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https://www.readbyqxmd.com/read/29220670/qm-mm-modeling-of-the-hydrolysis-and-transfructosylation-reactions-of-fructosyltransferase-from-aspergillus-japonicas-an-enzyme-that-produces-prebiotic-fructooligosaccharide
#1
Jitrayut Jitonnom, James R Ketudat-Cairns, Supa Hannongbua
Fructosyltransferases (FTs) act on sucrose by cleaving the β-(2→1) linkage, releasing glucose, and then transferring the fructosyl group to an acceptor molecule. These enzymes are capable of producing prebiotic fructooligosaccharides (FOSs) that are of industrial interest. While several FOS-synthesizing enzymes FTs have been investigated, their catalytic mechanism is not yet fully understood, especially the molecular details of how FOS are enzymatically synthesized from sucrose. Here, we present a comparative quantum mechanics/molecular mechanics (QM/MM) study on the hydrolysis and transfructosylation reactions catalyzed by A...
November 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29218637/specific-phosphorothioate-substitution-within-domain-6-of-a-group-ii-intron-ribozyme-leads-to-changes-in-local-structure-and-metal-ion-binding
#2
Michèle C Erat, Emina Besic, Michael Oberhuber, Silke Johannsen, Roland K O Sigel
Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29216511/architecture-and-physicochemical-characterization-of-bacillus-biofilm-as-a-potential-enzyme-immobilization-factory
#3
C M Romero, P V Martorell, A Gómez López, C G Nieto Peñalver, S Chaves, M Mechetti
Biocatalysis for industrial application is based on the use of enzymes to perform complex transformations. However, these systems have some disadvantage related to the costs of the biocatalyst. In this work, an alternative strategy for producing green immobilized biocatalysts based on biofilm was developed.A study of the rheological behavior of the biofilm from Bacillus sp. Mcn4, as well as the determination of its composition, was carried out. The dynamic rheological measurements, viscosity (G") and elasticity (G') module, showed that the biofilm presents appreciable elastic components, which is a recognized property for enzymes immobilization...
November 23, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29216039/corrigendum-persisting-positron-emission-tomography-lesion-activity-and-mycobacterium-tuberculosis-mrna-after-tuberculosis-cure
#4
Stephanus T Malherbe, Shubhada Shenai, Katharina Ronacher, Andre G Loxton, Gregory Dolganov, Magdalena Kriel, Tran Van, Ray Y Chen, James Warwick, Laura E Via, Taeksun Song, Myungsun Lee, Gary Schoolnik, Gerard Tromp, David Alland, Clifton E Barry, Jill Winter, Gerhard Walzl
This corrects the article DOI: 10.1038/nm.4177.
December 7, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29215891/combining-visible-light-photoredox-and-lewis-acid-catalysis-for-the-synthesis-of-indolizino-1-2-b-quinolin-9-11h-ones-and-irinotecan-precursor
#5
Wuheng Dong, Yao Yuan, Bei Hu, Xiaoshuang Gao, Huang Gao, Xiaomin Xie, Zhaoguo Zhang
One-step construction of substituted indolizino[1,2-b]quinolin-9(11H)-ones was achieved by combining visible-light-photoredox and Lewis acid catalysis for an intramolecular Povarov cycloaddition reaction under mild conditions. In this catalytic process, the visible-light-promoted dehydrogenation protocol of tetrahydroquinolines constitutes the key procedure. Moreover, this method can be applied to the formal synthesis of the precursor of irinotecan, which exhibited good anticancer activities.
