that the human homologue of Bre1, RNF20/RNF40, heterodimerizes through similar coiled coil interactions. PMID:25864391

  11. Antibody mapping and tissue localization of globular and cysteine-rich regions of perlecan domain III

    DEFF Research Database (Denmark)

    Couchman, J R; Ljubimov, A V; Sthanam, M;

    1995-01-01

    Perlecan is the best-characterized basement membrane heparan sulfate proteoglycan. It has a large (approximately 400 KD) core protein consisting of five distinct domains. Domain III, a centrally located domain, contains three globular domains separated by cysteine-rich epidermal growth factor (EGF...... blotting showed that six of the nine MAbs recognized Domain III of perlecan, three of them mapping to globular Subdomain IIIc, and the other three recognized epitopes within the cysteine-rich regions. All six MAbs stained every basement membrane of several mouse organs as well as some connective tissues...

  12. Asymmetric Catalytic Reactions Catalyzed by Chiral Titanium Complexes

    Institute of Scientific and Technical Information of China (English)

    FENG; XiaoMing

    2001-01-01

    Chiral titanium complexes is very importance catalyst to asymmetric catalytic reactions. A series of catalytic systems based on titanium-chiral ligands complexes has been reported. This presentation will discuss some of our recent progress on asymmetric catalytic reactions catalyzed by chiral titanium complexes.  ……

  13. Asymmetric Catalytic Reactions Catalyzed by Chiral Titanium Complexes

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Chiral titanium complexes is very importance catalyst to asymmetric catalytic reactions. A series of catalytic systems based on titanium-chiral ligands complexes has been reported. This presentation will discuss some of our recent progress on asymmetric catalytic reactions catalyzed by chiral titanium complexes.

  14. Peroxisomal multifunctional enzyme type 2 (MFE-2):the catalytic domains work as independent units

    OpenAIRE

    Haataja, T. (Tatu)

    2011-01-01

    Abstract Lipids are necessary for living organisms and have various roles as, energy sources, hormone precursors and as components of membrane structures. Fatty acid β-oxidation is a pathway of energy metabolism, in which the fatty acyl-CoAs are degraded in several steps. Peroxisomal β-oxidation systems are found in all eukaryotes studied thus far, but the existence of a mitochondrial system is established in mammals only. Multifunctional enzyme type 2 (MFE-2) has been characterized f...

  15. The earths innermost core

    International Nuclear Information System (INIS)

    A new earth model is advanced with a solid innermost core at the centre of the Earth where elements heavier than iron, over and above what can be retained in solution in the iron core, are collected. The innermost core is separated from the solid iron-nickel core by a shell of liquid copper. The innermost core has a natural vibration measured on the earth's surface as the long period 26 seconds microseisms. The earth was formed initially as a liquid sphere with a relatively thin solid crust above the Byerly discontinuity. The trace elements that entered the innermost core amounted to only 0.925 ppm of the molten mass. Gravitational differentiation must have led to the separation of an explosive thickness of pure 235U causing a fission explosion that could expel beyond the Roche limit a crustal scab which would form the centre piece of the moon. A reservoir of helium floats on the liquid copper. A small proportion of helium-3, a relic of the ancient fission explosion present there will spell the exciting magnetic field. The field is stable for thousands of years because of the presence of large quantity of helium-4 which accounts for most of the gaseous collisions that will not disturb the atomic spin of helium-3 atoms. This field is prone to sudden reversals after long periods of stability. (author). 14 refs

  16. Time Domain Induced Polarization

    DEFF Research Database (Denmark)

    Fiandaca, Gianluca; Auken, Esben; Christiansen, Anders Vest;

    2012-01-01

    Time-domain-induced polarization has significantly broadened its field of reference during the last decade, from mineral exploration to environmental geophysics, e.g., for clay and peat identification and landfill characterization. Though, insufficient modeling tools have hitherto limited the use...... of time-domaininduced polarization for wider purposes. For these reasons, a new forward code and inversion algorithm have been developed using the full-time decay of the induced polarization response, together with an accurate description of the transmitter waveform and of the receiver transfer...... is above 100%. Furthermore, the presence of low-pass filters in time-domain-induced polarization instruments affects the early times of the acquired decays (typically up to 100 ms) and has to be modeled in the forward response to avoid significant loss of resolution. The developed forward code has...

  17. AtPGL3 is an Arabidopsis BURP domain protein that is localized to the cell wall and promotes cell enlargement

    OpenAIRE

    Park, Jiyoung; Cui, Yong; Kang, Byung-Ho

    2015-01-01

    The BURP domain is a plant-specific domain that has been identified in secretory proteins, and some of these are involved in cell wall modification. The tomato polygalacturonase I complex involved in pectin degradation in ripening fruits has a non-catalytic subunit that has a BURP domain. This protein is called polygalacturonase 1 beta (PG1β) and the Arabidopsis genome encodes three proteins that exhibit strong amino acid similarities with PG1β? We generated Arabidopsis lines in which express...

