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Sample records for catalytic domain directed

  1. Catalytic domain surface residues mediating catecholamine inhibition in tyrosine hydroxylase.

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    Briggs, Gabrielle D; Bulley, Jesse; Dickson, Phillip W

    2014-03-01

    Tyrosine hydroxylase (TH) performs the rate-limiting step in catecholamine (CA) synthesis and is a tetramer composed of regulatory, catalytic and tetramerization domains. CAs inhibit TH by binding two sites in the active site; one with high affinity and one with low affinity. Only high affinity CA binding requires the regulatory domain, believed to interact with the catalytic domain in the presence of CA. Without a crystal structure of the regulatory domain, the specific areas involved in this process are largely undefined. It is not clear whether the regulatory domain-catalytic domain interaction is asymmetrical across the tetramer to produce the high and low affinity sites. To investigate this, pure dimeric TH was generated through double substitution of residues at the tetramerization interface and dimerization salt bridge (K170E/L480A). This was shown to be the core regulatory unit of TH for CA inhibition, possessing both high and low affinity CA binding sites, indicating that there is symmetry between dimers of the tetramer. We also examined possible regulatory domain-interacting regions on the catalytic domain that mediate high affinity CA binding. Using site-directed mutagenesis, A297, E362/E365 and S368 were shown to mediate high affinity dopamine inhibition through V(max) reduction and increasing the K(M) for the cofactor.

  2. Mutational analysis of a ras catalytic domain

    DEFF Research Database (Denmark)

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

    1986-01-01

    transformation of NIH 3T3 cells with approximately the same efficiency as the wild-type v-rasH gene to those that failed to induce any detectable morphologic changes. Correlation of transforming activity with the location of the mutations enabled us to identify three nonoverlapping segments within the catalytic...... domain that were dispensable for transformation and six other segments that were required for transformation. Segments that were necessary for guanosine nucleotide (GDP) binding corresponded to three of the segments that were essential for transformation; two of the three segments share strong sequence...... 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....

  3. Catalytic roles of lysines (K9, K27, K31) in the N-terminal domain in human adenylate kinase by random site-directed mutagenesis.

    Science.gov (United States)

    Ayabe, T; Park, S K; Takenaka, H; Sumida, M; Uesugi, S; Takenaka, O; Hamada, M

    1996-11-01

    To elucidate lysine residues in the N-terminal domain of human cytosolic adenylate kinase (hAK1, EC 2.7.4.3), random site-directed mutagenesis of K9, K27, and K31 residues was performed, and six mutants were analyzed by steady-state kinetics. K9 residue may play an important role in catalysis by interacting with AMP2-. K27 and K31 residues appear to play a functional role in catalysis by interacting with MgATP2-. In human AK, the epsilon-amino group in the side chain of these lysine residues would be essential for phosphoryl transfer between MgATP2- and AMP2- during transition state.

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

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    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.

  5. Crystal structure of the bacteriophage P2 integrase catalytic domain.

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    Skaar, Karin; Claesson, Magnus; Odegrip, Richard; Högbom, Martin; Haggård-Ljungquist, Elisabeth; Stenmark, Pål

    2015-11-30

    Bacteriophage P2 is a temperate phage capable of integrating its DNA into the host genome by site-specific recombination upon lysogenization. Integration and excision of the phage genome requires P2 integrase, which performs recognition, cleavage and joining of DNA during these processes. This work presents the high-resolution crystal structure of the catalytic domain of P2 integrase, and analysis of the structure-function relationship of several previously identified non-functional P2 integrase mutants. The DNA binding area is characterized by a large positively charged patch, harboring key residues. The structure reveals potential for large dimer flexibility, likely essential for rearrangement of DNA strands upon integration and excision of the phage DNA.

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

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    Tobias Haase

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

  7. Crystal structure of yeast DNA polymerase ε catalytic domain.

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    Rinku Jain

    Full Text Available DNA polymerase ε (Polε is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Here we report the ternary structure of the Polε catalytic subunit (Pol2 bound to a nascent G:C base pair (Pol2G:C. Pol2G:C has a typical B-family polymerase fold and embraces the template-primer duplex with the palm, fingers, thumb and exonuclease domains. The overall arrangement of domains is similar to the structure of Pol2T:A reported recently, but there are notable differences in their polymerase and exonuclease active sites. In particular, we observe Ca2+ ions at both positions A and B in the polymerase active site and also observe a Ca2+ at position B of the exonuclease site. We find that the contacts to the nascent G:C base pair in the Pol2G:C structure are maintained in the Pol2T:A structure and reflect the comparable fidelity of Pol2 for nascent purine-pyrimidine and pyrimidine-purine base pairs. We note that unlike that of Pol3, the shape of the nascent base pair binding pocket in Pol2 is modulated from the major grove side by the presence of Tyr431. Together with Pol2T:A, our results provide a framework for understanding the structural basis of high fidelity DNA synthesis by Pol2.

  8. Direct catalytic cross-coupling of alkenyllithium compounds

    NARCIS (Netherlands)

    Hornillos, Valentin; Giannerini, Massimo; Vila, Carlos; Fananas-Mastral, Martin; Feringa, Ben L.

    2015-01-01

    A catalytic method for the direct cross-coupling of alkenyllithium reagents with aryl and alkenyl halides is described. The use of a catalyst comprising Pd-2(dba)(3)/XPhos allows for the stereoselective preparation of a wide variety of substituted alkenes in high yields under mild conditions. In add

  9. Direct measurement of antiferromagnetic domain fluctuations.

    Energy Technology Data Exchange (ETDEWEB)

    Shpyrko, O. G.; Isaacs, E. D.; Logan, J. M.; Feng, Y.; Aeppli, G.; Jaramillo, R.; Kim, H. C.; Rosenbaum, T. F.; Zschack, P.; Sprung, M.; Narayanan, S.; Sandy, A.; Univ. of Chicago; Univ. College London

    2007-05-03

    Measurements of magnetic noise emanating from ferromagnets owing to domain motion were first carried out nearly 100 years ago1, and have underpinned much science and technology2, 3. Antiferromagnets, which carry no net external magnetic dipole moment, yet have a periodic arrangement of the electron spins extending over macroscopic distances, should also display magnetic noise. However, this must be sampled at spatial wavelengths of the order of several interatomic spacings, rather than the macroscopic scales characteristic of ferromagnets. Here we present a direct measurement of the fluctuations in the nanometer-scale superstructure of spin- and charge-density waves associated with antiferromagnetism in elemental chromium. The technique used is X-ray photon correlation spectroscopy, where coherent X-ray diffraction produces a speckle pattern that serves as a 'fingerprint' of a particular magnetic domain configuration. The temporal evolution of the patterns corresponds to domain walls advancing and retreating over micrometer distances. This work demonstrates a useful measurement tool for antiferromagnetic domain wall engineering, but also reveals a fundamental finding about spin dynamics in the simplest antiferromagnet: although the domain wall motion is thermally activated at temperatures above 100 K, it is not so at lower temperatures, and indeed has a rate that saturates at a finite value--consistent with quantum fluctuations--on cooling below 40 K.

  10. Improving the catalytic activity of semiconductor nanocrystals through selective domain etching.

    Science.gov (United States)

    Khon, Elena; Lambright, Kelly; Khnayzer, Rony S; Moroz, Pavel; Perera, Dimuthu; Butaeva, Evgeniia; Lambright, Scott; Castellano, Felix N; Zamkov, Mikhail

    2013-05-01

    Colloidal chemistry offers an assortment of synthetic tools for tuning the shape of semiconductor nanocrystals. While many nanocrystal architectures can be obtained directly via colloidal growth, other nanoparticle morphologies require alternative processing strategies. Here, we show that chemical etching of colloidal nanoparticles can facilitate the realization of nanocrystal shapes that are topologically inaccessible by hot-injection techniques alone. The present methodology is demonstrated by synthesizing a two-component CdSe/CdS nanoparticle dimer, constructed in a way that both CdSe and CdS semiconductor domains are exposed to the external environment. This structural morphology is highly desirable for catalytic applications as it enables both reductive and oxidative reactions to occur simultaneously on dissimilar nanoparticle surfaces. Hydrogen production tests confirmed the improved catalytic activity of CdSe/CdS dimers, which was enhanced 3-4 times upon etching treatment. We expect that the demonstrated application of etching to shaping of colloidal heteronanocrystals can become a common methodology in the synthesis of charge-separating nanocrystals, leading to advanced nanoparticles architectures for applications in areas of photocatalysis, photovoltaics, and light detection.

  11. The NMR structure of the inhibited catalytic domain of human stromelysin-1.

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    Gooley, P R; O'Connell, J F; Marcy, A I; Cuca, G C; Salowe, S P; Bush, B L; Hermes, J D; Esser, C K; Hagmann, W K; Springer, J P

    1994-02-01

    The three-dimensional structure of the catalytic domain of stromelysin-1 complexed with an N-carboxyl alkyl inhibitor has been determined by NMR methods. The global fold consists of three helices, a five stranded beta-sheet and a methionine located in a turn near the catalytic histidines, classifying stromelysin-1 as a metzincin. Stromelysin-1 is unique in having two independent zinc binding sites: a catalytic site and a structural site. The inhibitor binds in an extended conformation. The S1' subsite is a deep hydrophobic pocket, whereas S2' appears shallow and S3' open.

  12. Autoantibodies against the catalytic domain of BRAF are not specific serum markers for rheumatoid arthritis.

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    Wenli Li

    Full Text Available BACKGROUND: Autoantibodies to the catalytic domain of v-raf murine sarcoma viral oncogene homologue B1 (BRAF have been recently identified as a new family of autoantibodies involved in rheumatoid arthritis (RA. The objective of this study was to determine antibody responses to the catalytic domain of BRAF in RA and other autoimmune diseases. The association between RA-related clinical indices and these antibodies was also assessed. METHODOLOGY/PRINCIPAL FINDINGS: The presence of autoantibodies to the catalytic domain of BRAF (anti-BRAF or to peptide P25 (amino acids 656-675 of the catalytic domain of BRAF; anti-P25 was determined in serum samples from patients with RA, primary Sjögren's syndrome (pSS, systemic lupus erythematosus (SLE, and healthy controls by using indirect enzyme-linked immunosorbent assays (ELISAs based on the recombinant catalytic domain of BRAF or a synthesized peptide, respectively. Associations of anti-BRAF or anti-P25 with disease variables of RA patients were also evaluated. Our results show that the BRAF-specific antibodies anti-BRAF and anti-P25 are equally present in RA, pSS, and SLE patients. However, the erythrocyte sedimentation rate (ESR used to detect inflammation was significantly different between patients with and without BRAF-specific antibodies. The anti-BRAF-positive patients were found to have prolonged disease, and active disease occurred more frequently in anti-P25-positive patients than in anti-P25-negative patients. A weak but significant correlation between anti-P25 levels and ESRs was observed (r = 0.319, p = 0.004. CONCLUSIONS/SIGNIFICANCE: The antibody response against the catalytic domain of BRAF is not specific for RA, but the higher titers of BRAF-specific antibodies may be associated with increased inflammation in RA.

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

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    Swinglel, Mark; Honkanel, Richard; Ciszak, Ewa

    2003-01-01

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

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

    DEFF Research Database (Denmark)

    Windahl, Michael Skovbo; Boesen, Jane; Karlsen, Pernille Efferbach;

    2009-01-01

    Tryptophan hydroxylase exists in two isoforms: Isoform 1 catalyses the first and rate-limiting step in the synthesis of serotonin in the peripheral parts of the body while isoform 2 catalyses this step in the brain. The catalytic domains of human tryptophan hydroxylase 1 and 2 have been expressed...

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

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    Kyle D Grode

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

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

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

    2012-03-26

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

  17. The MLLE domain of the ubiquitin ligase UBR5 binds to its catalytic domain to regulate substrate binding.

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    Muñoz-Escobar, Juliana; Matta-Camacho, Edna; Kozlov, Guennadi; Gehring, Kalle

    2015-09-11

    E3 ubiquitin ligases catalyze the transfer of ubiquitin from an E2-conjugating enzyme to a substrate. UBR5, homologous to the E6AP C terminus (HECT)-type E3 ligase, mediates the ubiquitination of proteins involved in translation regulation, DNA damage response, and gluconeogenesis. In addition, UBR5 functions in a ligase-independent manner by prompting protein/protein interactions without ubiquitination of the binding partner. Despite recent functional studies, the mechanisms involved in substrate recognition and selective ubiquitination of its binding partners remain elusive. The C terminus of UBR5 harbors the HECT catalytic domain and an adjacent MLLE domain. MLLE domains mediate protein/protein interactions through the binding of a conserved peptide motif, termed PAM2. Here, we characterize the binding properties of the UBR5 MLLE domain to PAM2 peptides from Paip1 and GW182. The crystal structure with a Paip1 PAM2 peptide reveals the network of hydrophobic and ionic interactions that drive binding. In addition, we identify a novel interaction of the MLLE domain with the adjacent HECT domain mediated by a PAM2-like sequence. Our results confirm the role of the MLLE domain of UBR5 in substrate recruitment and suggest a potential role in regulating UBR5 ligase activity.

  18. Calpain-Mediated Processing of Adenylate Cyclase Toxin Generates a Cytosolic Soluble Catalytically Active N-Terminal Domain.

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    Kepa B Uribe

    Full Text Available Bordetella pertussis, the whooping cough pathogen, secretes several virulence factors among which adenylate cyclase toxin (ACT is essential for establishment of the disease in the respiratory tract. ACT weakens host defenses by suppressing important bactericidal activities of the phagocytic cells. Up to now, it was believed that cell intoxication by ACT was a consequence of the accumulation of abnormally high levels of cAMP, generated exclusively beneath the host plasma membrane by the toxin N-terminal catalytic adenylate cyclase (AC domain, upon its direct translocation across the lipid bilayer. Here we show that host calpain, a calcium-dependent Cys-protease, is activated into the phagocytes by a toxin-triggered calcium rise, resulting in the proteolytic cleavage of the toxin N-terminal domain that releases a catalytically active "soluble AC". The calpain-mediated ACT processing allows trafficking of the "soluble AC" domain into subcellular organella. At least two strategic advantages arise from this singular toxin cleavage, enhancing the specificity of action, and simultaneously preventing an indiscriminate activation of cAMP effectors throughout the cell. The present study provides novel insights into the toxin mechanism of action, as the calpain-mediated toxin processing would confer ACT the capacity for a space- and time-coordinated production of different cAMP "pools", which would play different roles in the cell pathophysiology.

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

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, Alexander I.; Rogals, Monique J.; De, Soumya [Cornell University, Department of Molecular Biology and Genetics (United States); Lu, Kun Ping [Cancer Biology Program and Biology of Aging Program, Beth Israel Deaconess Medical Center, Harvard Medical School (United States); Kovrigin, Evgenii L. [Marquette University, Chemistry Department (United States); Nicholson, Linda K., E-mail: lkn2@cornell.edu [Cornell University, Department of Molecular Biology and Genetics (United States)

    2011-09-15

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

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

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

    2011-09-01

    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, [Formula: see text] and apparent Michaelis constants, [Formula: see text]. 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 [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] 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.

  1. Molecular defect in factor IXBm Lake Elsinore. Substitution of Ala390 by Val in the catalytic domain.

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    Spitzer, S G; Pendurthi, U R; Kasper, C K; Bajaj, S P

    1988-08-05

    Earlier studies with factor IXBm Lake Elsinore (IXBmLE), a nonfunctional variant of factor IX, suggested that the defect in this protein may reside in the catalytic domain of the molecule (Usharani, P., Warn-Cramer, B. J., Kasper, C. K., and Bajaj, S. P. (1985) J. Clin. Invest. 75, 76-83). In this report, genomic DNA fragments from normal IX and IXBmLE alleles were cloned into phage lambda EMBL3 and the recombinant phage identified using normal IX cDNA and synthetic oligonucleotides. Exons VI, VII, and VIII of normal IX and IXBmLE gene were also amplified using a newly developed primer-directed polymerase chain reaction method. All eight exons and flanking regions of the normal IX and IXBmLE gene were sequenced by the dideoxy chain termination method. Comparison of the normal IX and IXBmLE sequences revealed a single base substitution (C----T) in the exon VIII of the BmLE variant, which results in the replacement of Ala390 by Val in the variant molecule. Although this mutation is in the catalytic domain of the molecule, purified factor IXaBmLE is indistinguishable from normal IXa in its activity toward a small synthetic substrate, L-tosylarginine methyl ester. These data, coupled with the previous data, identify a region (around residue 390) in the normal factor IXa which appears to play a major role in the extended macromolecular substrate binding site.

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

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

    2016-02-01

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

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

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    Marletta Michael A

    2008-10-01

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

  4. Direct catalytic cross-coupling of organolithium compounds

    NARCIS (Netherlands)

    Giannerini, Massimo; Fananas Mastral, Martin; Feringa, Ben L.

    2013-01-01

    Catalytic carbon-carbon bond formation based on cross-coupling reactions plays a central role in the production of natural products, pharmaceuticals, agrochemicals and organic materials. Coupling reactions of a variety of organometallic reagents and organic halides have changed the face of modern sy

  5. Cleavage mediated by the catalytic domain of bacterial RNase P RNA.

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    Wu, Shiying; Kikovska, Ema; Lindell, Magnus; Kirsebom, Leif A

    2012-09-14

    Like other RNA molecules, RNase P RNA (RPR) is composed of domains, and these have different functions. Here, we provide data demonstrating that the catalytic (C) domain of Escherichia coli (Eco) RPR when separated from the specificity (S) domain mediates cleavage using various model RNA hairpin loop substrates. Compared to full-length Eco RPR, the rate constant, k(obs), of cleavage for the truncated RPR (CP RPR) was reduced 30- to 13,000-fold depending on substrate. Specifically, the structural architecture of the -1/+73 played a significant role where a C(-1)/G(+73) pair had the most dramatic effect on k(obs). Substitution of A(248) (E. coli numbering), positioned near the cleavage site in the RNase P-substrate complex, with G in the CP RPR resulted in 30-fold improvement in rate. In contrast, strengthening the interaction between the RPR and the 3' end of the substrate only had a modest effect. Interestingly, although deleting the S-domain gave a reduction in the rate, it resulted in a less erroneous RPR with respect to cleavage site selection. These data support and extend our understanding of the coupling between the distal interaction between the S-domain and events at the active site. Our findings will also be discussed with respect to the structure of RPR derived from different organisms.

  6. 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.

  7. The acidic domain of the endothelial membrane protein GPIHBP1 stabilizes lipoprotein lipase activity by preventing unfolding of its catalytic domain

    DEFF Research Database (Denmark)

    Mysling, Simon; Kristensen, Kristian Kølby; Larsson, Mikael

    2016-01-01

    and their lipolytic processing. The current work conceptualizes a model for the GPIHBP1•LPL interaction based on biophysical measurements with hydrogen-deuterium exchange/mass spectrometry, surface plasmon resonance, and zero-length cross-linking. According to this model, GPIHBP1 comprises two functionally distinct...... stabilizes LPL catalytic activity by mitigating the global unfolding of LPL's catalytic domain. This study provides a conceptual framework for understanding intravascular lipolysis and GPIHBP1 and LPL mutations causing familial chylomicronemia....

  8. Cholinesterase-like domains in enzymes and structural proteins: functional and evolutionary relationships and identification of a catalytically essential aspartic acid.

    Science.gov (United States)

    Krejci, E; Duval, N; Chatonnet, A; Vincens, P; Massoulié, J

    1991-01-01

    Primary sequences of cholinesterases and related proteins have been systematically compared. The cholinesterase-like domain of these proteins, about 500 amino acids, may fulfill a catalytic and a structural function. We identified an aspartic acid residue that is conserved among esterases and lipases (Asp-397 in Torpedo acetylcholinesterase) but that had not been considered to be involved in the catalytic mechanism. Site-directed mutagenesis demonstrated that this residue is necessary for activity. Analysis of evolutionary relationships shows that the noncatalytic members of the family do not constitute a separate subgroup, suggesting that loss of catalytic activity occurred independently on several occasions, probably from bifunctional molecules. Cholinesterases may thus be involved in cell-cell interactions in addition to the hydrolysis of acetylcholine. This would explain their specific expression in well-defined territories during embryogenesis before the formation of cholinergic synapses and their presence in noncholinergic tissues. Images PMID:1862088

  9. Visualizing Dealumination of a Single Zeolite Domain in a Real-Life Catalytic Cracking Particle.

    Science.gov (United States)

    Kalirai, Sam; Paalanen, Pasi P; Wang, Jian; Meirer, Florian; Weckhuysen, Bert M

    2016-09-05

    Fluid catalytic cracking (FCC) catalysts play a central role in the chemical conversion of crude oil fractions. Using scanning transmission X-ray microscopy (STXM) we investigate the chemistry of one fresh and two industrially deactivated (ECAT) FCC catalysts at the single zeolite domain level. Spectro-microscopic data at the Fe L3 , La M5 , and Al K X-ray absorption edges reveal differing levels of deposited Fe on the ECAT catalysts corresponding with an overall loss in tetrahedral Al within the zeolite domains. Using La as a localization marker, we have developed a novel methodology to map the changing Al distribution of single zeolite domains within real-life FCC catalysts. It was found that significant changes in the zeolite domain size distributions as well as the loss of Al from the zeolite framework occur. Furthermore, inter- and intraparticle heterogeneities in the dealumination process were observed, revealing the complex interplay between metal-mediated pore accessibility loss and zeolite dealumination.

  10. 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

  11. Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA.

    Science.gov (United States)

    Sunita, S; Zhenxing, H; Swaathi, J; Cygler, Miroslaw; Matte, Allan; Sivaraman, J

    2006-06-16

    Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine (Psi) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E.coli RluF at 2.6A resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of Psi-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.

  12. Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA

    Energy Technology Data Exchange (ETDEWEB)

    Sunita,S.; Zhenxing, H.; Swaathi, J.; Cygler, M.; Matte, A.; Sivaraman, J.

    2006-01-01

    Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine ({psi}) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E. coli RluF at 2.6 Angstroms resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of {psi}-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

  14. Structure of the catalytic domain of the Clostridium thermocellum cellulase CelT.

    Science.gov (United States)

    Kesavulu, Muppuru M; Tsai, Jia Yin; Lee, Hsiao Lin; Liang, Po Huang; Hsiao, Chwan Deng

    2012-03-01

    Cellulases hydrolyze cellulose, a major component of plant cell walls, to oligosaccharides and monosaccharides. Several Clostridium species secrete multi-enzyme complexes (cellulosomes) containing cellulases. C. thermocellum CelT, a family 9 cellulase, lacks the accessory module(s) necessary for activity, unlike most other family 9 cellulases. Therefore, characterization of the CelT structure is essential in order to understand its catalytic mechanism. Here, the crystal structure of free CelTΔdoc, the catalytic domain of CelT, is reported at 2.1 Å resolution. Its structure differs in several aspects from those of other family 9 cellulases. CelTΔdoc contains an additional α-helix, α-helices of increased length and two additional surface-exposed β-strands. It also contains three calcium ions instead of one as found in C. cellulolyticum Cel9M. CelTΔdoc also has two flexible loops at the open end of its active-site cleft. Movement of these loops probably allows the substrate to access the active site. CelT is stable over a wide range of pH and temperature conditions, suggesting that CelT could be used to convert cellulose biomass into biofuel.

  15. 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

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

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

    Science.gov (United States)

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

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

    Science.gov (United States)

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

  18. Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases.

    Science.gov (United States)

    Francia, María Victoria; Clewell, Don B; de la Cruz, Fernando; Moncalián, Gabriel

    2013-08-13

    Plasmid pAD1 is a 60-kb conjugative element commonly found in clinical isolates of Enterococcus faecalis. The relaxase TraX and the primary origin of transfer oriT2 are located close to each other and have been shown to be essential for conjugation. The oriT2 site contains a large inverted repeat (where the nic site is located) adjacent to a series of short direct repeats. TraX does not show any of the typical relaxase sequence motifs but is the prototype of a unique family of relaxases (MOBC). The present study focuses on the genetic, biochemical, and structural analysis of TraX, whose 3D structure could be predicted by protein threading. The structure consists of two domains: (i) an N-terminal domain sharing the topology of the DNA binding domain of the MarR family of transcriptional regulators and (ii) a C-terminal catalytic domain related to the PD-(D/E)XK family of restriction endonucleases. Alignment of MOBC relaxase amino acid sequences pointed to several conserved polar amino acid residues (E28, D152, E170, E172, K176, R180, Y181, and Y203) that were mutated to alanine. Functional analysis of these mutants (in vivo DNA transfer and cleavage assays) revealed the importance of these residues for relaxase activity and suggests Y181 as a potential catalytic residue similarly to His-hydrophobe-His relaxases. We also show that TraX binds specifically to dsDNA containing the oriT2 direct repeat sequences, confirming their role in transfer specificity. The results provide insights into the catalytic mechanism of MOBC relaxases, which differs radically from that of His-hydrophobe-His relaxases.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-29

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

  20. Identification of collagen binding domain residues that govern catalytic activities of matrix metalloproteinase-2 (MMP-2).

    Science.gov (United States)

    Mikhailova, Margarita; Xu, Xiaoping; Robichaud, Trista K; Pal, Sanjay; Fields, Gregg B; Steffensen, Bjorn

    2012-01-01

    An innovative approach to enhance the selectivity of matrix metalloproteinase (MMP) inhibitors comprises targeting these inhibitors to catalytically required substrate binding sites (exosites) that are located outside the catalytic cleft. In MMP-2, positioning of collagen substrate molecules occurs via a unique fibronectin-like domain (CBD) that contains three distinct modular collagen binding sites. To characterize the contributions of these exosites to gelatinolysis by MMP-2, seven MMP-2 variants were generated with single, or concurrent double and triple alanine substitutions in the three fibronectin type II modules of the CBD. Circular dichroism spectroscopy verified that recombinant MMP-2 wild-type (WT) and variants had the same fold. Moreover, the MMP-2 WT and variants had the same activity on a short FRET peptide substrate that is hydrolyzed independently of CBD binding. Among single-point variants, substitution in the module 3 binding site had greatest impact on the affinity of MMP-2 for gelatin. Simultaneous substitutions in two or three CBD modules further reduced gelatin binding. The rates of gelatinolysis of MMP-2 variants were reduced by 20-40% following single-point substitutions, by 60-75% after double-point modifications, and by >90% for triple-point variants. Intriguingly, the three CBD modules contributed differentially to cleavage of dissociated α-1(I) and α-2(I) collagen chains. Importantly, kinetic analyses (k(cat)/K(m)) revealed that catalysis of a triple-helical FRET peptide substrate by MMP-2 relied primarily on the module 3 binding site. Thus, we have identified three collagen binding site residues that are essential for gelatinolysis and constitute promising targets for selective inhibition of MMP-2.

  1. Structures of the human poly (ADP-ribose glycohydrolase catalytic domain confirm catalytic mechanism and explain inhibition by ADP-HPD derivatives.

    Directory of Open Access Journals (Sweden)

    Julie A Tucker

    Full Text Available Poly(ADP-ribose glycohydrolase (PARG is the only enzyme known to catalyse hydrolysis of the O-glycosidic linkages of ADP-ribose polymers, thereby reversing the effects of poly(ADP-ribose polymerases. PARG deficiency leads to cell death whilst PARG depletion causes sensitisation to certain DNA damaging agents, implicating PARG as a potential therapeutic target in several disease areas. Efforts to develop small molecule inhibitors of PARG activity have until recently been hampered by a lack of structural information on PARG. We have used a combination of bio-informatic and experimental approaches to engineer a crystallisable, catalytically active fragment of human PARG (hPARG. Here, we present high-resolution structures of the catalytic domain of hPARG in unliganded form and in complex with three inhibitors: ADP-ribose (ADPR, adenosine 5'-diphosphate (hydroxymethylpyrrolidinediol (ADP-HPD and 8-n-octyl-amino-ADP-HPD. Our structures confirm conservation of overall fold amongst mammalian PARG glycohydrolase domains, whilst revealing additional flexible regions in the catalytic site. These new structures rationalise a body of published mutational data and the reported structure-activity relationship for ADP-HPD based PARG inhibitors. In addition, we have developed and used biochemical, isothermal titration calorimetry and surface plasmon resonance assays to characterise the binding of inhibitors to our PARG protein, thus providing a starting point for the design of new inhibitors.

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

    Science.gov (United States)

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

    2015-05-01

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

  3. Direct Catalytic Asymmetric Mannich-Type Reaction of Alkylamides.

    Science.gov (United States)

    Arteaga, Fernando Arteaga; Liu, Zijian; Brewitz, Lennart; Chen, Jianyang; Sun, Bo; Kumagai, Naoya; Shibasaki, Masakatsu

    2016-05-20

    Direct enolate formation coupled with subsequent enantioselective C-C bond formation remains a topic of intense interest in asymmetric catalysis. This methodology is achieved even with low acidic amides without an electron-withdrawing group at the α-position in the context of a Mannich-type reaction. Acetate-, propionate-, and butyrate-type 7-azaindoline amides served as enolate precursors to afford the desired Mannich adducts with high stereoselectivity, and ligand-enabled diastereo-divergency provided access to both anti/syn diastereomers. The facile transformation of the amide moiety ensures the synthetic utility of the Mannich adducts.

  4. Unprecedented diversity of catalytic domains in the first four modules of the putative pederin polyketide synthase.

    Science.gov (United States)

    Piel, Jörn; Wen, Gaiping; Platzer, Matthias; Hui, Dequan

    2004-01-03

    Polyketides of the pederin group are highly potent antitumor compounds found in terrestrial beetles and marine sponges. Pederin is used by beetles of the genera Paederus and Paederidus as a chemical defense. We have recently identified a group of putative pederin biosynthesis genes and localized them to the genome of an as yet unculturable Pseudomonas sp. symbiont, the likely true pederin producer. However, this polyketide synthase cluster lacks several genes expected for pederin production. Here we report an additional polyketide synthase encoded on a separate region of the symbiont genome. It contains at least three novel catalytic domains that are predicted to be involved in pederin chain initiation and the formation of an unusual exomethylene bond. The region is bordered by mobility pseudogenes; this suggests that gene transposition led to the disjointed cluster organization. With this work, all putative pederin genes have been identified. Their heterologous expression in a culturable bacterium will provide important insights into how sustainable sources of invertebrate-derived drug candidates can be created.

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

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

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

    DEFF Research Database (Denmark)

    Boesen, Thomas; Mohammad, Sarah S.; Pavitt, Graham D.;

    this motif is involved in binding to the N-terminal part of the eIF2β subunit The aliphatic residues in the AA box motifs are involved in specific contacts in the hydrophobic core of the C-terminal helices important for maintaining the overall structure, whereas acidic residues in the motifs form a clustered......-terminal two helices contain the catalytic part of the domain, whereas the C-terminal six helices harbor the two Aromatic Acidic (AA) box motifs. This motif is also found in initiation factor 5, the GTPase activator protein of eIF2, and furthermore in mammalian initiation factor 4G. In eIF2B and eIF5......, surface exposed acidic patch which might interact with the lysine boxes of eIF2β. Interestingly, Tryptophan 699 was found to be solvent exposed and involved in crystal packing. This residue could possibly be important for the specific interaction with eIF2β. Furthermore, the structure shows the location...

  7. Expression of Catalytic Domain of Protein Tyrosine Phosphatase 1B and Preparation of Its Polyclonal Antibody

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This study focuses on the expression of human protein tyrosine phosphatase 1B(PTP1B) catalytic domain (△PTP1B) and preparation of polyclonal antibody against △PTP1B. △PTP1B gene was PCR amplified with the cDNA of human PTP1B as the template, and cloned into the pT7 expression vector. The recombinant pT7-△PTP1B was expressed in E. coli Rosetta( DE3 ) host cells and purified. The antiserum was prepared by immunizing rabbit with purified recombinant △PTP1B. The polyclonal antibody against △PTP1B was purified by PVDF immobilized antigen affinity chromatography. △PTP1B was correctly cloned, expressed, and purified as confirmed by PCR, DNA sequence ratio) and 0. 1 ng, respectively. This study provides an important basis for further studying the biological function of PTP1B and its relationship with human diseases.

  8. Directed Evolution of L-Aspartase by Mobility of Domains

    Institute of Scientific and Technical Information of China (English)

    GOU Xiao-jun; LI Shuang; KONG Xiang-duo; LIU Wei; SUN Yan-hong; ZHANG Jin

    2004-01-01

    To enhance the relative movement of domains, we inserted a random sequence of fifteen-peptide into the three domains of L-aspartase. By means of directed screening, the three isoforms of monomeric, dimmeric and tetrameric enzymes were obtained. Compared to the wild-type tetrameric L-asparease, these mutants remained 19.7%, 42.3%, and 92% of the enzyme activity, respectively. Moreover, the examination of enzyme properties revealed that their kcat and KM changed in varying degrees, and the optimum pH shifted towards acidic pH, while the dependence of the activity of enzyme on Mg2+ concentration and thermostability increased. Therefore this strategy provides a novel approach to directed evolution of enzymes.

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

    Institute of Scientific and Technical Information of China (English)

    Niu Chuanfeng; Gao Yongcan; Dai Lishun; Li Dadong

    2008-01-01

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

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

    OpenAIRE

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

    1999-01-01

    I-TevI is a member of the GIY-YIG family of homing endonucleases. It is folded into two structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding domain, separated by a flexible linker. In this study we have used genetic analyses, computational sequence analysis andNMR spectroscopy to define the configuration of theN-terminal domain and its relationship to the flexible linker. The catalytic domain is an alpha/beta structure contained within the first 92 am...

  11. 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.

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

    Institute of Scientific and Technical Information of China (English)

    N.A.S.Amin; Sriraj Ammasi

    2006-01-01

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

  13. 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.

  14. 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

  15. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface.

    Science.gov (United States)

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, Lindsay R; Lammich, Lutz; Besenbacher, Flemming; Mavrikakis, Manos; Wendt, Stefan

    2015-08-25

    Within the area of surface science, one of the "holy grails" is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFT+U calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

  16. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface

    Energy Technology Data Exchange (ETDEWEB)

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, L. R.; Lammich, Lutz; Besenbacher, Fleming; Mavrikakis, Manos; Wendt, Stefen

    2015-08-25

    Within the area of surface science, one of the “holy grails” is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFTþU calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

  17. Direct data domain approach to space-time adaptive processing

    Institute of Scientific and Technical Information of China (English)

    Wen Xiaoqin; Han Chongzhao

    2006-01-01

    In non-homogeneous environment, traditional space-time adaptive processing doesn' t effectively suppress interference and detect target, because the secondary data don' t exactly reflect the statistical characteristic of the range cell under test. A novel methodology utilizing the direct data domain approach to space- time adaptive processing (STAP) in airborne radar non-homogeneous environments is presented. The deterministic least squares adaptive signal processing technique operates on a "snapshot-by-snapshot" basis to determine the adaptive weights for nulling interferences and estimating signal of interest (SOI). Furthermore, this approach eliminates the requirement for estimating the covariance through the data of neighboring range rell,which eliminates calculating the inverse of covariance, and can be implemented to operate in resl-time. Simulation results illustrate the efficiency of interference suppression in non-homogeneous environment.

  18. Redox-coupled structural changes of the catalytic a' domain of protein disulfide isomerase.

    Science.gov (United States)

    Inagaki, Koya; Satoh, Tadashi; Yagi-Utsumi, Maho; Le Gulluche, Anne-Charlotte; Anzai, Takahiro; Uekusa, Yoshinori; Kamiya, Yukiko; Kato, Koichi

    2015-09-14

    Protein disulfide isomerase functions as a folding catalyst in the endoplasmic reticulum. Its b' and a' domains provide substrate-binding sites and undergo a redox-dependent domain rearrangement coupled to an open-closed structural change. Here we determined the first solution structure of the a' domain in its oxidized form and thereby demonstrate that oxidation of the a' domain induces significant conformational changes not only in the vicinity of the active site but also in the distal b'-interfacial segment. Based on these findings, we propose that this conformational transition triggers the domain segregation coupled with the exposure of the hydrophobic surface.

  19. The Translocation Domain of Botulinum Neurotoxin A Moderates the Propensity of the Catalytic Domain to Interact with Membranes at Acidic pH

    Science.gov (United States)

    Araye, Anne; Goudet, Amélie; Barbier, Julien; Pichard, Sylvain; Baron, Bruno; England, Patrick; Pérez, Javier; Zinn-Justin, Sophie; Chenal, Alexandre; Gillet, Daniel

    2016-01-01

    Botulinum neurotoxin A (BoNT/A) is composed of three domains: a catalytic domain (LC), a translocation domain (HN) and a receptor-binding domain (HC). Like most bacterial toxins BoNT/A is an amphitropic protein, produced in a soluble form that is able to interact, penetrate and/or cross a membrane to achieve its toxic function. During intoxication BoNT/A is internalized by the cell by receptor-mediated endocytosis. Then, LC crosses the membrane of the endocytic compartment and reaches the cytosol. This translocation is initiated by the low pH found in this compartment. It has been suggested that LC passes in an unfolded state through a transmembrane passage formed by HN. We report here that acidification induces no major conformational change in either secondary or tertiary structures of LC and HN of BoNT/A in solution. GdnHCl-induced denaturation experiments showed that the stability of LC and HN increases as pH drops, and that HN further stabilizes LC. Unexpectedly we found that LC has a high propensity to interact with and permeabilize anionic lipid bilayers upon acidification without the help of HN. This property is downplayed when LC is linked to HN. HN thus acts as a chaperone for LC by enhancing its stability but also as a moderator of the membrane interaction of LC. PMID:27070312

  20. Exploring the origin of the catalytic power and product specificity of SET domain protein methyltransferase.

    Science.gov (United States)

    Lima, A H; Alves, C N; Prasad, R; Lameira, J

    2016-10-20

    Herein, we used computer simulation to evaluate the free energy activation barriers of the first and second methyl transfer for native SET8 PKMT and its Y334F mutant. The results suggest that the origin of SET8 catalytic power is mainly due to electrostatic preorganization.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-04-07

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

  2. Soluble Expression and Purification of the Catalytic Domain of Human Vascular Endothelial Growth Factor Receptor 2 in Escherichia coli.

    Science.gov (United States)

    Wei, Jia; Cao, Xiaodan; Zhou, Shengmin; Chen, Chao; Yu, Haijun; Zhou, Yao; Wang, Ping

    2015-08-01

    Vascular endothelial growth factor (VEGF) plays a key role in angiogenesis through binding to its specific receptors, which mainly occurs to VEGF receptor 2 (VEGFR-2), a kinase insert domain-containing receptor. Therefore, the disruption of VEGFR-2 signaling provides a promising therapeutic approach for the treatment of cancer by inhibiting abnormal or tumorinduced angiogenesis. To explore this potential, we expressed the catalytic domain of VEGFR- 2 (VEGFR-2-CD) as a soluble active kinase in Escherichia coli. The recombinant protein was purified and the VEGFR-2-CD activity was investigated. The obtained VEGFR-2-CD showed autophosphorylation activity and phosphate transfer activity comparable to the commercial enzyme. Furthermore, the IC50 value of known VEGFR-2 inhibitor was determined using the purified VEGFR-2-CD. These results indicated a possibility for functional and economical VEGFR-2-CD expression in E. coli to use for inhibitor screening.

  3. Redirection of the immune response to the functional catalytic domain of the cystein proteinase cruzipain improves protective immunity against Trypanosoma cruzi infection.

    Science.gov (United States)

    Cazorla, Silvia I; Frank, Fernanda M; Becker, Pablo D; Arnaiz, María; Mirkin, Gerardo A; Corral, Ricardo S; Guzmán, Carlos A; Malchiodi, Emilio L

    2010-07-01

    Despite the strong immune responses elicited after natural infection with Trypanosoma cruzi or vaccination against it, parasite survival suggests that these responses are insufficient or inherently inadequate. T. cruzi contains a major cystein proteinase, cruzipain, which has a catalytic N-terminal domain and a C-terminal extension. Immunizations that employed recombinant cruzipain or its N- and C-terminal domains allowed evaluation of the ability of cruzipain to circumvent responses against the catalytic domain. This phenomenon is not a property of the parasite but of cruzipain itself, because recombinant cruzipain triggers a response similar to that of cruzipain during natural or experimental infection. Cruzipain is not the only antigen with a highly immunogenic region of unknown function that somehow protects an essential domain for parasite survival. However, our studies show that this can be reverted by using the N-terminal domain as a tailored immunogen able to redirect host responses to provide enhanced protection.

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

    Indian Academy of Sciences (India)

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

    2000-12-01

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

  5. Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.

    Science.gov (United States)

    Mizutani, Kenji; Machida, Yoshitaka; Unzai, Satoru; Park, Sam-Yong; Tame, Jeremy R H

    2004-04-20

    The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.

  6. An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.

    Science.gov (United States)

    Chartrand, P; Harvey, S C; Ferbeyre, G; Usman, N; Cedergren, R

    1995-10-25

    A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oligomers shows that, although the all-deoxyribonucleotide oligomer is less efficient in catalysis, the DNA/substrate complex shares many of the properties of the all-RNA hammerhead domain such as multiple turnover kinetics and dependence on Mg2+ concentration. On the other hand, the values of kinetic parameters distinguish the DNA oligomer from the all-RNA oligomer. In addition, an analog of the oligomer having a single ribonucleotide in a strongly conserved position of the hammerhead domain is associated with more efficient catalysis than the all-RNA oligomer.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1990-01-01

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

  8. Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain.

    Science.gov (United States)

    Bohn, Markus-Frederik; Shandilya, Shivender M D; Albin, John S; Kouno, Takahide; Anderson, Brett D; McDougle, Rebecca M; Carpenter, Michael A; Rathore, Anurag; Evans, Leah; Davis, Ahkillah N; Zhang, Jingying; Lu, Yongjian; Somasundaran, Mohan; Matsuo, Hiroshi; Harris, Reuben S; Schiffer, Celia A

    2013-06-04

    Human APOBEC3F is an antiretroviral single-strand DNA cytosine deaminase, susceptible to degradation by the HIV-1 protein Vif. In this study the crystal structure of the HIV Vif binding, catalytically active, C-terminal domain of APOBEC3F (A3F-CTD) was determined. The A3F-CTD shares structural motifs with portions of APOBEC3G-CTD, APOBEC3C, and APOBEC2. Residues identified to be critical for Vif-dependent degradation of APOBEC3F all fit within a predominantly negatively charged contiguous region on the surface of A3F-CTD. Specific sequence motifs, previously shown to play a role in Vif susceptibility and virion encapsidation, are conserved across APOBEC3s and between APOBEC3s and HIV-1 Vif. In this structure these motifs pack against each other at intermolecular interfaces, providing potential insights both into APOBEC3 oligomerization and Vif interactions.

  9. Crystal Structure of 12-Lipoxygenase Catalytic-Domain-Inhibitor Complex Identifies a Substrate-Binding Channel for Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shu; Mueser, Timothy C.; Marnett, Lawrence J.; Funk, Jr., Max O. (Toledo); (Vanderbilt)

    2014-10-02

    Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and cancer. Crystals diffracting to high resolution (1.9 {angstrom}) were obtained for a complex between the catalytic domain of leukocyte 12-lipoxygenase and the isoform-specific inhibitor, 4-(2-oxapentadeca-4-yne)phenylpropanoic acid (OPP). In the three-dimensional structure of the complex, the inhibitor occupied a new U-shaped channel open at one end to the surface of the protein and extending past the redox-active iron site that is essential for catalysis. In models, the channel accommodated arachidonic acid, defining the binding site for the substrate of the catalyzed reaction. There was a void adjacent to the OPP binding site connecting to the surface of the enzyme and providing a plausible access channel for the other substrate, oxygen.

  10. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.

    Science.gov (United States)

    Vandavasi, Venu Gopal; Putnam, Daniel K; Zhang, Qiu; Petridis, Loukas; Heller, William T; Nixon, B Tracy; Haigler, Candace H; Kalluri, Udaya; Coates, Leighton; Langan, Paul; Smith, Jeremy C; Meiler, Jens; O'Neill, Hugh

    2016-01-01

    A cellulose synthesis complex with a "rosette" shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. This work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. This study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.

  11. Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

    Science.gov (United States)

    Selwa, Edithe; Huynh, Tru; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Thérèse E

    2014-10-01

    The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations.

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

    Science.gov (United States)

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

    1999-05-15

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

  13. A simple two step procedure for purification of the catalytic domain of chicken tryptophan hydroxylase 1 in a form suitable for crystallization

    DEFF Research Database (Denmark)

    Windahl, Michael Skovbo; Petersen, Charlotte R.; Munch, Astrid;

    2008-01-01

    Tryptophan hydroxylase (TPH) [EC 1.14.16.4] catalyzes the conversion of tryptophan to 5-hydroxytryptophan, which is the first and rate-determining step in the biosynthesis of the neurotransmitter serotonin. We have expressed the catalytic domain of chicken (Gallus gallus) TPH isoform 1 in Escheri...

  14. The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases.

    Science.gov (United States)

    Cerdà-Costa, Núria; Guevara, Tibisay; Karim, Abdulkarim Y; Ksiazek, Miroslaw; Nguyen, Ky-Anh; Arolas, Joan L; Potempa, Jan; Gomis-Rüth, F Xavier

    2011-01-01

    Metallopeptidases (MPs) are among virulence factors secreted by pathogenic bacteria at the site of infection. One such pathogen is Tannerella forsythia, a member of the microbial consortium that causes peridontitis, arguably the most prevalent infective chronic inflammatory disease known to mankind. The only reported MP secreted by T. forsythia is karilysin, a 52 kDa multidomain protein comprising a central 18 kDa catalytic domain (CD), termed Kly18, flanked by domains unrelated to any known protein. We analysed the 3D structure of Kly18 in the absence and presence of Mg(2+) or Ca(2+) , which are required for function and stability, and found that it evidences most of the structural features characteristic of the CDs of mammalian matrix metalloproteinases (MMPs). Unexpectedly, a peptide was bound to the active-site cleft of Kly18 mimicking a left-behind cleavage product, which revealed that the specificity pocket accommodates bulky hydrophobic side-chains of substrates as in mammalian MMPs. In addition, Kly18 displayed a unique Mg(2+) or Ca(2+) binding site and two flexible segments that could play a role in substrate binding. Phylogenetic and sequence similarity studies revealed that Kly18 is evolutionarily much closer to winged-insect and mammalian MMPs than to potential bacterial counterparts found by genomic sequencing projects. Therefore, we conclude that this first structurally characterized non-mammalian MMP is a xenologue co-opted through horizontal gene transfer during the intimate coexistence between T. forsythia and humans or other animals, in a very rare case of gene shuffling from eukaryotes to prokaryotes. Subsequently, this protein would have evolved in a bacterial environment to give rise to full-length karilysin that is furnished with unique flanking domains that do not conform to the general multidomain architecture of animal MMPs.

  15. 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.

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

    Science.gov (United States)

    Guevara, Tibisay; Ksiazek, Miroslaw; Skottrup, Peter Durand; Cerdà-Costa, Núria; Trillo-Muyo, Sergio; de Diego, Iñaki; Riise, Erik; Potempa, Jan; Gomis-Rüth, F Xavier

    2013-05-01

    Karilysin is the only metallopeptidase identified as a virulence factor in the odontopathogen Tannerella forsythia owing to its deleterious effect on the host immune response during bacterial infection. The very close structural and sequence-based similarity of its catalytic domain (Kly18) to matrix metalloproteinases suggests that karilysin was acquired by horizontal gene transfer from an animal host. Previous studies by phage display identified peptides with the consensus sequence XWFPXXXGGG (single-letter amino-acid codes; X represents any residue) as karilysin inhibitors with low-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-binding histidines from the protein scaffold, to an octahedral-minus-one metal-coordination sphere. The tryptophan side chain penetrates the deep partially water-filled specificity pocket of Kly18. Together with previous serendipitous product complexes of Kly18, the present results provide the structural 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.

  17. Expression in E. coli and characterization of the catalytic domain of Botrytis cinerea chitin synthase

    Directory of Open Access Journals (Sweden)

    Piffeteau Annie

    2010-11-01

    Full Text Available Abstract Background Chitin synthase 3a (CHS3a from Botrytis cinerea (Bc catalyses the multiple transfer of N-acetylglucosamine (GlcNAc residues to the growing chitin chain. Chitin, a β-1,4 linked GlcNAc homopolymer, is an essential cell wall component of filamentous fungi. Chitin synthase, processive membranous protein, has been recognized as a promising target for new antifungicides. Enzymatic characterizations of chitin synthases have been limited, mainly because purity and amounts of integral enzyme obtained after purification procedures have not been sufficient. Findings We undertook the preparation of two BcCHS3a fragment proteins, containing only the central domain and devoid of the N-terminal and transmembrane C-terminal regions. The central domain of CHS3a, named SGC (Spsa GntI Core, is conserved in all UDP-glycosyltransferases and it is believed to contain the active site of the enzyme. CHS3a-SGC protein was totally expressed as inclusion bodies in Escherichia coli. We performed recombinant CHS3a-SGC purification in denaturing conditions, followed by a refolding step. Although circular dichroism spectra clearly exhibited secondary structures of renatured CHS3a-SGC, no chitin synthase activity was detected. Nevertheless CHS3a-SGC proteins show specific binding for the substrate UDP-GlcNAc with a dissociation constant similar to the Michaelis constant and a major contribution of the uracil moiety for recognition was confirmed. Conclusions Milligram-scale quantities of CHS3a-SGC protein with native-like properties such as specific substrate UDP-GlcNAc binding could be easily obtained. These results are encouraging for subsequent heterologous expression of full-length CHS3a.

  18. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain.

    Directory of Open Access Journals (Sweden)

    Liangzhong Lim

    Full Text Available Previously we revealed that the extra domain of SARS 3CLpro mediated the catalysis via different mechanisms. While the R298A mutation completely abolished the dimerization, thus resulting in the inactive catalytic machinery, N214A inactivated the enzyme by altering its dynamics without significantly perturbing its structure. Here we studied another mutant with S284-T285-I286 replaced by Ala (STI/A with a 3.6-fold activity increase and slightly enhanced dimerization. We determined its crystal structure, which still adopts the dimeric structure almost identical to that of the wild-type (WT, except for slightly tighter packing between two extra-domains. We then conducted 100-ns molecular dynamics (MD simulations for both STI/A and WT, the longest reported so far for 3CLpro. In the simulations, two STI/A extra domains become further tightly packed, leading to a significant volume reduction of the nano-channel formed by residues from both catalytic and extra domains. The enhanced packing appears to slightly increase the dynamic stability of the N-finger and the first helix residues, which subsequently triggers the redistribution of dynamics over residues directly contacting them. This ultimately enhances the dynamical stability of the residues constituting the catalytic dyad and substrate-binding pockets. Further correlation analysis reveals that a global network of the correlated motions exists in the protease, whose components include all residues identified so far to be critical for the dimerization and catalysis. Most strikingly, the N214A mutation globally decouples this network while the STI/A mutation alters the correlation pattern. Together with previous results, the present study establishes that besides the classic structural allostery, the dynamic allostery also operates in the SARS 3CLpro, which is surprisingly able to relay the perturbations on the extra domain onto the catalytic machinery to manifest opposite catalytic effects. Our

  19. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain.