December 7, 2017: Organic Letters
https://www.readbyqxmd.com/read/29215053/selective-carbon-dioxide-sorption-and-heterogeneous-catalysis-by-a-new-3d-zn-mof-with-nitrogen-rich-1d-channels
#6
Hyun-Chul Kim, Seong Huh, Sung-Jin Kim, Youngmee Kim
We prepared a new C 2h-symmetric bridging ligand, 3,3'-(pyrazine-2,5-diyl)dibenzoic acid (3,3'-PDBA), through a Suzuki coupling reaction. 3,3'-PDBA contains a central pyrazine ring instead of the phenyl ring of 3,3'-terphenyldicarboxylic acid (3,3'-TPDC). Despite the geometrical similarity of the two bridging ligands, the reaction between Zn(NO3)2·6H2O and 3,3'-PDBA in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) yielded a structurally different Zn-based metal-organic framework (Zn-MOF). The Zn-MOF, [Zn2(3,3'-PDBA)2(DABCO)1...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29214725/euphorbia-tirucalli-%C3%AE-amyrin-cyclase-trp612-and-tyr736-%C3%AF-electrons-participate-in-a-cation-%C3%AF-interaction-with-the-transient-cation-and-a-ch-%C3%AF-interaction-with-leu734-respectively
#7
Yukari Aiba, Takumi Watanabe, Yuri Terasawa, Chiaki Nakano, Tsutomu Hoshino
The functions of Trp612, Leu734 and Tyr736 of Euphorbia tirucalli β-amyrin synthase were examined. The aliphatic variants (Ala, Val, Met) of Trp612 showed almost no activity, but the aromatic variants exhibited high activities: 12.5% of the wild-type activity for the W612H variant, 43% for W612F, and 63% for W612Y. That is, the enzymatic activities of the variants increased in proportion to the increase in π-electron density. Thus, the major function of Trp612 is to stabilize transient cations via a cation-π interaction...
December 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29212707/inherent-steroid-17%C3%AE-20-lyase-activity-in-defunct-cytochrome-p450-17a-enzymes
#8
Eric Gonzalez, Kevin M Johnson, Pradeep S Pallan, Thanh T N Phan, Wei Zhang, L I Lei, Zdzislaw Wawrzak, Francis K Yoshimoto, Martin Egli, F Peter Guengerich
Cytochrome P450 (P450) 17A1 catalyzes the oxidations of progesterone and pregnenolone and is the major source of androgens. The enzyme catalyzes both 17α-hydroxylation and a subsequent 17α, 20-lyase reaction, and several mechanisms have been proposed for the latter step. Zebrafish P450 17A2 catalyzes only the 17α-hydroxylations. We previously reported high similarity of the crystal structures of zebrafish P450 17A1 and 17A2 and human P450 17A1 (Pallan et al. (2015) J. Biol. Chem. 290, 3248- 3268). Five residues near the heme, which differed, were changed...
December 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29211459/an-organometallic-cu20-nanocluster-synthesis-characterization-immobilization-on-silica-and-click-chemistry
#9
Andrew W Cook, Zachary R Jones, Guang Wu, Susannah L Scott, Trevor W Hayton
The development of atomically-precise nanoclusters (APNCs) protected by organometallic ligands, such as acetylides and hydrides, is an emerging area of nanoscience. In principle, these organometallic APNCs should not require harsh pre-treatment for activation towards catalysis, such as calcination, which can lead to sintering. Herein, we report the synthesis of the mixed-valent organometallic copper APNC, [Cu20(CCPh)12(OAc)6)] (1), via reduction of Cu(OAc) with Ph2SiH2 in the presence of phenylacetylene. This cluster is a rare example of a two-electron copper superatom, and the first to feature a tetrahedral [Cu4]2+ core, which is a unique "kernel" for a Cu-only superatom...
December 6, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29211330/cross-coupling-of-sodium-sulfinates-with-aryl-heteroaryl-and-vinyl-halides-by-nickel-photoredox-dual-catalysis
#10
Huifeng Yue, Chen Zhu, Magnus Rueping
An efficient photoredox/nickel dual catalyzed sulfonylation reaction of aryl, heteroaryl, and vinyl halides has been achieved for the first time. This newly developed sulfonylation protocol provides a versatile method for the synthesis of diverse aromatic sulfones at room temperature and shows excellent functional group tolerance. The electrophilic coupling partners are not limited to aryl, heteroaryl and vinyl bromides but also less reactive aryl chlorides are suitable substrates for this transformation.