  18. Facile Synthesis of Au or Ag Nanoparticles-Embedded Hollow Carbon Microspheres from Metal-Organic Framework Hybrids and Their Efficient Catalytic Activities.

    Science.gov (United States)

    Choi, Sora; Lee, Hee Jung; Oh, Moonhyun

    2016-05-01

    Au or Ag nanoparticles-embedded hollow carbon spheres, which display outstanding catalytic activity and excellent recyclability, are prepared by a one-step pyrolysis of metal-organic framework (MOF) hybrids consisting of polystyrene cores and MOF shells loaded with noble metal ions (polystyrene@ZIF-8/M(n+) ; M(n+) = Au(3+) or Ag(+) ). PMID:27151828

  19. Induction functors for group corings

    OpenAIRE

    Chen, Quan-Guo; Wang, Ding-Guo

    2015-01-01

    In the paper, we prove that the induction functor stemming from every morphism of group coring versus coring has a left adjoint, called ad-induction functor. The separability of the induction functor is characterized, extending some results for corings.

  20. Domain-specific languages

    OpenAIRE

    Jasný, Vojtěch

    2009-01-01

    The topic of the thesis are domain-specific languages (DSL) and their use in software development. The target audience are developers interested in learning more about this progressive area of software development. It starts with a necessary theoretical introduction to programming languages. Then, a classification of DSLs is given and software development methodologies based on DSLs are described, notably Language Oriented Programming and Intentional Programming. Another important piece in co...

  1. Implementing maritime domain awareness

    OpenAIRE

    Watts, Robert B.

    2006-01-01

    CHDS State/Local As an attempt to gain understanding of everything in the global maritime environment that can impact the security of the United States, the Maritime Domain Awareness initiative is one of the most ambitious projects ever undertaken by the U.S. government. Information that falls under the prevue of MDA is tremendously diverse and complex, having application in the regulatory, law enforcement, and military arenas. As such, MDA is a multi-agency effort that encompasses 16 resp...

  2. Magnetic domain-wall dynamics in wide permalloy strips

    Science.gov (United States)

    Estévez, Virginia; Laurson, Lasse

    2016-02-01

    Domain walls in soft permalloy strips may exhibit various equilibrium micromagnetic structures depending on the width and thickness of the strip, ranging from the well-known transverse and vortex walls in narrow and thin strips to double and triple vortex walls recently reported in wider strips [V. Estévez and L. Laurson, Phys. Rev. B 91, 054407 (2015), 10.1103/PhysRevB.91.054407]. Here, we analyze the field driven dynamics of such domain walls in permalloy strips of widths from 240 nm up to 6 μ m , using the known equilibrium domain wall structures as initial configurations. Our micromagnetic simulations show that the domain wall dynamics in wide strips is very complex, and depends strongly on the geometry of the system, as well as on the magnitude of the driving field. We discuss in detail the rich variety of the dynamical behaviors found, including dynamic transitions between different domain wall structures, periodic dynamics of a vortex core close to the strip edge, transitions towards simpler domain wall structures of the multi-vortex domain walls controlled by vortex polarity, and the fact that for some combinations of the strip geometry and the driving field the system cannot support a compact domain wall.

  3. Expanding the Activity of Tissue Inhibitors of Metalloproteinase (TIMP)-1 against Surface-Anchored Metalloproteinases by the Replacement of Its C-Terminal Domain: Implications for Anti-Cancer Effects

    OpenAIRE

    Jing Xian Duan; Magdalini Rapti; Anastasia Tsigkou; Meng Huee Lee

    2015-01-01

    Tissue inhibitors of metalloproteinases (TIMPs) are the endogenous inhibitors of the matrix metalloproteinases (MMPs) and a disintegrin and metalloproteinases (ADAMs). TIMP molecules are made up of two domains: an N-terminal domain that associates with the catalytic cleft of the metalloproteinases (MP) and a smaller C-terminal domain whose role in MP association is still poorly understood. This work is aimed at investigating the role of the C-terminal domain in MP selectivity. In this study, ...

  4. Domain decomposition method for solving elliptic problems in unbounded domains

    International Nuclear Information System (INIS)

    Computational aspects of the box domain decomposition (DD) method for solving boundary value problems in an unbounded domain are discussed. A new variant of the DD-method for elliptic problems in unbounded domains is suggested. It is based on the partitioning of an unbounded domain adapted to the given asymptotic decay of an unknown function at infinity. The comparison of computational expenditures is given for boundary integral method and the suggested DD-algorithm. 29 refs.; 2 figs.; 2 tabs

  5. Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next?

    Directory of Open Access Journals (Sweden)

    Julien Boudet

    2015-01-01

    Primase activity has been studied in the last decades but the detailed molecular steps explaining some unique features remain unclear. High-resolution structures of free and bound primases domains have brought significant insights in the understanding of the primase reaction cycle. Here, we give a short review of the structural work conducted in the field of archaeo-eukaryotic primases and we underline the missing “pictures” of the active forms of the enzyme which are of major interest. We organized our analysis with respect to the progression through the catalytic pathway.