    Science.gov (United States)

    Lim, Liangzhong; Shi, Jiahai; Mu, Yuguang; Song, Jianxing

    2014-01-01

    Previously we revealed that the extra domain of SARS 3CLpro mediated the catalysis via different mechanisms. While the R298A mutation completely abolished the dimerization, thus resulting in the inactive catalytic machinery, N214A inactivated the enzyme by altering its dynamics without significantly perturbing its structure. Here we studied another mutant with S284-T285-I286 replaced by Ala (STI/A) with a 3.6-fold activity increase and slightly enhanced dimerization. We determined its crystal structure, which still adopts the dimeric structure almost identical to that of the wild-type (WT), except for slightly tighter packing between two extra-domains. We then conducted 100-ns molecular dynamics (MD) simulations for both STI/A and WT, the longest reported so far for 3CLpro. In the simulations, two STI/A extra domains become further tightly packed, leading to a significant volume reduction of the nano-channel formed by residues from both catalytic and extra domains. The enhanced packing appears to slightly increase the dynamic stability of the N-finger and the first helix residues, which subsequently triggers the redistribution of dynamics over residues directly contacting them. This ultimately enhances the dynamical stability of the residues constituting the catalytic dyad and substrate-binding pockets. Further correlation analysis reveals that a global network of the correlated motions exists in the protease, whose components include all residues identified so far to be critical for the dimerization and catalysis. Most strikingly, the N214A mutation globally decouples this network while the STI/A mutation alters the correlation pattern. Together with previous results, the present study establishes that besides the classic structural allostery, the dynamic allostery also operates in the SARS 3CLpro, which is surprisingly able to relay the perturbations on the extra domain onto the catalytic machinery to manifest opposite catalytic effects. Our results thus imply a

  20. Dynamically-driven inactivation of the catalytic machinery of the SARS 3C-like protease by the N214A mutation on the extra domain.

    Science.gov (United States)

    Shi, Jiahai; Han, Nanyu; Lim, Liangzhong; Lua, Shixiong; Sivaraman, J; Wang, Lushan; Mu, Yuguang; Song, Jianxing

    2011-02-01

    Despite utilizing the same chymotrypsin fold to host the catalytic machinery, coronavirus 3C-like proteases (3CLpro) noticeably differ from picornavirus 3C proteases in acquiring an extra helical domain in evolution. Previously, the extra domain was demonstrated to regulate the catalysis of the SARS-CoV 3CLpro by controlling its dimerization. Here, we studied N214A, another mutant with only a doubled dissociation constant but significantly abolished activity. Unexpectedly, N214A still adopts the dimeric structure almost identical to that of the wild-type (WT) enzyme. Thus, we conducted 30-ns molecular dynamics (MD) simulations for N214A, WT, and R298A which we previously characterized to be a monomer with the collapsed catalytic machinery. Remarkably, three proteases display distinctive dynamical behaviors. While in WT, the catalytic machinery stably retains in the activated state; in R298A it remains largely collapsed in the inactivated state, thus implying that two states are not only structurally very distinguishable but also dynamically well separated. Surprisingly, in N214A the catalytic dyad becomes dynamically unstable and many residues constituting the catalytic machinery jump to sample the conformations highly resembling those of R298A. Therefore, the N214A mutation appears to trigger the dramatic change of the enzyme dynamics in the context of the dimeric form which ultimately inactivates the catalytic machinery. The present MD simulations represent the longest reported so far for the SARS-CoV 3CLpro, unveiling that its catalysis is critically dependent on the dynamics, which can be amazingly modulated by the extra domain. Consequently, mediating the dynamics may offer a potential avenue to inhibit the SARS-CoV 3CLpro.

  1. Structure of catalytic domain of Matriptase in complex with Sunflower trypsin inhibitor-1

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    Huang Mingdong

    2011-06-01

    Full Text Available Abstract Background Matriptase is a type II transmembrane serine protease that is found on the surfaces of epithelial cells and certain cancer cells. Matriptase has been implicated in the degradation of certain extracellular matrix components as well as the activation of various cellular proteins and proteases, including hepatocyte growth factor and urokinase. Sunflower trypsin inhibitor-1 (SFTI-1, a cyclic peptide inhibitor originally isolated from sunflower seeds, exhibits potent inhibitory activity toward matriptase. Results We have engineered and produced recombinant proteins of the matriptase protease domain, and have determined the crystal structures of the protease:SFTI-1 complex at 2.0 Å as well as the protease:benzamidine complex at 1.2 Å. These structures elaborate the structural basis of substrate selectivity of matriptase, and show that the matriptase S1 substrate specificity pocket is larger enough to allow movement of benzamidine inside the S1 pocket. Our study also reveals that SFTI-1 binds to matriptase in a way similar to its binding to trypsin despite the significantly different isoelectric points of the two proteins (5.6 vs. 8.2. Conclusions This work helps to define the structural basis of substrate specificity of matriptase and the interactions between the inhibitor and protease. The complex structure also provides a structural template for designing new SFTI-1 derivatives with better potency and selectivity against matriptase and other proteases.

  2. Intracellular catalytic domain of symbiosis receptor kinase hyperactivates spontaneous nodulation in absence of rhizobia.

    Science.gov (United States)

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

    2014-12-01

    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.

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

    Institute of Scientific and Technical Information of China (English)

    Haisheng Zhu; Xianfeng Chen; Hongyun Chen; Xuewei Deng

    2009-01-01

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

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Eirini Trompouki

    2009-05-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    was investigated using current-voltage-power density curves. In the anode chamber, catalysts are mixed with the carbon-carbonate mixture. These catalysts include various manganese oxides (MnO2, Mn2O3, Mn3O4, MnO), metal carbonates (Ag2CO3, MnCO3, Ce2(CO3)3), metals (Ag, Ce, Ni), doped-ceria (CeO2, Ce1-xGdxO2-x/2......, Ce1-xREExO2-δ (REE = Pr, Sm)) and metal oxides (LiMn2O4, Ag2O). Materials showing the highest activity in carbon black (Mn2O3, CeO2, Ce0.6Pr0.4O2-δ, Ag2O) were subsequently tested for catalytic activity toward bituminous coal, as revealed by both I-V-P curves and electrochemical impedance......Hybrid direct carbon fuel cells (HDCFCs) consisting of a solid carbon (carbon black)-molten carbonate ((62–38 wt% Li-K)2CO3) mixtures in the anode chamber of an anode-supported solid oxide fuel cell type full-cell are tested for their electrochemical performance between 700 and 800°C. Performance...

  7. A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity

    Science.gov (United States)

    Lee, Yen-Chun; Patil, Sumersing; Golz, Christopher; Strohmann, Carsten; Ziegler, Slava; Kumar, Kamal; Waldmann, Herbert

    2017-02-01

    The selective transformation of different starting materials by different metal catalysts under individually optimized reaction conditions to structurally different intermediates and products is a powerful approach to generate diverse molecular scaffolds. In a more unified albeit synthetically challenging strategy, common starting materials would be exposed to a common metal catalysis, leading to a common intermediate and giving rise to different scaffolds by tuning the reactivity of the metal catalyst through different ligands. Herein we present a ligand-directed synthesis approach for the gold(I)-catalysed cycloisomerization of oxindole-derived 1,6-enynes that affords distinct molecular scaffolds following different catalytic reaction pathways. Varying electronic properties and the steric demand of the gold(I) ligands steers the fate of a common intermediary gold carbene to selectively form spirooxindoles, quinolones or df-oxindoles. Investigation of a synthesized compound collection in cell-based assays delivers structurally novel, selective modulators of the Hedgehog and Wnt signalling pathways, autophagy and of cellular proliferation.

  8. Direct Catalytic Conversion of Cellulose to 5-Hydroxymethylfurfural Using Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Sanan Eminov

    2016-10-01

    Full Text Available Cellulose is the single largest component of lignocellulosic biomass and is an attractive feedstock for a wide variety of renewable platform chemicals and biofuels, providing an alternative to petrochemicals and petrofuels. This potential is currently limited by the existing methods of transforming this poorly soluble polymer into useful chemical building blocks, such as 5-hydroxymethylfurfural (HMF. Ionic liquids have been used successfully to separate cellulose from the other components of lignocellulosic biomass and so the use of the same medium for the challenging transformation of cellulose into HMF would be highly attractive for the development of the biorefinery concept. In this report, ionic liquids based on 1-butyl-3-methylimidazolium cations [C4C1im]+ with Lewis basic (X = Cl− and Brønsted acidic (X = HSO4− anions were used to investigate the direct catalytic transformation of cellulose to HMF. Variables probed included the composition of the ionic liquid medium, the metal catalyst, and the reaction conditions (temperature, substrate concentration. Lowering the cellulose loading and optimising the temperature achieved a 58% HMF yield after only one hour at 150 °C using a 7 mol % loading of the CrCl3 catalyst. This compares favourably with current literature procedures requiring much longer reactions times or approaches that are difficult to scale such as microwave irradiation.

  9. Temperature Non-Homogeneieties in a Catalytic Reactor With a Periodic Change in the Direction of the Reaction Mixture Feed

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    Zheleva Ivanka

    2015-06-01

    Full Text Available Temperature non-homogeneities in a catalytic reactor with periodic change in the direction of the reaction mixture feed is investigated in the present work. The temperature of the reaction mixture is described using a numerical algorithm for simulation of the work of the catalytic reactor, graphically shown and commented. The influence of the higher catalyst layer porosity in the wall area upon the temperature distribution in the reactor is studied. The existence of two different regimes is shown - a high temperature one in the middle part of the layer and a low temperature one in the high porosity area of the layer in contact with the reactor wall. This leads to not very effective usage of the catalyst in these parts of the catalyst layer in the reactor. This simulation can be used for better understanding and controlling of the examined catalytic process.

  10. Antibodies against recombinant catalytic domain of lethal toxin of Clostridium sordellii neutralize lethal toxin toxicity in HeLa cells.

    Science.gov (United States)

    Arya, Preetika; Ponmariappan, S; Singh, Lokendra; Prasad, G B K S

    2013-02-01

    Lethal toxin of Clostridium sordellii (MLD 150 ng/kg) is one of the most potent Clostridial toxins and is responsible for most of the diseases including sudden death syndrome in cattle, sheep and toxic shock syndrome, necrotizing faciitis, neonatal omphalitis and gangrene in humans. Lethal toxin (TcsL) is a single chain protein of about 270 kDa. In the present study, 1.6 kb DNA fragment encoding for the catalytic domain of TcsL was PCR amplified, cloned in pQE30 UA vector and expressed in E. coli SG 13009. The expression of recombinant lethal toxin protein (rTcsL) was optimized and it was purified under native conditions using a single step Ni-NTA affinity chromatography. The purified recombinant protein was used for the production of polyclonal antibodies in mice and rabbit. The raised antibodies reacted specifically with the purified rTcsL and intact native lethal toxin on Western blot. The biological activity of the recombinant protein was tested in HeLa cells where it showed the cytotoxicity. Further, the polyclonal antibodies were used for in-vitro neutralization of purified rTcsL, acid precipitated C. sordellii and C. difficile native toxins in HeLa cells. Mice and rabbit anti-rTcsL sera effectively neutralized the cytotoxicity of rTcsL and C. sordellii native toxin but it did not neutralize the cytotoxicity of C. difficile toxin in HeLa cells.

  11. Structure-guided systems-level engineering of oxidation-prone methionine residues in catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica for significant improvement of both oxidative stability and catalytic efficiency.

    Directory of Open Access Journals (Sweden)

    Haiquan Yang

    Full Text Available High oxidative stability and catalytic efficiency are required for the alkaline α-amylases to keep the enzymatic performance under the harsh conditions in detergent industries. In this work, we attempted to significantly improve both the oxidative stability and catalytic efficiency of an alkaline α-amylase from Alkalimonas amylolytica by engineering the five oxidation-prone methionine residues around the catalytic domain via a systematic approach. Specifically, based on the tertiary structure analysis, five methionines (Met 145, Met 214, Met 229, Met 247 and Met 317 were individually substituted with oxidation-resistant threonine, isoleucine and alaline, respectively. Among the created 15 mutants, 7 mutants M145A, M145I, M214A, M229A, M229T, M247T and M317I showed significantly enhanced oxidative stability or catalytic efficiency. In previous work, we found that the replacement of M247 with leucine could significantly improve the oxidative stability. Thus, these 8 positive mutants (M145A, M145I, M214A, M229A, M229T, M247T, M247L and M317I were used to conduct the second round of combinational mutations. Among the constructed 85 mutants (25 two-point mutants, 36 three-point mutants, 16 four-point mutants and 8 five-point mutants, the mutant M145I-214A-229T-247T-317I showed a 5.4-fold increase in oxidative stability and a 3.0-fold increase in catalytic efficiency. Interestingly, the specific activity, alkaline stability and thermal stability of this mutant were also increased. The increase of salt bridge and hydrogen bonds around the catalytic domain contributed to the significantly improved catalytic efficiency and stability, as revealed by the three-dimensional structure model of wild-type alkaline α-amylase and its mutant M145I-214A-229T-247T-317I. With the significantly improved oxidative stability and catalytic efficiency, the mutant M145I-214A-229T-247T-317I has a great potential as a detergent additive, and this structure-guided systems

  12. Structure-guided systems-level engineering of oxidation-prone methionine residues in catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica for significant improvement of both oxidative stability and catalytic efficiency.

    Science.gov (United States)

    Yang, Haiquan; Liu, Long; Shin, Hyun-dong; Li, Jianghua; Du, Guocheng; Chen, Jian

    2013-01-01

    High oxidative stability and catalytic efficiency are required for the alkaline α-amylases to keep the enzymatic performance under the harsh conditions in detergent industries. In this work, we attempted to significantly improve both the oxidative stability and catalytic efficiency of an alkaline α-amylase from Alkalimonas amylolytica by engineering the five oxidation-prone methionine residues around the catalytic domain via a systematic approach. Specifically, based on the tertiary structure analysis, five methionines (Met 145, Met 214, Met 229, Met 247 and Met 317) were individually substituted with oxidation-resistant threonine, isoleucine and alaline, respectively. Among the created 15 mutants, 7 mutants M145A, M145I, M214A, M229A, M229T, M247T and M317I showed significantly enhanced oxidative stability or catalytic efficiency. In previous work, we found that the replacement of M247 with leucine could significantly improve the oxidative stability. Thus, these 8 positive mutants (M145A, M145I, M214A, M229A, M229T, M247T, M247L and M317I) were used to conduct the second round of combinational mutations. Among the constructed 85 mutants (25 two-point mutants, 36 three-point mutants, 16 four-point mutants and 8 five-point mutants), the mutant M145I-214A-229T-247T-317I showed a 5.4-fold increase in oxidative stability and a 3.0-fold increase in catalytic efficiency. Interestingly, the specific activity, alkaline stability and thermal stability of this mutant were also increased. The increase of salt bridge and hydrogen bonds around the catalytic domain contributed to the significantly improved catalytic efficiency and stability, as revealed by the three-dimensional structure model of wild-type alkaline α-amylase and its mutant M145I-214A-229T-247T-317I. With the significantly improved oxidative stability and catalytic efficiency, the mutant M145I-214A-229T-247T-317I has a great potential as a detergent additive, and this structure-guided systems engineering

  13. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.

    Science.gov (United States)

    Del Campo, Mark; Ofengand, James; Malhotra, Arun

    2004-02-01

    Escherichia coli pseudouridine synthase RluD makes pseudouridines 1911, 1915, and 1917 in the loop of helix 69 in 23S RNA. These are the most highly conserved ribosomal pseudouridines known. Of 11 pseudouridine synthases in E. coli, only cells lacking RluD have severe growth defects and abnormal ribosomes. We have determined the 2.0 A structure of the catalytic domain of RluD (residues 77-326), the first structure of an RluA family member. The catalytic domain folds into a mainly antiparallel beta-sheet flanked by several loops and helices. A positively charged cleft that presumably binds RNA leads to the conserved Asp 139. The RluD N-terminal S4 domain, connected by a flexible linker, is disordered in our structure. RluD is very similar in both catalytic domain structure and active site arrangement to the pseudouridine synthases RsuA, TruB, and TruA. We identify five sequence motifs, two of which are novel, in the RluA, RsuA, TruB, and TruA families, uniting them as one superfamily. These results strongly suggest that four of the five families of pseudouridine synthases arose by divergent evolution. The RluD structure also provides insight into its multisite specificity.

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

    Institute of Scientific and Technical Information of China (English)

    XIE Huan-ling; XU Wen-guo

    2008-01-01

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

  15. 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

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

    DEFF Research Database (Denmark)

    Bagatolli, Luis A

    2003-01-01

    The direct observation of temperature-dependent lipid phase equilibria, using two-photon excitation fluorescence microscopy on giant unilamellar vesicles (GUVs) composed of different lipid mixtures, provides novel information about the physical characteristics of lipid domain coexistence. Physica...

  17. Catalytic wet peroxide oxidation of azo dye (Direct Blue 15) using solvothermally synthesized copper hydroxide nitrate as catalyst.

    Science.gov (United States)

    Zhan, Yuzhong; Zhou, Xiang; Fu, Bei; Chen, Yiliang

    2011-03-15

    Copper hydroxide nitrate (Cu(2)(OH)(3)NO(3)) was synthesized solvothermally in anhydrous ethanol and characterized by XRD, FTIR, TG-DTA and SEM. The peroxide degradation of an azo dye (Direct Blue 15) on this material was evaluated by examining catalyst loading, initial pH, hydrogen peroxide dosage, initial dye concentration and temperature. The leaching of Cu from the copper hydroxide nitrate during the reaction was also measured. The copper hydroxide nitrate synthesized solvothermally, which was of a novel spherical morphology with complex secondary structures and contained high-dispersed Cu(2)O impurity, showed good performance for oxidation degradation of the azo dye, especially high catalytic activity, high utilization of hydrogen peroxide and a wide pH range, whereas the copper hydroxide nitrate synthesized by the direct reaction of copper nitrate and sodium hydroxide showed low catalytic activity.

  18. 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).

  19. The catalytic A1 domains of cholera toxin and heat-labile enterotoxin are potent DNA adjuvants that evoke mixed Th1/Th17 cellular immune responses.

    Science.gov (United States)

    Bagley, Kenneth; Xu, Rong; Ota-Setlik, Ayuko; Egan, Michael; Schwartz, Jennifer; Fouts, Timothy

    2015-01-01

    DNA encoded adjuvants are well known for increasing the magnitude of cellular and/or humoral immune responses directed against vaccine antigens. DNA adjuvants can also tune immune responses directed against vaccine antigens to better protect against infection of the target organism. Two potent DNA adjuvants that have unique abilities to tune immune responses are the catalytic A1 domains of Cholera Toxin (CTA1) and Heat-Labile Enterotoxin (LTA1). Here, we have characterized the adjuvant activities of CTA1 and LTA1 using HIV and SIV genes as model antigens. Both of these adjuvants enhanced the magnitude of antigen-specific cellular immune responses on par with those induced by the well-characterized cytokine adjuvants IL-12 and GM-CSF. CTA1 and LTA1 preferentially enhanced cellular responses to the intracellular antigen SIVmac239-gag over those for the secreted HIVBaL-gp120 antigen. IL-12, GM-CSF and electroporation did the opposite suggesting differences in the mechanisms of actions of these diverse adjuvants. Combinations of CTA1 or LTA1 with IL-12 or GM-CSF generated additive and better balanced cellular responses to both of these antigens. Consistent with observations made with the holotoxin and the CTA1-DD adjuvant, CTA1 and LTA1 evoked mixed Th1/Th17 cellular immune responses. Together, these results show that CTA1 and LTA1 are potent DNA vaccine adjuvants that favor the intracellular antigen gag over the secreted antigen gp120 and evoke mixed Th1/Th17 responses against both of these antigens. The results also indicate that achieving a balanced immune response to multiple intracellular and extracellular antigens delivered via DNA vaccination may require combining adjuvants that have different and complementary mechanisms of action.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  1. Catalytic modification of conventional SOFC anodes with a view to reducing their activity for direct internal reforming of natural gas

    Energy Technology Data Exchange (ETDEWEB)

    Boder, M.; Dittmeyer, R. [Research Group Technical Chemistry, Karl-Winnacker-Institut, DECHEMA e.V., Theodor-Heuss-Allee 25, D-60486 Frankfurt (Germany)

    2006-04-18

    When using natural gas as fuel for the solid oxide fuel cell (SOFC), direct internal reforming lowers the requirement for cell cooling and, theoretically, offers advantages with respect to capital cost and efficiency. The high metal content of a nickel/zirconia anode and the high temperature, however, cause the endothermic reforming reaction to take place very fast. The resulting drop of temperature at the inlet produces thermal stresses, which may lower the system efficiency and limit the stack lifetime. To reduce the reforming rate without lowering the electrochemical activity of the cell, a wet impregnation procedure for modifying conventional cermets by coverage with a less active metal was developed. As the coating material copper was chosen. Copper is affordable, catalytically inert for the reforming reaction and exhibits excellent electronic conductivity. The current density-voltage characteristics of the modified units showed that it is possible to maintain a good electrochemical performance of the cells despite the catalytic modification. A copper to nickel ratio of 1:3 resulted in a strong diminution of the catalytic reaction rate. This indicates that the modification could be a promising method to improve the performance of solid oxide fuel cells with direct internal reforming of hydrocarbons. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-01

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

  3. 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

  4. Characterization of zinc-binding sites in human stromelysin-1: stoichiometry of the catalytic domain and identification of a cysteine ligand in the proenzyme.

    Science.gov (United States)

    Salowe, S P; Marcy, A I; Cuca, G C; Smith, C K; Kopka, I E; Hagmann, W K; Hermes, J D

    1992-05-19

    A determination of the zinc stoichiometry of the catalytic domain of the human matrix metalloproteinase stromelysin-1 has been carried out using enzyme purified from recombinant Escherichia coli that express C-terminally truncated protein. Atomic absorption spectrometry revealed that both the proenzyme (prostrom255) and the mature active form (strom255) contained nearly 2 mol of Zn/mol of protein. Full-length prostromelysin purified from a mammalian cell culture line also contained zinc in excess of 1 equiv. While zinc in prostrom255 could not be removed by dialysis against o-phenanthroline, similar treatment of mature strom255 resulted in the loss of one-half of the original zinc content. The peptidase activity of the zinc-depleted protein was reduced by greater than 85% but could be restored upon addition of Zn2+ or Co2+. Addition of a thiol-containing inhibitor to a CoZn hybrid enzyme resulted in marked spectral changes in both the visible and ultraviolet regions characteristic of sulfur ligation to Co2+. This direct evidence for an integral role in catalysis and inhibitor binding confirms the location of the exchangeable metal at the active site. To examine the environment of zinc in the proenzyme, a fully cobalt-substituted proenzyme was prepared by in vivo metal replacement. The absorbance features of dicobalt prostrom255 were consistent with metal coordination by the single cysteine present in the propeptide, although the data do not allow assignment to a particular zinc site.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Direct in situ observations of single Fe atom catalytic processes and anomalous diffusion at graphene edges.

    Science.gov (United States)

    Zhao, Jiong; Deng, Qingming; Avdoshenko, Stanislav M; Fu, Lei; Eckert, Jürgen; Rümmeli, Mark H

    2014-11-01

    Single-atom catalysts are of great interest because of their high efficiency. In the case of chemically deposited sp(2) carbon, the implementation of a single transition metal atom for growth can provide crucial insight into the formation mechanisms of graphene and carbon nanotubes. This knowledge is particularly important if we are to overcome fabrication difficulties in these materials and fully take advantage of their distinct band structures and physical properties. In this work, we present atomically resolved transmission EM in situ investigations of single Fe atoms at graphene edges. Our in situ observations show individual iron atoms diffusing along an edge either removing or adding carbon atoms (viz., catalytic action). The experimental observations of the catalytic behavior of a single Fe atom are in excellent agreement with supporting theoretical studies. In addition, the kinetics of Fe atoms at graphene edges are shown to exhibit anomalous diffusion, which again, is in agreement with our theoretical investigations.

  6. Direct observation of dendritic domain growth in perpendicular magnetic anisotropy CoFe/Pt multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Liu Haoliang [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); He Wei, E-mail: hewei@aphy.iphy.ac.cn [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Du Haifeng; Wu Qiong; Fang Yapeng [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Zhu Yun [College of Physics and Electronic Information Science, Tianjin Normal University, Tianjin 300387 (China); Cai Jianwang [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Cheng Zhaohua, E-mail: zhcheng@aphy.iphy.ac.cn [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2011-09-15

    We present the experimental results on thermally activated magnetization reversal for [Co{sub 0.9}Fe{sub 0.1}(5.0 A)/Pt(20 A)]{sub 4} multilayer. Direct domain observations show that magnetization reversal is initiated with rare nucleation and followed by dendritic growth of domain walls. Based on macroscopic magnetic parameters from experimental data, the dendritic domain growth mode is qualitatively interpreted by Monte Carlo simulations in terms of a simple uniaxial magnetic anisotropy model. Moreover, both time evolution of domain growth observation and magnetic relaxation measurements reveal that CoFe/Pt multilayer has a relatively large activation volume compared with Co/Pt multilayers. - Highlights: > We investigate magnetization reversal of [Co{sub 0.9}Fe{sub 0.1}(5.0 A)/Pt(20 A)]{sub 4} multilayer. > Magnetization reversal is governed by thermally activated mechanism. > Magnetic domains evolve in dendritic domain growth mode. > Relatively large activation volume is obtained for the multilayer. > Monte Carlo simulation reproduces the domain growth mode well.

  7. Direct observation of multiferroic vortex domains in YMnO3.

    Science.gov (United States)

    Zhang, Qinghua; Tan, Guotai; Gu, Lin; Yao, Yuan; Jin, Changqing; Wang, Yanguo; Duan, Xiaofeng; Yu, Richeng

    2013-01-01

    Topological vortices with swirling ferroelectric, magnetic and structural anti-phase relationship in hexagonal RMnO3 (R = Ho to Lu, Y, and Sc) have attracted much attention because of their intriguing behaviors. Herein, we report the structure of multiferroic vortex domains in YMnO3 at atomic scale using state-of-the-art aberration-corrected scanning transmission electron microscopy (STEM). Two types of displacements were identified among six domain walls (DWs); six translation-ferroelectric domains denoted by α+, γ-, β+, α-, γ+ and β-, respectively, were recognized, demonstrating the interlocking nature of the anti-vortex domain. We found that the anti-vortex core is about four unit cells wide. In addition, we reconstructed the vortex model with three swirling pairs of DWs along the [001] direction. These results are very critical for the understanding of topological behaviors and unusual properties of the multiferroic vortex.

  8. Direct imaging of topological edge states at a bilayer graphene domain wall

    Science.gov (United States)

    Yin, Long-Jing; Jiang, Hua; Qiao, Jia-Bin; He, Lin

    2016-06-01

    The AB-BA domain wall in gapped graphene bilayers is a rare naked structure hosting topological electronic states. Although it has been extensively studied in theory, a direct imaging of its topological edge states is still missing. Here we image the topological edge states at the graphene bilayer domain wall by using scanning tunnelling microscope. The simultaneously obtained atomic-resolution images of the domain wall provide us unprecedented opportunities to measure the spatially varying edge states within it. The one-dimensional conducting channels are observed to be mainly located around the two edges of the domain wall, which is reproduced quite well by our theoretical calculations. Our experiment further demonstrates that the one-dimensional topological states are quite robust even in the presence of high magnetic fields. The result reported here may raise hopes of graphene-based electronics with ultra-low dissipation.

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

    DEFF Research Database (Denmark)

    Roher, N; Miró, F; Boldyreff, B

    2001-01-01

    The C-terminal domain (residues 518-803) of the 94 kDa glucose regulated protein (grp94) was expressed in Escherichia coli as a fusion protein with a His6-N-terminal tag (grp94-CT). This truncated form of grp94 formed dimers and oligomers that could be dissociated into monomers by treatment...... with dithiothreitol. Grp94-CT conferred protection against aggregation on the catalytic subunit of protein kinase CK2 (CK2alpha), although it did not protect against thermal inactivation. This anti-aggregation effect of grp94-CT was concentration dependent, with full protection achieved at grp94-CT/CK2alpha molar...

  10. Distortion of the catalytic domain of tissue-type plasminogen activator by plasminogen activator inhibitor-1 coincides with the formation of stable serpin-proteinase complexes.

    Science.gov (United States)

    Perron, Michel J; Blouse, Grant E; Shore, Joseph D

    2003-11-28

    Plasminogen activator inhibitor-1 (PAI-1) is a typical member of the serpin family that kinetically traps its target proteinase as a covalent complex by distortion of the proteinase domain. Incorporation of the fluorescently silent 4-fluorotryptophan analog into PAI-1 permitted us to observe changes in the intrinsic tryptophan fluorescence of two-chain tissue-type plasminogen activator (tPA) and the proteinase domain of tPA during the inhibition reaction. We demonstrated three distinct conformational changes of the proteinase that occur during complex formation and distortion. A conformational change occurred during the initial formation of the non-covalent Michaelis complex followed by a large conformational change associated with the distortion of the proteinase catalytic domain that occurs concurrently with the formation of stable proteinase-inhibitor complexes. Following distortion, a very slow structural change occurs that may be involved in the stabilization or regulation of the trapped complex. Furthermore, by comparing the inhibition rates of two-chain tPA and the proteinase domain of tPA by PAI-1, we demonstrate that the accessory domains of tPA play a prominent role in the initial formation of the non-covalent Michaelis complex.

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

    Energy Technology Data Exchange (ETDEWEB)

    1992-12-31

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

  12. Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1

    Science.gov (United States)

    Hinchliffe, Philip; Yang, Qiu E.; Portal, Edward; Young, Tom; Li, Hui; Tooke, Catherine L.; Carvalho, Maria J.; Paterson, Neil G.; Brem, Jürgen; Niumsup, Pannika R.; Tansawai, Uttapoln; Lei, Lei; Li, Mei; Shen, Zhangqi; Wang, Yang; Schofield, Christopher J.; Mulholland, Adrian J; Shen, Jianzhong; Fey, Natalie; Walsh, Timothy R.; Spencer, James

    2017-01-01

    The polymixin colistin is a “last line” antibiotic against extensively-resistant Gram-negative bacteria. Recently, the mcr-1 gene was identified as a plasmid-mediated resistance mechanism in human and animal Enterobacteriaceae, with a wide geographical distribution and many producer strains resistant to multiple other antibiotics. mcr-1 encodes a membrane-bound enzyme catalysing phosphoethanolamine transfer onto bacterial lipid A. Here we present crystal structures revealing the MCR-1 periplasmic, catalytic domain to be a zinc metalloprotein with an alkaline phosphatase/sulphatase fold containing three disulphide bonds. One structure captures a phosphorylated form representing the first intermediate in the transfer reaction. Mutation of residues implicated in zinc or phosphoethanolamine binding, or catalytic activity, restores colistin susceptibility of recombinant E. coli. Zinc deprivation reduces colistin MICs in MCR-1-producing laboratory, environmental, animal and human E. coli. Conversely, over-expression of the disulphide isomerase DsbA increases the colistin MIC of laboratory E. coli. Preliminary density functional theory calculations on cluster models suggest a single zinc ion may be sufficient to support phosphoethanolamine transfer. These data demonstrate the importance of zinc and disulphide bonds to MCR-1 activity, suggest that assays under zinc-limiting conditions represent a route to phenotypic identification of MCR-1 producing E. coli, and identify key features of the likely catalytic mechanism. PMID:28059088

  13. Preparation and electrochemistry of Pd-Ni/Si nanowire nanocomposite catalytic anode for direct ethanol fuel cell.

    Science.gov (United States)

    Miao, Fengjuan; Tao, Bairui; Chu, Paul K

    2012-04-28

    A new silicon-based anode suitable for direct ethanol fuel cells (DEFCs) is described. Pd-Ni nanoparticles are coated on Si nanowires (SiNWs) by electroless co-plating to form the catalytic materials. The electrocatalytic properties of the SiNWs and ethanol oxidation on the Pd-Ni catalyst (Pd-Ni/SiNWs) are investigated electrochemically. The effects of temperature and working potential limit in the anodic direction on ethanol oxidation are studied by cyclic voltammetry. The Pd-Ni/SiNWs electrode exhibits higher electrocatalytic activity and better long-term stability in an alkaline solution. It also yields a larger current density and negative onset potential thus boding well for its application to fuel cells.

  14. On the Direct Cauchy Theorem in Widom Domains: Positive and Negative Examples

    CERN Document Server

    Yuditskii, Peter

    2010-01-01

    We discuss several questions which remained open in our joint work with M. Sodin "Almost periodic Jacobi matrices with homogeneous spectrum, infinite-dimensional Jacobi inversion, and Hardy spaces of character--automorphic functions". In particular, we show that there exists a non-homogeneous set $E$ such that the Direct Cauchy Theorem (DCT) holds in the Widom domain $\\bbC\\setminus E$. On the other hand we demonstrate that the weak homogeneity condition on $E$ (introduced recently by Poltoratski and Remling) does not ensure that DCT holds in the corresponding Widom domain.

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

    CERN Document Server

    Zhang, Zhentao

    2016-01-01

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

  16. Site-selective C-H arylation of primary aliphatic amines enabled by a catalytic transient directing group

    Science.gov (United States)

    Liu, Yongbing; Ge, Haibo

    2017-01-01

    Transition-metal-catalysed direct C-H bond functionalization of aliphatic amines is of great importance in organic and medicinal chemistry research. Several methods have been developed for the direct sp3 C-H functionalization of secondary and tertiary aliphatic amines, but site-selective functionalization of primary aliphatic amines in remote positions remains a challenge. Here, we report the direct, highly site-selective γ-arylation of primary alkylamines via a palladium-catalysed C-H bond functionalization process on unactivated sp3 carbons. Using glyoxylic acid as an inexpensive, catalytic and transient directing group, a wide array of γ-arylated primary alkylamines were prepared without any protection or deprotection steps. This approach provides straightforward access to important structural motifs in organic and medicinal chemistry without the need for pre-functionalized substrates or stoichiometric directing groups and is demonstrated here in the synthesis of analogues of the immunomodulatory drug fingolimod directly from commercially available 2-amino-2-propylpropane-1,3-diol.

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

    Institute of Scientific and Technical Information of China (English)

    LIU Yun; LI Zhishun

    2004-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-07

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

  19. 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.

  20. A domain decomposition method for the efficient direct simulation of aeroacoustic problems

    OpenAIRE

    Utzmann, Jens

    2008-01-01

    A novel domain decomposition approach is developed in this thesis, which significantly accelerates the direct simulation of aeroacoustic problems. All relevant scales must be resolved with high accuracy, from the small, noise generating flow features (e.g., vortices) to the sound with small pressure amplitudes and large wavelengths. Furthermore, the acoustic waves must be propagated over great distances and without dissipation and dispersion errors. In order to keep the computational effort w...

  1. Localized domain wall nucleation dynamics in asymmetric ferromagnetic rings revealed by direct time-resolved magnetic imaging

    Science.gov (United States)

    Richter, Kornel; Krone, Andrea; Mawass, Mohamad-Assaad; Krüger, Benjamin; Weigand, Markus; Stoll, Hermann; Schütz, Gisela; Kläui, Mathias

    2016-07-01

    We report time-resolved observations of field-induced domain wall nucleation in asymmetric ferromagnetic rings using single direction field pulses and rotating fields. We show that the asymmetric geometry of a ring allows for controlling the position of nucleation events, when a domain wall is nucleated by a rotating magnetic field. Direct observation by scanning transmission x-ray microscopy (STXM) reveals that the nucleation of domain walls occurs through the creation of transient ripplelike structures. This magnetization state is found to exhibit a surprisingly high reproducibility even at room temperature and we determine the combinations of field strengths and field directions that allow for reliable nucleation of domain walls and directly quantify the stability of the magnetic states. Our analysis of the processes occurring during field induced domain wall nucleation shows how the effective fields determine the nucleation location reproducibly, which is a key prerequisite toward using domain walls for spintronic devices.

  2. Crystal Structure of the Human Pol α B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit.

    Science.gov (United States)

    Suwa, Yoshiaki; Gu, Jianyou; Baranovskiy, Andrey G; Babayeva, Nigar D; Pavlov, Youri I; Tahirov, Tahir H

    2015-06-05

    In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol δ and Pol ϵ. The C terminus of the Pol α catalytic subunit (p180C) in complex with the B subunit (p70) regulates the RNA priming and DNA polymerizing activities of Prim-Pol α. It tethers Pol α and primase, facilitating RNA primer handover from primase to Pol α. To understand these regulatory mechanisms and to reveal the details of human Pol α organization, we determined the crystal structure of p70 in complex with p180C. The structured portion of p70 includes a phosphodiesterase (PDE) domain and an oligonucleotide/oligosaccharide binding (OB) domain. The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. The p180C adopts an elongated asymmetric saddle shape, with a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. The extensive p180C-p70 interactions involve 20 hydrogen bonds and a number of hydrophobic interactions resulting in an extended buried surface of 4080 Å(2). Importantly, in the structure of the p180C-p70 complex with full-length p70, the residues from the N-terminal to the OB domain contribute to interactions with p180C. The comparative structural analysis revealed both the conserved features and the differences between the human and yeast Pol α complexes.

  3. Heterologous expression and catalytic properties of the C-terminal domain of starfish cdc25 dual-specificity phosphatase, a cell cycle regulator.

    Science.gov (United States)

    Deshimaru, Shungo; Miyake, Yasuo; Ohmiya, Tadamasa; Tatsu, Yoshiro; Endo, Yasuko; Yumoto, Noboru; Toraya, Tetsuo

    2002-05-01

    The 3'-terminal region of starfish Asterina pectinifera cdc25 cDNA encoding the C-terminal catalytic domain was overexpressed in Escherichia coli. The C-terminal domain consisted of 226 amino acid residues containing the signature motif HCxxxxxR, a motif highly conserved among protein tyrosine and dual-specificity phosphatases, and showed phosphatase activity toward p-nitrophenyl phosphate. The enzyme activity was strongly inhibited by SH inhibitors. Mutational studies indicated that the cysteine and arginine residues in the conserved motif are essential for activity, but the histidine residue is not. These results suggest that the enzyme catalyzes the reaction through a two-step mechanism involving a phosphocysteine intermediate like in the cases of other protein tyrosine and dual-specificity phosphatases. The C-terminal domain of Cdc25 activated the histone H1 kinase activity of the purified, inactive form of Cdc2.cyclin B complex (preMPF) from extracts of immature starfish oocytes. Synthetic diphosphorylated di- to nonadecapeptides mimicking amino acid sequences around the dephosphorylation site of Cdc2 still retained substrate activity. Phosphotyrosine and phosphothreonine underwent dephosphorylation in this order. This is the reverse order to that reported for the in vivo and in vitro dephosphorylation of preMPF. Monophosphopeptides having the same sequence served as much poorer substrates. As judged from the results with synthetic phosphopeptides, the presence of two phosphorylated residues was important for specific recognition of substrates by the Cdc25 phosphatase.

  4. The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants.

    Science.gov (United States)

    Liang, Zhe; Demko, Viktor; Wilson, Robert C; Johnson, Kenneth A; Ahmad, Rafi; Perroud, Pierre-François; Quatrano, Ralph; Zhao, Sen; Shalchian-Tabrizi, Kamran; Otegui, Marisa S; Olsen, Odd-Arne; Johansen, Wenche

    2013-09-01

    DEK1, the single calpain of land plants, is a member of the ancient membrane bound TML-CysPc-C2L calpain family that dates back 1.5 billion years. Here we show that the CysPc-C2L domains of land plant calpains form a separate sub-clade in the DEK1 clade of the phylogenetic tree of plants. The charophycean alga Mesostigma viride DEK1-like gene is clearly divergent from those in land plants, suggesting that a major evolutionary shift in DEK1 occurred during the transition to land plants. Based on genetic complementation of the Arabidopsis thaliana dek1-3 mutant using CysPc-C2L domains of various origins, we show that these two domains have been functionally conserved within land plants for at least 450 million years. This conclusion is based on the observation that the CysPc-C2L domains of DEK1 from the moss Physcomitrella patens complements the A. thaliana dek1-3 mutant phenotype. In contrast, neither the CysPc-C2L domains from M. viride nor chimeric animal-plant calpains complement this mutant. Co-evolution analysis identified differences in the interactions between the CysPc-C2L residues of DEK1 and classical calpains, supporting the view that the two enzymes are regulated by fundamentally different mechanisms. Using the A. thaliana dek1-3 complementation assay, we show that four conserved amino acid residues of two Ca²⁺-binding sites in the CysPc domain of classical calpains are conserved in land plants and functionally essential in A. thaliana DEK1.

  5. Unraveling the molecular structure of the catalytic domain of matrix metalloproteinase-2 in complex with a triple-helical peptide by means of molecular dynamics simulations.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas; Valdés, Haydeé

    2013-11-26

    Herein, we present the results of a computational study that employed various simulation methodologies to build and validate a series of molecular models of a synthetic triple-helical peptide (fTHP-5) both in its native state and in a prereactive complex with the catalytic domain of the MMP-2 enzyme. First, the structure and dynamical properties of the fTHP-5 substrate are investigated by means of molecular dynamics (MD) simulations. Then, the propensity of each of the three peptide chains in fTHP-5 to be distorted around the scissile peptide bond is assessed by carrying out potential of mean force calculations. Subsequently, the distorted geometries of fTHP-5 are docked within the MMP-2 active site following a semirigid protocol, and the most stable docked structures are fully relaxed and characterized by extensive MD simulations in explicit solvent. Following a similar approach, we also investigate a hypothetical ternary complex formed between two MMP-2 catalytic units and a single fTHP-5 molecule. Overall, our models for the MMP-2/fTHP-5 complexes unveil the extent to which the triple helix is distorted to allow the accommodation of an individual peptide chain within the MMP active site.

  6. The catalytic activity of the CD45 membrane-proximal phosphatase domain is required for TCR signaling and regulation

    DEFF Research Database (Denmark)

    Desai, D M; Sap, J; Silvennoinen, O;

    1994-01-01

    Cell surface expression of CD45, a receptor-like protein tyrosine phosphatase (PTPase), is required for T cell antigen receptor (TCR)-mediated signal transduction. Like the majority of transmembrane PTPases, CD45 contains two cytoplasmic phosphatase domains, whose relative in vivo function is not...

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

    DEFF Research Database (Denmark)

    Németh, Eszter; Körtvélyesi, Tamás; Thulstrup, Peter W.;

    2014-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

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

  9. Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.

    Science.gov (United States)

    Sevcík, Jozef; Hostinová, Eva; Solovicová, Adriana; Gasperík, Juraj; Dauter, Zbigniew; Wilson, Keith S

    2006-05-01

    Most glucoamylases (alpha-1,4-D-glucan glucohydrolase, EC 3.2.1.3) have structures consisting of both a catalytic and a starch binding domain. The structure of a glucoamylase from Saccharomycopsis fibuligera HUT 7212 (Glu), determined a few years ago, consists of a single catalytic domain. The structure of this enzyme with the resolution extended to 1.1 A and that of the enzyme-acarbose complex at 1.6 A resolution are presented here. The structure at atomic resolution, besides its high accuracy, shows clearly the influence of cryo-cooling, which is manifested in shrinkage of the molecule and lowering the volume of the unit cell. In the structure of the complex, two acarbose molecules are bound, one at the active site and the second at a site remote from the active site, curved around Tyr464 which resembles the inhibitor molecule in the 'sugar tongs' surface binding site in the structure of barley alpha-amylase isozyme 1 complexed with a thiomalto-oligosaccharide. Based on the close similarity in sequence of glucoamylase Glu, which does not degrade raw starch, to that of glucoamylase (Glm) from S. fibuligera IFO 0111, a raw starch-degrading enzyme, it is reasonable to expect the presence of the remote starch binding site at structurally equivalent positions in both enzymes. We propose the role of this site is to fix the enzyme onto the surface of a starch granule while the active site degrades the polysaccharide. This hypothesis is verified here by the preparation of mutants of glucoamylases Glu and Glm.

  10. 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.

  11. New Reactions to Obtain Aromatics and Hydrogen through Methane's Direct Catalytic Dehydroaromatization

    Institute of Scientific and Technical Information of China (English)

    XU Yide; XIE Maosong; BAO Xinhe; LIN Liwu; WANG Linsheng

    2007-01-01

    @@ Methane is the main component of natural gas and coal-bed gas. Structurally, its molecule is highly symmetric and hence, it becomes one of the most stable hydrocarbon compounds in nature. For a long time in the past, the research of methane transformation is a permanent "hot spot" and disciplinary frontier for chemists as it can be catalyzed directly into top-quality fuel and chemicals.

  12. Functional dissection of the N-terminal sequence of Clostridium sp. G0005 glucoamylase: identification of components critical for folding the catalytic domain and for constructing the active site structure.

    Science.gov (United States)

    Sakaguchi, Masayoshi; Matsushima, Yudai; Nagamine, Yusuke; Matsuhashi, Tomoki; Honda, Shotaro; Okuda, Shoi; Ohno, Misa; Sugahara, Yasusato; Shin, Yongchol; Oyama, Fumitaka; Kawakita, Masao

    2017-03-01

    Clostridium sp. G0005 glucoamylase (CGA) is composed of a β-sandwich domain (BD), a linker, and a catalytic domain (CD). In the present study, CGA was expressed in Escherichia coli as inclusion bodies when the N-terminal region (39 amino acid residues) of the BD was truncated. To further elucidate the role of the N-terminal region of the BD, we constructed N-terminally truncated proteins (Δ19, Δ24, Δ29, and Δ34) and assessed their solubility and activity. Although all evaluated proteins were soluble, their hydrolytic activities toward maltotriose as a substrate varied: Δ19 and Δ24 were almost as active as CGA, but the activity of Δ29 was substantially lower, and Δ34 exhibited little hydrolytic activity. Subsequent truncation analysis of the N-terminal region sequence between residues 25 and 28 revealed that truncation of less than 26 residues did not affect CGA activity, whereas truncation of 26 or more residues resulted in a substantial loss of activity. Based on further site-directed mutagenesis and N-terminal sequence analysis, we concluded that the 26XaaXaaTrp28 sequence of CGA is important in exhibiting CGA activity. These results suggest that the N-terminal region of the BD in bacterial GAs may function not only in folding the protein into the correct structure but also in constructing a competent active site for catalyzing the hydrolytic reaction.

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

    Directory of Open Access Journals (Sweden)

    Christian Feiler

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

  14. Green synthesis of silver nanoparticles using Terminalia cuneata and its catalytic action in reduction of direct yellow-12 dye

    Science.gov (United States)

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

    2016-05-01

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

  15. Direct optical observation of magnetic domains in Ni-Mn-Ga martensite

    Science.gov (United States)

    Ge, Y.; Heczko, O.; Söderberg, O.; Hannula, S.-P.

    2006-08-01

    This letter reports the direct optical observation, i.e., without polarization, of the magnetic domain structure explained by a large surface relief in Ni-Mn-Ga martensite. The authors suggest that the relief is due to the different straining of the surface and the bulk caused by the internal stresses associated with the magnetic shape memory effect. As a result of the relief the projection of the (011) twin traces upon the (010) plane creates the observed zigzag pattern. The surface tilt angle calculated from the zigzag pattern is ˜3°.

  16. Combination of direct-forcing fictitious domain method and sharp interface method for dielectrophoresis of particles

    Institute of Scientific and Technical Information of China (English)

    Yang Shi; Zhaosheng Yu; Xueming Shao

    2010-01-01

    In this paper,we combine the direct-forcing fictitious domain(DF/FD)method and the sharp interface method to resolve the problem of particle dielectrophoresis in two dimensions,The flow field and the motion of particles are solved with the DF/FD method,the electric field is solved with the sharp interface method,and the electrostatic force on the particles is computed using the Maxwell stress tensor method.The proposed method is validated via three problems: effective conductivity of particle composite between two planar plates,cell trapping in a channel,and motion of particles due to both conventional and traveling wave dielectrophoretic forces.

  17. Direct conversion of methane to aromatics in a catalytic co-ionic membrane reactor.

    Science.gov (United States)

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

    2016-08-01

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

  18. Direct Nanoscale Imaging of Evolving Electric Field Domains in Quantum Structures

    Science.gov (United States)

    Dhar, Rudra Sankar; Razavipour, Seyed Ghasem; Dupont, Emmanuel; Xu, Chao; Laframboise, Sylvain; Wasilewski, Zbig; Hu, Qing; Ban, Dayan

    2014-01-01

    The external performance of quantum optoelectronic devices is governed by the spatial profiles of electrons and potentials within the active regions of these devices. For example, in quantum cascade lasers (QCLs), the electric field domain (EFD) hypothesis posits that the potential distribution might be simultaneously spatially nonuniform and temporally unstable. Unfortunately, there exists no prior means of probing the inner potential profile directly. Here we report the nanoscale measured electric potential distribution inside operating QCLs by using scanning voltage microscopy at a cryogenic temperature. We prove that, per the EFD hypothesis, the multi-quantum-well active region is indeed divided into multiple sections having distinctly different electric fields. The electric field across these serially-stacked quantum cascade modules does not continuously increase in proportion to gradual increases in the applied device bias, but rather hops between discrete values that are related to tunneling resonances. We also report the evolution of EFDs, finding that an incremental change in device bias leads to a hopping-style shift in the EFD boundary – the higher electric field domain expands at least one module each step at the expense of the lower field domain within the active region. PMID:25431158

  19. Crystal structure of the catalytic domain of the initiation factor 2B epsilon subunit from saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Boesen, Thomas; Pavitt, Graham D.; Andersen, Gregers Rom

    -terminal domain harbors the two aa-box motifs involved in binding to the N-terminal part of the initiation factor 2 β subunit. Aliphatic residues in the aa-box motifs are involved in specific contacts in the hydrophobic core of the C-terminal bundle important for maintaining the overall structure, whereas, acidic...... residues in the motifs form a surface exposed acidic patch which might interact with the lysine boxes of initiation factor 2 β. Interestingly, tryptophan 699 was found to be solvent exposed and involved in crystal packing. This residue could possibly be important for the specific interaction...

  20. Evaluation of anode (electro)catalytic materials for the direct borohydride fuel cell: Methods and benchmarks

    Science.gov (United States)

    Olu, Pierre-Yves; Job, Nathalie; Chatenet, Marian

    2016-09-01

    In this paper, different methods are discussed for the evaluation of the potential of a given catalyst, in view of an application as a direct borohydride fuel cell DBFC anode material. Characterizations results in DBFC configuration are notably analyzed at the light of important experimental variables which influence the performances of the DBFC. However, in many practical DBFC-oriented studies, these various experimental variables prevent one to isolate the influence of the anode catalyst on the cell performances. Thus, the electrochemical three-electrode cell is a widely-employed and useful tool to isolate the DBFC anode catalyst and to investigate its electrocatalytic activity towards the borohydride oxidation reaction (BOR) in the absence of other limitations. This article reviews selected results for different types of catalysts in electrochemical cell containing a sodium borohydride alkaline electrolyte. In particular, propositions of common experimental conditions and benchmarks are given for practical evaluation of the electrocatalytic activity towards the BOR in three-electrode cell configuration. The major issue of gaseous hydrogen generation and escape upon DBFC operation is also addressed through a comprehensive review of various results depending on the anode composition. At last, preliminary concerns are raised about the stability of potential anode catalysts upon DBFC operation.

  1. Easy moment direction and antiferromagnetic domain wall motion in Mn2Au

    Science.gov (United States)

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

    2016-05-01

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

  2. Determine electric field directions at semiconductor surfaces by femtosecond frequency domain interferometric second harmonic (FDISH) generation

    Science.gov (United States)

    Nelson, C. A.; Zhu, X.-Y.

    2016-10-01

    Optical excitations at semiconductor surfaces or interfaces are accompanied by transient interfacial electric fields due to charge redistribution or transfer. While such transient fields may be probed by time-resolved second harmonic generation (TR-SHG), it is difficult to determine the field direction, which is invaluable to unveiling the underlying physics. Here we apply a time-resolved frequency domain interferometric second harmonic (TR-FDISH) generation technique to determine the phase relationship between the SH field emitted from bulk GaAs(1 0 0) and the transient SH field from the space charge region. The interference between these two SH fields allow us to unambiguously determine the directions of transient electric fields. Since SH fields from a static bulk contribution and a changing electric field contribution are present at most semiconductor surfaces or interfaces under optical excitation, the TR-FDISH technique is of general significance to probing the dynamics of interfacial charge transfer/redistribution.

