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Sample records for catalytic core domain

  1. Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon.

    Science.gov (United States)

    Zhang, Da-wei; Zhao, Ming-ming; He, Hong-qiu; Guo, Shun-xing

    2013-09-15

    HIV-1 integrase, an essential enzyme for retroviral replication, is a validated target for anti-HIV therapy development. The catalytic core domain of integrase (IN-CCD) is capable of catalyzing disintegration reaction. In this work, a hairpin-shaped disintegration substrate was designed and validated by enzyme-linked immunosorbent assay; a molecular beacon-based assay was developed for disintegration reaction of IN-CCD. Results showed that the disintegration substrate could be recognized and catalyzed by IN-CCD, and the disintegration reaction can be monitored according to the increase of fluorescent signal. The assay can be applied to real-time detection of disintegration with advantages of simplicity, high sensitivity, and excellent specificity. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication

    Directory of Open Access Journals (Sweden)

    Belhumeur Pierre

    2008-11-01

    Full Text Available Abstract Background HIV-1 integrase (IN is a key viral enzymatic molecule required for the integration of the viral cDNA into the genome. Additionally, HIV-1 IN has been shown to play important roles in several other steps during the viral life cycle, including reverse transcription, nuclear import and chromatin targeting. Interestingly, previous studies have demonstrated that the expression of HIV-1 IN induces the lethal phenotype in some strains of Saccharomyces cerevisiae. In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s and/or motif(s required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. Results Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. Chromatin binding assays in yeast and mammalian cells demonstrated that these IN mutants were impaired for the ability to bind chromatin. Additionally, we determined that while these IN mutants failed to interact with LEDGF/p75, they retained the ability to bind Integrase interactor 1. Furthermore, we observed that VSV-G-pseudotyped HIV-1 containing these IN mutants was unable to replicate in the C8166 T cell line and this defect was partially rescued by complementation with the catalytically inactive D64E IN mutant. Conclusion Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of

  3. Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 A resolution.

    Science.gov (United States)

    Varrot, A; Hastrup, S; Schülein, M; Davies, G J

    1999-01-15

    The three-dimensional structure of the catalytic core of the family 6 cellobiohydrolase II, Cel6A (CBH II), from Humicola insolens has been determined by X-ray crystallography at a resolution of 1.92 A. The structure was solved by molecular replacement using the homologous Trichoderma reesei CBH II as a search model. The H. insolens enzyme displays a high degree of structural similarity with its T. reesei equivalent. The structure features both O- (alpha-linked mannose) and N-linked glycosylation and a hexa-co-ordinate Mg2+ ion. The active-site residues are located within the enclosed tunnel that is typical for cellobiohydrolase enzymes and which may permit a processive hydrolysis of the cellulose substrate. The close structural similarity between the two enzymes implies that kinetics and chain-end specificity experiments performed on the H. insolens enzyme are likely to be applicable to the homologous T. reesei enzyme. These cast doubt on the description of cellobiohydrolases as exo-enzymes since they demonstrated that Cel6A (CBH II) shows no requirement for non-reducing chain-ends, as had been presumed. There is no crystallographic evidence in the present structure to support a mechanism involving loop opening, yet preliminary modelling experiments suggest that the active-site tunnel of Cel6A (CBH II) is too narrow to permit entry of a fluorescenyl-derivatized substrate, known to be a viable substrate for this enzyme.

  4. One Health Core Competency Domains

    Directory of Open Access Journals (Sweden)

    Rebekah Frankson

    2016-09-01

    Full Text Available The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting ‘One Health’ approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education as they describe the knowledge, skills and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  5. One Health Core Competency Domains.

    Science.gov (United States)

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting "One Health" approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  6. Catalytic properties of ADAM12 and its domain deletion mutants

    DEFF Research Database (Denmark)

    Jacobsen, Jonas; Visse, Robert; Sørensen, Hans Peter

    2008-01-01

    of pro, catalytic, disintegrin, cysteine-rich, and EGF domains. Here we present a novel activity of recombinant ADAM12-S and its domain deletion mutants on S-carboxymethylated transferrin (Cm-Tf). Cleavage of Cm-Tf occurred at multiple sites, and N-terminal sequencing showed that the enzyme exhibits...... restricted specificity but a consensus sequence could not be defined as its subsite requirements are promiscuous. Kinetic analysis revealed that the noncatalytic C-terminal domains are important regulators of Cm-Tf activity and that ADAM12-PC consisting of the pro domain and catalytic domain is the most...... 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...

  7. Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance

    Energy Technology Data Exchange (ETDEWEB)

    Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John; Steussy, C. Nicklaus; Carpita, Nicholas C.; Stauffacher, Cynthia V. (NEU); (Purdue)

    2016-11-22

    The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.

  8. Porous Core-Shell Nanostructures for Catalytic Applications

    Science.gov (United States)

    Ewers, Trevor David

    Porous core-shell nanostructures have recently received much attention for their enhanced thermal stability. They show great potential in the field of catalysis, as reactant gases can diffuse in and out of the porous shell while the core particle is protected from sintering, a process in which particles coalesce to form larger particles. Sintering is a large problem in industry and is the primary cause of irreversible deactivation. Despite the obvious advantages of high thermal stability, porous core-shell nanoparticles can be developed to have additional interactive properties from the combination of the core and shell together, rather than just the core particle alone. This dissertation focuses on developing new porous core-shell systems in which both the core and shell take part in catalysis. Two types of systems are explored; (1) yolk-shell nanostructures with reducible oxide shells formed using the Kirkendall effect and (2) ceramic-based porous oxide shells formed using sol-gel chemistry. Of the Kirkendall-based systems, Au FexOy and Cu CoO were synthesized and studied for catalytic applications. Additionally, ZnO was explored as a potential shelling material. Sol-gel work focused on optimizing synthetic methods to allow for coating of small gold particles, which remains a challenge today. Mixed metal oxides were explored as a shelling material to make dual catalysts in which the product of a reaction on the core particle becomes a reactant within the shell.

  9. Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains.

    Science.gov (United States)

    Harper, Stephen; Gratton, Hayley E; Cornaciu, Irina; Oberer, Monika; Scott, David J; Emsley, Jonas; Dreveny, Ingrid

    2014-05-13

    The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation.

  10. Updating the Psoriatic Arthritis (PsA) Core Domain Set

    DEFF Research Database (Denmark)

    Orbai, Ana-Maria; de Wit, Maarten; Mease, Philip J

    2017-01-01

    OBJECTIVE: To include the patient perspective in accordance with the Outcome Measures in Rheumatology (OMERACT) Filter 2.0 in the updated Psoriatic Arthritis (PsA) Core Domain Set for randomized controlled trials (RCT) and longitudinal observational studies (LOS). METHODS: At OMERACT 2016, research...... conducted to update the PsA Core Domain Set was presented and discussed in breakout groups. The updated PsA Core Domain Set was voted on and endorsed by OMERACT participants. RESULTS: We conducted a systematic literature review of domains measured in PsA RCT and LOS, and identified 24 domains. We conducted...... and breakout groups at OMERACT 2016 in which findings were presented and discussed. The updated PsA Core Domain Set endorsed with 90% agreement by OMERACT 2016 participants included musculoskeletal disease activity, skin disease activity, fatigue, pain, patient's global assessment, physical function, health...

  11. Modulation of catalytic activity in multi-domain protein tyrosine phosphatases.

    Directory of Open Access Journals (Sweden)

    Lalima L Madan

    Full Text Available Signaling mechanisms involving protein tyrosine phosphatases govern several cellular and developmental processes. These enzymes are regulated by several mechanisms which include variation in the catalytic turnover rate based on redox stimuli, subcellular localization or protein-protein interactions. In the case of Receptor Protein Tyrosine Phosphatases (RPTPs containing two PTP domains, phosphatase activity is localized in their membrane-proximal (D1 domains, while the membrane-distal (D2 domain is believed to play a modulatory role. Here we report our analysis of the influence of the D2 domain on the catalytic activity and substrate specificity of the D1 domain using two Drosophila melanogaster RPTPs as a model system. Biochemical studies reveal contrasting roles for the D2 domain of Drosophila Leukocyte antigen Related (DLAR and Protein Tyrosine Phosphatase on Drosophila chromosome band 99A (PTP99A. While D2 lowers the catalytic activity of the D1 domain in DLAR, the D2 domain of PTP99A leads to an increase in the catalytic activity of its D1 domain. Substrate specificity, on the other hand, is cumulative, whereby the individual specificities of the D1 and D2 domains contribute to the substrate specificity of these two-domain enzymes. Molecular dynamics simulations on structural models of DLAR and PTP99A reveal a conformational rationale for the experimental observations. These studies reveal that concerted structural changes mediate inter-domain communication resulting in either inhibitory or activating effects of the membrane distal PTP domain on the catalytic activity of the membrane proximal PTP domain.

  12. Plasma-activated core-shell gold nanoparticle films with enhanced catalytic properties

    Energy Technology Data Exchange (ETDEWEB)

    Llorca, Jordi, E-mail: jordi.llorca@upc.edu; Casanovas, Albert; Dominguez, Montserrat; Casanova, Ignasi [Universitat Politecnica de Catalunya, Institut de Tecniques Energetiques (Spain); Angurell, Inmaculada; Seco, Miquel; Rossell, Oriol [Universitat de Barcelona, Departament de Quimica Inorganica (Spain)

    2008-03-15

    Catalytically active gold nanoparticle films have been prepared from core-shell nanoparticles by plasma-activation and characterized by high-resolution transmission electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Methane can be selectively oxidized into formic acid with an O{sub 2}-H{sub 2} mixture in a catalytic wall reactor functionalized with plasma-activated gold nanoparticle films containing well-defined Au particles of about 3.5 nm in diameter. No catalytic activity was recorded over gold nanoparticle films prepared by thermal decomposition of core-shell nanoparticles due to particle agglomeration.

  13. Plasma-activated core-shell gold nanoparticle films with enhanced catalytic properties

    International Nuclear Information System (INIS)

    Llorca, Jordi; Casanovas, Albert; Dominguez, Montserrat; Casanova, Ignasi; Angurell, Inmaculada; Seco, Miquel; Rossell, Oriol

    2008-01-01

    Catalytically active gold nanoparticle films have been prepared from core-shell nanoparticles by plasma-activation and characterized by high-resolution transmission electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Methane can be selectively oxidized into formic acid with an O 2 -H 2 mixture in a catalytic wall reactor functionalized with plasma-activated gold nanoparticle films containing well-defined Au particles of about 3.5 nm in diameter. No catalytic activity was recorded over gold nanoparticle films prepared by thermal decomposition of core-shell nanoparticles due to particle agglomeration

  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)

    Solomon, A.; Akabayov, B.; Frenkel, A.; Millas, M.; Sagi, I.

    2007-01-01

    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. 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...... to measure RA flare. METHODS: Patient and healthcare professional (HCP) qualitative studies, focus groups, and literature review, followed by patient and HCP Delphi exercises including combined Delphi consensus at Outcome Measures in Rheumatology 10 (OMERACT 10), identified potential domains to measure flare...... Filter 2.0 methodology. RESULTS: A pre-meeting combined Delphi exercise for defining flare identified 9 domains as important (>70% consensus from patients or HCP). Four new patient-reported domains beyond those included in the RA disease activity core set were proposed for inclusion (fatigue...

  16. CORAL: aligning conserved core regions across domain families.

    Science.gov (United States)

    Fong, Jessica H; Marchler-Bauer, Aron

    2009-08-01

    Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

  17. The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity

    OpenAIRE

    Woodman, Zenda L.; Schwager, Sylva L. U.; Redelinghuys, Pierre; Carmona, Adriana K.; Ehlers, Mario R. W.; Sturrock, Edward D.

    2005-01-01

    sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test ...

  18. Domain decomposition methods for core calculations using the MINOS solver

    International Nuclear Information System (INIS)

    Guerin, P.; Baudron, A. M.; Lautard, J. J.

    2007-01-01

    Cell by cell homogenized transport calculations of an entire nuclear reactor core are currently too expensive for industrial applications, even if a simplified transport (SPn) approximation is used. In order to take advantage of parallel computers, we propose here two domain decomposition methods using the mixed dual finite element solver MINOS. The first one is a modal synthesis method on overlapping sub-domains: several Eigenmodes solutions of a local problem on each sub-domain are taken as basis functions used for the resolution of the global problem on the whole domain. The second one is an iterative method based on non-overlapping domain decomposition with Robin interface conditions. At each iteration, we solve the problem on each sub-domain with the interface conditions given by the solutions on the close sub-domains estimated at the previous iteration. For these two methods, we give numerical results which demonstrate their accuracy and their efficiency for the diffusion model on realistic 2D and 3D cores. (authors)

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

    KAUST Repository

    Wang, Jianfang; Li, Benxia; Gu, Ting; Ming, Tian; Wang, Junxin; Wang, Peng; Yu, Jimmy C.

    2014-01-01

    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.

  20. (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.

  1. 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.

  2. The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity.

    Science.gov (United States)

    Woodman, Zenda L; Schwager, Sylva L U; Redelinghuys, Pierre; Carmona, Adriana K; Ehlers, Mario R W; Sturrock, Edward D

    2005-08-01

    sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test this, we constructed two mutants: CNdom-ACE and CCdom-ACE. CNdom-ACE was shed less efficiently than sACE, whereas CCdom-ACE was shed as efficiently as tACE. Notably, cleavage occurred both within the stalk and the interdomain bridge in both mutants, suggesting that a sheddase recognition motif resides within the C domain and is capable of directly cleaving at both positions. Analysis of the catalytic properties of the mutants and comparison with sACE and tACE revealed that the k(cat) for sACE and CNdom-ACE was less than or equal to the sum of the kcat values for tACE and the N-domain, suggesting negative co-operativity, whereas the kcat value for the CCdom-ACE suggested positive co-operativity between the two domains. Taken together, the results provide support for (i) the existence of a sheddase recognition motif in the C domain and (ii) molecular flexibility of the N and C domains in sACE, resulting in occlusion of the C-domain recognition motif by the N domain as well as close contact of the two domains during hydrolysis of peptide substrates.

  3. Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP.

    Science.gov (United States)

    Perederina, Anna; Khanova, Elena; Quan, Chao; Berezin, Igor; Esakova, Olga; Krasilnikov, Andrey S

    2011-10-01

    Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding site corresponds to the protein binding site in bacterial RNase P RNA. Structural and evolutionary roles of the Pop5/Rpp1 heterodimer in RNases P and MRP are discussed.

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

    International Nuclear Information System (INIS)

    Greenwood, Alexander I.; Rogals, Monique J.; De, Soumya; Lu, Kun Ping; Kovrigin, Evgenii L.; Nicholson, Linda K.

    2011-01-01

    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 cat cis and apparent Michaelis constants, K M 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 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 13 C– 1 H constant time HSQC spectra to determine k cat cis , k cat trans , K D cis , and K D trans 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.

  5. Structural stability of human protein tyrosine phosphatase ρ catalytic domain: effect of point mutations.

    Directory of Open Access Journals (Sweden)

    Alessandra Pasquo

    Full Text Available Protein tyrosine phosphatase ρ (PTPρ belongs to the classical receptor type IIB family of protein tyrosine phosphatase, the most frequently mutated tyrosine phosphatase in human cancer. There are evidences to suggest that PTPρ may act as a tumor suppressor gene and dysregulation of Tyr phosphorylation can be observed in diverse diseases, such as diabetes, immune deficiencies and cancer. PTPρ variants in the catalytic domain have been identified in cancer tissues. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of the membrane-proximal catalytic domain of PTPρ. We expressed and purified as soluble recombinant proteins some of the mutants of the membrane-proximal catalytic domain of PTPρ identified in colorectal cancer and in the single nucleotide polymorphisms database. The mutants show a decreased thermal and thermodynamic stability and decreased activation energy relative to phosphatase activity, when compared to wild- type. All the variants show three-state equilibrium unfolding transitions similar to that of the wild- type, with the accumulation of a folding intermediate populated at ~4.0 M urea.

  6. Effective Domain Partitioning for Multi-Clock Domain IP Core Wrapper Design under Power Constraints

    Science.gov (United States)

    Yu, Thomas Edison; Yoneda, Tomokazu; Zhao, Danella; Fujiwara, Hideo

    The rapid advancement of VLSI technology has made it possible for chip designers and manufacturers to embed the components of a whole system onto a single chip, called System-on-Chip or SoC. SoCs make use of pre-designed modules, called IP-cores, which provide faster design time and quicker time-to-market. Furthermore, SoCs that operate at multiple clock domains and very low power requirements are being utilized in the latest communications, networking and signal processing devices. As a result, the testing of SoCs and multi-clock domain embedded cores under power constraints has been rapidly gaining importance. In this research, a novel method for designing power-aware test wrappers for embedded cores with multiple clock domains is presented. By effectively partitioning the various clock domains, we are able to increase the solution space of possible test schedules for the core. Since previous methods were limited to concurrently testing all the clock domains, we effectively remove this limitation by making use of bandwidth conversion, multiple shift frequencies and properly gating the clock signals to control the shift activity of various core logic elements. The combination of the above techniques gains us greater flexibility when determining an optimal test schedule under very tight power constraints. Furthermore, since it is computationally intensive to search the entire expanded solution space for the possible test schedules, we propose a heuristic 3-D bin packing algorithm to determine the optimal wrapper architecture and test schedule while minimizing the test time under power and bandwidth constraints.

  7. 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

  8. SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family.

    Science.gov (United States)

    Register, A C; Leonard, Stephen E; Maly, Dustin J

    2014-11-11

    Src-family kinases (SFKs) make up a family of nine homologous multidomain tyrosine kinases whose misregulation is responsible for human disease (cancer, diabetes, inflammation, etc.). Despite overall sequence homology and identical domain architecture, differences in SH3 and SH2 regulatory domain accessibility and ability to allosterically autoinhibit the ATP-binding site have been observed for the prototypical SFKs Src and Hck. Biochemical and structural studies indicate that the SH2-catalytic domain (SH2-CD) linker, the intramolecular binding epitope for SFK SH3 domains, is responsible for allosterically coupling SH3 domain engagement to autoinhibition of the ATP-binding site through the conformation of the αC helix. As a relatively unconserved region between SFK family members, SH2-CD linker sequence variability across the SFK family is likely a source of nonredundant cellular functions between individual SFKs via its effect on the availability of SH3 and SH2 domains for intermolecular interactions and post-translational modification. Using a combination of SFKs engineered with enhanced or weakened regulatory domain intramolecular interactions and conformation-selective inhibitors that report αC helix conformation, this study explores how SH2-CD sequence heterogeneity affects allosteric coupling across the SFK family by examining Lyn, Fyn1, and Fyn2. Analyses of Fyn1 and Fyn2, isoforms that are identical but for a 50-residue sequence spanning the SH2-CD linker, demonstrate that SH2-CD linker sequence differences can have profound effects on allosteric coupling between otherwise identical kinases. Most notably, a dampened allosteric connection between the SH3 domain and αC helix leads to greater autoinhibitory phosphorylation by Csk, illustrating the complex effects of SH2-CD linker sequence on cellular function.

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

    International Nuclear Information System (INIS)

    Piserchio, Andrea; Ghose, Ranajeet; Cowburn, David

    2009-01-01

    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

  10. Structure and Function of the Catalytic Domain of the Dihydrolipoyl Acetyltransferase Component in Escherichia coli Pyruvate Dehydrogenase Complex*

    Science.gov (United States)

    Wang, Junjie; Nemeria, Natalia S.; Chandrasekhar, Krishnamoorthy; Kumaran, Sowmini; Arjunan, Palaniappa; Reynolds, Shelley; Calero, Guillermo; Brukh, Roman; Kakalis, Lazaros; Furey, William; Jordan, Frank

    2014-01-01

    The Escherichia coli pyruvate dehydrogenase complex (PDHc) catalyzing conversion of pyruvate to acetyl-CoA comprises three components: E1p, E2p, and E3. The E2p is the five-domain core component, consisting of three tandem lipoyl domains (LDs), a peripheral subunit binding domain (PSBD), and a catalytic domain (E2pCD). Herein are reported the following. 1) The x-ray structure of E2pCD revealed both intra- and intertrimer interactions, similar to those reported for other E2pCDs. 2) Reconstitution of recombinant LD and E2pCD with E1p and E3p into PDHc could maintain at least 6.4% activity (NADH production), confirming the functional competence of the E2pCD and active center coupling among E1p, LD, E2pCD, and E3 even in the absence of PSBD and of a covalent link between domains within E2p. 3) Direct acetyl transfer between LD and coenzyme A catalyzed by E2pCD was observed with a rate constant of 199 s−1, comparable with the rate of NADH production in the PDHc reaction. Hence, neither reductive acetylation of E2p nor acetyl transfer within E2p is rate-limiting. 4) An unprecedented finding is that although no interaction could be detected between E1p and E2pCD by itself, a domain-induced interaction was identified on E1p active centers upon assembly with E2p and C-terminally truncated E2p proteins by hydrogen/deuterium exchange mass spectrometry. The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p. E2p domain-induced changes at the E1p active site were also manifested by the appearance of a circular dichroism band characteristic of the canonical 4′-aminopyrimidine tautomer of bound thiamin diphosphate (AP). PMID:24742683

  11. Structure and function of the catalytic domain of the dihydrolipoyl acetyltransferase component in Escherichia coli pyruvate dehydrogenase complex.

    Science.gov (United States)

    Wang, Junjie; Nemeria, Natalia S; Chandrasekhar, Krishnamoorthy; Kumaran, Sowmini; Arjunan, Palaniappa; Reynolds, Shelley; Calero, Guillermo; Brukh, Roman; Kakalis, Lazaros; Furey, William; Jordan, Frank

    2014-05-30

    The Escherichia coli pyruvate dehydrogenase complex (PDHc) catalyzing conversion of pyruvate to acetyl-CoA comprises three components: E1p, E2p, and E3. The E2p is the five-domain core component, consisting of three tandem lipoyl domains (LDs), a peripheral subunit binding domain (PSBD), and a catalytic domain (E2pCD). Herein are reported the following. 1) The x-ray structure of E2pCD revealed both intra- and intertrimer interactions, similar to those reported for other E2pCDs. 2) Reconstitution of recombinant LD and E2pCD with E1p and E3p into PDHc could maintain at least 6.4% activity (NADH production), confirming the functional competence of the E2pCD and active center coupling among E1p, LD, E2pCD, and E3 even in the absence of PSBD and of a covalent link between domains within E2p. 3) Direct acetyl transfer between LD and coenzyme A catalyzed by E2pCD was observed with a rate constant of 199 s(-1), comparable with the rate of NADH production in the PDHc reaction. Hence, neither reductive acetylation of E2p nor acetyl transfer within E2p is rate-limiting. 4) An unprecedented finding is that although no interaction could be detected between E1p and E2pCD by itself, a domain-induced interaction was identified on E1p active centers upon assembly with E2p and C-terminally truncated E2p proteins by hydrogen/deuterium exchange mass spectrometry. The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p. E2p domain-induced changes at the E1p active site were also manifested by the appearance of a circular dichroism band characteristic of the canonical 4'-aminopyrimidine tautomer of bound thiamin diphosphate (AP). © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. An Adaptor Domain-Mediated Auto-Catalytic Interfacial Kinase Reaction

    Science.gov (United States)

    Liao, Xiaoli; Su, Jing; Mrksich, Milan

    2010-01-01

    This paper describes a model system for studying the auto-catalytic phosphorylation of an immobilized substrate by a kinase enzyme. This work uses self-assembled monolayers (SAMs) of alkanethiolates on gold to present the peptide substrate on a planar surface. Treatment of the monolayer with Abl kinase results in phosphorylation of the substrate. The phosphorylated peptide then serves as a ligand for the SH2 adaptor domain of the kinase and thereby directs the kinase activity to nearby peptide substrates. This directed reaction is intramolecular and proceeds with a faster rate than does the initial, intermolecular reaction, making this an auto-catalytic process. The kinetic non-linearity gives rise to properties that have no counterpart in the corresponding homogeneous phase reaction: in one example, the rate for phosphorylation of a mixture of two peptides is faster than the sum of the rates for phosphorylation of each peptide when presented alone. This work highlights the use of an adaptor domain in modulating the activity of a kinase enzyme for an immobilized substrate and offers a new approach for studying biochemical reactions in spatially inhomogeneous settings. PMID:19821459

  13. A non-catalytic N-terminal domain negatively influences the nucleotide exchange activity of translation elongation factor 1Bα.

    Science.gov (United States)

    Trosiuk, Tetiana V; Shalak, Vyacheslav F; Szczepanowski, Roman H; Negrutskii, Boris S; El'skaya, Anna V

    2016-02-01

    Eukaryotic translation elongation factor 1Bα (eEF1Bα) is a functional homolog of the bacterial factor EF-Ts, and is a component of the macromolecular eEF1B complex. eEF1Bα functions as a catalyst of guanine nucleotide exchange on translation elongation factor 1A (eEF1A). The C-terminal domain of eEF1Bα is necessary and sufficient for its catalytic activity, whereas the N-terminal domain interacts with eukaryotic translation elongation factor 1Bγ (eEF1Bγ) to form a tight complex. However, eEF1Bγ has been shown to enhance the catalytic activity of eEF1Bα attributed to the C-terminal domain of eEF1Bα. This suggests that the N-terminal domain of eEF1Bα may in some way influence the guanine nucleotide exchange process. We have shown that full-length recombinant eEF1Bα and its truncated forms are non-globular proteins with elongated shapes. Truncation of the N-terminal domain of eEF1Bα, which is dispensable for catalytic activity, resulted in acceleration of the rate of guanine nucleotide exchange on eEF1A compared to full-length eEF1Bα. A similar effect on the catalytic activity of eEF1Bα was observed after its interaction with eEF1Bγ. We suggest that the non-catalytic N-terminal domain of eEF1Bα may interfere with eEF1A binding to the C-terminal catalytic domain, resulting in a decrease in the overall rate of the guanine nucleotide exchange reaction. Formation of a tight complex between the eEF1Bγ and eEF1Bα N-terminal domains abolishes this inhibitory effect. © 2015 FEBS.

  14. 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.

  15. 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

  16. Crystallization and preliminary X-ray characterization of the catalytic domain of collagenase G from Clostridium histolyticum

    International Nuclear Information System (INIS)

    Eckhard, Ulrich; Nüss, Dorota; Ducka, Paulina; Schönauer, Esther; Brandstetter, Hans

    2008-01-01

    The catalytic domain of collagenase G from C. histolyticum was expressed in E. coli BL21 (DE3) and purified using affinity and size-exclusion column-chromatographic methods. Crystals were obtained at 290 K by the sitting-drop vapour-diffusion method and diffraction data have been collected to 2.75 Å resolution. The catalytic domain of collagenase G from Clostridium histolyticum has been cloned, recombinantly expressed in Escherichia coli and purified using affinity and size-exclusion column-chromatographic methods. Crystals of the catalytic domain were obtained from 0.12 M sodium citrate and 23%(v/v) PEG 3350 at 293 K. The crystals diffracted to 2.75 Å resolution using synchrotron radiation. The crystals belong to an orthorhombic space group, with unit-cell parameters a = 57, b = 109, c = 181 Å. This unit cell is consistent with the presence of one molecule per asymmetric unit and a solvent content of approximately 53%

  17. Crystallization and preliminary X-ray characterization of the catalytic domain of collagenase G from Clostridium histolyticum

    Energy Technology Data Exchange (ETDEWEB)

    Eckhard, Ulrich, E-mail: ulrich.eckhard@sbg.ac.at; Nüss, Dorota; Ducka, Paulina; Schönauer, Esther; Brandstetter, Hans [Structural Biology Group, Department of Molecular Biology, University of Salzburg, 5020 Salzburg (Austria)

    2008-05-01

    The catalytic domain of collagenase G from C. histolyticum was expressed in E. coli BL21 (DE3) and purified using affinity and size-exclusion column-chromatographic methods. Crystals were obtained at 290 K by the sitting-drop vapour-diffusion method and diffraction data have been collected to 2.75 Å resolution. The catalytic domain of collagenase G from Clostridium histolyticum has been cloned, recombinantly expressed in Escherichia coli and purified using affinity and size-exclusion column-chromatographic methods. Crystals of the catalytic domain were obtained from 0.12 M sodium citrate and 23%(v/v) PEG 3350 at 293 K. The crystals diffracted to 2.75 Å resolution using synchrotron radiation. The crystals belong to an orthorhombic space group, with unit-cell parameters a = 57, b = 109, c = 181 Å. This unit cell is consistent with the presence of one molecule per asymmetric unit and a solvent content of approximately 53%.

  18. Catalytic cleavage activities of 10–23 DNAzyme analogs functionalized with an amino group in its catalytic core

    Directory of Open Access Journals (Sweden)

    Qi Wang

    2012-02-01

    Full Text Available Functionalization of the catalytic loop of 10–23 DNAzyme with an amino group was performed by incorporation of 7-(3-aminopropyl-8-aza-7-deaza-2′-deoxyadenosine in different single positions. Among the nine modified positions in the catalytic loop, A9 is the unique position with positive contribution by such modification. These results indicated that more efficient deoxyribozymes remain to be explored by introduction of exogenous functional groups in an appropriate position in the catalytic loop of 10–23 DNAzyme, such as the combination of 7-functional group substituted 8-aza-7-deaza-2′-deoxyadenosine analogs and A9 position.

  19. Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain.

    Science.gov (United States)

    Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Petitjean, Michel; Flatters, Delphine; Camproux, Anne-Claude

    2017-10-01

    While recent literature focuses on drug promiscuity, the characterization of promiscuous binding sites (ability to bind several ligands) remains to be explored. Here, we present a proteochemometric modeling approach to analyze diverse ligands and corresponding multiple binding sub-pockets associated with one promiscuous binding site to characterize protein-ligand recognition. We analyze both geometrical and physicochemical profile correspondences. This approach was applied to examine the well-studied druggable urokinase catalytic domain inhibitor binding site, which results in a large number of complex structures bound to various ligands. This approach emphasizes the importance of jointly characterizing pocket and ligand spaces to explore the impact of ligand diversity on sub-pocket properties and to establish their main profile correspondences. This work supports an interest in mining available 3D holo structures associated with a promiscuous binding site to explore its main protein-ligand recognition tendency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains

    Directory of Open Access Journals (Sweden)

    Huxley-Jones Julie

    2007-11-01

    Full Text Available Abstract Background The genomes of the three parasitic protozoa Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are the main subject of this study. These parasites are responsible for devastating human diseases known as Chagas disease, African sleeping sickness and cutaneous Leishmaniasis, respectively, that affect millions of people in the developing world. The prevalence of these neglected diseases results from a combination of poverty, inadequate prevention and difficult treatment. Protein phosphorylation is an important mechanism of controlling the development of these kinetoplastids. With the aim to further our knowledge of the biology of these organisms we present a characterisation of the phosphatase complement (phosphatome of the three parasites. Results An ontology-based scan of the three genomes was used to identify 86 phosphatase catalytic domains in T. cruzi, 78 in T. brucei, and 88 in L. major. We found interesting differences with other eukaryotic genomes, such as the low proportion of tyrosine phosphatases and the expansion of the serine/threonine phosphatase family. Additionally, a large number of atypical protein phosphatases were identified in these species, representing more than one third of the total phosphatase complement. Most of the atypical phosphatases belong to the dual-specificity phosphatase (DSP family and show considerable divergence from classic DSPs in both the domain organisation and sequence features. Conclusion The analysis of the phosphatome of the three kinetoplastids indicates that they possess orthologues to many of the phosphatases reported in other eukaryotes, including humans. However, novel domain architectures and unusual combinations of accessory domains, suggest distinct functional roles for several of the kinetoplastid phosphatases, which await further experimental exploration. These distinct traits may be exploited in the selection of suitable new targets for drug development to prevent

  1. A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

    Science.gov (United States)

    Mills, Jamie E; Whitford, Paul C; Shaffer, Jennifer; Onuchic, Jose N; Adams, Joseph A; Jennings, Patricia A

    2007-02-02

    The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of the SH2 domain were investigated. The kinase activity of full-length Csk decreases by an order of magnitude upon formation of the disulfide bond in the distal SH2 domain. NMR spectra of the fully oxidized and fully reduced SH2 domains exhibit similar chemical shift patterns and are indicative of similar, well-defined tertiary structures. The solvent-accessible disulfide bond in the isolated SH2 domain is highly stable and far from the small lobe of the kinase domain. However, reduction of this bond results in chemical shift changes of resonances that map to a cluster of residues that extend from the disulfide bond across the molecule to a surface that is in direct contact with the small lobe of the kinase domain in the intact molecule. Normal mode analyses and molecular dynamics calculations suggest that disulfide bond formation has large effects on residues within the kinase domain, most notably within the active-site cleft. Overall, the data indicate that reversible cross-linking of two cysteine residues in the SH2 domain greatly impacts catalytic function and interdomain communication in Csk.

  2. Pt@Ag and Pd@Ag core/shell nanoparticles for catalytic degradation of Congo red in aqueous solution

    Science.gov (United States)

    Salem, Mohamed A.; Bakr, Eman A.; El-Attar, Heba G.

    2018-01-01

    Platinum/silver (Pt@Ag) and palladium/silver (Pd@Ag) core/shell NPs have been synthesized in two steps reaction using the citrate method. The progress of nanoparticle formation was followed by the UV/Vis spectroscopy. Transmission electron microscopy revealed spherical shaped core/shell nanoparticles with average particle diameter 32.17 nm for Pt@Ag and 8.8 nm for Pd@Ag. The core/shell NPs were further characterized by FT-IR and XRD. Reductive degradation of the Congo red dye was chosen to demonstrate the excellent catalytic activity of these core/shell nanostructures. The nanocatalysts act as electron mediators for the transfer of electrons from the reducing agent (NaBH4) to the dye molecules. Effect of reaction parameters such as nanocatalyst dose, dye and NaBH4 concentrations on the dye degradation was investigated. A comparison between the catalytic activities of both nanocatalysts was made to realize which of them the best in catalytic performance. Pd@Ag was the higher in catalytic activity over Pt@Ag. Such greater activity is originated from the smaller particle size and larger surface area. Pd@Ag nanocatalyst was catalytically stable through four subsequent reaction runs under the utilized reaction conditions. These findings can thus be considered as possible economical alternative for environmental safety against water pollution by dyes.

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

    DEFF Research Database (Denmark)

    Lira-Navarrete, Erandi; de Las Rivas, Matilde; Compañón, Ismael

    2015-01-01

    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......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...... 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...

  4. 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.

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

    International Nuclear Information System (INIS)

    Shewamare, Sisay; Mal'nev, V.N.

    2012-01-01

    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.

  6. Remote Exosites of the Catalytic Domain of Matrix Metalloproteinase-12 Enhance Elastin Degradation┼

    Science.gov (United States)

    Fulcher, Yan G.; Van Doren, Steven R.

    2011-01-01

    How does matrix metalloproteinase-12 (MMP-12 or metalloelastase) degrade elastin with high specific activity? NMR suggested soluble elastin to cover surfaces of MMP-12 far from its active site. Two of these surfaces have been found, by mutagenesis guided by the BINDSIght approach, to affect degradation and affinity for elastin substrates but not a small peptide substrate. Main exosite 1 has been extended out to Asp124 that binds calcium. Novel exosite 2 comprises residues from the II–III loop and β-strand I near the back of the catalytic domain. The high exposure of these distal exosites may make them accessible to elastin made more flexible by partial hydrolysis. Importantly, combination of a lesion at each of exosites 1 and 2 and active site decreased catalytic competence towards soluble elastin by 13- to 18-fold to the level of MMP-3, homologue and poor elastase. Double mutant cycle analysis of conservative mutations of Met156 (exosite 2) and either Asp124 (exosite 1) or Ile180 (active site) had additive effects. Compared to polar substitutions observed in other MMPs, Met156 enhanced affinity and Ile180 kcat for soluble elastin. Both residues detracted from the higher folding stability with polar mutations. This resembles the trend in enzymes of an inverse relationship between folding stability and activity. Restoring Asp124 from combination mutants enhanced kcat for soluble elastin. In elastin degradation, exosites 1 and 2 contributed independently of each other and Ile180 at the active site, but with partial coupling to Ala182 near the active site. The concept of weak, separated interactions coalescing somewhat independently can be extended to this proteolytic digestion of a protein from fibrils. PMID:21967233

  7. Mobile sequences in the pyruvate dehydrogenase complex, the E2 component, the catalytic domain and the 2-oxogluturate dehydrogenase complex of Azotobacter vinelandii, as detected by 600 MHz 1H-NMR spectroscopy

    International Nuclear Information System (INIS)

    Hanemaaijer, R.; Vervoort, J.; Westphal, A.H.; Kok, A. de.; Veeger, C.

    1988-01-01

    600 MHz 1 H-NMR spectroscopy demonstrates that the pyruvate dehydrogenase complex of Azotobacter vinelandii contains regions of the polypeptide chain with intramolecular mobility. This mobility is located in the E 2 component and can probably be ascribed to alanine-proline-rich regions that link the lipoyl sibdiomains to each other as well as to the E 1 and E 3 binding domain. In the catalytic domain of E 2 which is thought to form a compact, rigid core, also conformational flexibility is observed. It is conceivable that the N-terminal region of the catalytic domain, which contains many alanine residues, is responsible for the observed mobility. In the low-field region of the 1 H-NMR spectrum of E 2 specific resonances are found, which can be ascribed to mobile phenylalanine, histidine and/or tyrosine residues which are located in the E 1 and E 3 binding domain that links the lipoyl domain to the catalytic domain. In the 1 H-NMR spectrum of the intact complex, these resonances cannot be observed, indicating a decreased mobility of the E 1 and E 3 binding domain. (author). 24 refs.; 2 figs

  8. LKIF Core: principled ontology development for the legal domain

    NARCIS (Netherlands)

    Hoekstra, R.; Breuker, J.; Di Bello, M.; Boer, A.; Breuker, J.; Casanovas, P.; Klein, M.C.A.; Francesconi, E.

    2009-01-01

    In this paper we describe a legal core ontology that is part of the Legal Knowledge Interchange Format: a knowledge representation formalism that enables the translation of legal knowledge bases written in different representation formats and formalisms. A legal (core) ontology can play an important

  9. Development of SiO2@TiO2 core-shell nanospheres for catalytic applications

    Science.gov (United States)

    Kitsou, I.; Panagopoulos, P.; Maggos, Th.; Arkas, M.; Tsetsekou, A.

    2018-05-01

    Silica-titania core-shell nanospheres, CSNp, were prepared via a simple and environmentally friendly two step route. First, silica cores were prepared through the hydrolysis-condensation reaction of silicic acid in the presence of hyperbranched poly(ethylene)imine (HBPEI) followed by repeating washing, centrifugation and, finally, calcination steps. To create the core-shell structure, various amounts of titanium isopropoxide were added to the cores and after that a HBPEI-water solution was added to hydrolyze the titanium precursor. Washing with ethanol and heat treatment followed. The optimization of processing parameters led to well-developed core-shell structures bearing a homogeneous nanocrystalline anatase coating over each silica core. The photocatalytic activity for NO was examined in a continuous flux photocatalytic reactor under real environmental conditions. The results revealed a very potent photocatalyst as the degradation percentage reached 84.27% for the core-shell material compared to the 82% of pure titania with the photodecomposition rates measured at 0.62 and 0.55 μg·m-2·s-1, respectively. In addition, catalytic activities of the CSNp and pure titania were investigated by monitoring the reduction of 4-nitrophenol to 4-aminophenol by an excess of NaBH4. Both materials exhibited excellent catalytic activity (100%), making the core-shell material a promising alternative catalyst to pure titania for various applications.

  10. Crystallization and preliminary X-ray diffraction analysis of the glucuronoyl esterase catalytic domain from Hypocrea jecorina

    International Nuclear Information System (INIS)

    Wood, S. J.; Li, X.-L.; Cotta, M. A.; Biely, P.; Duke, N. E. C.; Schiffer, M.; Pokkuluri, P. R.

    2008-01-01

    The catalytic domain of the glucuronoyl esterase from H. jecorina was overexpresssed, purified and crystallized in space group P2 1 2 1 2 1 . X-ray diffraction data were collected to 1.9 Å resolution. The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was overexpresssed, purified and crystallized by the sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. The crystals belonged to space group P2 1 2 1 2 1 and X-ray diffraction data were collected to 1.9 Å resolution. This is the first enzyme with glucoronoyl esterase activity to be crystallized; its structure will be valuable in lignocellulose-degradation research

  11. Crystallization and preliminary X-ray diffraction analysis of the glucuronoyl esterase catalytic domain from Hypocrea jecorina

    Energy Technology Data Exchange (ETDEWEB)

    Wood, S. J. [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Li, X.-L.; Cotta, M. A. [Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604 (United States); Biely, P. [Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava (Slovakia); Duke, N. E. C.; Schiffer, M.; Pokkuluri, P. R., E-mail: rajp@anl.gov [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2008-04-01

    The catalytic domain of the glucuronoyl esterase from H. jecorina was overexpresssed, purified and crystallized in space group P2{sub 1}2{sub 1}2{sub 1}. X-ray diffraction data were collected to 1.9 Å resolution. The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was overexpresssed, purified and crystallized by the sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1} and X-ray diffraction data were collected to 1.9 Å resolution. This is the first enzyme with glucoronoyl esterase activity to be crystallized; its structure will be valuable in lignocellulose-degradation research.

  12. Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain

    Science.gov (United States)

    Gallego-Bartolomé, Javier; Gardiner, Jason; Liu, Wanlu; Papikian, Ashot; Ghoshal, Basudev; Kuo, Hsuan Yu; Zhao, Jenny Miao-Chi; Jacobsen, Steven E.

    2018-01-01

    DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is fwa, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing up-regulation of FWA and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA up-regulation, and a heritable late-flowering phenotype. Additional ZF–TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCas9-based targeted demethylation system using the TET1cd and a modified SunTag system. Similar to the ZF–TET1cd fusions, the SunTag–TET1cd system is able to target demethylation and activate gene expression when directed to the FWA or CACTA1 loci. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons. PMID:29444862

  13. 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...

  14. Fabrication of ammonium perchlorate/copper-chromium oxides core-shell nanocomposites for catalytic thermal decomposition of ammonium perchlorate

    Energy Technology Data Exchange (ETDEWEB)

    Eslami, Abbas, E-mail: eslami@umz.ac.ir [Department of Inorganic Chemistry, Faculty of Chemistry, University of Mazandaran, P.O.Box 47416-95447, Babolsar (Iran, Islamic Republic of); Juibari, Nafise Modanlou [Department of Inorganic Chemistry, Faculty of Chemistry, University of Mazandaran, P.O.Box 47416-95447, Babolsar (Iran, Islamic Republic of); Hosseini, Seyed Ghorban [Department of Chemistry, Malek Ashtar University of Technology, P.O. Box 16765-3454, Tehran (Iran, Islamic Republic of)

    2016-09-15

    The ammonium perchlorate/Cu(II)-Cr(III)-oxides(AP/Cu-Cr-O) core-shell nanocomposites were in-situ prepared by deposition of copper and chromium oxides on suspended ammonium perchlorate particles in ethyl acetate as solvent. The results of differential scanning calorimetery (DSC) and thermal gravimetric analysis (TGA) experiments showed that the nanocomposites have excellent catalytic effect on the thermal decomposition of AP, so that the released heat increases up to about 3-fold over initial values, changing from 450 J/g for pure AP to 1510 J/g for most appropriate mixture. For better comparison, single metal oxide/AP core-shell nanocomposite have also been prepared and the results showed that they have less catalytic effect respect to mixed metal oxides system. Scanning electron microscopy (SEM) results revealed homogenous deposition of nanoparticles on the surface of AP and fabrication of core-shell structures. The kinetic parameters of thermal decomposition of both pure AP and AP/Cu-Cr-O samples have been calculated by Kissinger method and the results showed that the values of pre-exponential factor and activation energy are higher for AP/Cu-Cr-O nanocomposite. The better catalytic effect of Cu-Cr-O nanocomposites is probably attributed to the synergistic effect between Cu{sup 2+} and Cr{sup 3+} in the nanocomposites, smaller particle size and more crystal defect. - Highlights: • The Cu-Cr-O nanoparticles were synthesized by chemical liquid deposition method. • Then, the AP/Cu-Cr-O core-shell nanocomposites were prepared. • The core-shell samples showed high catalytic activity for AP decomposition. • Thermal decomposition of samples occurs at lower temperature range.

  15. Cooperation between catalytic and DNA binding domains enhances thermostability and supports DNA synthesis at higher temperatures by thermostable DNA polymerases.

    Science.gov (United States)

    Pavlov, Andrey R; Pavlova, Nadejda V; Kozyavkin, Sergei A; Slesarev, Alexei I

    2012-03-13

    We have previously introduced a general kinetic approach for comparative study of processivity, thermostability, and resistance to inhibitors of DNA polymerases [Pavlov, A. R., et al. (2002) Proc. Natl. Acad. Sci. U.S.A.99, 13510-13515]. The proposed method was successfully applied to characterize hybrid DNA polymerases created by fusing catalytic DNA polymerase domains with various sequence-nonspecific DNA binding domains. Here we use the developed kinetic analysis to assess basic parameters of DNA elongation by DNA polymerases and to further study the interdomain interactions in both previously constructed and new chimeric DNA polymerases. We show that connecting helix-hairpin-helix (HhH) domains to catalytic polymerase domains can increase thermostability, not only of DNA polymerases from extremely thermophilic species but also of the enzyme from a faculatative thermophilic bacterium Bacillus stearothermophilus. We also demonstrate that addition of Topo V HhH domains extends efficient DNA synthesis by chimerical polymerases up to 105 °C by maintaining processivity of DNA synthesis at high temperatures. We found that reversible high-temperature structural transitions in DNA polymerases decrease the rates of binding of these enzymes to the templates. Furthermore, activation energies and pre-exponential factors of the Arrhenius equation suggest that the mechanism of electrostatic enhancement of diffusion-controlled association plays a minor role in binding of templates to DNA polymerases.