  6. 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

    2004-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Tatjana P Kristensen

    2014-03-01

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

  8. A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein

    OpenAIRE

    Gleave, Emma S.; Schmidt, Helgo; Carter, Andrew P.

    2014-01-01

    Dyneins are large protein complexes that act as microtubule based molecular motors. The dynein heavy chain contains a motor domain which is a member of the AAA+ protein family (ATPases Associated with diverse cellular Activities). Proteins of the AAA+ family show a diverse range of functionalities, but share a related core AAA+ domain, which often assembles into hexameric rings. Dynein is unusual because it has all six AAA+ domains linked together, in one long polypeptide. The dynein motor do...

  9. Keeping Dublin Core Simple: Cross-Domain Discovery or Resource Description?; First Steps in an Information Commerce Economy: Digital Rights Management in the Emerging E-Book Environment; Interoperability: Digital Rights Management and the Emerging EBook Environment; Searching the Deep Web: Direct Query Engine Applications at the Department of Energy.

    Science.gov (United States)

    Lagoze, Carl; Neylon, Eamonn; Mooney, Stephen; Warnick, Walter L.; Scott, R. L.; Spence, Karen J.; Johnson, Lorrie A.; Allen, Valerie S.; Lederman, Abe

    2001-01-01

    Includes four articles that discuss Dublin Core metadata, digital rights management and electronic books, including interoperability; and directed query engines, a type of search engine designed to access resources on the deep Web that is being used at the Department of Energy. (LRW)

  10. Comparison of the domain and frequency domain state feedbacks

    International Nuclear Information System (INIS)

    In this paper, we present explicitly the equivalence of the time domain and frequency domain state feedbacks, as well as the dynamic state feedback and a modified frequency domain state feedback, from the closed-loop transfer function point of view. The difference of the two approaches is also shown

  11. On Free Z-domains%自由Z-domain

    Institute of Scientific and Technical Information of China (English)

    姚丽娟; 徐晓泉

    2011-01-01

    给出由偏序集生成的自由Z-domain,讨论自由Z-domain和偏序集的Dedekind-MacNeille完备化的一些性质.%The free Z-domains generated by posets are given.Some properties of tte free Z-domains and the Dedekind-MacNeille completions of posets are investigated.

  12. Reforming of methane in tubes with a catalytic active wall

    International Nuclear Information System (INIS)

    The heterogeneous steam reforming process in tubes with catalytic active inner surface is studied. The purpose of this ivestigation is to find a method of predicting the reaction rate of the catalytic conversion of methane by steam. The dependency of the reaction rate upon the temperature, pressure, gas composition, Reynolds number, geometrical sizes of tubes and catalytic behaviour of the catalytic active inner wall of these tubes has been examined. It was found that the reaction rate mainly depends on the temperature. The reaction rate is limited by the catalytic behaviour and the heat resisting properties of the materials used. (author)

  13. The Domain Structure of Centromeres Is Conserved from Fission Yeast to Humans

    OpenAIRE

    Kniola, Barbara; O'Toole, Eileen; McIntosh, J. Richard; Mellone, Barbara; Allshire, Robin; Mengarelli, Silwa; Hultenby, Kjell; Ekwall, Karl

    2001-01-01

    The centromeric DNA of fission yeast is arranged with a central core flanked by repeated sequences. The centromere-associated proteins, Mis6p and Cnp1p (SpCENP-A), associate exclusively with central core DNA, whereas the Swi6 protein binds the surrounding repeats. Here, electron microscopy and immunofluorescence light microscopy reveal that the central core and flanking regions occupy distinct positions within a heterochromatic domain. An “anchor” structure containing ...

  14. Analysis of hapten binding and catalytic determinants in a family of catalytic antibodies.

    Science.gov (United States)

    Ulrich, H D; Schultz, P G

    1998-01-01

    We report here the cloning and kinetic analysis of a family of catalytic antibodies raised against a common transition state (TS) analog hapten, which accelerate a unimolecular oxy-Cope rearrangement. Sequence analysis revealed close homologies among the heavy chains of the catalytically active members of this set of antibodies, which derive mainly from a single germline gene, whereas the light chains can be traced back to several different, but related germline genes. The requirements for hapten binding and catalytic activity were determined by the construction of hybrid antibodies. Characterization of the latter antibodies again indicates a strong conservation of binding site structure among the catalytically active clones. The heavy chain was found to be the determining factor for catalytic efficiency, while the light chain exerted a smaller modulating effect that depended on light chain gene usage and somatic mutations. Within the heavy chain, the catalytic activity of a clone, but not hapten binding affinity, depended on the sequence of the third complementarity determining region (CDR). No correlation between high affinity for the hapten and high rate enhancement was found in the oxy-Cope system, a result that stands in contrast to the expectations from transition state theory. A mechanistic explanation for this observation is provided based on the three-dimensional crystal structure of the most active antibody, AZ-28, in complex with the hapten. This study demonstrates the utility of catalytic antibodies in examining the relationship between binding energy and catalysis in the evolution of biological catalysis, as well as expanding our understanding of the molecular basis of an immune response. PMID:9451442

  15. Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway.