  3. Crystal structures of human RIP2 kinase catalytic domain complexed with ATP-competitive inhibitors: Foundations for understanding inhibitor selectivity.

    Science.gov (United States)

    Charnley, Adam K; Convery, Máire A; Lakdawala Shah, Ami; Jones, Emma; Hardwicke, Philip; Bridges, Angela; Ouellette, Michael; Totoritis, Rachel; Schwartz, Benjamin; King, Bryan W; Wisnoski, David D; Kang, James; Eidam, Patrick M; Votta, Bartholomew J; Gough, Peter J; Marquis, Robert W; Bertin, John; Casillas, Linda

    2015-11-01

    Receptor interacting protein 2 (RIP2) is an intracellular kinase and key signaling partner for the pattern recognition receptors NOD1 and NOD2 (nucleotide-binding oligomerization domain-containing proteins 1 and 2). As such, RIP2 represents an attractive target to probe the role of these pathways in disease. In an effort to design potent and selective inhibitors of RIP2 we established a crystallographic system and determined the structure of the RIP2 kinase domain in an apo form and also in complex with multiple inhibitors including AMP-PCP (β,γ-Methyleneadenosine 5'-triphosphate, a non-hydrolysable adenosine triphosphate mimic) and structurally diverse ATP competitive chemotypes identified via a high-throughput screening campaign. These structures represent the first set of diverse RIP2-inhibitor co-crystal structures and demonstrate that the protein possesses the ability to adopt multiple DFG-in as well as DFG-out and C-helix out conformations. These structures reveal key protein-inhibitor structural insights and serve as the foundation for establishing a robust structure-based drug design effort to identify both potent and highly selective inhibitors of RIP2 kinase.

  4. Direct Production of 5-Hydroxymethylfurfural via Catalytic Conversion of Simple and Complex Sugars over Phosphated TiO2.

    Science.gov (United States)

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

    2015-09-01

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

  5. Direct methane solid oxide fuel cells based on catalytic partial oxidation enabling complete coking tolerance of Ni-based anodes

    Science.gov (United States)

    Lee, Daehee; Myung, Jaeha; Tan, Jeiwan; Hyun, Sang-Hoon; Irvine, John T. S.; Kim, Joosun; Moon, Jooho

    2017-03-01

    Solid oxide fuel cells (SOFCs) can oxidize diverse fuels by harnessing oxygen ions. Benefited by this feature, direct utilization of hydrocarbon fuels without external reformers allows for cost-effective realization of SOFC systems. Superior hydrocarbon reforming catalysts such as nickel are required for this application. However, carbon coking on nickel-based anodes and the low efficiency associated with hydrocarbon fueling relegate these systems to immature technologies. Herein, we present methane-fueled SOFCs operated under conditions of catalytic partial oxidation (CPOX). Utilizing CPOX eliminates carbon coking on Ni and facilitates the oxidation of methane. Ni-gadolinium-doped ceria (GDC) anode-based cells exhibit exceptional power densities of 1.35 W cm-2 at 650 °C and 0.74 W cm-2 at 550 °C, with stable operation over 500 h, while the similarly prepared Ni-yttria stabilized zirconia anode-based cells exhibit a power density of 0.27 W cm-2 at 650 °C, showing gradual degradation. Chemical analyses suggest that combining GDC with the Ni anode prevents the oxidation of Ni due to the oxygen exchange ability of GDC. In addition, CPOX operation allows the usage of stainless steel current collectors. Our results demonstrate that high-performance SOFCs utilizing methane CPOX can be realized without deterioration of Ni-based anodes using cost-effective current collectors.

  6. Study on Direct Synthesis of Diphenyl Carbonate with Heterogeneous Catalytic Reaction (V) Screening Catalysts and Optimizing Synthesis Conditions

    Institute of Scientific and Technical Information of China (English)

    张光旭; 吴元欣; 马沛生; 田崎峰; 吴广文; 李定或; 王存文

    2003-01-01

    Pd/LaxPbyMnOz, Pd/C, Pd/molecular sieve and Pd-heteropoly acid catalysts for direct synthesis of diphenyl carbonate (DPC) by heterogeneous catalytic reaction were compared and the results of DPC synthesis indicated that the catalyst Pd/LaxPbyMnOz had higher activity. The Pd/LaxPbyMnOz catalyst and the support was characterized by XRD, SEM and TEM, the main phase was La0.62Pb0.38MnO3 and the average diameter could be about 25.4 nm. The optimum conditions for synthesis of DPC with Pd/LaxPbyMnOz were determined by orthogonal experiments and the experimental results showed that reaction temperature was the first factor of effect on the selectivity and yield of DPC, and the concentration of O2 in gas phase also had significant effect on selectivity of DPC. The optimum reaction conditions were catMyst/phenol mass ratio 1 to 50, pressure 4.5 MPa,volume concentration of O2 25%, reaction temperature 60° and reaction time 4 h. The maximum yield and average selectivity could reach 13% and 97% respectively in the batch operation.

  7. The Myc Transactivation Domain Promotes Global Phosphorylation of the RNA Polymerase II Carboxy-Terminal Domain Independently of Direct DNA Binding▿ †

    Science.gov (United States)

    Cowling, Victoria H.; Cole, Michael D.

    2007-01-01

    Myc is a transcription factor which is dependent on its DNA binding domain for transcriptional regulation of target genes. Here, we report the surprising finding that Myc mutants devoid of direct DNA binding activity and Myc target gene regulation can rescue a substantial fraction of the growth defect in myc−/− fibroblasts. Expression of the Myc transactivation domain alone induces a transcription-independent elevation of the RNA polymerase II (Pol II) C-terminal domain (CTD) kinases cyclin-dependent kinase 7 (CDK7) and CDK9 and a global increase in CTD phosphorylation. The Myc transactivation domain binds to the transcription initiation sites of these promoters and stimulates TFIIH binding in an MBII-dependent manner. Expression of the Myc transactivation domain increases CDK mRNA cap methylation, polysome loading, and the rate of translation. We find that some traditional Myc transcriptional target genes are also regulated by this Myc-driven translation mechanism. We propose that Myc transactivation domain-driven RNA Pol II CTD phosphorylation has broad effects on both transcription and mRNA metabolism. PMID:17242204

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

    DEFF Research Database (Denmark)

    Plasencia, I; Norlen, Lars; Bagatolli, Luis

    2007-01-01

    The main function of skin is to serve as a physical barrier between the body and the environment. This barrier capacity is in turn a function of the physical state and structural organization of the stratum corneum extracellular lipid matrix. This lipid matrix is essentially composed of very long...... chain saturated ceramides, cholesterol, and free fatty acids. Three unsolved key questions are i), whether the stratum corneum extracellular lipid matrix is constituted by a single gel phase or by coexisting crystalline (solid) domains; ii), whether a separate liquid crystalline phase is present......; and iii), whether pH has a direct effect on the lipid matrix phase behavior. In this work the lateral structure of membranes composed of lipids extracted from human skin stratum corneum was studied in a broad temperature range (10 degrees C-90 degrees C) using different techniques such as differential...

  9. Conformational transitions of the catalytic domain of heme-regulated eukaryotic initiation factor 2α kinase, a key translational regulatory molecule.

    Science.gov (United States)

    Sreejith, R K; Suresh, C G; Bhosale, Siddharth H; Bhavnani, Varsha; Kumar, Avinash; Gaikwad, Sushama M; Pal, Jayanta K

    2012-01-01

    In mammalian cells, the heme-regulated inhibitor (HRI) plays a critical role in the regulation of protein synthesis at the initiation step through phosphorylation of α-subunit of the eukaryotic initiation factor 2 (eIF2). In this study we have cloned and performed biophysical characterization of the kinase catalytic domain (KD) of rabbit HRI. The KD described here comprises kinase 1, the kinase insertion domain (KI) and kinase 2. We report here the existence of an active and stable monomer of HRI (KD). The HRI (KD) containing three tryptophan residues was examined for its conformational transitions occurring under various denaturing conditions using steady-state and time-resolved tryptophan fluorescence, circular dichroism (CD) and hydrophobic dye binding. The parameter A and phase diagram analysis revealed multi-state unfolding and existence of three stable intermediates during guanidine hydrochloride (Gdn-HCl) induced unfolding of HRI (KD). The protein treated with 6 M Gdn-HCl showed collisional and static mechanism of acrylamide quenching and the constants (K(sv) = 3.08 M(-1) and K(s)= 5.62 M(-1)) were resolved using time resolved fluorescence titration. Based on pH, guanidine hydrochloride and temperature mediated transitions, HRI (KD) appears to exemplify a rigid molten globule-like intermediate with compact secondary structure, altered tertiary structure and exposed hydrophobic patches at pH 3.0. The results indicate the inherent structural stability of HRI (KD), a member of the class of stress response proteins.

  10. The phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS-phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance.

    Directory of Open Access Journals (Sweden)

    Lorena Rodríguez-Rubio

    Full Text Available The increase in antibiotic resistance world-wide revitalized the interest in the use of phage lysins to combat pathogenic bacteria. In this work, we analyzed the specific cleavage sites on the staphylococcal peptidoglycan produced by three phage lytic proteins. The investigated cell wall lytic enzymes were the endolysin LysH5 derived from the S. aureus bacteriophage vB_SauS-phi-IPLA88 (phi-IPLA88 and two fusion proteins between lysostaphin and the virion-associated peptidoglycan hydrolase HydH5 (HydH5SH3b and HydH5Lyso. We determined that all catalytic domains present in these proteins were active. Additionally, we tested for the emergence of resistant Staphylococcus aureus to any of the three phage lytic proteins constructs. Resistant S. aureus could not be identified after 10 cycles of bacterial exposure to phage lytic proteins either in liquid or plate cultures. However, a quick increase in lysostaphin resistance (up to 1000-fold in liquid culture was observed. The lack of resistant development supports the use of phage lytic proteins as future therapeutics to treat staphylococcal infections.

  11. Direct catalytic conversion of methane and light hydrocarbon gases. Quarterly report No. 6, January 16, 1988--April 15, 1988

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-05-20

    The goal of this research is to develop catalysts that directly convert methane and light hydrocarbons to intermediates that later can be converted to either liquid fuels or value-added chemicals, as economics dictate. During this reporting period, we synthesized several phthalocyanine catalysts supported on magnesia (MgO) in Task 3. In Task 4 we have tested these catalysts for oxidation of methane and did a number of blank experiments to determine the cause of the low methanol yield we have observed. Magnesia supported catalysts were prepared by first synthesizing the various metal tetrasulfophthalocyanines (TSPCs), converting them to the acid form, and then supporting these complexes on a basic support (MgO) by a neutralization reaction. The metals used were Ru, Pd, Cu, Fe, Co, Mn, and Mo. CoTSPC was also synthesized in zeolite Y using our standard template techniques described in Quarterly Report No. 1. These complexes were examined for catalytic activity in the oxidation of methane. The PdTSPC/MgO had greater activity, and oxidized some of the methane (selectivity of 2.8% from the methane oxidized at 375{degrees}C) to ethane. This is a much lower temperature for this reaction than previously reported in the literature. We also examined the reactivity of various components of the system in the oxidation of the product methanol. The reactor showed some activity for the oxidation of methanol to carbon dioxide. When zeolite or magnesia were added, this activity increased. The magnesia oxidized most of the methanol to carbon dioxide, while the zeolite reduced some of the methanol to hydrocarbons. With oxygen in the feed gas stream (i.e., the conditions of our methane oxidation), a very large fraction of the methanol was oxidized to carbon dioxide when passed over magnesia. From this, we can conclude that any methanol formed in the oxidation of methane would probably be destroyed very quickly on the catalyst bed.

  12. Dissecting the Catalytic Mechanism of Betaine-Homocysteine S-Methyltransferase Using Intrinsic Tryptophan Fluorescence and Site-Directed Mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Castro, C.; Gratson, A.A.; Evans, J.C.; Jiracek, J.; Collinsova, M.; Ludwig, M.L.; Garrow, T.A. (ASCR); (UIUC); (Michigan)

    2010-03-05

    Betaine-homocysteine S-methyltransferase (BHMT) is a zinc-dependent enzyme that catalyzes the transfer of a methyl group from glycine betaine (Bet) to homocysteine (Hcy) to form dimethylglycine (DMG) and methionine (Met). Previous studies in other laboratories have indicated that catalysis proceeds through the formation of a ternary complex, with a transition state mimicked by the inhibitor S-({delta}-carboxybutyl)-l-homocysteine (CBHcy). Using changes in intrinsic tryptophan fluorescence to determine the affinity of human BHMT for substrates, products, or CBHcy, we now demonstrate that the enzyme-substrate complex reaches its transition state through an ordered bi-bi mechanism in which Hcy is the first substrate to bind and Met is the last product released. Hcy, Met, and CBHcy bind to the enzyme to form binary complexes with K{sub d} values of 7.9, 6.9, and 0.28 {micro}M, respectively. Binary complexes with Bet and DMG cannot be detected with fluorescence as a probe, but Bet and DMG bind tightly to BHMT-Hcy to form ternary complexes with K{sub d} values of 1.1 and 0.73 {micro}M, respectively. Mutation of each of the seven tryptophan residues in human BHMT provides evidence that the enzyme undergoes two distinct conformational changes that are reflected in the fluorescence of the enzyme. The first is induced when Hcy binds, and the second, when Bet binds. As predicted by the crystal structure of BHMT, the amino acids Trp44 and Tyr160 are involved in binding Bet, and Glu159 in binding Hcy. Replacing these residues by site-directed mutagenesis significantly reduces the catalytic efficiency (V{sub max}/K{sub m}) of the enzyme. Replacing Tyr77 with Phe abolishes enzyme activity.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-06-01

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

  14. The Human Mixed Lineage Leukemia 5 (MLL5), a Sequentially and Structurally Divergent SET Domain-Containing Protein with No Intrinsic Catalytic Activity

    Science.gov (United States)

    Teyssier, Catherine; Déméné, Hélène; Carvalho, João E.; Bird, Louise E.; Lebedev, Andrey; Fattori, Juliana; Schubert, Michael; Dumas, Christian; Bourguet, William; le Maire, Albane

    2016-01-01

    Mixed Lineage Leukemia 5 (MLL5) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. Chromatin binding is ensured by its plant homeodomain (PHD) through a direct interaction with the N-terminus of histone H3 (H3). In addition, MLL5 contains a Su(var)3-9, Enhancer of zeste, Trithorax (SET) domain, a protein module that usually displays histone lysine methyltransferase activity. We report here the crystal structure of the unliganded SET domain of human MLL5 at 2.1 Å resolution. Although it shows most of the canonical features of other SET domains, both the lack of key residues and the presence in the SET-I subdomain of an unusually large loop preclude the interaction of MLL5 SET with its cofactor and substrate. Accordingly, we show that MLL5 is devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptides. Hence, the three dimensional structure of MLL5 SET domain unveils the structural basis for its lack of methyltransferase activity and suggests a new regulatory mechanism. PMID:27812132

  15. A single domain direct carbon fuel cell (DCFC) 2-D modeling

    Energy Technology Data Exchange (ETDEWEB)

    Elleuch, A.; Boussetta, A.; Halouani, K. [Sfax Univ., Sfax (Tunisia). Inst. Preparatoire aux Etudes d' Ingenieurs de Sfax, Micro-Electro-Thermal Systems, Industrial Energy Systems Group; Sahraoui, M. [Tunis Univ., Tunis (Tunisia). LASMAP EPT IPEIT

    2010-07-01

    There has been a renewed interest in cells fuelled with solid carbon because they promise increased conversion efficiencies for coal-based power generation with less production of carbon dioxide (CO{sub 2}). In addition, the CO{sub 2} produced in a direct carbon fuel cell (DCFC) is capture-ready for sequestration. The DCFC is a special type of high temperature fuel cell in which solid carbon directly reacts with oxygen to form CO{sub 2} and electricity. This paper presented a numerical 2-D model that simulates the transport of gaseous species, electrochemical kinetics, energy transport, and ionic current distribution for all regions of the DCFC. The governing differential equations were solved over a single computational domain, which consisted of a cathode gas channel, cathode gas diffusion layer, and cathode catalyst layer for the cathode side of the cell, a simple bloc for the anode side as well as the molten carbonate electrolyte. The coupled set of differential equations was solved using a FORTRAN code, and was readily adaptable in terms of geometry and material property definitions. The results showed temperature, carbon dioxide and oxygen concentration profile in all DCFC compartments. It was concluded that the model contributes to a better understanding of the heat and mass transfer mechanisms occurring within the cell. 10 refs., 3 tabs., 8 figs.

  16. A rigid surface boundary element for soil-structure interaction analysis in the direct time domain

    Science.gov (United States)

    Rizos, D. C.

    Many soil-structure interaction problems involve studies of single or multiple rigid bodies of arbitrary shape and soil media. The commonly used boundary element methods implement the equations of the rigid body in a form that depends on the particulars of the geometry and requires partitioning and condensation of the associated algebraic system of equations. The present work employs the direct time domain B-Spline BEM for 3D elastodynamic analysis and presents an efficient implementation of rigid bodies of arbitrary shape in contact with, or embedded in, elastic media. The formulation of a rigid surface boundary element introduced herein is suitable for direct superposition in the BEM system of algebraic equations. Consequently, solutions are computed in a single analysis step, eliminating, thus, the need for partitioning of the system of equations. Computational efficiency is also achieved due to the extremely sparse form of the associated coefficient matrices. The proposed element can be used for the modeling of single or multiple rigid bodies of arbitrary shape within the framework of the BEM method. The efficiency and general nature of the proposed element is demonstrated through applications related to the dynamic analysis of rigid surface and embedded foundations and their interaction with embedded rigid bodies of arbitrary shape.

  17. Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter.

    Science.gov (United States)

    Kim, Dong-Sik; Song, Hyung-Nam; Nam, Hyo Jung; Kim, Sung-Geun; Park, Young-Seoub; Park, Jae-Chan; Woo, Eui-Jeon; Lim, Hyung-Kwon

    2014-01-01

    Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

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

    Science.gov (United States)

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

    2015-12-18

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

  19. Photo-activated psoralen binds the ErbB2 catalytic kinase domain, blocking ErbB2 signaling and triggering tumor cell apoptosis.

    Directory of Open Access Journals (Sweden)

    Wenle Xia

    Full Text Available Photo-activation of psoralen with UVA irradiation, referred to as PUVA, is used in the treatment of proliferative skin disorders. The anti-proliferative effects of PUVA have been largely attributed to psoralen intercalation of DNA, which upon UV treatment, triggers the formation of interstrand DNA crosslinks (ICL that inhibit transcription and DNA replication. Here, we show that PUVA exerts antitumor effects in models of human breast cancer that overexpress the ErbB2 receptor tyrosine kinase oncogene, through a new mechanism. Independent of ICL formation, the antitumor effects of PUVA in ErbB2+ breast cancer models can instead be mediated through inhibition of ErbB2 activation and signaling. Using a mass spectroscopy-based approach, we show for the first time that photo-activated 8MOP (8-methoxypsoralen interacts with the ErbB2 catalytic autokinase domain. Furthermore, PUVA can reverse therapeutic resistance to lapatinib and other ErbB2 targeted therapies, including resistance mediated via expression of a phosphorylated, truncated form of ErbB2 (p85(ErbB2 that is preferentially expressed in tumor cell nuclei. Current ErbB2 targeted therapies, small molecule kinase inhibitors or antibodies, do not block the phosphorylated, activated state of p85(ErbB2. Here we show that PUVA reduced p85(ErbB2 phosphorylation leading to tumor cell apoptosis. Thus, in addition to its effects on DNA and the formation of ICL, PUVA represents a novel ErbB2 targeted therapy for the treatment of ErbB2+ breast cancers, including those that have developed resistance to other ErbB2 targeted therapies.

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

    Science.gov (United States)

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

    2011-01-01

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

  1. The c-Myc Transactivation Domain Is a Direct Modulator of Apoptotic versus Proliferative Signals

    Science.gov (United States)

    Chang, David W.; Claassen, Gisela F.; Hann, Stephen R.; Cole, Michael D.

    2000-01-01

    We have assayed the oncogenic, proliferative, and apoptotic activities of the frequent mutations that occur in the c-myc gene in Burkitt's lymphomas. Some alleles have a modest (50 to 60%) increase in transforming activity; however, the most frequent Burkitt's lymphoma allele (T58I) had an unexpected substantial decrease in transforming activity (85%). All alleles restored the proliferation function of c-Myc in cells that grow slowly due to a c-myc knockout. There was discordance for some alleles between apoptotic and oncogenic activities, but only the T58A allele had elevated transforming activity with a concomitant reduced apoptotic potential. We discovered a novel missense mutation, MycS71F, that had a very low apoptotic activity compared to wild-type Myc, yet this mutation has never been found in lymphomas, suggesting that there is no strong selection for antiapoptotic c-Myc alleles. MycS71F also induced very low levels of cytochrome c release from mitochondria, suggesting a mechanism of action for this mutation. Phosphopeptide mapping provided a biochemical basis for the dramatically different biological activities of the transformation-defective T58I and transformation-enhanced T58A c-Myc alleles. Furthermore, the antiapoptotic survival factor insulin-like growth factor 1 was found to suppress phosphorylation of T58, suggesting that the c-Myc transactivation domain is a direct target of survival signals. PMID:10825194

  2. Direct injection of functional single-domain antibodies from E. coli into human cells.

    Directory of Open Access Journals (Sweden)

    Ana Blanco-Toribio

    Full Text Available Intracellular proteins have a great potential as targets for therapeutic antibodies (Abs but the plasma membrane prevents access to these antigens. Ab fragments and IgGs are selected and engineered in E. coli and this microorganism may be also an ideal vector for their intracellular delivery. In this work we demonstrate that single-domain Ab (sdAbs can be engineered to be injected into human cells by E. coli bacteria carrying molecular syringes assembled by a type III protein secretion system (T3SS. The injected sdAbs accumulate in the cytoplasm of HeLa cells at levels ca. 10⁵-10⁶ molecules per cell and their functionality is shown by the isolation of sdAb-antigen complexes. Injection of sdAbs does not require bacterial invasion or the transfer of genetic material. These results are proof-of-principle for the capacity of E. coli bacteria to directly deliver intracellular sdAbs (intrabodies into human cells for analytical and therapeutic purposes.

  3. Direct Data Domain Sparsity-Based STAP Utilizing Subaperture Smoothing Techniques

    Directory of Open Access Journals (Sweden)

    Zhaocheng Yang

    2015-01-01

    Full Text Available We propose a novel direct data domain (D3 sparsity-based space-time adaptive processing (STAP algorithm utilizing subaperture smoothing techniques for airborne radar applications. Different from either normal sparsity-based STAP or D3 sparsity-based STAP, the proposed algorithm firstly uses only the snapshot in the cell under test (CUT to generate multiple subsnapshots by exploiting the space-time structure of the steering vector and the uncorrelated nature of the components of the interference covariance matrix. Since the interference spectrum is sparse in the whole angle-Doppler plane, by employing a sparse regularization, the generated multiple subsnapshots are jointly used to recover the interference spectrum. The interference covariance matrix is then estimated from the interference spectrum, followed by the space-time filtering and the target detection. Simulation results illustrate that the proposed algorithm outperforms the generalized forward/backward method, the conventional D3 least squares STAP algorithm, and the existing D3 sparsity-based STAP algorithm. Furthermore, compared with the normal sparsity-based STAP algorithm using multiple snapshots, the proposed algorithm can also avoid the performance degradation caused by discrete interferers merely appearing in the CUT.

  4. A novel 3D Ag(I)-MOF: Surfactant-directed syntheses and catalytic degradation of o/m/p-Nitrophenol

    Science.gov (United States)

    Wu, Xue-Qian; Wen, Guo-Xuan; Wu, Ya-Pan; Dong, Wen-Wen; Zhao, Jun; Li, Dong-Sheng

    2016-10-01

    For the first time, sodium caprylate has been investigated to direct the crystal growth of 3D Ag-MOF, [Ag2(ddcba)(4,4‧-bipy)2] (1), constructing from 3,5-(di(2‧,5‧-dicarboxylphenyl)benozoic acid and 4,4‧-bipy. The single crystal diffraction analyses shows that complex 1 possess 3D neutral framework with a three-connected ThSi2 (103-b) topology. Compound 1 exhibits predominant catalytic activity towards the degradation of o-Nitrophenol (ONP), m-Nitrophenol (MNP) and p-Nitrophenol (PNP) in aqueous solution. The kinetics of such catalytic degradation reactions was also studied.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-30

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

  6. Direct observation of massless domain wall dynamics in nanostripes with perpendicular magnetic anisotropy.

    Science.gov (United States)

    Vogel, J; Bonfim, M; Rougemaille, N; Boulle, O; Miron, I M; Auffret, S; Rodmacq, B; Gaudin, G; Cezar, J C; Sirotti, F; Pizzini, S

    2012-06-15

    Domain wall motion induced by nanosecond current pulses in nanostripes with perpendicular magnetic anisotropy (Pt/Co/AlO(x)) is shown to exhibit negligible inertia. Time-resolved magnetic microscopy during current pulses reveals that the domain walls start moving, with a constant speed, as soon as the current reaches a constant amplitude, and no or little motion takes place after the end of the pulse. The very low "mass" of these domain walls is attributed to the combination of their narrow width and high damping parameter α. Such a small inertia should allow accurate control of domain wall motion by tuning the duration and amplitude of the current pulses.

  7. The Antitumor Effect of Single-domain Antibodies Directed Towards Membrane-associated Catalase and Superoxide Dismutase.

    Science.gov (United States)

    Bauer, Georg; Motz, Manfred

    2016-11-01

    Neutralizing single-domain antibodies directed towards catalase or superoxide dismutase (SOD) caused efficient reactivation of intercellular reactive oxygen species/reactive nitrogen species (ROS/RNS)-dependent apoptosis-inducing signaling specifically in human tumor cells. Single-domain antibodies targeted tumor cell-specific membrane-associated SOD and catalase, but not the corresponding intracellular enzymes. They were shown to be about 200-fold more effective than corresponding classical recombinant antigen-binding fragments and more than four log steps more efficient than monoclonal antibodies. Combined addition of single-domain antibodies against catalase and SOD caused a remarkable synergistic effect. Proof-of-concept experiments in immunocompromised mice using human tumor xenografts and single-domain antibodies directed towards SOD showed an inhibition of tumor growth. Neutralizing single-domain antibodies directed to catalase and SOD also caused a very strong synergistic effect with the established chemotherapeutic agent taxol, indicating an overlap of signaling pathways. This effect might also be useful in order to avoid unwanted side-effects and to drastically lower the costs for taxol-based therapy.

  8. Activation of p115-RhoGEF requires direct association of Gα13 and the Dbl homology domain.

    Science.gov (United States)

    Chen, Zhe; Guo, Liang; Hadas, Jana; Gutowski, Stephen; Sprang, Stephen R; Sternweis, Paul C

    2012-07-20

    RGS-containing RhoGEFs (RGS-RhoGEFs) represent a direct link between the G(12) class of heterotrimeric G proteins and the monomeric GTPases. In addition to the canonical Dbl homology (DH) and pleckstrin homology domains that carry out the guanine nucleotide exchange factor (GEF) activity toward RhoA, these RhoGEFs also possess RGS homology (RH) domains that interact with activated α subunits of G(12) and G(13). Although the GEF activity of p115-RhoGEF (p115), an RGS-RhoGEF, can be stimulated by Gα(13), the exact mechanism of the stimulation has remained unclear. Using combined studies with small angle x-ray scattering, biochemistry, and mutagenesis, we identify an additional binding site for activated Gα(13) in the DH domain of p115. Small angle x-ray scattering reveals that the helical domain of Gα(13) docks onto the DH domain, opposite to the surface of DH that binds RhoA. Mutation of a single tryptophan residue in the α3b helix of DH reduces binding to activated Gα(13) and ablates the stimulation of p115 by Gα(13). Complementary mutations at the predicted DH-binding site in the αB-αC loop of the helical domain of Gα(13) also affect stimulation of p115 by Gα(13). Although the GAP activity of p115 is not required for stimulation by Gα(13), two hydrophobic motifs in RH outside of the consensus RGS box are critical for this process. Therefore, the binding of Gα(13) to the RH domain facilitates direct association of Gα(13) to the DH domain to regulate its exchange activity. This study provides new insight into the mechanism of regulation of the RGS-RhoGEF and broadens our understanding of G protein signaling.

  9. Direct catalytic asymmetric addition of allyl cyanide to ketones via soft Lewis acid/hard Brønsted base/hard Lewis base catalysis.

    Science.gov (United States)

    Yazaki, Ryo; Kumagai, Naoya; Shibasaki, Masakatsu

    2010-04-21

    We report that a hard Lewis base substantially affects the reaction efficiency of direct catalytic asymmetric gamma-addition of allyl cyanide (1a) to ketones promoted by a soft Lewis acid/hard Brønsted base catalyst. Mechanistic studies have revealed that Cu/(R,R)-Ph-BPE and Li(OC(6)H(4)-p-OMe) serve as a soft Lewis acid and a hard Brønsted base, respectively, allowing for deprotonative activation of 1a as the rate-determining step. A ternary catalytic system comprising a soft Lewis acid/hard Brønsted base and an additional hard Lewis base, in which the basicity of the hard Brønsted base Li(OC(6)H(4)-p-OMe) was enhanced by phosphine oxide (the hard Lewis base) through a hard-hard interaction, outperformed the previously developed binary soft Lewis acid/hard Brønsted base catalytic system, leading to higher yields and enantioselectivities while using one-tenth the catalyst loading and one-fifth the amount of 1a. This second-generation catalyst allows efficient access to highly enantioenriched tertiary alcohols under nearly ideal atom-economical conditions (0.5-1 mol % catalyst loading and a substrate molar ratio of 1:2).

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chih-Hung, E-mail: chwang@phy.ncu.edu.tw [Department of Physics, Tamkang University, Taipei 25137, Taiwan (China); Department of Physics, National Central University, Chungli 320, Taiwan (China); Wu, Yu-Huei, E-mail: yhwu@phy.ncu.edu.tw [Center for Mathematics and Theoretical Physics, National Central University, Chungli 320, Taiwan (China); Department of Physics, National Central University, Chungli 320, Taiwan (China); Hsu, Stephen D.H., E-mail: hsu@uoregon.edu [Institute of Theoretical Science, University of Oregon, Eugene, OR 97403 (United States)

    2012-06-18

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

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

    Directory of Open Access Journals (Sweden)

    Shouyun Cheng

    2015-06-01

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

  12. Direct Evidence for a Phenylalanine Site in the Regulatory Domain of Phenylalanine Hydroxylase

    OpenAIRE

    Li, Jun; Ilangovan, Udayar; Daubner, S. Colette; Hinck, Andrew P.; Fitzpatrick, Paul F.

    2010-01-01

    The hydroxylation of phenylalanine to tyrosine by the liver enzyme phenylalanine hydroxylase is regulated by the level of phenylalanine. Whether there is a distinct allosteric binding site for phenylalanine outside of the active site has been unclear. The enzyme contains an N-terminal regulatory domain that extends through Thr117. The regulatory domain of rat phenylalanine hydroxylase was expressed in E. coli. The purified protein behaves as a dimer on a gel filtration column. In the presence...

  13. Directed evolution of the TALE N-terminal domain for recognition of all 5' bases.

    Science.gov (United States)

    Lamb, Brian M; Mercer, Andrew C; Barbas, Carlos F

    2013-11-01

    Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5'-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5' T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5' T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes.

  14. Functional roles of the non-catalytic calcium-binding sites in the N-terminal domain of human peptidylarginine deiminase 4.

    Science.gov (United States)

    Liu, Yi-Liang; Tsai, I-Chen; Chang, Chia-Wei; Liao, Ya-Fan; Liu, Guang-Yaw; Hung, Hui-Chih

    2013-01-01

    This study investigated the functional roles of the N-terminal Ca(2+) ion-binding sites, in terms of enzyme catalysis and stability, of peptidylarginine deiminase 4 (PAD4). Amino acid residues located in the N-terminal Ca(2+)-binding site of PAD4 were mutated to disrupt the binding of Ca(2+) ions. Kinetic data suggest that Asp155, Asp157 and Asp179, which directly coordinate Ca3 and Ca4, are essential for catalysis in PAD4. For D155A, D157A and D179A, the k(cat)/K(m,BAEE) values were 0.02, 0.63 and 0.01 s(-1)mM(-1) (20.8 s(-1)mM(-1) for WT), respectively. Asn153 and Asp176 are directly coordinated with Ca3 and indirectly coordinated with Ca5 via a water molecule. However, N153A displayed low enzymatic activity with a k(cat) value of 0.3 s(-1) (13.3 s(-1) for wild-type), whereas D176A retained some catalytic power with a k(cat) of 9.7 s(-1). Asp168 is the direct ligand for Ca5, and Ca5 coordination by Glu252 is mediated by two water molecules. However, mutation of these two residues to Ala did not cause a reduction in the k(cat)/K(m,BAEE) values, which indicates that the binding of Ca5 may not be required for PAD4 enzymatic activity. The possible conformational changes of these PAD4 mutants were examined. Thermal stability analysis of the PAD4 mutants in the absence or presence of Ca(2+) indicated that the conformational stability of the enzyme is highly dependent on Ca(2+) ions. In addition, the results of urea-induced denaturation for the N153, D155, D157 and D179 series mutants further suggest that the binding of Ca(2+) ions in the N-terminal Ca(2+)-binding site stabilizes the overall conformational stability of PAD4. Therefore, our data strongly suggest that the N-terminal Ca(2+) ions play critical roles in the full activation of the PAD4 enzyme.

  15. Functional roles of the non-catalytic calcium-binding sites in the N-terminal domain of human peptidylarginine deiminase 4.

    Directory of Open Access Journals (Sweden)

    Yi-Liang Liu

    Full Text Available This study investigated the functional roles of the N-terminal Ca(2+ ion-binding sites, in terms of enzyme catalysis and stability, of peptidylarginine deiminase 4 (PAD4. Amino acid residues located in the N-terminal Ca(2+-binding site of PAD4 were mutated to disrupt the binding of Ca(2+ ions. Kinetic data suggest that Asp155, Asp157 and Asp179, which directly coordinate Ca3 and Ca4, are essential for catalysis in PAD4. For D155A, D157A and D179A, the k(cat/K(m,BAEE values were 0.02, 0.63 and 0.01 s(-1mM(-1 (20.8 s(-1mM(-1 for WT, respectively. Asn153 and Asp176 are directly coordinated with Ca3 and indirectly coordinated with Ca5 via a water molecule. However, N153A displayed low enzymatic activity with a k(cat value of 0.3 s(-1 (13.3 s(-1 for wild-type, whereas D176A retained some catalytic power with a k(cat of 9.7 s(-1. Asp168 is the direct ligand for Ca5, and Ca5 coordination by Glu252 is mediated by two water molecules. However, mutation of these two residues to Ala did not cause a reduction in the k(cat/K(m,BAEE values, which indicates that the binding of Ca5 may not be required for PAD4 enzymatic activity. The possible conformational changes of these PAD4 mutants were examined. Thermal stability analysis of the PAD4 mutants in the absence or presence of Ca(2+ indicated that the conformational stability of the enzyme is highly dependent on Ca(2+ ions. In addition, the results of urea-induced denaturation for the N153, D155, D157 and D179 series mutants further suggest that the binding of Ca(2+ ions in the N-terminal Ca(2+-binding site stabilizes the overall conformational stability of PAD4. Therefore, our data strongly suggest that the N-terminal Ca(2+ ions play critical roles in the full activation of the PAD4 enzyme.

  16. Direct observation of domain walls in NiFe films using high-resolution Lorentz microscopy

    Science.gov (United States)

    Wong, Bunsen Y.; Laughlin, David E.

    1996-04-01

    A novel approach to observe the interaction between magnetic domain wall and nanoscale microstructural features is demonstrated. The method is based on Focault mode Lorentz microscopy and utilizes a Gatan energy image filter to provide additional magnification. A postexperimental image processing technique was applied to separate lattice diffraction from that induced by magnetic domains. The effect of NiFe thickness on the width of a 180° Néel wall has been studied. It was found that the thickness dependence has a similar profile to the theoretically predicted trend but the actual wall thickness is smaller than the calculated values.

  17. Direct observation of low frequency confined acoustic phonons in silver nanoparticles: Terahertz time domain spectroscopy.

    Science.gov (United States)

    Kumar, Sunil; Kamaraju, N; Karthikeyan, B; Tondusson, M; Freysz, E; Sood, A K

    2010-07-01

    Terahertz time domain spectroscopy has been used to study low frequency confined acoustic phonons of silver nanoparticles embedded in poly(vinyl alcohol) matrix in the spectral range of 0.1-2.5 THz. The real and imaginary parts of the dielectric function show two bands at 0.60 and 2.12 THz attributed to the spheroidal and toroidal modes of silver nanoparticles, thus demonstrating the usefulness of terahertz time domain spectroscopy as a complementary technique to Raman spectroscopy in characterizing the nanoparticles.

  18. Direct observation of nanoscale Peltier and Joule effects at metal-insulator domain walls in vanadium dioxide nanobeams.

    Science.gov (United States)

    Favaloro, Tela; Suh, Joonki; Vermeersch, Bjorn; Liu, Kai; Gu, Yijia; Chen, Long-Qing; Wang, Kevin X; Wu, Junqiao; Shakouri, Ali

    2014-05-14

    The metal to insulator transition (MIT) of strongly correlated materials is subject to strong lattice coupling, which brings about the unique one-dimensional alignment of metal-insulator (M-I) domains along nanowires or nanobeams. Many studies have investigated the effects of stress on the MIT and hence the phase boundary, but few have directly examined the temperature profile across the metal-insulating interface. Here, we use thermoreflectance microscopy to create two-dimensional temperature maps of single-crystalline VO2 nanobeams under external bias in the phase coexisting regime. We directly observe highly localized alternating Peltier heating and cooling as well as Joule heating concentrated at the M-I domain boundaries, indicating the significance of the domain walls and band offsets. Utilizing the thermoreflectance technique, we are able to elucidate strain accumulation along the nanobeam and distinguish between two insulating phases of VO2 through detection of the opposite polarity of their respective thermoreflectance coefficients. Microelasticity theory was employed to predict favorable domain wall configurations, confirming the monoclinic phase identification.

  19. New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading.

    Science.gov (United States)

    Sumitani, J; Tottori, T; Kawaguchi, T; Arai, M

    2000-09-01

    The alpha-amylase from Bacillus sp. no. 195 (BAA) consists of two domains: one is the catalytic domain similar to alpha-amylases from animals and Streptomyces in the N-terminal region; the other is the functionally unknown domain composed of an approx. 90-residue direct repeat in the C-terminal region. The gene coding for BAA was expressed in Streptomyces lividans TK24. Three active forms of the gene products were found. The pH and thermal profiles of BAAs, and their catalytic activities for p-nitrophenyl maltopentaoside and soluble starch, showed almost the same behaviours. The largest, 69 kDa, form (BAA-alpha) was of the same molecular mass as that of the mature protein estimated from the nucleotide sequence, and had raw-starch-binding and -degrading abilities. The second largest, 60 kDa, form (BAA-beta), whose molecular mass was the same as that of the natural enzyme from Bacillus sp. no. 195, was generated by proteolytic processing between the two repeat sequences in the C-terminal region, and had lower activities for raw starch binding and degrading than those of BAA-alpha. The smallest, 50 kDa, form (BAA-gamma) contained only the N-terminal catalytic domain as a result of removal of the C-terminal repeat sequence, which led to loss of binding and degradation of insoluble starches. Thus the starch adsorption capacity and raw-starch-degrading activity of BAAs depends on the existence of the repeat sequence in the C-terminal region. BAA-alpha was specifically adsorbed on starch or dextran (alpha-1,4 or alpha-1,6 glucan), and specifically desorbed with maltose or beta-cyclodextrin. These observations indicated that the repeat sequence of the enzyme was functional in the starch-binding domain (SBD). We propose the designation of the homologues to the SBD of glucoamylase from Aspergillus niger as family I SBDs, the homologues to that of glucoamylase from Rhizopus oryzae as family II, and the homologues of this repeat sequence of BAA as family III.

  20. Direct observation of intrinsic twin domains in tetragonal CH3NH3PbI3

    Science.gov (United States)

    Rothmann, Mathias Uller; Li, Wei; Zhu, Ye; Bach, Udo; Spiccia, Leone; Etheridge, Joanne; Cheng, Yi-Bing

    2017-01-01

    Organic–inorganic hybrid perovskites are exciting candidates for next-generation solar cells, with CH3NH3PbI3 being one of the most widely studied. While there have been intense efforts to fabricate and optimize photovoltaic devices using CH3NH3PbI3, critical questions remain regarding the crystal structure that governs its unique properties of the hybrid perovskite material. Here we report unambiguous evidence for crystallographic twin domains in tetragonal CH3NH3PbI3, observed using low-dose transmission electron microscopy and selected area electron diffraction. The domains are around 100–300 nm wide, which disappear/reappear above/below the tetragonal-to-cubic phase transition temperature (approximate 57 °C) in a reversible process that often ‘memorizes' the scale and orientation of the domains. Since these domains exist within the operational temperature range of solar cells, and have dimensions comparable to the thickness of typical CH3NH3PbI3 films in the solar cells, understanding the twin geometry and orientation is essential for further improving perovskite solar cells. PMID:28230064

  1. Large-scale production and purification of recombinant protein from an insect cell/baculovirus system in Erlenmeyer flasks: application to the chicken poly(ADP-ribose polymerase catalytic domain

    Directory of Open Access Journals (Sweden)

    Miranda E.A.

    1997-01-01

    Full Text Available A simple and inexpensive shaker/Erlenmeyer flask system for large-scale cultivation of insect cells is described and compared to a commercial spinner system. On the basis of maximum cell density, average population doubling time and overproduction of recombinant protein, a better result was obtained with a simpler and less expensive bioreactor consisting of Erlenmeyer flasks and an ordinary shaker waterbath. Routinely, about 90 mg of pure poly(ADP-ribose polymerase catalytic domain was obtained for a total of 3 x 109 infected cells in three liters of culture

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    The Her-2 receptor coded for by the proto-oncogenic erbB-2 gene is a clinically validated target for treatment of a significant genetic subclass of breast cancers, and Her-2 is also overexpressed or mutated in a range of other cancers. In an approach to exploit antisense mediated splicing...... oligomers that specifically induce skipping of exon 19 as this exon is coding for the ATP catalytic domain of Her-2, and if expressed such truncated version of the Her-2 protein should be functionally inactive in a dominant negative fashion. Therefore, antisense compounds having efficient erbB-2 exon 19...

  3. Flow patterns on spectral-domain optical coherence tomography reveal flow directions at retinal vessel bifurcations

    DEFF Research Database (Denmark)

    Willerslev, Anne; Li, Xiao Q; Munch, Inger C

    2014-01-01

    PURPOSE: To study intravascular characteristics of flowing blood in retinal vessels using spectral-domain optical coherence tomography (SD-OCT). METHODS: Examination of selected arterial bifurcations and venous sites of confluence in 25 healthy 11-year-old children recruited as an ad hoc subsample...... be determined using SD-OCT. This feature may assist the identification of flow reversal near sites of vascular occlusion, the analysis of blood flow near vascular malformations and the segmentation of retinal SD-OCT images....

  4. Direct evidence for a phenylalanine site in the regulatory domain of phenylalanine hydroxylase.

    Science.gov (United States)

    Li, Jun; Ilangovan, Udayar; Daubner, S Colette; Hinck, Andrew P; Fitzpatrick, Paul F

    2011-01-15

    The hydroxylation of phenylalanine to tyrosine by the liver enzyme phenylalanine hydroxylase is regulated by the level of phenylalanine. Whether there is a distinct allosteric binding site for phenylalanine outside of the active site has been unclear. The enzyme contains an N-terminal regulatory domain that extends through Thr117. The regulatory domain of rat phenylalanine hydroxylase was expressed in Escherichia coli. The purified protein behaves as a dimer on a gel filtration column. In the presence of phenylalanine, the protein elutes earlier from the column, consistent with a conformational change in the presence of the amino acid. No change in elution is seen in the presence of the non-activating amino acid proline. ¹H-¹⁵N HSQC NMR spectra were obtained of the ¹⁵N-labeled protein alone and in the presence of phenylalanine or proline. A subset of the peaks in the spectrum exhibits chemical shift perturbation in the presence of phenylalanine, consistent with binding of phenylalanine at a specific site. No change in the NMR spectrum is seen in the presence of proline. These results establish that the regulatory domain of phenylalanine hydroxylase can bind phenylalanine, consistent with the presence of an allosteric site for the amino acid.

  5. Direct visualization of solid ordered domains induced by polyene antibiotics in giant unilamellar vesicles.

    Science.gov (United States)

    Chulkov, Evgeny G; Efimova, Svetlana S; Schagina, Ludmila V; Ostroumova, Olga S

    2014-10-01

    Polyene antibiotics isolated from Streptomyces are frequently used in treatment of mycoses. Confocal fluorescence microscopy has been employed to investigate the influence of polyene macrolide antibiotics nystatin, amphotericin B, and filipin on the phase separation in giant unilamellar vesicles. It has been demonstrated that nystatin produced the solid ordered domains in vesicles made from DOPC/Chol, DOPC/Chol/SM, and POPC while DOPC vesicles remained homogenous in the presence of polyene antibiotics. The ability of various polyenes to produce the solid ordered phase in POPC membranes has been compared. It has been shown that amphotericin B produced phase separation at lower concentration as compared with nystatin and filipin. Filipin was less effective in promotion of gel domains. The observed efficiency of polyene antibiotics to induce phase separation in lipid bilayers correlates with their biological activity. Present findings probably indicate the limitations of using of polyenes as fluorescence membrane probes for determination of strerol-enriched domains in plasma membrane of live cells.

  6. Analysis of mucolipidosis II/III GNPTAB missense mutations identifies domains of UDP-GlcNAc:lysosomal enzyme GlcNAc-1-phosphotransferase involved in catalytic function and lysosomal enzyme recognition.

    Science.gov (United States)

    Qian, Yi; van Meel, Eline; Flanagan-Steet, Heather; Yox, Alex; Steet, Richard; Kornfeld, Stuart

    2015-01-30

    UDP-GlcNAc:lysosomal enzyme GlcNAc-1-phosphotransferase tags newly synthesized lysosomal enzymes with mannose 6-phosphate recognition markers, which are required for their targeting to the endolysosomal system. GNPTAB encodes the α and β subunits of GlcNAc-1-phosphotransferase, and mutations in this gene cause the lysosomal storage disorders mucolipidosis II and III αβ. Prior investigation of missense mutations in GNPTAB uncovered amino acids in the N-terminal region and within the DMAP domain involved in Golgi retention of GlcNAc-1-phosphotransferase and its ability to specifically recognize lysosomal hydrolases, respectively. Here, we undertook a comprehensive analysis of the remaining missense mutations in GNPTAB reported in mucolipidosis II and III αβ patients using cell- and zebrafish-based approaches. We show that the Stealth domain harbors the catalytic site, as some mutations in these regions greatly impaired the activity of the enzyme without affecting its Golgi localization and proteolytic processing. We also demonstrate a role for the Notch repeat 1 in lysosomal hydrolase recognition, as missense mutations in conserved cysteine residues in this domain do not affect the catalytic activity but impair mannose phosphorylation of certain lysosomal hydrolases. Rescue experiments using mRNA bearing Notch repeat 1 mutations in GNPTAB-deficient zebrafish revealed selective effects on hydrolase recognition that differ from the DMAP mutation. Finally, the mutant R587P, located in the spacer between Notch 2 and DMAP, was partially rescued by overexpression of the γ subunit, suggesting a role for this region in γ subunit binding. These studies provide new insight into the functions of the different domains of the α and β subunits.

  7. Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis.

    Science.gov (United States)

    Lee, Hyunji; Park, Jiyoung; Jung, Chaewon; Han, Dongfei; Seo, Jiyoung; Ahn, Joong-Hoon; Chong, Youhoon; Hur, Hor-Gil

    2015-11-01

    The enzyme ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4 catalyzes the decarboxylation reaction of lignin monomers and phenolic compounds such as p-coumaric acid, caffeic acid, and ferulic acid into their corresponding 4-vinyl derivatives, that is, 4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol, respectively. Among various ferulic acid decarboxylase enzymes, we chose the FADase from Enterobacter sp. Px6-4, whose crystal structure is known, and produced mutants to enhance its catalytic activity by random and site-directed mutagenesis. After three rounds of sequential mutations, FADase(F95L/D112N/V151I) showed approximately 34-fold higher catalytic activity than wild-type for the production of 4-vinylguaiacol from ferulic acid. Docking analyses suggested that the increased activity of FADase(F95L/D112N/V151I) could be due to formation of compact active site compared with that of the wild-type FADase. Considering the amount of phenolic compounds such as lignin monomers in the biomass components, successfully bioengineered FADase(F95L/D112N/V151I) from Enterobacter sp. Px6-4 could provide an ecofriendly biocatalytic tool for producing diverse styrene derivatives from biomass.

  8. 小球藻粉热解及其催化热解试验研究%Experimental Study on Direct and Catalytic Pyrolysis of Chlorella Vulgaris Powders

    Institute of Scientific and Technical Information of China (English)

    时艳; 王许云; 李芳; 仲卫成; 郭庆杰

    2013-01-01

    采用热重分析法考察小球藻粉的热解特性,以HZSM-5、HY分子筛为催化剂,对小球藻粉直接热解和催化热解后生物油的化学组成进行对比分析,研究2种分子筛催化剂对催化热解的影响.结果表明,小球藻粉的热解温度为160~600℃;小球藻粉加入HZSM-5分子筛催化剂催化热解后,十六酸及含氮化合物的含量大幅降低,烃类物质的含量提高,含有较多甲苯、二甲苯等芳香烃;经HY分子筛催化热解后,十六酸含量降低,含氮化合物的含量大幅提高,形成大量的萘等多环芳烃;HZSM-5分子筛具有较好的催化脱氧、择形芳构化功能,HY分子筛择形性较差,导致多环芳烃及含氮化合物的含量提高.%The pyrolysis characteristics of chlorella vulgaris powders were investigated by thermogravimetry technology.Using HZSM-5 zeolite and HY zeolite as catalysts,a comparison on chemical composition of bio-oil from chlorella vulgaris powders by direct and catalytic pyrolysis approaches was presented.The influence of the two kinds of catalysts on catalytic pyrolysis was explored.The results show that the pyrolysis temperature of chlorella vulgaris powders ranges from 160 to 600 ℃.The contents of hexadecanoic acid and nitrogenous compounds are greatly decreased by catalytic pyrolysis ofchlorella vulgaris powders with HZSM-5 zeolite.The amount of hydrocarbons is increased,including plentiful aromatic hydrocarbons such as toluene and xylenes.The content of hexadecanoic acid is reduced by catalytic pyrolysis of chlorella vulgaris powders with HY zeolite,but the content of nitrogenous compounds is greatly increased.The bio-oil contains abundant polycyclic aromatic hydrocarbon,especially naphthalene.HZSM-5 zeolite is highly active in deoxygenation and aromatization.Due to the poor shape-selectivity of HY zeolite,the contents of polycyclic aromatic hydrocarbon and nitrogenous compounds are increased.

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

    Energy Technology Data Exchange (ETDEWEB)

    Maruta, H.; Korn, E.D.

    1981-01-10

    The heavy chains of Acanthamoeba myosins, IA, IB and II, turkey gizzard myosin, and rabbit skeletal muscle myosin subfragment-1 were specifically labeled by radioactive ATP, ADP, and UTP, each of which is a substrate or product of myosin ATPase activity, when irradiated with uv light at 0/sup 0/C. With UTP, as much as 0.45 mol/mol of Acanthamoeba myosin IA heavy chain and 1 mol/mol of turkey gizzard myosin heavy chain was incorporated. Evidence that the ligands were associated with the catalytic site included the observations that reaction occurred only with nucleotides that are substrates or products of the ATPase activity; that the reaction was blocked by pyrophosphate which is an inhibitor of the ATPase activity; that ATP was bound as ADP; and that label was probably restricted to a single peptide following limited subtilisin proteolysis of labeled Acanthamoeba myosin IA heavy chain and extensive cleavage with CNBr and trypsin of labeled turkey gizzard myosin heavy chain.