  16. Evolutionary divergence in the catalytic activity of the CAM-1, ROR1 and ROR2 kinase domains.

    Directory of Open Access Journals (Sweden)

    Travis W Bainbridge

    Full Text Available Receptor tyrosine kinase-like orphan receptors (ROR 1 and 2 are atypical members of the receptor tyrosine kinase (RTK family and have been associated with several human diseases. The vertebrate RORs contain an ATP binding domain that deviates from the consensus amino acid sequence, although the impact of this deviation on catalytic activity is not known and the kinase function of these receptors remains controversial. Recently, ROR2 was shown to signal through a Wnt responsive, β-catenin independent pathway and suppress a canonical Wnt/β-catenin signal. In this work we demonstrate that both ROR1 and ROR2 kinase domains are catalytically deficient while CAM-1, the C. elegans homolog of ROR, has an active tyrosine kinase domain, suggesting a divergence in the signaling processes of the ROR family during evolution. In addition, we show that substitution of the non-consensus residues from ROR1 or ROR2 into CAM-1 and MuSK markedly reduce kinase activity, while restoration of the consensus residues in ROR does not restore robust kinase function. We further demonstrate that the membrane-bound extracellular domain alone of either ROR1 or ROR2 is sufficient for suppression of canonical Wnt3a signaling, and that this domain can also enhance Wnt5a suppression of Wnt3a signaling. Based on these data, we conclude that human ROR1 and ROR2 are RTK-like pseudokinases.

  17. The phospholipase PNPLA7 functions as a lysophosphatidylcholine hydrolase and interacts with lipid droplets through its catalytic domain.

    Science.gov (United States)

    Heier, Christoph; Kien, Benedikt; Huang, Feifei; Eichmann, Thomas O; Xie, Hao; Zechner, Rudolf; Chang, Ping-An

    2017-11-17

    Mammalian patatin-like phospholipase domain-containing proteins (PNPLAs) are lipid-metabolizing enzymes with essential roles in energy metabolism, skin barrier development, and brain function. A detailed annotation of enzymatic activities and structure-function relationships remains an important prerequisite to understand PNPLA functions in (patho-)physiology, for example, in disorders such as neutral lipid storage disease, non-alcoholic fatty liver disease, and neurodegenerative syndromes. In this study, we characterized the structural features controlling the subcellular localization and enzymatic activity of PNPLA7, a poorly annotated phospholipase linked to insulin signaling and energy metabolism. We show that PNPLA7 is an endoplasmic reticulum (ER) transmembrane protein that specifically promotes hydrolysis of lysophosphatidylcholine in mammalian cells. We found that transmembrane and regulatory domains in the PNPLA7 N-terminal region cooperate to regulate ER targeting but are dispensable for substrate hydrolysis. Enzymatic activity is instead mediated by the C-terminal domain, which maintains full catalytic competence even in the absence of N-terminal regions. Upon elevated fatty acid flux, the catalytic domain targets cellular lipid droplets and promotes interactions of PNPLA7 with these organelles in response to increased cAMP levels. We conclude that PNPLA7 acts as an ER-anchored lysophosphatidylcholine hydrolase that is composed of specific functional domains mediating catalytic activity, subcellular positioning, and interactions with cellular organelles. Our study provides critical structural insights into an evolutionarily conserved class of phospholipid-metabolizing enzymes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

    Science.gov (United States)

    Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

    2012-01-01

    The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

  19. Mutational analyses of the core domain of Avian Leukemia and Sarcoma Viruses integrase: critical residues for concerted integration and multimerization

    International Nuclear Information System (INIS)

    Moreau, Karen; Faure, Claudine; Violot, Sebastien; Gouet, Patrice; Verdier, Gerard; Ronfort, Corinne

    2004-01-01

    During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the cell DNA by the viral integrase (IN) enzyme. The central core domain of IN contains the catalytic site of the enzyme and is involved in binding viral ends and cell DNA as well as dimerization. We previously performed single amino acid substitutions in the core domain of an Avian Leukemia and Sarcoma Virus (ALSV) IN [Arch. Virol. 147 (2002) 1761]. Here, we modeled the resulting IN mutants and analyzed the ability of these mutants to mediate concerted DNA integration in an in vitro assay, and to form dimers by protein-protein cross-linking and size exclusion chromatography. The N197C mutation resulted in the inability of the mutant to perform concerted integration that was concomitant with a loss of IN dimerization. Surprisingly, mutations Q102G and A106V at the dimer interface resulted in mutants with higher efficiencies than the wild-type IN in performing two-ended concerted integration of viral DNA ends. The G139D and A195V mutants had a trend to perform one-ended DNA integration of viral ends instead of two-ended integration. More drastically, the I88L and L135G mutants preferentially mediated nonconcerted DNA integration although the proteins form dimers. Therefore, these mutations may alter the formation of IN complexes of higher molecular size than a dimer that would be required for concerted integration. This study points to the important role of core domain residues in the concerted integration of viral DNA ends as well as in the oligomerization of the enzyme

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

    KAUST Repository

    Wong, Aloysius Tze; Gehring, Christoph A

    2013-01-01

    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

  1. 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

  2. N- versus C-domain selectivity of catalytic inactivation of human angiotensin converting enzyme by lisinopril-coupled transition metal chelates.

    Science.gov (United States)

    Hocharoen, Lalintip; Joyner, Jeff C; Cowan, J A

    2013-12-27

    The N- and C-terminal domains of human somatic angiotensin I converting enzyme (sACE-1) demonstrate distinct physiological functions, with resulting interest in the development of domain-selective inhibitors for specific therapeutic applications. Herein, the activity of lisinopril-coupled transition metal chelates was tested for both reversible binding and irreversible catalytic inactivation of each domain of sACE-1. C/N domain binding selectivity ratios ranged from 1 to 350, while rates of irreversible catalytic inactivation of the N- and C-domains were found to be significantly greater for the N-domain, suggesting a more optimal orientation of M-chelate-lisinopril complexes within the active site of the N-domain of sACE-1. Finally, the combined effect of binding selectivity and inactivation selectivity was assessed for each catalyst (double-filter selectivity factors), and several catalysts were found to cause domain-selective catalytic inactivation. The results of this study demonstrate the ability to optimize the target selectivity of catalytic metallopeptides through both binding and catalytic factors (double-filter effect).

  3. Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.

    Science.gov (United States)

    Barski, Michal; Brennan, Benjamin; Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M; Schwarz-Linek, Ulrich

    2017-09-15

    Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83-248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in viruses encoding full-length NSs completely abrogated intranuclear filament formation in infected cells. We propose the fibrillar arrangement of the NSs core domain in crystals reveals the molecular basis of assembly of this key virulence factor in cell nuclei. Our findings have important implications for fundamental understanding of RVFV virulence.

  4. A Preliminary Core Domain Set for Clinical Trials of Shoulder Disorders: A Report from the OMERACT 2016 Shoulder Core Outcome Set Special Interest Group.

    Science.gov (United States)

    Buchbinder, Rachelle; Page, Matthew J; Huang, Hsiaomin; Verhagen, Arianne P; Beaton, Dorcas; Kopkow, Christian; Lenza, Mario; Jain, Nitin B; Richards, Bethan; Richards, Pamela; Voshaar, Marieke; van der Windt, Danielle; Gagnier, Joel J

    2017-12-01

    The Outcome Measures in Rheumatology (OMERACT) Shoulder Core Outcome Set Special Interest Group (SIG) was established to develop a core outcome set (COS) for clinical trials of shoulder disorders. In preparation for OMERACT 2016, we systematically examined all outcome domains and measurement instruments reported in 409 randomized trials of interventions for shoulder disorders published between 1954 and 2015. Informed by these data, we conducted an international Delphi consensus study including shoulder trial experts, clinicians, and patients to identify key domains that should be included in a shoulder disorder COS. Findings were discussed at a stakeholder premeeting of OMERACT. At OMERACT 2016, we sought consensus on a preliminary core domain set and input into next steps. There were 13 and 15 participants at the premeeting and the OMERACT 2016 SIG meeting, respectively (9 attended both meetings). Consensus was reached on a preliminary core domain set consisting of an inner core of 4 domains: pain, physical function/activity, global perceived effect, and adverse events including death. A middle core consisted of 3 domains: emotional well-being, sleep, and participation (recreation and work). An outer core of research required to inform the final COS was also formulated. Our next steps are to (1) analyze whether participation (recreation and work) should be in the inner core, (2) conduct a third Delphi round to finalize definitions and wording of domains and reach final endorsement for the domains, and (3) determine which instruments fulfill the OMERACT criteria for measuring each domain.

  5. HD-PTP is a catalytically inactive tyrosine phosphatase due to a conserved divergence in its phosphatase domain.

    Directory of Open Access Journals (Sweden)

    Marie-Claude Gingras

    Full Text Available The HD-PTP protein has been described as a tumor suppressor candidate and based on its amino acid sequence, categorized as a classical non-transmembrane protein tyrosine phosphatase (PTP. To date, no HD-PTP phosphorylated substrate has been identified and controversial results concerning its catalytic activity have been recently reported.Here we report a rigorous enzymatic analysis demonstrating that the HD-PTP protein does not harbor tyrosine phosphatase or lipid phosphatase activity using the highly sensitive DiFMUP substrate and a panel of different phosphatidylinositol phosphates. We found that HD-PTP tyrosine phosphatase inactivity is caused by an evolutionary conserved amino acid divergence of a key residue located in the HD-PTP phosphatase domain since its back mutation is sufficient to restore the HD-PTP tyrosine phosphatase activity. Moreover, in agreement with a tumor suppressor activity, HD-PTP expression leads to colony growth reduction in human cancer cell lines, independently of its catalytic PTP activity status.In summary, we demonstrate that HD-PTP is a catalytically inactive protein tyrosine phosphatase. As such, we identify one residue involved in its inactivation and show that its colony growth reduction activity is independent of its PTP activity status in human cancer cell lines.

  6. Core outcome domains for clinical trials in non-specific low back pain.

    Science.gov (United States)

    Chiarotto, Alessandro; Deyo, Richard A; Terwee, Caroline B; Boers, Maarten; Buchbinder, Rachelle; Corbin, Terry P; Costa, Leonardo O P; Foster, Nadine E; Grotle, Margreth; Koes, Bart W; Kovacs, Francisco M; Lin, Chung-Wei Christine; Maher, Chris G; Pearson, Adam M; Peul, Wilco C; Schoene, Mark L; Turk, Dennis C; van Tulder, Maurits W; Ostelo, Raymond W

    2015-06-01

    Inconsistent reporting of outcomes in clinical trials of patients with non-specific low back pain (NSLBP) hinders comparison of findings and the reliability of systematic reviews. A core outcome set (COS) can address this issue as it defines a minimum set of outcomes that should be reported in all clinical trials. In 1998, Deyo et al. recommended a standardized set of outcomes for LBP clinical research. The aim of this study was to update these recommendations by determining which outcome domains should be included in a COS for clinical trials in NSLBP. An International Steering Committee established the methodology to develop this COS. The OMERACT Filter 2.0 framework was used to draw a list of potential core domains that were presented in a Delphi study. Researchers, care providers and patients were invited to participate in three Delphi rounds and were asked to judge which domains were core. A priori criteria for consensus were established before each round and were analysed together with arguments provided by panellists on importance, overlap, aggregation and/or addition of potential core domains. The Steering Committee discussed the final results and made final decisions. A set of 280 experts was invited to participate in the Delphi; response rates in the three rounds were 52, 50 and 45%. Of 41 potential core domains presented in the first round, 13 had sufficient support to be presented for rating in the third round. Overall consensus was reached for the inclusion of three domains in this COS: 'physical functioning', 'pain intensity' and 'health-related quality of life'. Consensus on 'physical functioning' and 'pain intensity' was consistent across all stakeholders, 'health-related quality of life' was not supported by the patients, and all the other domains were not supported by two or more groups of stakeholders. Weighting all possible argumentations, the Steering Committee decided to include in the COS the three domains that reached overall consensus and

  7. Identification of preliminary core outcome domains for communication about childhood vaccination: An online Delphi survey.

    Science.gov (United States)

    Kaufman, Jessica; Ryan, Rebecca; Lewin, Simon; Bosch-Capblanch, Xavier; Glenton, Claire; Cliff, Julie; Oyo-Ita, Angela; Muloliwa, Artur Manuel; Oku, Afiong; Ames, Heather; Rada, Gabriel; Cartier, Yuri; Hill, Sophie

    2017-08-20

    Communication interventions for childhood vaccination are promising strategies to address vaccine hesitancy, but current research is limited by the outcomes measured. Most studies measure only vaccination-related outcomes, with minimal consideration of vaccine hesitancy-relevant intermediate outcomes. This impedes understanding of which interventions or elements are effective. It is also unknown which outcomes are important to the range of stakeholders affected by vaccine hesitancy. Outcome selection shapes the evidence base, informing future interventions and trials, and should reflect stakeholder priorities. Therefore, our aim was to identify which outcome domains (i.e. broad outcome categories) are most important to different stakeholders, identifying preliminary core outcome domains to inform evaluation of three common vaccination communication types: (i) communication to inform or educate, (ii) remind or recall, and (iii) enhance community ownership. We conducted a two-stage online Delphi survey, involving four stakeholder groups: parents or community members, healthcare providers, researchers, and government or non-governmental organisation representatives. Participants rated the importance of eight outcome domains for each of the three communication types. They also rated specific outcomes within one domain ("attitudes or beliefs") and provided feedback about the survey. Collectively, stakeholder groups prioritised outcome domains differently when considering the effects of different communication types. For communication that aims to (i) inform or educate, the most important outcome domain is "knowledge or understanding"; for (ii) reminder communication, "vaccination status and behaviours"; and for (iii) community engagement communication, "community participation". All stakeholder groups rated most outcome domains as very important or critical. The highest rated specific outcome within the "attitudes or beliefs" domain was "trust". This Delphi survey

  8. The Role of Factor XIa (FXIa) Catalytic Domain Exosite Residues in Substrate Catalysis and Inhibition by the Kunitz Protease Inhibitor Domain of Protease Nexin 2*

    Science.gov (United States)

    Su, Ya-Chi; Miller, Tara N.; Navaneetham, Duraiswamy; Schoonmaker, Robert T.; Sinha, Dipali; Walsh, Peter N.

    2011-01-01

    To select residues in coagulation factor XIa (FXIa) potentially important for substrate and inhibitor interactions, we examined the crystal structure of the complex between the catalytic domain of FXIa and the Kunitz protease inhibitor (KPI) domain of a physiologically relevant FXIa inhibitor, protease nexin 2 (PN2). Six FXIa catalytic domain residues (Glu98, Tyr143, Ile151, Arg3704, Lys192, and Tyr5901) were subjected to mutational analysis to investigate the molecular interactions between FXIa and the small synthetic substrate (S-2366), the macromolecular substrate (factor IX (FIX)) and inhibitor PN2KPI. Analysis of all six Ala mutants demonstrated normal Km values for S-2366 hydrolysis, indicating normal substrate binding compared with plasma FXIa; however, all except E98A and K192A had impaired values of kcat for S-2366 hydrolysis. All six Ala mutants displayed deficient kcat values for FIX hydrolysis, and all were inhibited by PN2KPI with normal values of Ki except for K192A, and Y5901A, which displayed increased values of Ki. The integrity of the S1 binding site residue, Asp189, utilizing p-aminobenzamidine, was intact for all FXIa mutants. Thus, whereas all six residues are essential for catalysis of the macromolecular substrate (FIX), only four (Tyr143, Ile151, Arg3704, and Tyr5901) are important for S-2366 hydrolysis; Glu98 and Lys192 are essential for FIX but not S-2366 hydrolysis; and Lys192 and Tyr5901 are required for both inhibitor and macromolecular substrate interactions. PMID:21778227

  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

    , and stiffness scores averaged ≥ 2 times higher (2 of 11 points) in flaring individuals. Correlations between flare domains and corresponding legacy instruments were obtained: r = 0.46 to 0.93. A combined definition (patient report of flare and 28-joint Disease Activity Score increase) was evaluated in 2 other...... provided input for stiffness, self-management, contextual factors, and measurement considerations. RESULTS: Flare data from 501 patients in an observational study indicated 39% were in flare, with mean (SD) severity of 6.0 (2.6) and 55% lasting > 14 days. Pain, physical function, fatigue, participation...

  10. N- vs. C-Domain Selectivity of Catalytic Inactivation of Human Angiotensin Converting Enzyme by Lisinopril-Coupled Transition Metal Chelates

    Science.gov (United States)

    Hocharoen, Lalintip; Joyner, Jeff C.; Cowan, J. A.

    2014-01-01

    The N- and C-terminal domains of human somatic Angiotensin I Converting Enzyme (sACE-1) demonstrate distinct physiological functions, with resulting interest in the development of domain-selective inhibitors for specific therapeutic applications. Herein, the activity of lisinopril-coupled transition metal chelates were tested for both reversible binding and irreversible catalytic inactivation of sACE-1. C/N domain binding selectivity ratios ranged from 1 to 350, while rates of irreversible catalytic inactivation of the N- and C-domains were found to be significantly greater for the N-domain, suggesting a more optimal orientation of the M-chelate-lisinopril complexes within the active site of the N-domain of sACE-1. Finally, the combined effect of binding selectivity and inactivation selectivity was assessed for each catalyst (double-filter selectivity factors), and several catalysts were found to cause domain-selective catalytic inactivation. The results of this study demonstrate the ability to optimize the target selectivity of catalytic metallopeptides through both binding and orientation factors (double-filter effect). PMID:24228790

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

    DEFF Research Database (Denmark)

    Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan

    2015-01-01

    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...

  12. 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 measuring shared decision making in intervention studies in adults with osteoarthritis (OA), from the perspectives of patients, health professionals, and researchers. METHODS: We followed the OMERACT Filter 2.0 method to develop a draft core domain set by (1) forming an OMERACT working group; (2) conducting...... a review of domains of shared decision making; and (3) obtaining opinions of all those involved using a modified nominal group process held at a session activity at the OMERACT 12 meeting. RESULTS: In all, 26 people from Europe, North America, and Australia, including 5 patient research partners...

  13. Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase.

    Science.gov (United States)

    Jana, Biman; Adkar, Bharat V; Biswas, Rajib; Bagchi, Biman

    2011-01-21

    The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations.

  14. The core domain as the force sensor of the yeast mechanosensitive TRP channel.

    Science.gov (United States)

    Su, Zhenwei; Anishkin, Andriy; Kung, Ching; Saimi, Yoshiro

    2011-12-01

    Stretch-activated conductances are commonly encountered in careful electric recordings. Those of known proteins (TRP, MscL, MscS, K(2p), Kv, etc.) all share a core, which houses the ion pathway and the gate, but no recognizable force-sensing domain. Like animal TRPs, the yeast TRPY1 is polymodal, activated by stretch force, Ca(2+), etc. To test whether its S5-S6 core senses the stretch force, we tried to uncouple it from the peripheral domains by strategic peptide insertions to block the covalent core-periphery interactions. Insertion of long unstructured peptides should distort, if not disrupt, protein structures that transmit force. Such insertions between S6 and the C-terminal tail largely removed Ca(2+) activation, showing their effectiveness. However, such insertions as well as those between S5 and the N-terminal region, which includes S1-S4, did not significantly alter mechanosensitivity. Even insertions at both locations flanking the S5-S6 core did not much alter mechanosensitivity. Tryptophan scanning mutations in S5 were also constructed to perturb possible noncovalent core-periphery contacts. The testable tryptophan mutations also have little or no effects on mechanosensitivity. Boltzmann fits of the wild-type force-response curves agree with a structural homology model for a stretch-induced core expansion of ~2 nm(2) upon opening. We hypothesize that membrane tension pulls on S5-S6, expanding the core and opening the TRPY1 gate. The core being the major force sensor offers the simplest, though not the only, explanation of why so many channels of disparate designs are mechanically sensitive. Compared with the bacterial MscL, TRPY1 is much less sensitive to force, befitting a polymodal channel that relies on multiple stimuli.

  15. Transforming p21 ras protein: flexibility in the major variable region linking the catalytic and membrane-anchoring domains

    DEFF Research Database (Denmark)

    Willumsen, B M; Papageorge, A G; Hubbert, N

    1985-01-01

    or increasing it to 50 amino acids has relatively little effect on the capacity of the gene to induce morphological transformation of NIH 3T3 cells. Assays of GTP binding, GTPase and autophosphorylating activities of such mutant v-rasH-encoded proteins synthesized in bacteria indicated that the sequences...... that is required for post-translational processing, membrane localization and transforming activity of the proteins. We have now used the viral oncogene (v-rasH) of Harvey sarcoma virus to study the major variable region by deleting or duplicating parts of the gene. Reducing this region to five amino acids...... that encode these biochemical activities are located upstream from the major variable region. In the context of transformation, we propose that the region of sequence heterogeneity serves principally to connect the N-terminal catalytic domain with amino acids at the C terminus that are required to anchor...

  16. Mixed first- and second-order transport method using domain decomposition techniques for reactor core calculations

    International Nuclear Information System (INIS)

    Girardi, E.; Ruggieri, J.M.

    2003-01-01

    The aim of this paper is to present the last developments made on a domain decomposition method applied to reactor core calculations. In this method, two kind of balance equation with two different numerical methods dealing with two different unknowns are coupled. In the first part the two balance transport equations (first order and second order one) are presented with the corresponding following numerical methods: Variational Nodal Method and Discrete Ordinate Nodal Method. In the second part, the Multi-Method/Multi-Domain algorithm is introduced by applying the Schwarz domain decomposition to the multigroup eigenvalue problem of the transport equation. The resulting algorithm is then provided. The projection operators used to coupled the two methods are detailed in the last part of the paper. Finally some preliminary numerical applications on benchmarks are given showing encouraging results. (authors)

  17. Mechanism of Diphtheria Toxin Catalytic Domain Delivery to the Eukaryotic Cell Cytosol and the Cellular Factors that Directly Participate in the Process

    Science.gov (United States)

    Murphy, John R.

    2011-01-01

    Research on diphtheria and anthrax toxins over the past three decades has culminated in a detailed understanding of their structure function relationships (e.g., catalytic (C), transmembrane (T), and receptor binding (R) domains), as well as the identification of their eukaryotic cell surface receptor, an understanding of the molecular events leading to the receptor-mediated internalization of the toxin into an endosomal compartment, and the pH triggered conformational changes required for pore formation in the vesicle membrane. Recently, a major research effort has been focused on the development of a detailed understanding of the molecular interactions between each of these toxins and eukaryotic cell factors that play an essential role in the efficient translocation of their respective catalytic domains through the trans-endosomal vesicle membrane pore and delivery into the cell cytosol. In this review, I shall focus on recent findings that have led to a more detailed understanding of the mechanism by which the diphtheria toxin catalytic domain is delivered to the eukaryotic cell cytosol. While much work remains, it is becoming increasingly clear that the entry process is facilitated by specific interactions with a number of cellular factors in an ordered sequential fashion. In addition, since diphtheria, anthrax lethal factor and anthrax edema factor all carry multiple coatomer I complex binding motifs and COPI complex has been shown to play an essential role in entry process, it is likely that the initial steps in catalytic domain entry of these divergent toxins follow a common mechanism. PMID:22069710

  18. Accumulating Data to Optimally Predict Obesity Treatment (ADOPT) Core Measures: Psychosocial Domain.

    Science.gov (United States)

    Sutin, Angelina R; Boutelle, Kerri; Czajkowski, Susan M; Epel, Elissa S; Green, Paige A; Hunter, Christine M; Rice, Elise L; Williams, David M; Young-Hyman, Deborah; Rothman, Alexander J

    2018-04-01

    Within the Accumulating Data to Optimally Predict obesity Treatment (ADOPT) Core Measures Project, the psychosocial domain addresses how psychosocial processes underlie the influence of obesity treatment strategies on weight loss and weight maintenance. The subgroup for the psychosocial domain identified an initial list of high-priority constructs and measures that ranged from relatively stable characteristics about the person (cognitive function, personality) to dynamic characteristics that may change over time (motivation, affect). This paper describes (a) how the psychosocial domain fits into the broader model of weight loss and weight maintenance as conceptualized by ADOPT; (b) the guiding principles used to select constructs and measures for recommendation; (c) the high-priority constructs recommended for inclusion; (d) domain-specific issues for advancing the science; and (e) recommendations for future research. The inclusion of similar measures across trials will help to better identify how psychosocial factors mediate and moderate the weight loss and weight maintenance process, facilitate research into dynamic interactions with factors in the other ADOPT domains, and ultimately improve the design and delivery of effective interventions. © 2018 The Obesity Society.

  19. Intracellular Catalytic Domain of Symbiosis Receptor Kinase Hyperactivates Spontaneous Nodulation in Absence of Rhizobia1[W

    Science.gov (United States)

    Saha, Sudip; Dutta, Ayan; Bhattacharya, Avisek; DasGupta, Maitrayee

    2014-01-01

    Symbiosis Receptor Kinase (SYMRK), a member of the Nod factor signaling pathway, is indispensible for both nodule organogenesis and intracellular colonization of symbionts in rhizobia-legume symbiosis. Here, we show that the intracellular kinase domain of a SYMRK (SYMRK-kd) but not its inactive or full-length version leads to hyperactivation of the nodule organogenic program in Medicago truncatula TR25 (symrk knockout mutant) in the absence of rhizobia. Spontaneous nodulation in TR25/SYMRK-kd was 6-fold higher than rhizobia-induced nodulation in TR25/SYMRK roots. The merged clusters of spontaneous nodules indicated that TR25 roots in the presence of SYMRK-kd have overcome the control over both nodule numbers and their spatial position. In the presence of rhizobia, SYMRK-kd could rescue the epidermal infection processes in TR25, but colonization of symbionts in the nodule interior was significantly compromised. In summary, ligand-independent deregulated activation of SYMRK hyperactivates nodule organogenesis in the absence of rhizobia, but its ectodomain is required for proper symbiont colonization. PMID:25304318

  20. Accumulating Data to Optimally Predict Obesity Treatment (ADOPT) Core Measures: Behavioral Domain.

    Science.gov (United States)

    Lytle, Leslie A; Nicastro, Holly L; Roberts, Susan B; Evans, Mary; Jakicic, John M; Laposky, Aaron D; Loria, Catherine M

    2018-04-01

    The ability to identify and measure behaviors that are related to weight loss and the prevention of weight regain is crucial to understanding the variability in response to obesity treatment and the development of tailored treatments. The overarching goal of the Accumulating Data to Optimally Predict obesity Treatment (ADOPT) Core Measures Project is to provide obesity researchers with guidance on a set of constructs and measures that are related to weight control and that span and integrate obesity-related behavioral, biological, environmental, and psychosocial domains. This article describes how the behavioral domain subgroup identified the initial list of high-priority constructs and measures to be included, and it describes practical considerations for assessing the following four behavioral areas: eating, activity, sleep, and self-monitoring of weight. Challenges and considerations for advancing the science related to weight loss and maintenance behaviors are also discussed. Assessing a set of core behavioral measures in combination with those from other ADOPT domains is critical to improve our understanding of individual variability in response to adult obesity treatment. The selection of behavioral measures is based on the current science, although there continues to be much work needed in this field. © 2018 The Obesity Society.

  1. 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)

    Littler, Dene R.; Walker, John R.; Davis, Tara; Wybenga-Groot, Leanne E.; Finerty, Patrick J. Jr; Newman, Elena; Mackenzie, Farell; Dhe-Paganon, Sirano

    2010-01-01

    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

  2. Crystal structures of wild-type Trichoderma reesei Cel7A catalytic domain in open and closed states

    Energy Technology Data Exchange (ETDEWEB)

    Bodenheimer, Annette M. [Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh NC USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, TN USA; Meilleur, Flora [Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh NC USA; Neutron Sciences Directorate, Oak Ridge National Laboratory, TN USA

    2016-11-07

    Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

  3. Functional analysis of TMLH variants and definition of domains required for catalytic activity and mitochondrial targeting.

    Science.gov (United States)

    Monfregola, Jlenia; Cevenini, Armando; Terracciano, Antonio; van Vlies, Naomi; Arbucci, Salvatore; Wanders, Ronald J A; D'Urso, Michele; Vaz, Frédéric M; Ursini, Matilde Valeria

    2005-09-01

    epsilon-N-Trimethyllysine hydroxylase (TMLH) (EC 1.14.11.8) is a non-heme-ferrous iron hydroxylase, Fe(++) and 2-oxoglutarate (2OG) dependent, catalyzing the first of four enzymatic reactions of the highly conserved carnitine biosynthetic pathway. Otherwise from all the other enzymes of carnitine biosynthesis, TMLH was found to be associated to the mitochondrial fraction. We here report molecular cloning of two alternative spliced forms of TMLH, which appear ubiquitously expressed in human adult and fetal tissues. The deduced proteins are designated TMLH-a and TMLH-b, and contain 421 and 399 amino acids, respectively. They share the first N-terminal 332 amino acids, including a mitochondrial targeting signal, but diverge at the C-terminal end. TMLH-a and TMLH-b exogenous expression in COS-1 cells shows that the first 15 amino acids are necessary and sufficient for mitochondrial import. Furthermore, comparative evolutionary analysis of the C-terminal portion of TMLH-a identifies a conserved domain characterized by a key triad of residues, His242-Glu244-His389 predicted to bind 2OG end. This sequence is conserved in the TMLH enzyme from all species but is partially substituted by a unique sequence in the TMLH-b variant. Indeed, TMLH-b is not functional by itself as well as a TMLH-H389L mutant produced by site directed mutagenesis. As great interest, we found that TMLH-b and TMLH-H389L, individually co-expressed with TMLH-a in COS-1 cells, negatively affect TMLH activity. Therefore, our studies on the TMLH alternative form provide relevant novel information, first that the C-terminal region of TMLH contains the main determinants for its enzymatic activity including a key H389 residue, and second that TMLH-b could act as a crucial physiological negative regulator of TMLH. Copyright 2005 Wiley-Liss, Inc.

  4. A chitinase with two catalytic domains is required for organization of the cuticular extracellular matrix of a beetle.

    Directory of Open Access Journals (Sweden)

    Mi Young Noh

    2018-03-01

    Full Text Available Insect cuticle or exoskeleton is an extracellular matrix formed primarily from two different structural biopolymers, chitin and protein. During each molt cycle, a new cuticle is deposited simultaneously with degradation of the inner part of the chitinous procuticle of the overlying old exoskeleton by molting fluid enzymes including epidermal chitinases. In this study we report a novel role for an epidermal endochitinase containing two catalytic domains, TcCHT7, from the red flour beetle, Tribolium castaneum, in organizing chitin in the newly forming cuticle rather than in degrading chitin present in the prior one. Recombinant TcCHT7 expressed in insect cells is membrane-bound and capable of hydrolyzing an extracellular chitin substrate, whereas in vivo, this enzyme is also released from the plasma membrane and co-localizes with chitin in the entire procuticle. RNAi of TcCHT7 reveals that this enzyme is nonessential for any type of molt or degradation of the chitinous matrix in the old cuticle. In contrast, TcCHT7 is required for maintaining the integrity of the cuticle as a compact structure of alternating electron-dense and electron-lucent laminae. There is a reduction in thickness of elytral and leg cuticles after RNAi for TcCHT7. TcCHT7 is also required for formation of properly oriented long chitin fibers inside pore canals that are vertically oriented columnar structures, which contribute to the mechanical strength of a light-weight, yet rigid, adult cuticle. The conservation of CHT7-like proteins harboring such a unique domain configuration among many insect and other arthropod species indicates a critical role for the group III class of chitinases in the higher ordered organization of chitin fibers for development of the structural integrity of many invertebrate exoskeletons.

  5. 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

    2010-09-01

    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.

  6. Specificity and versatility of substrate binding sites in four catalytic domains of human N-terminal acetyltransferases.

    Directory of Open Access Journals (Sweden)

    Cédric Grauffel

    Full Text Available Nt-acetylation is among the most common protein modifications in eukaryotes. Although thought for a long time to protect proteins from degradation, the role of Nt-acetylation is still debated. It is catalyzed by enzymes called N-terminal acetyltransferases (NATs. In eukaryotes, several NATs, composed of at least one catalytic domain, target different substrates based on their N-terminal sequences. In order to better understand the substrate specificity of human NATs, we investigated in silico the enzyme-substrate interactions in four catalytic subunits of human NATs (Naa10p, Naa20p, Naa30p and Naa50p. To date hNaa50p is the only human subunit for which X-ray structures are available. We used the structure of the ternary hNaa50p/AcCoA/MLG complex and a structural model of hNaa10p as a starting point for multiple molecular dynamics simulations of hNaa50p/AcCoA/substrate (substrate=MLG, EEE, MKG, hNaa10p/AcCoA/substrate (substrate=MLG, EEE. Nine alanine point-mutants of the hNaa50p/AcCoA/MLG complex were also simulated. Homology models of hNaa20p and hNaa30p were built and compared to hNaa50p and hNaa10p. The simulations of hNaa50p/AcCoA/MLG reproduce the interactions revealed by the X-ray data. We observed strong hydrogen bonds between MLG and tyrosines 31, 138 and 139. Yet the tyrosines interacting with the substrate's backbone suggest that their role in specificity is limited. This is confirmed by the simulations of hNaa50p/AcCoA/EEE and hNaa10p/AcCoA/MLG, where these hydrogen bonds are still observed. Moreover these tyrosines are all conserved in hNaa20p and hNaa30p. Other amino acids tune the specificity of the S1' sites that is different for hNaa10p (acidic, hNaa20p (hydrophobic/basic, hNaa30p (basic and hNaa50p (hydrophobic. We also observe dynamic correlation between the ligand binding site and helix [Formula: see text] that tightens under substrate binding. Finally, by comparing the four structures we propose maps of the peptide

  7. Amyloid cores in prion domains: Key regulators for prion conformational conversion.

    Science.gov (United States)

    Fernández, María Rosario; Batlle, Cristina; Gil-García, Marcos; Ventura, Salvador

    2017-01-02

    Despite the significant efforts devoted to decipher the particular protein features that encode for a prion or prion-like behavior, they are still poorly understood. The well-characterized yeast prions constitute an ideal model system to address this question, because, in these proteins, the prion activity can be univocally assigned to a specific region of their sequence, known as the prion forming domain (PFD). These PFDs are intrinsically disordered, relatively long and, in many cases, of low complexity, being enriched in glutamine/asparagine residues. Computational analyses have identified a significant number of proteins having similar domains in the human proteome. The compositional bias of these regions plays an important role in the transition of the prions to the amyloid state. However, it is difficult to explain how composition alone can account for the formation of specific contacts that position correctly PFDs and provide the enthalpic force to compensate for the large entropic cost of immobilizing these domains in the initial assemblies. We have hypothesized that short, sequence-specific, amyloid cores embedded in PFDs can perform these functions and, accordingly, act as preferential nucleation centers in both spontaneous and seeded aggregation. We have shown that the implementation of this concept in a prediction algorithm allows to score the prion propensities of putative PFDs with high accuracy. Recently, we have provided experimental evidence for the existence of such amyloid cores in the PFDs of Sup35, Ure2, Swi1, and Mot3 yeast prions. The fibrils formed by these short stretches may recognize and promote the aggregation of the complete proteins inside cells, being thus a promising tool for targeted protein inactivation.

  8. Ethics in Knowledge Organization: Two Conferences Point to a New Core in the Domain

    Directory of Open Access Journals (Sweden)

    Richard P. Smiraglia

    2015-01-01

    Full Text Available http://dx.doi.org/10.5007/1518-2924.2015v20nesp1p1 Two conferences called "Ethics in Information Organization (EIO," held in 2009 and 2013, brought together practitioners and scholars in knowledge organization (KO to discuss ethical decision-making for the organization of knowledge. Traditionally the notion of ethics as a component of knowledge organization has occupied a sort of background position. Concepts of cultural warrant clash with concepts of literary warrant to produce harmful knowledge organization systems. Here tools of domain analytical visualization are applied to the two EIO conferences to demonstrate the potential intension of ethics for KO. Co-word analysis helps to visualize the thematic core in the most frequently used terms: user, ethical, knowledge, national, description, and access. There clearly is a meta-level trajectory incorporating ethics and the user, while the intension includes all applied approaches to KO as well as strong recognition of national, regional, and social cultural identities. Another approach to domain analysis is to examine the social semantics (by analyzing the public record of discourse through citation patterns. Author co-citation analysis shows work anchored in the basic theoretical premises of KO, but also bringing ideas from outside the domain to bear on the problems of objective violence. A network visualization shows how the work on ethics in KO is based on the core principles of KO, but relies also on evidence from librarianship and philosophical guidance to bring forward the issues surrounding objective violence in KOS. The authors contributing to this small pair of conferences have laid out a pathway for expanding understanding of the role of ethics in KO.

  9. Centeredness Theory: Understanding and Measuring Well-Being Across Core Life Domains

    Directory of Open Access Journals (Sweden)

    Zephyr T. Bloch-Jorgensen

    2018-05-01

    Full Text Available Background: Centeredness Theory (CT is proposed as a new mental health paradigm that focuses on well-being at a systems-level, across the core life domains of the self, the family unit, relationships, community, and work. The current studies aimed to validate the psychometric properties of a new scale that measures CT against existing well-being and mental health measures.Methods: Study 1 included 488 anonymous online respondents (46% females, 28% males, 25% unknown with median age between 31 and 35 years across 38 countries who completed the CT scale. Study 2 included 49 first-year psychology students (90% females, mean age of 19 years from Sydney Australia that completed the CT scale and other well-being and mental health questionnaires at baseline and 2-weeks follow-up.Results: Exploratory and confirmatory factor analyses resulted in a refined 60-item CT scale with five domains, each with four sub-domains. The CT scale demonstrated good internal consistency reliability and test-retest reliability, and showed evidence of convergent validity against other well-being measures (e.g., COMPAS-W Wellbeing Scale, SWLS scale, and Ryff's Psychological Well-being scale.Conclusions: The CT scale appears to be a reliable measure of well-being at a systems-level. Future studies need to confirm these findings in larger heterogeneous samples.

  10. Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes.

    Science.gov (United States)

    Zhu, Wenyou; Liu, Yongjun; Ling, Baoping

    2015-08-25

    Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).

  11. Factor VII deficiency: Unveiling the cellular and molecular mechanisms underlying three model alterations of the enzyme catalytic domain.

    Science.gov (United States)

    Chollet, Maria Eugenia; Andersen, Elisabeth; Skarpen, Ellen; Myklebust, Christiane F; Koehler, Christian; Morth, Jens Preben; Chuansumrit, Ampaiwan; Pinotti, Mirko; Bernardi, Francesco; Thiede, Bernd; Sandset, Per Morten; Skretting, Grethe

    2018-03-01

    Activated factor (F) VII is a vitamin K-dependent glycoprotein that initiates blood coagulation upon interaction with tissue factor. FVII deficiency is the most common of the rare congenital bleeding disorders. While the mutational pattern has been extensively characterized, the pathogenic molecular mechanisms of mutations, particularly at the intracellular level, have been poorly defined. Here, we aimed at elucidating the mechanisms underlying altered FVII biosynthesis in the presence of three mutation types in the catalytic domain: a missense change, a microdeletion and a frameshift/elongation, associated with severe or moderate to severe phenotypes. Using CHO-K1 cells transiently transfected with expression vectors containing the wild-type FVII cDNA (FVIIwt) or harboring the p.I289del, p.G420V or p.A354V-p.P464Hfs mutations, we found that the secretion of the FVII mutants was severely decreased compared to FVIIwt. The synthesis rate of the mutants was slower than the FVIIwt and delayed, and no degradation of the FVII mutants by proteasomes, lysosomes or cysteine proteases was observed. Confocal immunofluorescence microscopy studies showed that FVII variants were localized into the endoplasmic reticulum (ER) but were not detectable within the Golgi apparatus. These findings suggested that a common pathogenic mechanism, possibly a defective folding of the mutant proteins, was triggered by the FVII mutations. The misfolded state led to impaired trafficking of these proteins causing ER retention, which would explain the low to very low FVII plasma levels observed in patients carrying these mutations. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 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

    2016-06-14

    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.

  13. Cooperation between Catalytic and DNA-binding Domains Enhances Thermostability and Supports DNA Synthesis at Higher Temperatures by Thermostable DNA Polymerases

    Science.gov (United States)

    Pavlov, Andrey R.; Pavlova, Nadejda V.; Kozyavkin, Sergei A.; Slesarev, Alexei I.

    2012-01-01

    We have previously introduced a general kinetic approach for comparative study of processivity, thermostability, and resistance to inhibitors of DNA polymerases (Pavlov et. al., (2002) Proc. Natl. Acad. Sci. USA 99, 13510–13515). The proposed method was successfully applied to characterize hybrid DNA polymerases created by fusing catalytic DNA polymerase domains with various non-specific DNA binding domains. Here we use the developed kinetic analysis to assess basic parameters of DNA elongation by DNA polymerases and to further study the interdomain interactions in both previously constructed and new chimeric DNA polymerases. We show that connecting Helix-hairpin-Helix (HhH) domains to catalytic polymerase domains can increase thermostability, not only of DNA polymerases from extremely thermophilic species, but also of the enzyme from a faculatative thermophilic bacterium Bacillus stearothermophilus. We also demonstrate that addition of TopoV HhH domains extends efficient DNA synthesis by chimerical polymerases up to 105°C by maintaining processivity of DNA synthesis at high temperatures. We also found that reversible high-temperature structural transitions in DNA polymerases decrease the rates of binding of these enzymes to the templates. Furthermore, activation energies and pre-exponential factors of the Arrhenius equation suggest that the mechanism of electrostatic enhancement of diffusion-controlled association plays a minor role in binding templates to DNA polymerases. PMID:22320201

  14. 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 single and three-phase transformers is also presented. This analysis leads to the conclusion that the method can be applied for modelling nonlinearities of three-phase autotransformers....

  15. 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.

  16. Domain Decomposition strategy for pin-wise full-core Monte Carlo depletion calculation with the reactor Monte Carlo Code

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Jingang; Wang, Kan; Qiu, Yishu [Dept. of Engineering Physics, LiuQing Building, Tsinghua University, Beijing (China); Chai, Xiao Ming; Qiang, Sheng Long [Science and Technology on Reactor System Design Technology Laboratory, Nuclear Power Institute of China, Chengdu (China)

    2016-06-15

    Because of prohibitive data storage requirements in large-scale simulations, the memory problem is an obstacle for Monte Carlo (MC) codes in accomplishing pin-wise three-dimensional (3D) full-core calculations, particularly for whole-core depletion analyses. Various kinds of data are evaluated and quantificational total memory requirements are analyzed based on the Reactor Monte Carlo (RMC) code, showing that tally data, material data, and isotope densities in depletion are three major parts of memory storage. The domain decomposition method is investigated as a means of saving memory, by dividing spatial geometry into domains that are simulated separately by parallel processors. For the validity of particle tracking during transport simulations, particles need to be communicated between domains. In consideration of efficiency, an asynchronous particle communication algorithm is designed and implemented. Furthermore, we couple the domain decomposition method with MC burnup process, under a strategy of utilizing consistent domain partition in both transport and depletion modules. A numerical test of 3D full-core burnup calculations is carried out, indicating that the RMC code, with the domain decomposition method, is capable of pin-wise full-core burnup calculations with millions of depletion regions.

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

    International Nuclear Information System (INIS)

    Haverkort, Maurits W.

    2016-01-01

    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. (paper)

  18. Accumulating Data to Optimally Predict Obesity Treatment (ADOPT) Core Measures: Environmental Domain.

    Science.gov (United States)

    Saelens, Brian E; Arteaga, S Sonia; Berrigan, David; Ballard, Rachel M; Gorin, Amy A; Powell-Wiley, Tiffany M; Pratt, Charlotte; Reedy, Jill; Zenk, Shannon N

    2018-04-01

    There is growing interest in how environment is related to adults' weight and activity and eating behaviors. However, little is known about whether environmental factors are related to the individual variability seen in adults' intentional weight loss or maintenance outcomes. The environmental domain subgroup of the Accumulating Data to Optimally Predict obesity Treatment (ADOPT) Core Measures Project sought to identify a parsimonious set of objective and perceived neighborhood and social environment constructs and corresponding measures to include in the assessment of response to adult weight-loss treatment. Starting with the home address, the environmental domain subgroup recommended for inclusion in future weight-loss or maintenance studies constructs and measures related to walkability, perceived land use mix, food outlet accessibility (perceived and objective), perceived food availability, socioeconomics, and crime-related safety (perceived and objective) to characterize the home neighborhood environment. The subgroup also recommended constructs and measures related to social norms (perceived and objective) and perceived support to characterize an individual's social environment. The 12 neighborhood and social environment constructs and corresponding measures provide a succinct and comprehensive set to allow for more systematic examination of the impact of environment on adults' weight loss and maintenance. © 2018 The Obesity Society.

  19. Liquid-phase pulsed laser ablation synthesis of graphitized carbon-encapsulated palladium core-shell nanospheres for catalytic reduction of nitrobenzene to aniline

    Science.gov (United States)

    Kim, Yu-jin; Ma, Rory; Reddy, D. Amaranatha; Kim, Tae Kyu

    2015-12-01

    Graphitized carbon-encapsulated palladium (Pd) core-shell nanospheres were produced via pulsed laser ablation of a solid Pd foil target submerged in acetonitrile. The microstructural features and optical properties of these nanospheres were characterized via high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and UV-visible spectroscopy. Microstructural analysis indicated that the core-shell nanostructures consisted of single-crystalline cubic metallic Pd spheres that serve as the core material, over which graphitized carbon was anchored as a heterogeneous shell. The absorbance spectrum of the synthesized nanostructures exhibited a broad (absorption) band at ∼264 nm; this band corresponded to the typical inter-band transition of a metallic system and resulted possibly from the absorbance of the ionic Pd2+. The catalytic properties of the Pd and Pd@C core-shell nanostructures were investigated using the reduction of nitrobenzene to aniline by an excess amount of NaBH4 in an aqueous solution at room temperature, as a model reaction. Owing to the graphitized carbon-layered structure and the high specific surface area, the resulting Pd@C nanostructures exhibited higher conversion efficiencies than their bare Pd counterparts. In fact, the layered structure provided access to the surface of the Pd nanostructures for the hydrogenation reaction, owing to the synergistic effect between graphitized carbon and the nanostructures. Their unique structure and excellent catalytic performance render Pd@C core-shell nanostructures highly promising candidates for catalysis applications.

  20. Toward the Development of a Core Set of Outcome Domains to Assess Shared Decision-making Interventions in Rheumatology

    DEFF Research Database (Denmark)

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

    2017-01-01

    OBJECTIVE: The aim of this Outcome Measures in Rheumatology (OMERACT) Working Group was to determine the core set of outcome domains and subdomains for measuring the effectiveness of shared decision-making (SDM) interventions in rheumatology clinical trials. METHODS: Following the OMERACT Filter 2.......0, and based on a previous literature review of SDM outcome domains and a nominal group process at OMERACT 2014, (1) an online Delphi survey was conducted to gather feedback on the draft core set and refine its domains and subdomains, and (2) a workshop was held at the OMERACT 2016 meeting to gain consensus...... ranged from 83% to 100% of respondents). At OMERACT 2016, only 8% of the 96 attendees were patients/caregivers. Despite initial votes of support in breakout groups, there was insufficient comfort about the conceptualization of these 7 domains and 17 subdomains for these to be endorsed at OMERACT 2016...