    Science.gov (United States)

    Sanchez, Jacint G; Chiang, Jessica J; Sparrer, Konstantin M J; Alam, Steven L; Chi, Michael; Roganowicz, Marcin D; Sankaran, Banumathi; Gack, Michaela U; Pornillos, Owen

    2016-08-01

    Antiviral response pathways induce interferon by higher-order assembly of signaling complexes called signalosomes. Assembly of the RIG-I signalosome is regulated by K63-linked polyubiquitin chains, which are synthesized by the E3 ubiquitin ligase, TRIM25. We have previously shown that the TRIM25 coiled-coil domain is a stable, antiparallel dimer that positions two catalytic RING domains on opposite ends of an elongated rod. We now show that the RING domain is a separate self-association motif that engages ubiquitin-conjugated E2 enzymes as a dimer. RING dimerization is required for catalysis, TRIM25-mediated RIG-I ubiquitination, interferon induction, and antiviral activity. We also provide evidence that RING dimerization and E3 ligase activity are promoted by binding of the TRIM25 SPRY domain to the RIG-I effector domain. These results indicate that TRIM25 actively participates in higher-order assembly of the RIG-I signalosome and helps to fine-tune the efficiency of the RIG-I-mediated antiviral response. PMID:27425606

  16. Domain-specific Web Service Discovery with Service Class Descriptions

    Energy Technology Data Exchange (ETDEWEB)

    Rocco, D; Caverlee, J; Liu, L; Critchlow, T J

    2005-02-14

    This paper presents DynaBot, a domain-specific web service discovery system. The core idea of the DynaBot service discovery system is to use domain-specific service class descriptions powered by an intelligent Deep Web crawler. In contrast to current registry-based service discovery systems--like the several available UDDI registries--DynaBot promotes focused crawling of the Deep Web of services and discovers candidate services that are relevant to the domain of interest. It uses intelligent filtering algorithms to match services found by focused crawling with the domain-specific service class descriptions. We demonstrate the capability of DynaBot through the BLAST service discovery scenario and describe our initial experience with DynaBot.

  17. Janus droplet as a catalytic micromotor

    CERN Document Server

    Shklyaev, Sergey

    2015-01-01

    Self-propulsion of a Janus droplet in a solution of surfactant, which reacts on a half of a drop surface, is studied theoretically. The droplet acts as a catalytic motor creating a concentration gradient, which generates its surface-tension-driven motion; the self-propulsion speed is rather high, $60\\; {\\rm \\mu m/s}$ and more. This catalytic motor has several advantages over other micromotors: simple manufacturing, easily attained neutral buoyancy. In contrast to a single-fluid droplet, which demonstrates a self-propulsion as a result of symmetry breaking instability, for Janus one no stability threshold exists; hence, the droplet radius can be scaled down to micrometers. The paper was finalized and submitted by Denis S. Goldobin after Sergey Sklyaev had sadly passed away on June 2, 2014.

  18. From Catalytic Reaction Networks to Protocells

    Science.gov (United States)

    Kaneko, Kunihiko

    2013-12-01

    In spite of recent advances, there still remains a large gape between a set of chemical reactions and a biological cell. Here we discuss several theoretical efforts to fill in the gap. The topics cover (i) slow relaxation to equilibrium due to glassy behavior in catalytic reaction networks (ii) consistency between molecule replication and cell growth, as well as energy metabolism (iii) control of a system by minority molecules in mutually catalytic system, which work as a carrier of genetic information, and leading to evolvability (iv) generation of a compartmentalized structure as a cluster of molecules centered around the minority molecule, and division of the cluster accompanied by the replication of minority molecule (v) sequential, logical process over several states from concurrent reaction dynamics, by taking advantage of discreteness in molecule number.

  19. Summarization by domain ontology navigation

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2013-01-01

    of the subject. In between these two extremes, conceptual summaries encompass selected concepts derived using background knowledge. We address in this paper an approach where conceptual summaries are provided through a conceptualization as given by an ontology. The ontology guiding the summarization can...... be a simple taxonomy or a generative domain ontology. A domain ontology can be provided by a preanalysis of a domain corpus and can be used to condense improved summaries that better reflects the conceptualization of a given domain....

  20. Domain Engineering: An Empirical Study

    OpenAIRE

    Harris, Charles; Frakes, William B.

