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https://www.readbyqxmd.com/read/28108654/revealing-the-role-of-the-product-metal-in-dna-polymerase-%C3%AE-catalysis
#1
Lalith Perera, Bret D Freudenthal, William A Beard, Lee G Pedersen, Samuel H Wilson
DNA polymerases catalyze a metal-dependent nucleotidyl transferase reaction during extension of a DNA strand using the complementary strand as a template. The reaction has long been considered to require two magnesium ions. Recently, a third active site magnesium ion was identified in some DNA polymerase product crystallographic structures, but its role is not known. Using quantum mechanical/ molecular mechanical calculations of polymerase β, we find that a third magnesium ion positioned near the newly identified product metal site does not alter the activation barrier for the chemical reaction indicating that it does not have a role in the forward reaction...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108278/comparison-of-the-redox-chemistry-of-sulfur-and-selenium-containing-analogs-of-uracil
#2
N Connor Payne, Andrew Geissler, Aileen Button, Alexandru R Sasuclark, Alayne L Schroll, Erik L Ruggles, Vadim N Gladyshev, Robert J Hondal
Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNA(Glu), tRNA(Gln) and tRNA(Lys). It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen...
January 17, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28107929/highly-sensitive-aptasensor-based-on-synergetic-catalysis-activity-of-mos2-au-he-composite-using-cdna-au-god-for-signal-amplification
#3
Hai-Yan Song, Tian-Fang Kang, Li-Ping Lu, Shui-Yuan Cheng
Single or few-layer nanosheets of MoS2 (MoS2 nanosheets) and a composite composed of MoS2 nanosheets, Au nanoparticles (AuNPs) and hemin (HE) (denoted as MoS2-Au-HE) were prepared. The composites possessed high synergetic catalysis activity towards the electroreduction of hydrogen peroxide. Furthermore, glucose oxidase (GOD) and AuNPs were used as marker of the complementary DNA (cDNA) strand of kanamycin aptamer to prepare a conjugate (reffered as cDNA-Au-GOD) that was designed as the signal probe. Both cDNA-Au-GOD and MoS2-Au-HE were applied to fabricate aptasensor for kanamycin...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107510/effect-of-the-crystal-environment-on-side-chain-conformational-dynamics-in-cyanovirin-n-investigated-through-crystal-and-solution-molecular-dynamics-simulations
#4
Logan S Ahlstrom, Ivan I Vorontsov, Jun Shi, Osamu Miyashita
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure...
2017: PloS One
https://www.readbyqxmd.com/read/28107007/chlorophyll-catalyzed-visible-light-mediated-synthesis-of-tetrahydroquinolines-from-n-n-dimethylanilines-and-maleimides
#5
Jun-Tao Guo, Da-Cheng Yang, Zhi Guan, Yan-Hong He
Natural pigment chlorophyll was used as a green photosensitizer for the first time in a visible light photoredox catalysis for the efficient synthesis of tetrahydroquinolines from N,N-dimethylanilines and maleimides in an air atmosphere. The reaction involves direct cyclization via sp3 C-H bond functionalization process to afford products in moderate to high yields (61-98%) from a wide range of substrates with a low loading of chlorophyll under mild conditions. This work demonstrates the potential benefits of chlorophyll as photosensitizer in visible light catalysis...