  1. Modeling of absorption and scattering properties of core -shell nanoparticles for application as nanoantenna in optical domain

    International Nuclear Information System (INIS)

    Devi, Jutika; Datta, Pranayee; Saikia, Rashmi

    2016-01-01

    The present paper describes the study of core-shell nanoparticles for application as nanoantenna in the optical domain. To obtain the absorption and extinction efficiencies as well as the angular distribution of the far field radiation pattern and the resonance wavelengths for these metal-dielectric, dielectric-metal and metal-metal core-shell nanoparticles in optical domain, we have used Finite Element Method based COMSOL Multiphysics Software and Mie Theory. From the comparative study of the extinction efficiencies of core-shell nanoparticles of different materials, it is found that for silica - gold core - shell nanoparticles, the resonant wavelength is greater than that of the gold - silver, silver-gold and gold-silica core - shell nanoparticles and also the radiation pattern of the silica-gold core-shell nanoparticle is the most suitable one from the point of view of directivity. The dielectric functions of the core and shell material as well as of the embedded matrix are extremely important and plays a very major role to tune the directivity and resonance wavelength. Such highly controllable parameters of the dielectric - metal core - shell nanoparticles make them suitable for efficient coupling of optical radiation into nanoscale structures for a broad range of applications in the field of communications. (paper)

  2. Modeling of absorption and scattering properties of core -shell nanoparticles for application as nanoantenna in optical domain

    Science.gov (United States)

    Devi, Jutika; Saikia, Rashmi; Datta, Pranayee

    2016-10-01

    The present paper describes the study of core-shell nanoparticles for application as nanoantenna in the optical domain. To obtain the absorption and extinction efficiencies as well as the angular distribution of the far field radiation pattern and the resonance wavelengths for these metal-dielectric, dielectric-metal and metal-metal core-shell nanoparticles in optical domain, we have used Finite Element Method based COMSOL Multiphysics Software and Mie Theory. From the comparative study of the extinction efficiencies of core-shell nanoparticles of different materials, it is found that for silica - gold core - shell nanoparticles, the resonant wavelength is greater than that of the gold - silver, silver-gold and gold-silica core - shell nanoparticles and also the radiation pattern of the silica-gold core-shell nanoparticle is the most suitable one from the point of view of directivity. The dielectric functions of the core and shell material as well as of the embedded matrix are extremely important and plays a very major role to tune the directivity and resonance wavelength. Such highly controllable parameters of the dielectric - metal core - shell nanoparticles make them suitable for efficient coupling of optical radiation into nanoscale structures for a broad range of applications in the field of communications.

  3. 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.

  4. Oxidative Unfolding of the Rubredoxin Domain and the Natively Disordered N-terminal Region Regulate the Catalytic Activity of Mycobacterium tuberculosis Protein Kinase G.

    Science.gov (United States)

    Wittwer, Matthias; Luo, Qi; Kaila, Ville R I; Dames, Sonja A

    2016-12-30

    Mycobacterium tuberculosis escapes killing in human macrophages by secreting protein kinase G (PknG). PknG intercepts host signaling to prevent fusion of the phagosome engulfing the mycobacteria with the lysosome and, thus, their degradation. The N-terminal NORS (no regulatory secondary structure) region of PknG (approximately residues 1-75) has been shown to play a role in PknG regulation by (auto)phosphorylation, whereas the following rubredoxin-like metal-binding motif (RD, residues ∼74-147) has been shown to interact tightly with the subsequent catalytic domain (approximately residues 148-420) to mediate its redox regulation. Deletions or mutations in NORS or the redox-sensitive RD significantly decrease PknG survival function. Based on combined NMR spectroscopy, in vitro kinase assay, and molecular dynamics simulation data, we provide novel insights into the regulatory roles of the N-terminal regions. The NORS region is indeed natively disordered and rather dynamic. Consistent with most earlier data, autophosphorylation occurs in our assays only when the NORS region is present and, thus, in the NORS region. Phosphorylation of it results only in local conformational changes and does not induce interactions with the subsequent RD. Although the reduced, metal-bound RD makes tight interactions with the following catalytic domain in the published crystal structures, it can also fold in its absence. Our data further suggest that oxidation-induced unfolding of the RD regulates substrate access to the catalytic domain and, thereby, PknG function under different redox conditions, e.g. when exposed to increased levels of reactive oxidative species in host macrophages. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site*

    Science.gov (United States)

    Lu, Shaoyong; Banerjee, Avik; Jang, Hyunbum; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth

    2015-01-01

    K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4BWT-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4BWT-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding. PMID:26453300

  6. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site.

    Science.gov (United States)

    Lu, Shaoyong; Banerjee, Avik; Jang, Hyunbum; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth

    2015-11-27

    K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4B(WT)-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4B(WT)-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. 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)

    Wang, Xiaoxiao; Zhao, Liangfu; Guo, Shaoqing

    2013-01-01

    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

  8. 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)

    Steinrigl, Adolf; Nosek, Dagmara; Ertl, Reinhard; Guenzburg, Walter H.; Salmons, Brian; Klein, Dieter

    2007-01-01

    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

  9. Backbone assignment of the little finger domain of a Y-family DNA polymerase.

    Science.gov (United States)

    Ma, Dejian; Fowler, Jason D; Suo, Zucai

    2011-10-01

    Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

  10. Small-angle scattering studies show distinct conformations of calmodulin in its complexes with two peptides based on the regulatory domain of the catalytic subunit of phosphorylase kinase

    International Nuclear Information System (INIS)

    Trewhella, J.; Blumenthal, D.K.; Rokop, S.E.; Seeger, P.A.

    1990-01-01

    Small-angle X-ray and neutron scattering have been used to study the solution structures of calmodulin complexed with synthetic peptides corresponding to residues 342-366 and 301-326, designated PhK5 and PhK13, respectively, in the regulatory domain of the catalytic subunit of skeletal muscle phosphorylase kinase. The scattering data show that binding of PhK5 to calmodulin induces a dramatic contraction of calmodulin, similar to that previously observed when calmodulin is complexed with the calmodulin-binding domain peptide from rabbit skeletal muscle myosin light chain kinase. In contrast, calmodulin remains extended upon binding PhK13. In the presence of both peptides, calmodulin also remains extended. Apparently, the presence of PhK13 inhibits calmodulin from undergoing the PhK5-induced contraction. These data indicate that there is a fundamentally different type of calmodulin-target enzyme interaction in the case of the catalytic subunit of phosphorylase kinase compared with that for myosin light chain kinase

  11. 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.

  12. Charge order-superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

    Science.gov (United States)

    Moskvin, A. S.; Panov, Yu. D.; Rybakov, F. N.; Borisov, A. B.

    2017-11-01

    We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.

  13. WD40 domain of Apc1 is critical for the coactivator-induced allosteric transition that stimulates APC/C catalytic activity.

    Science.gov (United States)

    Li, Qiuhong; Chang, Leifu; Aibara, Shintaro; Yang, Jing; Zhang, Ziguo; Barford, David

    2016-09-20

    The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric cullin-RING E3 ubiquitin ligase that orchestrates cell-cycle progression by targeting cell-cycle regulatory proteins for destruction via the ubiquitin proteasome system. The APC/C assembly comprises two scaffolding subcomplexes: the platform and the TPR lobe that together coordinate the juxtaposition of the catalytic and substrate-recognition modules. The platform comprises APC/C subunits Apc1, Apc4, Apc5, and Apc15. Although the role of Apc1 as an APC/C scaffolding subunit has been characterized, its specific functions in contributing toward APC/C catalytic activity are not fully understood. Here, we report the crystal structure of the N-terminal domain of human Apc1 (Apc1N) determined at 2.2-Å resolution and provide an atomic-resolution description of the architecture of its WD40 (WD40 repeat) domain (Apc1(WD40)). To understand how Apc1(WD40) contributes to APC/C activity, a mutant form of the APC/C with Apc1(WD40) deleted was generated and evaluated biochemically and structurally. We found that the deletion of Apc1(WD40) abolished the UbcH10-dependent ubiquitination of APC/C substrates without impairing the Ube2S-dependent ubiquitin chain elongation activity. A cryo-EM structure of an APC/C-Cdh1 complex with Apc1(WD40) deleted showed that the mutant APC/C is locked into an inactive conformation in which the UbcH10-binding site of the catalytic module is inaccessible. Additionally, an EM density for Apc15 is not visible. Our data show that Apc1(WD40) is required to mediate the coactivator-induced conformational change of the APC/C that is responsible for stimulating APC/C catalytic activity by promoting UbcH10 binding. In contrast, Ube2S activity toward APC/C substrates is not dependent on the initiation-competent conformation of the APC/C.

  14. Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

    Science.gov (United States)

    Pereira, Félix Monteiro; Oliveira, Samuel Conceição

    2016-11-01

    In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

  15. 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)

    Okazaki, Nobuo; Arimori, Takao; Nakazawa, Masami; Miyatake, Kazutaka; Ueda, Mitsuhiro; Tamada, Taro

    2011-01-01

    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-ChiC 89–252 ) 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 P6 1 22 or P6 5 22, with unit-cell parameters a = b = 100, c = 243 Å. The calculated Matthews coefficient was approximately 3.2, 2.4 or 1.9 Å 3 Da −1 assuming the presence of three, four or five Ra-ChiC 89–252 molecules in the asymmetric unit, respectively

  16. Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

    Directory of Open Access Journals (Sweden)

    Zhu Li

    Full Text Available The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

  17. Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

    Science.gov (United States)

    Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

    2017-01-01

    The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

  18. The Hippo pathway: key interaction and catalytic domains in organ growth control, stem cell self-renewal and tissue regeneration.

    Science.gov (United States)

    Cherrett, Claire; Furutani-Seiki, Makoto; Bagby, Stefan

    2012-01-01

    The Hippo pathway is a conserved pathway that interconnects with several other pathways to regulate organ growth, tissue homoeostasis and regeneration, and stem cell self-renewal. This pathway is unique in its capacity to orchestrate multiple processes, from sensing to execution, necessary for organ expansion. Activation of the Hippo pathway core kinase cassette leads to cytoplasmic sequestration of the nuclear effectors YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif), consequently disabling their transcriptional co-activation function. Components upstream of the core kinase cassette have not been well understood, especially in vertebrates, but are gradually being elucidated and include cell polarity and cell adhesion proteins.

  19. 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

    -micromolar binding affinities. Subsequent refinement revealed that inhibition comparable to that of longer peptides could be achieved using the tetrapeptide SWFP. To analyze its binding, the high-resolution crystal structure of the complex between Kly18 and SWFP was determined and it was found that the peptide binds...... 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...... determinants of inhibition of karilysin and open the field for the design of novel inhibitory strategies aimed at the treatment of human periodontal disease based on a peptidic hit molecule....

  20. Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae.

    Science.gov (United States)

    Kobayashi, Junya; Matsuura, Yoshiyuki

    2017-10-01

    In the budding yeast Saccharomyces cerevisiae, the protein phosphatase Cdc14p orchestrates various events essential for mitotic exit. We have determined the X-ray crystal structures at 1.85 Å resolution of the catalytic domain of Cdc14p in both the apo state, and as a complex with S160-phosphorylated Swi6p peptide. Each asymmetric unit contains two Cdc14p chains arranged in an intimately associated homodimer, consistent with its oligomeric state in solution. The dimerization interface is located on the backside of the substrate-binding cleft. Structure-based mutational analyses indicate that the dimerization of Cdc14p is required for normal growth of yeast cells. © 2017 The Protein Society.

  1. Phylogenetic analysis of the diacylglycerol kinase family of proteins and identification of multiple highly-specific conserved inserts and deletions within the catalytic domain that are distinctive characteristics of different classes of DGK homologs.

    Directory of Open Access Journals (Sweden)

    Radhey S Gupta

    Full Text Available Diacylglycerol kinase (DGK family of proteins, which phosphorylates diacylglycerol into phosphatidic acid, play important role in controlling diverse cellular processes in eukaryotic organisms. Most vertebrate species contain 10 different DGK isozymes, which are grouped into 5 different classes based on the presence or absence of specific functional domains. However, the relationships among different DGK isozymes or how they have evolved from a common ancestor is unclear. The catalytic domain constitutes the single largest sequence element within the DGK proteins that is commonly and uniquely shared by all family members, but there is limited understanding of the overall function of this domain. In this work, we have used the catalytic domain sequences to construct a phylogenetic tree for the DGK family members from representatives of the main vertebrate classes and have also examined the distributions of various DGK isozymes in eukaryotic phyla. In a tree based on catalytic domain sequences, the DGK homologs belonging to different classes formed strongly supported clusters which were separated by long branches, and the different isozymes within each class also generally formed monophyletic groupings. Further, our analysis of the sequence alignments of catalytic domains has identified >10 novel sequence signatures consisting of conserved signature indels (inserts or deletions, CSIs that are distinctive characteristics of either particular classes of DGK isozymes, or are commonly shared by members of two or more classes of DGK isozymes. The conserved indels in protein sequences are known to play important functional roles in the proteins/organisms where they are found. Thus, our identification of multiple highly specific CSIs that are distinguishing characteristics of different classes of DGK homologs points to the existence of important differences in the catalytic domain function among the DGK isozymes. The identified CSIs in conjunction with

  2. Association of mitochondrial lysyl-tRNA synthetase with HIV-1 GagPol involves catalytic domain of the synthetase and transframe and integrase domains of Pol

    Directory of Open Access Journals (Sweden)

    Shalak V. F.

    2011-10-01

    Full Text Available Aim. Analyze the interaction between Lysyl-tRNA synthetase (LysRS and HIV-1 GagPol to know whether a particular N-terminal sequence of mitochondrial LysRS triggers a specific recognition with GagPol. Methods. Yeast two-hybrid analysis, immunoprecipitation. Results. We have shown that LysRS associates with the Pol domain of GagPol. Conclusions. A model of the assembly of the LysRS:tRNA3Lys:GagPol packaging complex is proposed.

  3. Crystal structure of the catalytic domain of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14.

    Science.gov (United States)

    Lou, Xiangdi; Ran, Tingting; Han, Ning; Gao, Yanyan; He, Jianhua; Tang, Lin; Xu, Dongqing; Wang, Weiwu

    2014-04-25

    Prodigiosin, a tripyrrole red pigment synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway, MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. MAP is synthesized sequentially by PigD, PigE and PigB. PigE catalyzes the transamination of an amino group to the aldehyde group of 3-acetyloctanal, resulting in an aminoketone, which spontaneously cyclizes to form H2MAP. Here we report the crystal structure of the catalytic domain of PigE which involved in the biosynthesis of prodigiosin precursor MAP for the first time to a resolution of 2.3Å with a homodimer in the asymmetric unit. The monomer of PigE catalytic domain is composed of three domains with PLP as cofactor: a small N-terminal domain connecting the catalytic domain with the front part of PigE, a large PLP-binding domain and a C-terminal domain. The residues from both monomers build the PLP binding site at the interface of the dimer which resembles the other PLP-dependent enzymes. Structural comparison of PigE with Thermus thermophilus AcOAT showed a higher hydrophobic and smaller active site of PigE, these differences may be the reason for substrate specificity. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Consensus on core phenomena and statements describing Basic Body Awareness Therapy within the movement awareness domain in physiotherapy.

    Science.gov (United States)

    Skjaerven, L H; Mattsson, M; Catalan-Matamoros, D; Parker, A; Gard, G; Gyllensten, A Lundvik

    2018-02-26

    Physiotherapists are facing complex health challenges in the treatment of persons suffering from long-lasting musculoskeletal disorders and mental health problems. Basic Body Awareness Therapy (BBAT) is a physiotherapy approach within the movement awareness domain developed to bridge physical, mental, and relational health challenges. The purpose of this study was to reach a consensus on core phenomena and statements describing BBAT. A consensus-building process was conducted using the nominal group technique (NGT). Twenty-one BBAT experts from 10 European countries participated in a concentrated weekend workshop of 20 hours. All participants signed informed consent. Participants reached a consensus on 138 core phenomena, clustered in three overarching categories: clinical core, historical roots, and research and evaluation phenomena. Of the 106 clinical core phenomena, the participants agreed on three categories of phenomena: movement quality, movement awareness practice, and movement awareness therapy and pedagogy. Furthermore, the participants reached 100 percent consensus on 16 of 30 statements describing BBAT. This study provides a consensus on core phenomena and statements describing BBAT. The data reveal phenomena implemented when promoting movement quality through movement awareness. Data provide clarity in some aspects of the vocabulary as fundamental theory. Further reearch will be developed.

  5. Efficient multiscale magnetic-domain analysis of iron-core material under mechanical stress

    Science.gov (United States)

    Nishikubo, Atsushi; Ito, Shumpei; Mifune, Takeshi; Matsuo, Tetsuji; Kaido, Chikara; Takahashi, Yasuhito; Fujiwara, Koji

    2018-05-01

    For an efficient analysis of magnetization, a partial-implicit solution method is improved using an assembled domain structure model with six-domain mesoscopic particles exhibiting pinning-type hysteresis. The quantitative analysis of non-oriented silicon steel succeeds in predicting the stress dependence of hysteresis loss with computation times greatly reduced by using the improved partial-implicit method. The effect of cell division along the thickness direction is also evaluated.

  6. Performance Analysis of Fission and Surface Source Iteration Method for Domain Decomposed Monte Carlo Whole-Core Calculation

    International Nuclear Information System (INIS)

    Jo, Yu Gwon; Oh, Yoo Min; Park, Hyang Kyu; Park, Kang Soon; Cho, Nam Zin

    2016-01-01

    In this paper, two issues in the FSS iteration method, i.e., the waiting time for surface source data and the variance biases in local tallies are investigated for the domain decomposed, 3-D continuous-energy whole-core calculation. The fission sources are provided as usual, while the surface sources are provided by banking MC particles crossing local domain boundaries. The surface sources serve as boundary conditions for nonoverlapping local problems, so that each local problem can be solved independently. In this paper, two issues in the FSS iteration are investigated. One is quantifying the waiting time of processors to receive surface source data. By using nonblocking communication, 'time penalty' to wait for the arrival of the surface source data is reduced. The other important issue is underestimation of the sample variance of the tally because of additional inter-iteration correlations in surface sources. From the numerical results on a 3-D whole-core test problem, it is observed that the time penalty is negligible in the FSS iteration method and that the real variances of both pin powers and assembly powers are estimated by the HB method. For those purposes, three cases; Case 1 (1 local domain), Case 2 (4 local domains), Case 3 (16 local domains) are tested. For both Cases 2 and 3, the time penalties for waiting are negligible compared to the source-tracking times. However, for finer divisions of local domains, the loss of parallel efficiency caused by the different number of sources for local domains in symmetric locations becomes larger due to the stochastic errors in source distributions. For all test cases, the HB method very well estimates the real variances of local tallies. However, it is also noted that the real variances of local tallies estimated by the HB method show slightly smaller than the real variances obtained from 30 independent batch runs and the deviations become larger for finer divisions of local domains. The batch size used for the HB

  7. Purification and crystallization of the catalytic PRONE domain of RopGEF8 and its complex with Rop4 from Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Thomas, Christoph; Weyand, Michael; Wittinghofer, Alfred; Berken, Antje

    2006-01-01

    Crystals of the catalytic PRONE domain of the guanine nucleotide exchange factor RopGEF8 and its complex with the Rho-family protein Rop4 from A. thaliana were obtained that diffract to 2.2 and 3.1 Å resolution, respectively. The PRONE domain of the guanine nucleotide exchange factor RopGEF8 (PRONE8) was purified and crystallized free and in complex with the Rho-family protein Rop4 using the hanging-drop vapour-diffusion method. PRONE8 crystals were obtained using NaCl as precipitating agent and belong to the hexagonal space group P6 5 22. Native and anomalous data sets were collected using synchrotron radiation at 100 K to 2.2 and 2.8 Å resolution, respectively. Crystals of the Rop4–PRONE8 complex belonging to space group P6 3 were obtained using Tacsimate and PEG 3350 as precipitating agents and diffracted to 3.1 Å resolution

  8. Purification and crystallization of the catalytic PRONE domain of RopGEF8 and its complex with Rop4 from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Christoph; Weyand, Michael; Wittinghofer, Alfred; Berken, Antje, E-mail: antje.berken@mpi-dortmund.mpg.de [Department of Structural Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)

    2006-06-01

    Crystals of the catalytic PRONE domain of the guanine nucleotide exchange factor RopGEF8 and its complex with the Rho-family protein Rop4 from A. thaliana were obtained that diffract to 2.2 and 3.1 Å resolution, respectively. The PRONE domain of the guanine nucleotide exchange factor RopGEF8 (PRONE8) was purified and crystallized free and in complex with the Rho-family protein Rop4 using the hanging-drop vapour-diffusion method. PRONE8 crystals were obtained using NaCl as precipitating agent and belong to the hexagonal space group P6{sub 5}22. Native and anomalous data sets were collected using synchrotron radiation at 100 K to 2.2 and 2.8 Å resolution, respectively. Crystals of the Rop4–PRONE8 complex belonging to space group P6{sub 3} were obtained using Tacsimate and PEG 3350 as precipitating agents and diffracted to 3.1 Å resolution.

  9. Carbon Domains on MoS2/TiO2 System via Catalytic Acetylene Oligomerization: Synthesis, Structure, and Surface Properties

    Directory of Open Access Journals (Sweden)

    Sara Cravanzola

    2017-11-01

    Full Text Available Carbon domains have been obtained at the surface of a MoS2/TiO2 (Evonik, P25 system via oligomerization and cyclotrimerization reactions involved in the interaction of the photoactive material with acetylene. Firstly, MoS2 nanosheets have been synthesized at the surface of TiO2, via sulfidation of a molybdenum oxide precursor with H2S (bottom-up method. Secondly, the morphology and the structure, the optical and the vibrational properties of the obtained materials, for each step of the synthesis procedure, have been investigated by microscopy and spectroscopy methods. In particular, transmission electron microscopy images provide a simple tool to highlight the effectiveness of the sulfidation process, thus showing 1L, 2L, and stacked MoS2 nanosheets anchored to the surface of TiO2 nanoparticles. Lastly, in-situ FTIR spectroscopy investigation gives insights into the nature of the oligomerized species, showing that the formation of both polyenic and aromatic systems can be taken into account, being their formation promoted by both Ti and Mo catalytic sites. This finding gives an opportunity for the assembly of extended polyenic, polyaromatic, or mixed domains firmly attached at the surface of photoactive materials. The presented approach, somehow different from the carbon adding or doping processes of TiO2, is of potential interest for the advanced green chemistry and energy conversion/transport applications.

  10. Scanning microscopy of magnetic domains using the Fe 3p core level transverse magneto-optical Kerr effect

    Science.gov (United States)

    Friedrich, J.; Rozhko, I.; Voss, J.; Hillebrecht, F. U.; Kisker, E.; Wedemeier, V.

    1999-04-01

    We demonstrate the feasibility of the vacuum ultraviolet analog to visible-light magneto-optical imaging of magnetic structures using the resonantly enhanced transverse magneto-optical Kerr effect at core level thresholds with incident p-polarized radiation. The advantages are element specificity and a variable information depth. We used the scanning x-ray microscope at HASYLAB capable of obtaining about 1 μm resolution by means of its focusing ellipsoidal ring mirror. The p-polarized component of the reflected light was selected using multilayer reflection at an additional plane mirror downstream to the sample. Micrographs of the optical reflectivity were taken in the vicinity of the Fe 3p core level threshold at 53.7 and 56.5 eV photon energy where the magneto-optical effect is of opposite sign. Magnetic domains are visible in the difference of both recorded images.

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

    International Nuclear Information System (INIS)

    Choi, Kyoung-Jae; Lim, Chun-Woo; Yoon, Moon-Young; Ahn, Byung-Yoon; Yu, Yeon Gyu

    2004-01-01

    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 (K D app ) 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

  12. Residues in the membrane-spanning domain core modulate conformation and fusogenicity of the HIV-1 envelope glycoprotein

    International Nuclear Information System (INIS)

    Shang Liang; Hunter, Eric

    2010-01-01

    The membrane-spanning domain (MSD) of human immunodeficiency virus type I (HIV-1) envelope glycoprotein (Env) is critical for its biological activity. Initial studies have defined an almost invariant 'core' structure in the MSD and demonstrated that it is crucial for anchoring Env in the membrane and virus entry. We show here that amino acid substitutions in the MSD 'core' do not influence specific virus-cell attachment, nor CD4 receptor and CXCR4 coreceptor recognition by Env. However, substitutions within the MSD 'core' delayed the kinetics and reduced the efficiency of cell-cell fusion mediated by Env. Although we observed no evidence that membrane fusion mediated by the MSD core mutants was arrested at a hemifusion stage, impaired Env fusogenicity was correlated with minor conformational changes in the V2, C1, and C5 regions in gp120 and the immunodominant loop in gp41. These changes could delay initiation of the conformational changes required in the fusion process.

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

    International Nuclear Information System (INIS)

    Salfeld, J.; Pfaff, E.; Noah, M.; Schaller, H.

    1989-01-01

    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

  14. 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.

  15. Development of a Draft Core Set of Domains for Measuring Shared Decision Making in Osteoarthritis: An OMERACT Working Group on Shared Decision Making

    Science.gov (United States)

    Toupin April, Karine; Barton, Jennifer; Fraenkel, Liana; Li, Linda; Grandpierre, Viviane; Guillemin, Francis; Rader, Tamara; Stacey, Dawn; Légaré, France; Jull, Janet; Petkovic, Jennifer; Scholte Voshaar, Marieke; Welch, Vivian; Lyddiatt, Anne; Hofstetter, Cathie; De Wit, Maarten; March, Lyn; Meade, Tanya; Christensen, Robin; Gaujoux-Viala, Cécile; Suarez-Almazor, Maria E.; Boonen, Annelies; Pohl, Christoph; Martin, Richard; Tugwell, Peter

    2015-01-01

    Objective Despite the importance of shared decision making for delivering patient-centred care in rheumatology, there is no consensus on how to measure its process and outcomes. The aim of this OMERACT working group is to determine the core set of domains for measuring shared decision making in intervention studies in adults with osteoarthritis (OA), from the perspective of patients, health professionals and researchers. Methods We followed the OMERACT Filter 2.0 to develop a draft core domain set, which consisted of: (i) forming an OMERACT working group; (ii) conducting a review of domains of shared decision making; and (iii) obtaining the opinions of stakeholders using a modified nominal group process held at a session activity at the OMERACT 2014 meeting. Results 26 stakeholders from Europe, North America and Australia, including 5 patient research partners, participated in the session activity. Participants identified the following domains for measuring shared decision making to be included as part of the Draft Core Set: 1) Identifying the decision; 2) Exchanging Information; 3) Clarifying views; 4) Deliberating; 5) Making the decision; 6) Putting the decision into practice; and 7) Assessing the impact of the decision. Contextual factors were also suggested. Conclusion We propose a Draft Core Set of shared decision making domains for OA intervention research studies. Next steps include a workshop at OMERACT 2016 to reach consensus on these proposed domains in the wider OMERACT group, as well as detail sub-domains and assess instruments to develop a Core Outcome Measurement Set. PMID:25877502

  16. 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 ...

  17. Symptomatic type 1 protein C deficiency caused by a de novo Ser270Leu mutation in the catalytic domain

    DEFF Research Database (Denmark)

    Lind, B; Koefoed, P; Thorsen, S

    2001-01-01

    the intracellular content of mutant and wild-type protein was similar. Northern blot analysis of total mRNA from transfected cells showed no reduction of the mutant protein C mRNA compared with wild-type protein C mRNA. Collectively, these results indicate that the Ser270Leu mutation in the affected family caused......Heterozygosity for a C8524T transition in the protein C gene converting Ser270(TCG) to Leu(TTG) in the protease domain was identified in a family with venous thrombosis. The mutation was associated with parallel reduction in plasma levels of protein C anticoagulant activity and protein C antigen......, which is consistent with a type 1 deficiency. Transient expression of mutant protein C cDNA in human kidney 293 cells and analysis of protein C antigen in culture media and cell lysates showed that the secretion of mutant protein compared with wild-type protein was reduced by at least 97% while...

  18. The perturbation of tryptophan fluorescence by phenylalanine to alanine mutations identifies the hydrophobic core in a subset of bacterial Ig-like domains.

    Science.gov (United States)

    Raman, Rajeev; Ptak, Christopher P; Hsieh, Ching-Lin; Oswald, Robert E; Chang, Yung-Fu; Sharma, Yogendra

    2013-07-09

    Many host-parasite interactions are mediated via surface-exposed proteins containing bacterial immunoglobulin-like (Big) domains. Here, we utilize the spectral properties of a conserved Trp to provide evidence that, along with a Phe, these residues are positioned within the hydrophobic core of a subset of Big_2 domains. The mutation of the Phe to Ala decreases Big_2 domain stability and impairs the ability of LigBCen2 to bind to the host protein, fibronectin.

  19. Societal and individual burden of illness among fibromyalgia patients in France: Association between disease severity and OMERACT core domains

    Directory of Open Access Journals (Sweden)

    Perrot Serge

    2012-02-01

    Full Text Available Abstract Background Patients with fibromyalgia (FM report widespread pain, fatigue, and other functional limitations. This study aimed to provide an assessment of the burden of illness associated with FM in France and its association with disease severity and core domains as defined by Outcome Measures in Rheumatology Clinical Trials (OMERACT for FM. Methods This cross-sectional, observational study recruited patients with a prior diagnosis of FM from 18 community-based physician offices in France. Patients completed questions about FM impact (Fibromyalgia-Impact Questionnaire [FIQ], core symptoms (defined by OMERACT, health-related quality of life (EQ-5D, current overall health status (rated on a scale from 0 to 100, productivity, treatment satisfaction, and out-of-pocket expenses related to FM. Site staff recorded patients' treatment and health resource use based on medical record review. Costs were extrapolated from 4-week patient-reported data and 3-month clinical case report form data and calculated in 2008 Euros using a societal perspective. Tests of significance used the Kruskal-Wallis test or Fisher's Exact test where P Results Eighty-eight patients (mean 55.2 y; female:male 74:14 were recruited. The majority of patients (84.1% were prescribed medications for FM. Patients mainly described medications as a little/not at all effective (40.0% or somewhat effective (52.9%. Current Overall Health rating was 52.9 (± 17.8 and FIQ total score was 54.8 (± 17.3. FIQ total score was used to define FM severity, and 17 patients scored 0- Conclusions In a sample of 88 patients with FM from France, we found that FM poses a substantial economic and human burden on patients and society. FM severity level was significantly associated with patients' health status and core symptom domains.

  20. Unique biological properties of catalytic domain directed human anti-CAIX antibodies discovered through phage-display technology.

    Directory of Open Access Journals (Sweden)

    Chen Xu

    2010-03-01

    Full Text Available Carbonic anhydrase IX (CAIX, gene G250/MN-encoded transmembrane protein is highly expressed in various human epithelial tumors such as renal clear cell carcinoma (RCC, but absent from the corresponding normal tissues. Besides the CA signal transduction activity, CAIX may serve as a biomarker in early stages of oncogenesis and also as a reliable marker of hypoxia, which is associated with tumor resistance to chemotherapy and radiotherapy. Although results from preclinical and clinical studies have shown CAIX as a promising target for detection and therapy for RCC, only a limited number of murine monoclonal antibodies (mAbs and one humanized mAb are available for clinical testing and development. In this study, paramagnetic proteoliposomes of CAIX (CAIX-PMPLs were constructed and used for anti-CAIX antibody selection from our 27 billion human single-chain antibody (scFv phage display libraries. A panel of thirteen human scFvs that specifically recognize CAIX expressed on cell surface was identified, epitope mapped primarily to the CA domain, and affinity-binding constants (KD determined. These human anti-CAIX mAbs are diverse in their functions including induction of surface CAIX internalization into endosomes and inhibition of the carbonic anhydrase activity, the latter being a unique feature that has not been previously reported for anti-CAIX antibodies. These human anti-CAIX antibodies are important reagents for development of new immunotherapies and diagnostic tools for RCC treatment as well as extending our knowledge on the basic structure-function relationships of the CAIX molecule.

  1. Comparison of diagnostic classification systems for delirium with new research criteria that incorporate the three core domains.

    Science.gov (United States)

    Trzepacz, Paula T; Meagher, David J; Franco, José G

    2016-05-01

    Diagnostic classification systems do not incorporate phenomenological research findings about the three core symptom domains of delirium (Attentional/Cognitive, Circadian, Higher Level Thinking). We evaluated classification performances of novel Trzepacz, Meagher, and Franco research diagnostic criteria (TMF) that incorporate those domains and ICD-10, DSM-III-R, DSM-IV, and DSM-5. Primary data analysis of 641 patients with mixed neuropsychiatric profiles. Delirium (n=429) and nondelirium (n=212) reference standard groups were identified using cluster analysis of symptoms assessed using the Delirium Rating Scale-Revised-98. Accuracy, sensitivity, specificity, positive and negative predictive values (PPV, NPV), and likelihood ratios (LR+, LR-) are reported. TMF criteria had high sensitivity and specificity (87.4% and 89.2%), more balanced than DSM-III-R (100% and 31.6%), DSM-IV (97.7% and 74.1%), DSM-5 (97.7% and 72.6%), and ICD-10 (66.2% and 100%). PPV of DSM-III-R, DSM-IV, and DSM-5 were 90%. ICD-10 had the lowest NPV (59.4%). TMF had the highest LR+ (8.06) and DSM-III-R the lowest LR- (0.0). Overall, values for DSM-IV and DSM-5 were similar, whereas for ICD-10 and DSM-III-R were inverse of each other. In the pre-existing cognitive impairment/dementia subsample (n=128), TMF retained its highest LR+ though specificity (58.3%) became less well balanced with sensitivity (87.9%), which still exceeded that of DSM. TMF research diagnostic criteria performed well, with more balanced sensitivity and specificity and the highest likelihood ratio for delirium identification. Reflecting the three core domains of delirium, TMF criteria may have advantages in biological research where delineation of this syndrome is important. Copyright © 2016. Published by Elsevier Inc.

  2. 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.

  3. New experimental treatments for core social domain in autism spectrum disorders.

    Science.gov (United States)

    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 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 behaviors. 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 intervention. Another study of neural changes in response to treatment examined variations in EEG signaling in patients after an Early Start Denver Model (ESDM) intervention.

  4. 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.

  5. Development of a Draft Core Set of Domains for Measuring Shared Decision Making in Osteoarthritis: An OMERACT Working Group on Shared Decision Making.

    Science.gov (United States)

    Toupin-April, Karine; Barton, Jennifer; Fraenkel, Liana; Li, Linda; Grandpierre, Viviane; Guillemin, Francis; Rader, Tamara; Stacey, Dawn; Légaré, France; Jull, Janet; Petkovic, Jennifer; Scholte-Voshaar, Marieke; Welch, Vivian; Lyddiatt, Anne; Hofstetter, Cathie; De Wit, Maarten; March, Lyn; Meade, Tanya; Christensen, Robin; Gaujoux-Viala, Cécile; Suarez-Almazor, Maria E; Boonen, Annelies; Pohl, Christoph; Martin, Richard; Tugwell, Peter S

    2015-12-01

    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 measuring shared decision making in intervention studies in adults with osteoarthritis (OA), from the perspectives of patients, health professionals, and researchers. We followed the OMERACT Filter 2.0 method to develop a draft core domain set by (1) forming an OMERACT working group; (2) conducting a review of domains of shared decision making; and (3) obtaining opinions of all those involved using a modified nominal group process held at a session activity at the OMERACT 12 meeting. In all, 26 people from Europe, North America, and Australia, including 5 patient research partners, participated in the session activity. Participants identified the following domains for measuring shared decision making to be included as part of the draft core set: (1) identifying the decision, (2) exchanging information, (3) clarifying views, (4) deliberating, (5) making the decision, (6) putting the decision into practice, and (7) assessing the effect of the decision. Contextual factors were also suggested. We proposed a draft core set of shared decision-making domains for OA intervention research studies. Next steps include a workshop at OMERACT 13 to reach consensus on these proposed domains in the wider OMERACT group, as well as to detail subdomains and assess instruments to develop a core outcome measurement set.

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

    Science.gov (United States)

    Maortua, Hiart; Martínez-Bouzas, Cristina; Calvo, María-Teresa; Domingo, Maria-Rosario; Ramos, Feliciano; García-Ribes, Ainhoa; Martínez, María-Jesús; López-Aríztegui, María-Asunción; Puente, Nerea; Rubio, Izaskun; Tejada, María-Isabel

    2012-08-06

    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. 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). 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. 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.

  7. 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.

  8. Updating the Psoriatic Arthritis (PsA) Core Domain Set: A Report from the PsA Workshop at OMERACT 2016.

    Science.gov (United States)

    Orbai, Ana-Maria; de Wit, Maarten; Mease, Philip J; Callis Duffin, Kristina; Elmamoun, Musaab; Tillett, William; Campbell, Willemina; FitzGerald, Oliver; Gladman, Dafna D; Goel, Niti; Gossec, Laure; Hoejgaard, Pil; Leung, Ying Ying; Lindsay, Chris; Strand, Vibeke; van der Heijde, Désirée M; Shea, Bev; Christensen, Robin; Coates, Laura; Eder, Lihi; McHugh, Neil; Kalyoncu, Umut; Steinkoenig, Ingrid; Ogdie, Alexis

    2017-10-01

    To include the patient perspective in accordance with the Outcome Measures in Rheumatology (OMERACT) Filter 2.0 in the updated Psoriatic Arthritis (PsA) Core Domain Set for randomized controlled trials (RCT) and longitudinal observational studies (LOS). At OMERACT 2016, research conducted to update the PsA Core Domain Set was presented and discussed in breakout groups. The updated PsA Core Domain Set was voted on and endorsed by OMERACT participants. We conducted a systematic literature review of domains measured in PsA RCT and LOS, and identified 24 domains. We conducted 24 focus groups with 130 patients from 7 countries representing 5 continents to identify patient domains. We achieved consensus through 2 rounds of separate surveys with 50 patients and 75 physicians, and a nominal group technique meeting with 12 patients and 12 physicians. We conducted a workshop and breakout groups at OMERACT 2016 in which findings were presented and discussed. The updated PsA Core Domain Set endorsed with 90% agreement by OMERACT 2016 participants included musculoskeletal disease activity, skin disease activity, fatigue, pain, patient's global assessment, physical function, health-related quality of life, and systemic inflammation, which were recommended for all RCT and LOS. These were important, but not required in all RCT and LOS: economic cost, emotional well-being, participation, and structural damage. Independence, sleep, stiffness, and treatment burden were on the research agenda. The updated PsA Core Domain Set was endorsed at OMERACT 2016. Next steps for the PsA working group include evaluation of PsA outcome measures and development of a PsA Core Outcome Measurement Set.

  9. Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain

    International Nuclear Information System (INIS)

    Nishimura, Mitsuhiro; Kaminishi, Tatsuya; Kawazoe, Masahito; Shirouzu, Mikako; Takemoto, Chie; Yokoyama, Shigeyuki; Tanaka, Akiko; Sugano, Sumio; Yoshida, Takuya; Ohkubo, Tadayasu; Kobayashi, Yuji

    2007-01-01

    A truncated variant of human ribosomal protien L10 was prepared and crystallized. Diffraction data were collected to 2.5 Å resolution. Eukaryotic ribosomal protein L10 is an essential component of the large ribosomal subunit, which organizes the architecture of the aminoacyl-tRNA binding site. The human L10 protein is also called the QM protein and consists of 214 amino-acid residues. For crystallization, the L10 core domain (L10CD, Phe34–Glu182) was recombinantly expressed in Escherichia coli and purified to homogeneity. A hexagonal crystal of L10CD was obtained by the sitting-drop vapour-diffusion method. The L10CD crystal diffracted to 2.5 Å resolution and belongs to space group P3 1 21 or P3 2 21

  10. Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure.

    Science.gov (United States)

    Fuglestad, Brian; Stetz, Matthew A; Belnavis, Zachary; Wand, A Joshua

    2017-12-01

    Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately -115mlmol -1 and an average pressure dependent change in compressibility of approximately 30mlmol -1 kbar -1 . In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Multiple domains of fission yeast Cdc19p (MCM2) are required for its association with the core MCM complex.

    Science.gov (United States)

    Sherman, D A; Pasion, S G; Forsburg, S L

    1998-07-01

    The members of the MCM protein family are essential eukaryotic DNA replication factors that form a six-member protein complex. In this study, we use antibodies to four MCM proteins to investigate the structure of and requirements for the formation of fission yeast MCM complexes in vivo, with particular regard to Cdc19p (MCM2). Gel filtration analysis shows that the MCM protein complexes are unstable and can be broken down to subcomplexes. Using coimmunoprecipitation, we find that Mis5p (MCM6) and Cdc21p (MCM4) are tightly associated with one another in a core complex with which Cdc19p loosely associates. Assembly of Cdc19p with the core depends upon Cdc21p. Interestingly, there is no obvious change in Cdc19p-containing MCM complexes through the cell cycle. Using a panel of Cdc19p mutants, we find that multiple domains of Cdc19p are required for MCM binding. These studies indicate that MCM complexes in fission yeast have distinct substructures, which may be relevant for function.

  12. High-temperature catalytic reforming of n-hexane over supported and core-shell Pt nanoparticle catalysts: role of oxide-metal interface and thermal stability.

    Science.gov (United States)

    An, Kwangjin; Zhang, Qiao; Alayoglu, Selim; Musselwhite, Nathan; Shin, Jae-Youn; Somorjai, Gabor A

    2014-08-13

    Designing catalysts with high thermal stability and resistance to deactivation while simultaneously maintaining their catalytic activity and selectivity is of key importance in high-temperature reforming reactions. We prepared Pt nanoparticle catalysts supported on either mesoporous SiO2 or TiO2. Sandwich-type Pt core@shell catalysts (SiO2@Pt@SiO2 and SiO2@Pt@TiO2) were also synthesized from Pt nanoparticles deposited on SiO2 spheres, which were encapsulated by either mesoporous SiO2 or TiO2 shells. n-Hexane reforming was carried out over these four catalysts at 240-500 °C with a hexane/H2 ratio of 1:5 to investigate thermal stability and the role of the support. For the production of high-octane gasoline, branched C6 isomers are more highly desired than other cyclic, aromatic, and cracking products. Over Pt/TiO2 catalyst, production of 2-methylpentane and 3-methylpentane via isomerization was increased selectively up to 420 °C by charge transfer at Pt-TiO2 interfaces, as compared to Pt/SiO2. When thermal stability was compared between supported catalysts and sandwich-type core@shell catalysts, the Pt/SiO2 catalyst suffered sintering above 400 °C, whereas the SiO2@Pt@SiO2 catalyst preserved the Pt nanoparticle size and shape up to 500 °C. The SiO2@Pt@TiO2 catalyst led to Pt nanoparticle sintering due to incomplete protection of the TiO2 shells during the reaction at 500 °C. Interestingly, over the Pt/TiO2 catalyst, the average size of Pt nanoparticles was maintained even after 500 °C without sintering. In situ ambient pressure X-ray photoelectron spectroscopy demonstrated that the Pt/TiO2 catalyst did not exhibit TiO2 overgrowth on the Pt surface or deactivation by Pt sintering up to 600 °C. The extraordinarily high stability of the Pt/TiO2 catalyst promoted high reaction rates (2.0 μmol · g(-1) · s(-1)), which was 8 times greater than other catalysts and high isomer selectivity (53.0% of C6 isomers at 440 °C). By the strong metal-support interaction

  13. Common Core State Standards in the Middle Grades: What's New in the Geometry Domain and How Can Teachers Support Student Learning?

    Science.gov (United States)

    Teuscher, Dawn; Tran, Dung; Reys, Barbara J.

    2015-01-01

    The Common Core State Standards for Mathematics (CCSSM) is a primary focus of attention for many stakeholders' (e.g., teachers, district mathematics leaders, and curriculum developers) intent on improving mathematics education. This article reports on specific content shifts related to the geometry domain in the middle grades (6-8)…

  14. Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic.

    Science.gov (United States)

    Mahoney, Brendan J; Zhang, Meiling; Zintsmaster, John S; Peng, Jeffrey W

    2018-03-02

    Pin1 is a two-domain human protein that catalyzes the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs in numerous cell-cycle regulatory proteins. These pS/T-P motifs bind to Pin1's peptidyl-prolyl isomerase (PPIase) domain in a catalytic pocket, between an extended catalytic loop and the PPIase domain core. Previous studies showed that post-translational phosphorylation of S71 in the catalytic loop decreases substrate binding affinity and isomerase activity. To define the origins for these effects, we investigated a phosphomimetic Pin1 mutant, S71E-Pin1, using solution NMR. We find that S71E perturbs not only its host loop but also the nearby PPIase core. The perturbations identify a local network of hydrogen bonds and salt bridges that is more extended than previously thought, and includes interactions between the catalytic loop and the α2/α3 turn in the PPIase core. Explicit-solvent molecular dynamics simulations and phylogenetic analysis suggest that these interactions act as conserved "latches" between the loop and PPIase core that enhance binding of phosphorylated substrates, as they are absent in PPIases lacking pS/T-P specificity. Our results suggest that S71 is a hub residue within an electrostatic network primed for phosphorylation, and may illustrate a common mechanism of phosphorylation-mediated allostery. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Recommendation for measuring clinical outcome in distal radius fractures: a core set of domains for standardized reporting in clinical practice and research.

    Science.gov (United States)

    Goldhahn, Jörg; Beaton, Dorcas; Ladd, Amy; Macdermid, Joy; Hoang-Kim, Amy

    2014-02-01

    Lack of standardization of outcome measurement has hampered an evidence-based approach to clinical practice and research. We adopted a process of reviewing evidence on current use of measures and appropriate theoretical frameworks for health and disability to inform a consensus process that was focused on deriving the minimal set of core domains in distal radius fracture. We agreed on the following seven core recommendations: (1) pain and function were regarded as the primary domains, (2) very brief measures were needed for routine administration in clinical practice, (3) these brief measures could be augmented by additional measures that provide more detail or address additional domains for clinical research, (4) measurement of pain should include measures of both intensity and frequency as core attributes, (5) a numeric pain scale, e.g. visual analogue scale or visual numeric scale or the pain subscale of the patient-reported wrist evaluation (PRWE) questionnaires were identified as reliable, valid and feasible measures to measure these concepts, (6) for function, either the Quick Disability of the arm, shoulder and hand questionnaire or PRWE-function subscale was identified as reliable, valid and feasible measures, and (7) a measure of participation and treatment complications should be considered core outcomes for both clinical practice and research. We used a sound methodological approach to form a comprehensive foundation of content for outcomes in the area of distal radius fractures. We recommend the use of symptom and function as separate domains in the ICF core set in clinical research or practice for patients with wrist fracture. Further research is needed to provide more definitive measurement properties of measures across all domains.