    2006-01-01

    This paper presents a summary and analysis of data gathered from thirteen domain engineering projects, participant surveys, and demographic information. Taking a failure modes approach, project data is compared to an ideal model of the DARE methodology, revealing valuable insights into points of failure in the domain engineering process. This study suggests that success is a function of the domain analyst’s command of a specific set of domain engineering concepts and skills, the time invested...

  1. A Convenient Category of Domains

    OpenAIRE

    Battenfeld, Ingo; Schröder, Matthias; Simpson, Alexander

    2007-01-01

    We motivate and define a category of topological domains, whose objects are certain topological spaces, generalising the usual ω-continuous dcppos of domain theory. Our category supports all the standard constructions of domain theory, including the solution of recursive domain equations. It also supports the construction of free algebras for (in)equational theories, can be used as the basis for a theory of computability, and provides a model of parametric polymorphism.

  2. A convenient category of domains

    OpenAIRE

    Battenfeld, Ingo; Schröder, Matthias; Simpson, Alex

    2007-01-01

    We motivate and define a category of "topological domains", whose objects are certain topological spaces, generalising the usual $omega$-continuous dcppos of domain theory. Our category supports all the standard constructions of domain theory, including the solution of recursive domain equations. It also supports the construction of free algebras for (in)equational theories, provides a model of parametric polymorphism, and can be used as the basis for a theory of computab...

  3. Catalytic extraction processing of contaminated scrap metal

    International Nuclear Information System (INIS)

    Molten Metal Technology was awarded a contract to demonstrate the applicability of the Catalytic Extraction Process, a proprietary process that could be applied to US DOE's inventory of low level mixed waste. This paper is a description of that technology, and included within this document are discussions of: (1) Program objectives, (2) Overall technology review, (3) Organic feed conversion to synthetic gas, (4) Metal, halogen, and transuranic recovery, (5) Demonstrations, (6) Design of the prototype facility, and (7) Results

  4. Thermal and catalytic pyrolysis of plastic waste

    OpenAIRE

    Débora Almeida; Maria de Fátima Marques

    2016-01-01

    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. Zeolit...

  5. Materials for High-Temperature Catalytic Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Ersson, Anders

    2003-04-01

    Catalytic combustion is an environmentally friendly technique to combust fuels in e.g. gas turbines. Introducing a catalyst into the combustion chamber of a gas turbine allows combustion outside the normal flammability limits. Hence, the adiabatic flame temperature may be lowered below the threshold temperature for thermal NO{sub X} formation while maintaining a stable combustion. However, several challenges are connected to the application of catalytic combustion in gas turbines. The first part of this thesis reviews the use of catalytic combustion in gas turbines. The influence of the fuel has been studied and compared over different catalyst materials. The material section is divided into two parts. The first concerns bimetallic palladium catalysts. These catalysts showed a more stable activity compared to their pure palladium counterparts for methane combustion. This was verified both by using an annular reactor at ambient pressure and a pilot-scale reactor at elevated pressures and flows closely resembling the ones found in a gas turbine combustor. The second part concerns high-temperature materials, which may be used either as active or washcoat materials. A novel group of materials for catalysis, i.e. garnets, has been synthesised and tested in combustion of methane, a low-heating value gas and diesel fuel. The garnets showed some interesting abilities especially for combustion of low-heating value, LHV, gas. Two other materials were also studied, i.e. spinels and hexa aluminates, both showed very promising thermal stability and the substituted hexa aluminates also showed a good catalytic activity. Finally, deactivation of the catalyst materials was studied. In this part the sulphur poisoning of palladium, platinum and the above-mentioned complex metal oxides has been studied for combustion of a LHV gas. Platinum and surprisingly the garnet were least deactivated. Palladium was severely affected for methane combustion while the other washcoat materials were

  6. Materials for High-Temperature Catalytic Combustion

    OpenAIRE

    Ersson, Anders

    2003-01-01

    Catalytic combustion is an environmentally friendlytechnique to combust fuels in e.g. gas turbines. Introducing acatalyst into the combustion chamber of a gas turbine allowscombustion outside the normal flammability limits. Hence, theadiabatic flame temperature may be lowered below the thresholdtemperature for thermal NOXformation while maintaining a stable combustion.However, several challenges are connected to the application ofcatalytic combustion in gas turbines. The first part of thisthe...

  7. Catalytic fast pyrolysis of lignocellulosic biomass

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Changjun; Wang, Huamin; Karim, Ayman M.; Sun, Junming; Wang, Yong