  10. Domain-confined catalytic soot combustion over Co3O4 anchored on a TiO2 nanotube array catalyst prepared by mercaptoacetic acid induced surface-grafting

    Science.gov (United States)

    Ren, Jiale; Yu, Yifu; Dai, Fangfang; Meng, Ming; Zhang, Jing; Zheng, Lirong; Hu, Tiandou

    2013-11-01

    Herein, we introduce a specially designed domain-confined macroporous catalyst, namely, the Co3O4 nanocrystals anchored on a TiO2 nanotube array catalyst, which was synthesized by using the mercaptoacetic acid induced surface-grafting method. This catalyst exhibits much better performance for catalytic soot combustion than the conventional TiO2 powder supported one in gravitational contact mode (GMC).Herein, we introduce a specially designed domain-confined macroporous catalyst, namely, the Co3O4 nanocrystals anchored on a TiO2 nanotube array catalyst, which was synthesized by using the mercaptoacetic acid induced surface-grafting method. This catalyst exhibits much better performance for catalytic soot combustion than the conventional TiO2 powder supported one in gravitational contact mode (GMC). Electronic supplementary information (ESI) available: The images of XRD, UV-vis, EDX and soot-TPR. The table providing information on Co/Ti-NA catalysts. See DOI: 10.1039/c3nr03757f

  11. Site-directed antibody immobilization using a protein A-gold binding domain fusion protein for enhanced SPR immunosensing.

    Science.gov (United States)

    de Juan-Franco, Elena; Caruz, Antonio; Pedrajas, J R; Lechuga, Laura M

    2013-04-07

    We have implemented a novel strategy for the oriented immobilization of antibodies onto a gold surface based on the use of a fusion protein, the protein A-gold binding domain (PAG). PAG consists of a gold binding peptide (GBP) coupled to the immunoglobulin-binding domains of staphylococcal protein A. This fusion protein provides an easy and fast oriented immobilization of antibodies preserving its native structure, while leaving the antigen binding sites (Fab) freely exposed. Using this immobilization strategy, we have demonstrated the performance of the immunosensing of the human Growth Hormone by SPR. A limit of detection of 90 ng mL(-1) was obtained with an inter-chip variability lower than 7%. The comparison of this method with other strategies for the direct immobilization of antibodies over gold surfaces has showed the enhanced sensitivity provided by the PAG approach.

  12. Directional effects consideration to improve out-doors emissivity retrieval in the 3-13 mum domain.

    Science.gov (United States)

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

    2007-09-17

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

  13. Direct visualization of the thermomagnetic behavior of pseudo–single-domain magnetite particles

    Science.gov (United States)

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

    2016-01-01

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

  14. Direct visualization of the thermomagnetic behavior of pseudo-single-domain magnetite particles.

    Science.gov (United States)

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

    2016-04-01

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

  15. Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity.

    Science.gov (United States)

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

    2016-03-01

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

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

    DEFF Research Database (Denmark)

    Gerken, Thomas A; Revoredo, Leslie; Thome, Joseph J C

    2013-01-01

    Mucin type O-glycosylation is initiated by a large family of polypeptide GalNAc transferases (ppGalNAc Ts) that add α-GalNAc to the Ser and Thr residues of peptides. Of the 20 human isoforms, all but one are composed of two globular domains linked by a short flexible linker: a catalytic domain...... relative to the nonglycosylated control peptides. This N- and/or C-terminal selectivity is presumably due to weak glycopeptide binding to the lectin domain, whose orientation relative to the catalytic domain is dynamic and isoform-dependent. Such N- or C-terminal glycopeptide selectivity provides...

  17. Direct Time Domain Numerical Analysis of Transient Behavior of a VLFS during Unsteady External Loads in Wave Condition

    Directory of Open Access Journals (Sweden)

    Yong Cheng

    2014-01-01

    Full Text Available The transient response of the VLFS subjected to arbitrary external load is systematically investigated by a direct time domain modal expansion method, in which the BEM solutions based on time domain Kelvin sources are used for hydrodynamic forces. In the analysis, the time domain free-surface Green functions with sufficient accuracy are rapidly evaluated in finite water depth by the interpolation-tabulation method, and the boundary integral equation with a quarter VLFS model is established taking advantage of symmetry of flow field and structure. The validity of the present method is verified by comparing with the time histories of vertical displacements of the VLFS during a mass drop and airplane landing and takeoff in still water conditions, respectively. Then the developed numerical scheme is used in wave conditions to study the combined action taking into account the mass drop/airplane landing/takeoff loads as well as incident wave action. It is found that the elevation of structural waves due to mass drop load can be significantly changed near the impact region, while the vertical motion of runway in wave conditions is dominant as compared with that only generated by airplane.

  18. LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration

    Institute of Scientific and Technical Information of China (English)

    Mingzhu Fan; Chongyi Xu; Ke Xu; Yuxin Hu

    2012-01-01

    The remarkable regeneration capability of plant tissues or organs under culture conditions has underlain an extensive practice for decades.The initial step in plant in vitro regeneration often involves the induction of a pluripotent cell mass termed callus,which is driven by the phytohormone auxin and occurs via a root development pathway.However,the key molecules governing callus formation remain unknown.Here we demonstrate that Arabidopsis LATERAL ORGAN BOUNDARIES DOMAIN (LBD)/ASYMMETRIC LEAVES2-LIKE (ASL) transcription factors are involved in the control of callus formation program.The four LBD genes downstream of AUXIN RESPONSE FACTORs (ARFs),LBD16,LBD17,LBD18 and LBD29,are rapidly and dramatically induced by callus-inducing medium (CIM) in multiple organs.Ectopic expression of each of the four LBD genes in Arabidopsis is sufficient to trigger spontaneous callus formation without exogenous phytohormones,whereas suppression of LBD function inhibits the callus formation induced by CIM.Moreover,the callus triggered by LBD resembles that induced by CIM by characteristics of ectopically activated root meristem genes and efficient regeneration capacity.These findings define LBD transcription factors as key regulators in the callus induction process,thereby establishing a molecular link between auxin signaling and the plant regeneration program.

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

    CERN Document Server

    Babkovskaia, N; Brandenburg, A

    2010-01-01

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

  20. Directed self-assembled crystalline oligomer domains on graphene and graphite

    DEFF Research Database (Denmark)

    Balzer, Frank; Henrichsen, Henrik Hartmann; Klarskov, Mikkel Buster

    2014-01-01

    We observe the formation of thin films of fibre-like aggregates from the prototypical organic semiconductor molecule para-hexaphenylene (p-6P) on graphite thin flakes and on monolayer graphene. Using atomic force microscopy, scanning electron microscopy, x-ray diffraction, polarized fluorescence...... show that the graphene surface can be used as a growth substrate to direct the self-assembly of organic molecular thin films and nanofibres, both with and without lithographical processing....

  1. 1-D Directional Filter Based Texture Descriptor in Fractional Fourier Domain

    Institute of Scientific and Technical Information of China (English)

    Kai Tian; Hongzhang Jin; Liying Zheng

    2015-01-01

    Texture analysis is a fundamental field in computer vision. However, it is also a particularly difficult problem for no universal mathematical model of real world textures. By extending a new application of the fractional Fourier transform ( FrFT) in the field of texture analysis, this paper proposes an FrFT⁃based method for describing textures. Firstly, based on the Radon⁃Wigner transform, 1⁃D directional FrFT filters are designed to two types of texture features, i.e., the coarseness and directionality. Then, the frequencies with maximum and median amplitudes of the FrFT of the input signal are regarded as the output of the 1⁃D directional FrFT filter. Finally, the mean and the standard deviation are used to compose of the feature vector. Compared to the WD⁃based method, three benefits can be achieved with the proposed FrFT⁃based method, i. e., less memory size, lower computational load, and less disturbed by the cross⁃terms. The proposed method has been tested on 16 standard texture images. The experimental results show that the proposed method is superior to the popular Gabor filtering⁃based method.

  2. Direct observation of the uncapping of capping protein-capped actin filaments by CARMIL homology domain 3.

    Science.gov (United States)

    Fujiwara, Ikuko; Remmert, Kirsten; Hammer, John A

    2010-01-22

    Bulk solution assays have shown that the isolated CARMIL homology 3 (CAH3) domain from mouse and Acanthamoeba CARMIL rapidly and potently restores actin polymerization when added to actin filaments previously capped with capping protein (CP). To demonstrate this putative uncapping activity directly, we used total internal reflection microscopy to observe single, CP-capped actin filaments before and after the addition of the CAH3 domain from mouse CARMIL-1 (mCAH3). The addition of mCAH3 rapidly restored the polymerization of individual capped filaments, consistent with uncapping. To verify uncapping, filaments were capped with recombinant mouse CP tagged with monomeric green fluorescent protein (mGFP-CP). Restoration of polymerization upon the addition of mCAH3 was immediately preceded by the complete dissociation of mGFP-CP from the filament end, confirming the CAH3-driven uncapping mechanism. Quantitative analyses showed that the percentage of capped filaments that uncapped increased as the concentration of mCAH3 was increased, reaching a maximum of approximately 90% at approximately 250 nm mCAH3. Moreover, the time interval between mCAH3 addition and uncapping decreased as the concentration of mCAH3 increased, with the half-time of CP at the barbed end decreasing from approximately 30 min without mCAH3 to approximately 10 s with a saturating amount of mCAH3. Finally, using mCAH3 tagged with mGFP, we obtained direct evidence that the complex of CP and mCAH3 has a small but measurable affinity for the barbed end, as inferred from previous studies and kinetic modeling. We conclude that the isolated CAH3 domain of CARMIL (and presumably the intact molecule as well) possesses the ability to uncap CP-capped actin filaments.

  3. Direct Observation of the Uncapping of Capping Protein-capped Actin Filaments by CARMIL Homology Domain 3*

    Science.gov (United States)

    Fujiwara, Ikuko; Remmert, Kirsten; Hammer, John A.

    2010-01-01

    Bulk solution assays have shown that the isolated CARMIL homology 3 (CAH3) domain from mouse and Acanthamoeba CARMIL rapidly and potently restores actin polymerization when added to actin filaments previously capped with capping protein (CP). To demonstrate this putative uncapping activity directly, we used total internal reflection microscopy to observe single, CP-capped actin filaments before and after the addition of the CAH3 domain from mouse CARMIL-1 (mCAH3). The addition of mCAH3 rapidly restored the polymerization of individual capped filaments, consistent with uncapping. To verify uncapping, filaments were capped with recombinant mouse CP tagged with monomeric green fluorescent protein (mGFP-CP). Restoration of polymerization upon the addition of mCAH3 was immediately preceded by the complete dissociation of mGFP-CP from the filament end, confirming the CAH3-driven uncapping mechanism. Quantitative analyses showed that the percentage of capped filaments that uncapped increased as the concentration of mCAH3 was increased, reaching a maximum of ∼90% at ∼250 nm mCAH3. Moreover, the time interval between mCAH3 addition and uncapping decreased as the concentration of mCAH3 increased, with the half-time of CP at the barbed end decreasing from ∼30 min without mCAH3 to ∼10 s with a saturating amount of mCAH3. Finally, using mCAH3 tagged with mGFP, we obtained direct evidence that the complex of CP and mCAH3 has a small but measurable affinity for the barbed end, as inferred from previous studies and kinetic modeling. We conclude that the isolated CAH3 domain of CARMIL (and presumably the intact molecule as well) possesses the ability to uncap CP-capped actin filaments. PMID:19926785

  4. Domain of oscillatory growth in directional solidification of dilute binary alloys.

    Science.gov (United States)

    Babushkina, Evgenia; Bessonov, Nicholas M; Korzhenevskii, Alexander L; Bausch, Richard; Schmitz, Rudi

    2013-04-01

    The oscillatory growth of a dilute binary alloy has recently been described by a nonlinear oscillator equation that applies to small temperature gradients and large growth velocities in the setup of directional solidification. Based on a one-dimensional stability analysis of stationary solutions of this equation, we explore in the present paper the complete region where the solidification front propagates in an oscillatory way. The boundary of this region is calculated exactly, and the nature of the oscillations is evaluated numerically in several segments of the region.

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

    CERN Document Server

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

    2016-01-01

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

  6. Encapsulation of metal clusters within MFI via interzeolite transformations and direct hydrothermal syntheses and catalytic consequences of their confinement.

    Science.gov (United States)

    Goel, Sarika; Zones, Stacey I; Iglesia, Enrique

    2014-10-29

    The encapsulation of metal clusters (Pt, Ru, Rh) within MFI was achieved by exchanging cationic metal precursors into a parent zeolite (BEA, FAU), reducing them with H2 to form metal clusters, and transforming these zeolites into daughter structures of higher framework density (MFI) under hydrothermal conditions. These transformations required MFI seeds or organic templates for FAU parent zeolites, but not for BEA, and occurred with the retention of encapsulated clusters. Clusters uniform in size (1.3-1.7 nm) and exposing clean and accessible surfaces formed in BEA and FAU zeolites; their size remained essentially unchanged upon transformation into MFI. Encapsulation selectivities, determined from the relative hydrogenation rates of small (toluene) and large (alkyl arenes) molecules and defined as the ratio of the surface areas of all the clusters in the sample to that of external clusters, were very high (8.1-40.9) for both parent and daughter zeolites. Encapsulation into MFI via direct hydrothermal syntheses was unsuccessful because metal precursors precipitated prematurely at the pH and temperatures required for MFI synthesis. Delayed introduction of metal precursors and F(-) (instead of OH(-)) as the mineralizing agent in hydrothermal syntheses increased encapsulation selectivities, but they remained lower than those achieved via interzeolite transformations. These interconversions provide a general and robust strategy for encapsulation of metals when precursors can be introduced via exchange into a zeolite that can be transformed into target daughter zeolites with higher framework densities, whether spontaneously or by using seeds or structure-directing agents (SDA).

  7. Ligation of cancer cell surface GRP78 with antibodies directed against its COOH-terminal domain up-regulates p53 activity and promotes apoptosis.

    Science.gov (United States)

    Misra, Uma Kant; Mowery, Yvonne; Kaczowka, Steven; Pizzo, Salvatore Vincent

    2009-05-01

    Binding of activated α(2)-macroglobulin to GRP78 on the surface of human prostate cancer cells promotes proliferation by activating signaling cascades. Autoantibodies directed against the activated α(2)-macroglobulin binding site in the NH(2)-terminal domain of GRP78 are receptor agonists, and their presence in the sera of cancer patients is a poor prognostic indicator. We now show that antibodies directed against the GRP78 COOH-terminal domain inhibit [(3)H]thymidine uptake and cellular proliferation while promoting apoptosis as measured by DNA fragmentation, Annexin V assay, and clonogenic assay. These antibodies are receptor antagonists blocking autophosphorylation and activation of GRP78. Using 1-LN and DU145 prostate cancer cell lines and A375 melanoma cells, which express GRP78 on their cell surface, we show that antibodies directed against the COOH-terminal domain of GRP78 up-regulate the tumor suppressor protein p53. By contrast, antibody directed against the NH(2)-terminal domain of GRP78 shows negligible effects on p53 expression. PC-3 prostate cancer cells, which do not express GRP78 on their cell surface, are refractory to the effects of anti-GRP78 antibodies directed against either the COOH- or NH(2)-terminal domains. However, overexpression of GRP78 in PC-3 cells causes translocation of GRP78 to the cell surface and promotes apoptosis when these cells are treated with antibody directed against its COOH-terminal domain. Silencing GRP78 or p53 expression by RNA interference significantly blocked the increase in p53 induced by antibodies. Antibodies directed against the COOH-terminal domain may play a therapeutic role in cancer patients whose tumors trigger the production of autoantibodies directed against the NH(2)-terminal domain of GRP78.

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

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Starch-binding domains (SBDs) comprise distinct protein modules that bind starch, glycogen or related carbohydrates and have been classified into different families of carbohydrate-binding modules (CBMs). The present review focuses on SBDs of CBM20 and CBM48 found in amylolytic enzymes from sever...

  10. Cystatins as calpain inhibitors: engineered chicken cystatin- and stefin B-kininogen domain 2 hybrids support a cystatin-like mode of interaction with the catalytic subunit of mu-calpain.

    Science.gov (United States)

    Díaz, B G; Gross, S; Assfalg-Machleidt, I; Pfeiler, D; Gollmitzer, N; Gabrijelcic-Geiger, D; Stubbs, M T; Fritz, H; Auerswald, E A; Machleidt, W

    2001-01-01

    Within the cystatin superfamily, only kininogen domain 2 (KD2) is able to inhibit mu- and m-calpain. In an attempt to elucidate the structural requirements of cystatins for calpain inhibition, we constructed recombinant hybrids of human stefin B (an intracellular family 1 cystatin) with KD2 and deltaL110 deletion mutants of chicken cystatin-KD2 hybrids. Substitution of the N-terminal contact region of stefin B by the corresponding KD2 sequence resulted in a calpain inhibitor of Ki = 188 nM. Deletion of L110, which forms a beta-bulge in family 1 and 2 cystatins but is lacking in KD2, improved inhibition of mu-calpain 4- to 8-fold. All engineered cystatins were temporary inhibitors of calpain due to slow substrate-like cleavage of a single peptide bond corresponding to Gly9-Ala10 in chicken cystatin. Biomolecular interaction analysis revealed that, unlike calpastatin, the cystatin-type inhibitors do not bind to the calmodulin-like domain of the small subunit of calpain, and their interaction with the mu-calpain heterodimer is completely prevented by a synthetic peptide comprising subdomain B of calpastatin domain 1. Based on these results we propose that (i) cystatin-type calpain inhibitors interact with the active site of the catalytic domain of calpain in a similar cystatin-like mode as with papain and (ii) the potential for calpain inhibition is due to specific subsites within the papain-binding regions of the general cystatin fold.

  11. Directed Self-assembly of Block Copolymer with Sub-15 nm Domain Spacing Using Nanoimprinted Photoresist Templates

    Science.gov (United States)

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

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

  12. Adaptive extraction of emotion-related EEG segments using multidimensional directed information in time-frequency domain.

    Science.gov (United States)

    Petrantonakis, Panagiotis C; Hadjileontiadis, Leontios J

    2010-01-01

    Emotion discrimination from electroencephalogram (EEG) has gained attention the last decade as a user-friendly and effective approach to EEG-based emotion recognition (EEG-ER) systems. Nevertheless, challenging issues regarding the emotion elicitation procedure, especially its effectiveness, raise. In this work, a novel method, which not only evaluates the degree of emotion elicitation but localizes the emotion information in the time-frequency domain, as well, is proposed. The latter, incorporates multidimensional directed information at the time-frequency EEG representation, extracted using empirical mode decomposition, and introduces an asymmetry index for adaptive emotion-related EEG segment selection. Experimental results derived from 16 subjects visually stimulated with pictures from the valence/arousal space drawn from the International Affective Picture System database, justify the effectiveness of the proposed approach and its potential contribution to the enhancement of EEG-ER systems.

  13. Crystal structure of the ternary complex of the catalytic domain of human phenylalanine hydroxylase with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine, and its implications for the mechanism of catalysis and substrate activation.

    Science.gov (United States)

    Andersen, Ole Andreas; Flatmark, Torgeir; Hough, Edward

    2002-07-26

    Phenylalanine hydroxylase catalyzes the stereospecific hydroxylation of L-phenylalanine, the committed step in the degradation of this amino acid. We have solved the crystal structure of the ternary complex (hPheOH-Fe(II).BH(4).THA) of the catalytically active Fe(II) form of a truncated form (DeltaN1-102/DeltaC428-452) of human phenylalanine hydroxylase (hPheOH), using the catalytically active reduced cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) and 3-(2-thienyl)-L-alanine (THA) as a substrate analogue. The analogue is bound in the second coordination sphere of the catalytic iron atom with the thiophene ring stacking against the imidazole group of His285 (average interplanar distance 3.8A) and with a network of hydrogen bonds and hydrophobic contacts. Binding of the analogue to the binary complex hPheOH-Fe(II).BH(4) triggers structural changes throughout the entire molecule, which adopts a slightly more compact structure. The largest change occurs in the loop region comprising residues 131-155, where the maximum r.m.s. displacement (9.6A) is at Tyr138. This loop is refolded, bringing the hydroxyl oxygen atom of Tyr138 18.5A closer to the iron atom and into the active site. The iron geometry is highly distorted square pyramidal, and Glu330 adopts a conformation different from that observed in the hPheOH-Fe(II).BH(4) structure, with bidentate iron coordination. BH(4) binds in the second coordination sphere of the catalytic iron atom, and is displaced 2.6A in the direction of Glu286 and the iron atom, relative to the hPheOH-Fe(II).BH(4) structure, thus changing its hydrogen bonding network. The active-site structure of the ternary complex gives new insight into the substrate specificity of the enzyme, notably the low affinity for L-tyrosine. Furthermore, the structure has implications both for the catalytic mechanism and the molecular basis for the activation of the full-length tetrameric enzyme by its substrate. The large conformational change, moving

  14. Preconversion processing of bituminous coals: New directions to improved direct catalytic coal liquefaction. Quarterly report, January 1, 1992--March 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    1992-07-01

    A study of the high-temperature soaking started in this quarter, following the installation of reactors in the previous quarter. Two high-volatile bituminous coals and three coal liquids, which were identified in the previous report, were used. A cross-linked, three-dimensional macromolecular model has been widely accepted f or the structure of coal, but there is no direct evidence to prove this model. The conventional coal structure model has been recently re-examined by this investigator because of the importance of relatively strong intra- and intermolecular interactions in bituminous coals. It was reasonable to deduce that significant portions were physically associated after a study of multistep extractions, associative equilibria, the irreversibility and the dependence of coal concentration on solvent swelling, and consideration of the monophase concept. Physical dissociation which may be significant above 300{degree}C should be utilized for the treatment before liquefaction. The high-temperature soaking in a recycle oil was proposed to dissociate coal complexes.

  15. Preconversion processing of bituminous coals: New directions to improved direct catalytic coal liquefaction. [Effect of preconversion heat soak with coal liquids

    Energy Technology Data Exchange (ETDEWEB)

    1992-07-01

    A study of the high-temperature soaking started in this quarter, following the installation of reactors in the previous quarter. Two high-volatile bituminous coals and three coal liquids, which were identified in the previous report, were used. A cross-linked, three-dimensional macromolecular model has been widely accepted f or the structure of coal, but there is no direct evidence to prove this model. The conventional coal structure model has been recently re-examined by this investigator because of the importance of relatively strong intra- and intermolecular interactions in bituminous coals. It was reasonable to deduce that significant portions were physically associated after a study of multistep extractions, associative equilibria, the irreversibility and the dependence of coal concentration on solvent swelling, and consideration of the monophase concept. Physical dissociation which may be significant above 300{degree}C should be utilized for the treatment before liquefaction. The high-temperature soaking in a recycle oil was proposed to dissociate coal complexes.

  16. 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.

  17. Identification of amino acids related to catalytic function of Sulfolobus solfataricus P1 carboxylesterase by site-directed mutagenesis and molecular modeling

    Science.gov (United States)

    Choi, Yun-Ho; Lee, Ye-Na; Park, Young-Jun; Yoon, Sung-Jin; Lee, Hee-Bong

    2016-01-01

    The archaeon Sulfolobus solfataricus P1 carboxylesterase is a thermostable enzyme with a molecular mass of 33.5 kDa belonging to the mammalian hormone-sensitive lipase (HSL) family. In our previous study, we purified the enzyme and suggested the expected amino acids related to its catalysis by chemical modification and a sequence homology search. For further validating these amino acids in this study, we modified them using site-directed mutagenesis and examined the activity of the mutant enzymes using spectrophotometric analysis and then estimated by homology modeling and fluorescence analysis. As a result, it was identified that Ser151, Asp244, and His274 consist of a catalytic triad, and Gly80, Gly81, and Ala152 compose an oxyanion hole of the enzyme. In addition, it was also determined that the cysteine residues are located near the active site or at the positions inducing any conformational changes of the enzyme by their replacement with serine residues. [BMB Reports 2016; 49(6): 349-354] PMID:27222124

  18. Creation of domains by direct electron beam writing in magnesium-doped LiNbO{sub 3} and LiNbO{sub 3}:Fe single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Palatnikov, M.N. [Institute of Chemistry and Technology of Rare Elements and Mineral Raw Materials, 26a Akademgorodok, Apatity, Murmansk 184209 (Russian Federation); Kokhanchik, L.S.; Emelin, E.V. [Institute of Microelectronics Technology and High Purity Materials of Russian Academy of Sciences, 6 Academician Ossipyan st, Chernogolovka, Moscow 142432 (Russian Federation); Sidorov, N.V. [Institute of Chemistry and Technology of Rare Elements and Mineral Raw Materials, 26a Akademgorodok, Apatity, Murmansk 184209 (Russian Federation); Manukovskaya, D.V., E-mail: deenka@yandex.ru [Institute of Chemistry and Technology of Rare Elements and Mineral Raw Materials, 26a Akademgorodok, Apatity, Murmansk 184209 (Russian Federation)

    2016-03-01

    Highlights: • The periodic domains are created in crystal LiNbO{sub 3}:Mg by direct electron beam writing. • Periodic domains appear only at equilibrium between switching and screening times. • Equilibrium exists in crystal co-doped by Fe. • Shape and appearance of domains depend on the conductivity type. - Abstract: Domain structures in the Z-cut of highly doped LiNbO{sub 3}:Mg and LiNbO{sub 3}:Mg,Fe single crystals were created by direct electron beam writing (DEBW). It was found that the value and type of electron conductivity influence the shape and number of domains thus created. Controlled electron beam regular domains were created only in samples of the crystal LiNbO{sub 3}:Mg,Fe [MgO] = 5.16 mol.%, [Fe] = 0.007 mol.%. In highly doped LiNbO{sub 3}:Mg ([MgO] = 5.19 mol.%) crystal, the domains were formed chaotically and controlled creation of domains did not occur. The domain shapes were analyzed in the framework of the theory of screening of domain nuclei depolarizing electric fields and the influence of screening on the final shape of domains. It was found that screening of intrinsic electric fields is faster in the LiNbO{sub 3}:Mg,Fe crystal. This crystal has a high electronic conductivity of hopping type with a high mobility of charge carriers. Thus, a small amount of Fe provides equilibrium between the ferroelectric switching velocity and screening of the depolarizing electric field velocity. The results are discussed considering differences in the electron conductivity mechanisms, which control the screening of depolarizing electric field velocity and spatial charge area formed under an electron beam.

  19. Direct visualization of tear film on soft contact lens using ultra-high resolution spectral domain optical coherence tomography

    Science.gov (United States)

    Wang, Jianhua; Jiao, Shuliang; Ruggeri, Marco; Wehbe, Hassan M.

    2008-02-01

    The integrity of the tear film on the surface of contact lenses is essential to maintaining visual clarity and the overall health of the superficial structures of the eye (cornea and conjunctiva) for contact lens wearers. It is very critical to evaluate pre- and post-lens tear films in contact lens practice to make sure the lens is properly fitted. Improper lens fitting may cause ocular discomfort, visual distortion and ocular infection. It is very often for soft contact lens wearers to experience dry eye, especially in the afternoon after wearing the lens for a period of time. Dry eye has been a common cause of contact lens drop-off. There is currently no method available to directly visualize the tears on and underneath the contact lens in situ on human eye, mainly due to the extremely difficulty in imaging the micrometer-thin tear layer. An ultra-high resolution spectral domain optical coherence tomography has been developed with a telecentric light delivery system mounted with a slit-lamp. The system has a 3 micrometer depth resolution with a scan width up to 15 mm. The system was used to image soft contact lenses on the human eye. For the first time to our knowledge, tear films on the center and edge of the soft contact lens were directly visualized in vivo.

  20. Statistical characteristic in time-domain of direct current corona-generated audible noise from conductor in corona cage

    Science.gov (United States)

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

    2016-03-01

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

  1. 2.0A resolution crystal structures of the ternary complexes of human phenylalanine hydroxylase catalytic domain with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine or L-norleucine: substrate specificity and molecular motions related to substrate binding.

    Science.gov (United States)

    Andersen, Ole Andreas; Stokka, Anne J; Flatmark, Torgeir; Hough, Edward

    2003-10-31

    The crystal structures of the catalytic domain of human phenylalanine hydroxylase (hPheOH) in complex with the physiological cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) and the substrate analogues 3-(2-thienyl)-L-alanine (THA) or L-norleucine (NLE) have been determined at 2.0A resolution. The ternary THA complex confirms a previous 2.5A structure, and the ternary NLE complex shows that similar large conformational changes occur on binding of NLE as those observed for THA. Both structures demonstrate that substrate binding triggers structural changes throughout the entire protomer, including the displacement of Tyr138 from a surface position to a buried position at the active site, with a maximum displacement of 20.7A for its hydroxyl group. Two hinge-bending regions, centred at Leu197 and Asn223, act in consort upon substrate binding to create further large structural changes for parts of the C terminus. Thus, THA/L-Phe binding to the active site is likely to represent the epicentre of the global conformational changes observed in the full-length tetrameric enzyme. The carboxyl and amino groups of THA and NLE are positioned identically in the two structures, supporting the conclusion that these groups are of key importance in substrate binding, thus explaining the broad non-physiological substrate specificity observed for artificially activated forms of the enzyme. However, the specific activity with NLE as the substrate was only about 5% of that with THA, which is explained by the different affinities of binding and different catalytic turnover.

  2. Expression and Characterization of Catalytic Domain of T Cell Protein Tyrosine Phosphatase(ΔTC-PTP)——Immunohistochemical Study of ΔTC-PTP Expression in Non-small Cell Lung Carcinomas

    Institute of Scientific and Technical Information of China (English)

    ZHU Zhi-cheng; SUN Mei; ZHANG Xing-yi; LIU Ke-xiang; SHI Dong-lei; LI Jin-dong; SU Ji-quan; XU Yue-chi; FU Xue-qi

    2007-01-01

    This study objective was to express and characterize the catalytic domain of the human T cell protein tyrosine phosphatase(ΔTC-PTP) and to study immunohistochemically the expression of ΔTC-PTP in human non-small cell lung cancers. ΔTC-PTP gene was PCR amplified with the cDNA of human TC-PTP as template, and cloned into the pT7 expression vector. The recombinant pT7-ΔTC-PTP was expressed in E.coli Rosetta(DE3) host cells and purified. The enzymatic characteristics of ΔTC-PTP including enzyme activity and kinetics assay were measured. The antiserum was prepared by immunizing rabbit with the purified recombinant ΔTC-PTP. Rabbit polyclonal antibody against ΔTC-PTP was purified by PVDF immobilized antigen affinity chromatography. Immunohistochemical staining of lung cancer tissues was performed with antibody against ΔTC-PTP protein. ΔTC-PTP gene was correctly cloned, expressed, and purified. The recombinant ΔTC-PTP had a highly catalytic activity of PTPase. Squamous cell lung carcinoma showed a significantly higher expression rate of ΔTC-PTP(76.92%, 10/13) than adenocarcinoma(57.14%, 4/7) and normal lung tissue(20%, 1/5). This study represents the first demonstration that ΔTC-PTP is highly expressed in human squamous cell lung carcinomas. In addition, this study provides an important basis for further studying the biological function of TC-PTP and its relationship with lung carcinomas and other diseases.

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

    Directory of Open Access Journals (Sweden)

    Yu Shiratsuchi

    2015-11-01

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

  4. Lack of somatic mutations in the catalytic domains of CREBBP and EP300 genes implies a role for histone deacetylase inhibition in myeloproliferative neoplasms

    DEFF Research Database (Denmark)

    Andersen, C.L.; Grønbæk, K.; Hasselbalch, H.

    2012-01-01

    with myeloproliferative neoplasms (MPNs) has not previously been performed. DNA was purified from diagnostic samples of 56 MPN patients. We designed a mutation screening assay based on denaturing gradient gel electrophoresis and direct sequencing. Our results suggest that CREBBP and EP300 mutations are not major...... pathogenetic mechanisms of MPNs. The rationale for using HDACi in these patients seems reasonable. © 2011 Elsevier Ltd....

  5. A ROBUST PHASE-ONLY DIRECT DATA DOMAIN ALGORITHM BASED ON GENERALIZED RAYLEIGH QUOTIENT OPTIMIZATION USING HYBRID GENETIC ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    Shao Wei; Qian Zuping; Yuan Feng

    2007-01-01

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

  6. Bispecific antibodies directed to CD4 domain 2 and HIV envelope exhibit exceptional breadth and picomolar potency against HIV-1.

    Science.gov (United States)

    Pace, Craig S; Song, Ruijiang; Ochsenbauer, Christina; Andrews, Chasity D; Franco, David; Yu, Jian; Oren, Deena A; Seaman, Michael S; Ho, David D

    2013-08-13

    In the absence of an effective HIV-1 vaccine, passive immunization using broadly neutralizing Abs or Ab-like molecules could provide an alternative to the daily administration of oral antiretroviral agents that has recently shown promise as preexposure prophylaxis. Currently, no single broadly neutralizing Ab (bNAb) or combination of bNAbs neutralizes all HIV-1 strains at practically achievable concentrations in vivo. To address this problem, we created bispecific Abs that combine the HIV-1 inhibitory activity of ibalizumab (iMab), a humanized mAb directed to domain 2 of human CD4, with that of anti-gp120 bNAbs. These bispecific bNAbs (BibNAbs) exploit iMab's potent anti-HIV-1 activity and demonstrated clinical efficacy and safety to anchor and thereby concentrate a second broadly neutralizing agent at the site of viral entry. Two BibNabs, PG9-iMab and PG16-iMab, exhibit exceptional breadth and potency, neutralizing 100% of the 118 viruses tested at low picomolar concentrations, including viruses resistant to both parental mAbs. The enhanced potency of these BibNAbs was entirely dependent on CD4 anchoring, not on membrane anchoring per se, and required optimal Ab geometry and linker length. We propose that iMab-based BibNAbs, such as PG9-iMab and PG16-iMab, are promising candidates for passive immunization to prevent HIV-1 infection.

  7. Generalized focusing of time-lapse changes with applications to direct current and time-domain induced polarization inversions

    Science.gov (United States)

    Fiandaca, Gianluca; Doetsch, Joseph; Vignoli, Giulio; Auken, Esben

    2015-11-01

    Often in geophysical monitoring experiments time-lapse inversion models vary too smoothly with time, owing to the strong imprint of regularization. Several methods have been proposed for focusing the spatiotemporal changes of the model parameters. In this study, we present two generalizations of the minimum support norm, which favour compact time-lapse changes and can be adapted to the specific problem requirements. Inversion results from synthetic direct current resistivity models that mimic developing plumes show that the focusing scheme significantly improves size, shape and magnitude estimates of the time-lapse changes. Inversions of the synthetic data also illustrate that the focused inversion gives robust results and that the focusing settings are easily chosen. Inversions of full-decay time-domain induced polarization (IP) field data from a CO2 monitoring injection experiment show that the focusing scheme performs well for field data and inversions for all four Cole-Cole polarization parameters. Our tests show that the generalized minimum support norms react in an intuitive and predictable way to the norm settings, implying that they can be used in time-lapse experiments for obtaining reliable and robust results.

  8. Nonstationary Interference Excision in Time-Frequency Domain Using Adaptive Hierarchical Lapped Orthogonal Transform for Direct Sequence Spread Spectrum Communications

    Directory of Open Access Journals (Sweden)

    Zhu Yi-Sheng

    2003-01-01

    Full Text Available An adaptive hierarchical lapped orthogonal transform (HLOT exciser is proposed for tracking, localizing, and rejecting the nonstationary interference in direct sequence spread spectrum (DSSS communications. The method is based on HLOT. It utilizes a fast dynamic programming algorithm to search for the best basis, which matches the interference structure best, in a library of lapped orthogonal bases. The adaptive HLOT differs from conventional block transform and the more advanced modulated lapped transform (MLT in that the former produces arbitrary time-frequency tiling, which can be adapted to the signal structure, while the latter yields fixed tilings. The time-frequency tiling of the adaptive HLOT can be time varying, so it is also able to track the variations of the signal time-frequency structure. Simulation results show that the proposed exciser brings significant performance improvement in the presence of nonstationary time-localized interference with or without instantaneous frequency (IF information compared with the existing block transform domain excisers. Also, the proposed exciser is effective in suppressing narrowband interference and combined narrowband and time-localized impulsive interference.

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  10. 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.

  11. The influence of laser scribing on magnetic domain formation in grain oriented electrical steel visualized by directional neutron dark-field imaging

    Science.gov (United States)

    Rauscher, P.; Betz, B.; Hauptmann, J.; Wetzig, A.; Beyer, E.; Grünzweig, C.

    2016-12-01

    The performance and degree of efficiency of transformers are directly determined by the bulk magnetic properties of grain oriented electrical steel laminations. The core losses can be improved by post manufacturing methods, so-called domain refinement techniques. All these methods induce mechanical or thermal stress that refines the domain structure. The most commonly used technique is laser scribing due to the no-contact nature and the ease of integration in existing production systems. Here we show how directional neutron dark-field imaging allows visualizing the impact of laser scribing on the bulk and supplementary domain structure. In particular, we investigate the domain formation during magnetization of samples depending on laser treatment parameters such as laser energy and line distances. The directional dark-field imaging findings were quantitatively interpreted in the context with global magnetic hysteresis measurements. Especially we exploit the orientation sensitivity in the dark-field images to distinguish between different domain structures alignment and their relation to the laser scribing process.

  12. 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.

  13. Membrane docking geometry of GRP1 PH domain bound to a target lipid bilayer: an EPR site-directed spin-labeling and relaxation study.

    Directory of Open Access Journals (Sweden)

    Huai-Chun Chen

    Full Text Available The second messenger lipid PIP(3 (phosphatidylinositol-3,4,5-trisphosphate is generated by the lipid kinase PI3K (phosphoinositide-3-kinase in the inner leaflet of the plasma membrane, where it regulates a broad array of cell processes by recruiting multiple signaling proteins containing PIP(3-specific pleckstrin homology (PH domains to the membrane surface. Despite the broad importance of PIP(3-specific PH domains, the membrane docking geometry of a PH domain bound to its target PIP(3 lipid on a bilayer surface has not yet been experimentally determined. The present study employs EPR site-directed spin labeling and relaxation methods to elucidate the membrane docking geometry of GRP1 PH domain bound to bilayer-embedded PIP(3. The model target bilayer contains the neutral background lipid PC and both essential targeting lipids: (i PIP(3 target lipid that provides specificity and affinity, and (ii PS facilitator lipid that enhances the PIP(3 on-rate via an electrostatic search mechanism. The EPR approach measures membrane depth parameters for 18 function-retaining spin labels coupled to the PH domain, and for calibration spin labels coupled to phospholipids. The resulting depth parameters, together with the known high resolution structure of the co-complex between GRP1 PH domain and the PIP(3 headgroup, provide sufficient constraints to define an optimized, self-consistent membrane docking geometry. In this optimized geometry the PH domain engulfs the PIP(3 headgroup with minimal bilayer penetration, yielding the shallowest membrane position yet described for a lipid binding domain. This binding interaction displaces the PIP(3 headgroup from its lowest energy position and orientation in the bilayer, but the headgroup remains within its energetically accessible depth and angular ranges. Finally, the optimized docking geometry explains previous biophysical findings including mutations observed to disrupt membrane binding, and the rapid lateral

  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. Charge-Domain Signal Processing of Direct RF Sampling Mixer with Discrete-Time Filters in Bluetooth and GSM Receivers

    Directory of Open Access Journals (Sweden)

    Ho Yo-Chuol

    2006-01-01

    Full Text Available RF circuits for multi-GHz frequencies have recently migrated to low-cost digital deep-submicron CMOS processes. Unfortunately, this process environment, which is optimized only for digital logic and SRAM memory, is extremely unfriendly for conventional analog and RF designs. We present fundamental techniques recently developed that transform the RF and analog circuit design complexity to digitally intensive domain for a wireless RF transceiver, so that it enjoys benefits of digital and switched-capacitor approaches. Direct RF sampling techniques allow great flexibility in reconfigurable radio design. Digital signal processing concepts are used to help relieve analog design complexity, allowing one to reduce cost and power consumption in a reconfigurable design environment. The ideas presented have been used in Texas Instruments to develop two generations of commercial digital RF processors: a single-chip Bluetooth radio and a single-chip GSM radio. We further present details of the RF receiver front end for a GSM radio realized in a 90-nm digital CMOS technology. The circuit consisting of low-noise amplifier, transconductance amplifier, and switching mixer offers dB dynamic range with digitally configurable voltage gain of 40 dB down to dB. A series of decimation and discrete-time filtering follows the mixer and performs a highly linear second-order lowpass filtering to reject close-in interferers. The front-end gains can be configured with an automatic gain control to select an optimal setting to form a trade-off between noise figure and linearity and to compensate the process and temperature variations. Even under the digital switching activity, noise figure at the 40 dB maximum gain is 1.8 dB and dBm IIP2 at the 34 dB gain. The variation of the input matching versus multiple gains is less than 1 dB. The circuit in total occupies 3.1 . The LNA, TA, and mixer consume less than mA at a supply voltage of 1.4 V.

  16. Charge-Domain Signal Processing of Direct RF Sampling Mixer with Discrete-Time Filters in Bluetooth and GSM Receivers

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available RF circuits for multi-GHz frequencies have recently migrated to low-cost digital deep-submicron CMOS processes. Unfortunately, this process environment, which is optimized only for digital logic and SRAM memory, is extremely unfriendly for conventional analog and RF designs. We present fundamental techniques recently developed that transform the RF and analog circuit design complexity to digitally intensive domain for a wireless RF transceiver, so that it enjoys benefits of digital and switched-capacitor approaches. Direct RF sampling techniques allow great flexibility in reconfigurable radio design. Digital signal processing concepts are used to help relieve analog design complexity, allowing one to reduce cost and power consumption in a reconfigurable design environment. The ideas presented have been used in Texas Instruments to develop two generations of commercial digital RF processors: a single-chip Bluetooth radio and a single-chip GSM radio. We further present details of the RF receiver front end for a GSM radio realized in a 90-nm digital CMOS technology. The circuit consisting of low-noise amplifier, transconductance amplifier, and switching mixer offers 32.5 dB dynamic range with digitally configurable voltage gain of 40 dB down to 7.5 dB. A series of decimation and discrete-time filtering follows the mixer and performs a highly linear second-order lowpass filtering to reject close-in interferers. The front-end gains can be configured with an automatic gain control to select an optimal setting to form a trade-off between noise figure and linearity and to compensate the process and temperature variations. Even under the digital switching activity, noise figure at the 40 dB maximum gain is 1.8 dB and +50 dBm IIP2 at the 34 dB gain. The variation of the input matching versus multiple gains is less than 1 dB. The circuit in total occupies 3.1 mm 2 . The LNA, TA, and mixer consume less than 15.3 mA at a supply voltage of 1.4 V.

  17. The lectin domain of the polypeptide GalNAc transferase family of glycosyltransferases (ppGalNAc Ts) acts as a switch directing glycopeptide substrate glycosylation in an N- or C-terminal direction, further controlling mucin type O-glycosylation.

    Science.gov (United States)

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

    2013-07-01

    Mucin type O-glycosylation is initiated by a large family of polypeptide GalNAc transferases (ppGalNAc Ts) that add α-GalNAc to the Ser and Thr residues of peptides. Of the 20 human isoforms, all but one are composed of two globular domains linked by a short flexible linker: a catalytic domain and a ricin-like lectin carbohydrate binding domain. Presently, the roles of the catalytic and lectin domains in peptide and glycopeptide recognition and specificity remain unclear. To systematically study the role of the lectin domain in ppGalNAc T glycopeptide substrate utilization, we have developed a series of novel random glycopeptide substrates containing a single GalNAc-O-Thr residue placed near either the N or C terminus of the glycopeptide substrate. Our results reveal that the presence and N- or C-terminal placement of the GalNAc-O-Thr can be important determinants of overall catalytic activity and specificity that differ between transferase isoforms. For example, ppGalNAc T1, T2, and T14 prefer C-terminally placed GalNAc-O-Thr, whereas ppGalNAc T3 and T6 prefer N-terminally placed GalNAc-O-Thr. Several transferase isoforms, ppGalNAc T5, T13, and T16, display equally enhanced N- or C-terminal activities relative to the nonglycosylated control peptides. This N- and/or C-terminal selectivity is presumably due to weak glycopeptide binding to the lectin domain, whose orientation relative to the catalytic domain is dynamic and isoform-dependent. Such N- or C-terminal glycopeptide selectivity provides an additional level of control or fidelity for the O-glycosylation of biologically significant sites and suggests that O-glycosylation may in some instances be exquisitely controlled.

  18. Design of HIV-1 integrase inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75: a scaffold hopping approach using salicylate and catechol groups.

    Science.gov (United States)

    Fan, Xing; Zhang, Feng-Hua; Al-Safi, Rasha I; Zeng, Li-Fan; Shabaik, Yumna; Debnath, Bikash; Sanchez, Tino W; Odde, Srinivas; Neamati, Nouri; Long, Ya-Qiu

    2011-08-15

    HIV-1 integrase (IN) is a validated therapeutic target for antiviral drug design. However, the emergence of viral strains resistant to clinically studied IN inhibitors demands the discovery of novel inhibitors that are structurally as well mechanistically different. Herein, we describe the design and discovery of novel IN inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75, which is essential for the HIV-1 integration as an IN cofactor. By merging the pharmacophores of salicylate and catechol, the 2,3-dihydroxybenzamide (5a) was identified as a new scaffold to inhibit the strand transfer reaction efficiently. Further structural modifications on the 2,3-dihydroxybenzamide scaffold revealed that the heteroaromatic functionality attached on the carboxamide portion and the piperidin-1-ylsulfonyl substituted at the phenyl ring are beneficial for the activity, resulting in a low micromolar IN inhibitor (5p, IC(50)=5 μM) with more than 40-fold selectivity for the strand transfer over the 3'-processing reaction. More significantly, this active scaffold remarkably inhibited the interaction between IN and LEDGF/p75 cofactor. The prototype example, N-(cyclohexylmethyl)-2,3-dihydroxy-5-(piperidin-1-ylsulfonyl) benzamide (5u) inhibited the IN-LEDGF/p75 interaction with an IC(50) value of 8 μM. Using molecular modeling, the mechanism of action was hypothesized to involve the chelation of the divalent metal ions inside the IN active site. Furthermore, the inhibitor of IN-LEDGF/p75 interaction was properly bound to the LEDGF/p75 binding site on IN. This work provides a new and efficient approach to evolve novel HIV-1 IN inhibitors from rational integration and optimization of previously reported inhibitors.

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

    Directory of Open Access Journals (Sweden)

    Heidi J Chial

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-05

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

  1. Catalytic efficiency of designed catalytic proteins.

    Science.gov (United States)

    Korendovych, Ivan V; DeGrado, William F

    2014-08-01

    The de novo design of catalysts that mimic the affinity and specificity of natural enzymes remains one of the Holy Grails of chemistry. Despite decades of concerted effort we are still unable to design catalysts as efficient as enzymes. Here we critically evaluate approaches to (re)design of novel catalytic function in proteins using two test cases: Kemp elimination and ester hydrolysis. We show that the degree of success thus far has been modest when the rate enhancements seen for the designed proteins are compared with the rate enhancements by small molecule catalysts in solvents with properties similar to the active site. Nevertheless, there are reasons for optimism: the design methods are ever improving and the resulting catalyst can be efficiently improved using directed evolution.

  2. Poly(acrylic acid)-directed synthesis of colloidally stable single domain magnetite nanoparticles via partial oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Altan, Cem L. [Department of Chemical Engineering, Yeditepe University, Istanbul 34755 (Turkey); Laboratory of Materials and Interface Chemistry & Soft Matter cryoTEM Research Unit, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB (Netherlands); Gurten, Berna [Department of Chemical Engineering, Yeditepe University, Istanbul 34755 (Turkey); Sadza, Roel [Laboratory of Materials and Interface Chemistry & Soft Matter cryoTEM Research Unit, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB (Netherlands); Yenigul, Elcin [Department of Chemical Engineering, Yeditepe University, Istanbul 34755 (Turkey); Sommerdijk, Nico A.J.M., E-mail: n.sommerdijk@tue.nl [Laboratory of Materials and Interface Chemistry & Soft Matter cryoTEM Research Unit, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB (Netherlands); Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB (Netherlands); Bucak, Seyda, E-mail: seyda@yeditepe.edu.tr [Department of Chemical Engineering, Yeditepe University, Istanbul 34755 (Turkey)

    2016-10-15

    Octahedral, single domain magnetite nanoparticles with average size of ~55 nm were synthesized through oxidative aging of a ferrous hydroxide (Fe(OH){sub 2}) precursor at high pH in water. The synthesis was also carried out in the presence of the hydrophilic polymer poly(acrylic acid). Presence of the polymer changed the particle morphology from octahedral to spherical while average size decreased to 40–50 nm. Although these particles have a tendency to precipitate due to their high magnetic moment, dispersions of these particles were obtained in the presence of this particular polymer which made the particles stable in water for several days making them suitable for various biotechnological applications such as cell separation owing to their low toxicity. - Highlights: • Stable, single domain magnetite nanoparticles are synthesized via partial oxidation. • Particles are readily stabilized in water by a biocompatible polymer. • Steric barrier is essential for the stabilization of large magnetite nanoparticles.

  3. Direct binding of specific AUF1 isoforms to tandem zinc finger domains of tristetraprolin (TTP) family proteins.

    Science.gov (United States)

    Kedar, Vishram P; Zucconi, Beth E; Wilson, Gerald M; Blackshear, Perry J

    2012-02-17

    Tristetraprolin (TTP) is the prototype of a family of CCCH tandem zinc finger proteins that can bind to AU-rich elements in mRNAs and promote their decay. TTP binds to mRNA through its central tandem zinc finger domain; it then promotes mRNA deadenylation, considered to be the rate-limiting step in eukaryotic mRNA decay. We found that TTP and its related family members could bind to certain isoforms of another AU-rich element-binding protein, HNRNPD/AUF1, as well as a related protein, laAUF1. The interaction domain within AUF1p45 appeared to be a C-terminal "GY" region, and the interaction domain within TTP was the tandem zinc finger domain. Surprisingly, binding of AUF1p45 to TTP occurred even with TTP mutants that lacked RNA binding activity. In cell extracts, binding of AUF1p45 to TTP potentiated TTP binding to ARE-containing RNA probes, as determined by RNA gel shift assays; AUF1p45 did not bind to the RNA probes under these conditions. Using purified, recombinant proteins and a synthetic RNA target in FRET assays, we demonstrated that AUF1p45, but not AUF1p37, increased TTP binding affinity for RNA ∼5-fold. These data suggest that certain isoforms of AUF1 can serve as "co-activators" of TTP family protein binding to RNA. The results raise interesting questions about the ability of AUF1 isoforms to regulate the mRNA binding and decay-promoting activities of TTP and its family members as well as the ability of AUF1 proteins to serve as possible physical links between TTP and other mRNA decay proteins and structures.

  4. Activity of the TonEBP/OREBP transactivation domain varies directly with extracellular NaCl concentration

    OpenAIRE

    2002-01-01

    Hypertonicity-induced binding of the transcription factor TonEBP/OREBP to its cognate DNA element, ORE/TonE, is associated with increased transcription of several osmotically regulated genes. Previously, it was found that hypertonicity rapidly causes nuclear translocation and phosphorylation of TonEBP/OREBP and, more slowly, increases TonEBP/OREBP abundance. Also, the C terminus of TonEBP/OREBP was found to contain a transactivation domain (TAD). We have now tested for tonicity dependence of ...