January 20, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28106897/transition-metal-co-ni-nanoparticles-wrapped-with-carbon-and-their-superior-catalytic-activities-for-the-reversible-hydrogen-storage-of-magnesium-hydride
#6
Xu Huang, Xuezhang Xiao, Wei Zhang, Xiulin Fan, Liuting Zhang, Changjun Cheng, Shouquan Li, Hongwei Ge, Qidong Wang, Lixin Chen
Magnesium hydride (MgH2) exhibits long-term stability and has recently been developed as a safe alternative to store hydrogen in the solid state, due to its high capacity of 7.6 wt% H2 and low cost compared to other metal hydrides. However, the high activation energy and poor kinetics of MgH2 lead to inadequate hydrogen storage properties, resulting in low energy efficiency. Nano-catalysis is deemed to be the most effective strategy in improving the kinetics performance of hydrogen storage materials. In this work, robust and efficient architectures of carbon-wrapped transition metal (Co/C, Ni/C) nanoparticles (8-16 nm) were prepared and used as catalysts in the MgH2 system via ball milling to improve its de/rehydrogenation kinetics...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106397/kinetics-of-detergent-induced-activation-and-inhibition-of-a-minimal-lipase
#7
Daniel Kuebler, Anna Bergmann, Lukas Weger, Kim Nadine Ingenbosch, Kerstin Hoffmann-Jacobsen
Detergents are commonly applied in lipase assays to solubilize the sparingly soluble model substrates. However, detergents affect lipases as well as substrates in multiple ways. The effect of detergents on lipase activity is commonly attributed to conformational changes in the lid region. This study deals with the effect of the non-ionic detergent, polyethylene glycol dodecyl ether, on a lipase that does not contain a lid sequence, lipase A from Bacillus subtilis (BSLA). We show that BSLA activity depends strongly on detergent concentration and the dependency profile changes with pH...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106388/mechanistic-studies-of-single-step-styrene-production-using-a-rhodium-i-catalyst
#8
Benjamin A Vaughan, Sarah K Khani, J Brannon Gary, James D Kammert, Michael S Webster-Gardiner, Bradley A McKeown, Robert J Davis, Thomas R Cundari, T Brent Gunnoe
The direct and single-step conversion of benzene, ethylene, and a Cu(II) oxidant to styrene using the Rh(I) catalyst ((Fl)DAB)Rh(TFA)(η(2)-C2H4) [(Fl)DAB = N,N'-bis(pentafluorophenyl)-2,3-dimethyl-1,4-diaza-1,3-butadiene; TFA = trifluoroacetate] has been reported to give quantitative yields (with Cu(II) as the limiting reagent) and selectivity combined with turnover numbers >800. This report details mechanistic studies of this catalytic process using a combined experimental and computational approach. Examining catalysis with the complex ((Fl)DAB)Rh(OAc)(η(2)-C2H4) shows that the reaction rate has a dependence on catalyst concentration between first- and half-order that varies with both temperature and ethylene concentration, a first-order dependence on ethylene concentration with saturation at higher concentrations of ethylene, and a zero-order dependence on the concentration of Cu(II) oxidant...
January 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28106188/reversible-covalent-interactions-of-%C3%AE-aminoboronic-acids-with-carbohydrate-derivatives
#9
Graham E Garrett, Diego B Diaz, Andrei K Yudin, Mark S Taylor
β-Aminoalkylboronic acids are capable of binding to carbohydrate derivatives through reversible covalent interactions. An anthracene-bearing β-aminoboronic acid has been synthesized, enabling determinations of association constants for binding of sugars by fluorescence spectroscopy. The diol-binding properties of β-aminoboronic acids are also useful in catalysis: one such compound displays remarkably high activity for regioselective O-acylation of a pyranoside derivative.
January 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28105822/functional-group-coverage-and-conversion-quantification-in-nanostructured-silica-by-1-h-nmr
#10
Carina I C Crucho, Carlos Baleizão, José Paulo S Farinha
Silica nanostructured materials are important in many fields, including catalysis, imaging, and drug delivery, mainly due to the versatility of surface functionalization that can bestow a huge variety of chemical and physical properties. With most applications requiring precise control over this surface modification, characterization of surface composition and reactivity have become of extreme importance. We present a novel approach to track silica surface modification and quantify functional group coverage using only solution NMR...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28105772/reversing-the-regioselectivity-of-halofunctionalization-reactions-through-cooperative-photoredox-and-copper-catalysis
#11
Jeremy D Griffin, Cortney L Cavanaugh, David A Nicewicz
Halofunctionalization of alkenes is a classical method for olefin difunctionalization. It gives rise to adducts which are found in many natural products and biologically active molecules, and offers a synthetic handle for further manipulation. Classically, this reaction is performed with an electrophilic halogen source and leads to regioselective formation of the halofunctionalized adducts. Herein, we demonstrate a reversal of the native regioselectivity for alkene halofunctionalization through the use of an acridinium photooxidant in conjunction with a copper cocatalyst...