  16. Characterizing Mobile/Less-Mobile Porosity and Solute Exchange in Dual-Domain Media Using Tracer Experiments and Electrical Measurements in a Hassler-Type Core Holder

    Science.gov (United States)

    Falzone, S.; Slater, L. D.; Day-Lewis, F. D.; Parker, B. L.; Keating, K.; Robinson, J.

    2017-12-01

    Mass transfer is the process by which solute is retained in less-mobile porosity domains, and later released into the mobile porosity domain. This process is often responsible for the slow arrival and gradual release of contaminants and solute tracers. Recent studies have outlined methods using dual-domain mass transfer (DDMT) models for characterizing this phenomenon. These models use the non-linear relationship of bulk (σb) and fluid (σf) conductivity, collected from electrical methods during tracer experiments, to characterize the less-mobile/mobile porosity ratio (β) and the mass-transfer rate coefficient (α). DDMT models use the hysteretic σb-σf relationship observed while solute tracers are injected and then flushed from a sample media. Due to limitations in observing the hysteretic σb-σf relationship, this method has not been used to characterize low permeability samples. We have developed an experimental method for testing porous rock cores that allows us to develop a fundamental understanding of contaminant storage and release in consolidated rock. We test the approach on cores from sedimentary rock sites where mass transfer is expected to occur between hydraulically connected fractures and the adjacent low permeability rock matrix. Our method uses a Hassler-type core holder, designed to apply confining pressure around the outside of a sample core, which hydraulically isolates the sample core, allowing water to be injected into it at increased pressures. The experimental apparatus was also designed to measure σb with spectral induced polarization (SIP) measurements, and σf from a sampling port located at the center of the core. Cores were initially saturated with a solution with high electrical conductivity ( 80000 μS/cm). DI water was then injected into the cores at elevated pressures (>60 psi) and the saturating solution was flushed from the cores, in order to generate flow rates fast enough to capture the non-linear σb-σf relationship

  17. 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

  18. 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

  19. Catalytic oxidation of olefins and sulfides in the presence of hydrazone-oxidovanadium(V) complex containing VOCl.sub.2./sub..sup.+./sup. core

    Czech Academy of Sciences Publication Activity Database

    Bikas, R.; Ghorbanloo, M.; Jafari, S.; Eigner, Václav; Dušek, Michal

    2016-01-01

    Roč. 453, Nov (2016), s. 78-85 ISSN 0020-1693 R&D Projects: GA ČR(CZ) GA14-03276S; GA MŠk LO1603 Institutional support: RVO:68378271 Keywords : oxidovanadium(V) * catalytic oxidation * hydrazone ligand * crystal structure * VOCl 2 + Subject RIV: CA - Inorganic Chemistry Impact factor: 2.002, year: 2016

  20. Quantitative determination of vortex core dimensions in head‑to‑head domain walls using off‑axis electron holography

    DEFF Research Database (Denmark)

    Junginger, F; Klaui, M; Backes, D

    2008-01-01

    In this paper, we present a complete three-dimensional characterization of vortex core spin structures, which is important for future magnetic data storage based on vortex cores in disks and in wires. Using electron holography to examine vortices in patterned Permalloy devices we have quantitativ...

  1. Mechanisms of mono- and poly-ubiquitination: Ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine

    Directory of Open Access Journals (Sweden)

    Sadowski Martin

    2010-08-01

    Full Text Available Abstract Ubiquitination involves the attachment of ubiquitin to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Ubiquitin attachment to different lysine residues can generate diverse substrate-ubiquitin structures, targeting proteins to different fates. The mechanisms of lysine selection are not well understood. Ubiquitination by the largest group of E3 ligases, the RING-family E3 s, is catalyzed through co-operation between the non-catalytic ubiquitin-ligase (E3 and the ubiquitin-conjugating enzyme (E2, where the RING E3 binds the substrate and the E2 catalyzes ubiquitin transfer. Previous studies suggest that ubiquitination sites are selected by E3-mediated positioning of the lysine toward the E2 active site. Ultimately, at a catalytic level, ubiquitination of lysine residues within the substrate or ubiquitin occurs by nucleophilic attack of the lysine residue on the thioester bond linking the E2 catalytic cysteine to ubiquitin. One of the best studied RING E3/E2 complexes is the Skp1/Cul1/F box protein complex, SCFCdc4, and its cognate E2, Cdc34, which target the CDK inhibitor Sic1 for K48-linked polyubiquitination, leading to its proteasomal degradation. Our recent studies of this model system demonstrated that residues surrounding Sic1 lysines or lysine 48 in ubiquitin are critical for ubiquitination. This sequence-dependence is linked to evolutionarily conserved key residues in the catalytic region of Cdc34 and can determine if Sic1 is mono- or poly-ubiquitinated. Our studies indicate that amino acid determinants in the Cdc34 catalytic region and their compatibility to those surrounding acceptor lysine residues play important roles in lysine selection. This may represent a general mechanism in directing the mode of ubiquitination in E2 s.

  2. Synthesis of Superparamagnetic Core-Shell Structure Supported Pd Nanocatalysts for Catalytic Nitrite Reduction with Enhanced Activity, No Detection of Undesirable Product of Ammonium, and Easy Magnetic Separation Capability.

    Science.gov (United States)

    Sun, Wuzhu; Yang, Weiyi; Xu, Zhengchao; Li, Qi; Shang, Jian Ku

    2016-01-27

    Superparamagnetic nanocatalysts could minimize both the external and internal mass transport limitations and neutralize OH(-) produced in the reaction more effectively to enhance the catalytic nitrite reduction efficiency with the depressed product selectivity to undesirable ammonium, while possess an easy magnetic separation capability. However, commonly used qusi-monodispersed superparamagnetic Fe3O4 nanosphere is not suitable as catalyst support for nitrite reduction because it could reduce the catalytic reaction efficiency and the product selectivity to N2, and the iron leakage could bring secondary contamination to the treated water. In this study, protective shells of SiO2, polymethylacrylic acid, and carbon were introduced to synthesize Fe3O4@SiO2/Pd, Fe3O4@PMAA/Pd, and Fe3O4@C/Pd catalysts for catalytic nitrite reduction. It was found that SiO2 shell could provide the complete protection to Fe3O4 nanosphere core among these shells. Because of its good dispersion, dense structure, and complete protection to Fe3O4, the Fe3O4@SiO2/Pd catalyst demonstrated the highest catalytic nitrite reduction activity without the detection of NH4(+) produced. Due to this unique structure, the activity of Fe3O4@SiO2/Pd catalysts for nitrite reduction was found to be independent of the Pd nanoparticle size or shape, and their product selectivity was independent of the Pd nanoparticle size, shape, and content. Furthermore, their superparamagnetic nature and high saturation magnetization allowed their easy magnetic separation from treated water, and they also demonstrated a good stability during the subsequent recycling experiment.

  3. Examining the similarities and differences of OMERACT core sets using the ICF: first step towards an improved domain specification and development of an item pool to measure functioning and health.

    Science.gov (United States)

    Escorpizo, Reuben; Boers, Maarten; Stucki, Gerold; Boonen, Annelies

    2011-08-01

    To contribute to the discussion on a common approach for domain selection in the Outcomes in Rheumatology Clinical Trials (OMERACT) process. First, this article reports on the consistency in the selection and names of the domains of the current OMERACT core set, and next on the comparability of the specifications of concepts that are relevant within the domains. For this purpose, a convenience sample of 4 OMERACT core sets was used: rheumatoid arthritis (RA), psoriatic arthritis (PsA), longitudinal observational studies (LOS) in rheumatology, and ankylosing spondylitis (AS). Domains from the different core sets were compared directly. To be able to compare the specific content of the domains, the concepts contained in the questionnaires that were considered or proposed to measure the domains were identified and linked to the category of the International Classification of Functioning, Disability, and Health (ICF) that best fit that construct. Large differences in the domains, and lack of domain definitions, were noted among the 4 OMERACT core sets. When comparing the concepts in the questionnaires that represent the domains, core sets differed also in the number and type of constructs that were addressed within each of the domains. Especially for the specification of the concepts within the domains Discomfort and Disability, the ICF proved to be useful as external reference to classify the different constructs. Our exercise suggests that the OMERACT process could benefit from a standardized approach to select, define, and specify domains, and demonstrated that the ICF is useful for further classification of the more specific concepts of "what to measure" within the domains. A clear definition and classification of domains and their specification can be useful as a starting point to build a pool of items that could then be used to develop new instruments to assess functioning and health for rheumatological conditions.

  4. Core domain and outcome measurement sets for shoulder pain trials are needed: Systematic review of physical therapy trials

    NARCIS (Netherlands)

    M.J. Page (Matthew J.); J.E. McKenzie (Joanne E.); S.E. Green (Sally E.); D.E. Beaton (Dorcas E.); N.B. Jain (Nitin B.); M. Lenza (Mario); A.P. Verhagen (Arianne); S. Surace (Stephen); J. Deitch (Jessica); R. Buchbinder (Rachelle)

    2015-01-01

    textabstractObjectives To explore the outcome domains and measurement instruments reported in published randomized controlled trials of physical therapy interventions for shoulder pain (rotator cuff disease, adhesive capsulitis, or nonspecific shoulder pain). Study Design and Setting We included

  5. Characterization of the roles of the catalytic domains of Mycobacterium tuberculosis ligase D in Ku-dependent error-prone DNA end joining.

    Science.gov (United States)

    Wright, Douglas; DeBeaux, Austin; Shi, Runhua; Doherty, Aidan J; Harrison, Lynn

    2010-09-01

    We previously established an Escherichia coli strain capable of re-circularizing linear plasmid DNA by expressing the Mycobacterium tuberculosis Ku (Mt-Ku) and Mycobacterium tuberculosis ligase D (Mt-LigD) proteins from the E.coli chromosome. Repair was predominately mutagenic due to deletions at the termini. We hypothesized that these deletions could be due to a nuclease activity of Mt-LigD that was previously detected in vitro. Mt-LigD has three domains: an N-terminal polymerase domain (PolDom), a central domain with 3'-phosphoesterase and nuclease activity and a C-terminal ligase domain (LigDom). We generated bacterial strains expressing Mt-Ku and mutant versions of Mt-LigD. Plasmid re-circularization experiments in bacteria showed that the PolDom alone had no re-circularization activity. However, an increase in the total and accurate repair was found when the central domain was deleted. This provides further evidence that this central domain does have nuclease activity that can generate deletions during repair. Deletion of only the PolDom of Mt-LigD resulted in a complete loss of accurate repair and a significant reduction in total repair. This is in agreement with published in vitro work indicating that the PolDom is the major Mt-Ku-binding site. Interestingly, the LigDom alone was able to re-circularize plasmid DNA but only in an Mt-Ku-dependent manner, suggesting a potential second site for Ku-LigD interaction. This work has increased our understanding of the mutagenic repair by Mt-Ku and Mt-LigD and has extended the in vitro biochemical experiments by examining the importance of the Mt-LigD domains during repair in bacteria.

  6. Establishing Core Outcome Domains in Hemodialysis: Report of the Standardized Outcomes in Nephrology-Hemodialysis (SONG-HD) Consensus Workshop.

    Science.gov (United States)

    Tong, Allison; Manns, Braden; Hemmelgarn, Brenda; Wheeler, David C; Evangelidis, Nicole; Tugwell, Peter; Crowe, Sally; Van Biesen, Wim; Winkelmayer, Wolfgang C; O'Donoghue, Donal; Tam-Tham, Helen; Shen, Jenny I; Pinter, Jule; Larkins, Nicholas; Youssouf, Sajeda; Mandayam, Sreedhar; Ju, Angela; Craig, Jonathan C

    2017-01-01

    Evidence-informed decision making in clinical care and policy in nephrology is undermined by trials that selectively report a large number of heterogeneous outcomes, many of which are not patient centered. The Standardized Outcomes in Nephrology-Hemodialysis (SONG-HD) Initiative convened an international consensus workshop on November 7, 2015, to discuss the identification and implementation of a potential core outcome set for all trials in hemodialysis. The purpose of this article is to report qualitative analyses of the workshop discussions, describing the key aspects to consider when establishing core outcomes in trials involving patients on hemodialysis therapy. Key stakeholders including 8 patients/caregivers and 47 health professionals (nephrologists, policymakers, industry, and researchers) attended the workshop. Attendees suggested that identifying core outcomes required equitable stakeholder engagement to ensure relevance across patient populations, flexibility to consider evolving priorities over time, deconstruction of language and meaning for conceptual consistency and clarity, understanding of potential overlap and associations between outcomes, and an assessment of applicability to the range of interventions in hemodialysis. For implementation, they proposed that core outcomes must have simple, inexpensive, and validated outcome measures that could be used in clinical care (quality indicators) and trials (including pragmatic trials) and endorsement by regulatory agencies. Integrating these recommendations may foster acceptance and optimize the uptake and translation of core outcomes in hemodialysis, leading to more informative research, for better treatment and improved patient outcomes. Copyright © 2016 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  7. Establishing Core Outcome Domains in Hemodialysis: Report of the Standardized Outcomes in Nephrology−Hemodialysis (SONG-HD) Consensus Workshop

    Science.gov (United States)

    Tong, Allison; Manns, Braden; Hemmelgarn, Brenda; Wheeler, David C.; Evangelidis, Nicole; Tugwell, Peter; Crowe, Sally; Van Biesen, Wim; Winkelmayer, Wolfgang C.; O’Donoghue, Donal; Tam-Tham, Helen; Shen, Jenny; Pinter, Jule; Larkins, Nicholas; Youssouf, Sajeda; Mandayam, Sreedhar; Ju, Angela; Craig, Jonathan C.

    2017-01-01

    Evidence-informed decision-making in clinical care and policy in nephrology is undermined by trials that selectively report a large number of heterogeneous outcomes, many of which are not patient-centered. The Standardized Outcomes in Nephrology−Hemodialysis (SONG-HD) Initiative convened an international consensus workshop on November 7, 2015, to discuss the identification and implementation of a potential core outcome set for all trials in hemodialysis. The purpose of this article is to report qualitative analyses of the workshop discussions, describing the key aspects to consider when establishing core outcomes in trials involving patients on hemodialysis. Key stakeholders including eight patients/caregivers and 47 health professionals (nephrologists, policy makers, industry, researchers) attended the workshop. Attendees suggested that identifying core outcomes required equitable stakeholder engagement to ensure relevance across patient populations; flexibility to consider evolving priorities over time; deconstruction of language and meaning for conceptual consistency and clarity; understanding of potential overlap and associations between outcomes; and an assessment of applicability to the range of interventions in hemodialysis. For implementation, they proposed that core outcomes must have simple, inexpensive and validated outcome measures that could be used in clinical care (quality ndicators) and trials (including pragmatic trials), and endorsement by regulatory agencies. Integrating these recommendations may foster acceptance and optimize the uptake and translation of core outcomes in hemodialysis, leading to more informative research, for better treatment, and improved patient outcomes. PMID:27497527

  8. 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....... The protein sequence has low overall homology, apart from very small NH2- and COOH-terminal motifs. At the junctions between the distal globular domains and the coiled-coil regions lie glycosylation sites, with up to three N-linked oligosaccharides and probably three chondroitin chains. Three other Ser...

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

    KAUST Repository

    Liu, Chenggang; Axtell, Michael J.; Fedoroff, Nina V.

    2012-01-01

    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

  10. Identification and Analysis of the SET-Domain Family in Silkworm, Bombyx mori

    Directory of Open Access Journals (Sweden)

    Hailong Zhao

    2015-01-01

    Full Text Available As an important economic insect, Bombyx mori is also a useful model organism for lepidopteran insect. SET-domain-containing proteins belong to a group of enzymes named after a common domain that utilizes the cofactor S-adenosyl-L-methionine (SAM to achieve methylation of its substrates. Many SET-domain-containing proteins have been shown to display catalytic activity towards particular lysine residues on histones, but emerging evidence also indicates that various nonhistone proteins are specifically targeted by this clade of enzymes. To explore their diverse functions of SET-domain superfamily in insect, we identified, cloned, and analyzed the SET-domains proteins in silkworm, Bombyx mori. Firstly, 24 genes containing SET domain from silkworm genome were characterized and 17 of them belonged to six subfamilies of SUV39, SET1, SET2, SUV4-20, EZ, and SMYD. Secondly, SET domains of silkworm SET-domain family were intraspecifically and interspecifically conserved, especially for the catalytic core “NHSC” motif, substrate binding site, and catalytic site in the SET domain. Lastly, further analyses indicated that silkworm SET-domain gene BmSu(var3-9 owned different characterization and expression profiles compared to other invertebrates. Overall, our results provide a new insight into the functional and evolutionary features of SET-domain family.

  11. Using the International Classification of Functioning, Disability, and Health to identify outcome domains for a core outcome set for aphasia: a comparison of stakeholder perspectives.

    Science.gov (United States)

    Wallace, Sarah J; Worrall, Linda; Rose, Tanya; Le Dorze, Guylaine

    2017-11-12

    This study synthesised the findings of three separate consensus processes exploring the perspectives of key stakeholder groups about important aphasia treatment outcomes. This process was conducted to generate recommendations for outcome domains to be included in a core outcome set for aphasia treatment trials. International Classification of Functioning, Disability, and Health codes were examined to identify where the groups of: (1) people with aphasia, (2) family members, (3) aphasia researchers, and (4) aphasia clinicians/managers, demonstrated congruence in their perspectives regarding important treatment outcomes. Codes were contextualized using qualitative data. Congruence across three or more stakeholder groups was evident for ICF chapters: Mental functions; Communication; and Services, systems, and policies. Quality of life was explicitly identified by clinicians/managers and researchers, while people with aphasia and their families identified outcomes known to be determinants of quality of life. Core aphasia outcomes include: language, emotional wellbeing, communication, patient-reported satisfaction with treatment and impact of treatment, and quality of life. International Classification of Functioning, Disability, and Health coding can be used to compare stakeholder perspectives and identify domains for core outcome sets. Pairing coding with qualitative data may ensure important nuances of meaning are retained. Implications for rehabilitation The outcomes measured in treatment research should be relevant to stakeholders and support health care decision making. Core outcome sets (agreed, minimum set of outcomes, and outcome measures) are increasingly being used to ensure the relevancy and consistency of the outcomes measured in treatment studies. Important aphasia treatment outcomes span all components of the International Classification of Functioning, Disability, and Health. Stakeholders demonstrated congruence in the identification of important

  12. Catalytic pyrolysis of hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Vail' eva, N A; Buyanov, R A

    1979-01-01

    Catalytic pyrolysis of petroleum fractions (undecane) was performed with the object of clarifying such questions as the mechanism of action of the catalyst, the concepts of activity and selectivity of the catalyst, the role of transport processes, the temperature ranges and limitations of the catalytic process, the effect of the catalyst on secondary processes, and others. Catalysts such as quartz, MgO, Al/sub 2/O/sub 3/, were used. Analysis of the experimental findings and the fact that the distribution of products is independent of the nature of the surface, demonstrate that the pyrolysis of hydrocarbons in the presence of catalysts is based on the heterogeneous-homogeneous radical-chain mechanism of action, and that the role of the catalysts reduces to increasing the concentration of free radicals. The concept of selectivity cannot be applied to catalysts here, since they do not affect the mechanism of the unfolding of the process of pyrolysis and their role consists solely in initiating the process. In catalytic pyrolysis the concepts of kinetic and diffusive domains of unfolding of the catalytic reaction do not apply, and only the outer surface of the catalyst is engaged, whereas the inner surface merely promotes deletorious secondary processes reducing the selectivity of the process and the activity of the catalyst. 6 references, 2 figures.

  13. Dense SDM (12-core × 3-mode) transmission over 527 km with 33.2-ns mode-dispersion employing low-complexity parallel MIMO frequency-domain equalization

    DEFF Research Database (Denmark)

    Shibahara, K.; Mizuno, T.; Takara, H.

    We demonstrate 12-core × 3-mode dense SDM transmission over 527 km graded-index multi-core few-mode fiber without mode-dispersion management. Employing low baud rate multi-carrier signal and frequency-domain equalization enables 33.2-ns DMD compensation with low computational complexity. © 2015 OSA...

  14. Fuel rich and fuel lean catalytic combustion of the stabilized confined turbulent gaseous diffusion flames over noble metal disc burners

    Directory of Open Access Journals (Sweden)

    Amal S. Zakhary

    2014-03-01

    Full Text Available Catalytic combustion of stabilized confined turbulent gaseous diffusion flames using Pt/Al2O3 and Pd/Al2O3 disc burners situated in the combustion domain under both fuel-rich and fuel-lean conditions was experimentally studied. Commercial LPG fuel having an average composition of: 23% propane, 76% butane, and 1% pentane was used. The thermal structure of these catalytic flames developed over Pt/Al2O3 and Pd/Al2O3 burners were examined via measuring the mean temperature distribution in the radial direction at different axial locations along the flames. Under-fuel-rich condition the flames operated over Pt catalytic disc attained high temperature values in order to express the progress of combustion and were found to achieve higher activity as compared to the flames developed over Pd catalytic disc. These two types of catalytic flames demonstrated an increase in the reaction rate with the downstream axial distance and hence, an increase in the flame temperatures was associated with partial oxidation towards CO due to the lack of oxygen. However, under fuel-lean conditions the catalytic flame over Pd catalyst recorded comparatively higher temperatures within the flame core in the near region of the main reaction zone than over Pt disc burner. These two catalytic flames over Pt and Pd disc burners showed complete oxidation to CO2 since the catalytic surface is covered by more rich oxygen under the fuel-lean condition.

  15. Catalytic treatment

    Energy Technology Data Exchange (ETDEWEB)

    Bindley, W T.R.

    1931-04-18

    An apparatus is described for the catalytic treatment of liquids, semi-liquids, and gases comprising a vessel into which the liquid, semi-liquid, or gas to be treated is introduced through a common inlet to a chamber within the vessel whence it passes to contact with a catalyst through radially arranged channels or passages to a common outlet chamber.

  16. C-Terminal Substitution of HBV Core Proteins with Those from DHBV Reveals That Arginine-Rich 167RRRSQSPRR175 Domain Is Critical for HBV Replication

    Science.gov (United States)

    Kim, Taeyeung; Shin, Bo-Hye; Park, Gil-Soon; Park, Sun; Chwae, Yong-Joon; Shin, Ho-Joon; Kim, Kyongmin

    2012-01-01

    To investigate the contributions of carboxyl-terminal nucleic acid binding domain of HBV core (C) protein for hepatitis B virus (HBV) replication, chimeric HBV C proteins were generated by substituting varying lengths of the carboxyl-terminus of duck hepatitis B virus (DHBV) C protein for the corresponding regions of HBV C protein. All chimeric C proteins formed core particles. A chimeric C protein with 221–262 amino acids of DHBV C protein, in place of 146–185 amino acids of the HBV C protein, supported HBV pregenomic RNA (pgRNA) encapsidation and DNA synthesis: 40% amino acid sequence identity or 45% homology in the nucleic-acid binding domain of HBV C protein was sufficient for pgRNA encapsidation and DNA synthesis, although we predominantly detected spliced DNA. A chimeric C protein with 221–241 and 251–262 amino acids of DHBV C, in place of HBV C 146–166 and 176–185 amino acids, respectively, could rescue full-length DNA synthesis. However, a reciprocal C chimera with 242–250 of DHBV C (242RAGSPLPRS 250) introduced in place of 167–175 of HBV C (167RRRSQSPRR 175) significantly decreased pgRNA encapsidation and DNA synthesis, and full-length DNA was not detected, demonstrating that the arginine-rich 167RRRSQSPRR175 domain may be critical for efficient viral replication. Five amino acids differing between viral species (underlined above) were tested for replication rescue; R169 and R175 were found to be important. PMID:22911745

  17. 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.

  18. 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)

    Wang Aijun; Li Yongfang; Li Zhonghua; Feng Jiuju; Sun Yanli; Chen Jianrong

    2012-01-01

    Monodisperse Fe 3 O 4 magnetic nanoparticles (NPs) were prepared under facile solvothermal conditions and successively functionalized with silica and Au to form core/shell Fe 3 O 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 × 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 Fe 3 O 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: ► Synthesis of monodispersed Fe 3 O 4 nanoparticles. ► Fabrication of core/shell Fe 3 O 4 -silica-Au nanoparticles. ► Construction of a novel glucose sensor with wide linear range, high sensitivity and fast response.

  19. 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)

    Yang, Zhimin; Wang, Qiang; Shan, Xiaoye; Zhu, Hongjun; Li, Wei-qi; Chen, Guang-hui

    2015-01-01

    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

  20. Identification of distinct SET/TAF-Ibeta domains required for core histone binding and quantitative characterisation of the interaction.

    Science.gov (United States)

    Karetsou, Zoe; Emmanouilidou, Anastasia; Sanidas, Ioannis; Liokatis, Stamatis; Nikolakaki, Eleni; Politou, Anastasia S; Papamarcaki, Thomais

    2009-04-09

    The assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Ibeta belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Ibeta, we designed several SET/TAF-Ibeta truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays. Wild type SET/TAF-Ibeta binds to histones H2B and H3 with Kd values of 2.87 and 0.15 microM, respectively. The preferential binding of SET/TAF-Ibeta to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Ibeta, as well as the H3 amino-terminal tail, are dispensable for this interaction. This type of analysis allowed us to assess the relative affinities of SET/TAF-Ibeta for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Ibeta and can be valuable to understand the role of SET/TAF-Ibeta in chromatin function.

  1. Identification of distinct SET/TAF-Iβ domains required for core histone binding and quantitative characterisation of the interaction

    Science.gov (United States)

    Karetsou, Zoe; Emmanouilidou, Anastasia; Sanidas, Ioannis; Liokatis, Stamatis; Nikolakaki, Eleni; Politou, Anastasia S; Papamarcaki, Thomais

    2009-01-01

    Background The assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Iβ belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Iβ, we designed several SET/TAF-Iβ truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays. Results Wild type SET/TAF-Iβ binds to histones H2B and H3 with Kd values of 2.87 and 0.15 μM, respectively. The preferential binding of SET/TAF-Iβ to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Iβ, as well as the H3 amino-terminal tail, are dispensable for this interaction. Conclusion This type of analysis allowed us to assess the relative affinities of SET/TAF-Iβ for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Iβ and can be valuable to understand the role of SET/TAF-Iβ in chromatin function. PMID:19358706

  2. The C Terminus of the Core β-Ladder Domain in Japanese Encephalitis Virus Nonstructural Protein 1 Is Flexible for Accommodation of Heterologous Epitope Fusion.

    Science.gov (United States)

    Yen, Li-Chen; Liao, Jia-Teh; Lee, Hwei-Jen; Chou, Wei-Yuan; Chen, Chun-Wei; Lin, Yi-Ling; Liao, Ching-Len

    2016-02-01

    NS1 is the only nonstructural protein that enters the lumen of the endoplasmic reticulum (ER), where NS1 is glycosylated, forms a dimer, and is subsequently secreted during flavivirus replication as dimers or hexamers, which appear to be highly immunogenic to the infected host, as protective immunity can be elicited against homologous flavivirus infections. Here, by using a trans-complementation assay, we identified the C-terminal end of NS1 derived from Japanese encephalitis virus (JEV), which was more flexible than other regions in terms of housing foreign epitopes without a significant impact on virus replication. This mapped flexible region is located in the conserved tip of the core β-ladder domain of the multimeric NS1 structure and is also known to contain certain linear epitopes, readily triggering specific antibody responses from the host. Despite becoming attenuated, recombinant JEV with insertion of a neutralizing epitope derived from enterovirus 71 (EV71) into the C-terminal end of NS1 not only could be normally released from infected cells, but also induced dual protective immunity for the host to counteract lethal challenge with either JEV or EV71 in neonatal mice. These results indicated that the secreted multimeric NS1 of flaviviruses may serve as a natural protein carrier to render epitopes of interest more immunogenic in the C terminus of the core β-ladder domain. The positive-sense RNA genomes of mosquito-borne flaviviruses appear to be flexible in terms of accommodating extra insertions of short heterologous antigens into their virus genes. Here, we illustrate that the newly identified C terminus of the core β-ladder domain in NS1 could be readily inserted into entities such as EV71 epitopes, and the resulting NS1-epitope fusion proteins appeared to maintain normal virus replication, secretion ability, and multimeric formation from infected cells. Nonetheless, such an insertion attenuated the recombinant JEV in mice, despite having retained

  3. Risperidone for the core symptom domains of autism: results from the study by the autism network of the research units on pediatric psychopharmacology.

    Science.gov (United States)

    McDougle, Christopher J; Scahill, Lawrence; Aman, Michael G; McCracken, James T; Tierney, Elaine; Davies, Mark; Arnold, L Eugene; Posey, David J; Martin, Andrès; Ghuman, Jaswinder K; Shah, Bhavik; Chuang, Shirley Z; Swiezy, Naomi B; Gonzalez, Nilda M; Hollway, Jill; Koenig, Kathleen; McGough, James J; Ritz, Louise; Vitiello, Benedetto

    2005-06-01

    Risperidone has been found efficacious for decreasing severe tantrums, aggression, and self-injurious behavior in children and adolescents with autistic disorder (autism). The authors report on whether risperidone improves the core symptoms of autism, social and communication impairment and repetitive and stereotyped behavior. The database from an 8-week double-blind, placebo-controlled trial (N=101) and 16-week open-label continuation study (N=63) of risperidone for children and adolescents with autism was used to test for drug effects on secondary outcome measures: scores on the Ritvo-Freeman Real Life Rating Scale, the Children's Yale-Brown Obsessive Compulsive Scale, and the maladaptive behavior domain of the Vineland Adaptive Behavior Scales. Compared to placebo, risperidone led to a significantly greater reduction in the overall score on the Ritvo-Freeman Real Life Rating Scale, as well as the scores on the subscales for sensory motor behaviors (subscale I), affectual reactions (subscale III), and sensory responses (subscale IV). No statistically significant difference was observed, however, on the subscale for social relatedness (subscale II) or language (subscale V). Risperidone also resulted in significantly greater reductions in scores on the Children's Yale-Brown Obsessive Compulsive Scale and Vineland maladaptive behavior domain. This pattern of treatment response was maintained for 6 months. Risperidone led to significant improvements in the restricted, repetitive, and stereotyped patterns of behavior, interests, and activities of autistic children but did not significantly change their deficit in social interaction and communication. Further research is necessary to develop effective treatments for the core social and communicative impairments of autism.

  4. 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.

  5. The FA Core Complex Contains a Homo-dimeric Catalytic Module for the Symmetric Mono-ubiquitination of FANCI-FANCD2

    Directory of Open Access Journals (Sweden)

    Paolo Swuec

    2017-01-01

    Full Text Available Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core complex. FANCI and FANCD2 form a stable complex; however, the molecular basis of their ubiquitination is ill defined. FANCD2 mono-ubiquitination by FANCL is stimulated by the presence of the FANCB and FAAP100 core complex components, through an unknown mechanism. How FANCI mono-ubiquitination is achieved remains unclear. Here, we use structural electron microscopy, combined with crosslink-coupled mass spectrometry, to find that FANCB, FANCL, and FAAP100 form a dimer of trimers, containing two FANCL molecules that are ideally poised to target both FANCI and FANCD2 for mono-ubiquitination. The FANCC-FANCE-FANCF subunits bridge between FANCB-FANCL-FAAP100 and the FANCI-FANCD2 substrate. A transient interaction with FANCC-FANCE-FANCF alters the FANCI-FANCD2 configuration, stabilizing the dimerization interface. Our data provide a model to explain how equivalent mono-ubiquitination of FANCI and FANCD2 occurs.

  6. A Single-Domain Llama Antibody Potently Inhibits the Enzymatic Activity of Botulinum Neurotoxin by Binding to the Non-Catalytic [alpha]-Exosite Binding Region

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Jianbo; Thompson, Aaron A.; Fan, Yongfeng; Lou, Jianlong; Conrad, Fraser; Ho, Mengfei; Pires-Alves, Melissa; Wilson, Brenda A.; Stevens, Raymond C.; Marks, James D. (UIUC); (Scripps); (UCSF)

    2010-08-13

    Ingestion or inhalation of botulinum neurotoxin (BoNT) results in botulism, a severe and frequently fatal disease. Current treatments rely on antitoxins, which, while effective, cannot reverse symptoms once BoNT has entered the neuron. For treatments that can reverse intoxication, interest has focused on developing inhibitors of the enzymatic BoNT light chain (BoNT Lc). Such inhibitors typically mimic substrate and bind in or around the substrate cleavage pocket. To explore the full range of binding sites for serotype A light chain (BoNT/A Lc) inhibitors, we created a library of non-immune llama single-domain VHH (camelid heavy-chain variable region derived from heavy-chain-only antibody) antibodies displayed on the surface of the yeast Saccharomyces cerevisiae. Library selection on BoNT/A Lc yielded 15 yeast-displayed VHH with equilibrium dissociation constants (K{sub d}) from 230 to 0.03 nM measured by flow cytometry. Eight of 15 VHH inhibited the cleavage of substrate SNAP25 (synaptosome-associated protein of 25,000 Da) by BoNT/A Lc. The most potent VHH (Aa1) had a solution K{sub d} for BoNT/A Lc of 1.47 x 10{sup -10} M and an IC{sub 50} (50% inhibitory concentration) of 4.7 x 10{sup -10} M and was resistant to heat denaturation and reducing conditions. To understand the mechanism by which Aa1 inhibited catalysis, we solved the X-ray crystal structure of the BoNT/A Lc-Aa1 VHH complex at 2.6 {angstrom} resolution. The structure reveals that the Aa1 VHH binds in the {alpha}-exosite of the BoNT/A Lc, far from the active site for catalysis. The study validates the utility of non-immune llama VHH libraries as a source of enzyme inhibitors and identifies the BoNT/A Lc {alpha}-exosite as a target for inhibitor development.

  7. Modularized Functions of the Fanconi Anemia Core Complex

    Directory of Open Access Journals (Sweden)

    Yaling Huang

    2014-06-01

    Full Text Available The Fanconi anemia (FA core complex provides the essential E3 ligase function for spatially defined FANCD2 ubiquitination and FA pathway activation. Of the seven FA gene products forming the core complex, FANCL possesses a RING domain with demonstrated E3 ligase activity. The other six components do not have clearly defined roles. Through epistasis analyses, we identify three functional modules in the FA core complex: a catalytic module consisting of FANCL, FANCB, and FAAP100 is absolutely required for the E3 ligase function, and the FANCA-FANCG-FAAP20 and the FANCC-FANCE-FANCF modules provide nonredundant and ancillary functions that help the catalytic module bind chromatin or sites of DNA damage. Disruption of the catalytic module causes complete loss of the core complex function, whereas loss of any ancillary module component does not. Our work reveals the roles of several FA gene products with previously undefined functions and a modularized assembly of the FA core complex.

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

  9. Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high affinity agonist dysiherbaine and the functional antagonist 8,9-dideoxyneodysiherbaine

    DEFF Research Database (Denmark)

    Frydenvang, Karla Andrea; Lash, L Leanne; Naur, Peter

    2009-01-01

    The prevailing structural model for ligand activation of ionotropic glutamate receptors posits that agonist efficacy arises from the stability and magnitude of induced domain closure in the ligand-binding core structure. Here we describe an exception to the correlation between ligand efficacy and...

  10. Mutational analysis of a ras catalytic domain

    DEFF Research Database (Denmark)

    Willumsen, B M; Papageorge, A G; Kung, H F

    1986-01-01

    localization. We speculate that this latter region interacts with the putative cellular target of ras. The results suggest that transforming ras proteins require membrane localization, guanosine nucleotide binding, and an additional undefined function that may represent interaction with their target....

  11. Subtype-selective regulation of IP(3) receptors by thimerosal via cysteine residues within the IP(3)-binding core and suppressor domain.

    Science.gov (United States)

    Khan, Samir A; Rossi, Ana M; Riley, Andrew M; Potter, Barry V L; Taylor, Colin W

    2013-04-15

    IP(3)R (IP(3) [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca(2+) channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP(3)R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP(3)-evoked Ca(2+) release via IP(3)R1 and IP(3)R2, but inhibited IP(3)R3. Activation of IP(3)R is initiated by IP(3) binding to the IBC (IP(3)-binding core; residues 224-604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1-223). Thimerosal (100 μM) stimulated IP(3) binding to the isolated NT (N-terminal; residues 1-604) of IP(3)R1 and IP(3)R2, but not to that of IP(3)R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP(3)) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP(3)R activation. IP(3) binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP(3)R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP(3) binding to the chimaeric NT and IP(3)-evoked Ca(2+) release from the chimaeric IP(3)R. This is the first systematic analysis of the effects of a thiol reagent on each IP(3)R subtype. We conclude that thimerosal selectively sensitizes IP(3)R1 and IP(3)R2 to IP(3) by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor.

  12. Subtype-selective regulation of IP3 receptors by thimerosal via cysteine residues within the IP3-binding core and suppressor domain

    Science.gov (United States)

    Khan, Samir A.; Rossi, Ana M.; Riley, Andrew M.; Potter, Barry V. L.; Taylor, Colin W.

    2013-01-01

    IP3R (IP3 [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca2+ channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP3R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP3-evoked Ca2+ release via IP3R1 and IP3R2, but inhibited IP3R3. Activation of IP3R is initiated by IP3 binding to the IBC (IP3-binding core; residues 224–604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1–223). Thimerosal (100 μM) stimulated IP3 binding to the isolated NT (N-terminal; residues 1–604) of IP3R1 and IP3R2, but not to that of IP3R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP3) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP3R activation. IP3 binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP3R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP3 binding to the chimaeric NT and IP3-evoked Ca2+ release from the chimaeric IP3R. This is the first systematic analysis of the effects of a thiol reagent on each IP3R subtype. We conclude that thimerosal selectively sensitizes IP3R1 and IP3R2 to IP3 by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor. PMID:23282150

  13. Aggregation-primed molten globule conformers of the p53 core domain provide potential tools for studying p53C aggregation in cancer.

    Science.gov (United States)

    Pedrote, Murilo M; de Oliveira, Guilherme A P; Felix, Adriani L; Mota, Michelle F; Marques, Mayra de A; Soares, Iaci N; Iqbal, Anwar; Norberto, Douglas R; Gomes, Andre M O; Gratton, Enrico; Cino, Elio A; Silva, Jerson L

    2018-05-31

    The functionality of the tumor suppressor p53 is altered in more than 50% of human cancers, and many individuals with cancer exhibit amyloid-like buildups of aggregated p53. An understanding of what triggers the pathogenic amyloid conversion of p53 is required for the further development of cancer therapies. Here, perturbation of the p53 core domain (p53C) with sub-denaturing concentrations of guanidine hydrochloride and high hydrostatic pressure revealed native-like molten globule (MG) states, a subset of which were highly prone to amyloidogenic aggregation. We found that MG conformers of p53C, likely representing population-weighted averages of multiple states, have different volumetric properties, as determined by pressure perturbation and size-exclusion chromatography. We also found that they bind the fluorescent dye 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) and have a native-like tertiary structure that occludes the single Trp residue in p53. Fluorescence experiments revealed conformational changes of the single Trp and Tyr residues before p53 unfolding and the presence of MG conformers, some of which were highly prone to aggregation. P53C exhibited marginal unfolding cooperativity, which could be modulated from unfolding to aggregation pathways with chemical or physical forces. We conclude that trapping amyloid precursor states in solution is a promising approach for understanding p53 aggregation in cancer. Our findings support the use of single-Trp fluorescence as a probe for evaluating p53 stability, effects of mutations, and the efficacy of therapeutics designed to stabilize p53. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  14. The cysteine-rich core domain of REIC/Dkk-3 is critical for its effect on monocyte differentiation and tumor regression.

    Science.gov (United States)

    Kinoshita, Rie; Watanabe, Masami; Huang, Peng; Li, Shun-Ai; Sakaguchi, Masakiyo; Kumon, Hiromi; Futami, Junichiro

    2015-06-01

    Reduced expression in immortalized cells (REIC)/Dickkopf (Dkk)-3 is a tumor-suppressor gene and has been studied as a promising therapeutic gene for cancer gene therapy. Intratumoral injection of an adenovirus vector carrying the human REIC/Dkk-3 gene (Ad-REIC) elicits cancer cell-specific apoptosis and anticancer immune responses. The cytokine-like effect of secretory REIC/Dkk-3 on the induction of dendritic cell (DC)-like cell differentiation from monocytes plays a role in systemic anticancer immunity. In the present study, we generated recombinant full-length and N-terminally truncated REIC/Dkk-3 to characterize the biological activity of the protein. During the purification procedure, we identified a 17 kDa cysteine-rich stable product (C17-REIC) showing limited degradation. Further analysis showed that the C17-REIC domain was sufficient for the induction of DC-like cell differentiation from monocytes. Concomitant with the differentiation of DCs, the REIC/Dkk-3 protein induced the phosphorylation of glycogen synthase kinase 3β (GSK-3β) and signal transducers and activators of transcription (STAT) at a level comparable to that of granulocyte/macrophage colony-stimulating factor. In a mouse model of subcutaneous renal adenocarcinoma, intraperitoneal injection of full-length and C17-REIC proteins exerted anticancer effects in parallel with the activation of immunocompetent cells such as DCs and cytotoxic T lymphocytes in peripheral blood. Taken together, our results indicate that the stable cysteine-rich core region of REIC/Dkk-3 is responsible for the induction of anticancer immune responses. Because REIC/Dkk-3 is a naturally circulating serum protein, the upregulation REIC/Dkk-3 protein expression could be a promising option for cancer therapy.

  15. 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)

    NARCIS (Netherlands)

    C.A. Berrevoets (Cor); P. Doesburg (Paul); K. Steketee (Karine); J. Trapman (Jan); A.O. 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

  16. Multiple isoforms for the catalytic subunit of PKA in the basal fungal lineage Mucor circinelloides.

    Science.gov (United States)

    Fernández Núñez, Lucas; Ocampo, Josefina; Gottlieb, Alexandra M; Rossi, Silvia; Moreno, Silvia

    2016-12-01

    Protein kinase A (PKA) activity is involved in dimorphism of the basal fungal lineage Mucor. From the recently sequenced genome of Mucor circinelloides we could predict ten catalytic subunits of PKA. From sequence alignment and structural prediction we conclude that the catalytic core of the isoforms is conserved, and the difference between them resides in their amino termini. This high number of isoforms is maintained in the subdivision Mucoromycotina. Each paralogue, when compared to the ones form other fungi is more homologous to one of its orthologs than to its paralogs. All of these fungal isoforms cannot be included in the class I or II in which fungal protein kinases have been classified. mRNA levels for each isoform were measured during aerobic and anaerobic growth. The expression of each isoform is differential and associated to a particular growth stage. We reanalyzed the sequence of PKAC (GI 20218944), the only cloned sequence available until now for a catalytic subunit of M. circinelloides. PKAC cannot be classified as a PKA because of its difference in the conserved C-tail; it shares with PKB a conserved C2 domain in the N-terminus. No catalytic activity could be measured for this protein nor predicted bioinformatically. It can thus be classified as a pseudokinase. Its importance can not be underestimated since it is expressed at the mRNA level in different stages of growth, and its deletion is lethal. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  17. 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)

    Axelrod, Herbert L.; Das, Debanu; Abdubek, Polat; Astakhova, Tamara; Bakolitsa, Constantina; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Lam, Winnie W.; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    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

  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. A structural role for the PHP domain in E. coli DNA polymerase III.

    Science.gov (United States)

    Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; Lamers, Meindert H

    2013-05-14

    In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

  20. A Study on Dielectric Properties of Cadmium Sulfide-Zinc Sulfide Core-Shell Nanocomposites for Application as Nanoelectronic Filter Component in the Microwave Domain

    Science.gov (United States)

    Devi, Jutika; Datta, Pranayee

    2018-03-01

    Complex permittivities of cadmium sulfide (CdS), zinc sulfide (ZnS), and of cadmium sulfide-zinc sulfide (CdS/ZnS) core-shell nanoparticles embedded in a polyvinyl alcohol matrix (PVA) were measured in liquid phase using a VectorNetwork Analyzer in the frequency range of 500 MHz-10 GHz. These nanocomposites are modeled as an embedded capacitor, and their electric field distribution and polarization have been studied using COMSOL Multiphysics software. By varying the thickness of the shell and the number of inclusions, the capacitance values were estimated. It was observed that CdS, ZnS and CdS/ZnS core-shell nanoparticles embedded in a polyvinyl alcohol matrix show capacitive behavior. There is a strong influence of the dielectric properties in the capacitive behavior of the embedded nanocapacitor. The capping matrix, position and filling factors of nanoinclusions all affect the capacitive behavior of the tested nanocomposites. Application of the CdS, ZnS and CdS/ZnS core-shell nanocomposite as the passive low-pass filter circuit has also been investigated. From the present study, it has been found that CdS/ZnS core-shell nanoparticles embedded in PVA matrix are potential structures for application as nanoelectronic filter components in different areas of communication.

  1. Contribution to the development of methods for nuclear reactor core calculations with APOLLO3 code: domain decomposition in transport theory with nonlinear diffusion acceleration for 2D and 3D geometries

    International Nuclear Information System (INIS)

    Lenain, Roland

    2015-01-01

    This thesis is devoted to the implementation of a domain decomposition method applied to the neutron transport equation. The objective of this work is to access high-fidelity deterministic solutions to properly handle heterogeneities located in nuclear reactor cores, for problems' size ranging from color-sets of assemblies to large reactor cores configurations in 2D and 3D. The innovative algorithm developed during the thesis intends to optimize the use of parallelism and memory. The approach also aims to minimize the influence of the parallel implementation on the performances. These goals match the needs of APOLLO3 project, developed at CEA and supported by EDF and AREVA, which must be a portable code (no optimization on a specific architecture) in order to achieve best estimate modeling with resources ranging from personal computer to compute cluster available for engineers analyses. The proposed algorithm is a Parallel Multigroup-Block Jacobi one. Each sub-domain is considered as a multi-group fixed-source problem with volume-sources (fission) and surface-sources (interface flux between the sub-domains). The multi-group problem is solved in each sub-domain and a single communication of the interface flux is required at each power iteration. The spectral radius of the resolution algorithm is made similar to the one of a classical resolution algorithm with a nonlinear diffusion acceleration method: the well-known Coarse Mesh Finite Difference. In this way an ideal scalability is achievable when the calculation is parallelized. The memory organization, taking advantage of shared memory parallelism, optimizes the resources by avoiding redundant copies of the data shared between the sub-domains. Distributed memory architectures are made available by a hybrid parallel method that combines both paradigms of shared memory parallelism and distributed memory parallelism. For large problems, these architectures provide a greater number of processors and the amount of

  2. 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...