  5. Direct interaction of the N-terminal domain of ribosomal protein S1 with protein S2 in Escherichia coli.

    Science.gov (United States)

    Byrgazov, Konstantin; Manoharadas, Salim; Kaberdina, Anna C; Vesper, Oliver; Moll, Isabella

    2012-01-01

    Despite of the high resolution structure available for the E. coli ribosome, hitherto the structure and localization of the essential ribosomal protein S1 on the 30 S subunit still remains to be elucidated. It was previously reported that protein S1 binds to the ribosome via protein-protein interaction at the two N-terminal domains. Moreover, protein S2 was shown to be required for binding of protein S1 to the ribosome. Here, we present evidence that the N-terminal domain of S1 (amino acids 1-106; S1(106)) is necessary and sufficient for the interaction with protein S2 as well as for ribosome binding. We show that over production of protein S1(106) affects E. coli growth by displacing native protein S1 from its binding pocket on the ribosome. In addition, our data reveal that the coiled-coil domain of protein S2 (S2α(2)) is sufficient to allow protein S1 to bind to the ribosome. Taken together, these data uncover the crucial elements required for the S1/S2 interaction, which is pivotal for translation initiation on canonical mRNAs in gram-negative bacteria. The results are discussed in terms of a model wherein the S1/S2 interaction surface could represent a possible target to modulate the selectivity of the translational machinery and thereby alter the translational program under distinct conditions.

  6. Classification of Land-use Based on Remote Sensing Image Texture Features with Multi-scales and Cardinal Direction Inspired by Domain Knowledge

    Directory of Open Access Journals (Sweden)

    LAN Zeying

    2016-08-01

    Full Text Available Texture features based on grey level co-occurrence matrix (GLCM are effective for image analysis, and this paper proposed a new method to construct GLCM with multi-scales and cardinal direction factors inspired by domain knowledge, in order to improve the performance of texture features and solve the uncertainty problems in image classification of land-use. By simulating the process of human visual interpretation, an integrated computation pattern of GIS and RS data were performed. Firstly, on the basis of image registration, some classic GIS spatial data mining algorithms were employed to asymptotically extract domain morphological knowledge; Next, under the responding mechanism derived from correlated analysis, an algorithm for establishing GLCM multi-scale windows that can match categories one by one, an algorithm for determining GLCM weighted cardinal direction windows that can describe observation orientation were designed based on relevant morphology indexes. Experimental results indicate that, there is a strong correlation between domain morphological knowledge and GLCM construction factors, meanwhile, with lower computational complexity, the new method can extract stable texture features to describe actual spatial meanings of complex objects, thereby improve the image classification accuracy of land-use.

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

    Institute of Scientific and Technical Information of China (English)

    YANG Wanmin; ZHOU Lian; FENG Yong; ZHANG Pingxiang; R.Nicolsky; R.de Andrade Jr

    2004-01-01

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

  8. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage

    Energy Technology Data Exchange (ETDEWEB)

    Dahlke Ojennus, Deanna; Mitton-Fry, Rachel M.; Wuttke, Deborah S. [University of Colorado, Department of Chemistry and Biochemistry (United States)

    1999-06-15

    Large residual {sup 15}N-{sup 1}H dipolar couplings have been measured in a Src homology II domain aligned at Pf1 bacteriophage concentrations an order of magnitude lower than used for induction of a similar degree of alignment of nucleic acids and highly acidic proteins. An increase in {sup 1} H and {sup 15}N protein linewidths and a decrease in T{sub 2} and T{sub 1}{rho} relaxation time constants implicates a binding interaction between the protein and phage as the mechanism of alignment. However, the associated increased linewidth does not preclude the accurate measurement of large dipolar couplings in the aligned protein. A good correlation is observed between measured dipolar couplings and predicted values based on the high resolution NMR structure of the SH2 domain. The observation of binding-induced protein alignment promises to broaden the scope of alignment techniques by extending their applicability to proteins that are able to interact weakly with the alignment medium.

  9. Constant domain-regulated antibody catalysis.

    Science.gov (United States)

    Sapparapu, Gopal; Planque, Stephanie; Mitsuda, Yukie; McLean, Gary; Nishiyama, Yasuhiro; Paul, Sudhir

    2012-10-19

    Some antibodies contain variable (V) domain catalytic sites. We report the superior amide and peptide bond-hydrolyzing activity of the same heavy and light chain V domains expressed in the IgM constant domain scaffold compared with the IgG scaffold. The superior catalytic activity of recombinant IgM was evident using two substrates, a small model peptide that is hydrolyzed without involvement of high affinity epitope binding, and HIV gp120, which is recognized specifically by noncovalent means prior to the hydrolytic reaction. The catalytic activity was inhibited by an electrophilic phosphonate diester, consistent with a nucleophilic catalytic mechanism. All 13 monoclonal IgMs tested displayed robust hydrolytic activities varying over a 91-fold range, consistent with expression of the catalytic functions at distinct levels by different V domains. The catalytic activity of polyclonal IgM was superior to polyclonal IgG from the same sera, indicating that on average IgMs express the catalytic function at levels greater than IgGs. The findings indicate a favorable effect of the remote IgM constant domain scaffold on the integrity of the V-domain catalytic site and provide a structural basis for conceiving antibody catalysis as a first line immune function expressed at high levels prior to development of mature IgG class antibodies.

  10. Poly(acrylic acid)-directed synthesis of colloidally stable single domain magnetite nanoparticles via partial oxidation

    Science.gov (United States)

    Altan, Cem L.; Gurten, Berna; Sadza, Roel; Yenigul, Elcin; Sommerdijk, Nico A. J. M.; Bucak, Seyda

    2016-10-01

    Octahedral, single domain magnetite nanoparticles with average size of ~55 nm were synthesized through oxidative aging of a ferrous hydroxide (Fe(OH)2) precursor at high pH in water. The synthesis was also carried out in the presence of the hydrophilic polymer poly(acrylic acid). Presence of the polymer changed the particle morphology from octahedral to spherical while average size decreased to 40-50 nm. Although these particles have a tendency to precipitate due to their high magnetic moment, dispersions of these particles were obtained in the presence of this particular polymer which made the particles stable in water for several days making them suitable for various biotechnological applications such as cell separation owing to their low toxicity.

  11. Activity of the TonEBP/OREBP transactivation domain varies directly with extracellular NaCl concentration.

    Science.gov (United States)

    Ferraris, Joan D; Williams, Chester K; Persaud, Prita; Zhang, Zheng; Chen, Ye; Burg, Maurice B

    2002-01-22

    Hypertonicity-induced binding of the transcription factor TonEBP/OREBP to its cognate DNA element, ORE/TonE, is associated with increased transcription of several osmotically regulated genes. Previously, it was found that hypertonicity rapidly causes nuclear translocation and phosphorylation of TonEBP/OREBP and, more slowly, increases TonEBP/OREBP abundance. Also, the C terminus of TonEBP/OREBP was found to contain a transactivation domain (TAD). We have now tested for tonicity dependence of the TAD activity of the 983 C-terminal amino acids of TonEBP/OREBP. HepG2 cells were cotransfected with a reporter construct and one of several TAD expression vector constructs. The reporter construct contained GAL4 DNA binding elements, a minimal promoter, and the Photinus luciferase gene. TAD expression vectors generate chimeras comprised of the GAL4 DNA binding domain fused to (i) the 983 C-terminal amino acids of TonEBP/OREBP, (ii) 17 glutamine residues, (iii) the TAD of c-Jun, or (iv) no TAD. All TAD-containing chimeras were functional at normal extracellular osmolality (300 mosmol/kg), but the activity only of the chimera containing the 983 C-terminal amino acids of TonEBP/OREBP varied with extracellular NaCl concentration, decreasing by >80% at 200 mosmol/kg and increasing 8-fold at 500 mosmol/kg. The chimera containing the 983 C-terminal amino acids of TonEBP/OREBP was constitutively localized to the nucleus and showed tonicity-dependent posttranslational modification consistent with phosphorylation. The activity at 500 mosmol/kg was reduced by herbimycin, a tyrosine kinase inhibitor and by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, a protein kinase CK2 inhibitor. Thus, the 983 C-terminal amino acids of TonEBP/OREBP contain a TAD that is regulated osmotically, apparently by tonicity-dependent phosphorylation.

  12. Experimental demonstration of half cycle 64-QAM Nyquist-SCM direct-detection optical communication system with data-aided estimation and overlap frequency-domain equalization

    Science.gov (United States)

    Li, Danyu; He, Jing; Tang, Jin; Chen, Ming; Chen, Lin

    2014-12-01

    A half cycle 64-quadrature amplitude modulation (QAM) Nyquist subcarrier modulation (SCM) polarization division multiplexing (PDM) intensity modulation direct detection optical communication system is experimentally demonstrated. At the receiver, training sequences-based channel estimation and an overlap frequency domain equalization method are proposed to enhance the system performance. The experimental results show that the half cycle 64-QAM Nyquist-SCM PDM signal can be transmitted over 43-km standard single-mode fibers with a bit error rate below the forward error coding threshold of 2.4×10-2.

  13. The methoxychlor metabolite, HPTE, directly inhibits the catalytic activity of cholesterol side-chain cleavage (P450scc) in cultured rat ovarian cells.

    Science.gov (United States)

    Akgul, Yucel; Derk, Raymond C; Meighan, Terence; Rao, K Murali Krishna; Murono, Eisuke P

    2008-01-01

    Exposure to the pesticide methoxychlor in rodents is linked to impaired steroid production, ovarian atrophy and reduced fertility. Following in vivo administration, it is rapidly converted by the liver to 2,2-bis-(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE), the reported active metabolite. Both methoxychlor and HPTE have weak estrogenic and antiandrogenic activities, and these effects are thought to be mediated through the estrogen and androgen receptors, respectively. Previous in vivo studies on methoxychlor exposure to female animals have demonstrated decreased progesterone production but no change in serum estrogen levels. We recently showed that HPTE specifically inhibits the P450 cholesterol side-chain cleavage (P450scc, CYP11A1) step resulting in decreased androgen production by cultured rat testicular Leydig cells. The current studies examined the mechanism of action of HPTE on progesterone production by cultured ovarian cells (granulosa and theca-interstitial) from pregnant mare serum gonadotropin-primed immature rats. In addition, we evaluated whether the effects of HPTE on rat ovarian cell progesterone biosynthesis were mediated through the estrogen or androgen receptors. Exposure to HPTE (0, 10, 50 or 100nM) alone progressively inhibited progesterone formation in cultured theca-interstitial and granulosa cells and the P450scc catalytic activity in theca-interstitial cells in a dose-dependent manner with significant declines starting at 50nM. However, HPTE did not change mRNA levels of the P450scc system (P450scc, adrenodoxin reductase and adrenodoxin) as well as P450scc protein levels. Of interest, estradiol, xenoestrogens (bisphenol-A or 4-tert-octylphenol), a pure antiestrogen (ICI 182,780), or antiandrogens (4-hydroxyflutamide or the vinclozolin metabolite M-2), had no effect on progesterone production even at 1000nM. Co-treatment of HPTE with ICI 182,780 did not block the effect of HPTE on progesterone formation. These studies suggest that the

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

    Institute of Scientific and Technical Information of China (English)

    于秀敏; 董伟; 嵇全喜

    2011-01-01

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

  15. Application of tungsten-based catalytic materials to direct alcohol fuel cell production%钨基催化材料在直接醇类燃料电池中的应用研究

    Institute of Scientific and Technical Information of China (English)

    刘喜慧; 周阳; 梁福永; 曲慧男; 温和瑞

    2015-01-01

    直接醇类燃料电池(DAFC)具有能量密度高、携带方便以及环境友好等优点。电极催化剂是改善DAFC性能的关键材料,目前DAFC催化剂要解决的关键问题是提高催化剂的电催化活性、抗CO等中间产物毒化能力以及降低催化剂成本,文中综述了2种钨基催化材料的制备、性能表征及其在DAFC中的应用研究进展,指出了目前钨基复合催化剂需要重点研究的基础问题。%Direct alcohol fuel cell (DAFC) has the advantages of high energy density , convenient packaging and environment friendliness. The key problem of anode catalyst for DAFC is how to improve the catalytic activity of anodic oxidation, and enhance the ability of resistance to CO poisoning and lower the price of catalyst. This paper reviews the synthesis , electric catalytic properties and applications in DAFC of two kinds of tungsten-based catalysts. The existing basic problems of tungsten-based composite catalysts are proposed.

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

    KAUST Repository

    Guermond, Jean-Luc

    2012-01-01

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

  17. Designing on-demand education for simultaneous development of domain-specific and self-directed learning skills

    NARCIS (Netherlands)

    Taminiau, Elisabeth M C; Kester, L.; Corbalan, G.; Spector, J. M.; Kirschner, P. A.; Van Merriënboer, J. J G

    2015-01-01

    On-demand education enables individual learners to choose their learning pathways according to their own learning needs. They must use self-directed learning (SDL) skills involving self-assessment and task selection to determine appropriate pathways for learning. Learners who lack these skills must

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

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

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

  19. Signal transduction by the formyl peptide receptor. Studies using chimeric receptors and site-directed mutagenesis define a novel domain for interaction with G-proteins.

    Science.gov (United States)

    Amatruda, T T; Dragas-Graonic, S; Holmes, R; Perez, H D

    1995-11-24

    The binding of small peptide ligands to high affinity chemoattractant receptors on the surface of neutrophils and monocytes leads to activation of heterotrimeric G-proteins, stimulation of phosphatidylinositol-phospholipase C (PI-PLC), and subsequently to the inflammatory response. It was recently shown (Amatruda, T. T., Gerard, N. P., Gerard, C., and Simon, M. I. (1993) J. Biol. Chem. 268, 10139-10144) that the receptor for the chemoattractant peptide C5a specifically interacts with G alpha 16, a G-protein alpha subunit of the Gq class, to trigger ligand-dependent stimulation of PI-PLC in transfected cells. In order to further characterize this chemoattractant peptide signal transduction pathway, we transfected cDNAs encoding the formylmethionylleucylphenylalanine receptor (fMLPR) into COS cells and measured the production of inositol phosphates. Ligand-dependent activation of PI-PLC was seen in COS cells transfected with the fMLPR and G alpha 16 and stimulated with fMLP but not in cells transfected with receptor alone or with receptor plus G alpha q. Chimeric receptors in which the N-terminal extracellular domain, the second intracellular domain, or the intracellular C-terminal tail of the fMLP receptor was replaced with C5a receptor domains (Perez, H. D., Holmes, R., Vilander, L. R., Adams, R. R., Manzana, W., Jolley, D., and Andrews, W. H. (1993) J. Biol. Chem. 268, 2292-2295) were capable of ligand-dependent activation of PI-PLC when co-transfected with G alpha 16. A chimeric receptor exchanging the first intracellular domain of the fMLPR was constitutively activated, stimulating PI-PLC in the absence of ligand. Constitutive activation of PI-PLC, to a level 233% of that seen in cells transfected with wild-type fMLP receptors, was dependent on G alpha 16. Site-directed mutagenesis of the first intracellular domain of the fMLPR (amino acids 54-62) reveals this to be a domain necessary for ligand-dependent activation of G alpha 16. These results suggest that

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

    Directory of Open Access Journals (Sweden)

    Dagmara Zlotkowska

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

  1. Magnetic, high-field EPR studies and catalytic activity of Schiff base tetranuclear CuII2FeIII2 complexes obtained by direct synthesis.

    Science.gov (United States)

    Nesterova, Oksana V; Chygorin, Eduard N; Kokozay, Vladimir N; Bon, Volodymyr V; Omelchenko, Irina V; Shishkin, Oleg V; Titiš, Ján; Boča, Roman; Pombeiro, Armando J L; Ozarowski, Andrew

    2013-12-28

    Two novel heterometallic complexes [Cu2Fe2(HL(1))2(H2L(1))2]·10DMSO (1) and [Cu2Fe2(HL(2))2(H2L(2))2]·2DMF (2) have been prepared using the open-air reaction of copper powder, iron(II) chloride and DMSO (1) or DMF (2) solutions of the polydentate Schiff base (H4L(1), 1; H4L(2), 2) formed in situ from salicylaldehyde (1) or 5-bromo-salicylaldehyde (2) and tris(hydroxymethyl)aminomethane. Crystallographic analysis revealed that both compounds are based on the centrosymmetric tetranuclear core {Cu(II)2Fe(III)2(μ-O)6} where metal centres are joined by μ-O bridges from the deprotonated ligands forming a nonlinear chain-like arrangement. Variable-temperature (1.8-300 K) magnetic susceptibility measurements of 1 and 2 showed a decrease of the effective magnetic moment value at low temperature, indicative of antiferromagnetic coupling (JCu-Fe/hc = -10.2 cm(-1), JFe-Fe/hc = -10.5 cm(-1) in 1, JCu-Fe/hc = -10.5 cm(-1), JFe-Fe/hc = -8.93 cm(-1) in 2) between the magnetic centres in both compounds. They reveal an exceptionally high catalytic activity in the oxidation of cyclohexane with hydrogen peroxide under mild conditions, with the best observed yield/TON combined values of 36%/596 and 44%/1.1 × 10(3) for 1 and 2, respectively.

  2. Study on Direct Synthesis of Diphenyl Carbonate with Heterogeneous Catalytic Reaction (Ⅵ) Effect of Sn Loading Method and Content on Activity of Sn-Pd Supported Catalyst

    Institute of Scientific and Technical Information of China (English)

    张光旭; 吴元欣; 马沛生; 田崎峰; 吴广文; 李定或

    2004-01-01

    The compound metal oxide LaxPbyMnzO used as support was prepared by the sol-gel method, and the catalyst in which Pd was used as active component and Sn as co-active component for direct synthesis of diphenyl carbonate (DPC) with heterogeneous catalytic reaction was obtained by co-calcination and precipitation respectively.The catalyst was characterized by XRD, SEM and TEM respectively. The specific surface area of catalysts was measured by ChemBET3000 instrument, and the activity of the catalysts was tested by the synthesis of DPC in a pressured reactor. The results showed that when the co-active component Sn was added by co-calcination method A, its loading content was equal to 14.43% and active component Pd was loaded by precipitation, the yield and selectivity of DPC could reach 26.78% and 99% respectively.

  3. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    The domain concept, originally suggested by Schmidt-Rohr in the 1930’s (as credited in Fishman’s writings in the 1970s), was an attempt to sort out different areas of language use in multilingual societies, which are relevant for language choice. In Fishman’s version, domains were considered...... not described in terms of domains, and recent research e.g. about the multilingual communities in the Danish-German border area seems to confirm this....

  4. Mechanism of Neutralization of Herpes Simplex Virus by Antibodies Directed at the Fusion Domain of Glycoprotein B

    Science.gov (United States)

    Fontana, Juan; Huang, Zhen-Yu; Whitbeck, J. Charles; Atanasiu, Doina; Rao, Samhita; Shelly, Spencer S.; Lou, Huan; Ponce de Leon, Manuel; Steven, Alasdair C.; Eisenberg, Roselyn J.; Cohen, Gary H.

    2014-01-01

    ABSTRACT Glycoprotein B (gB), the fusogen of herpes simplex virus (HSV), is a class III fusion protein with a trimeric ectodomain of known structure for the postfusion state. Seen by negative-staining electron microscopy, it presents as a rod with three lobes (base, middle, and crown). gB has four functional regions (FR), defined by the physical location of epitopes recognized by anti-gB neutralizing monoclonal antibodies (MAbs). Located in the base, FR1 contains two internal fusion loops (FLs) and is the site of gB-lipid interaction (the fusion domain). Many of the MAbs to FR1 are neutralizing, block cell-cell fusion, and prevent the association of gB with lipid, suggesting that these MAbs affect FL function. Here we characterize FR1 epitopes by using electron microscopy to visualize purified Fab-gB ectodomain complexes, thus confirming the locations of several epitopes and localizing those of MAbs DL16 and SS63. We also generated MAb-resistant viruses in order to localize the SS55 epitope precisely. Because none of the epitopes of our anti-FR1 MAbs mapped to the FLs, we hyperimmunized rabbits with FL1 or FL2 peptides to generate polyclonal antibodies (PAbs). While the anti-FL1 PAb failed to bind gB, the anti-FL2 PAb had neutralizing activity, implying that the FLs become exposed during virus entry. Unexpectedly, the anti-FL2 PAb (and the anti-FR1 MAbs) bound to liposome-associated gB, suggesting that their epitopes are accessible even when the FLs engage lipid. These studies provide possible mechanisms of action for HSV neutralization and insight into how gB FR1 contributes to viral fusion. IMPORTANCE For herpesviruses, such as HSV, entry into a target cell involves transfer of the capsid-encased genome of the virus to the target cell after fusion of the lipid envelope of the virus with a lipid membrane of the host. Virus-encoded glycoproteins in the envelope are responsible for fusion. Antibodies to these glycoproteins are important biological tools, providing a

  5. Method of fabricating a catalytic structure

    Science.gov (United States)

    Rollins, Harry W.; Petkovic, Lucia M.; Ginosar, Daniel M.

    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.

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

    Science.gov (United States)

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

    2015-12-15

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

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

    Directory of Open Access Journals (Sweden)

    Robert A. Baldock

    2015-12-01

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

  8. Enhanced photo-catalytic activity of Sr and Ag co-doped TiO2 nanoparticles for the degradation of Direct Green-6 and Reactive Blue-160 under UV & visible light.

    Science.gov (United States)

    Naraginti, Saraschandra; Thejaswini, T V L; Prabhakaran, D; Sivakumar, A; Satyanarayana, V S V; Arun Prasad, A S

    2015-10-05

    This work is focused on sol-gel synthesis of silver and strontium co-doped TiO2 nanoparticles and their utilization as photo-catalysts in degradation of two textile dyes. Effect of pH, intensity of light, amount of photo-catalyst, concentration of dye, sensitizers, etc., were studied to optimize conditions for obtaining enhanced photo-catalytic activity of synthesized nanoparticles. XRD, BET, HR-TEM, EDAX and UV-Vis (diffused reflectance mode) techniques were used to characterize the nanoparticles. Interestingly, band gap of Sr and Ag co-doped TiO2 nanoparticles showed considerable narrowing (2.6 eV) when compared to Ag doped TiO2 (2.7 eV) and undoped TiO2 (3.17 eV) nanoparticles. Incorporation of Ag and Sr in the lattice of TiO2 could bring isolated energy levels near conduction and valence bands thus narrowing band gap. The XRD analysis shows that both Ag and Sr nanoparticles are finely dispersed on the surface of titania framework, without disturbing its crystalline structure. TEM images indicate that representative grain sizes of Ag-doped TiO2 & Sr and Ag co-doped TiO2 nanoparticles are in the range of 8-20 nm and 11-25 nm, respectively. Effective degradation of Direct Green-6 (DG-6) and Reactive Blue-160 (RB-160) under UV and visible light has been achieved using the photo-catalysts. Sr and Ag co-doped TiO2 photo-catalysts showed higher catalytic activity during degradation process in visible region when compared to Ag-doped and undoped TiO2 nanoparticles which could be attributed to the interactive effect caused by band gap narrowing and enhancement in charge separation. For confirming degradation of the dyes, total organic carbon (TOC) content was monitored periodically.

  9. Modeling magnetic photonic crystals with lossy ferrites using an efficient complex envelope alternating-direction-implicit finite-difference time-domain method.

    Science.gov (United States)

    Singh, Gurpreet; Tan, Eng Leong; Chen, Zhi Ning

    2011-04-15

    In this Letter, we present an efficient complex-envelope alternating-direction-implicit finite-difference time-domain (CE-ADI-FDTD) method for the transient analysis of magnetic photonic crystals with lossy ferrites. The proposed CE-ADI-FDTD method is generally formulated for a saturated ferrite with anisotropic permittivity tensor and ferrite loss. Auxiliary differential equations for modeling saturated ferrite and Maxwell's curl equations are first cast into a first-order differential system in a CE form. Then, by using an efficient ADI splitting formulas, the proposed CE-ADI-FDTD method is attained in a very concise form with few and simple right-hand side terms. The performance of the proposed method is validated and compared with the explicit FDTD method.

  10. Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases.

    Science.gov (United States)

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

    2008-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-08-11

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

  12. Using potassium catalytic gasification to improve the performance of solid oxide direct carbon fuel cells: Experimental characterization and elementary reaction modeling

    OpenAIRE

    Yu, Xiankai; Shi, Yixiang; Wang, Hongjian; Cai, Ningsheng; Li, Chen; Ghoniem, Ahmed F

    2013-01-01

    The performance of a solid oxide electrolyte direct carbon fuel cell (SO-DCFC) is limited by the slow carbon gasification kinetics at the typical operating temperatures of cell: 650–850 °C. To overcome such limitation, potassium salt is used as a catalyst to speed up the dry carbon gasification reactions, increasing the power density by five-fold at 700–850 °C. The cell performance is shown to be sensitive to the bed temperature, emphasizing the role of gasification rates and that of CO produ...

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

    Science.gov (United States)

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

    2015-12-01

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

  14. Electrochemical and catalytic properties of Ni/BaCe0.75Y0.25O3-δ anode for direct ammonia-fueled solid oxide fuel cells.

    Science.gov (United States)

    Yang, Jun; Molouk, Ahmed Fathi Salem; Okanishi, Takeou; Muroyama, Hiroki; Matsui, Toshiaki; Eguchi, Koichi

    2015-04-01

    In this study, Ni/BaCe0.75Y0.25O3-δ (Ni/BCY25) was investigated as an anode for direct ammonia-fueled solid oxide fuel cells. The catalytic activity of Ni/BCY25 for ammonia decomposition was found to be remarkably higher than Ni/8 mol % Y2O3-ZrO2 and Ni/Ce0.90Gd0.10O1.95. The poisoning effect of water and hydrogen on ammonia decomposition reaction over Ni/BCY25 was evaluated. In addition, an electrolyte-supported SOFC employing BaCe0.90Y0.10O3-δ (BCY10) electrolyte and Ni/BCY25 anode was fabricated, and its electrochemical performance was investigated at 550-650 °C with supply of ammonia and hydrogen fuel gases. The effect of water content in anode gas on the cell performance was also studied. Based on these results, it was concluded that Ni/BCY25 was a promising anode for direct ammonia-fueled SOFCs. An anode-supported single cell denoted as Ni/BCY25|BCY10|Sm0.5Sr0.5CoO3-δ was also fabricated, and maximum powder density of 216 and 165 mW cm(-2) was achieved at 650 and 600 °C, for ammonia fuel, respectively.

  15. Image Denoising Algorithm Based on Elliptic Directional Windows in Wavelet Domain%椭圆方向窗内的小波域图像去噪算法

    Institute of Scientific and Technical Information of China (English)

    金彩虹

    2015-01-01

    Exploiting the different spread characteristics of noise and information coefficients in the quadtree struc-ture, an image denoising algorithm based on elliptic directional windows in wavelet domain is proposed,in which the quadtree structure is first used to divide the wavelet coefficients into“noise” coefficients,“image” coefficients and “ mixture” coefficients. Then those “noise” coefficients are set to zero, and those “image” coefficients are kept completely. Finally utilizing the advantages of multidirection-selectivity, an optimal elliptic directional window is obtained, using the stein unbiased risk estimation in the wavelet domain, and those “mixture” coefficients are estimated in this optimal elliptic directional windows by minimum mean squared error criterion. The experimental results show that this method has effectively separated noise and image details, improved the accuracy of variance estimation, kept more image details and improved the peak signal-to-noise ratio.%利用噪声小波系数父子和图像小波系数父子在四叉树上的不同传播特性,首先,将小波系数区分为:噪声系数、图像系数和噪声与图像共存的系数(简称共存系数)。然后,将噪声系数置零,图像系数完整保留。最后,利用小波域内子带能量分布的方向聚类性,采用Stein无偏风险估计,为每个子带确定最佳大小的椭圆方向邻域窗,通过最小均方误差准则在该窗内对共存系数进行去噪估计。实验结果表明,该算法实现了信号和噪声的有效分离,提高了真实信号系数方差估计的准确度,在去除噪声的同时尽可能多地保留了图像的边缘细节,提高了恢复图像的PSNR值。

  16. Direct determination of tellurium and its redox speciation at the low nanogram level in natural waters by catalytic cathodic stripping voltammetry.

    Science.gov (United States)

    Biver, Marc; Quentel, François; Filella, Montserrat

    2015-11-01

    Tellurium is one of the elements recently identified as technologically critical and is becoming a new emergent contaminant. No reliable method exists for its determination in environmental samples such as natural waters. This gap is filled by the method described here; it allows the rapid detection of trace concentrations of Te(IV) and Te(VI) in surface waters by differential pulse cathodic stripping voltammetry. It is based on the proton reduction catalysed by the absorption of Te(IV) on the mercury electrode. Under our conditions (0.1 mol L(-1) HCl) a detection limit of about 5 ng L(-1) for a deposition time of 300 s is achieved. Organic matter does not represent a problem at low concentrations; higher concentrations are eliminated by adsorptive purification. Tellurium occurs primarily as Te(IV) and Te(VI) in natural waters. Thus, determining total Te requires the reduction of Te(VI) that it is not electroactive. A number of reduction procedures have been carefully evaluated and a method based on the addition of TiCl3 to the acidified samples has been proven to reduce Te(VI) at the trace level to Te(IV) reliably and quantitatively. Therefore, the procedure described allows the direct determination of total Te and its redox speciation. It is flexible, reliable and cost effective compared to any possible alternative method based on the common preconcentration-ICPMS approach. It is readily implementable as a routine method and can be deployed in the field with relative ease.

  17. Complete kinetic and thermodynamic characterization of the unisite catalytic pathway of Escherichia coli F1-ATPase. Comparison with mitochondrial F1-ATPase and application to the study of mutant enzymes.

    Science.gov (United States)

    Al-Shawi, M K; Senior, A E

    1988-12-25

    A complete analysis is presented of the component rate constants of the "unisite" reaction pathway in normal Escherichia coli F1-ATPase. Gibbs free energy profiles of the unisite reaction pathway were constructed for both normal E. coli F1 and bovine-heart mitochondrial F1, and comparison indicated that E. coli F1 is an ancestral form of the mitochondrial enzyme. Similar kinetic and thermodynamic analyses of the unisite reaction pathway were done for mutant beta-Asn-242 and beta-Val-242 E. coli F1-ATPases. Both mutations affected unisite binding and hydrolysis of MgATP but had little effect on release of products or binding of MgADP. It was apparent that a primary effect of the mutations was on the interaction between the catalytic nucleotide-binding domain and the substrate MgATP. The catalytic transition state [F1-ATP]++ was the most destabilized step in the reaction sequence. Measurements of delta delta G[F1.ATP]++ and linear free energy plots for the catalytic step were consistent with the view that, in normal enzyme, residue beta-Asp-242 accepts an H-bond from the transition-state substrate in order to facilitate catalysis. Both mutations impaired positive catalytic cooperativity. This was caused by energetic destabilization of the catalytic transition state and was an indirect effect, not a direct effect on signal transmission per se between catalytic nucleotide-binding domains on beta-subunits. Therefore, impairment of unisite catalysis and of positive catalytic cooperativity appeared to be linked. This may provide a unifying explanation as to why a series of other, widely separated mis-sense mutations within the catalytic nucleotide-binding domain on F1-beta-subunit, which have been reported to affect unisite catalysis, also impair positive catalytic cooperativity. Linear free energy plots for the ATP-binding step of unisite catalysis demonstrated that beta-Asn-242 and beta-Val-242 mutant enzymes did not suffer any gross disruptive change in structure of

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

    Directory of Open Access Journals (Sweden)

    Rajendra Kumar Singh

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

  19. The role of Y84 on domain 1 and Y87 on domain 2 of Paragonimus westermani taurocyamine kinase: Insights on the substrate binding mechanism of a trematode phosphagen kinase.

    Science.gov (United States)

    Jarilla, Blanca R; Tokuhiro, Shinji; Nagataki, Mitsuru; Uda, Kouji; Suzuki, Tomohiko; Acosta, Luz P; Agatsuma, Takeshi

    2013-12-01

    The two-domain taurocyamine kinase (TK) from Paragonimus westermani was suggested to have a unique substrate binding mechanism. We performed site-directed mutagenesis on each domain of this TK and compared the kinetic parameters Km(Tc) and Vmax with that of the wild-type to determine putative amino acids involved in substrate recognition and binding. Replacement of Y84 on domain 1 and Y87 on domain 2 with R resulted in the loss of activity for the substrate taurocyamine. Y84E mutant has a dramatic decrease in affinity and activity for taurocyamine while Y87E has completely lost catalytic activity. Substituting H and I on the said positions also resulted in significant changes in activity. Mutation of the residues A59 on the GS region of domain 1 also caused significant decrease in affinity and activity while mutation on the equivalent position on domain 2 resulted in complete loss of activity.

  20. Catalytic combustor for hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Mercea, J.; Grecu, E.; Fodor, T.; Kreibik, S.

    1982-01-01

    The performance of catalytic combustors for hydrogen using platinum-supported catalysts is described. Catalytic plates of different sizes were constructed using fibrous and ceramic supports. The temperature distribution as well as the reaction efficiency as a function of the fuel input rate was determined, and a comparison between the performances of different plates is discussed.

  1. Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD

    Science.gov (United States)

    Suh, Man-Hee; Ye, Ping; Zhang, Mincheng; Hausmann, Stéphane; Shuman, Stewart; Gnatt, Averell L.; Fu, Jianhua

    2005-01-01

    Fcp1 is an essential protein phosphatase that hydrolyzes phosphoserines within the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II). Fcp1 plays a major role in the regulation of CTD phosphorylation and, hence, critically influences the function of Pol II throughout the transcription cycle. The basic understanding of Fcp1–CTD interaction has remained ambiguous because two different modes have been proposed: the “dockingsite” model versus the “distributive” mechanism. Here we demonstrate biochemically that Fcp1 recognizes and dephosphorylates the CTD directly, independent of the globular non-CTD part of the Pol II structure. We point out that the recognition of CTD by the phosphatase is based on random access and is not driven by Pol II conformation. Results from three different types of experiments reveal that the overall interaction between Fcp1 and Pol II is not stable but dynamic. In addition, we show that Fcp1 also interacts with a region on the polymerase distinct from the CTD. We emphasize that this non-CTD site is functionally distinct from the docking site invoked previously as essential for the CTD phosphatase activity of Fcp1. We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously. PMID:16301539

  2. Formation of a “Pre-mouth Array” from the Extreme Anterior Domain Is Directed by Neural Crest and Wnt/PCP Signaling

    Directory of Open Access Journals (Sweden)

    Laura Jacox

    2016-08-01

    Full Text Available The mouth arises from the extreme anterior domain (EAD, a region where the ectoderm and endoderm are directly juxtaposed. Here, we identify a “pre-mouth array” in Xenopus that forms soon after the cranial neural crest has migrated to lie on either side of the EAD. Initially, EAD ectoderm comprises a wide and short epithelial mass that becomes narrow and tall with cells and nuclei changing shape, a characteristic of convergent extension. The resulting two rows of cells—the pre-mouth array—later split down the midline to surround the mouth opening. Neural crest is essential for convergent extension and likely signals to the EAD through the Wnt/planar cell polarity (PCP pathway. Fzl7 receptor is locally required in EAD ectoderm, while Wnt11 ligand is required more globally. Indeed, heterologous cells expressing Wnt11 can elicit EAD convergent extension. The study reveals a precise cellular mechanism that positions and contributes to the future mouth.

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

    Institute of Scientific and Technical Information of China (English)

    Zheng Zhaohui

    2004-01-01

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

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

    Science.gov (United States)

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

    2012-10-01

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

  5. Catalytic polarographic currents of oxidizers

    Energy Technology Data Exchange (ETDEWEB)

    Zajtsev, P.M.; Zhdanov, S.I.; Nikolaeva, T.D. (Vsesoyuznyj Nauchno-Issledovatel' skij Inst. Khimicheskikh Reaktivov i Osobo Chistykh Veshchestv, Moscow (USSR))

    1982-06-01

    The state of theory and practice of an important direction in polarography, i.e. catalytic currents of oxidizers-substrates that have found a wide application in the development of highly sensitive methods of determination of a large number of substrates, catalysts and polarographically nonactive ligands, is considered. Transition and some non-transition elements serve as catalysts of reactions that cause catalytic polarographic currents of substrates. Catalytic activity of an inorganic catalyst increases with the increase in the number of its d-orbit. Complex formation in most cases leads to the increase of catalyst activity, however, sometimes a reverse phenomenon takes place. For many catalysts the maximum activity is observed at pH values close to pK value of their hydrolysis. The properties of oxidizers-substrates is revealed by H/sub 2/O/sub 2/, ClO/sub 3//sup -/, BrO/sub 3//sup -/, IO/sub 3//sup -/, ClO/sub 4//sup -/, IO/sub 4//sup -/, NO/sub 2//sup -/, NO/sub 3//sup -/, NH/sub 2/OH, V(5), V(4), S/sub 2/O/sub 8//sup 2 -/, H/sub 2/SO/sub 4/, H/sub 2/C/sub 2/O/sub 4/, COHCOOH, alkenes compounds, organic halogen , sulfur- and amine-containing compounds.

  6. Facile electrochemical co-deposition of a graphene-cobalt nanocomposite for highly efficient water oxidation in alkaline media: direct detection of underlying electron transfer reactions under catalytic turnover conditions.

    Science.gov (United States)

    Guo, Si-Xuan; Liu, Yuping; Bond, Alan M; Zhang, Jie; Esakki Karthik, P; Maheshwaran, I; Senthil Kumar, S; Phani, K L N

    2014-09-21

    A facile electrochemical co-deposition method has been developed for the fabrication of graphene-cobalt nanocomposite modified electrodes that achieve exceptionally efficient water oxidation in highly alkaline media. In the method reported, a graphene-cobalt nanocomposite film was deposited electrochemically from a medium containing 1 mg ml(-1) graphene oxide, 0.8 mM cobalt nitrate and 0.05 M phytic acid (pH 7). The formation of the nanocomposite film was confirmed using electrochemical, Raman spectroscopic and scanning electron microscopic techniques. The nanocomposite film exhibits excellent activity and stability towards water oxidation to generate oxygen in 1 M NaOH aqueous electrolyte media. A turn over frequency of 34 s(-1) at an overpotential of 0.59 V and a faradaic efficiency of 97.7% were deduced from analysis of data obtained by rotating ring disk electrode voltammetry. Controlled potential electrolysis data suggests that the graphene supported catalyst exhibits excellent stability under these harsh conditions. Phytate anion acts as stabilizer for the electrochemical formation of cobalt nanoparticles. Fourier transformed ac voltammetry allowed the redox chemistry associated with catalysis to be detected directly under catalytic turnover conditions. Estimates of formal reversible potentials obtained from this method and derived from the overall reactions 3Co(OH)2 + 2OH(-) ⇌ Co3O4 + 4H2O + 2e(-), Co3O4 + OH(-) ⇌ 3CoOOH + e(-) and CoOOH + OH(-) ⇌ CoO2 + H2O + e(-) are 0.10, 0.44 and 0.59 V vs. Ag/AgCl, respectively.

  7. Phase matching method for echo detection in direct data domain%直接数据域的相位匹配回波检测

    Institute of Scientific and Technical Information of China (English)

    幸高翔; 艾锐峰; 蔡志明; 虢应华

    2013-01-01

    提出了一种利用相位匹配直接提取接收数据中的目标回波以进行主动声纳混响抑制、回波检测的新方法.该方法首先构造子阵化的直接数据域波束形成,得到期望信号方向的若干波束输出序列;然后利用序列中信号相位与目标方位的依从性,直接解算出回波序列;再通过设计对应的检测量进行目标检测.区别于传统相关接收和空时自适应处理(space-time adaptive processing,STAP)的方法,该方法无需考虑混响与信号的相关性和统计特性.通过试验分析,新方法较传统方法具备更好的检测性能.%A new method is proposed to extract the echo of targets from the receiving data with phase matching for the case of reverberation suppression and echo detection of active sonars. First, the sub-arrayed direct data domain beam-forming is constructed to obtain the output time sequences in signal orientation. Second, the echo of targets is calculated by using the relationship between signal phase and object orientation from output sequences. Then, some special functions are designed for detection in this scene. Unlike the traditional correlation techniques and space-time adaptive processing (STAP) methods, the proposed method does not need to know the statistical properties and correlation between signals and reverberation. By the analysis of experimental data, it is verified to be more efficient than the conventional process.

  8. Catalytic Functions of Standards

    NARCIS (Netherlands)

    K. Blind (Knut)

    2009-01-01

    textabstractThe three different areas and the examples have illustrated several catalytic functions of standards for innovation. First, the standardisation process reduces the time to market of inventions, research results and innovative technologies. Second, standards themselves promote the diffusi

  9. Catalytic Synthesis Lactobionic Acid

    Directory of Open Access Journals (Sweden)

    V.G. Borodina

    2014-07-01

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

  10. Catalytic distillation process

    Science.gov (United States)

    Smith, Jr., Lawrence A.

    1982-01-01

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

  11. 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.

  12. 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.

  13. SOFC system with integrated catalytic fuel processing

    Science.gov (United States)

    Finnerty, Caine; Tompsett, Geoff. A.; Kendall, Kevin; Ormerod, R. Mark

    In recent years, there has been much interest in the development of solid oxide fuel cell technology operating directly on hydrocarbon fuels. The development of a catalytic fuel processing system, which is integrated with the solid oxide fuel cell (SOFC) power source is outlined here. The catalytic device utilises a novel three-way catalytic system consisting of an in situ pre-reformer catalyst, the fuel cell anode catalyst and a platinum-based combustion catalyst. The three individual catalytic stages have been tested in a model catalytic microreactor. Both temperature-programmed and isothermal reaction techniques have been applied. Results from these experiments were used to design the demonstration SOFC unit. The apparatus used for catalytic characterisation can also perform in situ electrochemical measurements as described in previous papers [C.M. Finnerty, R.H. Cunningham, K. Kendall, R.M. Ormerod, Chem. Commun. (1998) 915-916; C.M. Finnerty, N.J. Coe, R.H. Cunningham, R.M. Ormerod, Catal. Today 46 (1998) 137-145]. This enabled the performance of the SOFC to be determined at a range of temperatures and reaction conditions, with current output of 290 mA cm -2 at 0.5 V, being recorded. Methane and butane have been evaluated as fuels. Thus, optimisation of the in situ partial oxidation pre-reforming catalyst was essential, with catalysts producing high H 2/CO ratios at reaction temperatures between 873 K and 1173 K being chosen. These included Ru and Ni/Mo-based catalysts. Hydrocarbon fuels were directly injected into the catalytic SOFC system. Microreactor measurements revealed the reaction mechanisms as the fuel was transported through the three-catalyst device. The demonstration system showed that the fuel processing could be successfully integrated with the SOFC stack.

  14. SOFC system with integrated catalytic fuel processing

    Energy Technology Data Exchange (ETDEWEB)

    Finnerty, C.; Tompsett, G.A.; Kendall, K.; Ormerod, R.M. [Birchall Centre for Inorganic Chemistry and Materials Science, Keele Univ. (United Kingdom)

    2000-03-01

    In recent years, there has been much interest in the development of solid oxide fuel cell technology operating directly on hydrocarbon fuels. The development of a catalytic fuel processing system, which is integrated with the solid oxide fuel cell (SOFC) power source is outlined here. The catalytic device utilises a novel three-way catalytic system consisting of an in situ pre-reformer catalyst, the fuel cell anode catalyst and a platinum-based combustion catalyst. The three individual catalytic stages have been tested in a model catalytic microreactor. Both temperature-programmed and isothermal reaction techniques have been applied. Results from these experiments were used to design the demonstration SOFC unit. The apparatus used for catalytic characterisation can also perform in situ electrochemical measurements as described in previous papers [C.M. Finnerty, R.H. Cunningham, K. Kendall, R.M. Ormerod, Chem. Commun. (1998) 915-916; C.M. Finnerty, N.J. Coe, R.H. Cunningham, R.M. Ormerod, Catal. Today 46 (1998) 137-145]. This enabled the performance of the SOFC to be determined at a range of temperatures and reaction conditions, with current output of 290 mA cm{sup -2} at 0.5 V, being recorded. Methane and butane have been evaluated as fuels. Thus, optimisation of the in situ partial oxidation pre-reforming catalyst was essential, with catalysts producing high H{sub 2}/CO ratios at reaction temperatures between 873 K and 1173 K being chosen. These included Ru and Ni/Mo-based catalysts. Hydrocarbon fuels were directly injected into the catalytic SOFC system. Microreactor measurements revealed the reaction mechanisms as the fuel was transported through the three-catalyst device. The demonstration system showed that the fuel processing could be successfully integrated with the SOFC stack. (orig.)

  15. Enhanced catalytic performance for direct synthesis of dimethyl ether from syngas over a La2O3 modified Cu-ZrO2/γ-Al2O3 hybrid catalyst

    Institute of Scientific and Technical Information of China (English)

    Zhuo Li; Jianqing Li; Cheng Yang; Jinhu Wu

    2012-01-01

    A series of hybrid catalysts were made by physically mixing Cu-ZrO2 and γ-Al2O3,for former it was modified with different loadings of La2O3 prepared by co-precipitation method.The catalysts were characterized by BET,XRD,N2O-adsorption,EXAFS,H2-TPR,NH3-TPD techniques and evaluated in the synthesis of dimethyl ether from syngas.The results show that La2O3 promoted catalysts displayed a significantly better catalytic performance compared with Cu-ZrO2/γ-Al2O3 catalyst in CO conversion and DME selectivity,and the optimum catalytic activity was obtained when the content of La2O3 was 12 wt%.The characterizations reveal that high copper dispersion,facile reducibility of copper particles and appropriate amount of acidic sites are responsible for the superior catalytic performance.

  16. C2株蓝氏贾第鞭毛虫 SU MO特异性蛋白酶基因的克隆、生物信息学分析及其催化活性区的原核表达%Cloning and bioinformatics analysis of Giardia lamblia C2 strain SENP gene and prokaryotic expression of SENP catalytic domain

    Institute of Scientific and Technical Information of China (English)

    李少东; 周英斌; 刘晓莉; 禇晗; 李思瑾; 田喜凤; 王洋

    2015-01-01

    目的:克隆C2株蓝氏贾第鞭毛虫(Giardia lamblia ,简称贾第虫)的SUMO‐Specific Protease(SENP)基因,并对其序列进行生物信息学分析,原核表达贾第虫SENP的催化活性区。方法提取C2株贾第虫基因组DNA ,以基因组DNA为模板获得SENP编码区全长片段,连入克隆载体pGM‐T ,测序后进行生物信息学分析;根据分析结果克隆SENP的催化活性区,构建其原核表达载体pET‐28a(+)‐SENPc ,在 E .coli Rosetta(DE3)中诱导表达,SDS‐PAGE及Western blot观察表达结果。结果成功克隆了C2株贾第虫SENP编码区全长序列,生物信息学分析显示C2株贾第虫SENP蛋白序列与WB株相同,二级结构以无规则卷曲为主,其催化活性区位于126‐497aa ,被一段插入序列分割成两个部分;构建了SENP催化活性区原核表达载体并在大肠杆菌中高效表达,在相对分子量约43 kD的位置出现目的蛋白条带,与理论值相符。结论成功克隆了贾第虫SENP基因并原核表达了其催化活性区,为贾第虫SENP蛋白功能的研究提供了基础。%SUMOylation is a post‐translational modification involved in various cellular processes .SUMO‐specific protease (SENP) regulates SUMOylation by removing SUMO from conjugated substrates (deSUMOylation) and promoting maturation of SUMO precursor .In order to express Giardia lambia (C2 strain) SENP catalytic domain in E .coli ,the full‐length open reading frame of SENP was amplified by PCR from Giardia lamblia genome DNA .The PCR product about 1 620 bp was cloned into cloning vector pGM‐T .Sequencing result showed the sequence of SENP in C2 strain was identical with that in Gi‐ardia WB strain .Bioinformatics analysis showed that SENP protein possessed a 372 aa discontinuous ULP catalytic domain at C‐terminal .The catalytic domain of SENP was cloned into prokaryotic expression vector pET‐28a(+ ) .The recombinant vector pET‐28a

  17. Catalytic hydrotreating process

    Science.gov (United States)

    Karr, Jr., Clarence; McCaskill, Kenneth B.

    1978-01-01

    Carbonaceous liquids boiling above about 300.degree. C such as tars, petroleum residuals, shale oils and coal-derived liquids are catalytically hydrotreated by introducing the carbonaceous liquid into a reaction zone at a temperature in the range of 300.degree. to 450.degree. C and a pressure in the range of 300 to 4000 psig for effecting contact between the carbonaceous liquid and a catalytic transition metal sulfide in the reaction zone as a layer on a hydrogen permeable transition metal substrate and then introducing hydrogen into the reaction zone by diffusing the hydrogen through the substrate to effect the hydrogenation of the carbonaceous liquid in the presence of the catalytic sulfide layer.

  18. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei

    2015-01-01

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

  19. Mechanistic insight into the function of the C-terminal PKD domain of the collagenolytic serine protease deseasin MCP-01 from deep sea Pseudoalteromonas sp. SM9913: binding of the PKD domain to collagen results in collagen swelling but does not unwind the collagen triple helix.

    Science.gov (United States)

    Wang, Yu-Kai; Zhao, Guo-Yan; Li, Yang; Chen, Xiu-Lan; Xie, Bin-Bin; Su, Hai-Nan; Lv, Yao-Hui; He, Hai-Lun; Liu, Hong; Hu, Jun; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2010-05-07

    Deseasin MCP-01 is a bacterial collagenolytic serine protease. Its catalytic domain alone can degrade collagen, and its C-terminal PKD domain is a collagen-binding domain (CBD) that can improve the collagenolytic efficiency of the catalytic domain by an unknown mechanism. Here, scanning electron microscopy (SEM), atomic force microscopy (AFM), zeta potential, and circular dichroism spectroscopy were used to clarify the functional mechanism of the PKD domain in MCP-01 collagenolysis. The PKD domain observably swelled insoluble collagen. Its collagen-swelling ability and its improvement to the collagenolysis of the catalytic domain are both temperature-dependent. SEM observation showed the PKD domain swelled collagen fascicles with an increase of their diameter from 5.3 mum to 8.8 mum after 1 h of treatment, and the fibrils forming the fascicles were dispersed. AFM observation directly showed that the PKD domain bound collagen, swelled the microfibrils, and exposed the monomers. The PKD mutant W36A neither bound collagen nor disturbed its structure. Zeta potential results demonstrated that PKD treatment increased the net positive charges of the collagen surface. PKD treatment caused no change in the content or the thermostability of the collagen triple helix. Furthermore, the PKD-treated collagen could not be degraded by gelatinase. Therefore, though the triple helix monomers were exposed, the PKD domain could not unwind the collagen triple helix. Our study reveals the functional mechanism of the PKD domain of the collagenolytic serine protease MCP-01 in collagen degradation, which is distinct from that of the CBDs of mammalian matrix metalloproteases.