    2014-11-21

    Increasing energy demand, especially in the transportation sector, and soaring CO2 emissions necessitate the exploitation of renewable sources of energy. Despite the large variety of new energy Q3 carriers, liquid hydrocarbon still appears to be the most attractive and feasible form of transportation fuel taking into account the energy density, stability and existing infrastructure. Biomass is an abundant, renewable source of energy; however, utilizing it in a cost-effective way is still a substantial challenge. Lignocellulose is composed of three major biopolymers, namely cellulose, hemicellulose and lignin. Fast pyrolysis of biomass is recognized as an efficient and feasible process to selectively convert lignocellulose into a liquid fuel—bio-oil. However bio-oil from fast pyrolysis contains a large amount of oxygen, distributed in hundreds of oxygenates. These oxygenates are the cause of many negative properties, such as low heating values, high corrosiveness, high viscosity, and instability; they also greatly Q4 limit the application of bio-oil particularly as transportation fuel. Hydrocarbons derived from biomass are most attractive because of their high energy density and compatibility with the existing infrastructure. Thus, converting lignocellulose into transportation fuels via catalytic fast pyrolysis has attracted much attention. Many studies related to catalytic fast pyrolysis of biomass have been published. The main challenge of this process is the development of active and stable catalysts that can deal with a large variety of decomposition intermediates from lignocellulose. This review starts with the current understanding of the chemistry in fast pyrolysis of lignocellulose and focuses on the development of catalysts in catalytic fast pyrolysis. Recent progress in the experimental studies on catalytic fast pyrolysis of biomass is also summarized with the emphasis on bio-oil yields and quality.

  8. Computer Aided Enzyme Design and Catalytic Concepts

    OpenAIRE

    Frushicheva, Maria P.; Mills, Matthew J. L.; Schopf, Patrick; Singh, Manoj K.; Warshel, Arieh

    2014-01-01

    Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration ...

  9. Ubiquitous "glassy" relaxation in catalytic reaction networks

    OpenAIRE

    Awazu, Akinori; Kaneko, Kunihiko

    2009-01-01

    Study of reversible catalytic reaction networks is important not only as an issue for chemical thermodynamics but also for protocells. From extensive numerical simulations and theoretical analysis, slow relaxation dynamics to sustain nonequlibrium states are commonly observed. These dynamics show two types of salient behaviors that are reminiscent of glassy behavior: slow relaxation along with the logarithmic time dependence of the correlation function and the emergence of plateaus in the rel...

  10. Structures of the spectrin-ankyrin interaction binding domains

    Energy Technology Data Exchange (ETDEWEB)

    Ipsaro, Jonathan J.; Huang, Lei; Mondragón, Alfonso; (NWU)

    2010-01-07

    As key components of the erythrocyte membrane skeleton, spectrin and ankyrin specifically interact to tether the spectrin cytoskeleton to the cell membrane. The structure of the spectrin binding domain of ankyrin and the ankyrin binding domain of spectrin have been solved to elucidate the structural basis for ankyrin-spectrin recognition. The structure of repeats 14 and 15 of spectrin shows that these repeats are similar to all other spectrin repeats. One feature that could account for the preference of ankyrin for these repeats is the presence of a conserved, negatively charged patch on one side of repeat 14. The structure of the ankyrin ZU5 domain shows a novel structure containing a {beta} core. The structure reveals that the canonical ZU5 consensus sequence is likely to be missing an important region that codes for a {beta} strand that forms part of the core of the domain. In addition, a positively charged region is suggestive of a binding surface for the negatively charged spectrin repeat 14. Previously reported mutants of ankyrin that map to this region lie mostly on the surface of the protein, although at least one is likely to be part of the core.

  11. Tyrosine Kinase 2-mediated Signal Transduction in T Lymphocytes Is Blocked by Pharmacological Stabilization of Its Pseudokinase Domain.

    Science.gov (United States)

    Tokarski, John S; Zupa-Fernandez, Adriana; Tredup, Jeffrey A; Pike, Kristen; Chang, ChiehYing; Xie, Dianlin; Cheng, Lihong; Pedicord, Donna; Muckelbauer, Jodi; Johnson, Stephen R; Wu, Sophie; Edavettal, Suzanne C; Hong, Yang; Witmer, Mark R; Elkin, Lisa L; Blat, Yuval; Pitts, William J; Weinstein, David S; Burke, James R

    2015-04-24

    Inhibition of signal transduction downstream of the IL-23 receptor represents an intriguing approach to the treatment of autoimmunity. Using a chemogenomics approach marrying kinome-wide inhibitory profiles of a compound library with the cellular activity against an IL-23-stimulated transcriptional response in T lymphocytes, a class of inhibitors was identified that bind to and stabilize the pseudokinase domain of the Janus kinase tyrosine kinase 2 (Tyk2), resulting in blockade of receptor-mediated activation of the adjacent catalytic domain. These Tyk2 pseudokinase domain stabilizers were also shown to inhibit Tyk2-dependent signaling through the Type I interferon receptor but not Tyk2-independent signaling and transcriptional cellular assays, including stimulation through the receptors for IL-2 (JAK1- and JAK3-dependent) and thrombopoietin (JAK2-dependent), demonstrating the high functional selectivity of this approach. A crystal structure of the pseudokinase domain liganded with a representative example showed the compound bound to a site analogous to the ATP-binding site in catalytic kinases with features consistent with high ligand selectivity. The results support a model where the pseudokinase domain regulates activation of the catalytic domain by forming receptor-regulated inhibitory interactions. Tyk2 pseudokinase stabilizers, therefore, represent a novel approach to the design of potent and selective agents for the treatment of autoimmunity. PMID:25762719