  3. Turning goals into results: the power of catalytic mechanisms.

    Science.gov (United States)

    Collins, J

    1999-01-01

    Most executives have a big, hairy, audacious goal. They write vision statements, formalize procedures, and develop complicated incentive programs--all in pursuit of that goal. In other words, with the best of intentions, they install layers of stultifying bureaucracy. But it doesn't have to be that way. In this article, Jim Collins introduces the catalytic mechanism, a simple yet powerful managerial tool that helps translate lofty aspirations into concrete reality. Catalytic mechanisms are the crucial link between objectives and performance; they are a galvanizing, nonbureaucratic means to turn one into the other. What's the difference between catalytic mechanisms and most traditional managerial controls? Catalytic mechanisms share five characteristics. First, they produce desired results in unpredictable ways. Second, they distribute power for the benefit of the overall system, often to the discomfort of those who traditionally hold power. Third, catalytic mechanisms have teeth. Fourth, they eject "viruses"--those people who don't share the company's core values. Finally, they produce an ongoing effect. Catalytic mechanisms are just as effective for reaching individual goals as they are for corporate ones. To illustrate how catalytic mechanisms work, the author draws on examples of individuals and organizations that have relied on such mechanisms to achieve their goals. The same catalytic mechanism that works in one organization, however, will not necessarily work in another. Catalytic mechanisms must be tailored to specific goals and situations. To help readers get started, the author offers some general principles that support the process of building catalytic mechanisms effectively.

  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 - others: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. Effects of Lateral and Terminal Chains of X-Shaped Bolapolyphiles with Oligo(phenylene ethynylene Cores on Self-Assembly Behavior. Part 2: Domain Formation by Self-Assembly in Lipid Bilayer Membranes

    Directory of Open Access Journals (Sweden)

    Stefan Werner

    2017-09-01

    Full Text Available Supramolecular self-assembly of membrane constituents within a phospholipid bilayer creates complex functional platforms in biological cells that operate in intracellular signaling, trafficking and membrane remodeling. Synthetic polyphilic compounds of macromolecular or small size can be incorporated into artificial phospholipid bilayers. Featuring three or four moieties of different philicities, they reach beyond ordinary amphiphilicity and open up avenues to new functions and interaction concepts. Here, we have incorporated a series of X-shaped bolapolyphiles into DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayers of giant unilamellar vesicles. The bolapolyphiles consist of a rod-like oligo(phenylene ethynylene (OPE core, hydrophilic glycerol-based headgroups with or without oligo(ethylene oxide expansions at both ends and two lateral alkyl chains attached near the center of the OPE core. In the absence of DPPC and water, the compounds showed thermotropic liquid-crystalline behavior with a transition between polyphilic and amphiphilic assembly (see part 1 in this issue. In DPPC membranes, various trends in the domain morphologies were observed upon structure variations, which entailed branched alkyl chains of various sizes, alkyl chain semiperfluorination and size expansion of the headgroups. Observed effects on domain morphology are interpreted in the context of the bulk behavior (part 1 and of a model that was previously developed based on spectroscopic and physicochemical data.

  6. SHORT COMMUNICATION CATALYTIC KINETIC ...

    African Journals Online (AJOL)

    IV) catalyzes the discoloring reaction of DBS-arsenazo oxidized by potassium bromate, a new catalytic kinetic spectrophotometric method for the determination of trace titanium (IV) was developed. The linear range of the determination of ...

  7. Catalytic distillation process

    Science.gov (United States)

    Smith, L.A. Jr.

    1982-06-22

    A method is described 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.

  8. Catalytic distillation structure

    Science.gov (United States)

    Smith, L.A. Jr.

    1984-04-17

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

  9. Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

    NARCIS (Netherlands)

    Breukers, J.A.P.J.; Hoekstra, R.J.

    2004-01-01

    For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The

  10. Synthesis and characterization of branched fcc/hcp ruthenium nanostructures and their catalytic activity in ammonia borane hydrolysis

    KAUST Repository

    AlYami, Noktan

    2018-01-30

    Several systems have shown the ability to stabilize uncommon crystal structures during the synthesis of metallic nanoparticles. By tailoring the nanoparticle crystal structure, the physical and chemical properties of the particles can also be controlled. Herein, we first synthesized branched nanoparticles of mixed hcp/fcc ruthenium, which were formed using tungsten carbonyl [W(CO)6] as both a reducing agent and a source of carbon monoxide. The branched particles were formed from multiple particulates off a central core. High-resolution transmission electron microscopy (HRTEM) clearly showed that the branched structures consisted of aligned hcp crystal domains, a mixture of fcc and hcp crystal domains with several defects and misalignments, and particles that contained multiple cores and branches. Branched particles were also formed with molybdenum carbonyl [Mo(CO)6], and faceted particles of hcp and fcc particles were formed with Re2(CO)10 as a carbon monoxide source. Without metal carbonyls, small particles of spherical hcp ruthenium were produced, and their size could be controlled by the selection of the precursor. The ruthenium nanoparticles were tested for ammonia borane hydrolysis; the branched nanoparticles were more reactive for catalytic hydrogen evolution than the faceted hcp/fcc nanoparticles or the spherical hcp nanoparticles. This work showcases the potential of crystal phase engineering of transition metal nanoparticles by different carbon monoxide precursors for tailoring their catalytic reactivity.

  11. Atomically Precise Metal Nanoclusters for Catalytic Application

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Rongchao [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    2016-11-18

    The central goal of this project is to explore the catalytic application of atomically precise gold nanoclusters. By solving the total structures of ligand-protected nanoclusters, we aim to correlate the catalytic properties of metal nanoclusters with their atomic/electronic structures. Such correlation unravel some fundamental aspects of nanocatalysis, such as the nature of particle size effect, origin of catalytic selectivity, particle-support interactions, the identification of catalytically active centers, etc. The well-defined nanocluster catalysts mediate the knowledge gap between single crystal model catalysts and real-world conventional nanocatalysts. These nanoclusters also hold great promise in catalyzing certain types of reactions with extraordinarily high selectivity. These aims are in line with the overall goals of the catalytic science and technology of DOE and advance the BES mission “to support fundamental research to understand, predict, and ultimately control matter and energy at the level of electrons, atoms, and molecules”. Our group has successfully prepared different sized, robust gold nanoclusters protected by thiolates, such as Au25(SR)18, Au28(SR)20, Au38(SR)24, Au99(SR)42, Au144(SR)60, etc. Some of these nanoclusters have been crystallographically characterized through X-ray crystallography. These ultrasmall nanoclusters (< 2 nm diameter) exhibit discrete electronic structures due to quantum size effect, as opposed to quasicontinuous band structure of conventional metal nanoparticles or bulk metals. The available atomic structures (metal core plus surface ligands) of nanoclusters serve as the basis for structure-property correlations. We have investigated the unique catalytic properties of nanoclusters (i.e. not observed in conventional nanogold catalysts) and revealed the structure-selectivity relationships. Highlights of our

  12. Catalytic nanoporous membranes

    Science.gov (United States)

    Pellin, Michael J; Hryn, John N; Elam, Jeffrey W

    2013-08-27

    A nanoporous catalytic membrane which displays several unique features Including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity. Also provided is a method for producing a catalytic membrane having flow-through pores and discreet catalytic clusters adhering to the inside surfaces of the pores.

  13. Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.

    Science.gov (United States)

    Nocek, Boguslaw; Reidl, Cory; Starus, Anna; Heath, Tahirah; Bienvenue, David; Osipiuk, Jerzy; Jedrzejczak, Robert; Joachimiak, Andrzej; Becker, Daniel P; Holz, Richard C

    2018-02-06

    The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclear Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn-Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ∼10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than ∼10 Å is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. These data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.

  14. Core Outcome Domains for early phase clinical trials of sound-, psychology-, and pharmacology-based interventions to manage chronic subjective tinnitus in adults: the COMIT'ID study protocol for using a Delphi process and face-to-face meetings to establish consensus.

    Science.gov (United States)

    Fackrell, Kathryn; Smith, Harriet; Colley, Veronica; Thacker, Brian; Horobin, Adele; Haider, Haúla F; Londero, Alain; Mazurek, Birgit; Hall, Deborah A

    2017-08-23

    The reporting of outcomes in clinical trials of subjective tinnitus indicates that many different tinnitus-related complaints are of interest to investigators, from perceptual attributes of the sound (e.g. loudness) to psychosocial impacts (e.g. quality of life). Even when considering one type of intervention strategy for subjective tinnitus, there is no agreement about what is critically important for deciding whether a treatment is effective. The main purpose of this observational study is, therefore to, develop Core Outcome Domain Sets for the three different intervention strategies (sound, psychological, and pharmacological) for adults with chronic subjective tinnitus that should be measured and reported in every clinical trial of these interventions. Secondary objectives are to identify the strengths and limitations of our study design for recruiting and reducing attrition of participants, and to explore uptake of the core outcomes. The 'Core Outcome Measures in Tinnitus: International Delphi' (COMIT'ID) study will use a mixed-methods approach that incorporates input from health care users at the pre-Delphi stage, a modified three-round Delphi survey and final consensus meetings (one for each intervention). The meetings will generate recommendations by stakeholder representatives on agreed Core Outcome Domain Sets specific to each intervention. A subsequent step will establish a common cross-cutting Core Outcome Domain Set by identifying the common outcome domains included in all three intervention-specific Core Outcome Domain Sets. To address the secondary objectives, we will gather feedback from participants about their experience of taking part in the Delphi process. We aspire to conduct an observational cohort study to evaluate uptake of the core outcomes in published studies at 7 years following Core Outcome Set publication. The COMIT'ID study aims to develop a Core Outcome Domain Set that is agreed as critically important for deciding whether a

  15. Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.

    Science.gov (United States)

    Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2009-04-01

    The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3'-5' exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn(2+)-dependent 3'-5' exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3'-5' exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity.

  16. Steam reformer with catalytic combustor

    Science.gov (United States)

    Voecks, Gerald E. (Inventor)

    1990-01-01

    A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.

  17. 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.

  18. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studies....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  19. Catalytic Conversion of Biofuels

    DEFF Research Database (Denmark)

    Jørgensen, Betina

    This thesis describes the catalytic conversion of bioethanol into higher value chemicals. The motivation has been the unavoidable coming depletion of the fossil resources. The thesis is focused on two ways of utilising ethanol; the steam reforming of ethanol to form hydrogen and the partial oxida...

  20. CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...

    African Journals Online (AJOL)

    Preferred Customer

    acetylchlorophosphonazo(CPApA) by hydrogen peroxide in 0.10 M phosphoric acid. A novel catalytic kinetic-spectrophotometric method is proposed for the determination of copper based on this principle. Copper(II) can be determined spectrophotometrically ...

  1. Catalytic methanol dissociation

    International Nuclear Information System (INIS)

    Alcinikov, Y.; Fainberg, V.; Garbar, A.; Gutman, M.; Hetsroni, G.; Shindler, Y.; Tatrtakovsky, L.; Zvirin, Y.

    1998-01-01

    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

  2. Membrane Guanylate Cyclase catalytic Subdomain: Structure and Linkage with Calcium Sensors and Bicarbonate

    Directory of Open Access Journals (Sweden)

    Sarangan Ravichandran

    2017-06-01

    Full Text Available Membrane guanylate cyclase (MGC is a ubiquitous multi-switching cyclic GMP generating signaling machine linked with countless physiological processes. In mammals it is encoded by seven distinct homologous genes. It is a single transmembrane spanning multi-modular protein; composed of integrated blocks and existing in homo-dimeric form. Its core catalytic domain (CCD module is a common transduction center where all incoming signals are translated into the production of cyclic GMP, a cellular signal second messenger. Crystal structure of the MGC’s CCD does not exist and its precise identity is ill-defined. Here, we define it at a sub-molecular level for the phototransduction-linked MGC, the rod outer segment guanylate cyclase type 1, ROS-GC1. (1 The CCD is a conserved 145-residue structural unit, represented by the segment V820-P964. (2 It exists as a homo-dimer and contains seven conserved catalytic elements (CEs wedged into seven conserved motifs. (3 It also contains a conserved 21-residue neurocalcin δ-modulated structural domain, V836-L857. (4 Site-directed mutagenesis documents that each of the seven CEs governs the cyclase’s catalytic activity. (5 In contrast to the soluble and the bacterium MGC which use Mn2+-GTP substrate for catalysis, MGC CCD uses the natural Mg2+-GTP substrate. (6 Strikingly, the MGC CCD requires anchoring by the Transmembrane Domain (TMD to exhibit its major (∼92% catalytic activity; in isolated form the activity is only marginal. This feature is not linked with any unique sequence of the TMD; there is minimal conservation in TMD. Finally, (7 the seven CEs control each of four phototransduction pathways- -two Ca2+-sensor GCAPs-, one Ca2+-sensor, S100B-, and one bicarbonate-modulated. The findings disclose that the CCD of ROS-GC1 has built-in regulatory elements that control its signal translational activity. Due to conservation of these regulatory elements, it is proposed that these elements also control the

  3. Bimetallic Nanoparticles in Alternative Solvents for Catalytic Purposes

    Directory of Open Access Journals (Sweden)

    Trung Dang-Bao

    2017-07-01

    Full Text Available Bimetallic nanoparticles represent attractive catalytic systems thanks to the synergy between both partners at the atomic level, mainly induced by electronic effects which in turn are associated with the corresponding structures (alloy, core-shell, hetero-dimer. This type of engineered material can trigger changes in the kinetics of catalyzed processes by variations on the electrophilicity/nucleophilicity of the metal centers involved and also promote cooperative effects to foster organic transformations, including multi-component and multi-step processes. Solvents become a crucial factor in the conception of catalytic processes, not only due to their environmental impact, but also because they can preserve the bimetallic structure during the catalytic reaction and therefore increase the catalyst life-time. In this frame, the present review focuses on the recent works described in the literature concerning the synthesis of bimetallic nanoparticles in non-conventional solvents, i.e., other than common volatile compounds, for catalytic applications.

  4. Conserved and variable domains of RNase MRP RNA.

    Science.gov (United States)

    Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

    2009-01-01

    Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

  5. Improved crystallization of Escherichia coli ATP synthase catalytic complex (F1) by introducing a phosphomimetic mutation in subunit ∊

    International Nuclear Information System (INIS)

    Roy, Ankoor; Hutcheon, Marcus L.; Duncan, Thomas M.; Cingolani, Gino

    2012-01-01

    A phosphomimetic mutation in subunit ∊ dramatically increases reproducibility for crystallization of Escherichia coli ATP synthase catalytic complex (F 1 ) (subunit composition α 3 β 3 γ∊). Diffraction data were collected to ∼3.15 Å resolution using synchrotron radiation. The bacterial ATP synthase (F O F 1 ) of Escherichia coli has been the prominent model system for genetics, biochemical and more recently single-molecule studies on F-type ATP synthases. With 22 total polypeptide chains (total mass of ∼529 kDa), E. coli F O F 1 represents nature’s smallest rotary motor, composed of a membrane-embedded proton transporter (F O ) and a peripheral catalytic complex (F 1 ). The ATPase activity of isolated F 1 is fully expressed by the α 3 β 3 γ ‘core’, whereas single δ and ∊ subunits are required for structural and functional coupling of E. coli F 1 to F O . In contrast to mitochondrial F 1 -ATPases that have been determined to atomic resolution, the bacterial homologues have proven very difficult to crystallize. In this paper, we describe a biochemical strategy that led us to improve the crystallogenesis of the E. coli F 1 -ATPase catalytic core. Destabilizing the compact conformation of ∊’s C-terminal domain with a phosphomimetic mutation (∊S65D) dramatically increased crystallization success and reproducibility, yielding crystals of E. coli F 1 that diffract to ∼3.15 Å resolution

  6. Concentric catalytic combustor

    Science.gov (United States)

    Bruck, Gerald J [Oviedo, FL; Laster, Walter R [Oviedo, FL

    2009-03-24

    A catalytic combustor (28) includes a tubular pressure boundary element (90) having a longitudinal flow axis (e.g., 56) separating a first portion (94) of a first fluid flow (e.g., 24) from a second portion (95) of the first fluid flow. The pressure boundary element includes a wall (96) having a plurality of separate longitudinally oriented flow paths (98) annularly disposed within the wall and conducting respective portions (100, 101) of a second fluid flow (e.g., 26) therethrough. A catalytic material (32) is disposed on a surface (e.g., 102, 103) of the pressure boundary element exposed to at least one of the first and second portions of the first fluid flow.

  7. Concrete domains

    OpenAIRE

    Kahn, G.; Plotkin, G.D.

    1993-01-01

    This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

  8. Catalytic exhaust control

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, H

    1973-09-01

    Recent achievements and problems in the development of exhaust control devices in the USA are reviewed. To meet the 1976 emission standards, catalytic systems for the oxidation of carbon monoxide and hydrocarbons and for the reduction of nitrogen oxides to nitrogen and water are needed. While oxidizing catalysts using platinum, palladium, copper, vanadium, and chromium appplied on alumina or ceramic materials are more or less effective in emission control, there are no catalytic devices for the reduction of nitrogen oxides with the required useful life of 25,000 to 50,000 miles as yet available. In the case of platinum catalysts on monolithic supports, the operating temperature of 650 to 750/sup 0/C as required for the oxidation process may cause inactivation of the catalysts and fusion of the support material. The oxidation of CO and hydrocarbons is inhibited by high concentrations of CO, nitric oxide, and hydrocarbons. The use of catalytic converters requires the use of lead-free or low-lead gasoline. The nitrogen oxides conversion efficiency is considerably influenced by the oxygen-to-CO ratio of the exhaust gas, which makes limitation of this ratio necessary.

  9. 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.

  10. 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 a...

  11. Catalytic biomass pyrolysis process

    Science.gov (United States)

    Dayton, David C.; Gupta, Raghubir P.; Turk, Brian S.; Kataria, Atish; Shen, Jian-Ping

    2018-04-17

    Described herein are processes for converting a biomass starting material (such as lignocellulosic materials) into a low oxygen containing, stable liquid intermediate that can be refined to make liquid hydrocarbon fuels. More specifically, the process can be a catalytic biomass pyrolysis process wherein an oxygen removing catalyst is employed in the reactor while the biomass is subjected to pyrolysis conditions. The stream exiting the pyrolysis reactor comprises bio-oil having a low oxygen content, and such stream may be subjected to further steps, such as separation and/or condensation to isolate the bio-oil.

  12. Catalytic reforming methods

    Science.gov (United States)

    Tadd, Andrew R; Schwank, Johannes

    2013-05-14

    A catalytic reforming method is disclosed herein. The method includes sequentially supplying a plurality of feedstocks of variable compositions to a reformer. The method further includes adding a respective predetermined co-reactant to each of the plurality of feedstocks to obtain a substantially constant output from the reformer for the plurality of feedstocks. The respective predetermined co-reactant is based on a C/H/O atomic composition for a respective one of the plurality of feedstocks and a predetermined C/H/O atomic composition for the substantially constant output.

  13. 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.

  14. 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.

  15. Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2008-12-01

    Full Text Available Abstract Background Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

  16. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    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 ...

  17. SH2 domains: modulators of nonreceptor tyrosine kinase activity

    OpenAIRE

    Filippakopoulos, Panagis; Müller, Susanne; Knapp, Stefan

    2009-01-01

    The Src homology 2 (SH2) domain is a sequence-specific phosphotyrosine-binding module present in many signaling molecules. In cytoplasmic tyrosine kinases, the SH2 domain is located N-terminally to the catalytic kinase domain (SH1) where it mediates cellular localization, substrate recruitment, and regulation of kinase activity. Initially, structural studies established a role of the SH2 domain stabilizing the inactive state of Src family members. However, biochemical characterization showed ...

  18. Catalytic detritiation of water

    International Nuclear Information System (INIS)

    Rogers, M.L.; Lamberger, P.H.; Ellis, R.E.; Mills, T.K.

    1977-01-01

    A pilot-scale system has been used at Mound Laboratory to investigate the catalytic detritiation of water. A hydrophobic, precious metal catalyst is used to promote the exchange of tritium between liquid water and gaseous hydrogen at 60 0 C. Two columns are used, each 7.5 m long by 2.5 cm ID and packed with catalyst. Water flow is 5-10 cm 3 /min and countercurrent hydrogen flow is 9,000-12,000 cm 3 /min. The equipment, except for the columns, is housed in an inert atmosphere glovebox and is computer controlled. The hydrogen is obtained by electrolysis of a portion of the water stream. Enriched gaseous tritium is withdrawn for further enrichment. A description of the system is included along with an outline of its operation. Recent experimental data are discussed

  19. 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.

  20. 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

  1. Lectin Domains of Polypeptide GalNAc Transferases Exhibit Glycopeptide Binding Specificity

    DEFF Research Database (Denmark)

    Pedersen, Johannes W; Bennett, Eric P; Schjoldager, Katrine T-B G

    2011-01-01

    UDP-GalNAc:polypeptide a-N-acetylgalactosaminyltransferases (GalNAc-Ts) constitute a family of up to 20 transferases that initiate mucin-type O-glycosylation. The transferases are structurally composed of catalytic and lectin domains. Two modes have been identified for the selection...... of glycosylation sites by GalNAc-Ts: confined sequence recognition by the catalytic domain alone, and concerted recognition of acceptor sites and adjacent GalNAc-glycosylated sites by the catalytic and lectin domains, respectively. Thus far, only the catalytic domain has been shown to have peptide sequence...... on sequences of mucins MUC1, MUC2, MUC4, MUC5AC, MUC6, and MUC7 as well as a random glycopeptide bead library, we examined the binding properties of four different lectin domains. The lectin domains of GalNAc-T1, -T2, -T3, and -T4 bound different subsets of small glycopeptides. These results indicate...

  2. Heterogeneous nanocomposites composed of silver sulfide and hollow structured Pd nanoparticles with enhanced catalytic activity toward formic acid oxidation

    International Nuclear Information System (INIS)

    Chen, Dong; Cui, Penglei; Liu, Hui; Yang, Jun

    2015-01-01

    Highlights: • Core–shell Ag-Ag/Pd nanoparticles with an Ag core and an Ag/Pd alloy shell are prepared via galvanic replacement reaction. • Heterogeneous Ag2S-hollow Pd nanocomposites are fabricated by converting the Ag component into Ag2S using element sulfur. • The heterogeneous Ag2S-hollow Pd nanocomposites display enhanced activity for formic acid oxidation due to electronic coupling effect. • The methodology may find applications to produce the semiconductor-metal nanocomposites with interesting architectures and tailored functionalities. - Abstract: Nanocomposites consisting semiconductor and noble metal domains are of great interest for their synergistic effect-based enhanced properties in a given application. Herein, we demonstrate a facile approach for the synthesis of heterogeneous nanocomposites consisting of silver sulfide (Ag 2 S) and hollow structured Pd nanoparticles (hPd). It begins with the preparation of core–shell nanoparticles with an Ag core and an alloy Ag/Pd shell in an organic solvent via galvanic replacement reaction (GRR) between Ag seed particles pre-synthesized and Pd 2+ ion precursors. The Ag component is then removed from the core and shell regions of core–shell Ag-Ag/Pd nanoparticles, and converted into Ag 2 S by elemental sulfur (S). The Ag 2 S forms the semiconductor domain in the nanocomposite and shares the solid-state interface with the resultant hollow structured Pd nanoparticle. As demonstrated, the Ag 2 S-hPd nanocomposites exhibit superior catalytic activity and durability for formic acid oxidation, compared to the pure Pd nanoparticles prepared by oleylamine reduction of Pd ion precursors and commercial Pd/C catalyst, due to the electronic coupling between semiconductor and noble metal domains in the nanocomposites. In addition, the structural transformation from core–shell to heterogeneous nanocomposites may provide new opportunities to design and fabricate hybrid nanostructures with interesting

  3. Incompleteness in the finite domain

    Czech Academy of Sciences Publication Activity Database

    Pudlák, Pavel

    2017-01-01

    Roč. 23, č. 4 (2017), s. 405-441 ISSN 1079-8986 EU Projects: European Commission(XE) 339691 - FEALORA Institutional support: RVO:67985840 Keywords : finite domain Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 0.742, year: 2016 https://www.cambridge.org/core/journals/bulletin-of-symbolic-logic/article/incompleteness-in-the-finite-domain/D239B1761A73DCA534A4805A76D81C76

  4. Catalytic cracking of lignites

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, M.; Nowak, S.; Naegler, T.; Zimmermann, J. [Hochschule Merseburg (Germany); Welscher, J.; Schwieger, W. [Erlangen-Nuernberg Univ. (Germany); Hahn, T. [Halle-Wittenberg Univ., Halle (Germany)

    2013-11-01

    A most important factor for the chemical industry is the availability of cheap raw materials. As the oil price of crude oil is rising alternative feedstocks like coal are coming into focus. This work, the catalytic cracking of lignite is part of the alliance ibi (innovative Braunkohlenintegration) to use lignite as a raw material to produce chemicals. With this new one step process without an input of external hydrogen, mostly propylene, butenes and aromatics and char are formed. The product yield depends on manifold process parameters. The use of acid catalysts (zeolites like MFI) shows the highest amount of the desired products. Hydrogen rich lignites with a molar H/C ratio of > 1 are to be favoured. Due to primary cracking and secondary reactions the ratio between catalyst and lignite, temperature and residence time are the most important parameter to control the product distribution. Experiments at 500 C in a discontinuous rotary kiln reactor show yields up to 32 wt-% of hydrocarbons per lignite (maf - moisture and ash free) and 43 wt-% char, which can be gasified. Particularly, the yields of propylene and butenes as main products can be enhanced four times to about 8 wt-% by the use of catalysts while the tar yield decreases. In order to develop this innovative process catalyst systems fixed on beads were developed for an easy separation and regeneration of the used catalyst from the formed char. (orig.)

  5. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    126, No. 2, March 2014, pp. 341–351. c Indian Academy of Sciences. ... enhancement was realized by catalyst design, appropriate choice of reactor, better injection and .... Gas–liquid and liquid–solid transport processes in catalytic reactors.5.

  6. The PWR cores management

    International Nuclear Information System (INIS)

    Barral, J.C.; Rippert, D.; Johner, J.

    2000-01-01

    During the meeting of the 25 january 2000, organized by the SFEN, scientists and plant operators in the domain of the PWR debated on the PWR cores management. The five first papers propose general and economic information on the PWR and also the fast neutron reactors chains in the electric power market: statistics on the electric power industry, nuclear plant unit management, the ITER project and the future of the thermonuclear fusion, the treasurer's and chairman's reports. A second part offers more technical papers concerning the PWR cores management: performance and optimization, in service load planning, the cores management in the other countries, impacts on the research and development programs. (A.L.B.)

  7. 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.

  8. Transformer core

    NARCIS (Netherlands)

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2008-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  9. Transformer core

    NARCIS (Netherlands)

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2010-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  10. Domain crossing

    DEFF Research Database (Denmark)

    Schraefel, M. C.; Rouncefield, Mark; Kellogg, Wendy

    2012-01-01

    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...

  11. Multi-core MgO NPs(at)C core-shell nanospheres for selective CO2 capture under mild conditions

    International Nuclear Information System (INIS)

    Tae Kyung Kim; Kyung Joo Lee; Hoi Ri Moon; Junhan Yuh; Sang Kyu Kwak

    2014-01-01

    The core-shell structures have attracted attention in catalysis, because the outer shells isolate the catalytically active NP cores and prevent the possibility of sintering of core particles during catalytic reaction under physically and chemically harsh conditions. We aimed to adopt this core-shell system for CO 2 sorption materials. In this study, a composite material of multi-core 3 nm-sized magnesium oxide nanoparticles embedded in porous carbon nanospheres (MgO NPs(at)C) was synthesized by a gas phase reaction via a solvent-free process. It showed selective CO 2 adsorption capacity over N 2 under mild regeneration conditions. (authors)

  12. Comparison of the kinetic parameters of the truncated catalytic subunit and holoenzyme of human DNA polymerase ε

    Science.gov (United States)

    Zahurancik, Walter J.; Baranovskiy, Andrey G.; Tahirov, Tahir H.; Suo, Zucai

    2015-01-01

    Numerous genetic studies have provided compelling evidence to establish DNA polymerase ε (Polε) as the primary DNA polymerase responsible for leading strand synthesis during eukaryotic nuclear genome replication. Polε is a heterotetramer consisting of a large catalytic subunit that contains the conserved polymerase core domain as well as a 3′ → 5′ exonuclease domain common to many replicative polymerases. In addition, Polε possesses three small subunits that lack a known catalytic activity but associate with components involved in a variety of DNA replication and maintenance processes. Previous enzymatic characterization of the Polε heterotetramer from budding yeast suggested that the small subunits slightly enhance DNA synthesis by Polε in vitro. However, similar studies of the human Polε heterote-tramer (hPolε) have been limited by the difficulty of obtaining hPolε in quantities suitable for thorough investigation of its catalytic activity. Utilization of a baculovirus expression system for overexpression and purification of hPolε from insect host cells has allowed for isolation of greater amounts of active hPolε, thus enabling a more detailed kinetic comparison between hPolε and an active N-terminal fragment of the hPolε catalytic subunit (p261N), which is readily overexpressed in Escherichia coli. Here, we report the first pre-steady-state studies of fully-assembled hPolε. We observe that the small subunits increase DNA binding by hPolε relative to p261N, but do not increase processivity during DNA synthesis on a single-stranded M13 template. Interestingly, the 3′ → 5′ exonuclease activity of hPolε is reduced relative to p261N on matched and mismatched DNA substrates, indicating that the presence of the small subunits may regulate the proofreading activity of hPolε and sway hPolε toward DNA synthesis rather than proofreading. PMID:25684708

  13. Core lifter

    Energy Technology Data Exchange (ETDEWEB)

    Pavlov, N G; Edel' man, Ya A

    1981-02-15

    A core lifter is suggested which contains a housing, core-clamping elements installed in the housing depressions in the form of semirings with projections on the outer surface restricting the rotation of the semirings in the housing depressions. In order to improve the strength and reliability of the core lifter, the semirings have a variable transverse section formed from the outside by the surface of the rotation body of the inner arc of the semiring aroung the rotation axis and from the inner a cylindrical surface which is concentric to the outer arc of the semiring. The core-clamping elements made in this manner have the possibility of freely rotating in the housing depressions under their own weight and from contact with the core sample. These semirings do not have weakened sections, have sufficient strength, are inserted into the limited ring section of the housing of the core lifter without reduction in its through opening and this improve the reliability of the core lifter in operation.

  14. 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...... of wireless standards, limited resources of embedded systems, etc. Taking these challenges into account, we present a Trusted Domain home automation platform, which dynamically and securely connects heterogeneous networks of Short-Range Wireless devices via simple non-expert user. interactions, and allows......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...

  15. Catalytic bioreactors and methods of using same

    Science.gov (United States)

    Worden, Robert Mark; Liu, Yangmu Chloe

    2017-07-25

    Various embodiments provide a bioreactor for producing a bioproduct comprising one or more catalytically active zones located in a housing and adapted to keep two incompatible gaseous reactants separated when in a gas phase, wherein each of the one or more catalytically active zones may comprise a catalytic component retainer and a catalytic component retained within and/or thereon. Each of the catalytically active zones may additionally or alternatively comprise a liquid medium located on either side of the catalytic component retainer. Catalytic component may include a microbial cell culture located within and/or on the catalytic component retainer, a suspended catalytic component suspended in the liquid medium, or a combination thereof. Methods of using various embodiments of the bioreactor to produce a bioproduct, such as isobutanol, are also provided.

  16. Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

    Science.gov (United States)

    Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

    2015-01-01

    Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

  17. Reactor core

    International Nuclear Information System (INIS)

    Azekura, Kazuo; Kurihara, Kunitoshi.

    1992-01-01

    In a BWR type reactor, a great number of pipes (spectral shift pipes) are disposed in the reactor core. Moderators having a small moderating cross section (heavy water) are circulated in the spectral shift pipes to suppress the excess reactivity while increasing the conversion ratio at an initial stage of the operation cycle. After the intermediate stage of the operation cycle in which the reactor core reactivity is lowered, reactivity is increased by circulating moderators having a great moderating cross section (light water) to extend the taken up burnup degree. Further, neutron absorbers such as boron are mixed to the moderator in the spectral shift pipe to control the concentration thereof. With such a constitution, control rods and driving mechanisms are no more necessary, to simplify the structure of the reactor core. This can increase the fuel conversion ratio and control great excess reactivity. Accordingly, a nuclear reactor core of high conversion and high burnup degree can be attained. (I.N.)

  18. 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...

  19. 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....

  20. Dense SDM (12-Core × 3-Mode) Transmission Over 527 km With 33.2-ns Mode-Dispersion Employing Low-Complexity Parallel MIMO Frequency-Domain Equalization

    DEFF Research Database (Denmark)

    Shibahara, Kohki; Lee, Doohwan; Kobayashi, Takayuki

    2016-01-01

    We propose long-haul space-division-multiplexing (SDM) transmission systems employing parallel multiple-input multiple-output (MIMO) frequency-domain equalization (FDE) and transmission fiber with low differential mode delay (DMD). We first discuss the advantages of parallel MIMO FDE technique in...

  1. SH2 domains: modulators of nonreceptor tyrosine kinase activity.

    Science.gov (United States)

    Filippakopoulos, Panagis; Müller, Susanne; Knapp, Stefan

    2009-12-01

    The Src homology 2 (SH2) domain is a sequence-specific phosphotyrosine-binding module present in many signaling molecules. In cytoplasmic tyrosine kinases, the SH2 domain is located N-terminally to the catalytic kinase domain (SH1) where it mediates cellular localization, substrate recruitment, and regulation of kinase activity. Initially, structural studies established a role of the SH2 domain stabilizing the inactive state of Src family members. However, biochemical characterization showed that the presence of the SH2 domain is frequently required for catalytic activity, suggesting a crucial function stabilizing the active state of many nonreceptor tyrosine kinases. Recently, the structure of the SH2-kinase domain of Fes revealed that the SH2 domain stabilizes the active kinase conformation by direct interactions with the regulatory helix alphaC. Stabilizing interactions between the SH2 and the kinase domains have also been observed in the structures of active Csk and Abl. Interestingly, mutations in the SH2 domain found in human disease can be explained by SH2 domain destabilization or incorrect positioning of the SH2. Here we summarize our understanding of mechanisms that lead to tyrosine kinase activation by direct interactions mediated by the SH2 domain and discuss how mutations in the SH2 domain trigger kinase inactivation.

  2. Catalytic properties of niobium compounds

    International Nuclear Information System (INIS)

    Tanabe, K.; Iizuka, T.

    1983-04-01

    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) [pt

  3. Catalytic Decoupling of Quantum Information

    DEFF Research Database (Denmark)

    Majenz, Christian; Berta, Mario; Dupuis, Frédéric

    2017-01-01

    The decoupling technique is a fundamental tool in quantum information theory with applications ranging from quantum thermodynamics to quantum many body physics to the study of black hole radiation. In this work we introduce the notion of catalytic decoupling, that is, decoupling in the presence...... and quantum state merging, and leads to a resource theory of decoupling....

  4. Synthesis, spectroscopic characterization and catalytic oxidation ...

    Indian Academy of Sciences (India)

    were characterized by infrared, electronic, electron paramagnetic resonance ... The catalytic oxidation property of ruthenium(III) complexes were also ... cies at room temperature. ..... aldehyde part of Schiff base ligands, catalytic activ- ity of new ...

  5. Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase.

    Science.gov (United States)

    Wang, Li Kai; Nair, Pravin A; Shuman, Stewart

    2008-08-22

    NAD(+)-dependent DNA ligases (LigAs) are ubiquitous in bacteria and essential for growth. LigA enzymes have a modular structure in which a central catalytic core composed of nucleotidyltransferase and oligonucleotide-binding (OB) domains is linked via a tetracysteine zinc finger to distal helix-hairpin-helix (HhH) and BRCT (BRCA1-like C-terminal) domains. The OB and HhH domains contribute prominently to the protein clamp formed by LigA around nicked duplex DNA. Here we conducted a structure-function analysis of the OB and HhH domains of Escherichia coli LigA by alanine scanning and conservative substitutions, entailing 43 mutations at 22 amino acids. We thereby identified essential functional groups in the OB domain that engage the DNA phosphodiester backbone flanking the nick (Arg(333)); penetrate the minor grove and distort the nick (Val(383) and Ile(384)); or stabilize the OB fold (Arg(379)). The essential constituents of the HhH domain include: four glycines (Gly(455), Gly(489), Gly(521), Gly(553)), which bind the phosphate backbone across the minor groove at the outer margins of the LigA-DNA interface; Arg(487), which penetrates the minor groove at the outer margin on the 3 (R)-OH side of the nick; and Arg(446), which promotes protein clamp formation via contacts to the nucleotidyltransferase domain. We find that the BRCT domain is required in its entirety for effective nick sealing and AMP-dependent supercoil relaxation.

  6. The Catalytic Diversity of Multimodular Polyketide Synthases: Natural Product Biosynthesis Beyond Textbook Assembly Rules.

    Science.gov (United States)

    Gulder, Tobias A M; Freeman, Michael F; Piel, Jörn

    2011-03-01

    Bacterial multimodular polyketide synthases (PKSs) are responsible for the biosynthesis of a wide range of pharmacologically active natural products. These megaenzymes contain numerous catalytic and structural domains and act as biochemical templates to generate complex polyketides in an assembly line-like fashion. While the prototypical PKS is composed of only a few different domain types that are fused together in a combinatorial fashion, an increasing number of enzymes is being found that contain additional components. These domains can introduce remarkably diverse modifications into polyketides. This review discusses our current understanding of such noncanonical domains and their role in expanding the biosynthetic versatility of bacterial PKSs.

  7. 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)

    Im, Dong-Won; Kim, Tae-O; Jung, Ha Yun; Oh, Ji Eun; Lee, Se Jin; Heo, Yong-Seok

    2011-01-01

    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 P4 1 or P4 3 , with unit-cell parameters a = b = 52.63, c = 110.31 Å. The asymmetric unit is likely to contain one molecule, with a corresponding V M of 1.77 Å 3 Da −1 and a solvent content of 30.7%

  8. Reactor core

    International Nuclear Information System (INIS)

    Matsuura, Tetsuaki; Nomura, Teiji; Tokunaga, Kensuke; Okuda, Shin-ichi

    1990-01-01

    Fuel assemblies in the portions where the gradient of fast neutron fluxes between two opposing faces of a channel box is great are kept loaded at the outermost peripheral position of the reactor core also in the second operation cycle in the order to prevent interference between a control rod and the channel box due to bending deformation of the channel box. Further, the fuel assemblies in the second row from the outer most periphery in the first operation cycle are also kept loaded at the second row in the second operation cycle. Since the gradient of the fast neutrons in the reactor core is especially great at the outer circumference of the reactor core, the channel box at the outer circumference is bent such that the surface facing to the center of the reactor core is convexed and the channel box in the second row is also bent to the identical direction, the insertion of the control rod is not interfered. Further, if the positions for the fuels at the outermost periphery and the fuels in the second row are not altered in the second operation cycle, the gaps are not reduced to prevent the interference between the control rod and the channel box. (N.H.)

  9. Catalytic process for tritium exchange reaction

    International Nuclear Information System (INIS)

    Hansoo Lee; Kang, H.S.; Paek, S.W.; Hongsuk Chung; Yang Geun Chung; Sook Kyung Lee

    2001-01-01

    The catalytic activities for a hydrogen isotope exchange were measured through the reaction of a vapor and gas mixture. The catalytic activity showed to be comparable with the published data. Since the gas velocity is relatively low, the deactivation was not found clearly during the 5-hour experiment. Hydrogen isotope transfer experiments were also conducted through the liquid phase catalytic exchange reaction column that consisted of a catalytic bed and a hydrophilic bed. The efficiencies of both the catalytic and hydrophilic beds were higher than 0.9, implying that the column performance was excellent. (author)

  10. 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.

  11. Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure

    Energy Technology Data Exchange (ETDEWEB)

    Korasick, David A. [Department of Biochemistry, University of Missouri, Columbia MO USA; Singh, Harkewal [Department of Chemistry, University of Missouri, Columbia MO USA; Pemberton, Travis A. [Department of Chemistry, University of Missouri, Columbia MO USA; Luo, Min [Department of Chemistry, University of Missouri, Columbia MO USA; Dhatwalia, Richa [Department of Chemistry, University of Missouri, Columbia MO USA; Tanner, John J. [Department of Biochemistry, University of Missouri, Columbia MO USA; Department of Chemistry, University of Missouri, Columbia MO USA

    2017-08-01

    Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-γ-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs.

  12. Catalytic processes for cleaner fuels

    International Nuclear Information System (INIS)

    Catani, R.; Marchionna, M.; Rossini, S.

    1999-01-01

    More stringent limitations on vehicle emissions require different measurement: fuel reformulation is one of the most important and is calling for a noticeable impact on refinery assets. Composition rangers of the future fuels have been defined on a time scale. In this scenario the evolution of catalytic technologies becomes a fundamental tool for allowing refinery to reach the fixed-by-law targets. In this paper, the refinery process options to meet each specific requirements of reformulated fuels are surveyed [it

  13. .Gov Domains API

    Data.gov (United States)

    General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...

  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......, does not allow omissions, and does not contain ignorable elements. We do so by identifying syntactic sugar, including default values, and ignorable elements in WS-BPEL. The analysis results in a translation from the full language to the core subset. Thus, we reduce the effort needed for working...

  15. Optical manipulation and catalytic activity enhanced by surface plasmon effect

    Science.gov (United States)

    Zou, Ningmu; Min, Jiang; Jiao, Wenxiang; Wang, Guanghui

    2017-02-01

    For optical manipulation, a nano-optical conveyor belt consisting of an array of gold plasmonic non-concentric nano-rings (PNNRs) is demonstrated for the realization of trapping and unidirectional transportation of nanoparticles by polarization rotation of excitation beam. These hot spots of an asymmetric plasmonic nanostructure are polarization dependent, therefore, one can use the incident polarization state to manipulate the trapped targets. Trapped particles could be transferred between adjacent PNNRs in a given direction just by rotating the polarization of incident beam due to unbalanced potential. The angular dependent distribution of electric field around PNNR has been solved using the three- dimensional finite-difference time-domain (FDTD) technique. For optical enhanced catalytic activity, the spectral properties of dimers of Au nanorod-Au nanorod nanostructures under the excitation of 532nm photons have been investigated. With a super-resolution catalytic mapping technique, we identified the existence of "hot spot" in terms of catalytic reactivity at the gap region within the twined plasmonic nanostructure. Also, FDTD calculation has revealed an intrinsic correlation between hot electron transfer.

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

    Science.gov (United States)

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

    2013-06-01

    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 Legionella pneumophila. 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-AlF3 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 Gln70 side-chain flipping towards GDP-AlF3 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.

  17. 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

  18. Catalytic Organometallic Reactions of Ammonia

    Science.gov (United States)

    Klinkenberg, Jessica L.

    2012-01-01

    Until recently, ammonia had rarely succumbed to catalytic transformations with homogeneous catalysts, and the development of such reactions that are selective for the formation of single products under mild conditions has encountered numerous challenges. However, recently developed catalysts have allowed several classes of reactions to create products with nitrogen-containing functional groups from ammonia. These reactions include hydroaminomethylation, reductive amination, alkylation, allylic substitution, hydroamination, and cross-coupling. This Minireview describes examples of these processes and the factors that control catalyst activity and selectivity. PMID:20857466

  19. Catalytic cracking of hydrocarbon oils

    Energy Technology Data Exchange (ETDEWEB)

    1940-09-12

    A process is described for the vapor phase catalytic cracking of hydrocarbon oils boiling substantially in the gas oil range. The reaction takes place in the presence of a solid catalyst between 700 to 900/sup 0/F under pressure between atmospheric and 400 psi. A gas containing between 20 and 90 mol % of free hydrogen is used. The reaction is allowed to proceed until consumption of the free begins. The reaction is discontinued at that point and the catalyst is regenerated for further use.

  20. 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.

  1. Catalytic enantioselective Reformatsky reaction with ketones

    NARCIS (Netherlands)

    Fernandez-Ibanez, M. Angeles; Macia, Beatriz; Minnaard, Adriaan J.; Feringa, Ben L.

    2008-01-01

    Chiral tertiary alcohols were obtained with good yields and enantioselectivities via a catalytic Reformatsky reaction with ketones, including the challenging diaryl ketones, using chiral BINOL derivatives.

  2. Petrochemical promoters in catalytic cracking

    International Nuclear Information System (INIS)

    Gomez, Maria; Vargas, Clemencia; Lizcano, Javier

    2010-01-01

    This study is based on the current scheme followed by a refinery with available Catalytic Cracking capacity to process new feedstocks such as Straight Run Naphtha and Naphthas from FCC. These feedstocks are of petrochemical interest to produce Ethane, Ethylene, Propylene, i-Butane, Toluene and Xylene. To evaluate the potential of these new streams versus the Cracking-charged Residues, it was performed a detailed chemical analysis on the structural groups in carbons [C1-C12] at the reactor product obtained in pilot plant. A catalyst with and without Propylene Promoter Additive was used. This study analyzes the differences in the chemical composition of the feedstocks, relating them to the yield of each petrochemical product. Straight Run Naphthas with a high content of Naphthenes, and Paraffines n[C5-C12] and i[C7-C12] are selective to the production of i-Butane and Propane, while Naphthas from FCC with a high content of n[C5-C12]Olefins, i-Olefins, and Aromatics are more selective to Propylene, Toluene, and Xylene. Concerning Catalytic Cracking of Naphthas, the Additive has similar selectivity for all the petrochemical products, their yields increase by about one point with 4%wt of Additive, while in cracking of Residues, the Additive increases in three points Propylene yield, corresponding to a selectivity of 50% (?C3= / ?LPG).

  3. 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).

  4. Catalytic converters in the fireplace

    International Nuclear Information System (INIS)

    Kouki, J.

    1995-01-01

    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

  5. Intramolecular Crosstalk between Catalytic Activities of Receptor Kinases

    KAUST Repository

    Kwezi, Lusisizwe

    2018-01-22

    Signal modulation is important for the growth and development of plants and this process is mediated by a number of factors including physiological growth regulators and their associated signal transduction pathways. Protein kinases play a central role in signaling, including those involving pathogen response mechanisms. We previously demonstrated an active guanylate cyclase (GC) catalytic center in the brassinosteroid insensitive receptor (AtBRI1) within an active intracellular kinase domain resulting in dual enzymatic activity. Here we propose a novel type of receptor architecture that is characterized by a functional GC catalytic center nested in the cytosolic kinase domain enabling intramolecular crosstalk. This may be through a cGMP-AtBRI1 complex forming that may induce a negative feedback mechanism leading to desensitisation of the receptor, regulated through the cGMP production pathway. We further argue that the comparatively low but highly localized cGMP generated by the GC in response to a ligand is sufficient to modulate the kinase activity. This type of receptor therefore provides a molecular switch that directly and/or indirectly affects ligand dependent phosphorylation of downstream signaling cascades and suggests that subsequent signal transduction and modulation works in conjunction with the kinase in downstream signaling.