  20. Expression and purification of catalytic domain of human macrophage elastase for high-throughput inhibitor screening%表达和纯化人巨噬细胞弹性蛋白酶的催化区以高通量筛选酶抑制剂

    Institute of Scientific and Technical Information of China (English)

    程东航; 沈强; 钱静; 钱蓁; 叶其壮

    2002-01-01

    目的:获得具有催化活性的人巨噬细胞弹性蛋白酶的催化区(hMECD),并建立有效的高通量筛选方法筛选其抑制剂.方法:在大肠杆菌中表达hMECD,并根据酶活性以比色法建立高通量筛选模型.对一批共8560个纯化合物和混合物进行了高通量筛选.结果:构建了有效的大肠杆菌表达系统.存在于包涵体中的表达蛋白在体外重折叠复性,经阴离子交换柱层析的方法纯化,l L大肠杆菌培养物可得到23mg纯化的活性蛋白.该蛋白的重折叠复性和酶活性需要钙锌离子,但高浓度的锌离子则抑制其重折叠复性和活性.hMECD剪切合成底物包括一个硫酯和几个荧光发生的肽类底物,并在pH 8.0显示最强的活性.对8560个化合物和混合物的高通量筛选发现了2了个纯化合物和14个天然产物在20mg/L的浓度下具有大于80%的抑制活性.结论:建立了有效的人巨噬细胞弹性蛋白酶的催化区表达和纯化的方法.该重组蛋白抑制剂的高通量筛选模型具有有效、可信和快速的特点.%AIM:To obtain a catalytically active human macrophage elastase catalytic domain (hMECD) and to establish an efficient high-throughput method for screening macrophage elastase inhibitors.METHODS:Catalytic domain of human macrophage elastase was expressed in E coli and characterized to establish a high-throughput screening assay using a colorimetric method.A set of 8560 pure compounds and mixtures were screened.RESULTS:We have constructed an efficient E coli system for this human protein expression,and the recombinant hMECD protein was purified to homogeneity using anion-exchange chromatography after in vitro refolding from inclusion bodies.The yield of active hMECD protein was 23 mg from one liter of E coli culture after purification.Calcium and zinc ions were required both in refolding and enzymatic activity,but high concentration of zinc inhibited the refolding and activity.The hMECD cleaved several

  1. Catalytic Phosphination and Arsination

    Institute of Scientific and Technical Information of China (English)

    Kwong Fuk Yee; Chan Kin Shing

    2004-01-01

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

  2. 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).

  3. 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.

  4. The Inner Centromere Protein (INCENP) Coil Is a Single α-Helix (SAH) Domain That Binds Directly to Microtubules and Is Important for Chromosome Passenger Complex (CPC) Localization and Function in Mitosis.

    Science.gov (United States)

    Samejima, Kumiko; Platani, Melpomeni; Wolny, Marcin; Ogawa, Hiromi; Vargiu, Giulia; Knight, Peter J; Peckham, Michelle; Earnshaw, William C

    2015-08-28

    The chromosome passenger complex (CPC) is a master regulator of mitosis. Inner centromere protein (INCENP) acts as a scaffold regulating CPC localization and activity. During early mitosis, the N-terminal region of INCENP forms a three-helix bundle with Survivin and Borealin, directing the CPC to the inner centromere where it plays essential roles in chromosome alignment and the spindle assembly checkpoint. The C-terminal IN box region of INCENP is responsible for binding and activating Aurora B kinase. The central region of INCENP has been proposed to comprise a coiled coil domain acting as a spacer between the N- and C-terminal domains that is involved in microtubule binding and regulation of the spindle checkpoint. Here we show that the central region (213 residues) of chicken INCENP is not a coiled coil but a ∼ 32-nm-long single α-helix (SAH) domain. The N-terminal half of this domain directly binds to microtubules in vitro. By analogy with previous studies of myosin 10, our data suggest that the INCENP SAH might stretch up to ∼ 80 nm under physiological forces. Thus, the INCENP SAH could act as a flexible "dog leash," allowing Aurora B to phosphorylate dynamic substrates localized in the outer kinetochore while at the same time being stably anchored to the heterochromatin of the inner centromere. Furthermore, by achieving this flexibility via an SAH domain, the CPC avoids a need for dimerization (required for coiled coil formation), which would greatly complicate regulation of the proximity-induced trans-phosphorylation that is critical for Aurora B activation.

  5. Mitsunobu Reactions Catalytic in Phosphine and a Fully Catalytic System.

    Science.gov (United States)

    Buonomo, Joseph A; Aldrich, Courtney C

    2015-10-26

    The Mitsunobu reaction is renowned for its mild reaction conditions and broad substrate tolerance, but has limited utility in process chemistry and industrial applications due to poor atom economy and the generation of stoichiometric phosphine oxide and hydrazine by-products that complicate purification. A catalytic Mitsunobu reaction using innocuous reagents to recycle these by-products would overcome both of these shortcomings. Herein we report a protocol that is catalytic in phosphine (1-phenylphospholane) employing phenylsilane to recycle the catalyst. Integration of this phosphine catalytic cycle with Taniguchi's azocarboxylate catalytic system provided the first fully catalytic Mitsunobu reaction.

  6. Direct interaction of the human I-mfa domain-containing protein, HIC, with HIV-1 Tat results in cytoplasmic sequestration and control of Tat activity.

    Science.gov (United States)

    Gautier, Virginie W; Sheehy, Noreen; Duffy, Margaret; Hashimoto, Kenichi; Hall, William W

    2005-11-08

    The primary function of the HIV-1 regulatory protein Tat, activation of transcription from the viral LTR, is highly regulated by complex interactions between Tat and a number of host cell proteins. Tat nuclear import, a process mediated by importin beta, is a prerequisite for its activity. Here, we report and characterize the interaction of the human inhibitor of MyoD family domain-containing protein (I-mfa), HIC, with Tat at a biochemical and a functional level. This interaction was shown to occur in vivo and in vitro and to involve the nuclear localization signal and the transactivation responsive element-binding domains of Tat and the I-mfa domain of HIC. Coexpression of HIC and Tat resulted in the down-regulation of transactivation of the HIV-1 LTR, and colocalization studies revealed the cytoplasmic sequestration of Tat by HIC. Functionally this sequestration appears to be the underlying mechanism of LTR transcriptional repression by HIC and represents a unique mechanism for the control of Tat activity and regulation of HIV-1 replication.

  7. Starch-binding domain shuffling in Aspergillus niger glucoamylase.

    Science.gov (United States)

    Cornett, Catherine A G; Fang, Tsuei-Yun; Reilly, Peter J; Ford, Clark

    2003-07-01

    Aspergillus niger glucoamylase (GA) consists mainly of two forms, GAI [from the N-terminus, catalytic domain + linker + starch-binding domain (SBD)] and GAII (catalytic domain + linker). These domains were shuffled to make RGAI (SBD + linker + catalytic domain), RGAIDeltaL (SBD + catalytic domain) and RGAII (linker + catalytic domain), with domains defined by function rather than by tertiary structure. In addition, Paenibacillus macerans cyclomaltodextrin glucanotransferase SBD replaced the closely related A.niger GA SBD to give GAE. Soluble starch hydrolysis rates decreased as RGAII approximately GAII approximately GAI > RGAIDeltaL approximately RGAI approximately GAE. Insoluble starch hydrolysis rates were GAI > RGAIDeltaL > RGAI > GAE approximately RGAII > GAII, while insoluble starch-binding capacities were GAI > RGAI > RGAIDeltaL > RGAII > GAII > GAE. These results indicate that: (i) moving the SBD to the N-terminus or replacing the native SBD somewhat affects soluble starch hydrolysis; (ii) SBD location significantly affects insoluble starch binding and hydrolysis; (iii) insoluble starch hydrolysis is imperfectly correlated with its binding by the SBD; and (iv) placing the P.macerans cyclomaltodextrin glucanotransferase SBD at the end of a linker, instead of closely associated with the rest of the enzyme, severely reduces its ability to bind and hydrolyze insoluble starch.

  8. Porous media for catalytic renewable energy conversion

    Science.gov (United States)

    Hotz, Nico

    2012-05-01

    A novel flow-based method is presented to place catalytic nanoparticles into a reactor by sol-gelation of a porous ceramic consisting of copper-based nanoparticles, silica sand, ceramic binder, and a gelation agent. This method allows for the placement of a liquid precursor containing the catalyst into the final reactor geometry without the need of impregnating or coating of a substrate with the catalytic material. The so generated foam-like porous ceramic shows properties highly appropriate for use as catalytic reactor material, e.g., reasonable pressure drop due to its porosity, high thermal and catalytic stability, and excellent catalytic behavior. The catalytic activity of micro-reactors containing this foam-like ceramic is tested in terms of their ability to convert alcoholic biofuel (e.g. methanol) to a hydrogen-rich gas mixture with low concentrations of carbon monoxide (up to 75% hydrogen content and less than 0.2% CO, for the case of methanol). This gas mixture is subsequently used in a low-temperature fuel cell, converting the hydrogen directly to electricity. A low concentration of CO is crucial to avoid poisoning of the fuel cell catalyst. Since conventional Polymer Electrolyte Membrane (PEM) fuel cells require CO concentrations far below 100 ppm and since most methods to reduce the mole fraction of CO (such as Preferential Oxidation or PROX) have CO conversions of up to 99%, the alcohol fuel reformer has to achieve initial CO mole fractions significantly below 1%. The catalyst and the porous ceramic reactor of the present study can successfully fulfill this requirement.

  9. Parkin mitochondrial translocation is achieved through a novel catalytic activity coupled mechanism

    Institute of Scientific and Technical Information of China (English)

    Xinde Zheng; Tony Hunter

    2013-01-01

    Pink1,a mitochondrial kinase,and Parkin,an E3 ubiquitin ligase,function in mitochondrial maintenance.Pink1 accumulates on depolarized mitochondria,where it recruits Parkin to mainly induce K63-1inked chain ubiquitination of outer membrane proteins and eventually mitophagy.Parkin belongs to the RBR E3 iigase family.Recently,it has been proposed that the RBR domain transfers ubiquitin to targets via a cysteine-ubiquitin enzyme intermediate,in a manner similar to HECT domain E3 ligases.However,direct evidence for a ubiquitin transfer mechanism and its importance for Parkin's in vivo function is still missing.Here,we report that Parkin E3 activity relies on cysteinemediated ubiquitin transfer during mitophagy.Mutating the putative catalytic cysteine to serine (Parkin C431S)traps ubiquitin,and surprisingly,also abrogates Parkin mitochondrial translocation,indicating that E3 activity is essential for Parkin translocation.We found that Parkin can bind to K63-1inked ubiquitin chains,and that targeting K63-mimicking ubiquitin chains to mitochondria restores Parkin C431S localization.We propose that Parkin translocation is achieved through a novel catalytic activity coupled mechanism.

  10. Parkin mitochondrial translocation is achieved through a novel catalytic activity coupled mechanism

    Science.gov (United States)

    Zheng, Xinde; Hunter, Tony

    2013-01-01

    Pink1, a mitochondrial kinase, and Parkin, an E3 ubiquitin ligase, function in mitochondrial maintenance. Pink1 accumulates on depolarized mitochondria, where it recruits Parkin to mainly induce K63-linked chain ubiquitination of outer membrane proteins and eventually mitophagy. Parkin belongs to the RBR E3 ligase family. Recently, it has been proposed that the RBR domain transfers ubiquitin to targets via a cysteine∼ubiquitin enzyme intermediate, in a manner similar to HECT domain E3 ligases. However, direct evidence for a ubiquitin transfer mechanism and its importance for Parkin's in vivo function is still missing. Here, we report that Parkin E3 activity relies on cysteine-mediated ubiquitin transfer during mitophagy. Mutating the putative catalytic cysteine to serine (Parkin C431S) traps ubiquitin, and surprisingly, also abrogates Parkin mitochondrial translocation, indicating that E3 activity is essential for Parkin translocation. We found that Parkin can bind to K63-linked ubiquitin chains, and that targeting K63-mimicking ubiquitin chains to mitochondria restores Parkin C431S localization. We propose that Parkin translocation is achieved through a novel catalytic activity coupled mechanism. PMID:23670163

  11. Absolute distance measurement method without a non-measurable range and directional ambiguity based on the spectral-domain interferometer using the optical comb of the femtosecond pulse laser

    Science.gov (United States)

    Park, J.; Jin, J.; Kim, J.-A.; Kim, J. W.

    2016-12-01

    With the help of the optical comb of a femtosecond pulse laser, a spectral-domain interferometer has been utilized for measuring absolute distances. Even if the technique can measure distances at a high speed and with good precision, it has two fundamental problems: non-measurable range and directional ambiguity. First, the non-measurable range arises due to the sampling limit of the interference spectra at very short distances or the integer multiple of a double non-ambiguity range. Second, the peak corresponding to the desired distance in the Fourier domain has a directional ambiguity owing to the repeated property of the optical comb. Therefore, due to these two fundamental problems, most previous works never measure the absolute distances by itself in a single operation. In this letter, an interferometric method for measuring arbitrary absolute distances based on a spectral-domain interferometer operating with two reference mirrors is proposed and demonstrated. The two reference mirrors generate two distinguishable signals, primary and secondary, with a predetermined offset, thus solving these fundamental problems clearly. More importantly, as a practical advantage, the simple layout of the proposed method makes it readily applicable to most previous studies.

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  13. SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE Directly Interacts with the Cytoplasmic Domain of SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE and Negatively Regulates Leaf Senescence in Arabidopsis.

    Science.gov (United States)

    Xiao, Dong; Cui, Yanjiao; Xu, Fan; Xu, Xinxin; Gao, Guanxiao; Wang, Yaxin; Guo, Zhaoxia; Wang, Dan; Wang, Ning Ning

    2015-10-01

    Reversible protein phosphorylation mediated by protein kinases and phosphatases plays an important role in the regulation of leaf senescence. We previously reported that the leucine-rich repeat receptor-like kinase SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (AtSARK) positively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). Here, we report the involvement of a protein serine/threonine phosphatase 2C-type protein phosphatase, SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE (SSPP), in the negative regulation of Arabidopsis leaf senescence. SSPP transcript levels decreased greatly during both natural senescence and SARK-induced precocious senescence. Overexpression of SSPP significantly delayed leaf senescence in Arabidopsis. Protein pull-down and bimolecular fluorescence complementation assays demonstrated that the cytosol-localized SSPP could interact with the cytoplasmic domain of the plasma membrane-localized AtSARK. In vitro assays showed that SSPP has protein phosphatase function and can dephosphorylate the cytosolic domain of AtSARK. Consistent with these observations, overexpression of SSPP effectively rescued AtSARK-induced precocious leaf senescence and changes in hormonal responses. All our results suggested that SSPP functions in sustaining proper leaf longevity and preventing early senescence by suppressing or perturbing SARK-mediated senescence signal transduction.

  14. Selective Catalytic Reduction of NO with Methane

    Institute of Scientific and Technical Information of China (English)

    Xiang Gao; Qi Yu; Limin Chen

    2003-01-01

    The removal of nitrogen oxides from exhaust gases has attracted great attention in recent years, and many approaches have been developed depending on the application. Methane, the main component of natural gas, has great potential as a NO reductant. In this paper, a number of catalysts previous reported for this catalytic reduction of NO have been reviewed, including a direct comparison of the relative activities and effective factors of the catalysts. Reaction mechanisms have also been explored preliminarily.

  15. Selectivity of catalytic methods of determination.

    Science.gov (United States)

    Otto, M; Mueller, H; Werner, G

    1978-03-01

    By means of catalytic analytical methods, extremely low levels can be determined at low cost and with a high sensitivity that is equal to that of physical methods of trace analysis. The selectivity of the catalytic determinations, is, however, usually rather lower than that of other methods of trace analysis. The selectivity can sometimes be improved by modification of the indicator reaction through variation of the reagents and their concentrations, or by use of masking reagents or activators, or by combination with a separation method. Modification of the indicator reaction can be exemplified by the selective determination of osmium and ruthenium by their catalysis of the nitrate oxidation of 1-naphthylamine. By variation of the nitrate concentration and the use of 1,10-phenanthroline and 8-hydroxyquinoline as complexing agents it is possible to determine these two elements simultaneously. An especially significant increase in the selectivity is made possible by use of a preliminary separation step. If the ion to be determined is separated by solvent extraction and then catalytically determined directly in the extract, a very specific determination is possible; this technique has been called "extractive catalytic determination". This method has been used for determination of molybdenum (0.5 ng/ml) in sea-water, iron (5 ng/ml) in heavy metal salts, and copper (3 ng/ml) in the presence of numerous elements.

  16. Catalytic properties of ADAM12 and its domain deletion mutants

    DEFF Research Database (Denmark)

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

    2008-01-01

    Human ADAM12 (a disintegrin and metalloproteinase) is a multidomain zinc metalloproteinase expressed at high levels during development and in human tumors. ADAM12 exists as two splice variants: a classical type 1 membrane-anchored form (ADAM12-L) and a secreted splice variant (ADAM12-S) consistin...

  17. 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.

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

    Science.gov (United States)

    Somech, Anit; Wenderow, Maayan

    2006-01-01

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

  19. 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...

  20. 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.

  1. Fluid-Bed Testing of Greatpoint Energy's Direct Oxygen Injection Catalytic Gasification Process for Synthetic Natural Gas and Hydrogen Coproduction Year 6 - Activity 1.14 - Development of a National Center for Hydrogen Technology

    Energy Technology Data Exchange (ETDEWEB)

    Swanson, Michael; Henderson, Ann

    2012-04-01

    The GreatPoint Energy (GPE) concept for producing synthetic natural gas and hydrogen from coal involves the catalytic gasification of coal and carbon. GPE’s technology “refines” coal by employing a novel catalyst to “crack” the carbon bonds and transform the coal into cleanburning methane (natural gas) and hydrogen. The GPE mild “catalytic” gasifier design and operating conditions result in reactor components that are less expensive and produce pipeline-grade methane and relatively high purity hydrogen. The system operates extremely efficiently on very low cost carbon sources such as lignites, subbituminous coals, tar sands, petcoke, and petroleum residual oil. In addition, GPE’s catalytic coal gasification process eliminates troublesome ash removal and slagging problems, reduces maintenance requirements, and increases thermal efficiency, significantly reducing the size of the air separation plant (a system that alone accounts for 20% of the capital cost of most gasification systems) in the catalytic gasification process. Energy & Environmental Research Center (EERC) pilot-scale gasification facilities were used to demonstrate how coal and catalyst are fed into a fluid-bed reactor with pressurized steam and a small amount of oxygen to “fluidize” the mixture and ensure constant contact between the catalyst and the carbon particles. In this environment, the catalyst facilitates multiple chemical reactions between the carbon and the steam on the surface of the coal. These reactions generate a mixture of predominantly methane, hydrogen, and carbon dioxide. Product gases from the process are sent to a gas-cleaning system where CO{sub 2} and other contaminants are removed. In a full-scale system, catalyst would be recovered from the bottom of the gasifier and recycled back into the fluid-bed reactor. The by-products (such as sulfur, nitrogen, and CO{sub 2}) would be captured and could be sold to the chemicals and petroleum industries, resulting in

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

    Science.gov (United States)

    Mansournia, Mohammadreza; Azizi, Fatemeh; Rakhshan, Narges

    2015-05-01

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

  3. Peptide ligands incorporated into the threefold spike capsid domain to re-direct gene transduction of AAV8 and AAV9 in vivo.

    Directory of Open Access Journals (Sweden)

    Stefan Michelfelder

    Full Text Available Efficiency and specificity of viral vectors are vital issues in gene therapy. Insertion of peptide ligands into the adeno-associated viral (AAV capsid at receptor binding sites can re-target AAV2-derived vectors to alternative cell types. Also, the use of serotypes AAV8 and -9 is more efficient than AAV2 for gene transfer to certain tissues in vivo. Consequently, re-targeting of these serotypes by ligand insertion could be a promising approach but has not been explored so far. Here, we generated AAV8 and -9 vectors displaying peptides in the threefold spike capsid domain. These peptides had been selected from peptide libraries displayed on capsids of AAV serotype 2 to optimize systemic gene delivery to murine lung tissue and to breast cancer tissue in PymT transgenic mice (PymT. Such peptide insertions at position 590 of the AAV8 capsid and position 589 of the AAV9 capsid changed the transduction properties of both serotypes. However, both peptides inserted in AAV8 did not result in the same changes of tissue tropism as they did in AAV2. While the AAV2 peptides selected on murine lung tissue did not alter tropism of serotypes 8 and -9, insertion of the AAV2-derived peptide selected on breast cancer tissue augmented tumor gene delivery in both serotypes. Further, this peptide mediated a strong but unspecific in vivo gene transfer for AAV8 and abrogated transduction of various control tissues for AAV9. Our findings indicate that peptide insertion into defined sites of AAV8 and -9 capsids can change and improve their efficiency and specificity compared to their wild type variants and to AAV2, making these insertion sites attractive for the generation of novel targeted vectors in these serotypes.

  4. Llama-derived single variable domains (nanobodies) directed against chemokine receptor CXCR7 reduce head and neck cancer cell growth in vivo.

    Science.gov (United States)

    Maussang, David; Mujić-Delić, Azra; Descamps, Francis J; Stortelers, Catelijne; Vanlandschoot, Peter; Stigter-van Walsum, Marijke; Vischer, Henry F; van Roy, Maarten; Vosjan, Maria; Gonzalez-Pajuelo, Maria; van Dongen, Guus A M S; Merchiers, Pascal; van Rompaey, Philippe; Smit, Martine J

    2013-10-11

    The chemokine receptor CXCR7, belonging to the membrane-bound G protein-coupled receptor superfamily, is expressed in several tumor types. Inhibition of CXCR7 with either small molecules or small interference (si)RNA has shown promising therapeutic benefits in several tumor models. With the increased interest and effectiveness of biologicals inhibiting membrane-bound receptors we made use of the "Nanobody platform" to target CXCR7. Previously we showed that Nanobodies, i.e. immunoglobulin single variable domains derived from naturally occurring heavy chain-only camelids antibodies, represent new biological tools to efficiently tackle difficult drug targets such as G protein-coupled receptors. In this study we developed and characterized highly selective and potent Nanobodies against CXCR7. Interestingly, the CXCR7-targeting Nanobodies displayed antagonistic properties in contrast with previously reported CXCR7-targeting agents. Several high affinity CXCR7-specific Nanobodies potently inhibited CXCL12-induced β-arrestin2 recruitment in vitro. A wide variety of tumor biopsies was profiled, showing for the first time high expression of CXCR7 in head and neck cancer. Using a patient-derived CXCR7-expressing head and neck cancer xenograft model in nude mice, tumor growth was inhibited by CXCR7-targeting Nanobody therapy. Mechanistically, CXCR7-targeting Nanobodies did not inhibit cell cycle progression but instead reduced secretion of the angiogenic chemokine CXCL1 from head and neck cancer cells in vitro, thus acting here as inverse agonists, and subsequent angiogenesis in vivo. Hence, with this novel class of CXCR7 inhibitors, we further substantiate the therapeutic relevance of targeting CXCR7 in head and neck cancer.

  5. Protein domain organisation: adding order

    Directory of Open Access Journals (Sweden)

    Kummerfeld Sarah K

    2009-01-01

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

  6. Visualizing domain wall and reverse domain superconductivity.

    Science.gov (United States)

    Iavarone, M; Moore, S A; Fedor, J; Ciocys, S T; Karapetrov, G; Pearson, J; Novosad, V; Bader, S D

    2014-08-28

    In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application.

  7. HYDROGEN TRANSFER IN CATALYTIC CRACKING

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Hydrogen transfer is an important secondary reaction of catalytic cracking reactions, which affects product yield distribution and product quality. It is an exothermic reaction with low activation energy around 43.3 kJ/mol. Catalyst properties and operation parameters in catalytic cracking greatly influence the hydrogen transfer reaction. Satisfactory results are expected through careful selection of proper catalysts and operation conditions.

  8. Catalytic quantum error correction

    CERN Document Server

    Brun, T; Hsieh, M H; Brun, Todd; Devetak, Igor; Hsieh, Min-Hsiu

    2006-01-01

    We develop the theory of entanglement-assisted quantum error correcting (EAQEC) codes, a generalization of the stabilizer formalism to the setting in which the sender and receiver have access to pre-shared entanglement. Conventional stabilizer codes are equivalent to dual-containing symplectic codes. In contrast, EAQEC codes do not require the dual-containing condition, which greatly simplifies their construction. We show how any quaternary classical code can be made into a EAQEC code. In particular, efficient modern codes, like LDPC codes, which attain the Shannon capacity, can be made into EAQEC codes attaining the hashing bound. In a quantum computation setting, EAQEC codes give rise to catalytic quantum codes which maintain a region of inherited noiseless qubits. We also give an alternative construction of EAQEC codes by making classical entanglement assisted codes coherent.

  9. 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.

  10. Catalytic pyrolysis of waste mandarin over nanoporous materials.

    Science.gov (United States)

    Park, Young-Kwon; Kim, Jeong Wook; Park, Sung Hoon; Kim, Seong-Soo; Jeon, Jong-Ki; Lee, See Hoon

    2013-01-01

    Catalytic pyrolysis of waste mandarin was performed using nanoporous catalysts. AI-MCM-41 and Meso-MFI, which had different acid characteristics, were used. In addition, the characteristics of Pt/Meso-MFI were compared with those of Meso-MFI. To analyze the characteristics of the catalyst samples, Brunauer-Emmett-Teller surface area, temperature programmed desorption of NH3, and N2 adsorption-desorption analyses were performed. In addition, pyrolysis gas chromatography/mass spectrometry was used to facilitate the direct analysis of the pyrolytic products. The products obtained from catalytic pyrolysis contained a greater amount of valuable components than did those obtained from non-catalytic pyrolysis, indicating that catalytic pyrolysis improved the quality of the bio-oil. Additionally, valuable products such as furan and aromatic compounds were produced in greater quantities when Meso-MFI was used. When Pt/Meso-MFI was used, the amounts of furan and aromatic compounds produced increased even further.

  11. 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...

  12. Domains in Ferroelectric Nanostructures

    Science.gov (United States)

    Gregg, Marty

    2010-03-01

    Ferroelectric materials have great potential in influencing the future of small scale electronics. At a basic level, this is because ferroelectric surfaces are charged, and so interact strongly with charge-carrying metals and semiconductors - the building blocks for all electronic systems. Since the electrical polarity of the ferroelectric can be reversed, surfaces can both attract and repel charges in nearby materials, and can thereby exert complete control over both charge distribution and movement. It should be no surprise, therefore, that microelectronics industries have already looked very seriously at harnessing ferroelectric materials in a variety of applications, from solid state memory chips (FeRAMs) to field effect transistors (FeFETs). In all such applications, switching the direction of the polarity of the ferroelectric is a key aspect of functional behavior. The mechanism for switching involves the field-induced nucleation and growth of domains. Domain coarsening, through domain wall propagation, eventually causes the entire ferroelectric to switch its polar direction. It is thus the existence and behavior of domains that determine the switching response, and ultimately the performance of the ferroelectric device. A major issue, associated with the integration of ferroelectrics into microelectronic devices, has been that the fundamental properties associated with ferroelectrics, when in bulk form, appear to change quite dramatically and unpredictably when at the nanoscale: new modes of behaviour, and different functional characteristics from those seen in bulk appear. For domains, in particular, the proximity of surfaces and boundaries have a dramatic effect: surface tension and depolarizing fields both serve to increase the equilibrium density of domains, such that minor changes in scale or morphology can have major ramifications for domain redistribution. Given the importance of domains in dictating the overall switching characteristics of a device

  13. Enhanced activity of Rhizomucor miehei lipase by directed evolution with simultaneous evolution of the propeptide.

    Science.gov (United States)

    Wang, Jue; Wang, Dan; Wang, Bo; Mei, Zhuo-Hang; Liu, Ji; Yu, Hong-Wei

    2012-10-01

    Propeptides are short sequences that facilitate the folding of their associated proteins. The present study found that the propeptide of Rhizomucor miehei lipase (RML) was not proteolytically removed in Escherichia coli. Moreover, RML was not expressed if the propeptide was removed artificially during the cloning process in E. coli. This behavior in E. coli permitted the application of directed evolution to full-length RML, which included both propeptide and catalytic domain, to explore the role played by the propeptide in governing enzyme activity. The catalytic rate constant, k (cat), of the most active mutant RML protein (Q5) was increased from 10.63 ± 0.80 to 71.44 ± 3.20 min(-1) after four rounds of screening. Sequence analysis of the mutant displayed three mutations in the propeptide (L57V, S65A, and V67A) and two mutations in the functional region (I111T and S168P). This result showed that improved activity was obtained with essential involvement by mutations in the propeptide, meaning that the majority of mutants with enhanced activity had simultaneous mutations in propeptide and catalytic domains. This observation leads to the hypothesis that directed evolution has simultaneous and synergistic effects on both functional and propeptide domains that arise from the role played by the propeptide in the folding and maturation of the enzyme. We suggest that directed evolution of full-length proteins including their propeptides is a strategy with general validity for extending the range of conformations available to proteins, leading to the enhancement of the catalytic rates of the enzymes.

  14. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold.

    Science.gov (United States)

    Ericsson, Ulrika B; Nordlund, Pär; Hallberg, B Martin

    2004-05-01

    Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.

  15. Structural and mechanistic analysis of trichodiene synthase using site-directed mutagenesis: probing the catalytic function of tyrosine-295 and the asparagine-225/serine-229/glutamate-233-Mg2+B motif.

    Science.gov (United States)

    Vedula, L Sangeetha; Jiang, Jiaoyang; Zakharian, Tatiana; Cane, David E; Christianson, David W

    2008-01-15

    Trichodiene synthase from Fusarium sporotrichioides contains two metal ion-binding motifs required for the cyclization of farnesyl diphosphate: the "aspartate-rich" motif D(100)DXX(D/E) that coordinates to Mg2+A and Mg2+C, and the "NSE/DTE" motif N(225)DXXSXXXE that chelates Mg2+B (boldface indicates metal ion ligands). Here, we report steady-state kinetic parameters, product array analyses, and X-ray crystal structures of trichodiene synthase mutants in which the fungal NSE motif is progressively converted into a plant-like DDXXTXXXE motif, resulting in a degradation in both steady-state kinetic parameters and product specificity. Each catalytically active mutant generates a different distribution of sesquiterpene products, and three newly detected sesquiterpenes are identified. In addition, the kinetic and structural properties of the Y295F mutant of trichodiene synthase were found to be similar to those of the wild-type enzyme, thereby ruling out a proposed role for Y295 in catalysis.

  16. Unsteady catalytic processes and sorption-catalytic technologies

    Energy Technology Data Exchange (ETDEWEB)

    Zagoruiko, A N [G.K. Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2007-07-31

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

  17. 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

  18. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    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...... 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...

  19. Direct Catalytic Conversion of Cellobiose into Sorbitol in Extremely Low Acid over Ruthenium Catalysts%超低酸性环境中Ru/C催化纤维二糖一步法制备山梨醇的研究

    Institute of Scientific and Technical Information of China (English)

    李计彪; 武书彬; 张军

    2012-01-01

    以Ru/C为催化剂,在超低酸环境和氢气气氛下,将纤维二糖一步转化制备山梨醇.考察了反应温度、反应时间以及催化剂用量对山梨醇产率的影响.实验结果表明,在0.05%H3PO4环境,Ru/C催化剂用量15%,转速为600 r/min,反应温度为458 K以及3 MPa氢气条件下反应1h,产物山梨醇的产率最高,可达到87.1%.同时,催化剂重复利用研究表明Ru/C是一种较理想的氢化反应催化剂,可重复利用且催化效率较高.%Ru/C catalyst and extremely low acid were employed for one-step conversion of cellobiose into sorbitol in the presence of hydrogen. Effects of reaction temperature, reaction time and catalyst usage on sorbitol yield were discussed. Experimental results showed that the highest sorbitol yield of 87. 1% was obtained at reaction temperature of 458 K and catalyst usage of 15 % for 1 h under 3 MPa H2 with the stirring rate of 600 r/min. Meanwhile, catalyst recycling showed that Ru/C was an ideal hydro-genation catalyst with high catalytic efficiency, which could be recycled several times.

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

    KAUST Repository

    Qu, Shuanglin

    2014-04-02

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

  1. Study on Direct Synthesis of Diphenyl Carbonate with Heterogeneous Catalytic Reaction (VI) Effect of Sn Loading Method and Content on Activity of Sn-Pd Supported Catalyst%非均相催化一步合成碳酸二苯酯的研究(VI)Sn的添加方法及添加量对Pd-Sn催化性能的影响

    Institute of Scientific and Technical Information of China (English)

    张光旭; 吴元欣; 马沛生; 田崎峰; 吴广文; 李定或

    2004-01-01

    The compound metal oxide LaxPbyMnzO used as support was prepared by the sol-gel method, and the catalyst in which Pd was used as active component and Sn as co-active component for direct synthesis of diphenyl carbonate (DPC) with heterogeneous catalytic reaction was obtained by co-calcination and precipitation respectively.The catalyst was characterized by XRD, SEM and TEM respectively. The specific surface area of catalysts was measured by ChemBET3000 instrument, and the activity of the catalysts was tested by the synthesis of DPC in a pressured reactor. The results showed that when the co-active component Sn was added by co-calcination method A, its loading content was equal to 14.43% and active component Pd was loaded by precipitation, the yield and selectivity of DPC could reach 26.78% and 99% respectively.

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

    Institute of Scientific and Technical Information of China (English)

    Jingjie Wu; Xiao-Dong Zhou

    2016-01-01

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

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

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-11-11

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

  4. Catalytic Membrane Sensors

    Energy Technology Data Exchange (ETDEWEB)

    Boyle, T.J.; Brinker, C.J.; Gardner, T.J.; Hughes, R.C.; Sault, A.G.

    1998-12-01

    The proposed "catalytic membrane sensor" (CMS) was developed to generate a device which would selectively identify a specific reagent in a complex mixture of gases. This was to be accomplished by modifying an existing Hz sensor with a series of thin films. Through selectively sieving the desired component from a complex mixture and identifying it by decomposing it into Hz (and other by-products), a Hz sensor could then be used to detect the presence of the select component. The proposed "sandwich-type" modifications involved the deposition of a catalyst layered between two size selective sol-gel layers on a Pd/Ni resistive Hz sensor. The role of the catalyst was to convert organic materials to Hz and organic by-products. The role of the membraneo was to impart both chemical specificity by molecukir sieving of the analyte and converted product streams, as well as controlling access to the underlying Pd/Ni sensor. Ultimately, an array of these CMS elements encompassing different catalysts and membranes were to be developed which would enable improved selectivity and specificity from a compiex mixture of organic gases via pattern recognition methodologies. We have successfully generated a CMS device by a series of spin-coat deposited methods; however, it was determined that the high temperature required to activate the catalyst, destroys the sensor.

  5. Catalytic gasification of biomass

    Science.gov (United States)

    Robertus, R. J.; Mudge, L. K.; Sealock, L. J., Jr.; Mitchell, D. H.; Weber, S. L.

    1981-12-01

    Methane and methanol synthesis gas can be produced by steam gasification of biomass in the presence of appropriate catalysts. This concept is to use catalysts in a fluidized bed reactor which is heated indirectly. The objective is to determine the technical and economic feasibility of the concept. Technically the concept has been demonstrated on a 50 lb per hr scale. Potential advantages over conventional processes include: no oxygen plant is needed, little tar is produced so gas and water treatment are simplified, and yields and efficiencies are greater than obtained by conventional gasification. Economic studies for a plant processing 2000 T/per day dry wood show that the cost of methanol from wood by catalytic gasification is competitive with the current price of methanol. Similar studies show the cost of methane from wood is competitive with projected future costs of synthetic natural gas. When the plant capacity is decreased to 200 T per day dry wood, neither product is very attractive in today's market.

  6. 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.)

  7. Catalytic creativity. The case of Linus Pauling.

    Science.gov (United States)

    Nakamura, J; Csikszentmihalyi, M

    2001-04-01

    This article illustrates how creativity is constituted by forces beyond the innovating individual, drawing examples from the career of the eminent chemist Linus Pauling. From a systems perspective, a scientific theory or other product is creative only if the innovation gains the acceptance of a field of experts and so transforms the culture. In addition to this crucial selective function vis-à-vis the completed work, the social field can play a catalytic role, fostering productive interactions between person and domain throughout a career. Pauling's case yields examples of how variously the social field contributes to creativity, shaping the individual's standards of judgment and providing opportunities, incentives, and critical evaluation. A formidable set of strengths suited Pauling for his scientific achievements, but examination of his career qualifies the notion of a lone genius whose brilliance carries the day.

  8. Immigration process in catalytic medium

    Institute of Scientific and Technical Information of China (English)

    洪文明; 王梓坤

    2000-01-01

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

  9. Immigration process in catalytic medium

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

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

  10. Mutation of domain III and domain VI in L gene conserved domain of Nipah virus

    Science.gov (United States)

    Jalani, Siti Aishah; Ibrahim, Nazlina

    2016-11-01

    Nipah virus (NiV) is the etiologic agent responsible for the respiratory illness and causes fatal encephalitis in human. NiV L protein subunit is thought to be responsible for the majority of enzymatic activities involved in viral transcription and replication. The L protein which is the viral RNA dependent RNA polymerase has high sequence homology among negative sense RNA viruses. In negative stranded RNA viruses, based on sequence alignment six conserved domain (domain I-IV) have been determined. Each domain is separated on variable regions that suggest the structure to consist concatenated functional domain. To directly address the roles of domains III and VI, site-directed mutations were constructed by the substitution of bases at sequences 2497, 2500, 5528 and 5532. Each mutated L gene can be used in future studies to test the ability for expression on in vitro translation.

  11. Domain Decomposition Based High Performance Parallel Computing

    CERN Document Server

    Raju, Mandhapati P

    2009-01-01

    The study deals with the parallelization of finite element based Navier-Stokes codes using domain decomposition and state-ofart sparse direct solvers. There has been significant improvement in the performance of sparse direct solvers. Parallel sparse direct solvers are not found to exhibit good scalability. Hence, the parallelization of sparse direct solvers is done using domain decomposition techniques. A highly efficient sparse direct solver PARDISO is used in this study. The scalability of both Newton and modified Newton algorithms are tested.

  12. Allosteric inhibition of Aurora-A kinase by a synthetic vNAR domain.

    Science.gov (United States)

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

    2016-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-05-03

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

  14. Site-directed spectroscopic probes of actomyosin structural dynamics.

    Science.gov (United States)

    Thomas, David D; Kast, David; Korman, Vicci L

    2009-01-01

    Spectroscopy of myosin and actin has entered a golden age. High-resolution crystal structures of isolated actin and myosin have been used to construct detailed models for the dynamic actomyosin interactions that move muscle. Improved protein mutagenesis and expression technologies have facilitated site-directed labeling with fluorescent and spin probes. Spectroscopic instrumentation has achieved impressive advances in sensitivity and resolution. Here we highlight the contributions of site-directed spectroscopic probes to understanding the structural dynamics of myosin II and its actin complexes in solution and muscle fibers. We emphasize studies that probe directly the movements of structural elements within the myosin catalytic and light-chain domains, and changes in the dynamics of both actin and myosin due to their alternating strong and weak interactions in the ATPase cycle. A moving picture emerges in which single biochemical states produce multiple structural states, and transitions between states of order and dynamic disorder power the actomyosin engine.

  15. A NEW ROUTE TO DIRECT CATALYTIC SYNTHESIS OF ACETIC ACID FROM METHANE BY A LOW-TEMPERATURE REACTION%甲烷低温催化直接合成乙酸的新途径

    Institute of Scientific and Technical Information of China (English)

    丁一慧; 黄伟; 晋萍; 谢克昌

    2001-01-01

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

  16. Generic domain models in software engineering

    Science.gov (United States)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  17. Texture of lipid bilayer domains

    DEFF Research Database (Denmark)

    Jensen, Uffe Bernchou; Brewer, Jonathan R.; Midtiby, Henrik Skov;

    2009-01-01

    We investigate the texture of gel (g) domains in binary lipid membranes composed of the phospholipids DPPC and DOPC. Lateral organization of lipid bilayer membranes is a topic of fundamental and biological importance. Whereas questions related to size and composition of fluid membrane domain...... are well studied, the possibility of texture in gel domains has so far not been examined. When using polarized light for two-photon excitation of the fluorescent lipid probe Laurdan, the emission intensity is highly sensitive to the angle between the polarization and the tilt orientation of lipid acyl...... chains. By imaging the intensity variations as a function of the polarization angle, we map the lateral variations of the lipid tilt within domains. Results reveal that gel domains are composed of subdomains with different lipid tilt directions. We have applied a Fourier decomposition method...

  18. .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...

  19. 直流电弧自催化合成β-SiC纳米线%Self-catalytic Synthesis of β-SiC Nanowires by Direct Current Arc Discharge

    Institute of Scientific and Technical Information of China (English)

    王峰; 王秋实; 崔启良; 张剑; 邹广田

    2009-01-01

    采用C,Si和SiO2为反应原料,利用直流电弧法制备出长直的β-SiC纳米线.纳米线的直径为100~200 nm,长度为10~20 μm,并且沿着方向生长.通过X射线衍射(XRD)、扫描电子显微术(SEM)、透射电子显微术(TEM)、拉曼光谱等手段,对β-SiC纳米线进行表征.探讨了β-SiC纳米线自催化气-液-固(VLS)生长机制.%Straight and long β-SiC nanowires were synthesized in direct current arc discharge using a mixture of graphite, silicon, and silicon dioxide as the precursor. The diameter of the nanowires is 100~200 nm, and the length is about 10~20 μm. The axis of the nanowire is preferentially along the direction. The morphology and structure of the nanowires were characterized by X-ray diffraction(XRD), scanning electron microscopy(SEM), energy dispersive spectroscopy (EDS), transmission electron microscopy (TEM) and Raman spectroscopy. The β-SiC nanowires are suggested to be formed via a self-catalyzed vapor-liquid-solid growth mechanism.

  20. Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation

    Science.gov (United States)

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

    2016-05-01

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

  1. ΔµH+ and ATP Function at Different Steps of the Catalytic Cycle of Preprotein Translocase

    NARCIS (Netherlands)

    Schiebel, Elmar; Driessen, Arnold J.M.; Hartl, Franz-Ulrich; Wickner, William

    1991-01-01

    Preprotein translocation in E. coli requires ATP, the membrane electrochemical potential ΔµH+, and translocase, an enzyme with an ATPase domain (SecA) and the membrane-embedded SecY/E. Studies of translocase and proOmpA reveal a five-step catalytic cycle: First, proOmpA binds to the SecA domain. Sec

  2. Engineering reactors for catalytic reactions

    Indian Academy of Sciences (India)

    Vivek V Ranade

    2014-03-01

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

  3. 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....

  4. 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...... of an uncorrelated ancilla system. This removes a restriction on the standard notion of decoupling, which becomes important for structureless resources, and yields a tight characterization in terms of the max-mutual information. Catalytic decoupling naturally unifies various tasks like the erasure of correlations...... and quantum state merging, and leads to a resource theory of decoupling....

  5. Hydrogen production via catalytic processing of renewable feedstocks

    Energy Technology Data Exchange (ETDEWEB)

    Nazim Muradov; Franklyn Smith; Ali T-Raissi [Florida Solar Energy Center, University of Central Florida, Cocoa, Florida, (United States)

    2006-07-01

    Landfill gas (LFG) and biogas can potentially become important feedstocks for renewable hydrogen production. The objectives of this work were: (1) to develop a catalytic process for direct reforming of CH{sub 4}-CO{sub 2} gaseous mixture mimicking LFG, (2) perform thermodynamic analysis of the reforming process using AspenPlus chemical process simulator, (3) determine operational conditions for auto-thermal (or thermo-neutral) reforming of a model CH{sub 4}-CO{sub 2} feedstock, and (4) fabricate and test a bench-scale hydrogen production unit. Experimental data obtained from catalytic reformation of the CH{sub 4}-CO{sub 2} and CH{sub 4}-CO{sub 2}-O{sub 2} gaseous mixtures using Ni-catalyst were in a good agreement with the simulation results. It was demonstrated that catalytic reforming of LFG-mimicking gas produced hydrogen with the purity of 99.9 vol.%. (authors)

  6. Catalytic enantioselective addition of Grignard reagents to aromatic silyl ketimines

    Science.gov (United States)

    Rong, Jiawei; Collados, Juan F.; Ortiz, Pablo; Jumde, Ravindra P.; Otten, Edwin; Harutyunyan, Syuzanna R.

    2016-12-01

    α-Chiral amines are of significant importance in medicinal chemistry, asymmetric synthesis and material science, but methods for their efficient synthesis are scarce. In particular, the synthesis of α-chiral amines with the challenging tetrasubstituted carbon stereocentre is a long-standing problem and catalytic asymmetric additions of organometallic reagents to ketimines that would give direct access to these molecules are underdeveloped. Here we report a highly enantioselective catalytic synthesis of N-sulfonyl protected α-chiral silyl amines via the addition of inexpensive, easy to handle and readily available Grignard reagents to silyl ketimines. The key to this success was our ability to suppress any unselective background addition reactions and side reduction pathway, through the identification of an inexpensive, chiral Cu-complex as the catalytically active structure.

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

    Directory of Open Access Journals (Sweden)

    Hirotaka Koga

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

  9. Catalytic conversion of biomass to fuels. Final report

    Energy Technology Data Exchange (ETDEWEB)

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

    1978-01-01

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

  10. Crystal structures of histone and p53 methyltransferase SmyD2 reveal a conformational flexibility of the autoinhibitory C-terminal domain.

    Directory of Open Access Journals (Sweden)

    Yuanyuan Jiang

    Full Text Available SmyD2 belongs to a new class of chromatin regulators that control gene expression in heart development and tumorigenesis. Besides methylation of histone H3 K4, SmyD2 can methylate non-histone targets including p53 and the retinoblastoma tumor suppressor. The methyltransferase activity of SmyD proteins has been proposed to be regulated by autoinhibition via the intra- and interdomain bending of the conserved C-terminal domain (CTD. However, there has been no direct evidence of a conformational change in the CTD. Here, we report two crystal structures of SmyD2 bound either to the cofactor product S-adenosylhomocysteine or to the inhibitor sinefungin. SmyD2 has a two-lobed structure with the active site located at the bottom of a deep crevice formed between the CTD and the catalytic domain. By extensive engagement with the methyltransferase domain, the CTD stabilizes the autoinhibited conformation of SmyD2 and restricts access to the catalytic site. Unexpectedly, despite that the two SmyD2 structures are highly superimposable, significant differences are observed in the first two helices of the CTDs: the two helices bend outwards and move away from the catalytic domain to generate a less closed conformation in the sinefungin-bound structure. Although the overall fold of the individual domains is structurally conserved among SmyD proteins, SmyD2 appear to be a conformational "intermediate" between a close form of SmyD3 and an open form of SmyD1. In addition, the structures reveal that the CTD is structurally similar to tetratricopeptide repeats (TPR, a motif through which many cochaperones bind to the heat shock protein Hsp90. Our results thus provide the first evidence for the intradomain flexibility of the TPR-like CTD, which may be important for the activation of SmyD proteins by Hsp90.

  11. Point mutations in firefly luciferase C-domain demonstrate its significance in green color of bioluminescence.

    Science.gov (United States)

    Modestova, Yulia; Koksharov, Mikhail I; Ugarova, Natalia N

    2014-09-01

    Firefly luciferase is a two-domain enzyme that catalyzes the bioluminescent reaction of firefly luciferin oxidation. Color of the emitted light depends on the structure of the enzyme, yet the exact color-tuning mechanism remains unknown by now, and the role of the C-domain in it is rarely discussed, because a very few color-shifting mutations in the C-domain were described. Recently we reported a strong red-shifting mutation E457K in the C-domain; the bioluminescence spectra of this enzyme were independent of temperature or pH. In the present study we investigated the role of the residue E457 in the enzyme using the Luciola mingrelica luciferase with a thermostabilized N-domain as a parent enzyme for site-directed mutagenesis. We obtained a set of mutants and studied their catalytic properties, thermal stability and bioluminescence spectra. Experimental spectra were represented as a sum of two components (bioluminescence spectra of putative "red" and "green" emitters); λmax of these components were constant for all the mutants, but the ratio of these emitters was defined by temperature and mutations in the C-domain. We suggest that each emitter is stabilized by a specific conformation of the active site; thus, enzymes with two forms of the active site coexist in the reactive media. The rigid structure of the C-domain is crucial for maintaining the conformation corresponding to the "green" emitter. We presume that the emitters are the keto- and enol forms of oxyluciferin.

  12. Polyurethane modified with an antithrombin-heparin complex via polyethylene oxide linker/spacers: influence of PEO molecular weight and PEO-ATH bond on catalytic and direct anticoagulant functions.

    Science.gov (United States)

    Sask, Kyla N; Berry, Leslie R; Chan, Anthony K C; Brash, John L

    2012-10-01

    A segmented polyurethane (PU) was modified with polyethylene oxides (PEO) of varying molecular weight and end group. The PEO served as linker/spacers to immobilize an antithrombin-heparin (ATH) anticoagulant complex on the PU. Isocyanate groups were introduced into the PU to enable attachment of either "conventional" homo-bifunctional dihydroxy-PEO (PEO-OH surface) or a hetero-bifunctional amino-carboxy-PEO (PEO-COOH surface). The PEO surfaces were functionalized with N-hydroxysuccinimide (NHS) groups using appropriate chemistries, and ATH was attached to the distal NHS end of the PEO (PEO-OH-ATH and PEO-COOH-ATH surfaces). Water contact angle and fibrinogen adsorption measurements showed increased hydrophilicity and reduced fibrinogen adsorption from buffer on all PEO surfaces compared to unmodified PU. ATH uptake on NHS-functionalized PEO was quantified by radiolabeling. Despite the different PEO molecular weights and end groups, and NHS-functionalization chemistries, the surface densities of ATH were similar. The adsorption of fibrinogen and antithrombin (AT) from plasma was measured in a single experiment using dual radiolabeling. On PEO-ATH surfaces fibrinogen adsorption was minimal while AT adsorption was high showing the selectivity of the heparin moiety of ATH for AT. The PEO-COOH-ATH surfaces showed slightly greater AT adsorption than the PEO-OH-ATH surfaces. Thrombin adsorption on all of the PEO-ATH surfaces was greater than on the corresponding PEO surfaces without ATH, and was highest on the PEO-OH-ATH, suggesting potential anticoagulant properties for this surface via direct thrombin inhibition by the AT portion of ATH.

  13. Simple, chemoselective, catalytic olefin isomerization.

    Science.gov (United States)

    Crossley, Steven W M; Barabé, Francis; Shenvi, Ryan A

    2014-12-01

    Catalytic amounts of Co(Sal(tBu,tBu))Cl and organosilane irreversibly isomerize terminal alkenes by one position. The same catalysts effect cycloisomerization of dienes and retrocycloisomerization of strained rings. Strong Lewis bases like amines and imidazoles, and labile functionalities like epoxides, are tolerated.

  14. Catalytic Asymmetric Bromocyclization of Polyenes.

    Science.gov (United States)

    Samanta, Ramesh C; Yamamoto, Hisashi

    2017-02-01

    The first catalytic asymmetric bromonium ion-induced polyene cyclization has been achieved by using a chiral BINOL-derived thiophosphoramide catalyst and 1,3-dibromo-5,5-dimethylhydantoin as an electrophilic bromine source. Bromocyclization products are obtained in high yields, with good enantiomeric ratios and high diastereoselectivity, and are abundantly found as scaffolds in natural products.

  15. Electrochemical promotion of sulfur dioxide catalytic oxidation

    DEFF Research Database (Denmark)

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

    2000-01-01

    The effect of electrochemical polarization on the catalytic SO2 oxidation in the molten V2O5-K2S2O7 system has been studied using a gold working electrode in the temperature range 400-460 degrees C. A similar experiment has been performed with the industrial catalyst VK-58. The aim of the present...... investigation was to study a possible non-Faradaic electrochemical promotion of the liquid-phase catalytic reaction. It has been shown that there are two negative potential promotion areas with maximum effects at approximately -0.1 and -0.2 V, and one positive potential promotion area with the maximum effect...... caused by the negative charge on the electrode. The Faradaic part of the promoting effect under positive polarization has been explained as the electrochemical pushing of the V(V) V(IV) equilibrium in the direction of V(V) formation. It has also been shown that when using the industrial VK-58 catalyst...