  12. Reactor core monitoring method

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Michitsugu [Tokyo Electric Power Co., Inc. (Japan); Kanemoto, Shigeru; Enomoto, Mitsuhiro; Ebata, Shigeo

    1998-05-06

    The present invention provides a method of monitoring the state of coolant flow in a reactor of a BWR power plant. Namely, a plurality of local power region monitors (LPRM) are disposed to the inside of the reactor core for monitoring a power distribution. Signals of at least two optional LPRM detectors situated at positions different in axial or radial positions of the reactor core are obtained. General fluctuation components which nuclear hydrothermally fluctuate in overall reactor core are removed from the components of the signals. Then, correlational functions between these signals are determined. The state of coolant flow in the reactor is monitored based on the correlational function. When the axial flowing rate and radial flow interference are monitored, the accuracy upon monitoring axial and radial local behaviors of coolants can be improved by thus previously removing the general fluctuation components from signals of LPRM detectors and extracting local void information near to LPRM detectors at high accuracy. (I.S.)

  13. Probing catalytic rate enhancement during intramembrane proteolysis.

    Science.gov (United States)

    Arutyunova, Elena; Smithers, Cameron C; Corradi, Valentina; Espiritu, Adam C; Young, Howard S; Tieleman, D Peter; Lemieux, M Joanne

    2016-09-01

    Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6-3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis. PMID:27071148

  14. Catalytic pyrolysis of olive mill wastewater sludge

    Science.gov (United States)

    Abdellaoui, Hamza

    From 2008 to 2013, an average of 2,821.4 kilotons/year of olive oil were produced around the world. The waste product of the olive mill industry consists of solid residue (pomace) and wastewater (OMW). Annually, around 30 million m3 of OMW are produced in the Mediterranean area, 700,000 m3 year?1 in Tunisia alone. OMW is an aqueous effluent characterized by an offensive smell and high organic matter content, including high molecular weight phenolic compounds and long-chain fatty acids. These compounds are highly toxic to micro-organisms and plants, which makes the OMW a serious threat to the environment if not managed properly. The OMW is disposed of in open air evaporation ponds. After evaporation of most of the water, OMWS is left in the bottom of the ponds. In this thesis, the effort has been made to evaluate the catalytic pyrolysis process as a technology to valorize the OMWS. The first section of this research showed that 41.12 wt. % of the OMWS is mostly lipids, which are a good source of energy. The second section proved that catalytic pyrolysis of the OMWS over red mud and HZSM-5 can produce green diesel, and 450 °C is the optimal reaction temperature to maximize the organic yields. The last section revealed that the HSF was behind the good fuel-like properties of the OMWS catalytic oils, whereas the SR hindered the bio-oil yields and quality.

  15. Modeling the Complete Catalytic Cycle of Aspartoacylase.

    Science.gov (United States)

    Kots, Ekaterina D; Khrenova, Maria G; Lushchekina, Sofya V; Varfolomeev, Sergei D; Grigorenko, Bella L; Nemukhin, Alexander V

    2016-05-12

    The complete catalytic cycle of aspartoacylase (ASPA), a zinc-dependent enzyme responsible for cleavage of N-acetyl-l-aspartate, is characterized by the methods of molecular modeling. The reaction energy profile connecting the enzyme-substrate (ES) and the enzyme-product (EP) complexes is constructed by the quantum mechanics/molecular mechanics (QM/MM) method assisted by the molecular dynamics (MD) simulations with the QM/MM potentials. Starting from the crystal structure of ASPA complexed with the intermediate analogue, the minimum-energy geometry configurations and the corresponding transition states are located. The stages of substrate binding to the enzyme active site and release of the products are modeled by MD calculations with the replica-exchange umbrella sampling technique. It is shown that the first reaction steps, nucleophilic attack of a zinc-bound nucleophilic water molecule at the carbonyl carbon and the amide bond cleavage, are consistent with the glutamate-assisted mechanism hypothesized for the zinc-dependent hydrolases. The stages of formation of the products, acetate and l-aspartate, and regeneration of the enzyme are characterized for the first time. The constructed free energy diagram from the reactants to the products suggests that the enzyme regeneration, but not the nucleophilic attack of the catalytic water molecule, corresponds to the rate-determining stage of the full catalytic cycle of ASPA. PMID:27089954

  16. Catalytic applications of bio-inspired nanomaterials

    Science.gov (United States)