January 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28105660/selective-reductions-of-n-n-bis-chloro-aryl-phosphino-amines-yielding-three-five-six-and-eight-membered-cyclic-azaphosphanes
#12
Uwe Rosenthal, Martha Hoehne, Markus Joksch, Katharina Konieczny, Bernd Harald Mueller, Anke Spannenberg, Normen Peulecke
To date a plethora of λ3-P nitrogen containing-compounds is known. A large part of them is used as ligands in coordination chemistry and homogeneous catalysis. PN-containing compounds tend to build up cyclic moieties which have received less attention in regard to their application as ligands in transition metal chemistry. Hence different dehalogenation reactions of N,N-Bis{chloro(aryl)-phosphino}-amines have being developed to synthesize different P-N-P containing cyclic compounds. Their coordination behaviour to group (VI) transition metal carbonyls was explored...
January 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28105572/proteome-wide-identification-of-iron-binding-proteins-of-xanthomonas-translucens-pv-undulosa-focus-on-secretory-virulent-proteins
#13
Ankita Sharma, Dixit Sharma, Shailender Kumar Verma
Xanthomonas translucens pv. undulosa (Xtu) causes Bacterial Leaf Streak disease in the staple food crops such as wheat and barley. The survival strategies of pathogen and host are determined by the complex interactions occurring between the host plants and the pathogenic microbes. Iron binding proteins are important in the plant-microbe interactions as they are indulged in enzyme catalysis, virulence, metabolic and transport activities. In the presented study, we have identified that ~9.8% of Xtu proteome possess iron binding sequence motifs...
January 19, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28105399/large-area-carbon-nanosheets-doped-with-phosphorus-a-high-performance-anode-material-for-sodium-ion-batteries
#14
Hongshuai Hou, Lidong Shao, Yan Zhang, Guoqiang Zou, Jun Chen, Xiaobo Ji
Large-area phosphorus-doped carbon nanosheets (P-CNSs) are first obtained from carbon dots (CDs) through self-assembly driving from thermal treatment with Na catalysis. This is the first time to realize the conversion from 0D CDs to 2D nanosheets doped with phosphorus. The sodium storage behavior of phosphorus-doped carbon material is also investigated for the first time. As anode material for sodium-ion batteries (SIBs), P-CNSs exhibit superb performances for electrochemical storage of sodium. When cycled at 0...
January 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/28104837/the-role-of-dimer-asymmetry-and-protomer-dynamics-in-enzyme-catalysis
#15
Tae Hun Kim, Pedram Mehrabi, Zhong Ren, Adnan Sljoka, Christopher Ing, Alexandr Bezginov, Libin Ye, Régis Pomès, R Scott Prosser, Emil F Pai
Freeze-trapping x-ray crystallography, nuclear magnetic resonance, and computational techniques reveal the distribution of states and their interconversion rates along the reaction pathway of a bacterial homodimeric enzyme, fluoroacetate dehalogenase (FAcD). The crystal structure of apo-FAcD exhibits asymmetry around the dimer interface and cap domain, priming one protomer for substrate binding. This asymmetry is dynamically averaged through conformational exchange on a millisecond time scale. During catalysis, the protomer conformational exchange rate becomes enhanced, the empty protomer exhibits increased local disorder, and water egresses...