  6. Intramolecular Crosstalk between Catalytic Activities of Receptor Kinases

    KAUST Repository

    Kwezi, Lusisizwe; Wheeler, Janet I; Marondedze, Claudius; Gehring, Christoph A; Irving, Helen R

    2018-01-01

    Signal modulation is important for the growth and development of plants and this process is mediated by a number of factors including physiological growth regulators and their associated signal transduction pathways. Protein kinases play a central role in signaling, including those involving pathogen response mechanisms. We previously demonstrated an active guanylate cyclase (GC) catalytic center in the brassinosteroid insensitive receptor (AtBRI1) within an active intracellular kinase domain resulting in dual enzymatic activity. Here we propose a novel type of receptor architecture that is characterized by a functional GC catalytic center nested in the cytosolic kinase domain enabling intramolecular crosstalk. This may be through a cGMP-AtBRI1 complex forming that may induce a negative feedback mechanism leading to desensitisation of the receptor, regulated through the cGMP production pathway. We further argue that the comparatively low but highly localized cGMP generated by the GC in response to a ligand is sufficient to modulate the kinase activity. This type of receptor therefore provides a molecular switch that directly and/or indirectly affects ligand dependent phosphorylation of downstream signaling cascades and suggests that subsequent signal transduction and modulation works in conjunction with the kinase in downstream signaling.

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

    International Nuclear Information System (INIS)

    Kozlov, Guennadi; Perreault, Audrey; Schrag, Joseph D.; Park, Morag; Cygler, Miroslaw; Gehring, Kalle; Ekiel, Irena

    2004-01-01

    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

  8. The starch-binding domain family CBM41 - an in silico analysis of evolutionary relationships

    DEFF Research Database (Denmark)

    Janeček, Štefan; Majzlová, Katarína; Svensson, Birte

    2017-01-01

    Within the CAZy database, there are 81 carbohydrate-binding module (CBM) families. A CBM represents a non-catalytic domain in a modular arrangement of glycoside hydrolases (GHs). The present in silico study has been focused on starch-binding domains from the family CBM41 that are usually part...

  9. Heterogeneous catalytic degradation of polyacrylamide solution | Hu ...

    African Journals Online (AJOL)

    Modified with trace metal elements, the catalytic activity of Fe2O3/Al2O3 could be changed greatly. Among various trace metal elements, Fe2O3/Al2O3 catalysts modified with Co and Cu showed great increase on catalytic activity. International Journal of Engineering, Science and Technology, Vol. 2, No. 7, 2010, pp. 110- ...

  10. Method of fabricating a catalytic structure

    Science.gov (United States)

    Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

    2009-09-22

    A precursor to a catalytic structure comprising zinc oxide and copper oxide. The zinc oxide has a sheet-like morphology or a spherical morphology and the copper oxide comprises particles of copper oxide. The copper oxide is reduced to copper, producing the catalytic structure. The catalytic structure is fabricated by a hydrothermal process. A reaction mixture comprising a zinc salt, a copper salt, a hydroxyl ion source, and a structure-directing agent is formed. The reaction mixture is heated under confined volume conditions to produce the precursor. The copper oxide in the precursor is reduced to copper. A method of hydrogenating a carbon oxide using the catalytic structure is also disclosed, as is a system that includes the catalytic structure.

  11. Catalytic hydrogenation of carbon monoxide

    International Nuclear Information System (INIS)

    Wayland, B.B.

    1993-12-01

    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 H 2 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

  12. Selective catalytic oxidation of ammonia

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-31

    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.)

  13. Non-catalytic recuperative reformer

    Science.gov (United States)

    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.

  14. Studies of Catalytic Model Systems

    DEFF Research Database (Denmark)

    Holse, Christian

    The overall topic of this thesis is within the field of catalysis, were model systems of different complexity have been studied utilizing a multipurpose Ultra High Vacuum chamber (UHV). The thesis falls in two different parts. First a simple model system in the form of a ruthenium single crystal...... of 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 X......-ray Photoelectron Electron Spectroscopy (XPS) and in situ Transmission Electron Microscopy (TEM). The surface composition of the nanoparticles changes reversibly as the nanoparticles exposed to cycles of high-pressure oxidation and reduction (200 mbar). Furthermore, the presence of metallic Zn is observed by XPS...

  15. 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.)

  16. Modelling of procecces in catalytic recombiners

    International Nuclear Information System (INIS)

    Boehm, J.

    2007-01-01

    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.)

  17. 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.

  18. Synthesis of Ni-SiO2/silicalite-1 core-shell micromembrane reactors and their reaction/diffusion performance

    KAUST Repository

    Khan, Easir A.; Rajendran, Arvind; Lai, Zhiping

    2010-01-01

    with catalytically active nickel, showed no reactant selectivity between hexene isomers, but the core-shell particles showed high selectivities up to 300 for a 1-hexene conversion of 90%. © 2010 American Chemical Society.

  19. Combinatorial geometry domain decomposition strategies for Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z. [Institute of Applied Physics and Computational Mathematics, Beijing, 100094 (China)

    2013-07-01

    Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)

  20. Combinatorial geometry domain decomposition strategies for Monte Carlo simulations

    International Nuclear Information System (INIS)

    Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z.

    2013-01-01

    Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)

  1. Expression, purification and preliminary crystallographic studies on the catalytic region of the nonreceptor tyrosine kinase Fes

    International Nuclear Information System (INIS)

    Gnemmi, Ilaria; Scotti, Claudia; Cappelletti, Donata; Canonico, Pier Luigi; Condorelli, Fabrizio; Rosano, Camillo

    2006-01-01

    The catalytic domain of human Fes tyrosine kinase has been cloned, expressed, purified and crystallized. The proto-oncogene tyrosine protein kinase c-fps/fes encodes a structurally unique protein (Fes) of the nonreceptor protein-tyrosine kinase (PTK) family. Its expression has been demonstrated in myeloid haematopoietic cells, vascular endothelial cells and in neurons. In human-derived and murine-derived cell lines, the activated form of this kinase can induce cellular transformation; moreover, it has been shown that Fes is involved in the regulation of cell–cell and cell–matrix interactions mediated by adherens junctions and focal adhesions. The N-terminus of Fes contains the FCH (Fps/Fes/Fer/CIP4 homology) domain, which is unique to the Fes/Fer kinase family. It is followed by three coiled-coil domains and an SH2 (Src-homology 2) domain. The catalytic region (Fes-CR) is located at the C-terminus of the protein. The successful expression, purification and crystallization of the catalytic part of Fes (Fes-CR) are described

  2. Functional domains of plant chimeric calcium/calmodulin-dependent protein kinase: regulation by autoinhibitory and visinin-like domains

    Science.gov (United States)

    Ramachandiran, S.; Takezawa, D.; Wang, W.; Poovaiah, B. W.

    1997-01-01

    A novel calcium-binding calcium/calmodulin-dependent protein kinase (CCaMK) with a catalytic domain, calmodulin-binding domain, and a neural visinin-like domain was cloned and characterized from plants [Patil et al., (1995) Proc. Natl. Acad. Sci. USA 92, 4797-4801; Takezawa et al. (1996) J. Biol. Chem. 271, 8126-8132]. The mechanisms of CCaMK activation by calcium and calcium/calmodulin were investigated using various deletion mutants. The use of deletion mutants of CCaMK lacking either one, two, or all three calcium-binding EF hands indicated that all three calcium-binding sites in the visinin-like domain were crucial for the full calcium/calmodulin-dependent kinase activity. As each calcium-binding EF hand was deleted, there was a gradual reduction in calcium/calmodulin-dependent kinase activity from 100 to 4%. Another mutant (amino acids 1-322) which lacks both the visinin-like domain containing three EF hands and the calmodulin-binding domain was constitutively active, indicating the presence of an autoinhibitory domain around the calmodulin-binding domain. By using various synthetic peptides and the constitutively active mutant, we have shown that CCaMK contains an autoinhibitory domain within the residues 322-340 which overlaps its calmodulin-binding domain. Kinetic studies with both ATP and the GS peptide substrate suggest that the autoinhibitory domain of CCaMK interacts only with the peptide substrate binding motif of the catalytic domain, but not with the ATP-binding motif.

  3. Side core lifter

    Energy Technology Data Exchange (ETDEWEB)

    Edelman, Ya A

    1982-01-01

    A side core lifter is proposed which contains a housing with guide slits and a removable core lifter with side projections on the support section connected to the core receiver. In order to preserve the structure of the rock in the core sample by means of guaranteeing rectilinear movement of the core lifter in the rock, the support and core receiver sections are hinged. The device is equipped with a spring for angular shift in the core-reception part.

  4. 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.

  5. Catalytic modification of cellulose and hemicellulose - Sugarefine

    Energy Technology Data Exchange (ETDEWEB)

    Repo, T. [Helsinki Univ. (Finland),Laboratory of Inorganic Chemistry], email: timo.repo@helsinki.fi

    2012-07-01

    The main goal of the project is to develop catalytic methods for the modification of lignocellulose-based saccharides in the biorefineries. The products of these reactions could be used for example as biofuel components, raw materials for the chemical industry, solvents and precursors for biopolymers. The catalyst development aims at creating efficient, selective and green catalytic methods for profitable use in biorefineries. The project is divided in three work packages: In WP1 (Catalytic dehydration of cellulose) the aim is at developing non-toxic, efficient methods for the catalytic dehydration of cellulose the target molecule being here 5-hydroxymethylfurfural (5-HMF). 5-HMF is an interesting platform chemical for the production of fuel additives, solvents and polymers. In WP2 (Catalytic reduction), the objective of the catalytic reduction studies is to produce commercially interesting monofunctional chemicals, such as 1-butanol or 2-methyltetrahydrofuran (2-MeTHF). In WP3 (Catalytic oxidation), the research focuses on developing a green and efficient oxidation method for producing acids. Whereas acetic and formic acids are bulk chemicals, diacids such as glucaric and xylaric acids are valuable specialty chemicals for detergent, polymer and food production.

  6. Beltless Translocation Domain of Botulinum Neurotoxin A Embodies a Minimum Ion-conductive Channel*

    OpenAIRE

    Fischer, Audrey; Sambashivan, Shilpa; Brunger, Axel T.; Montal, Mauricio

    2011-01-01

    Botulinum neurotoxin, the causative agent of the paralytic disease botulism, is an endopeptidase composed of a catalytic domain (or light chain (LC)) and a heavy chain (HC) encompassing the translocation domain (TD) and receptor-binding domain. Upon receptor-mediated endocytosis, the LC and TD are proposed to undergo conformational changes in the acidic endocytic environment resulting in the formation of an LC protein-conducting TD channel. The mechanism of channel formation and the conformat...

  7. 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...

  8. Catalytic Wittig and aza-Wittig reactions

    Directory of Open Access Journals (Sweden)

    Zhiqi Lao

    2016-11-01

    Full Text Available This review surveys the literature regarding the development of catalytic versions of the Wittig and aza-Wittig reactions. The first section summarizes how arsenic and tellurium-based catalytic Wittig-type reaction systems were developed first due to the relatively easy reduction of the oxides involved. This is followed by a presentation of the current state of the art regarding phosphine-catalyzed Wittig reactions. The second section covers the field of related catalytic aza-Wittig reactions that are catalyzed by both phosphine oxides and phosphines.

  9. Catalytic models developed through social work

    DEFF Research Database (Denmark)

    Jensen, Mogens

    2015-01-01

    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......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...

  10. Efficient catalytic combustion in integrated micropellistors

    International Nuclear Information System (INIS)

    Bársony, I; Ádám, M; Fürjes, P; Dücső, Cs; Lucklum, R; Hirschfelder, M; Kulinyi, S

    2009-01-01

    This paper analyses two of the key issues of the development of catalytic combustion-type sensors: the selection and production of active catalytic particles on the micropellistor surface as well as the realization of a reliable thermal conduction between heater element and catalytic surface, for the sensing of temperature increase produced by the combustion. The report also demonstrates that chemical sensor product development by a MEMS process is a continuous struggle for elimination of all uncertainties influencing reliability and sensitivity of the final product

  11. 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.

  12. Using context to improve protein domain identification

    Directory of Open Access Journals (Sweden)

    Llinás Manuel

    2011-03-01

    Full Text Available Abstract Background Identifying domains in protein sequences is an important step in protein structural and functional annotation. Existing domain recognition methods typically evaluate each domain prediction independently of the rest. However, the majority of proteins are multidomain, and pairwise domain co-occurrences are highly specific and non-transitive. Results Here, we demonstrate how to exploit domain co-occurrence to boost weak domain predictions that appear in previously observed combinations, while penalizing higher confidence domains if such combinations have never been observed. Our framework, Domain Prediction Using Context (dPUC, incorporates pairwise "context" scores between domains, along with traditional domain scores and thresholds, and improves domain prediction across a variety of organisms from bacteria to protozoa and metazoa. Among the genomes we tested, dPUC is most successful at improving predictions for the poorly-annotated malaria parasite Plasmodium falciparum, for which over 38% of the genome is currently unannotated. Our approach enables high-confidence annotations in this organism and the identification of orthologs to many core machinery proteins conserved in all eukaryotes, including those involved in ribosomal assembly and other RNA processing events, which surprisingly had not been previously known. Conclusions Overall, our results demonstrate that this new context-based approach will provide significant improvements in domain and function prediction, especially for poorly understood genomes for which the need for additional annotations is greatest. Source code for the algorithm is available under a GPL open source license at http://compbio.cs.princeton.edu/dpuc/. Pre-computed results for our test organisms and a web server are also available at that location.

  13. Vacuum-insulated catalytic converter

    Science.gov (United States)

    Benson, David K.

    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.

  14. Catalytic hydrotreatment of refinery waste

    Energy Technology Data Exchange (ETDEWEB)

    1989-01-01

    The object of the project is to produce liquid hydrocarbons by the catalytic hydroprocessing of solid refinery wastes (hard pitches) in order to improve the profitability of deep conversion processes and reduce the excess production of heavy fuels. The project was mostly carried out on the ASVAHL demonstration platform site, at Solaize, and hard pitches were produced primarily by deasphalting of atmospheric or vacuum distillation residues. The project includes two experimental phases and an economic evaluation study phase. In phase 1, two granular catalysts were used to transform pitch into standard low sulphur fuel oil: a continuously moving bed, with demetallation and conversion catalyst; a fixed bed, with hydrorefining catalyst. In phase 2 of the project, it was proven that a hydrotreatment process using a finely dispersed catalyst in the feedstock, can, under realistic operating conditions, transform with goods yields hard pitch into distillates that can be refined through standard methods. In phase 3 of the project, it was shown that the economics of such processes are tightly linked to the price differential between white and black oil products, which is expected to increase in the future. Furthermore, the evolution of environmental constraints will impel the use of such methods, thus avoiding the coproduction of polluting solid residues.

  15. Structure and function of C-terminal catalytic region of pasteurella multocida toxin

    International Nuclear Information System (INIS)

    Kitadokoro, Kengo; Kamitami, Shigeki; Horiguchi, Yasuhiko

    2008-01-01

    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. Structural domain walls in polar hexagonal manganites

    Science.gov (United States)

    Kumagai, Yu

    2014-03-01

    The domain structure in the multiferroic hexagonal manganites is currently intensely investigated, motivated by the observation of intriguing sixfold topological defects at their meeting points [Choi, T. et al,. Nature Mater. 9, 253 (2010).] and nanoscale electrical conductivity at the domain walls [Wu, W. et al., Phys. Rev. Lett. 108, 077203 (2012).; Meier, D. et al., Nature Mater. 11, 284 (2012).], as well as reports of coupling between ferroelectricity, magnetism and structural antiphase domains [Geng, Y. et al., Nano Lett. 12, 6055 (2012).]. The detailed structure of the domain walls, as well as the origin of such couplings, however, was previously not fully understood. In the present study, we have used first-principles density functional theory to calculate the structure and properties of the low-energy structural domain walls in the hexagonal manganites [Kumagai, Y. and Spaldin, N. A., Nature Commun. 4, 1540 (2013).]. We find that the lowest energy domain walls are atomically sharp, with {210}orientation, explaining the orientation of recently observed stripe domains and suggesting their topological protection [Chae, S. C. et al., Phys. Rev. Lett. 108, 167603 (2012).]. We also explain why ferroelectric domain walls are always simultaneously antiphase walls, propose a mechanism for ferroelectric switching through domain-wall motion, and suggest an atomistic structure for the cores of the sixfold topological defects. This work was supported by ETH Zurich, the European Research Council FP7 Advanced Grants program me (grant number 291151), the JSPS Postdoctoral Fellowships for Research Abroad, and the MEXT Elements Strategy Initiative to Form Core Research Center TIES.

  17. The EFR project: core and fuel

    International Nuclear Information System (INIS)

    Francillon, E.; Barnes, D.W.; Pay, A.; Wehmann, U.

    1991-01-01

    The draft studies on EFR has beginning, in March 1988. The first part of the summary draft has consisted in the core and fuel domains to harmonize the different approaches used in national projects (SPX2-SNR2-CDFR). Rapidly, the core First Consistent Design has been defined with references to the anterior conceptions. Since this definition, studies have been engaged on the management (mean burnup amelioration) and on the conception (breeding gain, sodium void coefficient reduction). After a presentation of the basis options and on the general conception of the fuel assemblies we make a point on the core and the interfaces with the fuel cycle [fr

  18. Chemistry and engineering of catalytic hydrodesulfurization

    NARCIS (Netherlands)

    Schuit, G.C.A.; Gates, B.C.

    1973-01-01

    A review with 74 refs. on catalytic hydrodesulfurization of pure compds. and petroleum feedstocks, with emphasis on reaction intermediates and structures of Al2O3-supported Ni-W and Co-Mo catalysts. [on SciFinder (R)

  19. Measuring and Reporting Leadership and Core Competency Domains

    Science.gov (United States)

    2015-09-04

    Management : Defense’s System for Army Military Payroll Is Unreliable,” GAO-93-32 (Washington, D.C.: GAO, September 30, 1993). 7 GAO, “DoD Systems...Deficiencies in Controls over Army Active Duty Military Payroll ,” GAO-13-28, (Washington, D.C.: GAO, December 2012); GAO, “DOD Financial Management : The...culture, regional/technical, and leadership/influence.   Examining the numerous military personnel information management systems across DoD, IDA found

  20. Catalytic Aminohalogenation of Alkenes and Alkynes.

    Science.gov (United States)

    Chemler, Sherry R; Bovino, Michael T

    2013-06-07

    Catalytic aminohalogenation methods enable the regio- and stereoselective vicinal difunctionalization of alkynes, allenes and alkenes with amine and halogen moieties. A range of protocols and reaction mechanisms including organometallic, Lewis base, Lewis acid and Brønsted acid catalysis have been disclosed, enabling the regio- and stereoselective synthesis of halogen-functionalized acyclic amines and nitrogen heterocycles. Recent advances including aminofluorination and catalytic enantioselective aminohalogenation reactions are summarized in this review.

  1. Kinetic catalytic studies of scorpion's hemocyanin

    International Nuclear Information System (INIS)

    Queinnec, E.; Vuillaume, M.; Gardes-Albert, M.; Ferradini, C.; Ducancel, F.

    1991-01-01

    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 10 7 mol -1 .l.s -1 [fr

  2. Animal MRI Core

    Data.gov (United States)

    Federal Laboratory Consortium — The Animal Magnetic Resonance Imaging (MRI) Core develops and optimizes MRI methods for cardiovascular imaging of mice and rats. The Core provides imaging expertise,...

  3. Cytochromes P450: History, Classes, Catalytic Mechanism, and Industrial Application.

    Science.gov (United States)

    Cook, D J; Finnigan, J D; Cook, K; Black, G W; Charnock, S J

    Cytochromes P450, a family of heme-containing monooxygenases that catalyze a diverse range of oxidative reactions, are so-called due to their maximum absorbance at 450nm, ie, "Pigment-450nm," when bound to carbon monoxide. They have appeal both academically and commercially due to their high degree of regio- and stereoselectivity, for example, in the area of active pharmaceutical ingredient synthesis. Despite this potential, they often exhibit poor stability, low turnover numbers and typically require electron transport protein(s) for catalysis. P450 systems exist in a variety of functional domain architectures, organized into 10 classes. P450s are also divided into families, each of which is based solely on amino acid sequence homology. Their catalytic mechanism employs a very complex, multistep catalytic cycle involving a range of transient intermediates. Mutagenesis is a powerful tool for the development of improved biocatalysts and has been used extensively with the archetypal Class VIII P450, BM3, from Bacillus megaterium, but with the increasing scale of genomic sequencing, a huge resource is now available for the discovery of novel P450s. © 2016 Elsevier Inc. All rights reserved.

  4. Evolutionary dynamics of protein domain architecture in plants

    Directory of Open Access Journals (Sweden)

    Zhang Xue-Cheng

    2012-01-01

    Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

  5. ROSA full-core and DNBR capabilities

    International Nuclear Information System (INIS)

    Gibcus, H.P.M.; Verhagen, F.C.M.; Wakker, P.H.

    2013-01-01

    The latest developments of the ROSA (Reloading Optimization by Simulated Annealing) code system with an emphasis on the first full-core version and the minimum DNBR (Departure from Nucleate Boiling Ratio) as a new optimization parameter are presented. Designing the core loading pattern of nuclear power plants is becoming a more and more complex task. This task becomes even more complicated if asymmetries in the core loading pattern arise, for instance due to damaged fuel assemblies. For over almost 2 decades ROSA, NRG's (Nuclear Research and consultancy Group) loading pattern optimization code system for PWRs, has proven to be a valuable tool to reactor operators in accomplishing this task. To improve the use of ROSA for designing asymmetric loading patterns, NRG has developed a full-core version of ROSA besides the original quarter-core version which requires rotational symmetry in the computational domain. The extension of ROSA with DNBR as an optimization parameter is part of ROSA's continuous development. (orig.)

  6. Extrinsic functions of lectin domains in O-N-acetylgalactosamine glycan biosynthesis

    DEFF Research Database (Denmark)

    Lorenz, Virginia; Ditamo, Yanina; Cejas, Romina B

    2016-01-01

    during O-GalNAc glycan biosynthesis. The presence of lectin domain T3lec or T4lec during ppGalNAc-T2 and ppGalNAc-T3 catalytic reaction had a clear inhibitory effect on GalNAc-T activity. Interaction of T3lec or T4lec with ppGalNAc-T2 catalytic domain was not mediated by carbohydrate. T3lec, but not T2......Glycan biosynthesis occurs mainly in Golgi. Molecular organization and functional regulation of this process are not well understood. We evaluated the extrinsic effect of lectin domains (β-trefoil fold) of polypeptide GalNAc-transferases (ppGalNAc-Ts) on catalytic activity of glycosyltransferases...

  7. Catalytic hydrogenation of carbon monoxide

    Energy Technology Data Exchange (ETDEWEB)

    Wayland, B.B.

    1992-12-01

    This project is focused on developing strategies to accomplish the reduction and hydrogenation of carbon monoxide to produce organic oxygenates at mild conditions. Our approaches to this issue are based on the recognition that rhodium macrocycles have unusually favorable thermodynamic values for producing a series of intermediate implicated in the catalytic hydrogenation of CO. Observations of metalloformyl complexes produced by reactions of H{sub 2} and CO, and reductive coupling of CO to form metallo {alpha}-diketone species have suggested a multiplicity of routes to organic oxygenates that utilize these species as intermediates. Thermodynamic and kinetic-mechanistic studies are used in constructing energy profiles for a variety of potential pathways, and these schemes are used in guiding the design of new metallospecies to improve the thermodynamic and kinetic factors for individual steps in the overall process. Variation of the 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. Emerging knowledge of the factors that contribute to M-H, M-C and M-O bond enthalpies is directing the search for ligand arrays that will expand the range of metal species that have favorable thermodynamic parameters to produce the primary intermediates for CO hydrogenation. Studies of rhodium complexes are being extended to non-macrocyclic ligand complexes that emulate the favorable thermodynamic features associated with rhodium macrocycles, but that also manifest improved reaction kinetics. Multifunctional catalyst systems designed to couple the ability of rhodium complexes to produce formyl and diketone intermediates with a second catalyst that hydrogenates these imtermediates are promising approaches to accomplish CO hydrogenation at mild conditions.

  8. A disappearing heritage: the clinical core of schizophrenia

    DEFF Research Database (Denmark)

    Parnas, Josef

    2011-01-01

    ("schizoidia" and "latent schizophrenia"). The fundamental features are manifest across all domains of consciousness: subjective experience, expression, cognition, affectivity, behavior, and willing. Yet, the specificity of the core was only graspable at a more comprehensive Gestalt-level, variously designated...

  9. Monte Carlo simulation of magnetic multi-core nanoparticles

    International Nuclear Information System (INIS)

    Schaller, Vincent; Wahnstroem, Goeran; Sanz-Velasco, Anke; Enoksson, Peter; Johansson, Christer

    2009-01-01

    In this paper, a Monte Carlo simulation is carried out to evaluate the equilibrium magnetization of magnetic multi-core nanoparticles in a liquid and subjected to a static magnetic field. The particles contain a magnetic multi-core consisting of a cluster of magnetic single-domains of magnetite. We show that the magnetization of multi-core nanoparticles cannot be fully described by a Langevin model. Inter-domain dipolar interactions and domain magnetic anisotropy contribute to decrease the magnetization of the particles, whereas the single-domain size distribution yields an increase in magnetization. Also, we show that the interactions affect the effective magnetic moment of the multi-core nanoparticles.

  10. Functional interchangeability of late domains, late domain cofactors and ubiquitin in viral budding.

    Directory of Open Access Journals (Sweden)

    Maria Zhadina

    2010-10-01

    Full Text Available The membrane scission event that separates nascent enveloped virions from host cell membranes often requires the ESCRT pathway, which can be engaged through the action of peptide motifs, termed late (L- domains, in viral proteins. Viral PTAP and YPDL-like L-domains bind directly to the ESCRT-I and ALIX components of the ESCRT pathway, while PPxY motifs bind Nedd4-like, HECT-domain containing, ubiquitin ligases (e.g. WWP1. It has been unclear precisely how ubiquitin ligase recruitment ultimately leads to particle release. Here, using a lysine-free viral Gag protein derived from the prototypic foamy virus (PFV, where attachment of ubiquitin to Gag can be controlled, we show that several different HECT domains can replace the WWP1 HECT domain in chimeric ubiquitin ligases and drive budding. Moreover, artificial recruitment of isolated HECT domains to Gag is sufficient to stimulate budding. Conversely, the HECT domain becomes dispensable if the other domains of WWP1 are directly fused to an ESCRT-1 protein. In each case where budding is driven by a HECT domain, its catalytic activity is essential, but Gag ubiquitination is dispensable, suggesting that ubiquitin ligation to trans-acting proteins drives budding. Paradoxically, however, we also demonstrate that direct fusion of a ubiquitin moiety to the C-terminus of PFV Gag can also promote budding, suggesting that ubiquitination of Gag can substitute for ubiquitination of trans-acting proteins. Depletion of Tsg101 and ALIX inhibits budding that is dependent on ubiquitin that is fused to Gag, or ligated to trans-acting proteins through the action of a PPxY motif. These studies underscore the flexibility in the ways that the ESCRT pathway can be engaged, and suggest a model in which the identity of the protein to which ubiquitin is attached is not critical for subsequent recruitment of ubiquitin-binding components of the ESCRT pathway and viral budding to proceed.

  11. Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2.

    Directory of Open Access Journals (Sweden)

    David Talens-Perales

    Full Text Available In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2. We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module with two β-sandwich domains (non-catalytic at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.

  12. Adsorbent catalytic nanoparticles and methods of using the same

    Energy Technology Data Exchange (ETDEWEB)

    Slowing, Igor Ivan; Kandel, Kapil

    2017-01-31

    The present invention provides an adsorbent catalytic nanoparticle including a mesoporous silica nanoparticle having at least one adsorbent functional group bound thereto. The adsorbent catalytic nanoparticle also includes at least one catalytic material. In various embodiments, the present invention provides methods of using and making the adsorbent catalytic nanoparticles. In some examples, the adsorbent catalytic nanoparticles can be used to selectively remove fatty acids from feedstocks for biodiesel, and to hydrotreat the separated fatty acids.

  13. Crystal structure of a catalytically active, non-toxic endopeptidase derivative of Clostridium botulinum toxin A.

    Science.gov (United States)

    Masuyer, Geoffrey; Thiyagarajan, Nethaji; James, Peter L; Marks, Philip M H; Chaddock, John A; Acharya, K Ravi

    2009-03-27

    Botulinum neurotoxins (BoNTs) modulate cholinergic nerve terminals to result in neurotransmitter blockade. BoNTs consists of catalytic (LC), translocation (Hn) and cell-binding domains (Hc). The binding function of the Hc domain is essential for BoNTs to bind the neuronal cell membrane, therefore, removal of the Hc domain results in a product that retains the endopeptidase activity of the LC but is non-toxic. Thus, a molecule consisting of LC and Hn domains of BoNTs, termed LHn, is a suitable molecule for engineering novel therapeutics. The structure of LHA at 2.6 A reported here provides an understanding of the structural implications and challenges of engineering therapeutic molecules that combine functional properties of LHn of BoNTs with specific ligand partners to target different cell types.

  14. Core homogenization method for pebble bed reactors

    International Nuclear Information System (INIS)

    Kulik, V.; Sanchez, R.

    2005-01-01

    This work presents a core homogenization scheme for treating a stochastic pebble bed loading in pebble bed reactors. The reactor core is decomposed into macro-domains that contain several pebble types characterized by different degrees of burnup. A stochastic description is introduced to account for pebble-to-pebble and pebble-to-helium interactions within a macro-domain as well as for interactions between macro-domains. Performance of the proposed method is tested for the PROTEUS and ASTRA critical reactor facilities. Numerical simulations accomplished with the APOLLO2 transport lattice code show good agreement with the experimental data for the PROTEUS reactor facility and with the TRIPOLI4 Monte Carlo simulations for the ASTRA reactor configuration. The difference between the proposed method and the traditional volume-averaged homogenization technique is negligible while only one type of fuel pebbles present in the system, but it grows rapidly with the level of pebble heterogeneity. (authors)

  15. Contributions to the theory of catalytic titrations-III Neutralization catalytic titrations.

    Science.gov (United States)

    Gaál, F F; Abramović, B F

    1985-07-01

    Neutralization catalytic titrations of weak monoprotic adds and bases with both volumetric and coulometric addition of the titrant (strong base/acid) have been simulated by taking into account the equilibrium concentration of the catalyst during the titration. The influence of several factors on the shape of the simulated catalytic titration curve has been investigated and is discussed.

  16. Domain architecture of protein-disulfide isomerase facilitates its dual role as an oxidase and an isomerase in Ero1p-mediated disulfide formation

    DEFF Research Database (Denmark)

    Kulp, M. S.; Frickel, E. M.; Ellgaard, Lars

    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......Native disulfide bond formation in eukaryotes is dependent on protein-disulfide isomerase (PDI) and its homologs, which contain varying combinations of catalytically active and inactive thioredoxin domains. However, the specific contribution of PDI to the formation of new disulfides versus...... catalytic (A) domain. The specific order of thioredoxin domains in PDI is important in establishing the asymmetry in the rate of oxidation of the two active sites thus allowing A and A', two thioredoxin domains that are similar in sequence and structure, to serve opposing functional roles as a disulfide...

  17. Core Hunter 3: flexible core subset selection.

    Science.gov (United States)

    De Beukelaer, Herman; Davenport, Guy F; Fack, Veerle

    2018-05-31

    Core collections provide genebank curators and plant breeders a way to reduce size of their collections and populations, while minimizing impact on genetic diversity and allele frequency. Many methods have been proposed to generate core collections, often using distance metrics to quantify the similarity of two accessions, based on genetic marker data or phenotypic traits. Core Hunter is a multi-purpose core subset selection tool that uses local search algorithms to generate subsets relying on one or more metrics, including several distance metrics and allelic richness. In version 3 of Core Hunter (CH3) we have incorporated two new, improved methods for summarizing distances to quantify diversity or representativeness of the core collection. A comparison of CH3 and Core Hunter 2 (CH2) showed that these new metrics can be effectively optimized with less complex algorithms, as compared to those used in CH2. CH3 is more effective at maximizing the improved diversity metric than CH2, still ensures a high average and minimum distance, and is faster for large datasets. Using CH3, a simple stochastic hill-climber is able to find highly diverse core collections, and the more advanced parallel tempering algorithm further increases the quality of the core and further reduces variability across independent samples. We also evaluate the ability of CH3 to simultaneously maximize diversity, and either representativeness or allelic richness, and compare the results with those of the GDOpt and SimEli methods. CH3 can sample equally representative cores as GDOpt, which was specifically designed for this purpose, and is able to construct cores that are simultaneously more diverse, and either are more representative or have higher allelic richness, than those obtained by SimEli. In version 3, Core Hunter has been updated to include two new core subset selection metrics that construct cores for representativeness or diversity, with improved performance. It combines and outperforms the

  18. The JH2 domain and SH2-JH2 linker regulate JAK2 activity: A detailed kinetic analysis of wild type and V617F mutant kinase domains.

    Science.gov (United States)

    Sanz Sanz, Arturo; Niranjan, Yashavanthi; Hammarén, Henrik; Ungureanu, Daniela; Ruijtenbeek, Rob; Touw, Ivo P; Silvennoinen, Olli; Hilhorst, Riet

    2014-10-01

    JAK2 tyrosine kinase regulates many cellular functions. Its activity is controlled by the pseudokinase (JH2) domain by still poorly understood mechanisms. The V617F mutation in the pseudokinase domain activates JAK2 and causes myeloproliferative neoplasms. We conducted a detailed kinetic analysis of recombinant JAK2 tyrosine kinase domain (JH1) and wild-type and V617F tandem kinase (JH1JH2) domains using peptide microarrays to define the functions of the kinase domains. The results show that i) JAK2 follows a random Bi-Bi reaction mechanism ii) JH2 domain restrains the activity of the JH1 domain by reducing the affinity for ATP and ATP competitive inhibitors iii) V617F decreases affinity for ATP but increases catalytic activity compared to wild-type and iv) the SH2-JH2 linker region participates in controlling activity by reducing the affinity for ATP. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. 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.

  20. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid.

    Science.gov (United States)

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-07-05

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.

  1. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid

    Science.gov (United States)

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-01-01

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

  2. k-core covers and the core

    NARCIS (Netherlands)

    Sanchez-Rodriguez, E.; Borm, Peter; Estevez-Fernandez, A.; Fiestras-Janeiro, G.; Mosquera, M.A.

    This paper extends the notion of individual minimal rights for a transferable utility game (TU-game) to coalitional minimal rights using minimal balanced families of a specific type, thus defining a corresponding minimal rights game. It is shown that the core of a TU-game coincides with the core of

  3. Reactivity of organic compounds in catalytic synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Minachev, Kh M; Bragin, O V

    1978-01-01

    A comprehensive review of 1976 Soviet research on catalysis delivered to the 1977 annual session of the USSR Academy of Science Council on Catalysis (Baku 6/16-20/77) covers hydrocarbon reactions, including hydrogenation and hydrogenolysis, dehydrogenation, olefin dimerization and disproportionation, and cyclization and dehydrocyclization (e.g., piperylene cyclization and ethylene cyclotrimerization); catalytic and physicochemical properties of zeolites, including cracking, dehydrogenation, and hydroisomerization catalytic syntheses and conversion of heterocyclic and functional hydrocarbon derivatives, including partial and total oxidation (e.g., of o-xylene to phthalic anhydride); syntheses of thiophenes from alkanes and hydrogen sulfide over certain dehydrogenation catalysts; catalytic syntheses involving carbon oxides ( e.g., the development of a new heterogeneous catalyst for hydroformylation of olefins), and of Co-MgO zeolitic catalysts for synthesis of aliphatic hydrocarbons from carbon dioxide and hydrogen, and fabrication of high-viscosity lubricating oils over bifunctional aluminosilicate catalysts.

  4. Catalytic Organic Transformations Mediated by Actinide Complexes

    Directory of Open Access Journals (Sweden)

    Isabell S. R. Karmel

    2015-10-01

    Full Text Available This review article presents the development of organoactinides and actinide coordination complexes as catalysts for homogeneous organic transformations. This chapter introduces the basic principles of actinide catalysis and deals with the historic development of actinide complexes in catalytic processes. The application of organoactinides in homogeneous catalysis is exemplified in the hydroelementation reactions, such as the hydroamination, hydrosilylation, hydroalkoxylation and hydrothiolation of alkynes. Additionally, the use of actinide coordination complexes for the catalytic polymerization of α-olefins and the ring opening polymerization of cyclic esters is presented. The last part of this review article highlights novel catalytic transformations mediated by actinide compounds and gives an outlook to the further potential of this field.

  5. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei

    2015-01-01

    -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......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...

  6. Modeling and simulation of heterogeneous catalytic processes

    CERN Document Server

    Dixon, Anthony

    2014-01-01

    Heterogeneous catalysis and mathematical modeling are essential components of the continuing search for better utilization of raw materials and energy, with reduced impact on the environment. Numerical modeling of chemical systems has progressed rapidly due to increases in computer power, and is used extensively for analysis, design and development of catalytic reactors and processes. This book presents reviews of the state-of-the-art in modeling of heterogeneous catalytic reactors and processes. Reviews by leading authorities in the respective areas Up-to-date reviews of latest techniques in modeling of catalytic processes Mix of US and European authors, as well as academic/industrial/research institute perspectives Connections between computation and experimental methods in some of the chapters.

  7. 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.

  8. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Science.gov (United States)

    Robert-Paganin, Julien; Nonin-Lecomte, Sylvie; Réty, Stéphane

    2012-01-01

    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.

  9. Catalytic Wastewater Treatment Using Pillared Clays

    Science.gov (United States)

    Perathoner, Siglinda; Centi, Gabriele

    After introduction on the use of solid catalysts in wastewater treatment technologies, particularly advanced oxidation processes (AOPs), this review discussed the use of pillared clay (PILC) materials in three applications: (i) wet air catalytic oxidation (WACO), (ii) wet hydrogen peroxide catalytic oxidation (WHPCO) on Cu-PILC and Fe-PILC, and (iii) behavior of Ti-PILC and Fe-PILC in the photocatalytic or photo-Fenton conversion of pollutants. Literature data are critically analyzed to evidence the main direction to further investigate, in particularly with reference to the possible practical application of these technologies to treat industrial, municipal, or agro-food production wastewater.

  10. Catalytic Kinetic Resolution of Biaryl Compounds.

    Science.gov (United States)

    Ma, Gaoyuan; Sibi, Mukund P

    2015-08-10

    Biaryl compounds with axial chirality are very common in synthetic chemistry, especially in catalysis. Axially chiral biaryls are important due to their biological activities and extensive applications in asymmetric catalysis. Thus the development of efficient enantioselective methods for their synthesis has attracted considerable attention. This Minireview discusses the progress made in catalytic kinetic resolution of biaryl compounds and chronicles significant advances made recently in catalytic kinetic resolution of biaryl scaffolds. © 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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.

  12. Janus droplet as a catalytic micromotor

    Science.gov (United States)

    Shklyaev, Sergey

    2015-06-01

    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 μ \\text{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 the Janus one no stability threshold exists; hence, the droplet radius can be scaled down to micrometers.

  13. Catalytic burners in larger boiler appliances

    Energy Technology Data Exchange (ETDEWEB)

    Silversand, Fredrik; Persson, Mikael (Catator AB, Lund (Sweden))

    2009-02-15

    This project focuses on the scale up of a Catator's catalytic burner technology to enable retrofit installation in existing boilers and the design of new innovative combinations of catalytic burners and boilers. Different design approaches are discussed and evaluated in the report and suggestions are made concerning scale-up. Preliminary test data, extracted from a large boiler installation are discussed together with an accurate analysis of technical possibilities following an optimization of the boiler design to benefit from the advantages of catalytic combustion. The experimental work was conducted in close collaboration with ICI Caldaie (ICI), located in Verona, Italy. ICI is a leading European boiler manufacturer in the effect segment ranging from about 20 kWt to several MWt. The study shows that it is possibly to scale up the burner technology and to maintain low emissions. The boilers used in the study were designed around conventional combustion and were consequently not optimized for implementation of catalytic burners. From previous experiences it stands clear that the furnace volume can be dramatically decreased when applying catalytic combustion. In flame combustion, this volume is normally dimensioned to avoid flame impingement on cold surfaces and to facilitate completion of the gas-phase reactions. The emissions of nitrogen oxides can be reduced by decreasing the residence time in the furnace. Even with the over-dimensioned furnace used in this study, we easily reached emission values close to 35 mg/kWh. The emissions of carbon monoxide and unburned hydrocarbons were negligible (less than 5 ppmv). It is possible to decrease the emissions of nitrogen oxides further by designing the furnace/boiler around the catalytic burner, as suggested in the report. Simultaneously, the size of the boiler installation can be reduced greatly, which also will result in material savings, i.e. the production cost can be reduced. It is suggested to optimize the

  14. 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.)

  15. Using electron beams to investigate catalytic materials

    International Nuclear Information System (INIS)

    Zhang, Bingsen; Su, Dang Sheng

    2014-01-01

    Transmission Electron microscopy (TEM) enables us, not only to reveal the morphology, but also to provide structural, chemical and electronic information about solid catalysts at the atomic level, providing a dramatic driving force for the development of heterogeneous catalysis. Almost all catalytic materials have been studied with TEM in order to obtain information about their structures, which can help us to establish the synthesis-structure-property relationships and to design catalysts with new structures and desired properties. Herein, several examples will be reviewed to illustrate the investigation of catalytic materials by using electron beams. (authors)

  16. Domain decomposition methods for fluid dynamics

    International Nuclear Information System (INIS)

    Clerc, S.

    1995-01-01

    A domain decomposition method for steady-state, subsonic fluid dynamics calculations, is proposed. The method is derived from the Schwarz alternating method used for elliptic problems, extended to non-linear hyperbolic problems. Particular emphasis is given on the treatment of boundary conditions. Numerical results are shown for a realistic three-dimensional two-phase flow problem with the FLICA-4 code for PWR cores. (from author). 4 figs., 8 refs

  17. Reactor core fuel management

    International Nuclear Information System (INIS)

    Silvennoinen, P.

    1976-01-01

    The subject is covered in chapters, entitled: concepts of reactor physics; neutron diffusion; core heat transfer; reactivity; reactor operation; variables of core management; computer code modules; alternative reactor concepts; methods of optimization; general system aspects. (U.K.)

  18. Nuclear reactor core catcher

    International Nuclear Information System (INIS)

    1977-01-01

    A nuclear reactor core catcher is described for containing debris resulting from an accident causing core meltdown and which incorporates a method of cooling the debris by the circulation of a liquid coolant. (U.K.)

  19. Seismic core shroud

    International Nuclear Information System (INIS)

    Puri, A.; Mullooly, J.F.

    1981-01-01

    A core shroud is provided, comprising: a coolant boundary, following the shape of the core boundary, for channeling the coolant through the fuel assemblies; a cylindrical band positioned inside the core barrel and surrounding the coolant boundary; and support members extending from the coolant boundary to the band, for transferring load from the coolant boundary to the band. The shroud may be assembled in parts using automated welding techniques, and it may be adjusted to fit the reactor core easily

  20. Domain-General Factors Influencing Numerical and Arithmetic Processing

    Directory of Open Access Journals (Sweden)

    André Knops

    2017-12-01

    Full Text Available This special issue contains 18 articles that address the question how numerical processes interact with domain-general factors. We start the editorial with a discussion of how to define domain-general versus domain-specific factors and then discuss the contributions to this special issue grouped into two core numerical domains that are subject to domain-general influences (see Figure 1. The first group of contributions addresses the question how numbers interact with spatial factors. The second group of contributions is concerned with factors that determine and predict arithmetic understanding, performance and development. This special issue shows that domain-general (Table 1a as well as domain-specific (Table 1b abilities influence numerical and arithmetic performance virtually at all levels and make it clear that for the field of numerical cognition a sole focus on one or several domain-specific factors like the approximate number system or spatial-numerical associations is not sufficient. Vice versa, in most studies that included domain-general and domain-specific variables, domain-specific numerical variables predicted arithmetic performance above and beyond domain-general variables. Therefore, a sole focus on domain-general aspects such as, for example, working memory, to explain, predict and foster arithmetic learning is also not sufficient. Based on the articles in this special issue we conclude that both domain-general and domain-specific factors contribute to numerical cognition. But the how, why and when of their contribution still needs to be better understood. We hope that this special issue may be helpful to readers in constraining future theory and model building about the interplay of domain-specific and domain-general factors.

  1. Core Values | NREL

    Science.gov (United States)

    Core Values Core Values NREL's core values are rooted in a safe and supportive work environment guide our everyday actions and efforts: Safe and supportive work environment Respect for the rights physical and social environment Integrity Maintain the highest standard of ethics, honesty, and integrity

  2. Sidewall coring shell

    Energy Technology Data Exchange (ETDEWEB)

    Edelman, Ya A; Konstantinov, L P; Martyshin, A N

    1966-12-12

    A sidewall coring shell consists of a housing and a detachable core catcher. The core lifter is provided with projections, the ends of which are situated in another plane, along the longitudinal axis of the lifter. The chamber has corresponding projections.

  3. Supersymmetric domain walls

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Kleinschmidt, Axel; Riccioni, Fabio

    2012-01-01

    We classify the half-supersymmetric "domain walls," i.e., branes of codimension one, in toroidally compactified IIA/IIB string theory and show to which gauged supergravity theory each of these domain walls belong. We use as input the requirement of supersymmetric Wess-Zumino terms, the properties of

  4. Interaction Between the Biotin Carboxyl Carrier Domain and the Biotin Carboxylase Domain in Pyruvate Carboxylase from Rhizobium etli†

    Science.gov (United States)

    Lietzan, Adam D.; Menefee, Ann L.; Zeczycki, Tonya N.; Kumar, Sudhanshu; Attwood, Paul V.; Wallace, John C.; Cleland, W. Wallace; Maurice, Martin St.

    2011-01-01

    Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family. PMID:21958016

  5. Fluid catalytic cracking : Feedstocks and reaction mechanism

    NARCIS (Netherlands)

    Dupain, X.