December 6, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29211314/biologically-inspired-ligand-design-for-asymmetric-dia-stereodivergent-1-3-dipolar-cycloaddition
#11
Wen-Jing Xiao, Bin Feng, Jia-Rong Chen, Yun-Fang Yang, Bin Lu
In contrast to the plethora of catalytic systems that enable access to any enantiomers of the chiral products by simply choosing between a pair of enantiomeric or pseudoenantiomeric chiral catalysts, few analogously effective protocols exist for the synthesis of compounds with multiple stereogenic centers with full control of the absolute and relative stereochemical configurations. Inspired by the functional diversification in proteins and enzymes that are resulted from conformational change, here, we report the development of a novel type of modular phosphoramidite-thioether ligands for the diastereodivergent asymmetric catalysis...
December 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29211080/can-electrostatic-catalysis-of-diels-alder-reactions-be-harnessed-with-ph-switchable-charged-functional-groups
#12
Heather M Aitken, Michelle L Coote
Quantum-chemical calculations at the M06-2X/6-31+G(d,p) and G3(MP2)CC levels of theory are used to assess the feasibility of harnessing charged functional groups to electrostatically catalyse Diels-Alder reactions and alter their regio selectivity. For the reaction of the polar diene 2-pyrone with substituted cyclopentene, pH switches of nearly 60 kJ mol-1 are observed in the gas-phase. To switch regioselectivity however it is necessary to toggle between negatively and positively charged functional groups. With the 6-membered cyclohexene derivatives, similar pH-switches are observed but this time an opportunity to pH-switch diastereomeric selectivity is also observed due to the asymmetry of the transition state...
December 6, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29210420/a-novel-approach-to-5h-pyrazino-2-3-b-indoles-via-annulation-of-3-diazoindolin-2-imines-with-2h-azirines-or-5-alkoxyisoxazoles-under-rh-ii-catalysis
#13
Julia O Ruvinskaya, Nikolai V Rostovskii, Ilya P Filippov, Alexander F Khlebnikov, Mikhail S Novikov
A novel one-step method for the preparation of 5H-pyrazino[2,3-b]indoles with different substitution patterns in all rings of the tricyclic system via the Rh2(OAc)4-catalyzed reaction of 2H-azirines with 3-diazoindolin-2-imines is reported. Alkyl 5H-pyrazino[2,3-b]indole-3-carboxylates were also prepared by a one-pot procedure from synthetic equivalents of alkyl 2H-azirine-2-carboxylates, 5-alkoxyisoxazoles. The reactions provide the first examples of the use of Rh(ii) catalysis for intermolecular annulations with 2H-azirines and isoxazoles...
December 6, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29210357/structural-basis-of-proton-translocation-and-force-generation-in-mitochondrial-atp-synthase
#14
Niklas Klusch, Bonnie J Murphy, Deryck J Mills, Özkan Yildiz, Werner Kühlbrandt
ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton pathway. We determined the structure of an intact mitochondrial ATP synthase dimer by electron cryo-microscopy at near-atomic resolution. Charged and polar residues of the a-subunit stator define two aqueous channels, each spanning one half of the membrane. Passing through a conserved membrane-intrinsic helix hairpin, the lumenal channel protonates an acidic glutamate in the c-ring rotor...