  16. Metal hybrid nanoparticles for catalytic organic and photochemical transformations.

    Science.gov (United States)

    Song, Hyunjoon

    2015-03-17

    In order to understand heterogeneous catalytic reactions, model catalysts such as a single crystalline surface have been widely studied for many decades. However, catalytic systems that actually advance the reactions are three-dimensional and commonly have multiple components including active metal nanoparticles and metal oxide supports. On the other hand, as nanochemistry has rapidly been developed and been applied to various fields, many researchers have begun to discuss the impact of nanochemistry on heterogeneous catalysis. Metal hybrid nanoparticles bearing multiple components are structurally very close to the actual catalysts, and their uniform and controllable morphology is suitable for investigating the relationship between the structure and the catalytic properties in detail. In this Account, we introduce four typical structures of metal hybrid nanoparticles that can be used to conduct catalytic organic and photochemical reactions. Metal@silica (or metal oxide) yolk-shell nanoparticles, in which metal cores exist in internal voids surrounded by thin silica (or metal oxide) shells, exhibited extremely high thermal and chemical stability due to the geometrical protection of the silica layers against the metal cores. The morphology of the metal cores and the pore density of the hollow shells were precisely adjusted to optimize the reaction activity and diffusion rates of the reactants. Metal@metal oxide core-shell nanoparticles and inverted structures, where the cores supported the shells serving an active surface, exhibited high activity with no diffusion barriers for the reactants and products. These nanostructures were used as effective catalysts for various organic and gas-phase reactions, including hydrogen transfer, Suzuki coupling, and steam methane reforming. In contrast to the yolk- and core-shell structures, an asymmetric arrangement of distinct domains generated acentric dumbbells and tipped rods. A large domain of each component added multiple

  17. S-layer homology domain proteins Csac_0678 and Csac_2722 are implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus.

    Science.gov (United States)

    Ozdemir, Inci; Blumer-Schuette, Sara E; Kelly, Robert M

    2012-02-01

    The genus Caldicellulosiruptor contains extremely thermophilic bacteria that grow on plant polysaccharides. The genomes of Caldicellulosiruptor species reveal certain surface layer homology (SLH) domain proteins that have distinguishing features, pointing to a role in lignocellulose deconstruction. Two of these proteins in Caldicellulosiruptor saccharolyticus (Csac_0678 and Csac_2722) were examined from this perspective. In addition to three contiguous SLH domains, the Csac_0678 gene encodes a glycoside hydrolase family 5 (GH5) catalytic domain and a family 28 carbohydrate-binding module (CBM); orthologs to Csac_0678 could be identified in all genome-sequenced Caldicellulosiruptor species. Recombinant Csac_0678 was optimally active at 75°C and pH 5.0, exhibiting both endoglucanase and xylanase activities. SLH domain removal did not impact Csac_0678 GH activity, but deletion of the CBM28 domain eliminated binding to crystalline cellulose and rendered the enzyme inactive on this substrate. Csac_2722 is the largest open reading frame (ORF) in the C. saccharolyticus genome (predicted molecular mass of 286,516 kDa) and contains two putative sugar-binding domains, two Big4 domains (bacterial domains with an immunoglobulin [Ig]-like fold), and a cadherin-like (Cd) domain. Recombinant Csac_2722, lacking the SLH and Cd domains, bound to cellulose and had detectable carboxymethylcellulose (CMC) hydrolytic activity. Antibodies directed against Csac_0678 and Csac_2722 confirmed that these proteins bound to the C. saccharolyticus S-layer. Their cellular localization and functional biochemical properties indicate roles for Csac_0678 and Csac_2722 in recruitment and hydrolysis of complex polysaccharides and the deconstruction of lignocellulosic biomass. Furthermore, these results suggest that related SLH domain proteins in other Caldicellulosiruptor genomes may also be important contributors to plant biomass utilization.

  18. Structural, catalytic/redox and electrical characterization of systems combining Cu-Ni with CeO{sub 2} or Ce{sub 1-x}M{sub x}O{sub 2-{delta}} (M = Gd or Tb) for direct methane oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Hornes, A.; Gamarra, D.; Conesa, J.C.; Bera, P.; Martinez-Arias, A. [Instituto de Catalisis y Petroleoquimica (CSIC), C/Marie Curie 2, Campus de Cantoblanco, 28049 Madrid (Spain); Munuera, G. [Universidad de Sevilla, C/Profesor Garcia Gonzalez s/n, Departamento de Quimica Inorganica, 41012 Sevilla (Spain); Fuerte, A.; Valenzuela, R.X.; Escudero, M.J. [CIEMAT, Avda, Complutense 22, 28040 Madrid (Spain); Daza, L. [Instituto de Catalisis y Petroleoquimica (CSIC), C/Marie Curie 2, Campus de Cantoblanco, 28049 Madrid (Spain); CIEMAT, Avda, Complutense 22, 28040 Madrid (Spain)

    2009-07-01

    The present work analyses bimetallic Cu-Ni formulations, in comparison to monometallic Cu ones, combined with CeO{sub 2} or other structurally related mixed oxides resulting from doping of the former with Gd or Tb, focusing to its possible use as anodes of solid oxide fuel cells (SOFC) for direct oxidation of methane. The main objective is the characterization of the various formulations at structural level as well as with regards to the redox changes taking place in the systems upon interaction with methane, in order to evaluate the effects induced by the presence of dopants. In the same sense, an analysis of thermal expansion and electrical properties of the systems is performed, considering its possible implantation in SOFC single cells. For the mentioned purposes, the systems have been analysed by means of CH{sub 4}-TPR tests subsequently followed by TPO tests, as well as by XRD, Raman and XPS, with the aim of exploring structural and redox changes produced in the systems and the formation of carbon deposits during such interactions. The results reveal significant modifications in the structural, catalytic/redox and electrical properties of the systems as a function of the presence of Ni and/or Gd and Tb dopants in the formulation. (author)

  19. 非均相羰基氧化一步合成碳酸二苯酯的研究(Ⅴ)筛选催化剂及优化合成条件%Study on Direct Synthesis of Diphenyl Carbonate with Heterogeneous Catalytic Reaction (Ⅴ) Screening Catalysts and Optimizing Synthesis Conditions

    Institute of Scientific and Technical Information of China (English)

    张光旭; 吴元欣; 马沛生; 田崎峰; 吴广文; 李定或; 王存文

    2003-01-01

    Pd/LaxPbyMnOz, Pd/C, Pd/molecular sieve and Pd-heteropoly acid catalysts for direct synthesis of diphenyl carbonate (DPC) by heterogeneous catalytic reaction were compared and the results of DPC synthesis indicated that the catalyst Pd/LaxPbyMnOz had higher activity. The Pd/LaxPbyMnOz catalyst and the support was characterized by XRD, SEM and TEM, the main phase was La0.62Pb0.38MnO3 and the average diameter could be about 25.4nm. The optimum conditions for synthesis of DPC with Pd/LaxPbyMnOz were determined by orthogonal experiments and the experimental results showed that reaction temperature was the first factor of effect on the selectivity and yield of DPC, and the concentration of O2 in gas phase also had significant effect on selectivity of DPC. The optimum reaction conditions were catalyst/phenol mass ratio 1 to 50, pressure 4.5 MPa,volume concentration of O2 25%, reaction temperature 60℃ and reaction time 4 h. The maximum yield and average selectivity could reach 13% and 97% respectively in the batch operation.

  20. Mg2+ coordination in catalytic sites of F1-ATPase.

    Science.gov (United States)

    Weber, J; Hammond, S T; Wilke-Mounts, S; Senior, A E

    1998-01-13

    Coordination of the Mg2+ ion in Mg-nucleotide substrates by amino acid residue side chains in the catalytic site of Escherichia coli F1-ATPase was investigated. From the X-ray structure of the mitochondrial enzyme [Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628], it may be inferred that the hydroxyl of betaThr-156 is a direct ligand of Mg2+, whereas the carboxyls of betaGlu-181, betaGlu-185, and betaAsp-242 might contribute via intervening water molecules. Elimination of each respective functional group by site-directed mutagenesis, followed by determination of Mg-nucleotide and uncomplexed nucleotide binding affinities using a tryptophan probe, showed that betaThr-156, betaGlu-185, and betaAsp-242 are all involved in Mg2+ coordination, whereas betaGlu-181 is not. A derived structural model for the octahedral coordination around the Mg2+ ion is presented. The results indicate that the ADP-containing site in the X-ray structure is the catalytic site of highest affinity. Correct Mg2+ coordination is required for catalytic activity at physiological rates. Elimination of any one of the Mg2+-coordinating residues led to complete loss of Mg2+-dependent nucleotide binding cooperativity of the catalytic sites.

  1. Domain Modeling: NP_115871.1 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_115871.1 chr19 Catalytic, N-terminal domain of histone methyltransferase Dot1l d1nw3a_ chr19/NP_115871....1/NP_115871.1_holo_5-332.pdb blast 133P,134E,135V,136Y,137G,138E,139T,161D,162L,163G,

  2. Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance1[OPEN

    Science.gov (United States)

    Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John

    2017-01-01

    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. PMID:27879387

  3. The Site-Directed A184S Mutation in the HTH Domain of the Global Regulator IrrE Enhances Deinococcus radiodurans R1 Tolerance to UV Radiation and MMC Shock.

    Science.gov (United States)

    Zhang, Chen; Zhou, Zhengfu; Zhang, Wei; Chen, Zhen; Song, Yuan; Lu, Wei; Lin, Min; Chen, Ming

    2015-12-28

    IrrE is a highly conserved global regulator in the Deinococcus genus and contributes to survival from high doses of UV radiation, ionizing radiation, and desiccation. Drad-IrrE and Dgob-IrrE from Deinococcus radiodurans and Deinococcus gobiensis I-0 each share 66% sequence identity. However, Dgob-IrrE showed a stronger protection phenotype against UV radiation than Drad- IrrE in the D. radiodurans irrE-deletion mutant (ΔirrE), which may be due to amino acid residues differences around the DNA-binding HTH domain. Site-directed mutagenesis was used to generate a Drad-IrrE A184S single mutant, which has been characterized and compared with the ΔirrE mutant complemented strain with Drad-irrE, designated ΔirrE-E. The effects of the A184S mutation following UV radiation and mitomycin C (MMC) shock were determined. The A184S mutant displayed significantly increased resistance to UV radiation and MMC shock. The corresponding A184 site in Dgob-IrrE was inversely mutated, generating the S131A mutant, which exhibited a loss of resistance against UV radiation, MMC shock, and desiccation. qPCR analysis revealed that critical genes in the DNA repair system, such as recA, pprA, uvrA, and ddrB, were remarkably induced after UV radiation and MMC shock in the ΔirrE-IE and A184S mutants. These data suggested that A184S improves the ability against UV radiation and MMC shock, providing new insights into the modification of IrrE. We speculated that the serine residue may determine the efficiency of DNA binding, leading to the increased expression of IrrE-dependent genes important for protection against DNA damage.

  4. Frequency of Natural Resistance within NS5a Replication Complex Domain in Hepatitis C Genotypes 1a, 1b: Possible Implication of Subtype-Specific Resistance Selection in Multiple Direct Acting Antivirals Drugs Combination Treatment

    Directory of Open Access Journals (Sweden)

    Sabrina Bagaglio

    2016-03-01

    Full Text Available Different HCV subtypes may naturally harbor different resistance selection to anti-NS5a inhibitors. 2761 sequences retrieved from the Los Alamos HCV database were analyzed in the NS5a domain 1, the target of NS5a inhibitors. The NS5a resistance-associated polymorphisms (RAPs were more frequently detected in HCV G1b compared to G1a. The prevalence of polymorphisms associated with cross-resistance to compounds in clinical use (daclatasvir, DCV, ledipasvir, LDV, ombitasvir, and OMV or scheduled to come into clinical use in the near future (IDX719, elbasvir, and ELV was higher in G1b compared to G1a (37/1552 (2.4% in 1b sequences and 15/1209 (1.2% in 1a isolates, p = 0.040. Interestingly, on the basis of the genotype-specific resistance pattern, 95 (6.1% G1b sequences had L31M RAP to DCV/IDX719, while 6 sequences of G1a (0.5% harbored L31M RAP, conferring resistance to DCV/LDV/IDX719/ELV (p < 0.0001. Finally, 28 (2.3% G1a and none of G1b isolates harbored M28V RAP to OMV (p < 0.0001. In conclusion, the pattern of subtype-specific resistance selection in the naturally occurring strains may guide the treatment option in association with direct acting antivirals (DAAs targeting different regions, particularly in patients that are difficult to cure, such as those with advanced liver disease or individuals who have failed previous DAAs.

  5. Preparation and Catalytic Performance of Fe-Zr-O Catalysts for Direct Synthesis of Dimethyl Carbonate Using CO2 and Methanol%CO2和甲醇直接合成碳酸二甲酯的Fe-Zr-O催化剂制备和性能研究

    Institute of Scientific and Technical Information of China (English)

    陈红萍; 梁英华; 郑小满; 赵新强

    2014-01-01

    采用共沉淀法制备的Fe-Zr-O催化剂对CO2与甲醇直接合成碳酸二甲酯(DMC)反应具有较高的催化活性,与其他制备方法比较具有催化活性高且可重复利用的特点。通过SEM、TEM和N2吸附-脱附的表征结果表明,所制备的催化剂粒径均匀,比表面积大,孔道直径集中在10~30 nm,便于反应物和产物的扩散;XRD和XPS分析结果表明,铁锆之间发生了相互作用,铁的价态略有升高,使其所对应的L酸性增强,铁锆原子分别插入到对方氧化物晶格中,使氧化铁和氧化锆的晶型均发生改变。%This study investigated the preparation and catalytic performance of Fe-Zr-O catalysts prepared by co-precipitation method. The prepared catalysts were used to directly synthesize the dimethyl carbonate (DMC) from methanol and carbon dioxide. The prepared catalyst shows higher catalytic activity than catalysts prepared by other methods and it is recyclable without the decrease of activity. The synthesized catalysts were fully characterized by SEM, TEM and N2-adsorption desorption. The results reveal that they have a uniform nano-scale particle size, large specific surface area, and mesoporous channels for mass transfer. XRD and XPS results show that iron and zirconium interact with each other in the system, which increases the iron valence values and leads to the enhancement of corresponding Lewis acids. Iron and zirconium insert into their oxide lattices, which leads to the change of crystal structures of both Fe2O3 and ZrO3.

  6. Speckle Reduction for Ultrasound Image Using Edge Directions in DTCWT Domain%基于DTCWT方向信息的超声图像斑点噪声消除

    Institute of Scientific and Technical Information of China (English)

    许慰玲; 沈民奋; 杨金耀

    2011-01-01

    针对一般的小波去噪方法在去除超声图像斑点噪声时不能有效保持图像边缘信息的问题,本文提出基于双树复小波变换(Dual tree complex wavelet transform,DTCWT)方向信息的超声图像斑点噪声消除算法.利用双树复小波变换6个方向复小波系数的相对方差来确定该点是否位于边缘或纹理上,对低于门限的像素高频复系数置零以实现超声图像DTCWT域的自适应滤波.实验结果表明,与Lee,Frost,Kuan滤波方法相比,本文算法具有明显的优势;在图像平滑效果接近的情况下,本文算法边缘保持度略优于Yu提出的各向异性斑点噪声抑制(Speckle reducing anisotropic diffusion,SRAD)方法.%In general, the edge information of an image can not be effectively preserved when traditional wavelet de-noising methods are adopted to reduce the speckle in ultrasound images. In view of this problem, a novel speckle reducing algorithm for ultrasound images is proposed based on the dual tree complex wavelet transform (DD-DTCWT) direction information. The relative variance of the six directional complex detail coefficients about DTCWT is used to determine whether points are located at the edges or in the textures. Specifically, speckle is reduced by resetting complex detail coefficients to zero for the pixels beyond the threshold. Through such a way the adaptive filter in DTCWT domain is realized. Experimental results show that the proposed method significantly outperforms the state-of-the-art competitors including Lee, Frost and Kuan filtering methods. Also, the degree of edge maintaining of the method is better than the speckle reducing anisotropic diffusion (SRAD) method proposed by Yu for images with similar smoothing effects.

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

    Energy Technology Data Exchange (ETDEWEB)

    Eteman, Shahrokh

    2013-06-30

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

  8. 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.

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

    Science.gov (United States)

    Zhao, Hailong; Zheng, Chunqin; Cui, Hongjuan

    2015-01-01

    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(var)3-9 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.

  10. Template electrodeposition of catalytic nanomotors.

    Science.gov (United States)

    Wang, Joseph

    2013-01-01

    The combination of nanomaterials with electrode materials has opened new horizons in electroanalytical chemistry, and in electrochemistry in general. Over the past two decades we have witnessed an enormous activity aimed at designing new electrochemical devices based on nanoparticles, nanotubes or nanowires, and towards the use of electrochemical routes--particularly template-assisted electrodeposition--for preparing nanostructured materials. The power of template-assisted electrochemical synthesis is demonstrated in this article towards the preparation and the realization of self-propelled catalytic nanomotors, ranging from Pt-Au nanowire motors to polymer/Pt microtube engines. Design considerations affecting the propulsion behavior of such catalytic nanomotors are discussed along with recent bioanalytical and environmental applications. Despite recent major advances, artificial nanomotors have a low efficiency compared to their natural counterparts. Hopefully, the present Faraday Discussion will stimulate other electrochemistry teams to contribute to the fascinating area of artificial nanomachines.

  11. Radiation/Catalytic Augmented Combustion.

    Science.gov (United States)

    1980-09-01

    NATIO& NAk H(fJI At tl TANUAHTOb 19 A ~omm.81-0287 LVL RADIATION/CATALYTIC AUGMENTED COMBUST ION MOSHE LAVID CORPORATE RESEARCH-TECHNOLOGY FEASIBILITY...refinements as necessary. i. Perform cannular combustor experiments to Investigate ignition and flame attachment in flowing, liquid -fuel, unpremixed...stabilizer, with a sintered metal disk on the downstream side through which hot gases or products of partial fuel oxidation can be passed. Experimental

  12. Thermodynamics of catalytic nanoparticle morphology

    Science.gov (United States)

    Zwolak, Michael; Sharma, Renu; Lin, Pin Ann

    Metallic nanoparticles are an important class of industrial catalysts. The variability of their properties and the environment in which they act, from their chemical nature & surface modification to their dispersion and support, allows their performance to be optimized for many chemical processes useful in, e.g., energy applications and other areas. Their large surface area to volume ratio, as well as varying sizes and faceting, in particular, makes them an efficient source for catalytically active sites. These characteristics of nanoparticles - i.e., their morphology - can often display intriguing behavior as a catalytic process progresses. We develop a thermodynamic model of nanoparticle morphology, one that captures the competition of surface energy with other interactions, to predict structural changes during catalytic processes. Comparing the model to environmental transmission electron microscope images of nickel nanoparticles during carbon nanotube (and other product) growth demonstrates that nickel deformation in response to the nanotube growth is due to a favorable interaction with carbon. Moreover, this deformation is halted due to insufficient volume of the particles. We will discuss the factors that influence morphology and also how the model can be used to extract interaction strengths from experimental observations.

  13. New directions for the catalytic conversion of methane

    Science.gov (United States)

    Lunsford, J. H.

    1992-02-01

    The addition of chlorine via HCl to a Li(+)-MgO catalyst improves its activity for the oxidative dehydrogenation (OXD) of ethane. The latter effect is greater than ethylene-to-ethane ratio (greater than 5) observed during the oxidative coupling reaction. During the OXD reaction at 620 C, an 80 percent conversion of C2H6 was achieved with 77 percent selectivity to C2H4 after 40 h on stream. To attain these favorable results, the Cl/Li ratio must be greater than or = 0.9. The absolute amounts of Li and Cl are of secondary importance, although an excess amount of promoters may serve to replace that which is slowly lost during the reaction. In the presence of chlorine, LiCl is formed rather than Li2CO3. The carbonate phase spreads over the surface and presumably blocks active sites. The chlorine in the catalyst also modifies the gross basicity of the catalyst, thus, making it less effective for the future oxidation of ethylene, which is the desired product.

  14. Lectin domains of polypeptide GalNAc transferases exhibit glycopeptide binding specificity.

    Science.gov (United States)

    Pedersen, Johannes W; Bennett, Eric P; Schjoldager, Katrine T-B G; Meldal, Morten; Holmér, Andreas P; Blixt, Ola; Cló, Emiliano; Levery, Steven B; Clausen, Henrik; Wandall, Hans H

    2011-09-16

    UDP-GalNAc:polypeptide α-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 specificity, whereas the primary function of the lectin domain is to increase affinity to previously glycosylated substrates. Whether the lectin domain also has peptide sequence selectivity has remained unclear. Using a glycopeptide array with a library of synthetic and recombinant glycopeptides based 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 an additional level of complexity in the initiation step of O-glycosylation by GalNAc-Ts.

  15. 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

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

    Institute of Scientific and Technical Information of China (English)

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

    2013-01-01

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

  17. Mechanism of Transition-Metal Nanoparticle Catalytic Graphene Cutting.

    Science.gov (United States)

    Ma, Liang; Wang, Jinlan; Yip, Joanne; Ding, Feng

    2014-04-03

    Catalytic cutting by transition-metal (TM) particles is a promising method for the synthesizing of high-quality graphene quantum dots and nanoribbons with smooth edges. Experimentally, it is observed that the cutting always results in channels with zigzag (ZZ) or armchair (AC) edges. However, the driving force that is responsible for such a cutting behavior remains a puzzle. Here, by calculating the interfacial formation energies of the TM-graphene edges with ab initio method, we show that the surface of a catalyst particle tends to be aligned along either AC or ZZ direction of the graphene lattice, and thus the cutting of graphene is guided as such. The different cutting behaviors of various catalysts are well-explained based on the competition between TM-passivated graphene edges and the etching-agent-terminated ones. Furthermore, the kinetics of graphene catalytic cutting along ZZ and AC directions, respectively, are explored at the atomic level.

  18. Production of filamentous carbon and H{sub 2} by solarthermal catalytic cracking of CH{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Kirillov, V.; Kuvshinov, G. [Boreskov Inst. of Catalysis (Russian Federation); Reller, A. [Hamburg Univ., Hamburg (Germany); Steinfeld, A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    The catalytic thermal decomposition of methane has been experimentally studied using high-temperature solar process heat. Nickel catalyst particles, fluidized in methane, were directly irradiated at the PSI solar furnace. Carbon deposition consisted of randomly interlaced filaments that grew as fibers and hollow nanotubes (of approx. 30 nm diameter) originating at each catalytic particle. (author) 4 figs., 7 refs.

  19. Trends in catalytic NO decomposition over transition metal surfaces

    DEFF Research Database (Denmark)

    Falsig, Hanne; Bligaard, Thomas; Rass-Hansen, Jeppe

    2007-01-01

    The formation of NOx from combustion of fossil and renewable fuels continues to be a dominant environmental issue. We take one step towards rationalizing trends in catalytic activity of transition metal catalysts for NO decomposition by combining microkinetic modelling with density functional...... theory calculations. We show specifically why the key problem in using transition metal surfaces to catalyze direct NO decomposition is their significant relative overbinding of atomic oxygen compared to atomic nitrogen....

  20. Carbon nanofibers grown on metallic filters as novel catalytic materials

    OpenAIRE

    Tribolet, Pascal; Kiwi-Minsker, Lioubov

    2005-01-01

    Carbon nanofibers (CNF) were synthesized on sintered metal fibers (SMF) filters of nickel and Ni-containing alloys (Inconel, stainless steel (SS)) by thermal chemical vapor deposition of ethane in the presence of hydrogen at not, vert, similar660 °C. The CNFs were formed directly over the SMF filters without deposition of metal particles. The catalytic active sites leading to the CNF formation were attained by oxidation–reduction of the SMF filter. The CNFs present platelet morphology as dete...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-02-17

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

  2. Calcineurin A versus NS5A-TP2/HD domain containing 2: a case study of site-directed low-frequency random mutagenesis for dissecting target specificity of peptide aptamers.

    Science.gov (United States)

    Dibenedetto, Silvia; Cluet, David; Stebe, Pierre-Nicolas; Baumle, Véronique; Léault, Jérémie; Terreux, Raphaël; Bickle, Marc; Chassey, Benoit D E; Mikaelian, Ivan; Colas, Pierre; Spichty, Martin; Zoli, Michele; Rudkin, Brian B

    2013-07-01

    We previously identified a peptide aptamer (named R5G42) via functional selection for its capacity to slow cell proliferation. A yeast two-hybrid screen of human cDNA libraries, using R5G42 as "bait," allowed the identification of two binding proteins with very different functions: calcineurin A (CnA) (PP2B/PPP3CA), a protein phosphatase well characterized for its role in the immune response, and NS5A-TP2/HD domain containing 2, a much less studied protein induced subsequent to hepatitis C virus non-structural protein 5A expression in HepG2 hepatocellular carcinoma cells, with no known activity. Our objective in the present study was to dissect the dual target specificity of R5G42 in order to have tools with which to better characterize the actions of the peptide aptamers toward their individual targets. This was achieved through the selection of random mutants of the variable loop, derived from R5G42, evaluating their specificity toward CnA and NS5A-TP2 and analyzing their sequence. An interdisciplinary approach involving biomolecular computer simulations with integration of the sequence data and yeast two-hybrid binding phenotypes of these mutants yielded two structurally distinct conformers affording the potential molecular basis of the binding diversity of R5G42. Evaluation of the biological impact of CnA- versus NS5A-TP2-specific peptide aptamers indicated that although both contributed to the anti-proliferative effect of R5G42, CnA-binding was essential to stimulate the nuclear translocation of nuclear factor of activated T cells, indicative of the activation of endogenous CnA. By dissecting the target specificity of R5G42, we have generated novel tools with which to study each target individually. Apta-C8 is capable of directly activating CnA independent of binding to NS5A-TP2 and will be an important tool in studying the role of CnA activation in the regulation of different signaling pathways, whereas Apta-E1 will allow dissection of the function of NS5A

  3. PEMFC electrode preparation: Influence of the solvent composition and evaporation rate on the catalytic layer microstructure

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, R.; Daza, L. [Instituto de Catalisis y Petroleoquimica, CSIC, C/ Marie Curie, 2, 28049 Madrid (Spain); Ferreira-Aparicio, P. [Centro de Investigaciones Energeticas Medioambientales y Tecnologicas (CIEMAT), Avda. Complutense, 22, 28040 Madrid (Spain)

    2005-10-10

    A series of parameters affecting the catalytic layer microstructure in polymer exchange fuel cell electrodes have been evaluated. The deposition of the catalytic layer in the gas diffusion support is shown to depend not only on the ink deposition method but also on the characteristics of the solvent used to disperse both the catalyst and the Nafion ionomer. The solvent viscosity and its dielectric constant are two important factors to control for the catalytic ink preparation. In particular, the solvent dielectric constant is shown to be directly related to the electrode performance in single cell tests. (author)

  4. SYNTHETIC AND CATALYTIC PROPERTY STUDIES ON SILICA SUPPORTED BIS-(ACETYLACETONATO ) COBALT(Ⅱ) COMPLEXES

    Institute of Scientific and Technical Information of China (English)

    LI Xiaohu; LU Yun; LIN Sicong

    1992-01-01

    This paper reports mainly the preparation of silica supported acetylacetone ligands and their cobalt complexes, the characterization of their chemical structure, and the evaluation of their catalytic activity in the reaction for the preparation of ethers directly from alkanols and benzyl chloride. The results indicate that those silica supported β-diketone cobalt complexes (SACO) not only can simplify the reaction procedure of the ether preparation but also show a much higher catalytic activity in comparison with other homogeneous catalysts. In addition, SACO can be recovered and reused although their catalytic activity descend gradually as a result of the decrease in their cobalt content.

  5. Structural basis for catalytically restrictive dynamics of a high-energy enzyme state

    Science.gov (United States)

    Kovermann, Michael; Ådén, Jörgen; Grundström, Christin; Elisabeth Sauer-Eriksson, A.; Sauer, Uwe H.; Wolf-Watz, Magnus

    2015-07-01

    An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or `invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power--a key aspect in rational design of enzymes catalysing novel reactions.

  6. 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.

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

    Science.gov (United States)

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

    2015-10-01

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

  8. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan

    2008-01-01

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

  9. Loss of Dnmt1 catalytic activity reveals multiple roles for DNA methylation during pancreas development and regeneration.

    Science.gov (United States)

    Anderson, Ryan M; Bosch, Justin A; Goll, Mary G; Hesselson, Daniel; Dong, P Duc Si; Shin, Donghun; Chi, Neil C; Shin, Chong Hyun; Schlegel, Amnon; Halpern, Marnie; Stainier, Didier Y R

    2009-10-01

    Developmental mechanisms regulating gene expression and the stable acquisition of cell fate direct cytodifferentiation during organogenesis. Moreover, it is likely that such mechanisms could be exploited to repair or regenerate damaged organs. DNA methyltransferases (Dnmts) are enzymes critical for epigenetic regulation, and are used in concert with histone methylation and acetylation to regulate gene expression and maintain genomic integrity and chromosome structure. We carried out two forward genetic screens for regulators of endodermal organ development. In the first, we screened for altered morphology of developing digestive organs, while in the second we screed for the lack of terminally differentiated cell types in the pancreas and liver. From these screens, we identified two mutant alleles of zebrafish dnmt1. Both lesions are predicted to eliminate dnmt1 function; one is a missense mutation in the catalytic domain and the other is a nonsense mutation that eliminates the catalytic domain. In zebrafish dnmt1 mutants, the pancreas and liver form normally, but begin to degenerate after 84 h post fertilization (hpf). Acinar cells are nearly abolished through apoptosis by 100 hpf, though neither DNA replication, nor entry into mitosis is halted in the absence of detectable Dnmt1. However, endocrine cells and ducts are largely spared. Surprisingly, dnmt1 mutants and dnmt1 morpholino-injected larvae show increased capacity for pancreatic beta cell regeneration in an inducible model of pancreatic beta cell ablation. Thus, our data suggest that Dnmt1 is dispensable for pancreatic duct or endocrine cell formation, but not for acinar cell survival. In addition, Dnmt1 may influence the differentiation of pancreatic beta cell progenitors or the reprogramming of cells toward the pancreatic beta cell fate.

  10. 合成方法对于生物质合成气一步法合成二甲醚催化剂性能的影响%Study on Synthesis Method on Catalytical Performance of Catalysts for Direct Synthesis of Dimethyl Ether from Bio-syngas

    Institute of Scientific and Technical Information of China (English)

    徐海燕; 雷廷宙; 任素霞; 何晓峰; 朱金陵

    2012-01-01

    以Cu-ZnO-Fe2O3-ZrO2作为甲醇合成活性组分并以HZSM-5作为甲醇脱水活性组分用3种不同的方法合成了催化剂,对催化剂进行了XRD和BET表征.研究了3种合成方法对于生物质合成气一步法制二甲醚Cu-ZnO-Fe2O3-ZrO2/HZSM-5催化剂催化性能的影响,结果表明,合成方法对于活性组分的分散度有很大的影响,从而进一步影响催化剂对于该反应的催化活性及目标产物的选择性.%Three catalysts were synthesized using Cu —ZnO -Fe2O3 — ZrO2 as methanol synthesis component and HZSM-5 as methanol dehydration component. The catalysts were characterized using X-ray diffraction (XRD), and Brunauer-Emmett-Teller (BET) surface area techniques. Synthesis methods on catalytical performance of catalysts for direct synthesis of dimethyl ether from bio—syngas were studied. The results show that synthesis methods have great impact on the dispersity of active components of the catalysts, and then affecting the conversion of CO and selectivity of DME for this reaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Timko, Michael P.

    1999-09-24

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-04-16

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

  13. Life and death of a single catalytic cracking particle

    Science.gov (United States)

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-30

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

  15. Membrane binding domains

    OpenAIRE

    Hurley, James H.

    2006-01-01

    Eukaryotic signaling and trafficking proteins are rich in modular domains that bind cell membranes. These binding events are tightly regulated in space and time. The structural, biochemical, and biophysical mechanisms for targeting have been worked out for many families of membrane binding domains. This review takes a comparative view of seven major classes of membrane binding domains, the C1, C2, PH, FYVE, PX, ENTH, and BAR domains. These domains use a combination of specific headgroup inter...

  16. 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

  17. 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.

  18. Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain

    Science.gov (United States)

    Melcher, Rebecca L. J.; Neumann, Marten; Fuenzalida Werner, Juan Pablo; Gröhn, Franziska; Moerschbacher, Bruno M.

    2017-01-01

    Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential. PMID:28327560

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

    DEFF Research Database (Denmark)

    Lenaerts, Tom; Ferkinghoff-Borg, Jesper; Stricher, Francois

    2008-01-01

    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...

  20. Some Aspects of the Catalytic Organic Synthesis

    Institute of Scientific and Technical Information of China (English)

    Anil; K.Saikia

    2007-01-01

    1 Results Catalytic reactions are gaining importance due to its low cost, operational simplicity, high efficiency and selectivity. It is also getting much attention in green synthesis. Many useful organic reactions, including the acylation of alcohols and aldehydes, carbon-carbon, carbon-nitrogen, carbon-sulfur bond forming and oxidation reactions are carried out by catalyst. We are exploring the catalytic acylation of alcohols and aldehydes in a simple and efficient manner. Catalytic activation of unr...

  1. Direct observation of temperature dependent magnetic domain structure of the multiferroic La{sub 0.66}Sr{sub 0.34}MnO{sub 3}/BiFeO{sub 3} bilayer system by x-ray linear dichroism- and x-ray magnetic circular dichroism-photoemission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mix, C.; Finizio, S.; Jakob, G.; Kläui, M. [Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 7, D-55128 Mainz (Germany); Buzzi, M.; Nolting, F. [Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Kronast, F. [Helmholtz-Zentrum-Berlin für Materialien und Energie GmbH, Albert-Einstein Straße 15, D-12489 Berlin (Germany)

    2014-05-21

    Low-thickness La{sub 0.66}Sr{sub 0.34}MnO{sub 3} (LSMO)/BiFeO{sub 3} (BFO) thin film samples deposited on SrTiO{sub 3} were imaged by high resolution x-ray microscopy at different temperatures. The ultra-thin thickness of the top layer allows to image both the ferromagnetic domain structure of LSMO and the multiferroic domain structure of the buried BFO layer, opening a path to a direct observation of coupling at the interface on a microscopic level. By comparing the domain size and structure of the BFO and LSMO, we observed that, in contrast to LSMO single layers, LSMO/BFO multilayers show a strong temperature dependence of the ferromagnetic domain structure of the LSMO. Particularly, at 40 K, a similar domain size for BFO and LSMO is observed. This indicates a persistence of exchange coupling on the microscopic scale at a temperature, where the exchange bias as determined by magnetometer measurements is vanishing.

  2. Switching direction in electric-signal-induced cell migration by cyclic guanosine monophosphate and phosphatidylinositol signaling.

    Science.gov (United States)

    Sato, Masayuki J; Kuwayama, Hidekazu; van Egmond, Wouter N; Takayama, Airi L K; Takagi, Hiroaki; van Haastert, Peter J M; Yanagida, Toshio; Ueda, Masahiro

    2009-04-21

    Switching between attractive and repulsive migration in cell movement in response to extracellular guidance cues has been found in various cell types and is an important cellular function for translocation during cellular and developmental processes. Here we show that the preferential direction of migration during electrotaxis in Dictyostelium cells can be reversed by genetically modulating both guanylyl cyclases (GCases) and the cyclic guanosine monophosphate (cGMP)-binding protein C (GbpC) in combination with the inhibition of phosphatidylinositol-3-OH kinases (PI3Ks). The PI3K-dependent pathway is involved in cathode-directed migration under a direct-current electric field. The catalytic domains of soluble GCase (sGC) and GbpC also mediate cathode-directed signaling via cGMP, whereas the N-terminal domain of sGC mediates anode-directed signaling in conjunction with both the inhibition of PI3Ks and cGMP production. These observations provide an identification of the genes required for directional switching in electrotaxis and suggest that a parallel processing of electric signals, in which multiple-signaling pathways act to bias cell movement toward the cathode or anode, is used to determine the direction of migration.

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

    Science.gov (United States)

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

    2016-06-22

    The direct catalytic conversion of methane to liquid oxygenated compounds, such as methanol or dimethyl ether, at low temperature using molecular oxygen is a grand challenge in C-H activation that has never been met with synthetic, heterogeneous catalysts. We report the first demonstration of direct, catalytic oxidation of methane into methanol with molecular oxygen over copper-exchanged zeolites at low reaction temperatures (483-498 K). Reaction kinetics studies show sustained catalytic activity and high selectivity for a variety of commercially available zeolite topologies under mild conditions (e.g., 483 K and atmospheric pressure). Transient and steady state measurements with isotopically labeled molecules confirm catalytic turnover. The catalytic rates and apparent activation energies are affected by the zeolite topology, with caged-based zeolites (e.g., Cu-SSZ-13) showing the highest rates. Although the reaction rates are low, the discovery of catalytic sites in copper-exchanged zeolites will accelerate the development of strategies to directly oxidize methane into methanol under mild conditions.

  4. Catalytic microrotor driven by geometrical asymmetry

    Science.gov (United States)

    Yang, Mingcheng; Ripoll, Marisol; Chen, Ke

    2015-02-01

    An asymmetric gear with homogeneous surface properties is, here, presented as a prototype to fabricate catalytic microrotors. The driving torque arises from the diffusiophoretic effect induced by the concentration gradients generated by catalytic chemical reactions at the gear surface. This torque produces a spontaneous and unidirectional rotation of the asymmetric gear. By means of mesoscopic simulations, we prove and characterize this scenario. The gear rotational velocity is determined by the gear-solvent interactions, the gear geometry, the solvent viscosity, and the catalytic reaction ratio. Our work presents a simple way to design self-propelled microrotors, alternative to existing catalytic bi-component, or thermophoretic ones.

  5. Nanostructured Catalytic Reactors for Air Purification Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I project proposes the development of lightweight compact nanostructured catalytic reactors for air purification from toxic gaseous organic...

  6. Nanostructured Catalytic Reactors for Air Purification Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase II project proposes the development of lightweight compact nanostructured catalytic reactors for air purification from toxic gaseous organic...

  7. 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.

  8. Oligomerization of DH Domain Is Essential for Dbl-Induced Transformation

    OpenAIRE

    Zhu, Kejin; Debreceni, Balazs; Bi, Feng; Zheng, Yi

    2001-01-01

    The dbl oncogene product (onco-Dbl) is the prototype member of a family of guanine nucleotide exchange factors (GEFs) for Rho GTPases. The Dbl homology (DH) domain of onco-Dbl is responsible for the GEF catalytic activity, and the DH domain, together with the immediately adjacent pleckstrin homology (PH) domain, constitutes the minimum module bearing transforming function. In the present study, we demonstrate that the onco-Dbl protein exists in oligomeric form in vitro and in cells. The oligo...

  9. A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange

    OpenAIRE

    Rossman, Kent L.; Worthylake, David K.; Snyder, Jason T; Siderovski, David P.; Campbell, Sharon L; Sondek, John

    2002-01-01

    Dbl-related oncoproteins are guanine nucleotide exchange factors (GEFs) specific for Rho guanosine triphosphatases (GTPases) and invariably possess tandem Dbl (DH) and pleckstrin homology (PH) domains. While it is known that the DH domain is the principal catalytic subunit, recent biochemical data indicate that for some Dbl-family proteins, such as Dbs and Trio, PH domains may cooperate with their associated DH domains in promoting guanine nucleotide exchange of Rho GTPases. In order to gain ...

  10. Catalytic reforming feed characterisation technique

    Energy Technology Data Exchange (ETDEWEB)

    Larraz Mora, R.; Arvelo Alvarez, R. [Univ. of La Laguna, Chemical Engineering Dept., La Laguna (Spain)

    2002-09-01

    The catalytic reforming of naphtha is one of the major refinery processes, designed to increase the octane number of naphtha or to produce aromatics. The naphtha used as catalytic reformer feedstock usually contains a mixture of paraffins, naphthenes, and aromatics in the carbon number range C{sub 6} to C{sub 10}. The detailed chemical composition of the feed is necessary to predict the aromatics and hydrogen production as well as the operation severity. The analysis of feed naphtha is usually reported in terms of its ASTM distillation curve and API or specific gravity. Since reforming reactions are described in terms of lumped chemical species (paraffins, naphthenes and aromatics), a feed characterisation technique should be useful in order to predict reforming operating conditions and detect feed quality changes. Unfortunately online analyzer applications as cromatography or recently introduced naphtha NMR [1] are scarce in most of refineries. This work proposes an algorithmic characterisation method focusing on its main steps description. The method could help on the subjects previously described, finally a calculation example is shown. (orig.)

  11. Domains via Graphs

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guoqiang; CHEN Yixiang

    2001-01-01

    This paper provides a concrete and simple introduction to two pillars of domain theory: (1) solving recursive domain equations, and (2) universal and saturated domains. Our exposition combines Larsen and Winskel's idea on solving domain equations using information systems with Girard's idea of stable domain theory in the form of coherence spaces, or graphs.Detailed constructions are given for universal and even homogeneous objects in two categories of graphs: one representing binary complete, prime algebraic domains with complete primes covering the bottom; the other representing ω-algebraic, prime algebraic lattices. The backand-forth argument in model theory helps to enlighten the constructions.

  12. Ultraviolet laser deposition of graphene thin films without catalytic layers

    KAUST Repository

    Sarath Kumar, S. R.

    2013-01-09

    In this letter, the formation of nanostructured graphene by ultraviolet laser ablation of a highly ordered pyrolytic graphite target under optimized conditions is demonstrated, without a catalytic layer, and a model for the growth process is proposed. Previously, graphene film deposition by low-energy laser (2.3 eV) was explained by photo-thermal models, which implied that graphene films cannot be deposited by laser energies higher than the C-C bond energy in highly ordered pyrolytic graphite (3.7 eV). Here, we show that nanostructured graphene films can in fact be deposited using ultraviolet laser (5 eV) directly over different substrates, without a catalytic layer. The formation of graphene is explained by bond-breaking assisted by photoelectronic excitation leading to formation of carbon clusters at the target and annealing out of defects at the substrate.

  13. Guiding catalytically active particles with chemically patterned surfaces

    CERN Document Server

    Uspal, W E; Dietrich, S; Tasinkevych, M

    2016-01-01

    Catalytically active Janus particles suspended in solution create gradients in the chemical composition of the solution along their surfaces, as well as along any nearby container walls. The former leads to self-phoresis, while the latter gives rise to chemi-osmosis, providing an additional contribution to self-motility. Chemi-osmosis strongly depends on the molecular interactions between the diffusing chemical species and the wall. We show analytically, using an approximate "point-particle" approach, that by chemically patterning a planar substrate one can direct the motion of Janus particles: the induced chemi-osmotic flows can cause particles to either "dock" at the chemical step between the two materials, or to follow a chemical stripe. These theoretical predictions are confirmed by full numerical calculations. Generically, docking occurs for particles which tend to move away from their catalytic caps, while stripe-following occurs in the opposite case. Our analysis reveals the physical mechanisms governi...

  14. Neutralization of botulinum neurotoxin by a human monoclonal antibody specific for the catalytic light chain.

    Directory of Open Access Journals (Sweden)

    Sharad P Adekar

    Full Text Available BACKGROUND: Botulinum neurotoxins (BoNT are a family of category A select bioterror agents and the most potent biological toxins known. Cloned antibody therapeutics hold considerable promise as BoNT therapeutics, but the therapeutic utility of antibodies that bind the BoNT light chain domain (LC, a metalloprotease that functions in the cytosol of cholinergic neurons, has not been thoroughly explored. METHODS AND FINDINGS: We used an optimized hybridoma method to clone a fully human antibody specific for the LC of serotype A BoNT (BoNT/A. The 4LCA antibody demonstrated potent in vivo neutralization when administered alone and collaborated with an antibody specific for the HC. In Neuro-2a neuroblastoma cells, the 4LCA antibody prevented the cleavage of the BoNT/A proteolytic target, SNAP-25. Unlike an antibody specific for the HC, the 4LCA antibody did not block entry of BoNT/A into cultured cells. Instead, it was taken up into synaptic vesicles along with BoNT/A. The 4LCA antibody also directly inhibited BoNT/A catalytic activity in vitro. CONCLUSIONS: An antibody specific for the BoNT/A LC can potently inhibit BoNT/A in vivo and in vitro, using mechanisms not previously associated with BoNT-neutralizing antibodies. Antibodies specific for BoNT LC may be valuable components of an antibody antidote for BoNT exposure.

  15. SERCA mutant E309Q binds two Ca ions but adopts a catalytically incompetent conformation

    DEFF Research Database (Denmark)

    Clausen, Johannes D.; Bublitz, Maike; Arnou, Bertrand;

    2013-01-01

    The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) couples ATP hydrolysis to transport of Ca2+. This directed energy transfer requires cross-talk between the two Ca2+ sites and the phosphorylation site over 50 Å distance. We have addressed the mechano-structural basis for this intramolecular...... signal by analysing the structure and the functional properties of SERCA mutant E309Q. Glu309 contributes to Ca2+ coordination at site II, and a consensus has been that E309Q only binds Ca2+ at site I. The crystal structure of E309Q in the presence of Ca2+ and an ATP analogue, however, reveals two...... occupied Ca2+ sites of a non-catalytic Ca2E1 state. Ca2+ is bound with micromolar affinity by both Ca2+ sites in E309Q, but without cooperativity. The Ca2+-bound mutant does phosphorylate from ATP, but at a very low maximal rate. Phosphorylation depends on the correct positioning of the A-domain, requiring...

  16. Detailed characterization of the cooperative mechanism of Ca(2+) binding and catalytic activation in the Ca(2+) transport (SERCA) ATPase.

    Science.gov (United States)

    Zhang, Z; Lewis, D; Strock, C; Inesi, G; Nakasako, M; Nomura, H; Toyoshima, C

    2000-08-01

    Expression of heterologous SERCA1a ATPase in Cos-1 cells was optimized to yield levels that account for 10-15% of the microsomal protein, as revealed by protein staining on electrophoretic gels. This high level of expression significantly improved our characterization of mutants, including direct measurements of Ca(2+) binding by the ATPase in the absence of ATP, and measurements of various enzyme functions in the presence of ATP or P(i). Mutational analysis distinguished two groups of amino acids within the transmembrane domain: The first group includes Glu771 (M5), Thr799 (M6), Asp800 (M6), and Glu908 (M8), whose individual mutations totally inhibit binding of the two Ca(2+) required for activation of one ATPase molecule. The second group includes Glu309 (M4) and Asn796 (M6), whose individual or combined mutations inhibit binding of only one and the same Ca(2+). The effects of mutations of these amino acids were interpreted in the light of recent information on the ATPase high-resolution structure, explaining the mechanism of Ca(2+) binding and catalytic activation in terms of two cooperative sites. The Glu771, Thr799, and Asp800 side chains contribute prominently to site 1, together with less prominent contributions by Asn768 and Glu908. The Glu309, Asn796, and Asp800 side chains, as well as the Ala305 (and possibly Val304 and Ile307) carbonyl oxygen, contribute to site 2. Sequential binding begins with Ca(2+) occupancy of site 1, followed by transition to a conformation (E') sensitive to Ca(2+) inhibition of enzyme phosphorylation by P(i), but still unable to utilize ATP. The E' conformation accepts the second Ca(2+) on site 2, producing then a conformation (E' ') which is able to utilize ATP. Mutations of residues (Asp813 and Asp818) in the M6/M7 loop reduce Ca(2+) affinity and catalytic turnover, suggesting a strong influence of this loop on the correct positioning of the M6 helix. Mutation of Asp351 (at the catalytic site within the cytosolic domain

  17. Domains of laminin

    DEFF Research Database (Denmark)

    Engvall, E; Wewer, U M

    1996-01-01

    Extracellular matrix molecules are often very large and made up of several independent domains, frequently with autonomous activities. Laminin is no exception. A number of globular and rod-like domains can be identified in laminin and its isoforms by sequence analysis as well as by electron...... microscopy. Here we present the structure-function relations in laminins by examination of their individual domains. This approach to viewing laminin is based on recent results from several laboratories. First, some mutations in laminin genes that cause disease have affected single laminin domains, and some...... laminin isoforms lack particular domains. These mutants and isoforms are informative with regard to the activities of the mutated and missing domains. These mutants and isoforms are informative with regard to the activities of the mutated and missing domains. Second, laminin-like domains have now been...

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

    Science.gov (United States)

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

    2004-01-01

    Serinekhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth. Here we report the 1.6 Angstrom resolution crystal structure of PP5 catalytic domain with metal and phosphate ions in the active site. The structure reveals a mechanism for PPS-mediated catalysis that requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1),-M(sub 2)-His(sup 427)-W(sup 2)-His(sup 304)-Asp(sup 274) catalytic motif, and provides a structural basis for the exceptional catalytic proficiency of protein phosphatases placing them among the most powerful catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of PP5 should aid development of specific inhibitors.

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

    Science.gov (United States)

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

    2004-01-01

    Serinehhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth and cellular responses to stress. Here we report the crystal structure of the PP5 catalytic domain (PP5c) at a resolution of 1.6 A. From this structure we resolved the mechanism for PP5-mediated hydrolysis of phosphoprotein substrates, which requires the precise positioning of two metal ions within a con served Aspn-271-M(sub 1):M(sub 2)-W(sup 1)-His-427-His-304-Asp-274 catalytic motif. The structure of PPSc provides a structural basis for explaining the exceptional catalytic proficiency of protein phosphatases, which are among the most powerful known catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of the PP5c should also aid development of type-specific inhibitors.

  20. Field induced domain switching as the origin of anomalous lattice strain along non-polar direction in rhombohedral BiScO{sub 3}-PbTiO{sub 3} close to the morphotropic phase boundary

    Energy Technology Data Exchange (ETDEWEB)

    Lalitha, K. V.; Ranjan, Rajeev, E-mail: rajeev@materials.iisc.ernt.in [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012 (India); Fancher, Chris M.; Jones, Jacob L. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695 (United States)

    2015-08-03

    The lattice strain and domain switching behavior of xBiScO{sub 3}–(1-x)PbTiO{sub 3} (x = 0.40) was investigated as a function of cyclic field and grain orientation by in situ X-ray diffraction during application of electric fields. The electric field induced 200 lattice strain was measured to be five times larger than the 111 lattice strain in pseudorhombohedral xBiScO{sub 3}–(1-x)PbTiO{sub 3} (x = 0.40). It is shown that the anomalous 200 lattice strain is not an intrinsic phenomenon, but arises primarily due to stress associated with the reorientation of the 111 domains in dense polycrystalline ceramic.

  1. Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum.

    Directory of Open Access Journals (Sweden)

    Binchun Li

    Full Text Available Flexible NC-loops between the catalytic domain and the cap domain of the α/β hydrolase fold enzymes show remarkable diversity in length, sequence, and configuration. Recent investigations have suggested that the NC-loop might be involved in catalysis and substrate recognition in many enzymes from the α/β hydrolase fold superfamily. To foster a deep understanding of its role in catalysis, stability, and divergent evolution, we here systemically investigated the function of the NC-loop (residues 131-151 in a lipase (FClip1 from thermophilic bacterium Fervidobacterium changbaicum by loop deletion, alanine-scanning mutagenesis and site-directed mutagenesis. We found that the upper part of the NC-loop (residues 131-138 was of great importance to enzyme catalysis. Single substitutions in this region could fine-tune the activity of FClip1 as much as 41-fold, and any deletions from this region rendered the enzyme completely inactive. The lower part of the NC-loop (residues 139-151 was capable of enduring extensive deletions without loss of activity. The shortened mutants in this region were found to show both improved activity and increased stability simultaneously. We therefore speculated that the NC-loop, especially the lower part, would be a perfect target for enzyme engineering to optimize the enzymatic properties, and might present a hot zone for the divergent evolution of α/β hydrolases. Our findings may provide an opportunity for better understanding of the mechanism of divergent evolution in the α/β hydrolase fold superfamily, and may also guide the design of novel biocatalysts for industrial applications.

  2. Electrochemical promotion of catalytic reactions

    Science.gov (United States)

    Imbihl, R.