    2006-01-01

    The Fluid Catalytic Cracking (FCC) process is one of the key units in a modern refinery. Traditionally, its design is primarily aimed for the production of gasoline from heavy oil fractions, but as co-products also diesel blends and valuable gasses (e.g. propene and butenes) are formed in

  6. Kinetic equation of heterogeneous catalytic isotope exchange

    Energy Technology Data Exchange (ETDEWEB)

    Trokhimets, A I [AN Belorusskoj SSR, Minsk. Inst. Fiziko-Organicheskoj Khimii

    1979-12-01

    A kinetic equation is derived for the bimolecular isotope exchange reaction between AXsub(n)sup(*) and BXsub(m)sup(o), all atoms of element X in each molecule being equivalent. The equation can be generalized for homogeneous and heterogeneous catalytic isotope exchange.

  7. Complementary structure sensitive and insensitive catalytic relationships

    NARCIS (Netherlands)

    Santen, van R.A.

    2009-01-01

    The burgeoning field of nanoscience has stimulated an intense interest in properties that depend on particle size. For transition metal particles, one important property that depends on size is catalytic reactivity, in which bonds are broken or formed on the surface of the particles. Decreased

  8. 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…

  9. 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...... understanding of the nature of the electrochemical promotion is also presented....

  10. 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.

  11. 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....

  12. CATALYTIC SPECTROPHOTOMETRIC DETERMINATION OF Mn(II ...

    African Journals Online (AJOL)

    Preferred Customer

    method is based on the catalytic effect of Mn(II) with the oxidation of Celestine blue .... water samples were filtered through a 0.45 μm pore size membrane filter to remove suspended .... slope of the calibration graph as the optimization criterion. ..... In presence of Phen as stability enhancement agent in indicator system. ( ) +.

  13. Catalytic asymmetric synthesis of the alkaloid (+)-myrtine

    NARCIS (Netherlands)

    Pizzuti, Maria Gabriefla; Minnaard, Adriaan J.; Feringa, Ben L.

    2008-01-01

    A new protocol for the asymmetric synthesis of trans-2,6-disubstituted-4-piperidones has been developed using a catalytic enantioselective conjugate addition reaction in combination with a diastereoselective lithiation-substitution sequence; an efficient synthesis of (+)-myrtine has been achieved

  14. Catalytic oxidation of cyclohexane to cyclohexanone

    Indian Academy of Sciences (India)

    ... a precursor and characterized by chemical analysis using the ICP–AES method, XRD, TEM, FTIR and BET surface area determination. The oxidation reaction was carried out at 70°C under atmospheric pressure. The results showed the catalytic performance of Pt/Al2O3 as being very high in terms of turnover frequency.

  15. Catalytic site interactions in yeast OMP synthase

    DEFF Research Database (Denmark)

    Hansen, Michael Riis; Barr, Eric W.; Jensen, Kaj Frank

    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...

  16. Flame assisted synthesis of catalytic ceramic membranes

    DEFF Research Database (Denmark)

    Johansen, Johnny; Mosleh, Majid; Johannessen, Tue

    2004-01-01

    technology it is possible to make supported catalysts, composite metal oxides, catalytically active surfaces, and porous ceramic membranes. Membrane layers can be formed by using a porous substrate tube (or surface) as a nano-particle filter. The aerosol gas from the flame is led through a porous substrate...

  17. Sintering of Catalytic Nanoparticles: Particle Migration or Ostwald Ripening?

    DEFF Research Database (Denmark)

    Hansen, Thomas Willum; DeLaRiva, Andrew T.; Challa, Sivakumar R.

    2013-01-01

    deactivation, is an important mechanism for the loss of catalyst activity. This is especially true for high temperature catalytic processes, such as steam reforming, automotive exhaust treatment, or catalytic combustion. With dwindling supplies of precious metals and increasing demand, fundamental...

  18. Catalytic characterization of bi-functional catalysts derived from Pd ...

    Indian Academy of Sciences (India)

    Unknown

    1995; Lyubovsky and Pfefferle 1999; Sales et al 1999;. Hill et al 2000). ... For a catalytic system, whose activity ... catalytic systems containing Pd, supported on various acid- ..... Further studies are needed to optimize a balance between.

  19. Catalytically favorable surface patterns in Pt-Au nanoclusters

    KAUST Repository

    Mokkath, Junais Habeeb; Schwingenschlö gl, Udo

    2013-01-01

    Motivated by recent experimental demonstrations of novel PtAu nanoparticles with highly enhanced catalytic properties, we present a systematic theoretical study that explores principal catalytic indicators as a function of the particle size

  20. Expression, purification and preliminary biochemical and structural characterization of the leucine rich repeat namesake domain of leucine rich repeat kinase 2.

    Science.gov (United States)

    Vancraenenbroeck, Renée; Lobbestael, Evy; Weeks, Stephen D; Strelkov, Sergei V; Baekelandt, Veerle; Taymans, Jean-Marc; De Maeyer, Marc

    2012-03-01

    Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease. Much research effort has been directed towards the catalytic core region of LRRK2 composed of GTPase (ROC, Ras of complex proteins) and kinase domains and a connecting COR (C-terminus of ROC) domain. In contrast, the precise functions of the protein-protein interaction domains, such as the leucine-rich repeat (LRR) domain, are not known. In the present study, we modeled the LRRK2 LRR domain (LRR(LRRK2)) using a template assembly approach, revealing the presence of 14 LRRs. Next, we focused on the expression and purification of LRR(LRRK2) in Escherichia coli. Buffer optimization revealed that the protein requires the presence of a zwitterionic detergent, namely Empigen BB, during solubilization and the subsequent purification and characterization steps. This indicates that the detergent captures the hydrophobic surface patches of LRR(LRRK2) thereby suppressing its aggregation. Circular dichroism (CD) spectroscopy measured 18% α-helices and 21% β-sheets, consistent with predictions from the homology model. Size exclusion chromatography (SEC) and dynamic light scattering measurements showed the presence of a single species, with a Stokes radius corresponding to the model dimensions of a protein monomer. Furthermore, no obvious LRR(LRRK2) multimerization was detected via cross-linking studies. Finally, the LRR(LRRK2) clinical mutations did not influence LRR(LRRK2) secondary, tertiary or quaternary structure as determined via SEC and CD spectroscopy. We therefore conclude that these mutations are likely to affect putative LRR(LRRK2) inter- and intramolecular interactions. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

    Science.gov (United States)

    Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

    2013-01-01

    The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

  2. Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.

    Science.gov (United States)

    Stamogiannos, Athanasios; Maben, Zachary; Papakyriakou, Athanasios; Mpakali, Anastasia; Kokkala, Paraskevi; Georgiadis, Dimitris; Stern, Lawrence J; Stratikos, Efstratios

    2017-03-14

    Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.

  3. Catalytic monolayer voltammetry and in situ scanning tunneling microscopy of copper nitrite reductase on cysteamine-modified Au(111) electrodes

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Welinder, A.C.; Hansen, Allan Glargaard

    2003-01-01

    electrochemical scanning tunneling microscopy (in situ STM) directly in aqueous acetate buffer, pH 6.0 has been used. High-resolution in situ STM shows that cysteamine packs into ordered domains with strip features of a periodic distance of 11.7 +/- 0.3 Angstrom. No voltammetric signals of the nitrite substrate...... on this surface could be detected. A strong cathodic catalytic wave appears in the presence of nitrite. The catalytic current follows a Michaelis-Menten pattern with a Michaelis constant of K-m approximate to 44 muM, which is close to the value for AxCuNiR in homogeneous solution. The apparent catalytic rate...

  4. Rotary core drills

    Energy Technology Data Exchange (ETDEWEB)

    1967-11-30

    The design of a rotary core drill is described. Primary consideration is given to the following component parts of the drill: the inner and outer tube, the core bit, an adapter, and the core lifter. The adapter has the form of a downward-converging sleeve and is mounted to the lower end of the inner tube. The lifter, extending from the adapter, is split along each side so that it can be held open to permit movement of a core. It is possible to grip a core by allowing the lifter to assume a closed position.

  5. 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.

  6. Core power capability verification for PWR NPP

    International Nuclear Information System (INIS)

    Xian Chunyu; Liu Changwen; Zhang Hong; Liang Wei

    2002-01-01

    The Principle and methodology of pressurized water reactor nuclear power plant core power capability verification for reload are introduced. The radial and axial power distributions of normal operation (category I or condition I) and abnormal operation (category II or condition II) are simulated by using neutronics calculation code. The linear power density margin and DNBR margin for both categories, which reflect core safety, are analyzed from the point view of reactor physics and T/H, and thus category I operating domain and category II protection set point are verified. Besides, the verification results of reference NPP are also given

  7. The death effector domains of caspase-8 induce terminal differentiation.

    Directory of Open Access Journals (Sweden)

    Ainhoa Mielgo

    2009-11-01

    Full Text Available The differentiation and senescence programs of metazoans play key roles in regulating normal development and preventing aberrant cell proliferation, such as cancer. These programs are intimately associated with both the mitotic and apoptotic pathways. Caspase-8 is an apical apoptotic initiator that has recently been appreciated to coordinate non-apoptotic roles in the cell. Most of these functions are attributed to the catalytic domain, however, the amino-terminal death effector domains (DEDs, which belong to the death domain superfamily of proteins, can also play key roles during development. Here we describe a novel role for caspase-8 DEDs in regulating cell differentiation and senescence. Caspase-8 DEDs accumulate during terminal differentiation and senescence of epithelial, endothelial and myeloid cells; genetic deletion or shRNA suppression of caspase-8 disrupts cell differentiation, while re-expression of DEDs rescues this phenotype. Among caspase-8 deficient neuroblastoma cells, DED expression attenuated tumor growth in vivo and proliferation in vitro via disruption of mitosis and cytokinesis, resulting in upregulation of p53 and induction of differentiation markers. These events occur independent of caspase-8 catalytic activity, but require a critical lysine (K156 in a microtubule-binding motif in the second DED domain. The results demonstrate a new function for the DEDs of caspase-8, and describe an unexpected mechanism that contributes to cell differentiation and senescence.

  8. The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases.

    Science.gov (United States)

    Jacobsen, Annette V; Murphy, James M

    2017-06-15

    Over the past decade, our understanding of the mechanisms by which pseudokinases, which comprise ∼10% of the human and mouse kinomes, mediate signal transduction has advanced rapidly with increasing structural, biochemical, cellular and genetic studies. Pseudokinases are the catalytically defective counterparts of conventional, active protein kinases and have been attributed functions as protein interaction domains acting variously as allosteric modulators of conventional protein kinases and other enzymes, as regulators of protein trafficking or localisation, as hubs to nucleate assembly of signalling complexes, and as transmembrane effectors of such functions. Here, by categorising mammalian pseudokinases based on their known functions, we illustrate the mechanistic diversity among these proteins, which can be viewed as a window into understanding the non-catalytic functions that can be exerted by conventional protein kinases. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  9. Domain observations of Fe and Co based amorphous wires

    International Nuclear Information System (INIS)

    Takajo, M.; Yamasaki, J.

    1993-01-01

    Domain observations were made on Fe and Co based amorphous magnetic wires that exhibit a large Barkhausen discontinuity during flux reversal. Domain patterns observed on the wire surface were compared with those found on a polished section through the center of the wire. It was confirmed that the Fe based wire consists of a shell and core region as previously proposed, however, there is a third region between them. This fairly thick transition region made up of domains at an angle of about 45 degree to the wire axis clearly lacking the closure domains of the previous model. The Co based wire does not have a clear core and shell domain structure. The center of the wire had a classic domain structure expected of uniaxial anisotropy with the easy axis normal to the wire axis. When a model for the residual stress quenched-in during cooling of large Fe bars is applied to the wire, the expected anisotropy is consistent with the domain patterns in the Fe based wire, however, shape anisotropy still plays a dominant role in defining the wire core in the Co based wire

  10. HYDRATE CORE DRILLING TESTS

    Energy Technology Data Exchange (ETDEWEB)

    John H. Cohen; Thomas E. Williams; Ali G. Kadaster; Bill V. Liddell

    2002-11-01

    The ''Methane Hydrate Production from Alaskan Permafrost'' project is a three-year endeavor being conducted by Maurer Technology Inc. (MTI), Noble, and Anadarko Petroleum, in partnership with the U.S. DOE National Energy Technology Laboratory (NETL). The project's goal is to build on previous and ongoing R&D in the area of onshore hydrate deposition. The project team plans to design and implement a program to safely and economically drill, core and produce gas from arctic hydrates. The current work scope includes drilling and coring one well on Anadarko leases in FY 2003 during the winter drilling season. A specially built on-site core analysis laboratory will be used to determine some of the physical characteristics of the hydrates and surrounding rock. Prior to going to the field, the project team designed and conducted a controlled series of coring tests for simulating coring of hydrate formations. A variety of equipment and procedures were tested and modified to develop a practical solution for this special application. This Topical Report summarizes these coring tests. A special facility was designed and installed at MTI's Drilling Research Center (DRC) in Houston and used to conduct coring tests. Equipment and procedures were tested by cutting cores from frozen mixtures of sand and water supported by casing and designed to simulate hydrate formations. Tests were conducted with chilled drilling fluids. Tests showed that frozen core can be washed out and reduced in size by the action of the drilling fluid. Washing of the core by the drilling fluid caused a reduction in core diameter, making core recovery very difficult (if not impossible). One successful solution was to drill the last 6 inches of core dry (without fluid circulation). These tests demonstrated that it will be difficult to capture core when drilling in permafrost or hydrates without implementing certain safeguards. Among the coring tests was a simulated hydrate

  11. Aziridine- and Azetidine-Pd Catalytic Combinations. Synthesis and Evaluation of the Ligand Ring Size Impact on Suzuki-Miyaura Reaction Issues

    Directory of Open Access Journals (Sweden)

    Hamza Boufroura

    2017-01-01

    Full Text Available The synthesis of new vicinal diamines based on aziridine and azetidine cores as well as the comparison of their catalytic activities as ligand in the Suzuki-Miyaura coupling reaction are described in this communication. The synthesis of three- and four-membered ring heterocycles substituted by a methylamine pendant arm is detailed from the parent nitrile derivatives. Complexation to palladium under various conditions has been examined affording vicinal diamines or amine-imidate complexes. The efficiency of four new catalytic systems is compared in the preparation of variously substituted biaryls. Aziridine- and azetidine-based catalytic systems allowed Suzuki-Miyaura reactions from aryl halides including chlorides with catalytic loadings until 0.001% at temperatures ranging from 100 °C to r.t. The evolution of the Pd-metallacycle ring strain moving from azetidine to aziridine in combination with a methylamine or an imidate pendant arm impacted the Suzuki-Miyaura reaction issue.

  12. Core Competencies for Injury and Violence Prevention

    Science.gov (United States)

    Stephens-Stidham, Shelli; Peek-Asa, Corinne; Bou-Saada, Ingrid; Hunter, Wanda; Lindemer, Kristen; Runyan, Carol

    2009-01-01

    Efforts to reduce the burden of injury and violence require a workforce that is knowledgeable and skilled in prevention. However, there has been no systematic process to ensure that professionals possess the necessary competencies. To address this deficiency, we developed a set of core competencies for public health practitioners in injury and violence prevention programs. The core competencies address domains including public health significance, data, the design and implementation of prevention activities, evaluation, program management, communication, stimulating change, and continuing education. Specific learning objectives establish goals for training in each domain. The competencies assist in efforts to reduce the burden of injury and violence and can provide benchmarks against which to assess progress in professional capacity for injury and violence prevention. PMID:19197083

  13. 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.

  14. Akt1 binds focal adhesion kinase via the Akt1 kinase domain independently of the pleckstrin homology domain.

    Science.gov (United States)

    Basson, M D; Zeng, B; Wang, S

    2015-10-01

    Akt1 and focal adhesion kinase (FAK) are protein kinases that play key roles in normal cell signaling. Individually, aberrant expression of these kinases has been linked to a variety of cancers. Together, Akt1/FAK interactions facilitate cancer metastasis by increasing cell adhesion under conditions of increased extracellular pressure. Pathological and iatrogenic sources of pressure arise from tumor growth against constraining stroma or direct perioperative manipulation. We previously reported that 15 mmHg increased extracellular pressure causes Akt1 to both directly interact with FAK and to phosphorylate and activate it. We investigated the nature of the Akt1/FAK binding by creating truncations of recombinant FAK, conjugated to glutathione S-transferase (GST), to pull down full-length Akt1. Western blots probing for Akt1 showed that FAK/Akt1 binding persisted in FAK truncations consisting of only amino acids 1-126, FAK(NT1), which contains the F1 subdomain of its band 4.1, ezrin, radixin, and moesin (FERM) domain. Using FAK(NT1) as bait, we then pulled down truncated versions of recombinant Akt1 conjugated to HA (human influenza hemagglutinin). Probes for GST-FAK(NT1) showed Akt1-FAK binding to occur in the absence of the both the Akt1 (N)-terminal pleckstrin homology (PH) domain and its adjacent hinge region. The Akt1 (C)-terminal regulatory domain was equally unnecessary for Akt1/FAK co-immunoprecipitation. Truncations involving the Akt1 catalytic domain showed that the domain by itself was enough to pull down FAK. Additionally, a fragment spanning from the PH domain to half way through the catalytic domain demonstrated increased FAK binding compared to full length Akt1. These results begin to delineate the Akt1/FAK interaction and can be used to manipulate their force-activated signal interactions. Furthermore, the finding that the N-terminal half of the Akt1 catalytic domain binds so strongly to FAK when cleaved from the rest of the protein may suggest a means

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

    Directory of Open Access Journals (Sweden)

    Yu-Tung Chien

    2013-01-01

    Full Text Available 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 results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

  16. Effect of inlet cone pipe angle in catalytic converter

    Science.gov (United States)

    Amira Zainal, Nurul; Farhain Azmi, Ezzatul; Arifin Samad, Mohd

    2018-03-01

    The catalytic converter shows significant consequence to improve the performance of the vehicle start from it launched into production. Nowadays, the geometric design of the catalytic converter has become critical to avoid the behavior of backpressure in the exhaust system. The backpressure essentially reduced the performance of vehicles and increased the fuel consumption gradually. Consequently, this study aims to design various models of catalytic converter and optimize the volume of fluid flow inside the catalytic converter by changing the inlet cone pipe angles. Three different geometry angles of the inlet cone pipe of the catalytic converter were assessed. The model is simulated in Solidworks software to determine the optimum geometric design of the catalytic converter. The result showed that by decreasing the divergence angle of inlet cone pipe will upsurge the performance of the catalytic converter.

  17. The core paradox.

    Science.gov (United States)

    Kennedy, G. C.; Higgins, G. H.

    1973-01-01

    Rebuttal of suggestions from various critics attempting to provide an escape from the seeming paradox originated by Higgins and Kennedy's (1971) proposed possibility that the liquid in the outer core was thermally stably stratified and that this stratification might prove a powerful inhibitor to circulation of the outer core fluid of the kind postulated for the generation of the earth's magnetic field. These suggestions are examined and shown to provide no reasonable escape from the core paradox.

  18. Zeolitic catalytic conversion of alcohols to hydrocarbons

    Science.gov (United States)

    Narula, Chaitanya K.; Davison, Brian H.; Keller, Martin

    2018-04-10

    A method for converting an alcohol to a hydrocarbon, the method comprising contacting said alcohol with a metal-loaded zeolite catalyst at a temperature of at least 100.degree. C. and up to 550.degree. C., wherein said alcohol can be produced by a fermentation process, said metal is a positively-charged metal ion, and said metal-loaded zeolite catalyst is catalytically active for converting said alcohol to said hydrocarbon.

  19. Method to produce catalytically active nanocomposite coatings

    Science.gov (United States)

    Erdemir, Ali; Eryilmaz, Osman Levent; Urgen, Mustafa; Kazmanli, Kursat

    2016-02-09

    A nanocomposite coating and method of making and using the coating. The nanocomposite coating is disposed on a base material, such as a metal or ceramic; and the nanocomposite consists essentially of a matrix of an alloy selected from the group of Cu, Ni, Pd, Pt and Re which are catalytically active for cracking of carbon bonds in oils and greases and a grain structure selected from the group of borides, carbides and nitrides.

  20. Enantioselective catalytic fluorinative aza-semipinacol rearrangement.

    Science.gov (United States)

    Romanov-Michailidis, Fedor; Pupier, Marion; Besnard, Céline; Bürgi, Thomas; Alexakis, Alexandre

    2014-10-03

    An efficient and highly stereoselective fluorinative aza-semipinacol rearrangement is described. The catalytic reaction requires use of Selectfluor in combination with the chiral, enantiopure phosphate anion derived from acid L3. Under optimized conditions, cyclopropylamines A were transformed into β-fluoro cyclobutylimines B in good yields and high levels of diastereo- and enantiocontrol. Furthermore, the optically active cyclobutylimines were reduced diastereoselectively with L-Selectride in the corresponding fluorinated amines C, compounds of significant interest in the pharmacological industry.

  1. Zeolitic catalytic conversion of alochols to hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Narula, Chaitanya K.; Davison, Brian H.; Keller, Martin

    2017-01-03

    A method for converting an alcohol to a hydrocarbon, the method comprising contacting said alcohol with a metal-loaded zeolite catalyst at a temperature of at least 100.degree. C. and up to 550.degree. C., wherein said alcohol can be produced by a fermentation process, said metal is a positively-charged metal ion, and said metal-loaded zeolite catalyst is catalytically active for converting said alcohol to said hydrocarbon.

  2. 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

  3. Catalytic extraction processing of contaminated scrap metal

    International Nuclear Information System (INIS)

    Griffin, T.P.; Johnston, J.E.; Payea, B.M.; Zeitoon, B.M.

    1995-01-01

    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. Method to produce catalytically active nanocomposite coatings

    Energy Technology Data Exchange (ETDEWEB)

    Erdemir, Ali; Eryilmaz, Osman Levent; Urgen, Mustafa; Kazmanli, Kursat

    2017-12-19

    A nanocomposite coating and method of making and using the coating. The nanocomposite coating is disposed on a base material, such as a metal or ceramic; and the nanocomposite consists essentially of a matrix of an alloy selected from the group of Cu, Ni, Pd, Pt and Re which are catalytically active for cracking of carbon bonds in oils and greases and a grain structure selected from the group of borides, carbides and nitrides.

  5. Nuclear reactor core flow baffling

    International Nuclear Information System (INIS)

    Berringer, R.T.

    1979-01-01

    A flow baffling arrangement is disclosed for the core of a nuclear reactor. A plurality of core formers are aligned with the grids of the core fuel assemblies such that the high pressure drop areas in the core are at the same elevations as the high pressure drop areas about the core periphery. The arrangement minimizes core bypass flow, maintains cooling of the structure surrounding the core, and allows the utilization of alternative beneficial components such as neutron reflectors positioned near the core

  6. Stability of a Bifunctional Cu-Based Core@Zeolite Shell Catalyst for Dimethyl Ether Synthesis Under Redox Conditions Studied by Environmental Transmission Electron Microscopy and In Situ X-Ray Ptychography

    DEFF Research Database (Denmark)

    Baier, Sina; Damsgaard, Christian Danvad; Klumpp, Michael

    2017-01-01

    When using bifunctional core@shell catalysts, the stability of both the shell and core-shell interface is crucial for catalytic applications. In the present study, we elucidate the stability of a CuO/ZnO/Al2O3@ZSM-5 core@shell material, used for one-stage synthesis of dimethyl ether from synthesi...

  7. Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases

    Directory of Open Access Journals (Sweden)

    Lu Liu

    2017-09-01

    Full Text Available Product-releasing enzyme (PRE domains in fungal non-reducing polyketide synthases (NR-PKSs play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII. It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE, reductase (R, and metallo-β-lactamase-type TE (MβL-TE. The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.

  8. Sediment Core Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Provides instrumentation and expertise for physical and geoacoustic characterization of marine sediments.DESCRIPTION: The multisensor core logger measures...

  9. Catalytic hydrogen recombination for nuclear containments

    International Nuclear Information System (INIS)

    Koroll, G.W.; Lau, D.W.P.; Dewit, W.A.; Graham, W.R.C.

    1994-01-01

    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 H 2 -O 2 , 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 m 3 and 10 m 3 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

  10. Electrochemical catalytic treatment of phenol wastewater

    International Nuclear Information System (INIS)

    Ma Hongzhu; Zhang Xinhai; Ma Qingliang; Wang Bo

    2009-01-01

    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.

  11. 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.

  12. Vapor-Driven Propulsion of Catalytic Micromotors

    Science.gov (United States)

    Dong, Renfeng; Li, Jinxing; Rozen, Isaac; Ezhilan, Barath; Xu, Tailin; Christianson, Caleb; Gao, Wei; Saintillan, David; Ren, Biye; Wang, Joseph

    2015-08-01

    Chemically-powered micromotors offer exciting opportunities in diverse fields, including therapeutic delivery, environmental remediation, and nanoscale manufacturing. However, these nanovehicles require direct addition of high concentration of chemical fuel to the motor solution for their propulsion. We report the efficient vapor-powered propulsion of catalytic micromotors without direct addition of fuel to the micromotor solution. Diffusion of hydrazine vapor from the surrounding atmosphere into the sample solution is instead used to trigger rapid movement of iridium-gold Janus microsphere motors. Such operation creates a new type of remotely-triggered and powered catalytic micro/nanomotors that are responsive to their surrounding environment. This new propulsion mechanism is accompanied by unique phenomena, such as the distinct off-on response to the presence of fuel in the surrounding atmosphere, and spatio-temporal dependence of the motor speed borne out of the concentration gradient evolution within the motor solution. The relationship between the motor speed and the variables affecting the fuel concentration distribution is examined using a theoretical model for hydrazine transport, which is in turn used to explain the observed phenomena. The vapor-powered catalytic micro/nanomotors offer new opportunities in gas sensing, threat detection, and environmental monitoring, and open the door for a new class of environmentally-triggered micromotors.

  13. 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.

  14. Antibody proteases: induction of catalytic response.

    Science.gov (United States)

    Gabibov, A G; Friboulet, A; Thomas, D; Demin, A V; Ponomarenko, N A; Vorobiev, I I; Pillet, D; Paon, M; Alexandrova, E S; Telegin, G B; Reshetnyak, A V; Grigorieva, O V; Gnuchev, N V; Malishkin, K A; Genkin, D D

    2002-10-01

    Most of the data accumulated throughout the years on investigation of catalytic antibodies indicate that their production increases on the background of autoimmune abnormalities. The different approaches to induction of catalytic response toward recombinant gp120 HIV-1 surface protein in mice with various autoimmune pathologies are described. The peptidylphosphonate conjugate containing structural part of gp120 molecule is used for reactive immunization of NZB/NZW F1, MRL, and SJL mice. The specific modification of heavy and light chains of mouse autoantibodies with Val-Ala-Glu-Glu-Glu-Val-PO(OPh)2 reactive peptide was demonstrated. Increased proteolytic activity of polyclonal antibodies in SJL mice encouraged us to investigate the production of antigen-specific catalytic antibodies on the background of induced experimental autoimmune encephalomyelitis (EAE). The immunization of autoimmune-prone mice with the engineered fusions containing the fragments of gp120 and encephalitogenic epitope of myelin basic protein (MBP(89-104)) was made. The proteolytic activity of polyclonal antibodies isolated from the sera of autoimmune mice immunized by the described antigen was shown. Specific immune response of SJL mice to these antigens was characterized. Polyclonal antibodies purified from sera of the immunized animals revealed proteolytic activity. The antiidiotypic approach to raise the specific proteolytic antibody as an "internal image" of protease is described. The "second order" monoclonal antibodies toward subtilisin Carlsberg revealed pronounced proteolytic activity.

  15. Electrochemical catalytic treatment of phenol wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Ma Hongzhu, E-mail: hzmachem@snnu.edu.cn [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Zhang Xinhai [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Ma Qingliang [Department of Applied Physics, College of Sciences, Taiyuan University of Technology, 030024 Taiyuan (China); Wang Bo [Institute of Energy Chemistry, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China)

    2009-06-15

    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.

  16. Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.

    Directory of Open Access Journals (Sweden)

    Pascal F Egea

    Full Text Available In all organisms the Signal Recognition Particle (SRP, binds to signal sequences of proteins destined for secretion or membrane insertion as they emerge from translating ribosomes. In Archaea and Eucarya, the conserved ribonucleoproteic core is composed of two proteins, the accessory protein SRP19, the essential GTPase SRP54, and an evolutionarily conserved and essential SRP RNA. Through the GTP-dependent interaction between the SRP and its cognate receptor SR, ribosomes harboring nascent polypeptidic chains destined for secretion are dynamically transferred to the protein translocation apparatus at the membrane. We present here high-resolution X-ray structures of SRP54 and SRP19, the two RNA binding components forming the core of the signal recognition particle from the hyper-thermophilic archaeon Pyrococcus furiosus (Pfu. The 2.5 A resolution structure of free Pfu-SRP54 is the first showing the complete domain organization of a GDP bound full-length SRP54 subunit. In its ras-like GTPase domain, GDP is found tightly associated with the protein. The flexible linker that separates the GTPase core from the hydrophobic signal sequence binding M domain, adopts a purely alpha-helical structure and acts as an articulated arm allowing the M domain to explore multiple regions as it scans for signal peptides as they emerge from the ribosomal tunnel. This linker is structurally coupled to the GTPase catalytic site and likely to propagate conformational changes occurring in the M domain through the SRP RNA upon signal sequence binding. Two different 1.8 A resolution crystal structures of free Pfu-SRP19 reveal a compact, rigid and well-folded protein even in absence of its obligate SRP RNA partner. Comparison with other SRP19*SRP RNA structures suggests the rearrangement of a disordered loop upon binding with the RNA through a reciprocal induced-fit mechanism and supports the idea that SRP19 acts as a molecular scaffold and a chaperone, assisting the SRP

  17. Functional analysis of TMLH variants and definition of domains required for catalytic activity and mitochondrial targeting

    NARCIS (Netherlands)

    Monfregola, Jlenia; Cevenini, Armando; Terracciano, Antonio; van Vlies, Naomi; Arbucci, Salvatore; Wanders, Ronald J. A.; D'Urso, Michele; Vaz, Frédéric M.; Ursini, Matilde Valeria

    2005-01-01

    epsilon-N-Trimethyllysine hydroxylase (TMLH) (EC 1.14.11.8) is a non-heme-ferrous iron hydroxylase, Fe(++) and 2-oxoglutarate (2OG) dependent, catalyzing the first of four enzymatic reactions of the highly conserved carnitine biosynthetic pathway. Otherwise from all the other enzymes of carnitine

  18. Localization of catalytic active sites in the large cytoplasmic domain of Na+/K+-ATPase

    Czech Academy of Sciences Publication Activity Database

    Krumscheid, R.; Sušánková, Klára; Ettrich, R.; Teisinger, Jan; Amler, Evžen; Schoner, W.

    2003-01-01

    Roč. 986, - (2003), s. 242-244 ISSN 0077-8923 R&D Projects: GA ČR GA309/02/1479; GA ČR GA204/01/0254; GA ČR GA204/01/1001 Grant - others:CZ-DE(CZ) TSR-088-97; CZ-DE(CZ) CZE 00/033 Institutional research plan: CEZ:AV0Z5011922 Keywords : H4H5 loop * TNP-ATP phosphotase activity Subject RIV: BO - Biophysics Impact factor: 1.892, year: 2003

  19. Can Psychiatric Rehabilitation Be Core to CORE?

    Science.gov (United States)

    Olney, Marjorie F.; Gill, Kenneth J.

    2016-01-01

    Purpose: In this article, we seek to determine whether psychiatric rehabilitation principles and practices have been more fully incorporated into the Council on Rehabilitation Education (CORE) standards, the extent to which they are covered in four rehabilitation counseling "foundations" textbooks, and how they are reflected in the…

  20. The role of glycosylation and domain interactions in the thermal stability of human angiotensin-converting enzyme.

    Science.gov (United States)

    O'Neill, Hester G; Redelinghuys, Pierre; Schwager, Sylva L U; Sturrock, Edward D

    2008-09-01

    The N and C domains of somatic angiotensin-converting enzyme (sACE) differ in terms of their substrate specificity, inhibitor profiling, chloride dependency and thermal stability. The C domain is thermally less stable than sACE or the N domain. Since both domains are heavily glycosylated, the effect of glycosylation on their thermal stability was investigated by assessing their catalytic and physicochemical properties. Testis ACE (tACE) expressed in mammalian cells, mammalian cells in the presence of a glucosidase inhibitor and insect cells yielded proteins with altered catalytic and physicochemical properties, indicating that the more complex glycans confer greater thermal stabilization. Furthermore, a decrease in tACE and N-domain N-glycans using site-directed mutagenesis decreased their thermal stability, suggesting that certain N-glycans have an important effect on the protein's thermodynamic properties. Evaluation of the thermal stability of sACE domain swopover and domain duplication mutants, together with sACE expressed in insect cells, showed that the C domain contained in sACE is less dependent on glycosylation for thermal stabilization than a single C domain, indicating that stabilizing interactions between the two domains contribute to the thermal stability of sACE and are decreased in a C-domain-duplicating mutant.

  1. Voltage-sensing phosphatase modulation by a C2 domain

    Directory of Open Access Journals (Sweden)

    Paul M. Castle

    2015-04-01

    Full Text Available The voltage-sensing phosphatase (VSP is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD, the inter-domain linker, the cytosolic catalytic domain and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate (PI(4,5P2 (Kalli et al., 2014. Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in

  2. Voltage-sensing phosphatase modulation by a C2 domain.

    Science.gov (United States)

    Castle, Paul M; Zolman, Kevin D; Kohout, Susy C

    2015-01-01

    The voltage-sensing phosphatase (VSP) is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD), the inter-domain linker, the cytosolic catalytic domain, and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate (PIP) lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] (Kalli et al., 2014). Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5)P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry (VCF) were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5)P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in

  3. Inter-domain cross-talk controls the NifA protein activity of Herbaspirillum seropedicae.

    Science.gov (United States)

    Monteiro, R A; de Souza, E M; Wassem, R; Yates, M G; Pedrosa, F O; Chubatsu, L S

    2001-11-09

    Herbaspirillum seropedicae is an endophytic diazotroph, which colonizes sugar cane, wheat, rice and maize. The activity of NifA, a transcriptional activator of nif genes in H. seropedicae, is controlled by ammonium ions through a mechanism involving its N-terminal domain. Here we show that this domain interacts specifically in vitro with the N-truncated NifA protein, as revealed by protection against proteolysis, and this interaction caused an inhibitory effect on both the ATPase and DNA-binding activities of the N-truncated NifA protein. We suggest that the N-terminal domain inhibits NifA-dependent transcriptional activation by an inter-domain cross-talk between the catalytic domain of the NifA protein and its regulatory N-terminal domain in response to fixed nitrogen.

  4. Experimental studies on catalytic hydrogen recombiners for light water reactors

    International Nuclear Information System (INIS)

    Drinovac, P.

    2006-01-01

    In the course of core melt accidents in nuclear power plants a large amount of hydrogen can be produced and form an explosive or even detonative gas mixture with aerial oxygen in the reactor building. In the containment atmosphere of pressurized water reactors hydrogen combines a phlogistically with the oxygen present to form water vapor even at room temperature. In the past, experimental work conducted at various facilities has contributed little or nothing to an understanding of the operating principles of catalytic recombiners. Hence, the purpose of the present study was to conduct detailed investigations on a section of a recombiner essentially in order to deepen the understanding of reaction kinetics and heat transport processes. The results of the experiments presented in this dissertation form a large data base of measurements which provides an insight into the processes taking place in recombiners. The reaction-kinetic interpretation of the measured data confirms and deepens the diffusion theory - proposed in an earlier study. Thus it is now possible to validate detailed numeric models representing the processes in recombiners. Consequently the present study serves to broaden and corroborate competence in this significant area of reactor technology. In addition, the empirical knowledge thus gained may be used for a critical reassessment of previous numeric model calculations. (orig.)

  5. Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation.

    Science.gov (United States)

    Filippakopoulos, Panagis; Kofler, Michael; Hantschel, Oliver; Gish, Gerald D; Grebien, Florian; Salah, Eidarus; Neudecker, Philipp; Kay, Lewis E; Turk, Benjamin E; Superti-Furga, Giulio; Pawson, Tony; Knapp, Stefan

    2008-09-05

    The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase alphaC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.

  6. PWR core design calculations

    International Nuclear Information System (INIS)

    Trkov, A.; Ravnik, M.; Zeleznik, N.

    1992-01-01

    Functional description of the programme package Cord-2 for PWR core design calculations is presented. Programme package is briefly described. Use of the package and calculational procedures for typical core design problems are treated. Comparison of main results with experimental values is presented as part of the verification process. (author) [sl

  7. Ubuntu Core Snaps for Science

    Science.gov (United States)

    Wyngaard, J.

    2017-12-01

    A key challenge in the burgeoning sector of IoT (Internet of Things) is ensuring device and communication security. Ubuntu Core's approach to this is the use of 'snaps'. Along side this growth, scientists are increasingly utilising the many new low cost sensors now available. This work prototypes the use of snaps as a possible avenue to reducing the barrier to entry for scientific use of these low cost sensors while also ensuring proper meta-data is captured. Snaps are contained applications that have been signed. This means that a snap application is unable to read or write to any area of the system beyond its assigned reach, thereby significantly limiting the possible impact of any break in security higher up the stack. Further, application and system updates are automatically verified as authentic before being applied. Additionally, on an embedded system running Ubuntu Core the hardware interface (Gadget), kernel, and OS (Core) are all also snaps and therefore also have acquired these same gains. The result is an architecture that enables: (1) Secure, robust, remote automatic updates of both the OS and applications. (2) A user friendly deployment mechanism.(3) A easy to maintain means of supporting multiple platforms. The above is primarily targeted at non-academic domains, however, it is proposed that the Scientific community can benefit from it too. This work therefore prototypes a snap for sensors on board a small Unmanned Aircraft System (sUAS). For demonstration purposes this snap specifically targets connecting a popular low cost CO2 meter to a Raspberry Pi3 and the popular open source sUAS autopilot Arducopter.

  8. Concerted action of the PHD, chromo and motor domains regulates the human chromatin remodelling ATPase CHD4

    OpenAIRE

    Morra, Rosa; Lee, Benjamin M; Shaw, Heather; Tuma, Roman; Mancini, Erika J

    2012-01-01

    CHD4, the core subunit of the Nucleosome Remodelling and Deacetylase (NuRD) complex, is a chromatin remodelling ATPase that, in addition to a helicase domain, harbors tandem plant homeo finger and chromo domains. By using a panel of domain constructs we dissect their roles and demonstrate that DNA binding, histone binding and ATPase activities are allosterically regulated. Molecular shape reconstruction from small-angle X-ray scattering reveals extensive domain-domain interactions, which prov...

  9. Effect of support on the catalytic activity of manganese oxide catalyts for toluene combustion

    International Nuclear Information System (INIS)

    Pozan, Gulin Selda

    2012-01-01

    Highlights: ► α-Al 2 O 3 , obtained from Bohmite, as a support for enhancing of the activity. ► The support material for catalytic oxidation. ► The manganese state and oxygen species effect on the catalytic combustion reaction. - Abstract: The aim of this work was to study combustion of toluene (1000 ppm) over MnO 2 modified with different supports. α-Al 2 O 3 and γ-Al 2 O 3 obtained from Boehmite, γ-Al 2 O 3 (commercial), SiO 2 , TiO 2 and ZrO 2 were used as commercial support materials. In view of potential interest of this process, the influence of support material on the catalytic performance was discussed. The deposition of 9.5MnO 2 was performed by impregnation over support. The catalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and oxidation (TPR/TPO) and thermogravimetric analysis (TGA). The catalytic tests were carried out at atmospheric pressure in a fixed-bed flow reactor. 9.5MnO 2 /α-Al 2 O 3 (B) (synthesized from Boehmite) catalyst exhibits the highest catalytic activity, over which the toluene conversion was up to 90% at a temperature of 289 °C. Considering all the characterization and reaction data reported in this study, it was concluded that the manganese state and oxygen species played an important role in the catalytic activity.

  10. Replaceable LMFBR core components

    International Nuclear Information System (INIS)

    Evans, E.A.; Cunningham, G.W.

    1976-01-01

    Much progress has been made in understanding material and component performance in the high temperature, fast neutron environment of the LMFBR. Current data have provided strong assurance that the initial core component lifetime objectives of FFTF and CRBR can be met. At the same time, this knowledge translates directly into the need for improved core designs that utilize improved materials and advanced fuels required to meet objectives of low doubling times and extended core component lifetimes. An industrial base for the manufacture of quality core components has been developed in the US, and all procurements for the first two core equivalents for FFTF will be completed this year. However, the problem of fabricating recycled plutonium while dramatically reducing fabrication costs, minimizing personnel exposure, and protecting public health and safety must be addressed

  11. Lunar Core and Tides

    Science.gov (United States)

    Williams, J. G.; Boggs, D. H.; Ratcliff, J. T.

    2004-01-01

    Variations in rotation and orientation of the Moon are sensitive to solid-body tidal dissipation, dissipation due to relative motion at the fluid-core/solid-mantle boundary, and tidal Love number k2 [1,2]. There is weaker sensitivity to flattening of the core-mantle boundary (CMB) [2,3,4] and fluid core moment of inertia [1]. Accurate Lunar Laser Ranging (LLR) measurements of the distance from observatories on the Earth to four retroreflector arrays on the Moon are sensitive to lunar rotation and orientation variations and tidal displacements. Past solutions using the LLR data have given results for dissipation due to solid-body tides and fluid core [1] plus Love number [1-5]. Detection of CMB flattening, which in the past has been marginal but improving [3,4,5], now seems significant. Direct detection of the core moment has not yet been achieved.

  12. Internal core tightener

    International Nuclear Information System (INIS)

    Brynsvold, G.V.; Snyder, H.J. Jr.

    1976-01-01

    An internal core tightener is disclosed which is a linear actuated (vertical actuation motion) expanding device utilizing a minimum of moving parts to perform the lateral tightening function. The key features are: (1) large contact areas to transmit loads during reactor operation; (2) actuation cam surfaces loaded only during clamping and unclamping operation; (3) separation of the parts and internal operation involved in the holding function from those involved in the actuation function; and (4) preloaded pads with compliant travel at each face of the hexagonal assembly at the two clamping planes to accommodate thermal expansion and irradiation induced swelling. The latter feature enables use of a ''fixed'' outer core boundary, and thus eliminates the uncertainty in gross core dimensions, and potential for rapid core reactivity changes as a result of core dimensional change. 5 claims, 12 drawing figures

  13. Construction of hybrid peptide synthetases by module and domain fusions.

    Science.gov (United States)

    Mootz, H D; Schwarzer, D; Marahiel, M A

    2000-05-23

    Nonribosomal peptide synthetases are modular enzymes that assemble peptides of diverse structures and important biological activities. Their modular organization provides a great potential for the rational design of novel compounds by recombination of the biosynthetic genes. Here we describe the extension of a dimodular system to trimodular ones based on whole-module fusion. The recombinant hybrid enzymes were purified to monitor product assembly in vitro. We started from the first two modules of tyrocidine synthetase, which catalyze the formation of the dipeptide dPhe-Pro, to construct such hybrid systems. Fusion of the second, proline-specific module with the ninth and tenth modules of the tyrocidine synthetases, specific for ornithine and leucine, respectively, resulted in dimodular hybrid enzymes exhibiting the combined substrate specificities. The thioesterase domain was fused to the terminal module. Upon incubation of these dimodular enzymes with the first tyrocidine module, TycA, incorporating dPhe, the predicted tripeptides dPhe-Pro-Orn and dPhe-Pro-Leu were obtained at rates of 0.15 min(-1) and 2.1 min(-1). The internal thioesterase domain was necessary and sufficient to release the products from the hybrid enzymes and thereby facilitate a catalytic turnover. Our approach of whole-module fusion is based on an improved definition of the fusion sites and overcomes the recently discovered editing function of the intrinsic condensation domains. The stepwise construction of hybrid peptide synthetases from catalytic subunits reinforces the inherent potential for the synthesis of novel, designed peptides.

  14. Effective particle magnetic moment of multi-core particles

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

  15. 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.

  16. 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.

  17. Heterogeneous catalytic materials solid state chemistry, surface chemistry and catalytic behaviour

    CERN Document Server

    Busca, Guido

    2014-01-01

    Heterogeneous Catalytic Materials discusses experimental methods and the latest developments in three areas of research: heterogeneous catalysis; surface chemistry; and the chemistry of catalysts. Catalytic materials are those solids that allow the chemical reaction to occur efficiently and cost-effectively. This book provides you with all necessary information to synthesize, characterize, and relate the properties of a catalyst to its behavior, enabling you to select the appropriate catalyst for the process and reactor system. Oxides (used both as catalysts and as supports for cata

  18. Catalytic methods using molecular oxygen for treatment of PMMS and ECLSS waste streams, volume 2

    Science.gov (United States)

    Akse, James R.

    1992-01-01

    Catalytic oxidation has proven to be an effective addition to the baseline sorption, ion exchange water reclamation technology which will be used on Space Station Freedom (SSF). Low molecular weight, polar organics such as alcohols, aldehydes, ketones, amides, and thiocarbamides which are poorly removed by the baseline multifiltration (MF) technology can be oxidized to carbon dioxide at low temperature (121 C). The catalytic oxidation process by itself can reduce the Total Organic Carbon (TOC) to below 500 ppb for solutions designed to model these waste waters. Individual challenges by selected contaminants have shown only moderate selectivity towards particular organic species. The combined technology is applicable to the more complex waste water generated in the Process Materials Management System (PMMS) and Environmental Control and Life Support System (ECLSS) aboard SSF. During the phase 3 Core Module Integrated Facility (CMIF) water recovery tests at NASA MSFC, real hygiene waste water and humidity condensate were processed to meet potable specifications by the combined technology. A kinetic study of catalytic oxidation demonstrates that the Langmuir-Hinshelwood rate equation for heterogeneous catalysts accurately represent the kinetic behavior. From this relationship, activation energy and rate constants for acetone were determined.