January 20, 2017: Science
https://www.readbyqxmd.com/read/28103688/structure-based-substrate-specificity-analysis-of-heparan-sulfate-6-o-sulfotransferases
#16
Yongmei Xu, Andrea F Moon, Shuqin Xu, Juno M Krahn, Jian Liu, Lars C Pedersen
Heparan sulfate (HS) is a sulfated polysaccharide exhibiting essential physiological functions. HS 6-O-sulfotransferase (6-OST) transfers a sulfo group to the 6-OH position of glucosamine units to confer a variety of HS biological activities. There are three different isoforms of 6-OST in the human genome. Here, we report crystal structures of the ternary complex of 6-OST with the sulfo donor analog 3'-phosphoadenosine 5'-phosphate and three different oligosaccharide substrates at 1.95 to 2.1 Å resolutions...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28103251/active-hydrogen-bond-network-ahbn-and-applications-for-improvement-of-thermal-stability-and-ph-sensitivity-of-pullulanase-from-bacillus-naganoensis
#17
Qing-Yan Wang, Neng-Zhong Xie, Qi-Shi Du, Yan Qin, Jian-Xiu Li, Jian-Zong Meng, Ri-Bo Huang
A method, so called "active hydrogen bond network" (AHBN), is proposed for site-directed mutations of hydrolytic enzymes. In an enzyme the AHBN consists of the active residues, functional residues, and conservative water molecules, which are connected by hydrogen bonds, forming a three dimensional network. In the catalysis hydrolytic reactions of hydrolytic enzymes AHBN is responsible for the transportation of protons and water molecules, and maintaining the active and dynamic structures of enzymes. The AHBN of pullulanase BNPulA324 from Bacillus naganoensis was constructed based on a homologous model structure using Swiss Model Protein-modeling Server according to the template structure of pullulanase BAPulA (2WAN)...
2017: PloS One
https://www.readbyqxmd.com/read/28103007/glutamate-350-plays-an-essential-role-in-conformational-gating-of-long-range-radical-transport-in-e-coli-class-ia-ribonucleotide-reductase
#18
Kanchana R Ravichandran, Ellen C Minnihan, Qinghui Lin, Kenichi Yokoyama, Alexander T Taguchi, Jimin Shao, Daniel G Nocera, JoAnne Stubbe
E. coli Ia ribonucleotide reductase is composed of two subunits that form an active α2β2 complex. The nucleoside diphosphate substrates (NDP) are reduced in α2, 35 Å from the essential diferric-tyrosyl radical (Y122•) cofactor in β2. The Y122• mediated oxidation of C439 in α2 occurs by a pathway (Y122 ↔ [W48] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2) across the α/β interface. The absence of an α2β2 structure precludes insight into the location of Y356 and Y731 at the subunit interface...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28102678/a-self-assembled-cofacial-cobalt-porphyrin-prism-for-oxygen-reduction-catalysis
#19
Amanda N Oldacre, Alan E Friedman, Timothy R Cook
Herein we report the first study of the oxygen reduction reaction (ORR) catalyzed by a cofacial porphyrin scaffold accessed in high yield (overall 53%) using coordination-driven self-assembly with no chromatographic purification steps. The ORR activity was investigated using chemical and electrochemical techniques on monomeric cobalt(II) tetra(meso-4-pyridyl)porphyrinate (CoTPyP) and its cofacial analogue [Ru8(η(6)-iPrC6H4Me)8(dhbq)4(CoTPyP)2][OTf]8 (Co Prism) (dhbq = 2,5-dihydroxy-1,4-benzoquinato, OTf = triflate) as homogeneous oxygen reduction catalysts...
January 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28102576/printable-functional-chips-based-on-nanoparticle-assembly
#20
REVIEW
Yu Huang, Wenbo Li, Meng Qin, Haihua Zhou, Xingye Zhang, Fengyu Li, Yanlin Song
With facile manufacturability and modifiability, impressive nanoparticles (NPs) assembly applications were performed for functional patterned devices, which have attracted booming research attention due to their increasing applications in high-performance optical/electrical devices for sensing, electronics, displays, and catalysis. By virtue of easy and direct fabrication to desired patterns, high throughput, and low cost, NPs assembly printing is one of the most promising candidates for the manufacturing of functional micro-chips...
January 2017: Small
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