    2010-05-01

    The electrochemical promotion of heterogeneously catalyzed reactions (EPOC) became feasible through the use of porous metal electrodes interfaced to a solid electrolyte. With the O 2- conducting yttrium stabilized zirconia (YSZ), the Na + conducting β″-Al 2O 3 (β-alumina), and several other types of solid electrolytes the EPOC effect has been demonstrated for about 100 reaction systems in studies conducted mainly in the mbar range. Surface science investigations showed that the physical basis for the EPOC effect lies in the electrochemically induced spillover of oxygen and alkali metal, respectively, onto the surface of the metal electrodes. For the catalytic promotion effect general concepts and mechanistic schemes were proposed but these concepts and schemes are largely speculative. Applying surface analytical tools to EPOC systems the proposed mechanistic schemes can be verified or invalidated. This report summarizes the progress which has been achieved in the mechanistic understanding of the EPOC effect.

  3. Catalytic Graphitization of Phenolic Resin

    Institute of Scientific and Technical Information of China (English)

    Mu Zhao; Huaihe Song

    2011-01-01

    The catalytic graphitization of thermal plastic phenolic-formaldehyde resin with the aid of ferric nitrate (FN) was studied in detail. The morphologies and structural features of the products including onion-like carbon nanoparticles and bamboo-shaped carbon nanotubes were investigated by transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction and Raman spectroscopy measurements. It was found that with the changes of loading content of FN and residence time at 1000℃, the products exhibited various morphologies. The TEM images showed that bamboo-shaped carbon nanotube consisted of tens of bamboo sticks and onion-like carbon nanoparticle was made up of quasi-spherically concentrically closed carbon nanocages.

  4. Unsteady processes in catalytic reactors

    Energy Technology Data Exchange (ETDEWEB)

    Matros, Yu.Sh.

    1985-01-01

    In recent years a realization has occurred that reaction and reactor dynamics must be considered when designing and operating catalytic reactors. In this book, the author has focussed on both the processes occurring on individual porous-catalyst particles as well as the phenomena displayed by collections of these particles in fixed-bed reactors. The major topics discussed include the effects of unsteady-state heat and mass transfer, the influence of inhomogeneities and stagnant regions in fixed beds, and reactor operation during forced cycling of operating conditions. Despite the title of the book, attention is also paid to the determination of the number and stability of fixed-bed steady states, with the aim of describing the possibility of controlling reactors at unstable steady states. However, this development is somewhat dated, given the recent literature on multiplicity phenomena and process control.

  5. Non-catalytic recuperative reformer

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-22

    A non-catalytic recuperative reformer has a flue gas flow path for conducting hot flue gas from a thermal process and a reforming mixture flow path for conducting a reforming mixture. At least a portion of the reforming mixture flow path is embedded in the flue gas flow path to permit heat transfer from the hot flue gas to the reforming mixture. The reforming mixture flow path contains substantially no material commonly used as a catalyst for reforming hydrocarbon fuel (e.g., nickel oxide, platinum group elements or rhenium), but instead the reforming mixture is reformed into a higher calorific fuel via reactions due to the heat transfer and residence time. In a preferred embodiment, extended surfaces of metal material such as stainless steel or metal alloy that are high in nickel content are included within at least a portion of the reforming mixture flow path.

  6. 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.)

  7. A mesoporous catalytic membrane architecture for lithium-oxygen battery systems.

    Science.gov (United States)

    Ryu, Won-Hee; Gittleson, Forrest S; Schwab, Mark; Goh, Tenghooi; Taylor, André D

    2015-01-14

    Controlling the mesoscale geometric configuration of catalysts on the oxygen electrode is an effective strategy to achieve high reversibility and efficiency in Li-O2 batteries. Here we introduce a new Li-O2 cell architecture that employs a catalytic polymer-based membrane between the oxygen electrode and the separator. The catalytic membrane was prepared by immobilization of Pd nanoparticles on a polyacrylonitrile (PAN) nanofiber membrane and is adjacent to a carbon nanotube electrode loaded with Ru nanoparticles. During oxide product formation, the insulating PAN polymer scaffold restricts direct electron transfer to the Pd catalyst particles and prevents the direct blockage of Pd catalytic sites. The modified Li-O2 battery with a catalytic membrane showed a stable cyclability for 60 cycles with a capacity of 1000 mAh/g and a reduced degree of polarization (∼ 0.3 V) compared to cells without a catalytic membrane. We demonstrate the effects of a catalytic membrane on the reaction characteristics associated with morphological and structural features of the discharge products via detailed ex situ characterization.

  8. Generation of a phage-display library of single-domain camelid VH H antibodies directed against Chlamydomonas reinhardtii antigens, and characterization of VH Hs binding cell-surface antigens.

    Science.gov (United States)

    Jiang, Wenzhi; Rosenberg, Julian N; Wauchope, Akelia D; Tremblay, Jacqueline M; Shoemaker, Charles B; Weeks, Donald P; Oyler, George A

    2013-11-01

    Single-domain antibodies (sdAbs) are powerful tools for the detection, quantification, purification and subcellular localization of proteins of interest in biological research. We have generated camelid (Lama pacos) heavy chain-only variable VH domain (VH H) libraries against antigens in total cell lysates from Chlamydomonas reinhardtii. The sdAbs in the sera from immunized animals and VH H antibody domains isolated from the library show specificity to C. reinhardtii and lack of reactivity to antigens from four other algae: Chlorella variabilis, Coccomyxa subellipsoidea, Nannochloropsis oceanica and Thalassiosira pseudonana. Antibodies were produced against a diverse representation of antigens as evidenced by sera ELISA and protein-blot analyses. A phage-display library consisting of the VH H region contained at least 10(6) individual transformants, and thus should represent a wide range of C. reinhardtii antigens. The utility of the phage library was demonstrated by using live C. reinhardtii cells to pan for VH H clones with specific recognition of cell-surface epitopes. The lead candidate VH H clones (designated B11 and H10) bound to C. reinhardtii with EC50 values ≤ 0.5 nm. Treatment of cells with VH H B11 fused to the mCherry or green fluorescent proteins allowed brilliant and specific staining of the C. reinhardtii cell wall and analysis of cell-wall genesis during cell division. Such high-complexity VH H antibody libraries for algae will be valuable tools for algal researchers and biotechnologists.

  9. Titanium-Containing Mesoporous Materials: Synthesis and Application in Selective Catalytic Oxidation

    Institute of Scientific and Technical Information of China (English)

    Jie Li; Chunhui Zhou; Huali Xie; Zhonghua Ge; Liangcai Yuan; Xiaonian Li

    2006-01-01

    Titanium-containing mesoporous molecular sieves are of great significance in selective catalytic oxidation processes with bulky molecules. Recent researches and developments on the designing and synthesis of Ti-containing mesoporous materials have been reviewed. Various strategies for the preparation of Ti-containing mesoporous materials, such as direct synthesis and post-synthesis, are described. Modifications of Ti-containing mesoporous materials by surface-grafting and atom-planting are also discussed. All approaches aimed mainly at the improving of the stability, the hydrophobicity, and mostly the catalytic activity. Structural and mechanistic features of various synthetic systems are discussed. Ticontaining mesoporous materials in liquid phase catalytic oxidation of organic compounds with H2O2 as an oxidant is briefly summarized, showing their broad utilities for green synthesis of fine chemicals by catalytic oxidative reactions.

  10. Fabrication of bimetallic nanostructures via aerosol-assisted electroless silver deposition for catalytic CO conversion.

    Science.gov (United States)

    Byeon, Jeong Hoon; Kim, Jang-Woo

    2014-03-12

    Bimetallic nanostructures were fabricated via aerosol-assisted electroless silver deposition for catalytic CO conversion. An ambient spark discharge was employed to produce nanocatalysts, and the particles were directly deposited on a polytetrafluoroethylene substrate for initiating silver deposition to form Pd-Ag, Pt-Ag, Au-Ag bimetallic nanostructures as well as a pure Ag nanostructure. Kinetics and morphological evolutions in the silver deposition with different nanocatalysts were comparatively studied. The Pt catalyst displayed the highest catalytic activity for electroless silver deposition, followed by the order Pd > Au > Ag. Another catalytic activity of the fabricated bimetallic structures in the carbon monoxide conversion was further evaluated at low-temperature conditions. The bimetallic systems showed significantly higher catalytic activity than that from a pure Ag system.

  11. Development and test of a new catalytic converter for natural gas fuelled engine

    Indian Academy of Sciences (India)

    M A Kalam; H H Masjuki; M Redzuan; T M I Mahlia; M A Fuad; M Mohibah; K H Halim; A Ishak; M Khair; A Shahrir; A Yusoff

    2009-06-01

    This paper presents characteristics of a new catalytic converter (catco) to be used for natural gas fuelled engine. The catco were developed based on catalyst materials consisting of metal oxides such as titanium dioxide (TiO2) and cobalt oxide (CoO) with wire mesh substrate. Both of the catalyst materials (such as TiO2 and CoO) are inexpensive in comparison with conventional catalysts (noble metals) such as palladium or platinum. In addition, the noble metals such as platinum group metals are now identified as human health risk due to their rapid emissions in the environment from various resources like conventional catalytic converter, jewelers and other medical usages. It can be mentioned that the TiO2/CoO based catalytic converter and a new natural gas engine such as compressed natural gas (CNG) direct injection (DI) engine were developed under a research collaboration program. The original engine manufacture catalytic conveter (OEM catco) was tested for comparison purposes. The OEM catco was based on noble metal catalyst with honeycomb ceramic substrate. It is experimentally found that the conversion efficiencies of TiO2/CoO based catalytic converter are 93%, 89% and 82% for NOx, CO and HC emissions respectively. It is calculated that the TiO2/CoO based catalytic converter reduces 24%, 41% and 40% higher NOx, CO and HC emissions in comparison to OEM catco respectively. The objective of this paper is to develop a low-cost three way catalytic converter to be used with the newly developed CNG-DI engine. Detailed review on catalytic converter, low-cost catalytic converter development characteristics and CNGDI engine test results have been presented with discussions.

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

    Science.gov (United States)

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

    2016-07-31

    Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30Å from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction.

  13. Using advanced electron microscopy for the characterization of catalytic materials

    Science.gov (United States)

    Pyrz, William D.

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

  14. High-Resolution Single-Molecule Fluorescence Imaging of Zeolite Aggregates within Real-Life Fluid Catalytic Cracking Particles**

    Science.gov (United States)

    Ristanović, Zoran; Kerssens, Marleen M; Kubarev, Alexey V; Hendriks, Frank C; Dedecker, Peter; Hofkens, Johan; Roeffaers, Maarten B J; Weckhuysen, Bert M

    2015-01-01

    Fluid catalytic cracking (FCC) is a major process in oil refineries to produce gasoline and base chemicals from crude oil fractions. The spatial distribution and acidity of zeolite aggregates embedded within the 50–150 μm-sized FCC spheres heavily influence their catalytic performance. Single-molecule fluorescence-based imaging methods, namely nanometer accuracy by stochastic chemical reactions (NASCA) and super-resolution optical fluctuation imaging (SOFI) were used to study the catalytic activity of sub-micrometer zeolite ZSM-5 domains within real-life FCC catalyst particles. The formation of fluorescent product molecules taking place at Brønsted acid sites was monitored with single turnover sensitivity and high spatiotemporal resolution, providing detailed insight in dispersion and catalytic activity of zeolite ZSM-5 aggregates. The results point towards substantial differences in turnover frequencies between the zeolite aggregates, revealing significant intraparticle heterogeneities in Brønsted reactivity. PMID:25504139

  15. Revolutionary systems for catalytic combustion and diesel catalytic particulate traps.

    Energy Technology Data Exchange (ETDEWEB)

    Stuecker, John Nicholas; Witze, Peter O.; Ferrizz, Robert Matthew; Cesarano, Joseph, III; Miller, James Edward

    2004-12-01

    This report is a summary of an LDRD project completed for the development of materials and structures conducive to advancing the state of the art for catalyst supports and diesel particulate traps. An ancillary development for bio-medical bone scaffolding was also realized. Traditionally, a low-pressure drop catalyst support, such as a ceramic honeycomb monolith, is used for catalytic reactions that require high flow rates of gases at high-temperatures. A drawback to the traditional honeycomb monoliths under these operating conditions is poor mass transfer to the catalyst surface in the straight-through channels. ''Robocasting'' is a unique process developed at Sandia National Laboratories that can be used to manufacture ceramic monoliths with alternative 3-dimensional geometries, providing tortuous pathways to increase mass transfer while maintaining low-pressure drops. These alternative 3-dimensional geometries may also provide a foundation for the development of self-regenerating supports capable of trapping and combusting soot particles from a diesel engine exhaust stream. This report describes the structures developed and characterizes the improved catalytic performance that can result. The results show that, relative to honeycomb monolith supports, considerable improvement in mass transfer efficiency is observed for robocast samples synthesized using an FCC-like geometry of alternating rods. Also, there is clearly a trade-off between enhanced mass transfer and increased pressure drop, which can be optimized depending on the particular demands of a given application. Practical applications include the combustion of natural gas for power generation, production of syngas, and hydrogen reforming reactions. The robocast lattice structures also show practicality for diesel particulate trapping. Preliminary results for trapping efficiency are reported as well as the development of electrically resistive lattices that can regenerate the structure

  16. Molecular basis for TPR domain-mediated regulation of protein phosphatase 5.

    Science.gov (United States)

    Yang, Jing; Roe, S Mark; Cliff, Matthew J; Williams, Mark A; Ladbury, John E; Cohen, Patricia T W; Barford, David

    2005-01-12

    Protein phosphatase 5 (Ppp5) is a serine/threonine protein phosphatase comprising a regulatory tetratricopeptide repeat (TPR) domain N-terminal to its phosphatase domain. Ppp5 functions in signalling pathways that control cellular responses to stress, glucocorticoids and DNA damage. Its phosphatase activity is suppressed by an autoinhibited conformation maintained by the TPR domain and a C-terminal subdomain. By interacting with the TPR domain, heat shock protein 90 (Hsp90) and fatty acids including arachidonic acid stimulate phosphatase activity. Here, we describe the structure of the autoinhibited state of Ppp5, revealing mechanisms of TPR-mediated phosphatase inhibition and Hsp90- and arachidonic acid-induced stimulation of phosphatase activity. The TPR domain engages with the catalytic channel of the phosphatase domain, restricting access to the catalytic site. This autoinhibited conformation of Ppp5 is stabilised by the C-terminal alphaJ helix that contacts a region of the Hsp90-binding groove on the TPR domain. Hsp90 activates Ppp5 by disrupting TPR-phosphatase domain interactions, permitting substrate access to the constitutively active phosphatase domain, whereas arachidonic acid prompts an alternate conformation of the TPR domain, destabilising the TPR-phosphatase domain interface.

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

    Science.gov (United States)

    Talens-Perales, David; Górska, Anna; Huson, Daniel H; Polaina, Julio; Marín-Navarro, Julia

    2016-01-01

    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.

  18. Chimeric Plant Calcium/Calmodulin-Dependent Protein Kinase Gene with a Neural Visinin-Like Calcium-Binding Domain

    Science.gov (United States)

    Patil, Shameekumar; Takezawa, D.; Poovaiah, B. W.

    1995-01-01

    Calcium, a universal second messenger, regulates diverse cellular processes in eukaryotes. Ca-2(+) and Ca-2(+)/calmodulin-regulated protein phosphorylation play a pivotal role in amplifying and diversifying the action of Ca-2(+)- mediated signals. A chimeric Ca-2(+)/calmodulin-dependent protein kinase (CCaMK) gene with a visinin-like Ca-2(+)- binding domain was cloned and characterized from lily. The cDNA clone contains an open reading frame coding for a protein of 520 amino acids. The predicted structure of CCaMK contains a catalytic domain followed by two regulatory domains, a calmodulin-binding domain and a visinin-like Ca-2(+)-binding domain. The amino-terminal region of CCaMK contains all 11 conserved subdomains characteristic of serine/threonine protein kinases. The calmodulin-binding region of CCaMK has high homology (79%) to alpha subunit of mammalian Ca-2(+)/calmodulin-dependent protein kinase. The calmodulin-binding region is fused to a neural visinin-like domain that contains three Ca-2(+)-binding EF-hand motifs and a biotin-binding site. The Escherichia coli-expressed protein (approx. 56 kDa) binds calmodulin in a Ca-2(+)-dependent manner. Furthermore, Ca-45-binding assays revealed that CCaMK directly binds Ca-2(+). The CCaMK gene is preferentially expressed in developing anthers. Southern blot analysis revealed that CCaMK is encoded by a single gene. The structural features of the gene suggest that it has multiple regulatory controls and could play a unique role in Ca-2(+) signaling in plants.

  19. Topological entropy of catalytic sets: Hypercycles revisited

    Science.gov (United States)

    Sardanyés, Josep; Duarte, Jorge; Januário, Cristina; Martins, Nuno

    2012-02-01

    The dynamics of catalytic networks have been widely studied over the last decades because of their implications in several fields like prebiotic evolution, virology, neural networks, immunology or ecology. One of the most studied mathematical bodies for catalytic networks was initially formulated in the context of prebiotic evolution, by means of the hypercycle theory. The hypercycle is a set of self-replicating species able to catalyze other replicator species within a cyclic architecture. Hypercyclic organization might arise from a quasispecies as a way to increase the informational containt surpassing the so-called error threshold. The catalytic coupling between replicators makes all the species to behave like a single and coherent evolutionary multimolecular unit. The inherent nonlinearities of catalytic interactions are responsible for the emergence of several types of dynamics, among them, chaos. In this article we begin with a brief review of the hypercycle theory focusing on its evolutionary implications as well as on different dynamics associated to different types of small catalytic networks. Then we study the properties of chaotic hypercycles with error-prone replication with symbolic dynamics theory, characterizing, by means of the theory of topological Markov chains, the topological entropy and the periods of the orbits of unimodal-like iterated maps obtained from the strange attractor. We will focus our study on some key parameters responsible for the structure of the catalytic network: mutation rates, autocatalytic and cross-catalytic interactions.

  20. Development of Catalytic Cooking Plates

    Energy Technology Data Exchange (ETDEWEB)

    Hjelm, Anna-Karin; Silversand, Fredrik [CATATOR AB, Lund (Sweden); Tena, Emmanuel; Berger, Marc [Gaz de France (France)

    2004-04-01

    Gas catalytic combustion for gas stoves or cooking plates (closed catalytic burner system with ceramic plates) is a very promising technique in terms of ease of cleaning, power modulation and emissions. Previous investigations show that wire mesh catalysts, prepared and supplied by Catator AB (CAT), seem to be very well suited for such applications. Beside significantly reducing the NOx-emissions, these catalysts offer important advantages such as good design flexibility, low pressure drop and high heat transfer capacity, where the latter leads to a quick thermal response. Prior to this project, Gaz de France (GdF) made a series of measurements with CAT's wire mesh catalysts in their gas cooking plates and compared the measured performance with similar results obtained with theirs cordierite monolith catalysts. Compared to the monolith catalyst, the wire mesh catalyst was found to enable very promising results with respect to both emission levels (<10 mg NO{sub x} /kWh, <5 mg CO/kWh) and life-time (>8000 h vs. 700 h at 200 kW/m{sup 2}). It was however established that the radiation and hence, the thermal efficiency of the cooking plate, was significantly less than is usually measured in combination with the monolith (15 % vs. 32 %). It was believed that the latter could be improved by developing new burner designs based on CAT's wire mesh concept. As a consequence, a collaboration project between GdF, CAT and the Swedish Gas Technology AB was created. This study reports on the design, the construction and the evaluation of new catalytic burners, based on CAT's wire mesh catalysts, used for the combustion of natural gas in gas cooking stoves. The evaluation of the burners was performed with respect to key factors such as thermal efficiency, emission quality and pressure drop, etc, by the use of theoretical simulations and experimental tests. Impacts of parameters such as the the wire mesh number, the wire mesh structure (planar or folded), the

  1. Model catalytic oxidation studies using supported monometallic and heterobimetallic oxides

    Energy Technology Data Exchange (ETDEWEB)

    Ekerdt, J.G.

    1992-02-03

    This research program is directed toward a more fundamental understanding of the effects of catalyst composition and structure on the catalytic properties of metal oxides. Metal oxide catalysts play an important role in many reactions bearing on the chemical aspects of energy processes. Metal oxides are the catalysts for water-gas shift reactions, methanol and higher alcohol synthesis, isosynthesis, selective catalytic reduction of nitric oxides, and oxidation of hydrocarbons. A key limitation to developing insight into how oxides function in catalytic reactions is in not having precise information of the surface composition under reaction conditions. To address this problem we have prepared oxide systems that can be used to study cation-cation effects and the role of bridging (-O-) and/or terminal (=O) surface oxygen anion ligands in a systematic fashion. Since many oxide catalyst systems involve mixtures of oxides, we selected a model system that would permit us to examine the role of each cation separately and in pairwise combinations. Organometallic molybdenum and tungsten complexes were proposed for use, to prepare model systems consisting of isolated monomeric cations, isolated monometallic dimers and isolated bimetallic dimers supported on silica and alumina. The monometallic and bimetallic dimers were to be used as models of more complex mixed- oxide catalysts. Our current program was to develop the systems and use them in model oxidation reactions.

  2. Key parameters controlling the performance of catalytic motors

    Science.gov (United States)

    Esplandiu, Maria J.; Afshar Farniya, Ali; Reguera, David

    2016-03-01

    The development of autonomous micro/nanomotors driven by self-generated chemical gradients is a topic of high interest given their potential impact in medicine and environmental remediation. Although impressive functionalities of these devices have been demonstrated, a detailed understanding of the propulsion mechanism is still lacking. In this work, we perform a comprehensive numerical analysis of the key parameters governing the actuation of bimetallic catalytic micropumps. We show that the fluid motion is driven by self-generated electro-osmosis where the electric field originates by a proton current rather than by a lateral charge asymmetry inside the double layer. Hence, the surface potential and the electric field are the key parameters for setting the pumping strength and directionality. The proton flux that generates the electric field stems from the proton gradient induced by the electrochemical reactions taken place at the pump. Surprisingly the electric field and consequently the fluid flow are mainly controlled by the ionic strength and not by the conductivity of the solution, as one could have expected. We have also analyzed the influence of the chemical fuel concentration, electrochemical reaction rates, and size of the metallic structures for an optimized pump performance. Our findings cast light on the complex chemomechanical actuation of catalytic motors and provide important clues for the search, design, and optimization of novel catalytic actuators.

  3. 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.

  4. Catalytic production of conjugated fatty acids and oils.

    Science.gov (United States)

    Philippaerts, An; Goossens, Steven; Jacobs, Pierre A; Sels, Bert F

    2011-06-20

    The reactive double bonds in conjugated vegetable oils are of high interest in industry. Traditionally, conjugated vegetable oils are added to paints, varnishes, and inks to improve their drying properties, while recently there is an increased interest in their use in the production of bioplastics. Besides the industrial applications, also food manufactures are interested in conjugated vegetable oils due to their various positive health effects. While the isomer type is less important for their industrial purposes, the beneficial health effects are mainly associated with the c9,t11, t10,c12 and t9,t11 CLA isomers. The production of CLA-enriched oils as additives in functional foods thus requires a high CLA isomer selectivity. Currently, CLAs are produced by conjugation of oils high in linoleic acid, for example soybean and safflower oil, using homogeneous bases. Although high CLA productivities and very high isomer selectivities are obtained, this process faces many ecological drawbacks. Moreover, CLA-enriched oils can not be produced directly with the homogeneous bases. Literature reports describe many catalytic processes to conjugate linoleic acid, linoleic acid methyl ester, and vegetable oils rich in linoleic acid: biocatalysts, for example enzymes and cells; metal catalysts, for example homogeneous metal complexes and heterogeneous catalysts; and photocatalysts. This Review discusses state-of-the-art catalytic processes in comparison with some new catalytic production routes. For each category of catalytic process, the CLA productivities and the CLA isomer selectivity are compared. Heterogeneous catalysis seems the most attractive approach for CLA production due to its easy recovery process, provided that the competing hydrogenation reaction is limited and the CLA production rate competes with the current homogeneous base catalysis. The most important criteria to obtain high CLA productivity and isomer selectivity are (1) absence of a hydrogen donor, (2

  5. Structure of the kinase domain of Gilgamesh from Drosophila melanogaster.

    Science.gov (United States)

    Han, Ni; Chen, CuiCui; Shi, Zhubing; Cheng, Dianlin

    2014-04-01

    The CK1 family kinases regulate multiple cellular aspects and play important roles in Wnt/Wingless and Hedgehog signalling. The kinase domain of Drosophila Gilgamesh isoform I (Gilgamesh-I), a homologue of human CK1-γ, was purified and crystallized. Crystals of methylated Gilgamesh-I kinase domain with a D210A mutation diffracted to 2.85 Å resolution and belonged to space group P43212, with unit-cell parameters a = b = 52.025, c = 291.727 Å. The structure of Gilgamesh-I kinase domain, which was determined by molecular replacement, has conserved catalytic elements and an active conformation. Structural comparison indicates that an extended loop between the α1 helix and the β4 strand exists in the Gilgamesh-I kinase domain. This extended loop may regulate the activity and function of Gilgamesh-I.

  6. Halogen Chemistry on Catalytic Surfaces.

    Science.gov (United States)

    Moser, Maximilian; Pérez-Ramírez, Javier

    2016-01-01

    Halogens are key building blocks for the manufacture of high-value products such as chemicals, plastics, and pharmaceuticals. The catalytic oxidation of HCl and HBr is an attractive route to recover chlorine and bromine in order to ensure the sustainability of the production processes. Very few materials withstand the high corrosiveness and the strong exothermicity of the reactions and among them RuO2 and CeO2-based catalysts have been successfully applied in HCl oxidation. The search for efficient systems for HBr oxidation was initiated by extrapolating the results of HCl oxidation based on the chemical similarity of these reactions. Interestingly, despite its inactivity in HCl oxidation, TiO2 was found to be an outstanding HBr oxidation catalyst, which highlighted that the latter reaction is more complex than previously assumed. Herein, we discuss the results of recent comparative studies of HCl and HBr oxidation on both rutile-type (RuO2, IrO2, and TiO2) and ceria-based catalysts using a combination of advanced experimental and theoretical methods to provide deeper molecular-level understanding of the reactions. This knowledge aids the design of the next-generation catalysts for halogen recycling.

  7. Catalytic Chemistry on Oxide Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Asthagiri, Aravind; Dixon, David A.; Dohnalek, Zdenek; Kay, Bruce D.; Rodriquez, Jose A.; Rousseau, Roger J.; Stacchiola, Dario; Weaver, Jason F.

    2016-05-29

    Metal oxides represent one of the most important and widely employed materials in catalysis. Extreme variability of their chemistry provides a unique opportunity to tune their properties and to utilize them for the design of highly active and selective catalysts. For bulk oxides, this can be achieved by varying their stoichiometry, phase, exposed surface facets, defect, dopant densities and numerous other ways. Further, distinct properties from those of bulk oxides can be attained by restricting the oxide dimensionality and preparing them in the form of ultrathin films and nanoclusters as discussed throughout this book. In this chapter we focus on demonstrating such unique catalytic properties brought by the oxide nanoscaling. In the highlighted studies planar models are carefully designed to achieve minimal dispersion of structural motifs and to attain detailed mechanistic understanding of targeted chemical transformations. Detailed level of morphological and structural characterization necessary to achieve this goal is accomplished by employing both high-resolution imaging via scanning probe methods and ensemble-averaged surface sensitive spectroscopic methods. Three prototypical examples illustrating different properties of nanoscaled oxides in different classes of reactions are selected.

  8. Direct observation of the autophosphorylation of insulin receptor kinase by mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Zhi Li Li

    2009-01-01

    The catalytic and signaling activities of insulin receptor kinase(IRK)are regulated by the autophosphorylation of three tyrosine residues in a cytoplasmic protein-tyrosine kinase domain at Tyro 1158,Tyro 1162 and Tyro 1163.In this study,time-course of the auphosphorylation of the core kinase(residues 978-1283)from IRK was directly investigated by online electrospray ionization mass spectrometry.It is found that two tyrosine residues were phosphorylated in reaction time range of 30 min.This study implies that mass spectrometric technique must be a powerful tool to directly monitor the biological macromolecular modification and will also provide the information of the order and the mechanism of autophosphorylation at the tyrosine sites coupled with tandem mass spectrometric technique.

  9. Time Domain Stability Margin Assessment Method

    Science.gov (United States)

    Clements, Keith

    2017-01-01

    The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

  10. Frustratingly Easy Domain Adaptation

    CERN Document Server

    Daumé, Hal

    2009-01-01

    We describe an approach to domain adaptation that is appropriate exactly in the case when one has enough ``target'' data to do slightly better than just using only ``source'' data. Our approach is incredibly simple, easy to implement as a preprocessing step (10 lines of Perl!) and outperforms state-of-the-art approaches on a range of datasets. Moreover, it is trivially extended to a multi-domain adaptation problem, where one has data from a variety of different domains.

  11. Staggered domain wall fermions

    CERN Document Server

    Hoelbling, Christian

    2016-01-01

    We construct domain wall fermions with a staggered kernel and investigate their spectral and chiral properties numerically in the Schwinger model. In some relevant cases we see an improvement of chirality by more than an order of magnitude as compared to usual domain wall fermions. Moreover, we present first results for four-dimensional quantum chromodynamics, where we also observe significant reductions of chiral symmetry violations for staggered domain wall fermions.

  12. Translation domains in multiferroics

    OpenAIRE

    Meier, D; Leo, N; Jungk, T.; Soergel, E.; Becker, P.; Bohaty, L.; Fiebig, M.

    2010-01-01

    Translation domains differing in the phase but not in the orientation of the corresponding order parameter are resolved in two types of multiferroics. Hexagonal (h-) YMnO$_3$ is a split-order-parameter multiferroic in which commensurate ferroelectric translation domains are resolved by piezoresponse force microscopy whereas MnWO$_4$ is a joint-order-parameter multiferroic in which incommensurate magnetic translation domains are observed by optical second harmonic generation. The pronounced ma...

  13. Catalytic models developed through social work

    DEFF Research Database (Denmark)

    Jensen, Mogens

    2015-01-01

    The article develops the concept of catalytic processes in relation to social work with adolescents in an attempt to both reach a more nuanced understanding of social work and at the same time to develop the concept of catalytic processes in psychology. The social work is pedagogical treatment...... of adolescents placed in out-of-home care and is characterised using three situated cases as empirical data. Afterwards the concept of catalytic processes is briefly presented and then applied in an analysis of pedagogical treatment in the three cases. The result is a different conceptualisation of the social...... work with new possibilities of development of the work, but also suggestions for development of the concept of catalytic processes....

  14. Catalytic converters as a source of platinum

    Directory of Open Access Journals (Sweden)

    A. Fornalczyk

    2011-10-01

    Full Text Available The increase of Platinum Group Metals demand in automotive industry is connected with growing amount of cars equipped with the catalytic converters. The paper presents the review of available technologies during recycling process. The possibility of removing platinum from the used catalytic converters applying pyrometallurgical and hyrdometallurgical methods were also investigated. Metals such as Cu, Pb, Ca, Mg, Cd were used in the pyrometallurgical research (catalytic converter was melted with Cu, Pb and Ca or Mg and Cd vapours were blown through the whole carrier. In hydrometallurgical research catalytic converters was dissolved in aqua regia. Analysis of Pt contents in the carrier before and after the process was performed by means of atomic absorption spectroscopy. Obtained result were discussed.

  15. Catalytic Asymmetric Synthesis of Phosphine Boronates

    NARCIS (Netherlands)

    Hornillos, Valentin; Vila, Carlos; Otten, Edwin; Feringa, Ben L.

    2015-01-01

    The first catalytic enantioselective synthesis of ambiphilic phosphine boronate esters is presented. The asymmetric boration of ,-unsaturated phosphine oxides catalyzed by a copper bisphosphine complex affords optically active organoboronate esters that bear a vicinal phosphine oxide group in good y

  16. Pragmatic circuits frequency domain

    CERN Document Server

    Eccles, William

    2006-01-01

    Pragmatic Circuits: Frequency Domain goes through the Laplace transform to get from the time domain to topics that include the s-plane, Bode diagrams, and the sinusoidal steady state. This second of three volumes ends with a-c power, which, although it is just a special case of the sinusoidal steady state, is an important topic with unique techniques and terminology. Pragmatic Circuits: Frequency Domain is focused on the frequency domain. In other words, time will no longer be the independent variable in our analysis. The two other volumes in the Pragmatic Circuits series include titles on DC

  17. Catalytic Radical Domino Reactions in Organic Synthesis

    Science.gov (United States)

    Sebren, Leanne J.; Devery, James J.; Stephenson, Corey R.J.

    2014-01-01

    Catalytic radical-based domino reactions represent important advances in synthetic organic chemistry. Their development benefits synthesis by providing atom- and step-economical methods to complex molecules. Intricate combinations of radical, cationic, anionic, oxidative/reductive, and transition metal mechanistic steps result in cyclizations, additions, fragmentations, ring-expansions, and rearrangements. This Perspective summarizes recent developments in the field of catalytic domino processes. PMID:24587964

  18. MOBILE COMPLEX FOR CATALYTIC THERMAL WASTE TREATMENT

    Directory of Open Access Journals (Sweden)

    Vedi V.E.

    2012-12-01

    Full Text Available The design and purpose of the basic units of the mobile waste processing complex “MPK” are described. Experimental data of catalytic purification of exhaust gases are presented. Experimental data on catalytic clearing of final gases of a designed mobile incinerator plant are shown. It is defined, that concentrating of parasitic bridging in waste gases of the complex are considerably smaller, rather than allowed by normative documents.

  19. Temperature Modulation of a Catalytic Gas Sensor

    OpenAIRE

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

    2014-01-01

    The use of catalytic gas sensors usually offers low selectivity, only based on their different sensitivities for various gases due to their different heats of reaction. Furthermore, the identification of the gas present is not possible, which leads to possible misinterpretation of the sensor signals. The use of micro-machined catalytic gas sensors offers great advantages regarding the response time, which allows advanced analysis of the sensor response. By using temperature modulation, additi...

  20. 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.

  1. Molecular basis of the general base catalysis of an α/β-hydrolase catalytic triad.

    Science.gov (United States)

    Sun, Yueru; Yin, Shuhui; Feng, Yitao; Li, Jie; Zhou, Jiahai; Liu, Changdong; Zhu, Guang; Guo, Zhihong

    2014-05-30

    The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the α-helical cap domain, which causes extensive structural changes in the α/β-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. NMR analysis shows that the inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.

  2. Domain Walls on Singularities

    CERN Document Server

    Halyo, Edi

    2009-01-01

    We describe domain walls that live on $A_2$ and $A_3$ singularities. The walls are BPS if the singularity is resolved and non--BPS if it is deformed and fibered. We show that these domain walls may interpolate between vacua that support monopoles and/or vortices.

  3. A Domain Analysis Bibliography

    Science.gov (United States)

    1990-06-01

    Bauhaus , a prototype CASE workstation for D-SAPS development. [ARAN88A] Guillermo F. Arango. Domain Engineering for Software Reuse. PhD thesis...34 VITA90B: Domain Analysis within the ISEC Rapid Center 48 CMU/SEI-90-SR-3 Appendix III Alphabetical by Organization/Project BAUHAUS * ALLE87A

  4. Phage Endolysin: A Way To Understand A Binding Function Of C-Terminal Domains A Mini Review

    OpenAIRE

    Jarábková Veronika; Tišáková Lenka; Godány Andrej

    2015-01-01

    Endolysins are bacteriophage-encoded peptidoglycan hydrolases, which are synthesized in the end of phage reproduction cycle, in an infected host cell. Usually, for endolysins from phages that infect Gram-positive bacteria, a modular structure is typical. Therefore, these are composed of at least two separate functional domains: an N-terminal catalytic domain (EAD) and a C-terminal cell wall binding domain (CBD). Specific ligand recognition of CBDs and following peptidoglycan (PG) binding most...

  5. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

    Directory of Open Access Journals (Sweden)

    Weinzierl Robert OJ

    2010-10-01

    Full Text Available Abstract Background Cellular RNA polymerases (RNAPs are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC. BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.

  6. 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.

  7. Nucleotide occupancy of F1-ATPase catalytic sites under crystallization conditions.

    Science.gov (United States)

    Löbau, S; Weber, J; Senior, A E

    1997-03-03

    Using site-directed tryptophan fluorescence we studied nucleotide occupancy of the catalytic sites of Escherichia coli F1-ATPase, under conditions used previously for crystallization and X-ray structure analysis of the bovine mitochondrial enzyme [Abrahams et al. (1994) Nature 370, 621-628]. We found that only two of the three catalytic sites were filled in the E. coli enzyme under these conditions (250 microM MgAMPPNP plus 5 microM MgADP), consistent with what was reported in the bovine F1 X-ray structure. However, subsequent addition of a physiological concentration of MgATP readily filled the third catalytic site. Therefore the enzyme form seen in the X-ray structure results from the fact that it is obtained under sub-saturating nucleotide conditions. The data show that the X-ray structure is compatible with a catalytic mechanism in which all three F1-ATPase catalytic sites must fill with MgATP to initiate steady-state hydrolysis [e.g. Weber and Senior (1996) Biochim. Biophys. Acta 1275, 101-104]. The data further demonstrate that the site-directed tryptophan fluorescence technique can provide valuable support for F1 crystallography studies.

  8. Catalytic partial oxidation of pyrolysis oils

    Science.gov (United States)

    Rennard, David Carl

    2009-12-01

    details the catalytic partial oxidation of glycerol without preheat: droplets of glycerol are sprayed directly onto the top of the catalyst bed, where they react autothermally with contact times on the order of tau ≈ 30 ms. The reactive flash volatilization of glycerol results in equilibrium syngas production over Rh-Ce catalysts. In addition, water can be added to the liquid glycerol, resulting in true autothermal reforming. This highly efficient process can increase H2 yields and alter the H2 to CO ratio, allowing for flexibility in syngas quality depending on the purpose. Chapter 5 details the results of a time on stream experiment, in which optimal syngas conditions are chosen. Although conversion is 100% for 450 hours, these experiments demonstrate the deactivation of the catalyst over time. Deactivation is exhibited by decreases in H2 and CO 2 production accompanied by a steady increase in CO and temperature. These results are explained as a loss of water-gas shift equilibration. SEM images suggest catalyst sintering may play a role; EDS indicates the presence of impurities on the catalyst. In addition, the instability of quartz in the reactor is demonstrated by etching, resulting in a hole in the reactor tube at the end of the experiment. These results suggest prevaporization may be desirable in this application, and that quartz is not a suitable material for the reactive flash volatilization of oxygenated fuels. In Chapter 6, pyrolysis oil samples from three sources - poplar, pine, and hardwoods - are explored in the context of catalytic partial oxidation. Lessons derived from the tests with model compounds are applied to reactor design, resulting in the reactive flash vaporization of bio oils. Syngas is successfully produced, though deactivation due to coke and ash deposition keeps H2 below equlibrium. Coke formation is observed on the reactor walls, but is avoided between the fuel injection site and catalyst by increasing the proximity of these in the reactor

  9. 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.

  10. APP蛋白家族胞内段释放与神经干细胞向神经元细胞定向分化的关系研究%Study on the Relationship between the Release of Intracellular Domain of Amyloid-β Precursor Protein and Directional Differentiation of Neural Stem Cells into Neuron Cells

    Institute of Scientific and Technical Information of China (English)

    章建国; Amy Yong Chen Low; 杨武林

    2012-01-01

    [Objective] The research aimed to study the effects of the intracellular domain of APP family on the directional differentiation of neuron. [Method ] Neural stem cells were isolated and cultured in vitro, which were then transfected with plasmids containing the intracellular domains of APP family for overexpression. Their effects on the directional differentiation of neural stem cells into neurons were studied. [Result ] The over-expression of the intracellular domain of APP protein family can inhibit the differentiation of neural stem cells into neurons, and the effects of intracellular segments of APP and APLP2 were particularly significant. Mutagenesis experiments showed that it was necessary to release 31 amino acid terminal fragment through Capase hydrolysis in this process. The directional differentiation of neural stem cells into neuron cells was controlled through releasing APP-ICD31 by the intracellular domain of APP family. [Conclusion] This research further proved the relationship between APP protein and the incidence of Alzheimers disease,and provided new targets for the treatment of Alzheimers disease.%[目的]研究APP家族胞内段时神经细胞定向分化的影响.[方法]通过分离体外培养神经干细胞,转染导入APP蛋白家族胞内段以过表达后,研究其对神经干细胞向神经元定向分化的影响.[结果]APP家族蛋白胞内段的过表达可以抑制神经干细胞向神经元细胞的分化,其中APP和APLP2胞内段的影响尤为显著.突变试验表明,通过Capase水解释放末端31氧基酸片断是这个过程必需的.APP家族胞内段是通过释放APP-ICD31来抑制神经干细胞向神经元细胞的定向分化.[结论]该研究进一步证实了APP蛋白和老年痴呆病发生的联系,也为老年痴呆症的治疗提供新的靶点.

  11. Safe domain and elementary geometry

    CERN Document Server

    Richard, J M

    2004-01-01

    A classical problem of mechanics involves a projectile fired from a given point with a given velocity whose direction is varied. This results in a family of trajectories whose envelope defines the border of a 'safe' domain. In the simple cases of a constant force, harmonic potential and Kepler or Coulomb motion, the trajectories are conic curves whose envelope in a plane is another conic section which can be derived either by simple calculus or by geometrical considerations. The case of harmonic forces reveals a subtle property of the maximal sum of distances within an ellipse.

  12. Catalytic coal liquefaction. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Weller, S W

    1981-01-01

    Monolith catalysts of MoO/sub 3/-CoO-Al/sub 2/O/sub 3/ were prepared and tested for coal liquefaction in a stirred autoclave. In general, the monolith catalysts were not as good as particulate catalysts prepared on Corning alumina supports. Measurement of O/sub 2/ chemisorption and BET surface area has been made on a series of Co/Mo/Al/sub 2/O/sub 3/ catalysts obtained from PETC. The catalysts were derived from Cyanamid 1442A and had been tested for coal liquefaction in batch autoclaves and continuous flow units. MoO/sub 3/-Al/sub 2/O/sub 3/ catalysts over the loading range 3.9 to 14.9 wt % MoO/sub 3/ have been studied with respect to BET surface (before and after reduction), O/sub 2/ chemisorption at -78/sup 0/C, redox behavior at 500/sup 0/C, and activity for cyclohexane dehydrogenation at 500/sup 0/C. In connection with the fate of tin catalysts during coal liquefaction, calculations have been made of the relative thermodynamic stability of SnCl/sub 2/, Sn, SnO/sub 2/, and SnS in the presence of H/sub 2/, HCl, H/sub 2/S and H/sub 2/O. Ferrous sulfate dispersed in methylnaphthalene has been shown to be reduced to ferrous sulfide under typical coal hydroliquefaction conditions (1 hour, 450/sup 0/C, 1000 psi initial p/sub H/sub 2//). This suggests that ferrous sulfide may be the common catalytic ingredient when either (a) ferrous sulfate impregnated on powdered coal, or (b) finely divided iron pyrite is used as the catalyst. Old research on impregnated ferrous sulfate, impregnated ferrous halides, and pyrite is consistent with this assumption. Eight Co/Mo/Al/sub 2/O/sub 3/ catalysts from commercial suppliers, along with SnCl/sub 2/, have been studied for the hydrotreating of 1-methylnaphthalene (1-MN) in a stirred autoclave at 450 and 500/sup 0/C.

  13. Modulation of oncogenic DBL activity by phosphoinositol phosphate binding to pleckstrin homology domain.

    Science.gov (United States)

    Russo, C; Gao, Y; Mancini, P; Vanni, C; Porotto, M; Falasca, M; Torrisi, M R; Zheng, Y; Eva, A

    2001-06-01

    The Dbl family guanine nucleotide exchange factors (GEFs) contain a region of sequence similarity consisting of a catalytic Dbl homology (DH) domain in tandem with a pleckstrin homology (PH) domain. PH domains are involved in the regulated targeting of signaling molecules to plasma membranes by protein-protein and/or protein-lipid interactions. Here we show that Dbl PH domain binding to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-triphosphate results in the inhibition of Dbl GEF activity on Rho family GTPase Cdc42. Phosphatidylinositol 4,5-bisphosphate binding to the PH domain significantly inhibits the Cdc42 interactive activity of the DH domain suggesting that the DH domain is subjected to the PH domain modulation under the influence of phosphoinositides (PIPs). We generated Dbl mutants unable to interact with PIPs. These mutants retained GEF activity on Cdc42 in the presence of PIPs and showed a markedly enhanced activating potential for both Cdc42 and RhoA in vivo while displaying decreased cellular transforming activity. Immunofluorescence analysis of NIH3T3 transfectants revealed that whereas the PH domain localizes to actin stress fibers and plasma membrane, the PH mutants are no longer detectable on the plasma membrane. These results suggest that modulation of PIPs in both the GEF catalytic activity and the targeting to plasma membrane determines the outcome of the biologic activity of Dbl.

  14. Domain Organization in Clostridium botulinum Neurotoxin Type E is Unique: Its Implication in Faster Translocation

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran, D.; Eswaramoorthy, S; Furey, W; Navaza, J; Sax, M; Swaminathan, S

    2009-01-01

    Clostridium botulinum produces seven antigenically distinct neurotoxins [C. botulinum neurotoxins (BoNTs) A-G] sharing a significant sequence homology. Based on sequence and functional similarity, it was believed that their three-dimensional structures will also be similar. Indeed, the crystal structures of BoNTs A and B exhibit similar fold and domain association where the translocation domain is flanked on either side by binding and catalytic domains. Here, we report the crystal structure of BoNT E holotoxin and show that the domain association is different and unique, although the individual domains are similar to those of BoNTs A and B. In BoNT E, both the binding domain and the catalytic domain are on the same side of the translocation domain, and all three have mutual interfaces. This unique association may have an effect on the rate of translocation, with the molecule strategically positioned in the vesicle for quick entry into cytosol. Botulism, the disease caused by BoNT E, sets in faster than any other serotype because of its speedy internalization and translocation, and the present structure offers a credible explanation. We propose that the translocation domain in other BoNTs follows a two-step process to attain translocation-competent conformation as in BoNT E. We also suggest that this translocation-competent conformation in BoNT E is a probable reason for its faster toxic rate compared to BoNT A. However, this needs further experimental elucidation.

  15. Influence of Preparation Conditions on the Catalytic Performance of MoNx/SBA-15 for Ammonia Decomposition

    Institute of Scientific and Technical Information of China (English)

    Hongchao Liu; Hua Wang; Jianghan Shen; Ying Sun; Zhongmin Liu

    2006-01-01

    The influence of preparation conditions (e.g. H2-N2 ratios, final nitriding temperatures) on the performance of MoNx/SBA-15 catalysts for ammonia decomposition was investigated. The variation of catalytic activity with H2-N2 ratios may be attributed to the variation of surface compositions and particle sizes of the active components. The variation of nitriding temperatures leads to the formation of molybdenum nitride domains of varying compositions, which are responsible for the difference in their catalytic performance with respect to ammonia decomposition. At 923 K, ammonia could be completely decomof ammonia.

  16. Evolution of toxicity upon wet catalytic oxidation of phenol.

    Science.gov (United States)

    Santos, A; Yustos, P; Quintanilla, A; García-Ochoa, F; Casas, J A; Rodríguez, J J

    2004-01-01

    This work reports on the evolution of the toxicity of phenol-containing simulated wastewater upon catalytic wet oxidation with a commercial copper-based catalyst (Engelhard Cu-0203T). The results of the study show that this catalyst enhances detoxification, in addition to its effect on the oxidation rate. The EC50 values of the intermediates identified throughout the oxidation route of phenol have been determined and used to predict the evolution of toxicity upon oxidation. The predicted values have been compared with the ones measured directly from the aqueous solution during the oxidation process. To learn about the evolution of toxicity through out the routes of phenol oxidation, experiments have been performed with simulated wastewaters containing separately phenol, catechol, and hydroquinone as original pollutants. The significant increase of toxicity observed during the early stages of phenol oxidation is not directly related to the development of the brown color that derives mainly from catechol oxidation. This increase of toxicity is caused by the formation of hydroquinone and p-benzoquinone as intermediates, the former showing the highest toxicity. Furthermore, synergistic effects, giving rise to a significant increase of toxicity, have been observed. These effects derive from the interactions among copper leached from the catalyst and catechol, hydroquinone, and p-benzoquinone and demand that close attention be paid to this potential problem in catalytic wet oxidation.

  17. Crystal structures of yeast beta-alanine synthase complexes reveal the mode of substrate binding and large scale domain closure movements.

    Science.gov (United States)

    Lundgren, Stina; Andersen, Birgit; Piskur, Jure; Dobritzsch, Doreen

    2007-12-07

    Beta-alanine synthase is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of uracil and thymine in higher organisms. The fold of the homodimeric enzyme from the yeast Saccharomyces kluyveri identifies it as a member of the AcyI/M20 family of metallopeptidases. Its subunit consists of a catalytic domain harboring a di-zinc center and a smaller dimerization domain. The present site-directed mutagenesis studies identify Glu(159) and Arg(322) as crucial for catalysis and His(262) and His(397) as functionally important but not essential. We determined the crystal structures of wild-type beta-alanine synthase in complex with the reaction product beta-alanine, and of the mutant E159A with the substrate N-carbamyl-beta-alanine, revealing the closed state of a dimeric AcyI/M20 metallopeptidase-like enzyme. Subunit closure is achieved by a approximately 30 degrees rigid body domain rotation, which completes the active site by integration of substrate binding residues that belong to the dimerization domain of the same or the partner subunit. Substrate binding is achieved via a salt bridge, a number of hydrogen bonds, and coordination to one of the zinc ions of the di-metal center.

  18. The PE-PPE Domain in Mycobacterium Reveals a Serine α/β Hydrolase Fold and Function: An In-Silico Analysis

    Science.gov (United States)

    Sultana, Rafiya; Tanneeru, Karunakar; Guruprasad, Lalitha

    2011-01-01

    The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards the C-terminus of some PE and PPE proteins and hypothetical proteins. Our in-silico sequence analysis revealed that this domain is present in all Mycobacteria, some Rhodococcus and Nocardia farcinica genomes. This domain comprises a pentapeptide sequence motif GxSxG/S at the N-terminus and conserved amino acid residues Ser, Asp and His that constitute a catalytic triad characteristic of lipase, esterase and cutinase activity. The fold prediction and comparative modeling of the 3-D structure of the PE-PPE domain revealed a “serine α/β hydrolase” structure with a central β-sheet flanked by α-helices on either side. The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site. The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified. Our findings add to the growing list of serine hydrolases in mycobacterium, which are essential for the maintenance of their impermeable cell wall and virulence. These results provide the directions for the design of experiments to establish the function of PE and PPE proteins. PMID:21347309

  19. 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

  20. Structure of the Tribolium castaneum Telomerase Catalytic Subunit TERT

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-01

    A common hallmark of human cancers is the overexpression of telomerase, a ribonucleoprotein complex that is responsible for maintaining the length and integrity of chromosome ends. Telomere length deregulation and telomerase activation is an early, and perhaps necessary, step in cancer cell evolution. Here we present the high-resolution structure of the Tribolium castaneum catalytic subunit of telomerase, TERT. The protein consists of three highly conserved domains, organized into a ring-like structure that shares common features with retroviral reverse transcriptases, viral RNA polymerases and B-family DNA polymerases. Domain organization places motifs implicated in substrate binding and catalysis in the interior of the ring, which can accommodate seven to eight bases of double-stranded nucleic acid. Modelling of an RNA-DNA heteroduplex in the interior of this ring demonstrates a perfect fit between the protein and the nucleic acid substrate, and positions the 3'-end of the DNA primer at the active site of the enzyme, providing evidence for the formation of an active telomerase elongation complex.