December 6, 2017: ELife
https://www.readbyqxmd.com/read/29208921/fe4s4-cubane-type-cluster-immobilized-on-a-graphene-support-a-high-performance-h2-evolution-catalysis-in-acidic-water
#15
Ameerunisha Begum, Aasif Hassan Sheikh, Golam Moula, Sabyasachi Sarkar
The development of alternate catalysts that utilize non-precious metal based electrode materials such as the first row transition metal complexes is an important goal for economic fuel cell design. In this direction, a new Fe4S4 cubane type cluster, [PPh4]2[Fe4S4(DMET)4] (1) (DMET = cis-1,2-dicarbomethoxyethylene dithiolate) and its composite with functionalized graphene, (1@graphene) have been synthesized and characterized. The presence of nanocrystalline structures on graphene matrix in TEM and SEM images of 1@graphene indicate that the cluster (1) has been immobilized...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208911/initiation-of-prolyl-cis-trans-isomerisation-in-the-cdr-h3-loop-of-an-antibody-in-response-to-antigen-binding
#16
Keiko Shinoda, Hideaki Fujitani
Proline cis-trans isomerisation is a regulatory mechanism used in a range of biological processes, and is related to various diseases such as Alzheimers disease and cancer. However, the details of the exact molecular mechanism by which it occurs are not known. Using X-ray crystallography, proline isomerisation has been shown to occur following formation of an antigen-antibody complex between the target epiregulin (EPR) and the antibody 9E5, at proline (Pro103), located in the third complementarity-determining region (CDR) of the heavy chain of 9E5...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208762/a-dimeric-catalytic-core-relates-the-short-and-long-forms-of-atp-phosphoribosyltransferase
#17
Gerd Mittelstädt, Wanting Jiao, Emma Livingstone, Gert-Jan Moggré, Ali Reza Nazmi, Emily J Parker
ATP-phosphoribosyltransferase (ATP-PRT) catalyses the first committed step of histidine biosynthesis in plants and micro-organisms. Two forms of ATP-PRT have been reported, which differ in their molecular architecture and mechanism of allosteric regulation. The short-form ATP-PRT is a hetero-octamer, with four HisG chains that comprise only the catalytic domains and four separate chains of HisZ required for allosteric regulation by histidine. The long-form ATP-PRT is homohexameric, with each chain comprising two catalytic domains and a covalently linked regulatory domain that binds histidine as an allosteric inhibitor...
December 5, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29208656/pvdo-is-required-for-the-oxidation-of-dihydropyoverdine-as-last-step-of-fluorophore-formation-in-pseudomonas-fluorescens
#18
Michael T Ringel, Gerald Draeger, Thomas Brüser
Pyoverdines are important siderophores that guarantee iron supply to important pathogenic and non-pathogenic pseudomonads in host habitats. A key characteristic of all pyoverdines is the fluorescent dihydroxyquinoline group that contributes two ligands to the iron complexes. Pyoverdines are derived from the non-ribosomally synthesized peptide ferribactin and their fluorophore is generated by periplasmic oxidation and cyclization reactions of D-tyrosine and L-diaminobutyric acid. The formation of the fluorophore is known to be driven by the periplasmic tyrosinase PvdP...
December 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29207569/the-uv-plasmonic-behavior-of-distorted-rhodium-nanocubes
#19
Yael Gutiérrez, Dolores Ortiz, José M Saiz, Francisco González, Henry O Everitt, Fernando Moreno
For applications of surface-enhanced spectroscopy and photocatalysis, the ultraviolet (UV) plasmonic behavior and charge distribution within rhodium nanocubes is explored by a detailed numerical analysis. The strongest plasmonic hot-spots and charge concentrations are located at the corners and edges of the nanocubes, exactly where they are the most spectroscopically and catalytically active. Because intense catalytic activity at corners and edges will reshape these nanoparticles, distortions of the cubical shape, including surface concavity, surface convexity, and rounded corners and edges, are also explored to quantify how significantly these distortions deteriorate their plasmonic and photocatalytic properties...
December 4, 2017: Nanomaterials
https://www.readbyqxmd.com/read/29206473/carbonyl-iron-powder-a-reagent-for-nitro-group-reductions-under-aqueous-micellar-catalysis-conditions
#20
Nicholas R Lee, Agata A Bikovtseva, Margery Cortes-Clerget, Fabrice Gallou, Bruce H Lipshutz
An especially mild, safe, efficient, and environmentally responsible reduction of aromatic and heteroaromatic nitro-group-containing educts is reported that utilizes very inexpensive carbonyl iron powder (CIP), a highly active commercial grade of iron powder. These reductions are conducted in the presence of nanomicelles composed of TPGS-750-M in water, a recyclable aqueous micellar reaction medium. This new technology also shows broad scope and scalability and presents opportunities for multistep one-pot sequences involving this reducing agent...
December 5, 2017: Organic Letters
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