  19. Novel catalytic micromotor of porous zeolitic imidazolate framework-67 for precise drug delivery.

    Science.gov (United States)

    Wang, Linlin; Zhu, Hongli; Shi, Ying; Ge, You; Feng, Xiaomiao; Liu, Ruiqing; Li, Yi; Ma, Yanwen; Wang, Lianhui

    2018-06-07

    Micromotors hold promise as drug carriers for targeted drug delivery owing to the characteristics of self-propulsion and directional navigation. However, several defects still exist, including high cost, short movement life, low drug loading and slow release rate. Herein, a novel catalytic micromotor based on porous zeolitic imidazolate framework-67 (ZIF-67) synthesized by a greatly simplified wet chemical method assisted with ultrasonication is described as an efficient anticancer drug carrier. These porous micromotors display effective autonomous motion in hydrogen peroxide and long durable movement life of up to 90 min. Moreover, the multifunctional micromotor ZIF-67/Fe3O4/DOX exhibits excellent performance in precise drug delivery under external magnetic field with high drug loading capacity of fluorescent anticancer drug DOX up to 682 μg mg-1 owing to its porous nature, high surface area and rapid drug release based on dual stimulus of catalytic reaction and solvent effects. Therefore, these porous ZIF-67-based catalytic micromotors combine the domains of metal-organic frameworks (MOFs) and micomotors, thus developing potential resources for micromotors and holding great potential as label-free and precisely controlled high-quality candidates of drug delivery systems for biomedical applications.

  20. Designing Domain-Specific Heterogeneous Architectures from Dataflow Programs

    Directory of Open Access Journals (Sweden)

    Süleyman Savas

    2018-04-01

    Full Text Available The last ten years have seen performance and power requirements pushing computer architectures using only a single core towards so-called manycore systems with hundreds of cores on a single chip. To further increase performance and energy efficiency, we are now seeing the development of heterogeneous architectures with specialized and accelerated cores. However, designing these heterogeneous systems is a challenging task due to their inherent complexity. We proposed an approach for designing domain-specific heterogeneous architectures based on instruction augmentation through the integration of hardware accelerators into simple cores. These hardware accelerators were determined based on their common use among applications within a certain domain.The objective was to generate heterogeneous architectures by integrating many of these accelerated cores and connecting them with a network-on-chip. The proposed approach aimed to ease the design of heterogeneous manycore architectures—and, consequently, exploration of the design space—by automating the design steps. To evaluate our approach, we enhanced our software tool chain with a tool that can generate accelerated cores from dataflow programs. This new tool chain was evaluated with the aid of two use cases: radar signal processing and mobile baseband processing. We could achieve an approximately 4 × improvement in performance, while executing complete applications on the augmented cores with a small impact (2.5–13% on area usage. The generated accelerators are competitive, achieving more than 90% of the performance of hand-written implementations.

  1. Earth's inner core: Innermost inner core or hemispherical variations?

    NARCIS (Netherlands)

    Lythgoe, K. H.; Deuss, A.|info:eu-repo/dai/nl/412396610; Rudge, J. F.; Neufeld, J. A.

    2014-01-01

    The structure of Earth's deep inner core has important implications for core evolution, since it is thought to be related to the early stages of core formation. Previous studies have suggested that there exists an innermost inner core with distinct anisotropy relative to the rest of the inner core.

  2. Dependence of Core and Extended Flux on Core Dominance ...

    Indian Academy of Sciences (India)

    Abstract. Based on two extragalactic radio source samples, the core dominance parameter is calculated, and the correlations between the core/extended flux density and core dominance parameter are investi- gated. When the core dominance parameter is lower than unity, it is linearly correlated with the core flux density, ...

  3. Domain decomposition methods for the neutron diffusion problem

    International Nuclear Information System (INIS)

    Guerin, P.; Baudron, A. M.; Lautard, J. J.

    2010-01-01

    The neutronic simulation of a nuclear reactor core is performed using the neutron transport equation, and leads to an eigenvalue problem in the steady-state case. Among the deterministic resolution methods, simplified transport (SPN) or diffusion approximations are often used. The MINOS solver developed at CEA Saclay uses a mixed dual finite element method for the resolution of these problems. and has shown his efficiency. In order to take into account the heterogeneities of the geometry, a very fine mesh is generally required, and leads to expensive calculations for industrial applications. In order to take advantage of parallel computers, and to reduce the computing time and the local memory requirement, we propose here two domain decomposition methods based on the MINOS solver. The first approach is a component mode synthesis method on overlapping sub-domains: several Eigenmodes solutions of a local problem on each sub-domain are taken as basis functions used for the resolution of the global problem on the whole domain. The second approach is an iterative method based on a non-overlapping domain decomposition with Robin interface conditions. At each iteration, we solve the problem on each sub-domain with the interface conditions given by the solutions on the adjacent sub-domains estimated at the previous iteration. Numerical results on parallel computers are presented for the diffusion model on realistic 2D and 3D cores. (authors)

  4. Korrelasjon mellom core styrke, core stabilitet og utholdende styrke i core

    OpenAIRE

    Berg-Olsen, Andrea Marie; Fugelsøy, Eivor; Maurstad, Ann-Louise

    2010-01-01

    Formålet med studien var å se hvilke korrelasjon det er mellom core styrke, core stabilitet og utholdende styrke i core. Testingen bestod av tre hoveddeler hvor vi testet core styrke, core stabilitet og utholdende styrke i core. Innenfor core styrke og utholdende styrke i core ble tre ulike tester utført. Ved måling av core stabilitet ble det gjennomført kun en test. I core styrke ble isometrisk abdominal fleksjon, isometrisk rygg ekstensjon og isometrisk lateral fleksjon testet. Sit-ups p...

  5. Windscale pile core surveys

    International Nuclear Information System (INIS)

    Curtis, R.F.; Mathews, R.F.

    1996-01-01

    The two Windscale Piles were closed down, defueled as far as possible and mothballed for thirty years following a fire in the core of Pile 1 in 1957 resulting from the spontaneous release of stored Wigner energy in the graphite moderator. Decommissioning of the reactors commenced in 1987 and has reached the stage where the condition of both cores needs to be determined. To this end, non-intrusive and intrusive surveys and sampling of the cores have been planned and partly implemented. The objectives for each Pile differ slightly. The location and quantity of fuel remaining in the damaged core of Pile 1 needed to be established, whereas the removal of all fuel from Pile 2 needed to be confirmed. In Pile 1, the possible existence of a void in the core is to be explored and in Pile 2, the level of Wigner energy remaining required to be quantified. Levels of radioactivity in both cores needed to be measured. The planning of the surveys is described including strategy, design, safety case preparation and the remote handling and viewing equipment required to carry out the inspection, sampling and monitoring work. The results from the completed non-intrusive survey of Pile 2 are summarised. They confirm that the core is empty and the graphite is in good condition. The survey of Pile 1 has just started. (UK)

  6. Domain: Labour market

    NARCIS (Netherlands)

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

    This domain chapter is dedicated to summarize research on the effects of labour market contextual factors on labour market participation of older workers (aged 50+) and identify research gaps. While employment participation and the timing of (early) retirement is often modelled as an individual

  7. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  8. Domain-Specific Multimodeling

    DEFF Research Database (Denmark)

    Hessellund, Anders

    the overall level of abstraction. It does, however, also introduce a new problem of coordinating multiple different languages in a single system. We call this problem the coordination problem. In this thesis, we present the coordination method for domain-specific multimodeling that explicitly targets...

  9. GlycoDomainViewer

    DEFF Research Database (Denmark)

    Joshi, Hiren J; Jørgensen, Anja; Schjoldager, Katrine T

    2018-01-01

    features, which enhances visibility and accessibility of the wealth of glycoproteomic data being generated. The GlycoDomainViewer enables visual exploration of glycoproteomic data, incorporating information from recent N- and O-glycoproteome studies on human and animal cell lines and some organs and body...

  10. Engineering Metallic Nanoparticles for Enhancing and Probing Catalytic Reactions.

    Science.gov (United States)

    Collins, Gillian; Holmes, Justin D

    2016-07-01

    Recent developments in tailoring the structural and chemical properties of colloidal metal nanoparticles (NPs) have led to significant enhancements in catalyst performance. Controllable colloidal synthesis has also allowed tailor-made NPs to serve as mechanistic probes for catalytic processes. The innovative use of colloidal NPs to gain fundamental insights into catalytic function will be highlighted across a variety of catalytic and electrocatalytic applications. The engineering of future heterogenous catalysts is also moving beyond size, shape and composition considerations. Advancements in understanding structure-property relationships have enabled incorporation of complex features such as tuning surface strain to influence the behavior of catalytic NPs. Exploiting plasmonic properties and altering colloidal surface chemistry through functionalization are also emerging as important areas for rational design of catalytic NPs. This news article will highlight the key developments and challenges to the future design of catalytic NPs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Catalytic cracking models developed for predictive control purposes

    Directory of Open Access Journals (Sweden)

    Dag Ljungqvist

    1993-04-01

    Full Text Available The paper deals with state-space modeling issues in the context of model-predictive control, with application to catalytic cracking. Emphasis is placed on model establishment, verification and online adjustment. Both the Fluid Catalytic Cracking (FCC and the Residual Catalytic Cracking (RCC units are discussed. Catalytic cracking units involve complex interactive processes which are difficult to operate and control in an economically optimal way. The strong nonlinearities of the FCC process mean that the control calculation should be based on a nonlinear model with the relevant constraints included. However, the model can be simple compared to the complexity of the catalytic cracking plant. Model validity is ensured by a robust online model adjustment strategy. Model-predictive control schemes based on linear convolution models have been successfully applied to the supervisory dynamic control of catalytic cracking units, and the control can be further improved by the SSPC scheme.

  12. Synthesis and characterization of mesoporous ZSM-5 core-shell particles for improved catalytic properties

    DEFF Research Database (Denmark)

    Kustova, Marina; Holm, Martin Spangsberg; Christensen, Claus H.

    2008-01-01

    samples were tested in the MTG reaction, and the results showed that both the shell-coated and the desilicated zeolites are significantly more resistant to coke formation. These results are ascribed to the effect of the removal of structural defects rather than to an improvement of the diffusion......HZSM-5 is a unique catalyst for the conversion of methanol, dimethyl ether and other oxygenates into gasoline. During this process, catalyst deactivation by coking requires frequent regeneration and the improvement of catalyst life time is one of the challenges in catalyst development...

  13. Protein structure based prediction of catalytic residues.

    Science.gov (United States)

    Fajardo, J Eduardo; Fiser, Andras

    2013-02-22

    Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases.

  14. Catalytic oxidation of soot over alkaline niobates

    International Nuclear Information System (INIS)

    Pecchi, G.; Cabrera, B.; Buljan, A.; Delgado, E.J.; Gordon, A.L.; Jimenez, R.

    2013-01-01

    Highlights: ► No previous reported studies about alkaline niobates as catalysts for soot oxidation. ► NaNbO 3 and KNbO 3 perovskite-type oxides show lower activation energy than other lanthanoid perovskite-type oxides. ► The alkaline niobate does not show deactivation by metal loss. - Abstract: The lack of studies in the current literature about the assessment of alkaline niobates as catalysts for soot oxidation has motivated this research. In this study, the synthesis, characterization and assessment of alkaline metal niobates as catalysts for soot combustion are reported. The solids MNbO 3 (M = Li, Na, K, Rb) are synthesized by a citrate method, calcined at 450 °C, 550 °C, 650 °C, 750 °C, and characterized by AAS, N 2 adsorption, XRD, O 2 -TPD, FTIR and SEM. All the alkaline niobates show catalytic activity for soot combustion, and the activity depends basically on the nature of the alkaline metal and the calcination temperature. The highest catalytic activity, expressed as the temperature at which combustion of carbon black occurs at the maximum rate, is shown by KNbO 3 calcined at 650 °C. At this calcination temperature, the catalytic activity follows an order dependent on the atomic number, namely: KNbO 3 > NaNbO 3 > LiNbO 3 . The RbNbO 3 solid do not follow this trend presumably due to the perovskite structure was not reached. The highest catalytic activity shown by of KNbO 3 , despite the lower apparent activation energy of NaNbO 3 , stress the importance of the metal nature and suggests the hypothesis that K + ions are the active sites for soot combustion. It must be pointed out that alkaline niobate subjected to consecutive soot combustion cycles does not show deactivation by metal loss, due to the stabilization of the alkaline metal inside the perovskite structure.

  15. Tritium stripping by a catalytic exchange stripper

    International Nuclear Information System (INIS)

    Heung, L.K.; Gibson, G.W.; Ortman, M.S.

    1991-01-01

    A catalytic exchange process for stripping elemental tritium from gas streams has been demonstrated. The process uses a catalyzed isotopic exchange reaction between tritium in the gas phase and protium or deuterium in the solid phase on alumina. The reaction is catalyzed by platinum deposited on the alumina. The process has been tested with both tritium and deuterium. Decontamination factors (ration of inlet and outlet tritium concentrations) as high as 1000 have been achieved, depending on inlet concentration. The test results and some demonstrated applications are presented

  16. Plasma-catalytic reforming of liquid hydrocarbons

    International Nuclear Information System (INIS)

    Nedybaliuk, O.A.; Chernyak, V.Ya; Kolgan, V.V.; Iukhymenko, V.V.; Solomenko, O.V.; Fedirchyk, I.I.; Martysh, E.V.; Demchina, V.P.; Klochok, N.V.; Dragnev, S.V.

    2015-01-01

    The series of experiments studying the plasma-catalytic reforming of liquid hydrocarbons was carried out. The dynamic plasma-liquid system based on a low-power rotating gliding arc with solid electrodes was used for the investigation of liquid hydrocarbons reforming process. Conversion was done via partial oxidation. A part of oxidant flow was activated by the discharge. Synthesis-gas composition was analysed by means of mass-spectrometry and gas-chromatography. A standard boiler, which operates on natural gas and LPG, was used for the burning of synthesis-gas

  17. Methane combustion in catalytic premixed burners

    International Nuclear Information System (INIS)

    Cerri, I.; Saracco, G.; Specchia, V.

    1999-01-01

    Catalytic premixed burners for domestic boiler applications were developed with the aim of achieving a power modularity from 10 to 100% and pollutant emissions limited to NO x 2 , where the combustion took place entirely inside the burner heating it to incandescence and allowing a decrease in the flame temperature and NO x emissions. Such results were confirmed through further tests carried out in a commercial industrial-scale boiler equipped with the conical panels. All the results, by varying the excess air and the heat power employed, are presented and discussed [it

  18. The framing of scientific domains

    DEFF Research Database (Denmark)

    Dam Christensen, Hans

    2014-01-01

    domains, and UNISIST helps understanding this navigation. Design/methodology/approach The UNISIST models are tentatively applied to the domain of art history at three stages, respectively two modern, partially overlapping domains, as well as an outline of an art historical domain anno c1820...

  19. Core shroud corner joints

    Science.gov (United States)

    Gilmore, Charles B.; Forsyth, David R.

    2013-09-10

    A core shroud is provided, which includes a number of planar members, a number of unitary corners, and a number of subassemblies each comprising a combination of the planar members and the unitary corners. Each unitary corner comprises a unitary extrusion including a first planar portion and a second planar portion disposed perpendicularly with respect to the first planar portion. At least one of the subassemblies comprises a plurality of the unitary corners disposed side-by-side in an alternating opposing relationship. A plurality of the subassemblies can be combined to form a quarter perimeter segment of the core shroud. Four quarter perimeter segments join together to form the core shroud.

  20. 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

  1. Direct catalytic hydrothermal liquefaction of spirulina to biofuels with hydrogen

    Science.gov (United States)

    Zeng, Qin; Liao, Hansheng; Zhou, Shiqin; Li, Qiuping; Wang, Lu; Yu, Zhihao; Jing, Li

    2018-01-01

    We report herein on acquiring biofuels from direct catalytic hydrothermal liquefaction of spirulina. The component of bio-oil from direct catalytic hydrothermal liquefaction was similar to that from two independent processes (including liquefaction and upgrading of biocrude). However, one step process has higher carbon recovery, due to the less loss of carbons. It was demonstrated that the yield and HHV of bio-oil from direct catalytic algae with hydrothermal condition is higher than that from two independent processes.

  2. Including lateral interactions into microkinetic models of catalytic reactions

    DEFF Research Database (Denmark)

    Hellman, Anders; Honkala, Johanna Karoliina

    2007-01-01

    In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three differ...... different approximations are investigated: site, mean-field, and quasichemical approximations. The obtained results are compared to accurate Monte Carlo numbers. In the end, we apply the approximations to a real catalytic reaction, namely, ammonia synthesis....

  3. A study on naphtha catalytic reforming reactor simulation and analysis.

    Science.gov (United States)

    Liang, Ke-min; Guo, Hai-yan; Pan, Shi-wei

    2005-06-01

    A naphtha catalytic reforming unit with four reactors in series is analyzed. A physical model is proposed to describe the catalytic reforming radial flow reactor. Kinetics and thermodynamics equations are selected to describe the naphtha catalytic reforming reactions characteristics based on idealizing the complex naphtha mixture by representing the paraffin, naphthene, and aromatic groups by single compounds. The simulation results based above models agree very well with actual operation unit data.

  4. A study on naphtha catalytic reforming reactor simulation and analysis

    OpenAIRE

    Liang, Ke-min; Guo, Hai-yan; Pan, Shi-wei

    2005-01-01

    A naphtha catalytic reforming unit with four reactors in series is analyzed. A physical model is proposed to describe the catalytic reforming radial flow reactor. Kinetics and thermodynamics equations are selected to describe the naphtha catalytic reforming reactions characteristics based on idealizing the complex naphtha mixture by representing the paraffin, naphthene, and aromatic groups by single compounds. The simulation results based above models agree very well with actual operation uni...

  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. ROSA full-core and DNBR capabilities

    International Nuclear Information System (INIS)

    Gibcus, H.P.M.; Verhagen, F.C.M.; Wakker, P.H.

    2012-01-01

    This paper presents the latest developments of the ROSA (Reloading Optimization by Simulated Annealing) code system with an emphasis on the first full-core version and the minimum DNBR (Departure from Nucleate Boiling Ratio) as a new optimization parameter. Designing the core loading pattern of nuclear power plants is becoming a more and more complex task. This task becomes even more complicated if asymmetries in the core loading pattern arise, for instance due to damaged fuel assemblies. For over almost two decades ROSA, NRG's (Nuclear Research and consultancy Group) loading pattern optimization code system for PWRs, has proven to be a valuable tool to reactor operators in accomplishing this task. To improve the use of ROSA for designing asymmetric loading patterns, NRG has developed a full-core version of ROSA besides the original quarter-core version which requires rotational symmetry in the computational domain. The extension of ROSA with DNBR as an optimization parameter is part of ROSA's continuous development. (orig.)

  7. Monodisperse metal nanoparticle catalysts on silica mesoporous supports: synthesis, characterizations, and catalytic reactions

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.

    2009-09-14

    addition, Pt-mesoporous silica core-shell structured NPs (Pt{at}mSiO{sub 2}) were prepared, where the individual Pt NP is encapsulated by the mesoporous silica layer. The Pt{at}mSiO{sub 2} catalysts showed promising catalytic activity in high temperature CO oxidation. The design of catalytic structures with tunable parameters by rational synthetic methods presents a major advance in the field of catalyst synthesis, which would lead to uncover the structure-function relationships in heterogeneous catalytic reactions.

  8. Big Data analytics in the Geo-Spatial Domain

    NARCIS (Netherlands)

    R.A. Goncalves (Romulo); M.G. Ivanova (Milena); M.L. Kersten (Martin); H. Scholten; S. Zlatanova; F. Alvanaki (Foteini); P. Nourian (Pirouz); E. Dias

    2014-01-01

    htmlabstractBig data collections in many scientific domains have inherently rich spatial and geo-spatial features. Spatial location is among the core aspects of data in Earth observation sciences, astronomy, and seismology to name a few. The goal of our project is to design an efficient data

  9. Hydrogen Recombination Rates of Plate-type Passive Auto-catalytic Recombiner

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jongtae; Hong, Seong-Wan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Gun Hong [Kyungwon E-C Co., Seongnam (Korea, Republic of)

    2014-10-15

    The hydrogen mitigation system may include igniters, passive autocatalytic recombiner (PAR), and venting or dilution system. Recently PAR is commonly used as a main component of HMS in a NPP containment because of its passive nature. PARs are categorized by the shape and material of catalytic surface. Catalytic surface coated by platinum is mostly used for the hydrogen recombiners. The shapes of the catalytic surface can be grouped into plate type, honeycomb type and porous media type. Among them, the plate-type PAR is well tested by many experiments. PAR performance analysis can be approached by a multi-scale method which is composed of micro, meso and macro scales. The criterion of the scaling is the ratio of thickness of boundary layer developed on a catalytic surface to representative length of a computational domain. Mass diffusion in the boundary layer must be resolved in the micro scale analysis. In a lumped parameter (LP) analysis using a system code such as MAAP or MELCOR, the chamber of the PAR is much smaller than a computational node. The hydrogen depletion by a PAR is modeled as a source of mass and energy conservation equations. Te catalytic surface reaction of hydrogen must be modeled by a volume-averaged correlation. In this study, a micro scale analysis method is developed using libraries in OpenFOAM to evaluate a hydrogen depletion rate depending on parameters such as size and number of plates and plate arrangement. The analysis code is validated by simulating REKO-3 experiment. And hydrogen depletion analysis is conducted by changing the plate arrangement as a trial of the performance enhancement of a PAR. In this study, a numerical code for an analysis of a PAR performance in a micro scale has been developed by using OpenFOAM libraries. The physical and numerical models were validated by simulating the REKO-3 experiment. As a try to enhance the performance of the plate-type PAR, it was proposed to apply a staggered two-layer arrangement of the

  10. Hydrogen Recombination Rates of Plate-type Passive Auto-catalytic Recombiner

    International Nuclear Information System (INIS)

    Kim, Jongtae; Hong, Seong-Wan; Kim, Gun Hong

    2014-01-01

    The hydrogen mitigation system may include igniters, passive autocatalytic recombiner (PAR), and venting or dilution system. Recently PAR is commonly used as a main component of HMS in a NPP containment because of its passive nature. PARs are categorized by the shape and material of catalytic surface. Catalytic surface coated by platinum is mostly used for the hydrogen recombiners. The shapes of the catalytic surface can be grouped into plate type, honeycomb type and porous media type. Among them, the plate-type PAR is well tested by many experiments. PAR performance analysis can be approached by a multi-scale method which is composed of micro, meso and macro scales. The criterion of the scaling is the ratio of thickness of boundary layer developed on a catalytic surface to representative length of a computational domain. Mass diffusion in the boundary layer must be resolved in the micro scale analysis. In a lumped parameter (LP) analysis using a system code such as MAAP or MELCOR, the chamber of the PAR is much smaller than a computational node. The hydrogen depletion by a PAR is modeled as a source of mass and energy conservation equations. Te catalytic surface reaction of hydrogen must be modeled by a volume-averaged correlation. In this study, a micro scale analysis method is developed using libraries in OpenFOAM to evaluate a hydrogen depletion rate depending on parameters such as size and number of plates and plate arrangement. The analysis code is validated by simulating REKO-3 experiment. And hydrogen depletion analysis is conducted by changing the plate arrangement as a trial of the performance enhancement of a PAR. In this study, a numerical code for an analysis of a PAR performance in a micro scale has been developed by using OpenFOAM libraries. The physical and numerical models were validated by simulating the REKO-3 experiment. As a try to enhance the performance of the plate-type PAR, it was proposed to apply a staggered two-layer arrangement of the

  11. Effect of support on the catalytic activity of manganese oxide catalyts for toluene combustion.

    Science.gov (United States)

    Pozan, Gulin Selda

    2012-06-30

    The aim of this work was to study combustion of toluene (1000ppm) over MnO(2) modified with different supports. α-Al(2)O(3) and γ-Al(2)O(3) obtained from Boehmite, γ-Al(2)O(3) (commercial), SiO(2), TiO(2) and ZrO(2) were used as commercial support materials. In view of potential interest of this process, the influence of support material on the catalytic performance was discussed. The deposition of 9.5MnO(2) was performed by impregnation over support. The catalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and oxidation (TPR/TPO) and thermogravimetric analysis (TGA). The catalytic tests were carried out at atmospheric pressure in a fixed-bed flow reactor. 9.5MnO(2)/α-Al(2)O(3)(B) (synthesized from Boehmite) catalyst exhibits the highest catalytic activity, over which the toluene conversion was up to 90% at a temperature of 289°C. Considering all the characterization and reaction data reported in this study, it was concluded that the manganese state and oxygen species played an important role in the catalytic activity. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Catalytic membrane in reduction of aqueous nitrates: operational principles and catalytic performance

    NARCIS (Netherlands)

    Ilinitch, O.M.; Cuperus, F.P.; Nosova, L.V.; Gribov, E.N.

    2000-01-01

    The catalytic membrane with palladium-copper active component supported over the macroporous ceramic membrane, and a series of γ-Al 2O 3 supported Pd-Cu catalysts were prepared and investigated. In reduction of nitrate ions by hydrogen in water at ambient temperature, pronounced internal diffusion

  13. Non-thermal plasmas for non-catalytic and catalytic VOC abatement

    International Nuclear Information System (INIS)

    Vandenbroucke, Arne M.; Morent, Rino; De Geyter, Nathalie; Leys, Christophe

    2011-01-01

    Highlights: → We review the current status of catalytic and non-catalytic VOC abatement based on a vast number of research papers. → The underlying mechanisms of plasma-catalysis for VOC abatement are discussed. → Critical process parameters that determine the influent are discussed and compared. - Abstract: This paper reviews recent achievements and the current status of non-thermal plasma (NTP) technology for the abatement of volatile organic compounds (VOCs). Many reactor configurations have been developed to generate a NTP at atmospheric pressure. Therefore in this review article, the principles of generating NTPs are outlined. Further on, this paper is divided in two equally important parts: plasma-alone and plasma-catalytic systems. Combination of NTP with heterogeneous catalysis has attracted increased attention in order to overcome the weaknesses of plasma-alone systems. An overview is given of the present understanding of the mechanisms involved in plasma-catalytic processes. In both parts (plasma-alone systems and plasma-catalysis), literature on the abatement of VOCs is reviewed in close detail. Special attention is given to the influence of critical process parameters on the removal process.

  14. Identification and characterization of a core fucosidase from the bacterium Elizabethkingia meningoseptica.

    Science.gov (United States)

    Li, Tiansheng; Li, Mengjie; Hou, Linlin; Guo, Yameng; Wang, Lei; Sun, Guiqin; Chen, Li

    2018-01-26

    All reported α-l-fucosidases catalyze the removal of nonreducing terminal l-fucoses from oligosaccharides or their conjugates, while having no capacity to hydrolyze core fucoses in glycoproteins directly. Here, we identified an α-fucosidase from the bacterium Elizabethkingia meningoseptica with catalytic activity against core α-1,3-fucosylated substrates, and we named it core fucosidase I (cFase I). Using site-specific mutational analysis, we found that three acidic residues (Asp-242, Glu-302, and Glu-315) in the predicted active pocket are critical for cFase I activity, with Asp-242 and Glu-315 acting as a pair of classic nucleophile and acid/base residues and Glu-302 acting in an as yet undefined role. These findings suggest a catalytic mechanism for cFase I that is different from known α-fucosidase catalytic models. In summary, cFase I exhibits glycosidase activity that removes core α-1,3-fucoses from substrates, suggesting cFase I as a new tool for glycobiology, especially for studies of proteins with core fucosylation. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Core Health Outcomes In Childhood Epilepsy (CHOICE): protocol for the selection of a core outcome set.

    Science.gov (United States)

    Morris, Christopher; Dunkley, Colin; Gibbon, Frances M; Currier, Janet; Roberts, Deborah; Rogers, Morwenna; Crudgington, Holly; Bray, Lucy; Carter, Bernie; Hughes, Dyfrig; Tudur Smith, Catrin; Williamson, Paula R; Gringras, Paul; Pal, Deb K

    2017-11-28

    There is increasing recognition that establishing a core set of outcomes to be evaluated and reported in trials of interventions for particular conditions will improve the usefulness of health research. There is no established core outcome set for childhood epilepsy. The aim of this work is to select a core outcome set to be used in evaluative research of interventions for children with rolandic epilepsy, as an exemplar of common childhood epilepsy syndromes. First we will identify what outcomes should be measured; then we will decide how to measure those outcomes. We will engage relevant UK charities and health professional societies as partners, and convene advisory panels for young people with epilepsy and parents of children with epilepsy. We will identify candidate outcomes from a search for trials of interventions for childhood epilepsy, statutory guidance and consultation with our advisory panels. Families, charities and health, education and neuropsychology professionals will be invited to participate in a Delphi survey following recommended practices in the development of core outcome sets. Participants will be able to recommend additional outcome domains. Over three rounds of Delphi survey participants will rate the importance of candidate outcome domains and state the rationale for their decisions. Over the three rounds we will seek consensus across and between families and health professionals on the more important outcomes. A face-to-face meeting will be convened to ratify the core outcome set. We will then review and recommend ways to measure the shortlisted outcomes using clinical assessment and/or patient-reported outcome measures. Our methodology is a proportionate and pragmatic approach to expediently produce a core outcome set for evaluative research of interventions aiming to improve the health of children with epilepsy. A number of decisions have to be made when designing a study to develop a core outcome set including defining the scope

  16. Microwave Catalytic Oxidation of Hydrocarbons in Aqueous Solutions

    National Research Council Canada - National Science Library

    Cha, Chang

    2003-01-01

    .... A sufficient amount of experimental work has been completed evaluating the performance of the microwave catalytic oxidation process and determining the effect of different operating parameters...

  17. Catalytically favorable surface patterns in Pt-Au nanoclusters

    KAUST Repository

    Mokkath, Junais Habeeb

    2013-01-01

    Motivated by recent experimental demonstrations of novel PtAu nanoparticles with highly enhanced catalytic properties, we present a systematic theoretical study that explores principal catalytic indicators as a function of the particle size and composition. We find that Pt electronic states in the vicinity of the Fermi level combined with a modified electron distribution in the nanoparticle due to Pt-to-Au charge transfer are the origin of the outstanding catalytic properties. From our model we deduce the catalytically favorable surface patterns that induce ensemble and ligand effects. © The Royal Society of Chemistry 2013.

  18. Core outcome sets in dermatology: report from the second meeting of the International Cochrane Skin Group Core Outcome Set Initiative.

    Science.gov (United States)

    Kottner, J; Jacobi, L; Hahnel, E; Alam, M; Balzer, K; Beeckman, D; Busard, C; Chalmers, J; Deckert, S; Eleftheriadou, V; Furlan, K; Horbach, S E R; Kirkham, J; Nast, A; Spuls, P; Thiboutot, D; Thorlacius, L; Weller, K; Williams, H C; Schmitt, J

    2018-04-01

    Results of clinical trials are the most important information source for generating external clinical evidence. The use of different outcomes across trials, which investigate similar interventions for similar patient groups, significantly limits the interpretation, comparability and clinical application of trial results. Core outcome sets (COSs) aim to overcome this limitation. A COS is an agreed standardized collection of outcomes that should be measured and reported in all clinical trials for a specific clinical condition. The Core Outcome Set Initiative within the Cochrane Skin Group (CSG-COUSIN) supports the development of core outcomes in dermatology. In the second CSG-COUSIN meeting held in 2017, 11 COS development groups working on skin diseases presented their current work. The presentations and discussions identified the following overarching methodological challenges for COS development in dermatology: it is not always easy to define the disease focus of a COS; the optimal method for outcome domain identification and level of detail needed to specify such domains is challenging to many; decision rules within Delphi surveys need to be improved; appropriate ways of patient involvement are not always clear. In addition, there appear to be outcome domains that may be relevant as potential core outcome domains for the majority of skin diseases. The close collaboration between methodologists in the Core Outcome Set Initiative and the international Cochrane Skin Group has major advantages for trialists, systematic reviewers and COS developers. © 2018 British Association of Dermatologists.

  19. Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

    Science.gov (United States)

    Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A

    2016-01-29

    Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Characterization of the catalytic center of the Ebola virus L polymerase.

    Science.gov (United States)

    Schmidt, Marie Luisa; Hoenen, Thomas

    2017-10-01

    Ebola virus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP) proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp) of L, which is one of the most promising molecular targets, has never been experimentally characterized. Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication. We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target regulating an essential

  1. Characterization of the catalytic center of the Ebola virus L polymerase.

    Directory of Open Access Journals (Sweden)

    Marie Luisa Schmidt

    2017-10-01

    Full Text Available Ebola virus (EBOV causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp of L, which is one of the most promising molecular targets, has never been experimentally characterized.Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication.We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target

  2. Heterogeneous gas core reactor

    International Nuclear Information System (INIS)

    Diaz, N.J.; Dugan, E.T.

    1983-01-01

    A heterogeneous gas core nuclear reactor is disclosed comprising a core barrel provided interiorly with an array of moderator-containing tubes and being otherwise filled with a fissile and/or fertile gaseous fuel medium. The fuel medium may be flowed through the chamber and through an external circuit in which heat is extracted. The moderator may be a fluid which is flowed through the tubes and through an external circuit in which heat is extracted. The moderator may be a solid which may be cooled by a fluid flowing within the tubes and through an external heat extraction circuit. The core barrel is surrounded by moderator/coolant material. Fissionable blanket material may be disposed inwardly or outwardly of the core barrel

  3. 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...

  4. Core Flight Software

    Data.gov (United States)

    National Aeronautics and Space Administration — The AES Core Flight Software (CFS) project purpose is to analyze applicability, and evolve and extend the reusability of the CFS system originally developed by...

  5. PWR degraded core analysis

    International Nuclear Information System (INIS)

    Gittus, J.H.

    1982-04-01

    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.)

  6. Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation.

    Directory of Open Access Journals (Sweden)

    Sulyman Barkho

    Full Text Available The Src family of tyrosine kinases (SFKs regulate numerous aspects of cell growth and differentiation and are under the principal control of the C-terminal Src Kinase (Csk. Although Csk and SFKs share conserved kinase, SH2 and SH3 domains, they differ considerably in three-dimensional structure, regulatory mechanism, and the intrinsic kinase activities. Although the SH2 and SH3 domains are known to up- or down-regulate tyrosine kinase function, little is known about the global motions in the full-length kinase that govern these catalytic variations. We use a combination of accelerated Molecular Dynamics (aMD simulations and experimental methods to provide a new view of functional motions in the Csk scaffold. These computational studies suggest that high frequency vibrations in the SH2 domain are coupled through the N-terminal lobe of the kinase domain to motions in the SH3 domain. The effects of these reflexive movements on the kinase domain can be viewed using both Deuterium Exchange Mass Spectrometry (DXMS and steady-state kinetic methods. Removal of several contacts, including a crystallographically unobserved N-terminal segment, between the SH3 and kinase domains short-circuit these coupled motions leading to reduced catalytic efficiency and stability of N-lobe motifs within the kinase domain. The data expands the model of Csk's activation whereby separate domains productively interact with two diametrically opposed surfaces of the kinase domain. Such reversible transitions may organize the active structure of the tyrosine kinase domain of Csk.

  7. 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

  8. Restraint system for core elements of a reactor core

    International Nuclear Information System (INIS)

    Class, G.

    1975-01-01

    In a nuclear reactor, a core element bundle formed of a plurality of side-by-side arranged core elements is surrounded by restraining elements that exert a radially inwardly directly restraining force generating friction forces between the core elements in a restraining plane that is transverse to the core element axes. The adjoining core elements are in rolling contact with one another in the restraining plane by virtue of rolling-type bearing elements supported in the core elements. (Official Gazette)

  9. Heterogeneous gas core reactor

    International Nuclear Information System (INIS)

    Han, K.I.

    1977-01-01

    Preliminary investigations of a heterogeneous gas core reactor (HGCR) concept suggest that this potential power reactor offers distinct advantages over other existing or conceptual reactor power plants. One of the most favorable features of the HGCR is the flexibility of the power producing system which allows it to be efficiently designed to conform to a desired optimum condition without major conceptual changes. The arrangement of bundles of moderator/coolant channels in a fissionable gas or mixture of gases makes a truly heterogeneous nuclear reactor core. It is this full heterogeneity for a gas-fueled reactor core which accounts for the novelty of the heterogeneous gas core reactor concept and leads to noted significant advantages over previous gas core systems with respect to neutron and fuel economy, power density, and heat transfer characteristics. The purpose of this work is to provide an insight into the design, operating characteristics, and safety of a heterogeneous gas core reactor system. The studies consist mainly of neutronic, energetic and kinetic analyses of the power producing and conversion systems as a preliminary assessment of the heterogeneous gas core reactor concept and basic design. The results of the conducted research indicate a high potential for the heterogeneous gas core reactor system as an electrical power generating unit (either large or small), with an overall efficiency as high as 40 to 45%. The HGCR system is found to be stable and safe, under the conditions imposed upon the analyses conducted in this work, due to the inherent safety of ann expanding gaseous fuel and the intrinsic feedback effects of the gas and water coolant

  10. Computational and Physical Analysis of Catalytic Compounds

    Science.gov (United States)

    Wu, Richard; Sohn, Jung Jae; Kyung, Richard

    2015-03-01

    Nanoparticles exhibit unique physical and chemical properties depending on their geometrical properties. For this reason, synthesis of nanoparticles with controlled shape and size is important to use their unique properties. Catalyst supports are usually made of high-surface-area porous oxides or carbon nanomaterials. These support materials stabilize metal catalysts against sintering at high reaction temperatures. Many studies have demonstrated large enhancements of catalytic behavior due to the role of the oxide-metal interface. In this paper, the catalyzing ability of supported nano metal oxides, such as silicon oxide and titanium oxide compounds as catalysts have been analyzed using computational chemistry method. Computational programs such as Gamess and Chemcraft has been used in an effort to compute the efficiencies of catalytic compounds, and bonding energy changes during the optimization convergence. The result illustrates how the metal oxides stabilize and the steps that it takes. The graph of the energy computation step(N) versus energy(kcal/mol) curve shows that the energy of the titania converges faster at the 7th iteration calculation, whereas the silica converges at the 9th iteration calculation.

  11. New separation technique. Catalytically functionated separation membrane

    Energy Technology Data Exchange (ETDEWEB)

    Urgami, Tadashi [Kansai Univ., Osaka (Japan)

    1989-02-01

    This report introduces research examples, showing the fundamental principle of the membrane by separating the catalytically functionated separation membrane into enzyme fixing separation membrane, polymerized metal complex separation membrane and polymer catalyst separation membrane. This membrane can achieve both functions of separation and catalytic reaction simultaneously and has sufficient possibility to combine powerful functions. Enzyme fixing separation membrane is prepared by carrier combination method, bridging method or covering method and the enzyme fixing method with polymerized complex in which enzyme is controlled to prevent the activity lowering as much as possible and enzyme is fixed from an aqueous solution into polymer membrane. This membrane is applied to the continuous manufacturing of invert sugar from cane sugar and adsorption and removing of harmful substances from blood by utilizing both micro-capsuled urease and active carbon. Alginic acid-copper (II) complex membrane is used for the polymerized metal complex membrane and polystyrene sulfonate membrane is used for the polymer catalyst separation membrane. 28 refs., 4 figs., 1 tabs.

  12. Study of catalytic phenomena in radiation chemistry

    International Nuclear Information System (INIS)

    Dran, J.C.

    1965-01-01

    Two phenomena have been studied: the action of γ rays from radio-cobalt on the adsorption and catalytic properties of ZnO and NiO in. relationship with the heterogeneous oxidation of CO, and the homogeneous catalysis by OsO 4 of the oxidation of various aqueous phase solutes by the same radiation. The prior irradiation of ZnO and of NiO does not modify their catalytic activity but generally increases the adsorption energy of -the gases CO and O 2 . The influence of the radiations appears to be connected with the presence of traces of water on ZnO and of an excess of oxygen on NiO. Osmium tetroxide which is not degraded by irradiation in acid solution, accelerates the radiolytic oxidation of certain compounds (Te IV , Pt 11 , As 111 ) in the presence of oxygen, as a result of its sensitizing effect on the oxidation by H 2 O 2 . In the case of phosphites on the other hand, OsO 4 has a protecting action under certain conditions of acidity and may suppress entirely the chain reaction which characterizes the oxidation of this solute byγ rays. A general mechanism is proposed for these phenomena. The rate constant for the OsO 4 + HO 2 reaction is calculated to be 5.7 x 10 5 l.mol -1 . sec -1 . (author) [fr

  13. Catalytic hydroprocessing of heavy oil feedstocks

    International Nuclear Information System (INIS)

    Okunev, A G; Parkhomchuk, E V; Lysikov, A I; Parunin, P D; Semeikina, V S; Parmon, V N

    2015-01-01

    A grave problem of modern oil refining industry is continuous deterioration of the produced oil quality, on the one hand, and increase in the demand for motor fuels, on the other hand. This necessitates processing of heavy oil feedstock with high contents of sulfur, nitrogen and metals and the atmospheric residue. This feedstock is converted to light oil products via hydrogenation processes catalyzed by transition metal compounds, first of all, cobalt- or nickel-promoted molybdenum and tungsten compounds. The processing involves desulfurization, denitrogenation and demetallization reactions as well as reactions converting heavy hydrocarbons to lighter fuel components. The review discusses the mechanisms of reactions involved in the heavy feedstock hydroprocessing, the presumed structure and state of the catalytically active components and methods for the formation of supports with the desired texture. Practically used and prospective approaches to catalytic upgrading of heavy oil feedstock as well as examples of industrial processing of bitumen and vacuum residues in the presence of catalysts are briefly discussed. The bibliography includes 140 references

  14. Catalytic hydroprocessing of heavy oil feedstocks

    Science.gov (United States)

    Okunev, A. G.; Parkhomchuk, E. V.; Lysikov, A. I.; Parunin, P. D.; Semeikina, V. S.; Parmon, V. N.

    2015-09-01

    A grave problem of modern oil refining industry is continuous deterioration of the produced oil quality, on the one hand, and increase in the demand for motor fuels, on the other hand. This necessitates processing of heavy oil feedstock with high contents of sulfur, nitrogen and metals and the atmospheric residue. This feedstock is converted to light oil products via hydrogenation processes catalyzed by transition metal compounds, first of all, cobalt- or nickel-promoted molybdenum and tungsten compounds. The processing involves desulfurization, denitrogenation and demetallization reactions as well as reactions converting heavy hydrocarbons to lighter fuel components. The review discusses the mechanisms of reactions involved in the heavy feedstock hydroprocessing, the presumed structure and state of the catalytically active components and methods for the formation of supports with the desired texture. Practically used and prospective approaches to catalytic upgrading of heavy oil feedstock as well as examples of industrial processing of bitumen and vacuum residues in the presence of catalysts are briefly discussed. The bibliography includes 140 references.

  15. Catalytic reactor for low-Btu fuels

    Science.gov (United States)

    Smith, Lance; Etemad, Shahrokh; Karim, Hasan; Pfefferle, William C.

    2009-04-21

    An improved catalytic reactor includes a housing having a plate positioned therein defining a first zone and a second zone, and a plurality of conduits fabricated from a heat conducting material and adapted for conducting a fluid therethrough. The conduits are positioned within the housing such that the conduit exterior surfaces and the housing interior surface within the second zone define a first flow path while the conduit interior surfaces define a second flow path through the second zone and not in fluid communication with the first flow path. The conduit exits define a second flow path exit, the conduit exits and the first flow path exit being proximately located and interspersed. The conduits define at least one expanded section that contacts adjacent conduits thereby spacing the conduits within the second zone and forming first flow path exit flow orifices having an aggregate exit area greater than a defined percent of the housing exit plane area. Lastly, at least a portion of the first flow path defines a catalytically active surface.

  16. FBR type reactor core

    International Nuclear Information System (INIS)

    Tamiya, Tadashi; Kawashima, Katsuyuki; Fujimura, Koji; Murakami, Tomoko.

    1995-01-01

    Neutron reflectors are disposed at the periphery of a reactor core fuel region and a blanket region, and a neutron shielding region is disposed at the periphery of them. The neutron reflector has a hollow duct structure having a sealed upper portion, a lower portion opened to cooling water, in which a gas and coolants separately sealed in the inside thereof. A driving pressure of a primary recycling pump is lowered upon reduction of coolant flow rate, then the liquid level of coolants in the neutron reflector is lowered due to imbalance between the driving pressure and a gas pressure, so that coolants having an effect as a reflector are eliminated from the outer circumference of the reactor core. Therefore, the amount of neutrons leaking from the reactor core is increased, and negative reactivity is charged to the reactor core. The negative reactivity of the neutron reflector is made greater than a power compensation reactivity. Since this enables reactor scram by using an inherent performance of the reactor core, the reactor core safety of an LMFBR-type reactor can be improved. (I.N.)

  17. The earths innermost core

    International Nuclear Information System (INIS)

    Nanda, J.N.

    1989-01-01

    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 235 U 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

  18. Structured materials for catalytic and sensing applications

    Science.gov (United States)

    Hokenek, Selma

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

  19. Catalytic combustion in gas stoves - Phase II

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, Anna-Karin [CATATOR AB, Lund (Sweden)

    2003-06-01

    Several independent studies show that gas stoves to some degree contribute to the indoor emissions of NO{sub x} especially in situations were the ventilation flow is poor. The peak-NO{sub x} concentrations can reach several hundred ppb but the integral concentration seldom exceeds about 20 - 50 ppb, which corresponds to an indoor-outdoor ratio of about 1 - 2.5. Epidemiological studies indicate increasing problems with respiratory symptoms in sensitive people at concentrations as low as 15 ppb of NO{sub 2}. Consequently, the NO{sub x}-concentration in homes where gas stoves are used is high enough to cause health effects. However, in situations where the ventilation flow is high (utilisation of ventilation hoods) the NO{sub x}-emissions are not likely to cause any health problems. This study has been aimed at investigating the possibilities to reduce the NO{sub x} emissions from gas stoves by replacing the conventional flame combustion with catalytic combustion. The investigation is requested by Swedish Gas Center, and is a following-up work of an earlier conducted feasibility study presented in April-2002. The present investigation reports on the possibility to use cheap and simple retro-fit catalytic design suggestions for traditional gas stoves. Experiments have been conducted with both natural and town gas, and parameters such as emissions of NO{sub x}, CO and unburned fuel gas and thermal efficiency, etc, have been examined and are discussed. The results show that it is possible to reduce the NO{sub x} emissions up to 80% by a simple retro-fit installation, without decreasing the thermal efficiency of the cooking plate. The measured source strengths correspond to indoor NO{sub x} concentrations that are below or equal to the average outdoor concentration, implying that no additional detrimental health effects are probable. The drawback of the suggested installations is that the concentration of CO and in some cases also CH{sub 4} are increased in the flue gases

  20. TENCompetence Domain Model

    NARCIS (Netherlands)

    2006-01-01

    This is the version 1.1 of the TENCompetence Domain Model (version 1.0 released at 19-6-2006; version 1.1 at 9-11-2008). It contains several files: a) a pdf with the model description, b) three jpg files with class models (also in the pdf), c) a MagicDraw zip file with the model itself, d) a release