    Pacardo, Dennis Kien Balaong

    The biomimetic synthesis of Pd nanoparticles was presented using the Pd4 peptide, TSNAVHPTLRHL, isolated from combinatorial phage display library. Using this approach, nearly monodisperse and spherical Pd nanoparticles were generated with an average diameter of 1.9 +/- 0.4 nm. The peptide-based nanocatalyst were employed in the Stille coupling reaction under energy-efficient and environmentally friendly reaction conditions of aqueous solvent, room temperature and very low catalyst loading. To this end, the Pd nanocatalyst generated high turnover frequency (TOF) value and quantitative yields using ≥ 0.005 mol% Pd as well as catalytic activities with different aryl halides containing electron-withdrawing and electron-donating groups. The Pd4-capped Pd nanoparticles followed the atom-leaching mechanism and were found to be selective with respect to substrate identity. On the other hand, the naturally-occurring R5 peptide (SSKKSGSYSGSKGSKRRIL) was employed in the synthesis of biotemplated Pd nanomaterials which showed morphological changes as a function of Pd:peptide ratio. TOF analysis for hydrogenation of olefinic alcohols showed similar catalytic activity regardless of nanomorphology. Determination of catalytic properties of these bio-inspired nanomaterials are important as they serve as model system for alternative green catalyst with applications in industrially important transformations.

  17. Catalytic hydrogen recombination for nuclear containments

    International Nuclear Information System (INIS)

    Catalytic recombiners appear to be a credible option for hydrogen mitigation in nuclear containments. The passive operation, versatility and ease of back fitting are appealing for existing stations and new designs. Recently, a generation of wet-proofed catalyst materials have been developed at AECL which are highly specific to H2-O2, are active at ambient temperatures and are being evaluated for containment applications. Two types of catalytic recombiners were evaluated for hydrogen removal in containments based on the AECL catalyst. The first is a catalytic combustor for application in existing air streams such as provided by fans or ventilation systems. The second is an autocatalytic recombiner which uses the enthalpy of reaction to produce natural convective flow over the catalyst elements. Intermediate-scale results obtained in 6 m3 and 10 m3 spherical and cylindrical vessels are given to demonstrate self-starting limits, operating limits, removal capacity, scaling parameters, flow resistance, mixing behaviour in the vicinity of an operating recombiner and sensitivity to poisoning, fouling and radiation. (author). 13 refs., 10 figs

  18. IFP solutions for revamping catalytic reforming units

    Energy Technology Data Exchange (ETDEWEB)

    Gendler, J.L. [HRI, Inc., Princeton, NJ (United States); Domergue, B.; Mank, L. [Inst. Francais du Petrole, Rueil Malmaison (France)

    1996-12-01

    The decision-making process for the refiner considering a revamp of a catalytic reforming unit comprises many factors. These may be grouped in two broad areas: technical and economic. This paper presents the results of a study performed by IFP that illustrates catalytic reforming unit revamp options. Three IFP processes are described and operating conditions, expected yields, and economic data are presented. The following options are discussed: base case Conventional, fixed-bed, semi-regenerative catalytic reformer; Case 1--revamp using IFP Dualforming technology; Case 2--revamp using IFP Dualforming Plus technology; and Case 3--revamp to IFP Octanizing technology. The study illustrates various options for the refiner to balance unit performance improvements with equipment, site, and economic constraints. The study was performed assuming design feedrate of 98.2 tons/hour (20,000 BPSD) in all cases. Because of the increased need for octane in many refineries, the study assumed that operating severity was set at a design value of 100 research octane number clear (RON). In all of the cases in this study, it was assumed that the existing recycle compressor was reused. Operating pressure differences between the cases is discussed separately. Also, in all cases, a booster compressor was included in order to return export hydrogen pressure to that of the conventional unit.

  19. Electrochemical catalytic treatment of phenol wastewater

    International Nuclear Information System (INIS)

    The slurry bed catalytic treatment of contaminated water appears to be a promising alternative for the oxidation of aqueous organic pollutants. In this paper, the electrochemical oxidation of phenol in synthetic wastewater catalyzed by ferric sulfate and potassium permanganate adsorbed onto active bentonite in slurry bed electrolytic reactor with graphite electrode has been investigated. In order to determine the optimum operating condition, the orthogonal experiments were devised and the results revealed that the system of ferric sulfate, potassium permanganate and active bentonite showed a high catalytic efficiency on the process of electrochemical oxidation phenol in initial pH 5. When the initial concentration of phenol was 0.52 g/L (the initial COD 1214 mg/L), up to 99% chemical oxygen demand (COD) removal was obtained in 40 min. According to the experimental results, a possible mechanism of catalytic degradation of phenol was proposed. Environmental estimation was also done and the results showed that the treated wastewater have little impact on plant growth and could totally be applied to irrigation.

  20. Domain Bridging Associations Support Creativity

    OpenAIRE

    Kötter, Tobias; Thiel, Kilian; Berthold, Michael R

    2010-01-01

    This paper proposes a new approach to support creativity through assisting the discovery of unexpected associations across different domains. This is achieved by integrating information from heterogeneous domains into a single network, enabling the interactive discovery of links across the corresponding information resources. We discuss three different pattern of domain crossing associations in this context.